Apoptosis A Practical Approach Practical Approach Series

Apoptosis
The Practical Approach Series
SERIES EDITOR
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Apoptosis
A Practical Approach
Edited by
GEORGE P. STUDZINSKI
Department of Pathology and Laboratory Medicine
UMD—New Jersey Medical School
Newark, N.J., USA
OXFORD
UNIVERSITY PRESS
OXFORD
UNIVERSITY PRESS
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Preface
Apoptosis, a concept derived from pathological observations dating back to
the availability of the microscope, has been recently afforded treatment
reminiscent of the ancient apocalyptic writings. Revelations are reported daily
of new, and so it is claimed, profound insights into cellular survival mecha-
nisms, and their principal default pathway, apoptosis. The preoccupation of
many scientists with this cellular programme, or programmes, appears to be
driven by several currents. There is a bewildering array of commercial
reagents and accompanying literature reporting to provide, often quick and
easy, means of discovering important secrets of nature. There is also the
fascination of the scientists with the beauty of an almost endless cascades of
protein-protein interactions that lead to an irrevocable end-point—cell death.
And of course, there is the legitimate expectation that important components
of therapy for cancer and immune diseases will be based on our understanding
of the precise mechanisms of these apoptotic cascades.
This volume presents the techniques essential for contemporary research on
diverse aspects of apoptosis. In addition to the basic methodology for recogni-
tion of the apoptotic phenotype and its characteristic DNA fragmentation, the
text contains a wide variety of procedures used to investigate the mechanistic
aspects of the programmes for survival or death of mammalian cells. A team of
scientists who are among the leaders in apoptosis research has provided
numerous protocols which describe in detail how to perform these procedures
and discusses them from the individual points of view of each contributor. The
protocols most frequently used in current investigations of apopotosis research
are presented with variations that have been found particularly useful for a par-
ticular application, thus allowing the reader to benefit from the experience of
laboratories which focus on different aspects of apoptosis research.
Attention is also directed to the choice of the procedures, to pitfalls in their
execution, and to critical interpretation of the results. It is believed that the
nuances of technical approaches discussed here will be helpful to the experi-
enced as well as the beginning investigators. The credit for this must go to the
team of authors and the OUP staff.
New Jersey G.P.S.

1999
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Contents
List of Contributors xv
Abbreviations xix
1. Overview of apoptosis 1
George P. Studzinski
1. General introduction and overview of contents 1
2. Historical perspective 5
3. Distinction of apoptosis from other forms of cell death 5
4. Apoptotic cascades 8
5. Time course of apoptotic cascades 8
6. Selection of methods 11
Procedure for determination of increased mitochondrial to nuclear
DNA ratio, for the detection and quantitation of apoptosis 12
7. Pitfalls 14
References 16
2. Morphological recognition of apoptotic cells 19

James W. Wilson and Christopher S. Potten
1. Introduction 19
Key morphological features of apoptotic cells 19
2. Light and fluorescent microscopy techniques for the
assessment of apoptosis 20
Preparation of cell or tissue samples 20
Nuclear counterstains 23
3. Electron microscopic techniques 27
4. Quantitation of apoptotic events 29
Methods 29
Problems in scoring apoptotic events 31
5. In situ detection of DNA strand breaks 33
6. Other techniques 37
7. Conclusions 38
References 38
Contents
3. Assessment of DNA damage in apoptosis 41

Akira Yoshida, Rong-Guang Shao, and Yves Pommier
1. Introduction 41
2. Types of DNA fragmentation 41
3. Measurement of high molecular weight DNA fragmentation
by pulse-field gel electrophoresis 43
Pulse-field gel electrophoresis procedures 44
Strategies for electrophoretic separations 46
4. Detection of internucleosomal DNA fragmentation by
standard agarose gel electrophoresis 47
5. Filter elution assay to measure apoptotic DNA fragmentation 48
Equipment 49
Filters and solutions 49
DNA labelling and preparation of experimental cell cultures 50
Protocols 51
Counting samples and computations 52
References 53
4. Analysis of cell death by flow and

laser-scanning cytometry 57
Zbigniew Darzynkiewicz, Elzbieta Bedner, and Xun Li
\. Introduction 57
2. Preparation of cells for analysis by LSC. Detection of
apoptotic cells based on changes in nuclear chromatin 59
3. Light-scattering properties of apoptotic and necrotic cells 61
4. Analysis of mitochondrial transmembrane potential (Av m ) 63
5. Detection of apoptotic cells exposing phosphatidylserine on
plasma membrane 67
6. Detection of apoptotic cells based on their fractional DNA
content 68
7. Identification of apoptotic cells based on the presence of
DNA strand breaks 71
8. Identification of apoptotic cells based on the increased
DNA sensitivity to denaturation 75
9. General comments 77
References 78
x
Contents
5. Cell-mediated cytotoxicity and cell death

receptors 81
Javier Naval and Alberto Anel
1. Overview of pathways for cell-mediated cytotoxicity 81
Fas-based cytotoxicity 82
Perforin/granzyme-based cytotoxicity 83
2. Standard methods for the evaluation of cell-mediated
cytotoxicity 84
Chromium release assay 84
[125I]Iododeoxyuridine (125IUdR) release assay 87
The JAM test 89
BLT-esterase release assay 91
Estimation of target cell nuclear fragmentation using fluorescent dyes 92
Activation-induced cell death (AICD) 94
3. Separate studies of Fas- and perforin/granzyme-based
cytotoxicity 95
Fas-based cytotoxicity in the absence of perforin/granzyme
contribution 95
Perforin/granzyme-based cytotoxicity in the absence of FasL
contribution 96
4. Use of caspase and granzyme inhibitors in cell-mediated
cytotoxicity assays 97
Caspase inhibitors 97
Granzyme inhibitors 99
References 100
6. Sphingolipids as messengers of cell death 105

Gary M. Jenkins and Yusuf A. Hannun
1. Introduction 105
2. Sphingolipids and their role in apoptosis 105
Overview of Sphingolipids 105
Role of Sphingolipids in apoptosis 106
Strategies and considerations in evaluating Sphingolipids 107
3. Extraction of Sphingolipids and normalization by lipid
phosphate 108
Extraction of sphingosines, ceramides, and sphingomyelins 108
Alkaline hydrolysis of Sphingolipids 111
Lipid phosphate measurement for normalization of experimental
samples 112
4. Analysis of sphingoid backbones 113
HPLC on sphingoid backbones 113
xi
Contents
5. Analysis of ceramides 115
6. Analysis of sphingomyelins 118
7. Measurement of SMase and SM synthase activities 120
References 123
7. Cytochemical detection of cytoskeletal and

nucleoskeletal changes during apoptosis 125
Manon van Engeland, Bert Schutte, Anton H. N. Hopman,
Frans C. S. Ramaekers, and Chris P. M. Reutelingsperger
1. Introduction 125
2. Cyto- and nucleoskeletal changes during apoptosis 126
General 126
Microfilaments and microfilament-associated proteins 126
Microtubules 126
Intermediate filaments 127
Nucleoskeletal components 128
Generation of neo-epitopes in cytoskeletal proteins during apoptosis 128
3. Apoptosis detection systems 129
Overview 129
The annexin V affinity assay 129
Detection of apoptosis using the TUNEL assay 135
References 138
8. Metabolic alterations associated with

apoptosis 141
Ana P. Costa-Pereira and Thomas G. Cotter
1. Introduction 141
2. Detection of changes in the mitochondrial transmembrane
potential 142
3. Detection of intracellular reactive oxygen intermediates
(ROI) 144
4. Determination of glutathione levels and its oxidative state 146
5. Measurement of catalase in cells undergoing apoptosis 153
References 155
xii
Contents
9. Methods of measuring Bcl-2 family proteins

and their functions 157
John C. Reed, Zhihua Xie, Shinichi Kitada, Juan M. Zapata,
Qunli Xu, Sharon Schendel, Maryla Krajewska, and
Stanislaw Krajewski
1. Introduction 157
2. Immunoblot analysis 157
Cell lysis and tissue processing procedures 158
Immunoblotting procedure 161
3. Detection of Bcl-2 family proteins by flow cytometry (FACS) 165
Indirect immunofluorescence procedure 166
Antibodies 167
4. Northern blot analysis of BCL-2 m RNA 167
General guidelines for RNA blotting 168
Pre-hybridization and hybridization procedures 169
Solutions 170
5. Reverse transcriptase-polymerase chain reaction (RT-PCR) 171
cDNA synthesis 172
PCR amplication 172
Southern blot analysis of PCR products 173
Primers and probes for PCR 174
6. Immunohistochemical detection of Bcl-2 family proteins
in tissues 175
Procedures for tissue preparation, embedding, and sectioning 177
Pre-staining sample preparation 180
Immunostaining 183
Counterstaining and mounting 185
Solutions 186
7. Immunohistochemical detection of Bcl-2 protein in
cultured cells 187
Procedures 188
Immunostaining 189
Solutions 191
8. Production of recombinant Bcl-2 family proteins in bacteria 191
Human Bcl-2 192
Human Bcl-XL protein 194
Mouse Bax protein 197
Human Bid protein 199
9. Measurements of pore formation by Bcl-2 family proteins 201
Liposome preparation 202
Channel activity measurements 204
xiii
Contents
10. Methods of assaying Bcl-2 and Bax family protein function

in yeast 205
Plasmid considerations 205
Saccharomyces cerevisiae strains 207
Media and growth conditions 207
Transformation of S. cerevisiae by the LiOAc method 209
Assay for Bax-induced lethality in S. cerevisiae 210
11. Summary 212
References 212
10. Methods for detecting proteolysis during

apoptosis in intact cells 215
April L. Blajeski and Scott H. Kaufmann
1. Introduction 215
2. Involvement of proteases in apoptosis 215
3. Caspase nomenclature and classification 217
4. Detection of procaspases and their cleavage products by
immunoblotting 218
Theoretical considerations 218
Practical considerations in immunoblotting for caspases 222
Sample preparation and immunoblotting 222
5. Cleavage of caspase targets 224
Establishing that proteases are activated in situ 224
Establishing that a polypeptide is cleaved by caspases 224
6. Assays of caspase activity 226
Theoretical considerations of caspase activity assays 227
Measuring caspase activity in cell lysates 227
7. Detection of active caspases by affinity labelling 230
Theoretical considerations in affinity labelling 230
Practical considerations in the use of affinity labelling reagents 232
Labelling and detecting enzymatically active caspases 232
8. Studying the biological effects of caspase cleavages 234
A molecular approach for analysis of the effects of substrate
cleavage 235
Use of caspase inhibitors: promises and pitfalls 235
References 236
List of Suppliers 239
Index 243
xiv
Contributors
ALBERTO ANEL
Department Bioquimica y Biologia Molecular y Celular, Faculty of Sciences,
University of Zaragoza, Zaragoza, 50009, Spain
ELZBIETA BEDNER
Brander Cancer Research Institute, 19 Bradhurst Avenue, Hawthorne, NY.,
10532, USA
APRIL L.BLAJESKI
Department of Pharmacology, Mayo Graduate School, Rochester, MN 55905,
USA
ANA P. COSTA-PEREIRA
Tumour Biology Laboratory, Department of Biochemistry, University College,
Cork, Ireland
THOMAS G. COTTER
Tumour Biology Laboratory, Department of Biochemistry, University College,
Cork, Ireland
ZBIGNIEW D ARZYNKIEWICZ
10532, USA
YUSUFA.HANNUN
114 Doughty St, Rm. 603, Strom Thurmond Bldg, Charleston, SC 29425, USA
ANTON H. N. HOPMAN
Department of Molecular Cell Biology and Genetics, University of Maastricht,
PO Box 616,6200 MD Maastricht, The Netherlands
GARY JENKINS
114 Doughty St, Rm. 603, Strom Thurmond Bldg, Charleston, SC 29425, USA
SCOTT H. KAUFMANN
Guggenheim 1342C, Mayo Clinic, 200 First St., S.W., Rochester, MN 55905,
USA
SHINICHI KITADA
The Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA, 93037,
USA
MARYLA KRAJEWSK A
USA
Contributors
STANISLAW KRAJEWSKI
USA
XUNLI
10532, USA
JAVIER NAVAL
Department Bioquimica y Biologia Molecular y Celular, Faculty of Sciences,
University of Zaragoza, Zaragoza, 50009, Spain
YVESPOMMIER
Laboratory of Molecular Pharmacology, Division of Basic Sciences, National
Cancer Institute, National Institute of Health, Bethesda, Maryland, USA
CHRISTOPHER S. POTTEN
CRC Epithelial Biology Laboratory, Section of Cell and Tumour Biology,
Paterson Institute for Cancer Research, Wilmslow Road, Withington,
Manchester M20 4BX, UK
FRANS C. S. RAMAEKERS
JOHN C. REED
USA
CHRIS P. M. REUTELINGSPERGER
Department of Biochemistry, University of Maastricht, PO Box 616, 6200 MD
Maastricht, The Netherlands
SHARON SCHENDEL
USA
BERT SCHUTTE
RONG-GUANG SHAO
Department of Oncology, Institute of Medicinal Biotechnology, Chinese
Academy of Medical Sciences, 1 Tiantan xili, Beijing 100050, P. R. China
Department of Pathology and Laboratory Medicine, UMDNJ-New Jersey
Medical School, 185 S. Orange Avenue, University Heights, Newark, NJ
07103, USA
xvi
Contributors
MANON VAN ENGELAND
JAMES W. WILSON
CRC Epithelial Biology Laboratory, Section of Cell and Tumour Biology,
Paterson Institute for Cancer Research, Wilmslow Road, Withington,
Manchester M20 4BX, UK
ZHIHUA XIE
USA
QUNLIXU
Oncology Disease Group, Hoechst & Marion Roussel, Inc., Route 202-206,
Bridgewater, NJ 08807, USA
AKIRAYOSHIDA
First Department of Internal Medicine, Fukui Medical School, Shimoaizuki
23, Matsuoka-cho, Fukui, 910-1193, Japan
xvii
Abbreviations
125 125
IUdR I-deoxyuridine
2-VP 2-vinylpyridine
ABC avidin-biotin complex
Ac-DEVD-CHO acetyl-Asp-Glu-Val-Asp-aldehyde
Ac-YVAD-cmk acetyl-Tyr-Val-Ala-Asp-chloromethylketone
AEC 3-amino-9-ethylcarbasole
AFC 7-amino-4-trifluoromethylcoumarin
AI apoptotic index
AICD activation-induced cell death
AID activation-induced death
ALS alkali-labile sites
AMC 7-amino-4-methylcoumarin
APAF apoptotic protease activating factor
APES 3-aminopropyl triethoxy silane
B-CLL B cell chronic lymphocytic leukaemia
BCA bicinchoninic acid
BCIP bromochloroindolyl phosphate
BLT TV-benzyloxycarbonyl-L-lysine thiobenzyl est
Boc-D-fmk f-butyloxycarbonyl-Asp-fluoromethylketone
(3OG B-octyl glucoside
bp base pair
BSA bovine serum albumin
BSO DL-buthionine-S,R-sulfoximine
CAD caspase-activated DNase
CAPK ceramide-activated protein kinase
CAPP ceramide-activated protein phosphatase
CARD caspase recruitment domain
CD cluster designation
CHEF clamped homogeneous electric field
CoA co-enzyme A
CPT comptothecin
CTL cytotoxic T lymphocyte
Cu/ZnSOD copper/zinc superoxide dismutase
D-FPR-cmk D-Phe-Pro-Arg-clhoromethylketone
DAB 3'3' -diaminobenzidine
DAG diacylglycerol
DAPI 4' ,6-diamidino-2-phenylindole
DCFH/DA 2' ,7' -dichlorofluorescein diacetate
DCI 3,4-dichloroisocoumarin
Abbreviations
BED death effector domains
DEP diethyl pyrocarbonate
DFF DNA fragmentation factor
DGK diacylglycerol kinase
DHE dihydroethidium
DMF dimethylformamide
DMG dimethyl glutaric acid
DMSO dimethyl sulfoxide
DOPG dioleoylphosphatidlylglycerol
DPC DNA-protein cross-links
DSB double-stranded breaks
DTNB 5,5' -dithio-few(2-nitrobenzoic acid)
DTT dithiothreitol
dUTP deoxyuridine triphosphate
AlKn mitochondrial transmembrane potential
E:T effector to target ratio
ECL enhanced chemiluminescence
EDTA ethylenediaminotetra-acetic acid
EGTA ethylene glycol tetra-acetic acid
ERK extracellular signal regulated kinases
FACS fluorescence-activated cell sorting
FADD Fas-associated death domain
FAK focal adhesion kinase
PCS fetal calf serum
FITC fluoroscein isothiocyanate
GFP green fluorescent protein
GSH glutathione
GSSG glutathione disulfide
GST glutathione S-transferase
GuHCl guanidine hydrochloride
H&E haematoxylin and eosin
H202 hydrogen peroxide
HBSS Hank's balanced salt solution
HIV human immunodeficiency virus
HMW high molecular weight
HO' hydroxyl radical
HPLC high performance liquid chromatography
HRPase horseraddish peroxidase
ICAD inhibitor of CAD
ICE interleukin-lp-converting enzyme
IGA 7-(phenyl-ureido)-4-chloro-3-(2-isothioureidoethoxy)-
isocoumarin
IPTG isopropylthio-p-D-galactoside
ISC interstrand DNA cross-links
xx
Abbreviations
ISEL in situ end labelling
ISNT in situ nick translation
JC-1 5,5',6,6'-tetrachloro-l,l',3,3'-tetraethyl-
benzimidazolylcarbocyanine iodide
kb kilobase pair
LB Luria-Bertani broth
LSC laser-scanning cytometry
LUV large unilamellar vesicles
MAD multiple antigen detection procedures
mBCl monochlorobimane
MHC major histocompatibility complex
MI mitotic index
MLC mixed lymphocyte culture
MnSOD manganese superoxide dismutase
mPBS modified PBS
MTT 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium
bromide
mtDNA mitochondrial DNA
NET nitroblue tetrazolium
NEM Af-ethylmaleimide
NK natural killer
nuDNA nuclear DNA
o-PA ortho-phthaldialdehyde
02' superoxide anion
OCX optimal cutting temperature
OTC outside tissue compound
PAGE polyacrylaminde gel electrophoresis
PAP peroxidase anti-peroxidase complex
PASB protein-associated strand breaks
PBS phosphate-buffered saline
PHA phytohaemagglutinin
PI propidium iodide
PKC protein kinase C
PMSF a-phenylmethylsulfonyl fluoride
pNA p-nitroaniline
PPDA p-phenylenediamine
PS phosphatidylserine
PT permeability transition
PVC polyvinal chloride
PVDF polyvinylidene fluoride
ROI reactive oxygen intermediates
RT-PCR reverse transcriptase-polymerase chain reaction
SDS sodium dodecyl sulfate
SE standard error
xxi
Abbreviations
SG designation of a commercial chromogenic substrate
SM sphingomyelin
SMase sphingomyelinase
SSA 5-sulfosalicylic acid
SSB single-strand breaks
SSC sodium chloride (0.15M), trisodium citrate (0.015 M),
buffer (pH 7.0)
SUV small unilamellar vesicles
TAB Tris-acetate buffer
TBE Tris-borate buffer
TCR T cell antigen receptor
TdT terminal deoxynucleotidyl transferase
TEM transmission electron microscopy
TLC thin layer chromatography
TLCK N-p-tosyl-L-lysine chloromethyl ketone
TMB 3,3', 5,5'-tetramethyl benzidene
TNB 5-thio-2-nitrobenzoic acid
TNF tumour necrosis factor
TPCK N-a-tosyl-L-phenylalanine chloromethyl ketone
TUNEL terminal deoxynucleotidyl transferase (TdT)-mediated
dUTP nick end-labelling
YVK(bio)D-aomk Af-(acetyltyrosinylvalinyl-(Nbiotinyllysyl) aspartic acid
[(2,6-dimethylbenzoyl)oxy]methyl ketone
Z-AAD-cmk benzyloxycarbonyl-Ala-Ala-Asp-clhoromethylketone
Z-EK(bio)D-aomk .N-(Nx-benzyloxycarbonylglutamyl-.Ne-
biotinyllysyl)aspartic acid [(2,6-
dimethylbenzoyl)oxy]methyl ketone
Z-VAD-fmk benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone
Z-VDVAD-fmk benzyloxycarbonyl-Val-Asp-Val-Ala-Asp-
fluoromethylketone
xxii
1
Overview of apoptosis
1. General introduction and overview of contents

When cells receive mixed signals for growth they usually die. For instance,
when the developmental programme requires cell division but external growth
signals are lacking, or when a growth-related gene such as c-myc is highly
expressed but the cellular environment has insufficient nutrient content, or
a toxic xenobiotic is present, the cell dies by a process termed apoptosis.
Although there are differences in the phenomena observed during the
apoptotic sequence of events, depending on the cell type, and agent or
circumstance which initiates the cell's demise, there are morphological and
biochemical similarities which suggest that these are variants of the same
biological process, designed to control the size of cell populations.
It is important to distinguish apoptosis from the other major form of cell
death, necrosis. First, at the tissue level, apoptosis produces little or no in-
flammation, since shrunken portions of the cell are engulfed by the neigh-
bouring cells, especially macrophages, rather than being released into the
extracellular fluid. In contrast, in necrosis, cellular contents are released into
the extracellular fluid, and thus have an irritant effect on the nearby cells,
causing inflammation. Secondly, there is the expectation that elucidation of
the steps of the cellular mechanisms that lead to apoptosis may allow this
form of cell death to be induced more effectively by cancer therapeutic
agents. Thirdly, the apoptotic mechanism of cell death is fundamental to the
normal development of tissues and organisms. In contrast, cell death by
necrosis is usually accidental and therefore does not have such significance.
The role of apoptosis in cell population control during development has
suggested that there are inherent cellular programmes that lead the cell to
self-destruct. This has been confirmed in a number of instances; e.g. in a small
nematode, Caenorhabditis elegans (C. elegans), where each individual cell can
be recognized, it has been found that in the hermaphrodite form of the worm
the same set of 113 cells is destined for programmed cell death during
embryogenesis, and another set of 18 cells later in life, for a total of 131 cells
(1). Also, inhibition of RNA or protein synthesis can, in many cases, abrogate
cell death by apoptosis (2), although it usually accelerates necrosis. Thus, it
appears that gene expression is necessary for cell death. Yet, there is, another
level of complexity, as, in some instances, inhibition of protein or RNA
synthesis, or even cxplusion of nuclei, does not prevent what otherwise
appears to he programmed cell death (3). Such cells are thought to he primed
for apoptosis.
The original use of the term apoptosis was primarily descriptive of the
cellular morphology of dying cells (4). Although in the current literature most
authors blur the precision of this term (3), it is still tenable to define apoptosis
as cell death that differs from necrosis on a morphological basis, observable
by light or by electron microscopy. The key features originally described
included shrinkage and blebbing of the cytoplasm; preservation of the
structure of cellular organellcs, including the mitochondria; and condensation
and margination of chromatin, although not all of these arc seen in all cell
types (Figure 1), It is generally assumed that these morphological changes
result from a developmental programme for cell death that can be triggered
by deprivation of a growth factor, or by addition of a xenobiotic compound
such as a cancer therapeutic drug. The morphological criteria are still the
most important when complex cell populations, such as tissues, are examined.
Figure 1. An illustration of the light microscopic appearance of apoptotic cells and their
modification by a differentiation-inducing agent, (a) HL60 cells were exposed to calcium
ionophore A23187 (10 uM for 8 h), embedded in epon, and 10 um sections were stained
with toluidine blue. Note the densely stained fragments of chromatin in the nuclei and
cytoplasm of most celts, (b) HL60 cells treated as in (a), but first exposed to 1,25-
dihydroxyvitamin D3 (10-8 M for 48 h), which protects HL60 cells against apoptosis (10).
Note the smaller (differentiated) cells, only a few of which show apoptotic nuclei.
2
1: Overview of apoptosis
and overall cell shrinkage and nuclear condensation are the easiest to
recogni/e. These are presented in detail in Chapter 2, with special emphasis
on the detection and quantitation of apoptosis in vivo, since this is a much
more challenging task than recognition of apoptosis in tissue culture.
In pure cell populations, biochemical changes in chromatin and DNA
degradation provide useful and often quantifiable means of detecting
apoptosis. It is often forgotten, however, that random DNA degradation is not
a specific test for apoptosis but simply demonstrates cell death. Although
detection of DNA degradation may be useful as an adjunct method of
quantitation, occurrence of apoptosis has be shown by morphological or by
more specific biochemical methods.
The classical biochemical method for demonstrating apoptosis is the presence
of oligonuclcosomc-sized fragments of DNA, which, when run on agarose gels,
produce 'ladders1, as discussed in Chapter 3 and illustrated in Figure 2 (5,6). It
has been shown also that an earlier endonucleolytic cleavage of ehromatin
produces DNA fragments from 300 kb down to 50 kb in size (7, 8). Also, the
observation that mitochondrial DNA is intact in early stages of apoptosis
Figure 2. DNA ladder formation in HL60-G1 cells (a subclone of human leukaemia HL60
cells), but not in K562 human leukaemia cells, following exposure to doxorubicin (5 uM
for HL60 cells and 10 uM for K562 cells, both for 24 h). DNA was extracted and run on 2%
agarose gels and stained with ethidiurn bromide. DNA ladders indicative of nucleosomal
DNA fragmentation became apparent after 8 h, concident with morphological
appearances due to apoptosis (not shown). Microscopic examination of doxorubicin-
treated K562 cells showed that these cells became necrotic [not shown}.
3
provides a basis for a method which can detect and quantify apoptosis (9), as
illustrated in Fig 7 and discussed further in Section 6. These methods prove that
apoptosis has occurred, although sometimes a lag period of several hours is
necessary for the signs of apoptosis to become detectable, as will be discussed
later in this chapter. It is possible that this lag can explain some situations in
which morphological apoptosis is not accompanied by DNA fragmentation.
Analysis of all aspects of cell death has been greatly aided by application of
flow cytometry (see Chapter 4). The instrumentation is now widely available
in most academic or industrial centres, and can provide quantifiable data for
practically every method of detection of apoptosis described in this volume.
In the author's laboratory, determination of the sub-Gl/GO cellular DNA
content of propidium iodide-stained cells (see Chapter 4, Protocol 4) has been
found to be excellent for routine use in studies of the effects of chemo-
therapeutic drugs on cultured cancer cells (e.g. ref. 10). A more specialized
and less accessible instrument, the laser-scanning cytometer, combines the
advantages of flow cytometry with image analysis, providing information on
cell morphology, and, if necessary, tissue architecture. The recent modifica-
tions of flow cytometric procedures for laser-scanning cytometry presented in
Chapter 4 may prove particularly valuable for groups with access to this
instrument.
The cascades which signal and execute cell death by apoptosis can be initi-
ated by internal cues or by agents present in the extracellular environment.
The cell death receptors described in Chapter 5 participate in the T cell-
mediated cytotoxicity of target cells, and serve to illustrate the procedures
used to study receptor-mediated pathways to apoptosis. Chapter 5 also
presents an overview of pathways to cell-mediated cytotoxicity and methods
which can distinguish cytoplasmic from nuclear manifestations of apoptosis.
Induction of apoptotic pathways by extracellular agents can also occur by
membrane events that include liberation of sphingolipids, which act as
messengers of cell death. Chapter 6 describes the sphingomyelin cycle in
which a stress signal activates a cell membrane-associated enzyme, sphingo-
myelinase, resulting in the formation of ceramide from sphingomyelin. In this
way various cytokines, such as TNF-a, interleukin-1, and -y-interferon, chemo-
therapeutic agents, and serum starvation can induce ceramide formation,
which activates cellular protein kinases and protein phosphatases involved in
cellular life and death decisions.
A well-known event in cell death is exteriorization of phosphatidylserine on
plasma membrane. This change allows binding of the anticoagulant protein
annexin V to this negatively charged phospholipid with great affinity, but is
not entirely specific for apoptosis. Approaches that allow the distinction of
apoptosis from necrosis based on annexin V techniques are the principal focus
of Chapter 7, which also discusses other cytoskeletal and nucleoskeletal
alterations associated with apoptosis.
Signals for apoptosis generated within the cell do not appear to be well
4
understood, but are known to include metabolic alterations in the mito-
chondria that result in the disruption of mitochondrial transmembrane
potential and changes in the cellular redox state. Chapter 8 addresses the
mitochondrial permeability transitions and the role of various aspects of
oxidative stress in the process of apoptosis. In particular, determination of
peroxide and superoxide levels and cellular glutathione content are pre-
sented, to illustrate how surrogate end-points can be used to investigate and
quantitate apoptosis-related phenomena.
An intermediate level of co-ordination of cell death versus survival signals is
largely controlled by members of the Bcl-2 family of protein. These are dis-
cussed in Chapter 9, with a wealth of techniques optimized in the Reed
laboratory, while investigation of the functioning of the caspase cascade is con-
sidered in Chapter 10. Extensive tabulation of the properties of caspases and of
polypeptides cleaved during apoptosis concludes Chapter 10 and this volume.
2. Historical perspective
It is not always realized that apoptosis affects cells one at a time. Indeed, this
form of cell death had been recognized earlier, as 'single cell necrosis'. The
original descriptions were reported over a hundred years ago by pathologists
studying liver diseases, but referred to as 'hyaline' or 'acidophilic bodies'. For
instance, Councilman described hyaline bodies in the livers of patients dying
of yellow fever (11), and subsequent electron microscopic studies concluded
that these structures, also often called 'Councilman bodies', represent the re-
mains of single dead hepatocytes (12, 13). Until recently, they were stated to
result from coagulative necrosis of single cells (14), but, interestingly, they were
noted to be eventually phagocytosed by macrophages. When the description
'apoptosis' was introduced by Kerr et al. in 1972 (4), this form of cell death fitted
right into the definition, and, indeed, this was experimentally confirmed (12).
In the strictest sense, apoptosis refers to manifestations of a process, a
programme leading to cell death, recognizable by morphological or a variety
of biochemical criteria, which are discussed in subsequent chapters. The
process itself, cell death, cannot, of course, be seen, and is detected by a com-
bination of its manifestations. Thus, the terms ' apoptosis' and 'programmed
cell death' are not exactly equivalent, nor is the phrase 'physiological cell
death', which generally implies a developmentally determined programme,
as opposed to 'chemoaptosis', in which the programme is triggered by
xenobiotics such as cancer chemotherapeutic drugs.
3. Distinction of apoptosis from other forms of cell

death
The current literature contains many examples of loose use of the term
'apoptosis'. There are several forms of cell death, and in all of them nuclear
5
DNA becomes degraded, at some point. As mentioned above, demonstration
of DNA damage or release of products of DNA degradation is by itself
insufficient to justify description of the phenomenon as apoptosis. The dis-
tinction is more than a semantic debate, since the concept behind the term
'apoptosis' is the existence of an inherent cellular programme, somewhat
similar to the programmes which drive cell differentiation, whereas 'necrosis'
results entirely from circumstances outside the cell. Other forms of cell death,
e.g. mitotic cell death, are insufficiently characterized to be considered at this
time as biologically distinct entities.
The distinction between apoptosis and necrosis can be made biochemically
(discussed on pp. 12-15) but is also very clear on purely morphological
grounds. As sketched in Figure 3, the apoptotic cell shrinks, nuclear chromatin
undergoes marked condensation, and it is expelled from the cells as apoptotic
bodies that are phagocytosed by neighbouring cells. In contrast, necrotic cells
first increase their cellular water content and thus their volume, the nuclei
lose the typical chromatin structure which is often seen as irregular clumping
and/or dissolution, and the cell membrane ruptures, discharging the cellular
contents into the environment. Many of the manifestations of necrosis appear
to be due to the depletion of cellular ATP by the agents or conditions
precipitating necrosis, and it is known that there are steps in the apoptotic
cascade that require ATP or dATP (15). This may be an incompletely
explored area for the study of how to distinguish controversial cases of cell
death; for further discussion of this interesting topic the report by Eguchi et al.
should be consulted (16).
The criteria currently most useful for distinguishing apoptosis from necrosis
are listed in Tables 1 and 2. Importantly, there are also similarities between
Table 1. Morphological differences and similarities between apoptosis and necrosis
Differences Similarities or
confounding variables
Apoptosis Necrosis
1. Nuclei Pyknosis Karyolysis Damage
and karyorrhexis preceded by occurs in
(dense condensation irregular chromatin both
of chromatin) clumping
2. Cytoplasmic Morphologically Disrupted Secondary damage
organelles intact in apoptosis
3. Cell membrane Apoptotic bodies, Blebbing and Changes seen
blebbing loss of integrity in both
4. Cell volume Cells shrink Cells swell There may be no
detectable changes
5. In tissues Single cells affected Groups of cells In epithelia superficial
affected cells are apoptotic and
in groups
6. Tissue response None Inflammation
6
Figure 3. A sketch of the key morphological differences between apoptosis and necrosis.
When a normal cell, depicted in (a), receives overriding signals to undergo apoptosis, it
first exhibits an irregular contour and appears smaller (b). The chromatin then shows
dense condensation, especially at the nuclear periphery, and small pieces of the cell,
usually containing condensed chromatin, break off (c). The pieces, called apoptotic
bodies, are taken up by phagocytosis by neighbouring cells, particularly macrophages if
these happen to be present (d). The apoptotic bodies are then gradually digested by the
phagocytic cells. In necrosis, the cells swell and chromatin often is alternatively diffuse or
finely clumped (e). The cytoplasmic organelles, such as the mitochondria, may be
swollen but remain intact. The necrotic cell eventually lyses, releasing all of its contents
into the extracellular space, and thus eliciting an inflammatory response by the tissue.
apoptosis and necrosis, and, in view of these and a frequent overlap of charac-
teristic features, conclusive evidence of the occurrence of apoptosis should
demonstrate more than one morphological or biochemical criterion of
apoptosis.
7
Table 2. Biochemical differences and similarities between apoptosis and necrosis
Differences Similarities or
confounding variables
Apoptosis Necrosis
1. Nuclear DNA Nucleosomal and/or Random Takes place in both,
damage 50-300 kb fragments —» smears easier to detect in
—» ladders on gels on gels apoptosis
2. Nuclear gene Usually needed Not needed Not needed in cells
expression primed for apoptosis
3. Mitochondrial Spared Occurs early
DNA damage
(a) DNases Necessary Not necessary Lysosomal DNase and
(b) Proteases Necessary proteases are activated
(c) Transglutaminase Frequent in necrosis
5. Membrane function Inact Loss of function —
6. Cell internal milieu
(a)pH Slightly acidic (pH 6.4) Acidic Both acidic
(b) Ca2+ Often increases Always increases Seen in both
(c) NaVK* pump May be intact Defective
(d) ATP Required Depleted
4. Apoptotic cascades
There appears to be an intricate but precisely ordered cellular machinery for
self-destruction. This machinery is a subject of intense current investigations
(discussed in several chapters in this volume) but some general principles have
already emerged. First, the initiating signals can be either extracellular or
intracellular. Secondly, many proteolytic enzymes are involved in apoptosis,
which can be subdivided into classes which either initiate the process, prop-
agate and amplify the signal, and those which attack the cellular structures to
cause their collapse (Figure 4). Third, the mitochondria play an important role
in this process, and many serve to integrate the various signals for apoptosis.
Fourth, the pro-apoptotic machinery interacts with cellular survival mechan-
isms at several levels, including the mitochondria and the execution caspases
(Figure 5). The suggested role for mitochondria in activation of the
executioner caspase-3 is further illustrated in Figure 6.
5. Time course of apoptotic cascades

A wide range of times has been reported for the duration of apoptosis. The
discrepancy is particularly marked when in vivo and tissue culture experi-
ments are compared. For instance, Figure 2 shows that DNA ladders, which
signify a late stage of apoptosis, are evident at 8 h after addition of 5 uM
doxorubicin to HL60 cells, and disruption of the inner mitochondria trans-
8
Figure 4. A conceptual outline of the major steps in the proteolytic cascade characteristic
of apoplosis. Note that signals for apoptosis can be generated from the outside or the
inside of a cell. The sequential activation of successive proteases (caspases) provides a
fail-safe mechanism that makes it possible to abort a premature apoptotic signal, and
also serves to amplify the signal to allow rapid finalizatiori of an irrevocable decision to
self-destruct.
membrane potential, an early event in apoptosis, can be detected in a similar

in vitro system (human myeloma cells treated with a retinoid) within 1 h (17).
In contrast, in an in vivo model of apoptosis that occurs in rat ventral prostate
after castration, the process was reported to take 44 h, and more detailed
analysis of this model suggested that the time gap between the apoptotic
trigger and the appearance of minimally abnormal morphology was 12-16 h.
The disassembly of apoptotic ceils into apoptotie bodies was estimated to take
9
Figure 5. A more detailed outline of apoptosis-signalling pathways. The mitochondria are

shown to act as the principal integrators of signals for apoptosis that do not have
dedicated membrane receptors for that purpose. The survival signals which counter the
pro-death signals are not shown, but components of the intracellular machinery that
promotes survival are indicated (Bcl-2, survivin). A few examples of cellular targets for
executioner caspases are also shown.
4-5 h, but the digestion of apoptotic bodies by the neighbouring cells, which
phagocytose these remnants, appeared to be a slow process, requiring
approximately 24 h (18).
Although these observations suggest that finding evidence of apoptosis in
animal tissues allows a reasonable window of time, this situation is not always
the case. Apoptotic bodies are frequently cleared from the tissues more
rapidly than in the central prostate, and there is an additional uncertainty as
to how rapidly the in vivo stimuli for apoptosis can reach the cell and be
summated before they exceed the threshold for initiation of cell death pro-
10
Figure 6. A detail of the role of mitochondria in triggering the caspase cascade. Note the
release of cytochrome c and the requirement for dATP. (Modified from Li et at., Cell, 91,
479,1997).
grammes. Thus, when looking for evidence of apoptosis in tissues, the old
adage, 'the absence of proof is not necessarily the proof of absence', becomes
particularly appropriate. The apoptotic cells and bodies may have been
missed.
The importance of careful selection of the time parameters for detection of
apoptotic is further discussed in Chapter 5.
6. Selection of methods
There are no infallible guidelines on how to chose a procedure that is ideal for
the study of apoptosis and its manifestations. The first basic rule is to consider
the objective of the study.
• If it is necessary to show simply that cells are dying, cell membrane
permeability tests are sufficient and very convenient, e.g. trypan blue
exclusion or permeability to propidium iodide.
• If it is to be demonstrated that apoptosis is the mode of cell death that has
taken place, simple morphology gives an excellent indication of this process,
11
both in vitro and in vivo, though it is more fashionable to include more
expensive procedures such as TUNEL or annexin V studies. When flow
cytometric equipment is available for determination of sub-Gl/GO DNA
content, this has been found to be exceedingly useful in daily use in the
author's laboratory. Demonstration of DNA ladders, if it can be done, is
very helpful in validating other procedures in the initial investigation of a
new system.
• If the objective is to study mechanistic aspects of apoptosis, any of the tech-
niques described in this volume may be appropriate, but in vitro systems
and isolated components of apoptotic cascades are particularly important
here. Examples are the release of cytochrome c from mitochondria and a
demonstration of the cleavage of procaspase-3 (10).
The second basic rule for the selection of methods for the investigation of
apoptosis is to decide which of the following is most important for the study:
sensitivity, specificity, ability to quantitate, and speed/economy with which
the determinations can be made. Sensitivity can be increased by enrichment
for fractions containing dead cells, such as the floating cells in adherent cell
populations, but, in general, these choices will vary depending on the
circumstances of the individual laboratory, and careful review of the following
chapters will provide guidelines for most investigators.
One procedure which is not described elsewhere, provides extraordinary
specificity and reasonable quantitation in an in vitro setting, although it
requires a significant amount of work and set-up for Southern analysis of
DNA. The test depends on the established fact that although the mito-
chondria show functional aberrations early in apoptosis, the mitochondrial
DNA remains intact, while in necrosis, mitochondrial DNA is subject to rapid
degradation (9,19).
6.1 Procedure for the determination of the increased

mitochondrial to nuclear DNA ratio, for detection and
quantitation of apoptosis
6.1.1 Principle
Mitochondria and other cellular organelles are preserved in apoptosis, but
undergo rapid degradation in necrosis (4,19). Mitochondria contain multiple
copies of a 16.5 kb circular DNA genome which encodes several mito-
chondrial proteins, and mitochondrial ribosomal and transfer RNAs (20, 21).
Nuclear DNA (nuDNA) is degraded in all forms of cell death. In contrast,
mitochondrial DNA (mtDNA) remains relatively intact in apoptosis, but
becomes degraded in necrosis (9, 19). Thus, determination of the integrity of
any mitochondrial gene relative to the integrity of a nuclear gene provides an
accurate procedure for distinguishing apoptosis form necrosis. In addition, the
12
ratio of the signal intensity of the mitochondrial to the nuclear gene allows
quantitation of the extent of apoptosis in the cell population (9).
DNA extracted from cells consists primarily of nuclear DNA (nuDNA) but
also contains mitochondrial DNA (mtDNA), and the mixture can be subjected
to restriction enzyme digestion and Southern blot analysis. The integrity of
the mitochondrial DNA is determined by the ratio of the abundance of a
mitochondrial gene representative of mtDNA (e.g. p72, ref. 22), to the abun-
dance of a nuclear gene representative of nuDNA. An example of such a
determination is shown in Figure 7, and its quantitation in Table 3.
Protocol 1. Analysis of cell death by comparison of mitochondrial

vs. nuclear DNA degradation assay
A. DNA isolation
Equipment and reagents
• Beckman J-6 centrifuge or equivalent • phenol/chloroform/isoamyl alcohol (25:24:1)
• digestion buffer: aqueous solution of 100 (Ameresco)
mM NaCI, 10 mM Tris-HCI (pH 8.0), 25 mM • ammonium acetate, 7.5 M
EDTA (pH 8.0), 0.5% SDS, 0.2 mg/ml . ethanol, 100%, 70%
proteinase K (PK) • TE buffer (pH 8.0): aqueous solution of 10
• chloroform/isoamyl alcohol (24:1) mM Tris-HCI, 5 mM EDTA
Method
1. Lyse the cells with the digestion buffer.
2. Incubate the lysed cells at 50°C for 12 h.
3. Extract the lysates once with phenol/chloroform/isoamyl alcohol, and
twice with chloroform/isoamyl alcohol.
4. Precipitate the DNA by adding ammonium acetate to 2.5 M, mix well,
then add 2 volumes of 100% ethanol.
5. Incubate at 4°C for at least 2 h.
6. Pellet the DNA by centrifugation at 4000 r.p.m. (12000 g) for 30 min at
RT.
7. Wash the pellets with 70% ethanol and repeat the centrifugation
step.
8. Aspirate the supernatant and air-dry the pellet.
9. Dissolve the pellet in TE buffer.
10. Take an aliquot for spectrophotometric readings at 260 and 280 nm.
11. The DNA extract obtained as described here can be used for part B.
13
Protocol 1. Continued
B. Restriction enzyme digestion of extracted DNA, and Southern analysis
• mt-gene probe (e.g. p72, 16S ribosomal . EcoRI (Gibco BRL)
RNA; see ref. 22) • Hindlll (Gibco BRL)
• nu-gene probe (e.g. c-myc) (Oncor) . NaCI, 0.2 M
Method
1. Digest 100 ug of the DNA samples from part A with EcoRI or H/ndlll
(3.5 U/ug DNA) for 8 h 37 °C.
2. Treat the reaction mixture with 2 units of DNase-free RNase for 1 h at
37°C.
3. Extract the samples with organic solvents as described in part A
(step 3).
4. Precipitate the digested DNA samples with 0.2 M NaCI and 100%
ethanol, wash the pellets with 70% ethanol, aspirate the supernatant,
and air-dry the pellet.
5. Dissolve the pellet in TE buffer and quantitate using a spectro-
photometer.
6. Electrophorese 10 ug of the DNA sample as described in Chapter 3,
Protocol 2.
7. Depurinate and denature the samples in the gel as described in ref. 23.
8. Transfer the DNA as described by Southern (24) and immobilize the
DNA on the membrane by drying and baking at 80°C for 2-5 h.
9. Nick translate the probes as described in ref. 25.
10. Add probes to the hybridization buffer.
11. Wash the membranes in SSC solution.
12. Wrap the membranes in plastic and expose to autoradiographic film
at -80°C for variable periods of time.
13. Analyse the film by densitometric image analysis for intensity.
7. Pitfalls
There is no doubt that apoptosis research will remain a vitally important area
of biological and medical research for some time to come. This very fact
provides some downsides, however. These include the sometimes exaggerated
claims of specificity for methods or reagents, the profusion of reports that may
be contradictory, and the expectation of some that the quality of the science
14
Figure 7. A Southern blot of the DNA shown in Figure 2, hybridized first to a nriito-
chondrial DNA probe (p72), then rehybridized to immunoglobulin lambda constant
region gene (c). Note that the mitochondrial gene signal increases during doxorubicin-
induced apoptosis of HL60 cells, but decreases during doxorubicin-induced necrosis of
K562 cells. In contrast, the nuclear gene signal decreased during apoptosis of HL60 cells,
but increased slightly during necrosis of K562 cells. The slight increase in the nuclear
gene signal is due to the enrichment of the DNA sample with nuclear DNA because of the
loss of mitochondrial DNA,
in a project or report may be elevated by the simple expedient of including an

experiment or two on apoptosis, It is therefore probably more important than
in any other field of science to maintain a highly critical attitude to assertions
that a particular experimental manoeuver results in the occurrence of
apoptosis.
The usual precaution is to demonstrate features of apoptosis by more than
one independent approach. It is also important to prevent artefactual DNA
damage that may mimic apoptotic DNA fragmentation. The loading of intact
cells to be lysed in the gel is described in Chapter 3, Protocol 1. Overloading
of gels with DNA produces smears rather than ladders, and attention to this
point is a simple way to improve one's credibility. Another precaution often
overlooked is to establish precisely the diploid DNA content of the cells
under investigation before determining the sub-Gl values, since tumour cell
populations are not infrequently composed of a mixture of diploid and
15
Table 3. Ratios of mtDNA to nuDNA during apoptosis in leukaemic cell lines
p72/c-myc ratioa
Cell line Treatment Concentration Duration EcoRI Hind III
(mM) (h)
MOLT-4 Control 1.00 1.00
Doxorubicin 10 12 3.43±0.56 2.50±0.51
Dox 10 24 7.50±1.27 7.70±0.92
U937 Control 1.00
Teniposide 5 12 4.18±0.57 NDb
ARA-C 10 12 4.24±0.11 ND
"Nuclear DNA and mtDNA levels were compared directly by sequential hybridization of the same
membrane with probes for c-myc as a representative nuclear gene, and p72, a probe for mtDNA.
Following densitometry of the autoradiographs, the ratios of the relative values of mtDNA/nuclear
gene were obtained for untreated cells ('controls') and for each treated group. Control mtDNA/nuDNA
ratios were converted to a value of 1.00, and the 'treated' mtDNA/nuDNA ratios were mutliplied by the
same conversion factor yielding the values presented, ±S.E.M.
b
Not done.
aneuploid cells. Under these circumstances the diploid peak can mimic the
apoptotic sub-Gl peak.
The avoidance of these and other pitfalls and shortcuts should accelerate
the acquisition of meaningful advances in apoptosis research.
Acknowledgements
I thank Dr Xuening Wang for help with the figures and Ms Claudine Marshall
for secretarial assistance. The experimental work in my laboratory is
supported by USPHS grant RO1-CA44722 from the National Cancer
Institute.
References
1. Sulston, J.E., Schierenberg, E., White, J.G., and Thomson, J.N. (1983). Dev. Biol.,
100, 64.
2. Wylie, A.H.,Morris, R.G., Smith, A.L., and Dunlop, D. (1984). J. Pathol., 142, 67.
3. Eastman, A., Grant, S., Lock, R., Tritton, T., VanHouten, N., and Yuan, J. (1994).
Cancer Res., 54, 2812.
4. Kerr, J.F.R., Wylie, A.M., and Currie, A.R. (1972). Br. J. Cancer, 26,239.
5. Skalka, M., Matyasova, J., and Cejkovan, M. (1976). FEBS Lett., 72,271.
6. Wylie, A.H. (1980). Nature, 284,555.
7. Oberhamner, F., Wilson, J.W., Dive, C., Morris, I.D., Hickman, J.A., Wakeling,
A.E., Walker, P.R., and Sikorska, M. (1993). EMBO J., 12, 3679.
8. Walker, R.P., Weaver, V.M., Lach, B., Leblanc, J., and Sikorska, M. (1994). Exp.
Cell Res., 213,100.
16
9. Tepper, C.G. and Studzinski, G.P. (1993). J. Cell. Biochem., 52,352.
10. Wang, X. and Studzinski, G.P. (1997). Exp. Cell Res., 235,210.
11. Councilman, W.T. (1890). In Report on the etiology and prevention of yellow fever
(ed. G.M. Sternberg), United States Marine Hospital Service, Treasury Dept.,
Document No 1328 (Public Health Bulletin 2), pp. 151-159. Government Printing
Office, Washington, D.C.
12. Kerr, J.F., Cooksley, W.G., Searle, J., Halliday, J.W., Halliday, W.J., Holder, L,
Roberts, L, Burnett, W., and Powell, L.W. (1979). Lancet, 2, 827.
13. Lacronique, V., Mignon, A., Fabre, M., Viollet, B., Rouquet, N., Molina,T.,
Porteu, A., Henrion, A., Bouscary, D., Varlet, P., Joulin, V., and Kahn, A. (1996).
Nat. Med. 2, 80.
14. Farber, J.L. and Rubin, E. (1988), in: Pathology, J.B. Lippincott Co., Philadelphia,
P15.
15. Liu, X, Kim, C.N., Yang, J., Jemmerson, R., and Wang, X. (1996). Cell, 86,147.
16. Eguchi, Y., Shimizu, S., and Tsujimoto, Y. (1997). Cancer Res., 57,1835.
17. Marchetti, P., Schraen-Maschke, S., Thomas, A.M., Dhuiege, E., Belin, M.T., and
Formstecher, P. (1999), In Proceedings of the steroid receptor superfamily AACR
special conference (ed. M.G. Rosenfeld and C.K. Glass), AACR, Philadelphia,
PA. p. A23.
18. Hu, Z., Ito, T., Yuri, K., Xie, C, Ozawa, H., and Kawata, M. (1998). Cell Tissue
Res, 294,153.
19. Murgia, M., Pizzo, P., Sandonia, D., Zanovello, P., Rizzuto, R., and DiVirgillio, F.
(1992). J. Biol. Chem., 267,127.
20. Anderson, S., Bankier, A.T., Barrell, B.G., deBruijn, M.H.L., Coulson, A.R.,
Drouin, J., Eperon, I.C., Nierlich, D.P., Roe, B.A., Sanger, F., Schreire, P.H.,
Smith, A.J.H., Staden, R., and Young, I.G. (1981). Nature, 290, 457.
21. Clayton, D.A. (1984). Annu. Rev. Biochem., 53, 573.
22. Tepper, C.G., Pater, M.M., Pater, A.M., Xu, H.M., and Studzinski, G.P. (1992).
Anal. Biochem., 203,127.
23. Wahl, G.M. Stern, M., and Stark, G.R. (1979). Proc. Natl. Acad. Sci. USA, 76,
3683.
24. Southern, E.M. (1975). J. Mol. Biol., 98,503.
25. Maniatis, T., Fritsch, E.F., and Sambrook, J. (1982). Molecular cloning: a
laboratory manual. Cold Spring Harbor Lab., New York.
17
2
Morphological recognition of
apoptotic cells
JAMES W. WILSON and CHRISTOPHER S. POTTEN
1. Introduction
In this chapter we outline the basic techniques that can be used to identify
apoptotic cells on the basis of morphology. All these techniques require the
use of some type of microscope, and obviously, the better the microscope then
the easier your job is in assessing cell morphology. In addition to the
subjective assessment of cellular/nuclear appearance, the use of immuno-
cytochemical techniques specifically designed for the recognition of apoptotic
cells is also outlined. Finally, we discuss how to extract quantitative informa-
tion from such observations, and how such quantitative data may be inter-
preted. Techniques for detecting the biochemical changes accompanying
apoptosis are described in subsequent chapters.
1.1 Key morphological features of apoptotic cells

A seminal paper in apoptosis research was that by Kerr et al. (1). Their
electron microscopic study of prednisolone-induced cell death in the kidney
defined the term apoptosis and provided the standard reference for the key
morphological features associated with this form of cell death. A cell under-
going apoptosis proceeds through various stages of morphological change
(see Figure 1). These are shrinkage of the cell away from its neighbours,
plasma membrane blebbing, cytoplasmic and nuclear condensation, non-
random cleavage of chromatin, margination of chromatin in the nucleus,
nuclear fragmentation, and cellular fragmentation into smaller apoptotic
bodies. Cells and cell fragments are ultimately phagocytosed by neighbouring
cells and 'professional' phagocytes.
James W. Wilson and Christopher S. Fatten
Figure 1. Schematic diagram of morphological changes associated with apoptosis.
2. Light and fluorescent microscopy techniques for

the assessment of apoptosis
2.1 Preparation of cell or tissue samples
2.1,1 Slide preparation
The majority of protocols outlined in this chapter require the mounting of
samples on glass microscope slides. In order to increase the adhesiveness of
cel] or tissue sections, slides need to be coated, or 'subbed'. The two most
eommon subbing agents are gelatine and 3-aminopropyl triethoxysilane
(APES), Gelatine is a good general purpose reagent, however, if microwave-
based antigen retrieval is used for immunohistochemistry that is to be carried
out in parallel with morphological assessment, then APES is recommended.
Protocol 1. Gelatine subbing
Reagents
. 10% acetic acid * 0,5 g gelatin
• ethanol (90, 9E, 100%)
Method
1. Acid-wash the slides or covers lips for 1-2 days, in 10% acetic acid/90%
ethanol.
2. Rinse (x 5) in deionized water, then 95% ethanol, and finally 100%
ethanol. Store in 100% ethanol.
20
2: Morphological recognition of apoptosis
3. Dissolve 0.5 g gelatin in 100 ml of deionized water (at 65°C). Allow the
solution to cool to room temperature prior to filtering through
Whatman number 1 filter paper. Store the gelatine at 4°C.
4. When required, re-melt the gelatine using gentle heat (i.e. in a water
bath).
5. Dip slides/coverslips in liquid gelatine, in a dust-free environment (i.e.
a microbiological safety cabinet).
6. Place the slides/coverslips in a rack and allow to dry vertically.
Protocol 2. APES subbing
Reagents
• decon-90 • acetone
. 2% APES
Method
1. Wash the slides in decon-90 (2% in water) for 5 min, and warm water
for 5 min.
2. Place the slides in an acetone bath for 1 min, prior to immersion in 2%
APES in acetone, for 5 min.
3. Rinse the slides in fresh acetone for 1 min, and in running deionized
water for 5 min.
4. Place the slides at 60°C for 1 min to dry.
2.1.2 Preparation of tissue sections
Protocol 3. Using formaldehyde-fixed, paraffin wax-embedded

tissue

• PBS, pH 7.4 • ethanol
• 4% formaldehyde • microtome
• chloroform
Method
1. Wash the tissue (animal/human) in ice-cold, phosphate-buffered saline
(PBS, pH 7.4), prior to fixation in 4% formaldehyde in PBS overnight, at
4°C.
2. Dehydrate the tissue through a series of graded alcohols (70% x 3,
21
James W. Wilson and Christopher S. potten
90%, 95%, 100% X 3). Allow 30-60 min for each step, depending on
the size of the tissue sample.
3. Transfer the tissue to chloroform/ethanol. After 30-60 min, transfer to
100% chloroform. Change to fresh chloroform for a further 30-60 min.
4. Place the tissue in molten wax at 60°C, for 30 min. Place under partial
vacuum and leave for a further 30 min. Change to fresh wax (at 60°C)
and place under full vacuum for 2 h.
5. Dispense fresh wax into a mould, place on a cooling tray, and allow to
begin to set.
6. Place the tissue in the required orientation within the wax and allow to
set fully.
7. Section at 3-5 um using a microtome. Expand the sections by floating
on deionized water, at about 48-50°C. Pick up the sections on to APES-
or gelatin-coated slides. Rack the slides and dry at 37°C overnight.
8. Store the slides in a dry, cool place. If slides are also to be used for
immunohistochemistry, store at 4°C.
Protocol 4. Using frozen tissue sections

• PBS . APES
• liquid nitrogen • acetone
• OCT compound (optimal cutting temperature: OCT) • methanol
• cryostat and cryovials
Method
1. Wash the tissue in ice-cold PBS (pH 7.4). Remove excess moisture by
blotting on a paper towel.
2. Freeze the tissue in the vapour phase of liquid nitrogen, by placing in a
small petri dish and floating this on the surface of the liquid nitrogen.
Store in cryovials, under liquid nitrogen, until use. For some tissues,
i.e. skeletal muscle, freezing the tissue in liquid nitrogen-cooled
isopentane is advised to give better preservation of tissue architecture.
3. Embed in OCT compound and section using a cryostat (tissue may be
stored in cryovials at -80°C or lower, until required).
4. Pick up sections on to APES- or gelatin-coated microscope slides or
coverslips.
5. Fix sections in acetone/methanol (1:1), for 3 min at -20°C, in a spark-
proof freezer. Air-dry the sections for 10 min and store at -80°C until
use.
22
2.1.3 Preparation of cell culture samples

The preparation of samples from cell cultures is relatively straightforward and
less labour intensive than the preparation of tissue sections.
Protocol 5. Preparation of cells in suspension cultures
Method
1. Harvest the cells from tissue culture.
2. Resuspend the cells at a density of ~1 x 106 cells/ml.
3. Load 100-200 ul of cell suspension into the reservoir of a cytospin
slide, and spin on to coated slides, at 500 r.p.m. (c. 30g) for 2-3 min
(Shandon Cytospin 3). Allow to air-dry.
Cells may be fixed immediately after harvesting or after spun slides have been air-dried.
Common fixation techniques are 30 min in 4% paraformaldehyde in PBS (pH 7.4) at 4°C or 3
min in acetone/methanol (1:1), at-20°C.
Unfixed cells in suspension may also be mixed directly with nuclear stains, as detailed in
Protocol 70.
Protocol 6. Preparation of cells from monolayer cultures
Method
1. Either, harvest cells using trypsin/EDTA treatment and treat as in
Protocol 5.
2. Or, if cells are able, grow them on glass coverslips (or slides). Cover-
slips can be easily removed from the tissue culture dish using a
suitable implement. Cells on slides/coverslips can be fixed according
to the methods in Protocol 5.
3. Alternatively, grow cells in chamber slides. Fixation of cells on
chamber slides should be carried out using 100% methanol at -20°C;
acetone will dissolve the plastic slide. As an alternative to chamber
slides, cells can be grown in conventional culture flasks, and when
assessment of morphology is required the top and side of the flask
may be removed by a model-makers electric cutting tool, or by other
means.
2.2 Nuclear counterstains

There are numerous stains and dyes that are employed to assess nuclear
morphology. This chapter will concentrate on the methods we currently
23
James W. Wiison and Christopher S. Potten
employ in our laboratory, which we feel allow accurate assessment of nuclear
morphology and apoptosis. Stains and dyes arc separated according to their
use in either light or fluorescent microscopy.
2.2,1 Stains for light microscopy
Haematoxylin and thionin blue are the two nuclear counterstains that are
most frequently used in our laboratory. They are both used for conventional
light microscopic examination of sections of formaldehyde-fixed, wax-em-
bedded tissue. They give a blue stain to all nuclei and have good contrast. The
condensed chromatin within apoplotie cells stains particularly heavily. Mitotic
nuclei also stain darkly, but can be differentiated because of their larger size
and more fuzzy appearance. The chromalin masses within apoptotic cells tend
to have 'sharp' borders. In the intestinal epithelium, mitotic cells tend to
appear more displaced towards the centre of the crypt lumen, although this
can also be true of some apoptotic cells/bodies. In our laboratory we routinely
use haematoxylin and eosin staining for assessment of apoptosis in tissue
sections, in parallel with whole-tissue autoradiography for studying tritiated
thymidine incorporation. Thionin blue is most commonly used as a counter-
stain when apoptosis is being assessed in parallel with immunoreaetivity in
wax-embedded tissue sections. Examples of apoptotic cells in haernatoxylm-
and thionin-stained small intestinal epilhelia are shown in Figure 2.
Wax-embedded tissue sections need to be hydrated prior to staining, as in
Protocol 7, If the staining is carried out at the end of a procedure such as
Figure 2. H&E staining of large intestinal crypt (A) and thionin blue staining of small
intestinal crypt (B), from a mouse, 4 h after exposure to 16 Gy y-radiation. Apoplotic
cells/bodies are indicated by arrow heads.
24
immunocytochemistry or autoradiography, the sections will already be in a
hydrated state and can be used directly, as detailed in Protocol 8.
Protocol 7. Rehydration of slides
Reagents
• xylene • ethanol
Method
1. Warm the slides to 60°C for 10-15 min in an oven, to melt the wax.
2. Place in fresh xylene for 5 min, with constant agitation.
3. Transfer the slides to absolute alcohol for 5 min.
4. Rehydrate the slides through a graded series of alcohols: three further
changes of 100%, then 95%, 90%, 70%, and 40%, with 3 min in each.
5. Finally, rinse the slides in deionized water.
Protocol 8. Haematoxylin (and eosin: H&E)
Reagents
• Gill's haematoxylin • ethanol
• ammonia solution • xylene
• eosin
Method
1. Place slides in Gill's x 2 haematoxylin for 3 min.
2. Rinse slides in running water for 1 min.
3. Give slides three dips in alkali water (deionized water with 4-5 drops of
ammonia solution) and return to running water for a further minute.
This results in the pink staining turning blue. If the blue coloration is
too dark (this can be checked quickly using a microscope), it can
hinder morphological assessment and the scoring of any parallel
autoradiography. The stain may be lightened by placing slides in acid
water (deionized water with a few drops of HCI) for a few seconds.
Then rinse the slide in running water and re-examine.
4. Transfer to alcoholic eosin (0.4% eosin in 70% ethanol) for 1 min.
5. Rinse in running water for 1 min.
6. Dehydrate through a series of graded alcohols (40%, 70%, 90%, 95%,
and 3-4 changes of 100% alcohol), with 5 min in each.
7. Place in xylene for 30 min, then mount slides using a permanent
mount (XAM, DPX).
25
8. Allow slides to dry overnight, prior to microscopic examination of
sections.
Gill's haematoxylin no. 2 (product code 6765007, Shandon Inc.) is the stain of choice in our
laboratory as it is relatively stable and gives reproducible and uniform staining. There are
other, commomly used haematoxylins, including Ehrlich's, Meyer's, and Harris's. Ehrlich's
stain requires two months to ripen prior to use, although it is very stable and gives excellent
morphology. Meyer's stain is prepared with chloral hydrate, and Harris's with mercuric oxide,
which make them unattractive for general laboratory use. Both the latter stains go off quickly
compared with Gill's. More information regarding the applications of different haematoxylin
stains can be obtained in: Theory and practice of histological hechniques (ed. J.D. Bancroft and
A. Stevens), p. 107. Churchill Livingstone, Edinburgh (1990).
Protocol 9. Thionin blue
Reagents
• Thionin blue (4 parts solution A and 1 part • solution B: 8 ml glacial acetic acid, 18 ml 5
solution B) M sodium hydroxide, made up to 100 ml
• 80% methanol with deionized water
• solution A: 0.5 g thionin acetate (Sigma, • 100% ethanol
T7029) in 100 ml methanol (filtered)
Method
1. Place the slides in thionin blue for 10 min.
2. Transfer to 80% methanol for 10 min.
3. Give the slides 10 dips in 95% ethanol. Repeat.
4. Transfer to absolute ethanol for 10 min.
5. Treat as for Protocol 8, steps 7 and 8.
Thionin may be reused many times before staining intensity is impaired. Methanol (80%) may
also be reused, until it becomes too discoloured.
2.2.2 Stains for fluorescence microscopy

Fluorescent nuclear counterstains are most appropriate for use with cultured
cell systems, and when fluorescent detection methods are being used in para-
llel for immunohistochemistry. The most commonly used are 4',6-diamidino-
2-phenylindole (DAPI), Hoechst 33258 and 33342, acridine orange, and
propidium iodide. As with the stains used for light microscopy, the tissue must
be hydrated prior to staining.
Hoechst 33258 stains non-apoptotic human and murine nuclei differentially.
Human nuclei have a uniform, diffuse stain, whereas murine nuclei demon-
strate several small, brightly staining bodies (2). Although there are no data to
suggest that apoptotic cells from different species are stained differentially,
26
this property of the Hoechst dye can be very useful when carrying out
morphological assessment of xenografted human tissues in immune-deficient
mice (3, 4), as it permits a distinction to be made between mouse and human
tissue. One possible caveat with the use of Hoechst dyes is that they have
been shown to induce apoptosis (5). However, this is only going to be a
problem in unfixed tissue, and the length of time required to induce this effect
(3 h) means that it should be irrelevant in all but exceptional circumstances.
Protocol 10. Fluorescent stains
Reagents
Make up stains as follows: • Acridine orange: 2 mg/ml stock in PBS,
• DAPI: 5 mg/ml stock in methanol. Prior to pH7.4. Prior to use dilute 1:400 in PBS
use, dilute 1:10000 in PBS, pH 7.4 (Sigma (Sigma)
D9542). • Propidium iodide: 2 mg/ml stock in PBS, pH
. Hoechst 33258 and 33342: 100 ug/ml stock 7.4. Prior to use, dilute 1:1500 in PBS
in PBS, pH 7.4. Prior to use, dilute 1:10 in (Sigma P4170).
PBS (Sigma B2883 and B2261).
Method
1. Incubate the cells/sections with stain for 3-5 min. For cell suspensions,
resuspend the cells at a density of ~2 x 106 cells/ml and mix with an
equal volume of dye.
2. Wash the cells/sections twice in PBS.
3. Mount using an aqueous-based mountant, with an anti-fade additive
(Vectorshield, H1000; Vector Labs Inc.).
Acridine orange has been the dye of choice for many years for researchers
studying developmental cell death in Drosophila (6-8). Acridine orange is a
vital dye, i.e. it is excluded by viable cells. Staining of non-fixed, whole
embryos with acridine orange allows the investigator to examine the spatial
and temporal aspects of cell death in developing Drosophila embryos, using
confocal fluorescence microscopy. Experimental details concerning this
technique can be found in refs 6-8.
3. Electron microscopic techniques

Electron microscopy was the original technique used by Kerr et al. (1) in their
seminal publication on apoptosis. It provides the most detailed information
for the assessment of cell morphology, and hence the most accurate deter-
mination of apoptosis in tissues. However, it requires more expensive equip-
ment and takes longer than other methods. Protocol 11 describes a method
for transmission electron microscopic study of cell lines and isolated cells
from tissues. Prior to starting Protocol 11, cultured cells must be harvested by
27
conventional means. Cells from normal tissues and tumours may be isolated
by a variety of methods, including scraping and mechanical disaggregation, in
combination with mild enzymatic treatment or chelating agents. Readers are
advised to seek more specialized texts for the optimal preparation of specific
tissues. Particular care needs to be taken when preparing samples for electron
microscopy that are also going to be used for immunolabelling of proteins and
RNAs. Here, the use of low-temperature embedding procedures is recom-
mended in order to preserve antigenicity (9,10).
Protocol 11. Preparation of cells for transmission electron

microscopy (TEM)
Reagents
• 0.1 M sodium cocodylate buffer (pH 7.2-7.4) • 2% magnesium uranyl acetate
• 2% paraformaldehyde • Spurr's resin mixture
• glutaraldehyde • 0.3% lead citrate
• 1% osmium tetroxide
Method
11. Resuspend the cells at a density of ~2 X 107/ml in 0.1 M sodium
cacodylate buffer. For this protocol a 1.5 ml plastic centrifuge tube is
a useful size to carry out the procedures in.
12. After 5 min, pellet the cells by centrifugation, and resuspend in 2%
paraformaldehyde/2% glutaraldehyde in 0.1 M sodium cacodylate
buffer (Tooze fixative). Leave the cells in the Tooze fix for 1 h.
13. Pellet the cells by centrifugation, and resuspend in 0.1 M sodium
cacodylate buffer.
14. Pellet the cells again after a further 5 min, and resuspend in 1%
osmium tetroxide, in 0.1 M sodium cacodylate buffer. Leave for 1 h.
15. After 1 h, pellet and resuspend the cells in 2% magnesium uranyl
acetate (in 70% ethanol). Leave overnight, in the dark.
16. The following day, dehydrate the cells in a graded series of alcohols
(3 x 70%, 90%, 95%), allowing 15 min in each.
17. Carry out three further changes in 100% ethanol, allowing 1 h between
each change.
18. After dehydration, allow 1-2 h for infiltration of absolute alcohol/
Spurr's resin mixture (1:1).
19. Change the alcohol/resin mixture for 100% Spurr's resin and allow
further infiltration overnight.
10. The next day carry out a further three changes of resin, and finally
polymerize the block overnight at 60°C.
28
11. Cut the sections (at 30-50 nm thickness) on to water using an
ultra microtome,
12. Expand the sections with chloroform, prior to transferring to copper
mesh support grids. Allow the sections to dry.
13. Stain the sections with 2% uranyl acetate (in 70% ethanol) for 20 min.
14. Wash the sections three times with deionized water, prior to staining
in 0.3% lead citrate (lead nitrate and lead acetate are also used
routinely) for 3-4 min.
15. Wash three times in deionized water and allow to air-dry.
16. Examine the sections using a transmission electron microscope.
Electron microscopic (EM) evidence of apoptosis is illustarted in Figure 3.
4. Quantitation of apoptotic events

4.1 Methods
This is a very labour-intensive task, requiring much time being spent on the
microscopic examination of prepared samples. Cells in suspension, stained
with fluorescent nuclear dyes, are loaded on a haemocytometer and viable
Figure 3. (a) Transmission electron micrograph of several apoptotic bodies which have
been phagocytosed by a neighbouring cell. One of the phagocytosed bodies appears to
be a celt which itself has previously phagocytosed another cell. The micrograph is of the
base of a small intestinal crypt. The elecron-opaque bodies marked G are Paneth cell
granules. To the bottom right of the picture is the nucleus of the phagocytosing cell (N).
We are grateful to Dr T.D. Allen for the production of this electron micrograph.
(b) Budding apoptotic bodies and crescents in HL60 cells treated with 20 uM etoposide
for 6 h (supplied by G.P. Studzinski).
29
cells and apoptotic cells are logged simply by use of a tally counter. Cytospun
slides, cell monolayers, and tissue sections may be scored in a similar way,
except that a graticule can be placed in the eye piece of the microscope to
substitute for the haemocytometer.
Methods do exist to make counting easier and to reduce the time spent
staring down a microscope, which include flow cytometry (see Chapter 4). In
our laboratory we use a Zeiss Axiohome system. This consists of a microscope
linked to a computer, which can monitor the co-ordinate position of the
microscope stage and allows the user to overlay a projected image of tally
symbols on the counted cells. The microscope automatically keeps a record of
the total number of each symbol used. This system is particularly useful when
scoring tissue sections with little or no structural organization, i.e. tumours
and hair follicles. When scoring, it is the general practice to record observa-
tions of 1000 cells from 10 random fields. Video capture of slide images is one
method which allows the observer more independence from the microscope.
Digital images can then be analysed on screen; however, this does not allow
the observer to focus up and down on an object in the slide that may be
slightly out of plane (focus), which can be critical for assessing the number of
small apoptotic bodies. The use of serial images from confocal microscopy is
desirable, since it eliminates this problem.
For structurally organized tissue such as the intestine, it is possible to score
the cells on a positional basis. This technique has revealed important bio-
logical differences between cells and allowed a number of issues to be
addressed. One critical procedure to carry out this scoring is the optimal
preparation and orientation of tissue sections. The method used in our
laboratory is outlined in Protocol 12.
Protocol 12. Preparation of tissue for the positional scoring of

apoptotic events in gastrointestinal epithelia of
mice
Method
1. Excise the small and large intestine and flush with ice-cold PBS.
2. Separate the intestine into different regions, i.e. duodenum, jejunum,
upper ileum, lower ileum, caecum, mid-colon/rectum.
3. Cut into 1 cm lengths.
4. 'Bundle' together up to 10 pieces of intestine:
(a) cut an 8-10 cm length of micropore tape and form a loop by
sticking the two ends together,
(b) lay the pieces of intestine parallel to each other within the loop
and bind together with micropore tape,
(c) cut a 4-5 mm thick cross-sectional disc from the taped bundle.
30
5. Process these smaller bundles for histology, as described in Protocol 3.
6. Cut sections through the bundles and process by one of the protocols
described in Section 2.2.
7. Examine the slides.
If the tissue is prepared as described in Protocol 12, slides with good

transverse sections of the intestine and good longitudinal crypt sections will
be obtained. Cells can be numbered from the base of the crypt, starting at cell
position one, with each side of a crypt (half-crypt) being scored separately.
Fifty half-crypts are commonly scored for each region of the intestine; ideally
from 4-5 bundles containing 5-10 individual cross-sections. The average length
of a small intestinal half-crypt is 20 cells, i.e. 50 half-crypts is equivalent to
1000 cells. The data are recorded on a laptop computer, using custom-written
software for data acquisition and analysis (PC Crypts, Steve Roberts, Bio-
statistics and Computing Department, PICR). The recording of data in this
way allows the frequency distributions of events (i.e. apoptosis, mitosis) to be
plotted for each cell position. This is illustrated in Figure 4. All positions can
be related to cell lineage position and, thus, stem cell properties can be
studied (11,12).
4.2 Problems in scoring apoptotic events

Quantitation of apoptotic events in cellular/tissue systems is always a topic
that raises much debate. The major problem is whether the methods used
accurately determine the frequency of apoptotic events, i.e. cell deaths, and
how to interpret such numbers (11,12). A number of factors can influence the
frequency of apoptotic events, or 'apoptotic index'. These include:
(a) Half-life. The half-life of apoptotic cells differs between cell systems/
tissues. In a tissue/cell line where apoptotic cells have a long half-life,
samples at different times over a given period will show a higher
frequency of events, compared with tissue where apoptotic cells have a
short half-life, even though the absolute number of cell deaths may be the
same.
Half-life itself is influenced by other factors. These include the rate at which
cells are cleared by phagocytosis, migration of cells in a hierarchical system
such as the intestinal tract, and the rate at which degradative changes take
place. We have previously published data that suggest that the half-life of
apoptotic cells may vary according to the cytotoxic agent used to induce
apoptosis (see ref. 12 and references therein).
(b) Section thickness. Apoptotic cells are smaller than neighbouring, viable
cells. They also fragment into yet smaller apoptotic bodies. Therefore, if
very thin sections are cut through a tissue block, the apoptotic nuclei may
31
Figure 4. Scoring of apoptosis on a cell positional basis in the intestinal crypts. Small
intestinal crypts from a mouse exposed to -y-radiation are shown in (a). Individual cells
can be assigned a numerical value, according to their histological appearance. This is
recorded on a laptop computer as a string of numbers, as demonstrated in (b). Pooling of
data from 50 half-crypts can then be used to construct frequency distributions (c): the
data shown are for irradiated crypts 4 h after exposure to 16 Gy y-radiation (solid line)
and unirradiated crypts (broken line). In addition to apoptosis, we commonly use this
technique to analyse mitotic events, incorporation of tritiated thymidine, and the
expression of nuclear antigens.
be 'missed', resulting in an underestimation of apoptotic frequency. The

use of thicker sections may allow better visualization of apoplolic events.
hut overall the structural organization of the tissue may become less clear,
as is the case with the intestinal tract. Whole-mount preparation of crypts
can give better estimates of the frequency of apoptotic events (13, 14);
however, their use is not suitable for routine examination of a large
number of tissue samples,
(c) Criteria selected for scoring. It is important for observers to be consistent
in their application of selection criteria for apoptotic cells. Most workers
would tend to err on the side of caution and only score those cells that are
unambiguously apoptotic. Apart from recognizing apoptotic cells, there is
the question of whether one should count every apoptotic body or try to
assess how many apoptotic events are represented by a group of
apoptotic bodies. This situation can be illuslarted by a comparison of the
32
scoring of small intestinal epithelium and of proliferating hair follicles.
The well-ordered structure of the small intestinal epithelium may allow
the determination of whether given apoptotic bodies are the result of a
single apoptotic event. In contrast, the hair follicle does not visibly
demonstrate a highly ordered structure (although there is a cellular
hierarchy), making this kind of assessment impossible. In this case, it is
better to score all apoptotic bodies. As with the half-life of apoptotic
cells/bodies, the number of apoptotic fragments arising from a single cell
death may vary according to the cytotoxic insult.
(d) Circadian rhythm. This is certainly of relevance in the gastrointestinal
tract, and probably also in other tissues, although diurnal variation in
some tissues is less well characterized. We have shown that the rate of cell
proliferation and cell migration in the intestinal crypts varies according to
the time of day at which observations are made (15). When making
comparisons between different treatments/experiments, therefore, it is
essential that observations that are being contrasted are made at the same
time of day.
(e) Cellular hierarchies. In hierarchical tissues, such as the intestinal
epithelium, the sensitivity of any given cell to an apoptotic stimulus is
determined by its position in that hierarchy. It is therefore useful to
represent the frequency of apoptotic events in relation to this position
within the hierarchy. This information can be very useful in determining
whether effects are observed in selected cell types.
(f) The denominator of the apoptotic index. The apoptotic index (AI) is the
number of apoptotic cells/bodies divided by the total number of cells.
Within the well-ordered intestinal epithelium, the denominator can be
determined reasonably accurately. For tissues with less visible organ-
ization, i.e. tumours and hair follicles, cell counts will be less accurate.
Also, in heterogeneous tissue such as tumours, there can be variation in
the rates of cell proliferation and cell death in different regions of the
tissue. Consequently, it can be useful to determine the ratio of the
apoptotic index in relation to the proliferation index (cell in S phase,
measured by bromodeoxyuridine or tritiated thymidine incorporation) or
the mitotic index (MI). The AI:MI ratio effectively eliminates the
denominator and any uncertainties associated with it. It also provides
useful information on any net changes in cell number that are occurring
within a tissue.
5. In situ detection of DNA strand breaks

In the last few years, techniques based on the detection of DNA strand breaks
have gained popularity as methods for the identification of apoptotic cells.
Two main techniques exist. They are: terminal deoxynucleotide transferase-
33
James W. Wilson and Christopher S. Potton
mediated dUTP-hiotin nick-end labelling ( 1 6 ) , usually known by the acronym
TUNEL.: and DNA polymerase l-mediated in side end-labelling, or ISHI. ( 1 7 ,
I S ) , The incorporation of b i o t i n y l a t e d or digoxygen in-labelled bases into
damaged DNA allows their subsequent detection by anti-biotin. or anti-
digoxygenin i m m u n o g l o b u l i n s . Conventional immunohistoeheniieal detection
t e c h n i q u e s are t h e n used. The T U N E , t e c h n i q u e labels all DNA ends, i.e. V-
overhangs. 3'-overhangs, and blunt ends. However, the 1SEL technique only
labels 3''-overhanging ends, m a k i n g it less sensitive t h a n T U N K L ,
The lediniqLies have been reported to be much more sensitive in delectinil
apopiotic cells, especially at an early stage, in comparison with morphological
scoring of cells in H&F sections and flow eylomelric analysis ( 1 9 ) . For some
tissues t h i s technique seems to work q u i t e well; however, we have f o u n d that
the technique has many problems, as previously reported (14, 20). In our
studies of radiation-induced apoplosis in the i n t e s t i n a l e p i t h e l i u m , we have
obtained s l a i n i n g p a t t e r n s using a modified T U N E L assay that were, in
general, mostly consistent with observed morphological changes. However, a
large n u m b e r of cells t h a t were obviously apoptolie, as assessed by morph-
Figure 5. (A) Individual cell at the tip of a small intestinal villus. showing positive
immunoreactivity using the TUNEL technique; the insert shows a high magnification
view. Note that the tell does not demonstrate any visible changes in morphology that are
commonly associated with apoptosis; however, alterations in the apical plasma
membrane can be seen (see text). (B) Small intestinal crypt from an irradiated mouse,
with positively stained apoptotic cells/bodes. These sections were stained with a
modified version of the TUNEL technique, using the Oncor ApopTag® kit, as outlined in
Protocol 13.
34
ology, were not stained. Previously published data showed that nearly 18% of
false-negatives were obtained by TUNEL (14). Small alterations in TUNEL
assay conditions, most notably in the concentration of the terminal deoxy-
nucleotide transferase (TdT) and the duration of the proteolytic digestion,
can result in the labelling of many non-apoptotic epithelial cells, especially on
the villi.
The ISEL technique has been used to demonstrate that a small number of
cells at the tip of the villi are undergoing apoptosis at any one time, prior to
being shed into the intestinal lumen (21). We have been able to manipulate
further the TUNEL assay conditions, to achieve a similar pattern of positively
stained cells at the villus tip (as outlined in Protocol 13). It was also possible to
observe abnormalities in the appearance of the brush border of these cells; a
feature which has been demonstrated previously by scanning electron
microscopy (22) and is associated with cells in the process of extrusion (see
Figure 5).
Protocol 13. TUNEL staining using the Oncor Apoptag® kit
N.B. The protocol described below is specifically optimized for sections of

formalin-fixed, wax-embedded murine small intestine; we found it to be
unsuitable for the study of human tumour samples. It is recommended
that workers determine empirically the conditions required for optimal
staining of their own tissue samples.
This technique follows the protocol in the ApopTag® kit handbook and
uses the majority of the reagents supplied by the kit (product code S7100,
Oncor). Listed below are the specific modifications we have made to the
standard kit protocol.
Reagents
• proteinase K • Oncor reaction buffer
. PBS • Oncor stop-wash
. 0.3% H202 • Oncor anti-digoxigenin peroxidase conjugate
• Oncor equilibration buffer .TdT
Method
11. Dewax and rehydrate sections as detailed in Protocol 7.
12. Incubate sections with proteinase K in PBS (40 ug/ml) for 20 min. N.B.
This step is usually carried out on the bench. Day to day changes in
room temperature can, therefore, have a significant effect on the
degree of digestion and, hence, the final results. An ambient
temperature of 18-20°C is recommended.
13. Wash twice with PBS (5 min each wash), prior to incubation in 0.3%
H2O2/PBS for 15 min.
35
fames W. Wilson and Christopher S. Potten
14. Wash twice with PBS (5 min each wash) and incubate with x 1 Oncor
equilibration buffer for 30 min.
15. Tap-off the buffer and apply either 54 ul of working strength TdT (38 ul
Oncor reaction buffer plus 16 ul TdT, as supplied) or 54 ul of control
buffer (38 uj Oncor reaction buffer plus 16 ul distilled water) to each
section. Coverslip and incubate for 1 h at 37°C.
16. Place slides in the Oncor stop-wash for 10 min, in a dish on a rocking
table.
17. Wash in PBS for 5 min.
18. Incubate sections with x 1 Oncor anti-digoxigenin peroxidase
conjugate for 1 h at room temperature.
19. Wash in PBS for 5 min prior to incubation in 3'3'-diaminobenzidine
(DAB: 0.5 mg/ml) in 0.03% H2O2/PBS for 5 min.
10. Wash in PBS and counterstain with thionin blue, as described in
Protocol 9.
See Oncor's web site at www.oncor.com.

N.B. This technique varies from the one previously published by Merritt et at. (14), which
utilized non-Apoptag kit reagents.
Using an improved ISEL technique, Pompeiano et al. (23) have demon-

strated that the majority of cells on the villi show positive staining, a pattern
that we observed using the original TUNEL assay conditions (20). The fact
that cells demonstrate DNA fragmentation prior to (in this case by 1-2 days)
the morphological changes of apoptosis does not fit well with the current
models of apoptotic events. It is very unlikely that, if DNA fragmentation has
occurred in the villus cells, this is due to activation of the apoptotic endo-
nuclease. DNA fragmentation could occur as part of the terminal differ-
entiation of enterocytes. This low level of fragmentation would be detected by
TUNEL (using the original assay condition (see ref. 20) and modified ISEL
techniques (23). The less sensitive ISEL technique (21) and modified TUNEL
technique (20) would be more specific in staining apoptotic cells, as they
would only be capable of detecting the higher levels of DNA fragmentation
associated with apoptosis, and not the low levels present in terminally
differentiated cells.
Other workers have also reported caveats of the TUNEL assay. Bio-
tinylated and digoxygenin-labelled nucleotides have been shown to bind to
matrix vesicles in atherosclerotic plaques (24, 25). It was demonstrated that
many of the nuclei labelled by the TUNEL assay were, in fact, transcrip-
tionally active, as assayed by the expression of RNA splicing factor and the
presence of poly A RNA tails (25). It is unlikely, therefore, that these were
36
nuclei of apoptotic cells, and, in addition, they did not show any morpho-
logical changes characteristic of apoptosis. The duration of proteolytic
treatment and TdT concentration are clearly factors that have been found to
greatly influence results in our own and others' laboratories (25, 26). The
occurrence of DNA strand breaks in a non-apoptotic context has been a
matter of concern for other workers, and has been discussed in Chapter 7 of
Cell growth and apoptosis: a practical approach, Oxford Univerisity Press,
Oxford (1995). It has been reported that end-labelling techniques, when used
alone, cannot differentiate between apoptosis and necrosis (27). The
accumulation of strand breaks in post-mortem tissue prior to fixation could
also result in a number of false-positive events (28).
It would seem that it is best to approach end-labelling techniques with
caution. Always determine empirically what assay conditions give staining that
best matches the morphological criteria; always ensure that tissue is fixed as
rapidly as possible; and employ additional techniques, such as those to establish
transcriptional activity (25). The use of in situ hybridization for the identifi-
cation of cell-type-specific markers, in parallel with TUNEL/ISEL techniques,
can also be useful when studying heterogeneous cell populations (29).
6. Other techniques
Other immunologically based techniques have also been developed, as com-
plementary methods for the identification of apoptotic cells. These include
the development of antibodies to single-strand DNA breaks (30); biotin-
labelled, hairpin oligonucleotides that bind to double-stranded DNA breaks
(31) and antibodies to caspase-cleavage products, such as the carboxyl termi-
nus fragment of actin (28). One of the most common techniques used is the
detection of phosphatidylserine in the outer leaflet of the plasma membrane
of apoptotic cells, using labelled annexin V. This technique is the subject of
Chapter 7. Here, it is sufficient to say that the technique can be used in con-
junction with both light and electron microscopy. Tissue culture cells have
been mixed with labelled annexin V, prior to fixation and histological
examination (32). Annexin V has also been injected (intracardiac) into viable
embryos, which were subsequently fixed and sectioned for microscopy (33).
The discovery of other techniques for the identification of apoptotic cells
has been more serendipitous. Antibodies to both c-jun (34) and epidermal
growth factor receptor (35) have been shown to have specific immuno-
reactivity for apoptotic cells. Studies on nuclear pore protein regulation re-
vealed that the nuclear pore protein POM121 was depleted from the nuclear
membrane in apoptotic cells (36). This loss could be monitored in cells trans-
fected with a vector expressing a POM121-GFP (green fluorescent protein)
fusion protein, using fluorescence microscopy, and used to recognize
apoptotic cells.
37
7. Conclusions
Morphological assessment of apoptosis still has a key role in the study of cell
death. The most important aspect of performing such analysis has to be the
consistency of the investigator. It is always useful for anyone approaching the
subject for the first time to have their scoring of apoptotic events checked by
an investigator who has regular experience of the technique. There is no
doubt that the recent development of DNA end-labelling and other tech-
niques has helped in establishing the role of dysregulated apoptosis in various
pathological conditions. However, caution must be urged in interpreting
results obtained using these techniques—all that glitters is not gold. When
contrasting data from different laboratories always be aware of what criteria
and end-point the investigators have selected for the scoring of apoptotic
cells.
Acknowledgements
Thanks to Dr Mike Bromley and Garry Ashton for informative discussions.
Thanks to Dr Danielle Hargreaves and Nicola Crag for information on the
modified TUNEL technique.
References
1. Kerr, J.F.R., Wyllie, A.M. and Currie, A.R. (1972). Br. J. Cancer, 26,239.
2. Cunha, G.R. and Vanderslice, K.D. (1984). Stain TechnoL, 59,7.
3. Grimwood, R.E., Ferris, C.F., Nielsen, L.D., Huff, J.C. and Clark, R.A.F. (1986).
J. Invest. Dermatol., 87,42.
4. Kischer, C.W., Sheridan, D. and Pindur J. (1989). Anatom. Rec., 225,189.
5. Zhang, X. and Kiechle, F.L. (1997). Ann. Clin. Lab. ScL, 27,260.
6. Spreij, T.E. (1971). NethldsJ. Zool., 21,221.
7. Abrams, J.M., White, K., Fessler, L.I. and Steller, H. (1993). Development, 117,29.
8. Hay, B.A., Wolff, T. and Rubin, G.M. (1994). Development, 120,2121.
9. Carlemalm, E., Villinger, W., Acetarin, J.D. and Kellenberger, E. (1985). In Proc.
4th Pfefferkorn Conference 1985, Science of biological specimen preparation, SEM
Inc., p. 147. AMF O'Hare, Chicago.
10. Hamilton, G., Hamilton, B. and Mallinger, R. (1992). Histochem., 7, 87.
11. Potten, C.S. (1995). In Radiation and gut (ed. C.S. Potten and J.H. Hendry), p. 61.
Elsevier Science B.V., Amsterdam.
12. Potten, C.S. (1996). Br. J. Cancer, 74,1743.
13. Potten, C.S., Roberts, S.A., Chwalinski, S., Loeffler, M. and Paulus, U. (1988). Cell
Tissue Kinet., 21, 231.
14. Merritt, A.J., Jones, L.S. and Potten, C.S. (1996). In Techniques in apoptosis: a
users guide (ed. T.G. Cotter and S.J. Martin), p. 269. Portland Press Ltd, London.
15. Qiu, J.M., Roberts, S.A. and Potten, C.S. (1994). Epith. Cell Biol., 3,137.
16. Gavrieli, Y., Sherman, Y. and Ben-Sasson, S.A. (1992). J. Cell Biol., 119,493.
38
17. Ansari, B., Coates, P.J., Greenstein, B.D., and Hall, P.A. (1993). J. PathoL, 170,1.
18. Wijsman, J.H., Jonker, R.R., Keijzer, R., Van de Velde, C.J.H., Cornelisse, CJ.
and Van Dierendonck, J.H. (1993). J. Histochem. Cytochem., 41,7.
19. Fujita, K., Ohyama, H. and Yamada, T. (1997). Histochem. J., 29,823.
20. Merritt, A.J., Potten, C.S., Watson, A.J.M., Loh, D.Y., Nakayama, K., Nakayama,
K. and Hickman, J.A. (1994). J. Cell Sci., 108,2261.
21. Hall, P.A., Coates, P.J., Ansari, B. and Hopwood, D. (1994). J. Cell Sci., 107, 3569.
22. Potten, C.S. and Allen, T.D. (1977). Ultrastruct. Res., 60, 272.
23. Pompeiano, M., Hvala, M. and Chun, J. (1998). Cell Death Different., 5,702.
24. Kockx, M.M., de Meyer, G.R.Y., Muhring, J., Bull H., Bultinck, J. and Herman,
A. (1996). Atherosclerosis, 120,115
25. Kockx, M.M., Muhring, J., Knaapen, M.W.M. and de Meyer, G.R.Y. (1998). Am.
J. PathoL, 152,885.
26. Hegyi, L., Hardwick, S.J. and Mitchinson, M.J. (1997). Am. J. PathoL, 105, 371.
27. Mundle, S. and Raza, A. (1995). Lab. Invest., 72, 611.
28. Yang , F., Sun, X., Beech, W., Teter, B., Wu, S., Sigel, J., Vinters, H.V., Frautschy,
S.A. and Cole, G.M. (1998). Am. J. PathoL, 152,379.
29. Gochuico, B.R., Williams, M.C. and Fine, A. (1997). Histochem. J., 29,413.
30. Naruse, I., Keino, H. and Kawarada, Y. (1994). Histochem., 101,73.
31. Didenko, V.V., Tunstead, J.R. and Horsby, P.J. (1998). Am. J. PathoL, 152,897.
32. Pellicciari, C., Bottone, M.G. and Biggiogera, M. (1997). Eur. J. Histochem., 41,
211.
33. Van-den-Eijnde, S.M., Boshart, L., Reutelingsperger, C.P., De-Zeeuw, C.I. and
Vermeij-Keers, C. (1997). Cell Death Different., 4,311.
34. Garrah, J.M., Bisby, M.A. and Rossiter, J.P. (1998). Acta Neuropathol. Berl, 95,
223.
35. Booth, C. and Potten, C.S. (1996). Apoptosis, 1,191.
36. Imreh, G., Beckman, M., Iverfeldt, K. and Hallberg-E. (1998). Exptl Cell Res.,
238,371.
39
3
Assessment of DNA damage in

apoptosis
AKIRA YOSHIDA, RONG-GUANG SHAO, and YVES POMMIER
1. Introduction
Apoptosis is morphologically characterized by early cell shrinkage, chromatin
condensation, nuclear fragmentation, cell surface blebbing, and membrane-
bound apoptotic bodies (1) and these changes are described in Chapter 2.
One of the most extensively studied biochemical events in apoptosis is
chromatin fragmentation by endonuclease activation. DNA double-strand
cleavage occurs in the linker regions between nucleosomes, and produces
DNA fragments that are multiples of approximately 185 base pairs (bp) (2-4).
These fragments can readily be demonstrated by agarose gel electrophoresis
as DNA ladders, and this method has been widely used to detect and define
apoptosis. In contrast, necrosis is accompanied by random DNA breakdown,
with diffuse smear in agarose gels. The appearance of the nucleosomal DNA
ladder in agarose gels is an important biochemical hallmark of apoptosis,
although several investigators have observed apoptosis with no detectable
internucleosomal DNA digestion (5, 6). In the absence of detectable inter-
nucleosomal DNA fragmentation, high molecular weight fragments (HMW)
ranging in size between 50 and 300 kb provide another characteristic feature
of apoptosis (7, 8). In this chapter, we describe the commonly used methods
to detect apoptotic internucleosomal and high molecular weight DNA frag-
mentation and a sensitive filter elution method that can be used to quantitate
these DNA fragmentations.
2. Types of DNA fragmentation

DNA fragmentation during apoptosis is considered to occur in two stages.
Walker et al. (9) reported sequential degradation of genomic DNA, initially to
high molecular weight (HMW) DNA fragments of approximately 300 kb,
followed by the appearance of 50 kb loop-size chromatin fragments which
were detected using pulse-field gel electrophoresis. Oligonucleosomal DNA
Akira Yoshida et al.
fragments that produce the characteristic DNA ladder are released when the
50 kb fragments are further degraded. Certain cells, such as Molt-4 human T
cell leukaemia cells (5) and DU145 human prostate cells (8,10) do not display
internucleosomal DNA fragmentation, although these cells die with a typical
apoptotic morphology. In these cells, however, HMW DNA fragmentation
can be observed, suggesting that HMW DNA cleavage is also an important
biochemical marker of apoptosis and that internucleosomal DNA cleavage is
dispensable for apoptosis (7,11,12). In general, haematopoietic cells, such as
human leukaemia HL60 and Jurkat, are very sensitive to induction of
apoptosis and undergo internucleosomal DNA fragmentation upon exposure
to various apoptotic stimuli, including inhibitors of topoisomerase I (campto-
thecin) or topoisomerase II (etoposide = VP-16) or staurosporine (13-17).
On the other hand, epithelial cells (e.g. MCF7 human breast cancer or DU1-45
prostatic carcinoma cells) are generally more resistant to apoptosis (8,10).
The presence of 5'-phosphate (5'-P) and 3'-hydroxyl (3'-OH) DNA termini
in apoptotic cells is an important biochemical feature of apoptotic DNA frag-
ments. Indeed, the terminal deoxynucleotidyl transferase-mediated dUTP-
biotin nick end-labelling (TUNEL) method, which is commonly used to
detect apoptotic cells, is based on the presence of 3'-OH termini (18). This
method is described in Chapter 2. Another characteristic feature of apoptotic
DNA fragmentation is that single-stranded DNA breaks are produced as well
as double-strand breaks. Peitsch et al. (19) and Walker et al. (20) found that
numerous single-strand breaks are generated in internucleosomal DNA
regions during apoptosis. They proposed that DNA single-strand breaks
accumulate in the linker regions between nucleosomes, eventually causing
double-strand scissions which release oligonucleosomes.
Several nucleases are probably responsible for the DNA fragmentation in
apoptosis (Table 1). Among the first reported were DNase I (21, 22) and
Nucl8 (23). NuclS (cyclophilin) was isolated from apoptotic rat thymocytes
(24). Recently, a 33 kDa DNase I-related nuclease (DNase Y) has been
isolated from rat cells. Its gene encodes a 36 kDa protein that is ubiquitously
expressed and is activated by proteolytic cleavage to a 33 kDa endonuclease
(25). This nuclease resembles the DNase 7, a 34 kDa nuclease that was
recently purified from rat thymocytes (26). Interestingly, DNase Y is not
transcriptionally regulated in apoptosis (25). An acidic endonuclease, DNase
II (27, 28) has also been proposed to be involved, as well as several
Ca2+/Mg2+-dependent endonucleases (26, 29-31). However, it should be
noted that DNase II produces 5'-OH and 3'-P DNA termini (32), which is not
consistent with the characteristics of apoptotic DNA fragmentation. Two
other Ca2+/Mg2+-dependent endonucleases have also been isolated from
apoptotic rodent cells and another endonuclease was isolated from apoptotic
mouse T cell hybridoma (30). It consists of three molecular forms (A, B, and
C) with apparent molecular weights of 49, 47, and 45 kDa, respectively (30).
In addition, a 97-kDa Ca2+/Mg2+-dependent nuclease producing internucleo-
42
3: Assessment of DNA damage in apoptosis
Table 1. Overview of the apoptotic nucleases
Name Ion dependency MW (kDa) Source Reference

NucIS Ca2+/Mg2+ 18 Rat thymocyte 23
ILCME Ca2+/Mg2+ 49, 47, 45 Mouse T cell hybridoma 30
(not named) Ca2+/Mg2+ 97 Rat hepatoma 31
(not named) Ca2+/Mg2+ 28 Human spleen 29
DNase 1 Ca2+/Mg2+ 31 Rat prostate 22
DNase-y Ca2+/Mg2+ 34 Rat thymocyte 26
DNase Y Ca2+/Mg2+ 33 Rat tissues 25
DNase II (-) 40 Bovine spleen 28
CAD/DFF40 ? 40 Rodent and human cells 33,35
AN34 Mg2+ 34 Human leukaemia HL60 37
somal DNA cleavage cells has been reported to be present in untreated rat
hepatoma (31).
Very recently, a caspase-activated DNase (CAD) has been reported by S.
Nagata and co-workers (33). CAD is a 40 kDa protein that induces internucle-
osomal DNA cleavage in isolated nuclei in the presence of Mg2+. CAD
activity does not require Ca2+, and CAD forms a complex and co-purifies with
an inhibitor of CAD (ICAD) that can be cleaved by caspase-3 during apoptosis
(33, 34). CAD and ICAD have been isolated independently by X. Wang and
co-workers who showed that DNA fragmentation and chromatin condensation
depend on a heterodimeric protein composed of two DNA fragmentation
factors of 45 and 40 kDa (DFF45 and DFF40 corresponding to ICAD and
CAD, respectively) (35, 36). In our laboratory, we purified a 34 kDa Mg2+-
dependent and Ca2+-independent endonuclease from etoposide-treated HL60
cells undergoing apoptosis (37), and designated this 34 kDa Mg2+-dependent
endonuclease, AN34 (apoptotic nuclease 34 kDa) (37). AN34 introduces single-
and double-strand breaks in purified DNA and internucleosomal DNA cleav-
age in isolated nuclei (37). AN34-induced DNA breaks terminate with 3'-OH,
consistent with characteristic products of apoptotic chromatin fragmentation
(37). Interestingly, our data using caspase inhibitor (zVAD-fmk) suggest that
the action of AN34 is also controlled by caspase (37), although AN34 is not in-
hibited by ICAD (DFF45) (A. Yoshida and Y. Pommier, unpublished data).
3. Measurement of high molecular weight DNA

fragmentation by pulse-field gel electrophoresis
Since DNA degradation to oligonucleosomes is not essential for apoptosis and
all cells must undergo DNA degradation to produce the large fragments (12),
high molecular weight (HMW) DNA fragmentation has been considered a
more reliable biochemical marker for apoptosis. When internucleosomal
DNA cannot be demonstrated in some cells, there is considerable HMW
43
DNA fragmentation, producing fragments of 50-300 kb that can be identified
by pulse-field gel electrophoresis.
Pulse-field gel electrophoresis is a specialized technique for resolving DNA
molecules in the range of kilo- to mega-bases (Mb). By alternating the electric
field between spatially distinct pairs of electrodes, HMW DNA fragments and
chromosome-size DNA from 200 to over 12000 kb can be separated because
they are able to reorient and move differentially through the pores of an
agarose gel.
3.1 Pulse-field gel electrophoresis procedures

We routinely use the CHEF-DR II or III pulse-field electrophoresis system
(BioRad). The basic equipment is as described by the manufacturer. The
CHEF-DR II system is an advanced pulse-field system based on the CHEF
(clamped homogeneous electric fields) technique. The key to high resolution,
sharp bands, straight lanes, and reproducible separations is a uniform electric
field at all points of a gel, and an optimal 120 "angle of alternating pulses. The
CHEF-DR II system accomplishes both of these by establishing the electric
field along the contour of the hexagonal array of 24 electrodes. The basic unit
of the CHEF-DR II system includes:
• gel chamber
• drive module
• pump
• Pulsewave 760 switcher
• model 200/2.0 power supply
The procedures used are as described in Protocol 1.
Protocol 1. Pulse-field gel electrophoresis procedures
Solutions
. TEN buffer: 5 mM Tris-HCI, 5 mM EDTA, 75• plug-washing buffer: 10 mM Tris-HCI, 1
mM NaCI, pH 7.8. mM EDTA, pH 7.8.
• deproteinizing solution: 0.1 mg/ml pro- • 0.5 x TBE running buffer: 45 mM Tris base,
teinase K, 1% sarkosyl, 50 mM EDTA, 50 45 mM boric acid, 1 mM EDTA, pH 8.2.
mM Tris-HCI, pH 7.8.
A. Sample preparation in agarose blocks

Any technique for the analysis of high molecular weight DNA frag-
mentation is critically dependent on its ability to isolate intact DNA from
control cells and prevent further degradation of DNA from apoptotic cells.
The technique of embedding cells in agarose plugs was evolved to solve
this problem. Large DNA fragments are so fragile that they are broken by
mechanical forces during their isolation. To prevent breakage of these
44
large DNA fragments, intact cells embedded in agarose are lysed and
deproteinized. The agarose matrix protects the embedded DNA from
shear forces and provides an easy way to manipulate samples. Processed
agarose plug-DNA inserts are loaded directly into sample wells of
agarose electrophoresis gels.
Method
1. Wash ~2 x 106 cells in phosphate-buffered saline (PBS).
2. Pellet the cells by centrifugation at 4°C for 10 min at 3000 r.p.m. (450 g).
3. Discard the supernatant and resuspend the cells with an equal volume
of TEN buffer.
4. Prepare 1% low-melt preparative grade agarose (low melting point
agarose) solution in TEN buffer by melting agarose in a microwave
oven. Let the agarose solution cool to 50°C.
5. Add the 1% melted agarose to the cell suspension to give a final
agarose concentration of 0.75%.
6. Pipette into mould chambers and allow cooling to 4°C for ~20 min.
7. The agarose plugs are removed from the mould and then incubated in
deproteinizing solution at 45°C for 16 h.
8. Wash with plug-washing buffer once an hour, three times.
B. Gel casting
Method
1. Place the casting stand on a levelled surface.
2. Attach a comb to the holder and adjust the height of the comb to
~2 mm above the casting stand surface.
3. Prepare the desired concentration of agarose (see Section 3.2) in 0.5 x
Tris-borate electrophoresis buffer.
4. Melt the agarose in a microwave oven.
5. Pour the molten agarose into the casting stand and allow to cool for
1 h at room temperature.
6. Carefully remove the comb holder and comb.
7. Sample plugs can be added to the wells while the electrophoresis gel
remains in the casting stand.
C. Loading the sample

Method
1. Place the sample plugs on a smooth clean surface, and cut them to
size. Samples should be less than 90% of the height of the wells.
45
2. Fill each sample well with low-melt agarose at an agarose concentra-
tion equal to that of the gel, and allow the agarose to harden at room
temperature for 15 min.
D. Running the gel

Method
1. Pour 0.5 x TBE buffer into the chamber.
2. Turn on the recirculating pump, and allow the buffer to equilibrate to
the desired temperature (14°C is recommended).
3. Slide the gel on to the surface of the chamber. Check the buffer level
so that the gel is covered by about 2 mm buffer.
4. Turn on the Pulsewave 760 switcher and power supply. Set the Pulse-
wave 760 parameters (the initial and final pulse time, ratio, running
time) and voltage. For details of the conditions for electrophoretic
separations see Section 3.2.
E. Staining the gel

Method
1. After electrophoresis, place the gel into 0.5 ug/ml ethidium bromide
solution and let it stain for 20-30 min.
2. Destaining is performed in distilled water for 1-3 h.
3. The DNA can be visualized by placing the gel on a UV transilluminator
(254-360 nm).
3.2 Strategies for electrophoretic separations

Several parameters must be considered before performing an electrophoretic
separation of HMW DNA. The separation of large DNA molecules in agarose
gels is affected by the agarose concentration, buffer concentration, tempera-
ture, pulse times, voltage, and total electrophoresis running time.
• The agarose concentration determines the size range of DNA molecules
separated, and the sharpness or tightness of the bands. Agarose concentra-
tions of 1 % are useful in separating DNA molecules up to 3 Mb in size.
• Tris-borate buffer (TBE), at a concentration of 0.5 X and chilled to 14 °C, is
recommended for use in pulse-field electrophoresis.
• The migration rate of DNA molecules through agarose gel is determined by
voltage, pulse time, and running time. The DNA migration velocity
increases with increasing voltage and temperature, and decreases with
increasing agarose concentration. Greater migration is accompanied by
46
Table 2. Run parameters
DNAsize(Mb) <0.1 0.1-0.2 2-4 >4

Agarose (%) 1.5 1-1.5 0.8-1 0.5-0.8
TBE buffer 0.5 x 0.5 x 0.5 X 0.5 X
Temperature (°C) 14 14 14 14
Voltage (V) 200 150-200 125-175 40-75
Pulse time (s) 1-10 1-10 1-10 10-60 min
Run time (h) 6-12 18-24 24-72 3-6 days
Table 3. Examplies for pulse motde
DNA size (Mb) 0.2-23 kb 0.05-1 0.2-2.2 1-5 3.5-5.7

Mode 2 2 3 3 1
Agarose (%) 1.5 1 1 0.8 0.6
Pulse time (s) 1-4 50-90 60-90 120-240 60 min
Run time (h) 5 24 15-19 24-36 160
Voltage (V) 200 200 200 150 50
decreased band sharpness. Increased band sharpness requires longer run

times at low voltage. Therefore, a compromise in voltage, temperature, and
agarose concentration should be used to give the maximum allowable band
sharpness within a reasonable run time. Table 2 gives a general starting
point for parameters to separate DNA molecules in the various size
categories.
There are three common pulse modes used in CHEF analysis (see Table 3).
Mode 1 is a single pulse time for the duration of the run. Mode 2 is an abrupt
change in pulse time, with one pulse setting for the first part of the run and a
second pulse setting for the remainder of the run. Mode 3 is a gradual linear
change of the pulse time from the initial to the final pulse time.
4. Detection of internucleosomal DNA fragmentation

by standard agarose gel electrophoresis
Internucleosomal DNA fragments can readily be detected by agarose gel
electrophoresis. The small DNA fragments that are isolated from apoptotic
cells are well resolved by gels. The simple and reproducible detection of inter-
nucleosomal DNA fragmentation has made it a biochemical hallmark of
apoptosis. However, it should be noted that some cell lines (e.g. MCF-7,
DU145) show almost no DNA ladders, although they show the typical
morphological changes of apoptosis (see Section 1).
47
Protocol 2. DNA extraction and standard agarose gel

electrophoresis
• horizontal agarose gel electrophoresis . TAE (40 mM Tris-acetate, 1 mM EDTA) or
chamber TBE buffer (45 mM Tris-borate, 1 mM
• electric power supply EDTA)
• sample comb • DNA sample loading solution (0.25%
• ethidium bromide solution bromophenol blue, 0.25% xylene cyanol FF,
• UV transilluminator 15% Ficol in water
Method
1. After harvesting the cells, samples are washed with phosphate-
buffered saline (PBS) and pelleted by centrifugation.
2. The cell pellets are lysed in a solution containing 50 mM Tris-HCI
(pH 8.0), 20 mM EDTA, 10 mM NaCI, 1% (w/v) sodium dodecylsulfate
(SDS).
3. Lysates are incubated sequentially with 20 ug/ml RNase A at 37°C for
60 min and 100 ug/ml proteinase K, at 37°C for 3-5 h.
4. Lysates can then be applied directly on 1.2% agarose gel in TAE or TBE
buffer in a horizontal gel support. In order to get clear DNA ladder
images, it is important to optimize the cell number and the volume of
cell lysis buffer because too many cells make the sample viscosity too
high, and reduce the gel resolution.
5. Pour 1.2% agarose gel in TAE or TBE buffer in a horizontal gel support.
Insert the comb and let the gel solidify.
6. Load samples to the gel wells, and perform electrophoresis.
7. Stain gels with 5 ug/ml ethidium bromide in TAE, TBE buffer, or water
for 30 min. Resolved DNA fragments can be viewed on a UV trans-
illuminator box and photographed.
8. Alternatively, DNA can be extracted from cell lysates by standard
phenol/chloroform/isoamyl alcohol extraction procedures if sharp
images cannot be obtained with whole-cell lysates.
5. Filter elution assay to measure apoptotic DNA

fragmentation
DNA filter elution is commonly used to study the effects and mechanisms of
action of chemotherapeutic drugs and carcinogens (38, 39). The basic DNA
elution filter methods were originally designed to assay DNA damage in
intact cells or tissues from living animals (38). More recently, DNA elution
filter assays were adapted to study drug mechanisms in isolated nuclei (40,41)
and in a reconstituted cell-free system (13,16). Altogether, the various elution
48
methods are currently applied in the study of the DNA effects of a variety of
anticancer agents (topoisomerase inhibitors, DNA cross-linking and
alkylating drugs) in cells in culture, and in the analysis of DNA fragmentation
associated with programmed cell death (apoptosis).
A variety of DNA lesions can be detected and quantitated by filter elution
methods. Such lesions include DNA single-strand breaks (SSB), as well as
double-strand breaks (DSB). SSB and DSB are either protein-associated
(PASB) or protein-free ('frank') breaks. Alkaline elutions can also measure
DNA-protein cross-links (DPC), interstrand DNA cross-links (ISC), and
alkali-labile sites (ALS). More recently, we have used a simple filter elution
method to quantitatively measure apoptosis-associated DNA fragmentation
(42). We will only describe here this filter elution method. Details of the other
alkaline elution methods can be found in detailed reviews and methods
chapters (e.g. 38,39,43).
The filter elution assay can detect both internucleosomal and high
molecular weight DNA fragmentation in apoptotic cells. Comparison with the
pulse-field electrophoresis method indicated that filter elution can detect
DNA fragmentation in the absence of internucleosomal DNA fragmentation
and that DNA fragments up to 50-80 kb were detectable by filter elution.
5.1 Equipment
The basic equipment (38, 39) consists of filtration funnels (25 mm poly-
ethylene filter holder, Swinnex, Millipore Corp.) connected and cemented
with epoxy to a 50 ml polyethylene syringe (Swinnex funnel). The syringe
orifice should be enlarged with a 0.125 in (3.2 mm) diameter drill to facilitate
filling the upper section of the filter without trapping air. The bottom of the
filter holder is connected to a 15 gauge stainless steel needle inserted through
a rubber stopper to fit a filtration funnel holder (Figure 1). A set of elution
funnels is mounted on a support, with a rack under this support to
accommodate liquid scintillation vials (Figure 1).
5.2 Filters and solutions

• Filters: protein-adsorbent membrane filters 25 mm diameter, 0.8 um pore
size can be obtained from Gelman Sciences Inc. (Ann Arbor, MI) [PVC
(polyvinyl chloride)/acrylic co-polymers, Metricel®] or from Poretics
Corporation (Livermore, CA) (PVC).
• EDTA washing solution pH 10.0:
(a) Prepare Na2EDTA (0.1 M) from 37.2 g Na2EDTA.2H2O(ethylene-
diaminetetraacetic acid disodium salt: dihydrate) and 8 g NaOH made
up to 1 litre with H20. Adjust pH to 10.0 with NaOH (5 M).
(b) For 500 ml of 0.02 M EDTA, mix 100 ml of Na2EDTA (0.1 M) and
400 ml of H20 and adjust the pH to 10.0.
• LS-10 (lysis solution pH 10.0): add 116.8 g NaCl, 400 ml 0.1 M Na2EDTA,
49
Figure 1. Photograph of a filter elution assay set-up, including a custom-designed rack to

hold elution funnels and scinitillation vials. Front right: a rubber stopper with central
needle (see text); front midle: the same with the assembled lower part of a Swinnex filter
holder; front left and second row: four assembled elution funnels.
6.7 ml of 30% sarkosyl solution, and distilled water to a final volume of 1

litre. Adjust to pH 10.0 with NaOH/HCl.
• nucleus buffer: add 0,136 g KH2PO4, 1.016 g MgCb., 8.76 g NaCl, 0.380 g
EGTA, and distilled water to a final volume of 1 litre. Adjust the pH to 6.4
with NaOH/HCL Add DTT (dithiothrcitol) to 0.1 mM final concentration
immediately before use.
• nucleus buffer + Triton X-100: add 1 ml of Triton X-100 (30% stock
solution) to 100 ml of nucleus buffer.
5.3 DNA labelling and preparation of experimental cell

cultures
The DNA of exponentially growing cells is labelled with [ l 4 C]lhymidine
(0.01-0.02 u,Ci/ml) for approximately one doubling time. Cells are then post-
50
incubated for at least 4 h in isotope-free medium to chase radioactivity into
high molecular weight DNA.
Control and drug-treated monolayer cells are detached by gentle scraping
with a rubber 'policeman' and dispersed by repeated pipetting in their medium.
Suspended cells are dispersed by repeated pipetting in their medium.
Typically, 0.5-1.0 X 106 cells (corresponding to at least 5000 dpm.) are diluted
in 5-10 ml of ice-cold Hank's balanced salt solution and loaded on to an
elution funnel. The first 3 ml of cell suspension are loaded with a 1 ml
automatic micropipette (the pipette tip needs to be inserted into the Swinnex
hole but not too deep, to avoid puncturing the filter).
5.4 Protocols
Protocol 3. DNA fragmentation assay
Reagents
• Hank's balanced salt solution (HBSS) • LS-10 lysis solution
• PBS • 0.02 M EDTA solution
Method
1. Prepare Swinnex elution funnels and solutions (see Sections 5.1 and
5.2).
2. Load the cells or isolated nuclei (~0.5 x 106) directly on to the filter
and wash immediately with an additional 5 ml of Hank's balanced salt
solution (HBSS) or PBS. Allow this solution to flow through by gravity.
This represents the 'supernatant' or 'soluble' fraction (S).
3. Add 5 ml LS-10 lysis solution and collect immediately. This represents
the 'lysis' fraction (L).
4. Wash the lysis solution by adding 5 ml of 0.02 M EDTA solution, pH
10.0. Collect. This represents the 'wash' fraction (W).
5. Remove the filter and process the samples as indicated in Section 5.5.
The 'filter' vial is labelled (F).
Protocol 4. Preparation of isolated nuclei
DNA filter elution assays can also be done using isolated nuclei. This
application can be used to study nuclease activities and examine bio-
chemical pathways that regulate nuclear apoptosis (see Protocol 5).
Reagents
• nucleus buffer . 0.3% Triton X-100
51
Method
1. Wash the cells twice in ice-cold nucleus buffer (see Section 5.2).
2. Incubate the cells (~1 X 106/ml) on ice with gentle rocking for 10 min
in nucleus buffer containing 0.3% Triton X-100.
3. Centrifuge (450 g, 10 min at 4°C) to pellet the nuclei. Supernatants
contain the cytoplasm and plasma membrane debris.
4. Wash the nuclear pellets twice by centrifugation/resuspension in lysis
buffer without Triton X-100. Isolated nuclei are then ready to be used
for experiments.
Protocol 5. Reconstituted cell-free system using isolated nuclei
Endonuclease activities that are associated with apoptosis can be

detected from a reconstituted cell-free system (16, 37, 42).
Method
1. Prepare the nuclear and cytoplasmic fractions from control and
apoptotic cells as in Protocol 4.
2. Centrifuge (12000 g, 10 min at 4°C) the supernatants obtained as in
Protocol 4 to obtain soluble components of cytoplasmic fractions.
3. Incubate the control nuclei with either control or drug-treated
(apoptotic) cytoplasmic fractions at 30°C for up to 30 min.
4. Load these extracts directly on to filters and carry out the DNA filter
binding assay as in Protocol 3above.
5.5 Counting samples and computations

• All fractions contained in scintillation bottles are collected and the volume
adjusted to ~5 ml to keep the ratio of water to liquid scintillation cocktail at
around 0.5 for optimum counting efficiency.
• Filters are placed at the bottom of a scintillation bottle and then add 0.4 ml
of 0.1 M HC1 is added. The vial is sealed and heated for 1 h at 65 °C to
depurinate the DNA. After removing the vials from the oven, 2.5 ml of
0.4 M NaOH is added and the vial is allowed to stand at room temperature
for 45-60 min to release the DNA from the filter into solution and to allow
maximum counting efficiency. Then, 2 ml H2O is added to the 'filter' vial.
• Scintillation cocktail (10 ml) is added [Aquassure R (New England
Nuclear)]. Radioactivity is then measured in each fraction by double-
52
isotope counting (3H for internal standard cells and 14C for experimental
cells) by liquid scintillation spectrometry.
• DNA fragmentation is determined as the fraction of labelled DNA in the
lysis fraction + EDTA wash relative to total intracellular DNA. Results are
expressed as the percentage of DNA fragmented in treated cells compared
with DNA fragmented in untreated control cells (background) using the
formula:
%DNA fragmentations = [(F-F0)/(1-F0)] X 100
where F and F0 represent DNA fragmentation in treated and control cells,
respectively. Experimental data are usually plotted as the percentage of
DNA fragmented versus the time, as shown in Figure 2,
Figure 2. Apoptosis-associated DNA fragmentation measured by filter elution assay from

cultured cells or from a reconstituted cell-free system, (a) HL60 cells were treated at
0.1 p.M (open circles) and 1 uM (closed circles) staurosporine concentrations (14). DNA
fragmentation was determined by the DNA filter elution assay at specified times after
drug removal, (b) DNA fragmentation induced in a reconstituted cell-free system by
cytoplasmic fractions obtained from HL60 cells treated with staurosporine (1 uM for 3 h).
Cytoplasm from untreated HL60 cells (open circles) or staurosporine-treated cells (closed
circles) was incubated with nuclei isolated from untreated cells at 30°C for the indicated
times. DNA fragmentation was determined as described in Section 5.5.
References
1. Wyllie, A. H., Kerr, J. F. R., and Carrie, A. R. (1980). Int. Rev. Cytol. 68,251—306.
2. Wyllie, A. H. (1995). Curr. Opin. Genet. Dev. 5, 97-104.
3. Wyllie, A. H. (1980). Nature 284, 555-6.
53
4. Arends, M. J., Morris, R. G., and Wyllie, A. H. (1990). Am. J. Pathol. 136,
593-608.
5. Falcieri, E., Martelli, A. M., Bareggi, R., Cataldi, A., and Cocco, L. (1993).
Biochem. Biophys. Res. Commun. 193,19-25.
6. Catchpoole, D. R. and Stewart, B. W. (1993). Cancer Res. 53,4287-96.
7. Cohen, G. M., Sun, X. M., Snowden, R. T., Dinsdale, D., and Skilleter, D. N.
(1992). Biochem. J. 286,331-4.
8. Oberhammer, F., Wilson, J. W., Dive, C., Morris, I. D., Hickman, J. A., Wakeling,
A. E., Walker, P. R., and Sikorska, M. (1993). EMBO J. 12,3679-84.
9. Walker, P. R., Smith, C., Youdale, T., Leblanc, J., Whitfield, J. F., and Sikorska,
M. (1991). Cancer Res. 51,1078-85.
10. Pandey, S., Walker, P. R., and Sikorska, M. (1994). Biochem. Cell Biol. 72, 625-9.
11. Cohen, G. M., Sun, X. M., Fearnhead, H., MacFarlane, M., Brown, D. G.,
Snowden, R. T., and Dinsdale, D. (1994). J. Immunol. 153, 507-16.
12. Walker, P. R. and Sikorska, M. (1997). Biochem. Cell Biol. 75,287-99.
13. Bertrand, R., Sarang, M., Jenkins, J., Kerrigan, D., and Pommier, Y. (1991).
Cancer Res. 51, 6280-5.
14. Bertrand, R., Solary, E., O'Connor, P., Kohn, K. W., and Pommier, Y. (1994).
Exp. Cell Res. 211,314-21.
15. Solary, E., Bertrand, R., and Pommier, Y. (1994). Leuk. Lymph. 15, 21-32.
16. Solary, E., Bertrand, R., Kohn, K. W., and Pommier, Y. (1993). Blood 81,
1359-68.
17. Pommier, Y., Leteurtre, F., Fesen, M. R., Fujimori, A., Bertrand, R., Solary, E.,
Kohlhagen, G., and Kohn, K. W. (1994). Cancer Invest. 12, 530-42.
18. Gavrieli, Y., Sherman, Y., and Ben-Sasson, S. A. (1992). J. Cell Biol. 119,
493-501.
19. Peitsch, M. C., Muller, C., and Tschopp, J. (1993). Nucl. Acids Res. 21,4206-9.
20. Walker, P. R., Leblanc, J., and Sikorska, M. (1997). Cell Death Differ. 4, 506-15.
21. Peitsch, M. C., Polzar, B., Stephan, H., Crompton, T., MacDonald, H. R.,
Mannherz, H. G., and Tschopp, J. (1993). EMBO J. 12, 371-7.
22. Rauch, F., Polzar, B., Stephan, H., Zanotti, S., Paddenberg, R., and Mannherz,
H. G. (1997). J. Cell Biol. 137, 909-23.
23. Gaido, M. L. and Cidlowski, J. A. (1991). J. Biol. Chem. 266,18580-5.
24. Montague, J. W., Gaido, M. L., Frye, C., and Cidlowski, J. A. (1994). J. Biol.
Chem. 269,18877-80.
25. Liu, Q. Y., Pandey, S., Singh, R. K., Ribecco, M., Borowy-Borowski, H., Smith, B.,
LeBlanc, J., Walker, P. R., and Sikorska, M. (1998). Biochemistry 37,10134-^3.
26. Shiokawa, D., Ohyama, H., Yamada, T., and Tanuma, S. (1997). Biochem. J. 326,
675-81.
27. Barry, A. and Eastman, A. (1993). Arch. Biochem. Biophys. 300, 440-50.
28. Krieser, R. J. and Eastman, A. (1998). J. Biol. Chem. 273, 30909-14.
29. Ribeiro, J. M. and Carson, D. A. (1993). Biochemistry 32, 9129-36.
30. Khodarev, N. N. and Ashwell, J. D. (1996). J. Immunol. 156, 922-31.
31. Pandey, S., Walker, P. R., and Sikorska, M. (1997). Biochemistry 36,711-20.
32. Bernardi, G. (1968). Adv. Enzymol. 31,1-7.
33. Enari, M., Sakahira, H., Yokoyama, H., Okawa, K., Iwamatsu, A., and Nagata, S.
(1998). Nature 391, 43-50.
34. Sakahira, H., Enari, M., and Nagata, S. (1998). Nature 391, 96-9.
54
35. Liu, X., Li, P., Widlak, P., Zou, H., Luo, X., Garrard, W. T., and Wang, X. (1998).
Proc. Natl. Acad. Sci. USA 95, 8461-6.
36. Zhang, J., Liu, X., Scherer, D. C, van Kaer, L., Wang, X., and Xu, M. (1998).
Proc. Natl. Acad. Sci. USA 95,12480-5.
37. Yoshida, A., Pourquier, P., and Pommier, Y. (1998). Cancer Res. 58, 2576-82.
38. Kohn, K. W., Ewig, R. A. G., Erickson, L. C., and Zwelling, L. A. (1981). In DNA
repair: a laboratory manual of research procedures (ed. E. C. Friedberg and P. C.
Hanawalt), pp. 379-401. Marcel Dekker Inc., New York.
39. Bertrand, R. and Pommier, Y. (1995). In Cell growth and apoptosis: a practical
approach (ed. G. Studzinski), pp. 96-117. IRL Press, Oxford University Press,
Oxford.
40. Filipski, J., Yin, J., and Kohn, K. W. (1983). Biochim. Biophys. Acta 741,116-22.
41. Pommier, Y., Schwartz, R. E., Kohn, K. W., and Zwelling, L. A. (1984).
Biochemistry 23, 3194-201.
42. Bertrand, R., Kohn, K. W., Solary, E., and Pommier, Y. (1995). Drug Develop.
Res. 34,138-44.
43. Kohn, K. W. (1996). Bioessays 18, 505-13.
55
4
Analysis of cell death by flow and

laser-scanning cytometry
ZBIGNIEW DARZYNKIEWICZ, ELZBIETA BEDNER,
and XUN LI
1. Introduction
Flow cytometry, by providing the possibility of rapid, accurate, and unbiased
measurements of a variety of cell components on a cell by cell basis, has
become an indispensable methodology in the analysis of cell death (see
reviews in refs 1-6). One area of application of flow cytometry is in studies of
the mechanism of cell death. In this application, flow cytometry is primarily
used to immunocytochemically detect and measure the cellular levels of
proteins such as members of the Bcl-2 family, proto-oncogenes c-myc or ras,
tumour suppressor genes p53, pRB, and other molecules that play a role in
cell death. It is also used in studies of cell function, particularly mitochondrial
metabolism, which is closely associated with mechanisms regulating cell
sensitivity to apoptosis (e.g. 7, 8). The major virtue of flow cytometry in this
application is that it offers the possibility of multiparametric analysis of a
multitude of cell attributes. This allows one to study the mutual relationship
between the measured constituents. When one of the measured attributes is
cellular DNA content, a relationship of other parameters to the cell cycle
position or DNA ploidy is analysed. Because individual cells are measured
the intercellular variability can be assessed, cell subpopulations identified, and
rare cells detected.
Another area of application of flow cytometry is in the identification and
quantitation of apoptotic or necrotic cells. Their recognition is generally
based on the presence of a particular biochemical or molecular marker that is
characteristic for either apoptosis or necrosis. A variety of methods have been
developed, especially for identification of apoptotic cells. The apoptosis-
associated changes in cell size and granularity can be detected by analysis of
laser light scattered by the cell in forward and side directions (9). Some of the
methods rely on the apoptosis-associated changes in the distribution of
plasma membrane phospholipids (5,10). Others measure the transport func-
tion of the plasma membrane. Still other methods probe the mitochondrial
Zbigniew Darzynkiewicz et al.
transmembrane potential, which decreases early during apoptosis (7, 8, 11).
Endonucleolytic DNA degradation that results in extraction of low MW
DNA from the cell provides yet another marker of apoptosis. Apoptotic cells
are then recognized either by their fractional DNA content (12,13) or by the
presence of DNA strand breaks which can be detected by labelling their 3'-
OH ends with fluorochrome-conjugated nucleotides in a reaction utilizing
exogenous terminal deoxynucleotidyl transferase (TdT) (14-18).
The common drawback of flow cytometric methods is that the identification
of apoptotic or necrotic cells relies on a single parameter reflecting a change
in a biochemical or molecular feature of the cell that is assumed to represent
apoptosis or necrosis. However, such a feature may be absent when apoptosis
is atypical, as is known to occur, e.g. in cells of epithelial and fibroblast lineage
(19-21). Atypical apoptosis is also caused by agents that inhibit apoptotic
effectors. For example, induction of apoptosis by an inhibitor of the endo-
nuclease results in a lack of DNA fragmentation, while inhibitors of proteases
prevent degradation of particular proteins such as 'death substrates' (e.g. ref.
22). Identification of apoptotic cells based on the missing attribute(s) (e.g.
DNA fragmentation or degradation of a particular protein) is impossible in
such cases. Therefore, the characteristic changes in cell morphology, as
originally described (23, 24) and discussed in Chapter 2, still remain the gold
standard for recognition of apoptotic cell death.
The laser-scanning cytometer (CompuCyte, Cambridge, MA) is a
microscope-based cytofluorometer that offers advantages of both flow cyto-
metry and image analysis (for reviews see refs 25 and 26). Thus, fluorescence
of individual cells is measured rapidly by laser-scanning cytometry (LSC) and
with an accuracy similar to that of flow cytometry. Since cell position on the
slide is recorded together with other measured cell parameters in a list-
mode fashion, the cells can be relocated after measurements and re-examined
visually or subjected to image analysis (e.g. 27, 28). Furthermore, the
geometry of cells attached to the slide, especially when flattened by cytocen-
trifugation, is more favourable for their morphometric analysis than when in
suspension. More information on cell morphology, therefore, can be obtained
by LSC than by flow cytometry. In the analysis of apoptosis and necrosis, an
opportunity to examine measured cells visually, as offered by LSC, is of par-
ticular value. Furthermore, cell analysis on slides eliminates cell loss, which
generally occurs during repeated centrifugations in sample preparation for
flow cytometry.
Several flow cytometric methods developed for the identification of apoptotic
and necrotic cells have been modified and adapted so that they may be used
for LSC (e.g. 29-31). These modifications and changes in methodology re-
quired by the adaptation of flow cytometric methods to LSC are presented in
this chapter. Also discussed are difficulties in the measurement of apoptosis
or necrosis, as well as common errors in the analysis and interpretation of
data.
58
4: Analysis of cell death by flow and laser-scanning-cytometry
2. Preparation of cells for analysis by LSC. Detection

of apoptotic cells based on changes in nuclear
chromatin
Several assays of apoptosis by LSC require cell fixation. In these assays the
cells are attached to microscope slides by standard methods that include
smear films, tissue sections, 'touch' preparations from the tissues, or cyto-
centrifuging cell suspensions. Cytocentrifugation is often preferred over
'touch' or smear preparations because it flattens the cells on the slides, so
more morphological details are revealed.
LSC measurement of total nuclear or cellular fluorescence is done by
integration of the light intensity of individual pixels over the area of nucleus
and/or cytoplasm (25, 26). Thus, the intensity of individual pixels, as well as
the fluorescence area (number of pixels), is being measured. The intensity of
the maximal pixel within the measured area is also recorded. Because of the
high degree of chromatin condensation in apoptotic cells, DNA stains with a
greater intensity per unit of the projected nuclear area in these cells (hyper-
chromasia). The maximal pixel value of the DNA-associated fluorescence
measured in the chromatin of apoptotic cells, therefore, is greater than in the
non-apoptotic nuclei (30). The situation is analogous to that of the chromatin
of mitotic cells, which is also strongly condensed. Apoptotic cells, therefore,
similarly to mitotic cells (31), can be identified by high values of the maximal
pixel of DNA-associated fluorescence (Figure 1).
Figure 1. Detection of apoptotic cells by LSC based on DNA hyperchromicity in

condensed chromatin. Apoptosis was induced by treatment of HL60 cells with 0.15 uM
camptothecin (CRT) for 3 or 4 h, as described (16, 17). The cells were stained with PI
according to Protocol 1. In the untreated, control culture (CTRL) only mitotic cells (M)
have a high value of red fluorescence maximal pixel. In the CRT-treated cultures,
concomitant with a loss of S phase cells, the cells with high values of red maximal pixel
become apparent. After relocation, when viewed by fluorescence microcopy, their
morphology, as well as the morphology of the cells with fractional DNA content, was
typical of apoptotic cells (shown in the four illustrations on the right).
59
Protocol 1. Identification of apoptotic cells by changes in nuclear

chromatin
Reagents
• stock solution of propidium iodide (PI): • prepare a working solution of PI by adding
dissolve 1 mg of PI (available from 200 ul of the stock solution of PI into 10 ml
Molecular Probes, Inc., Eugene, OR) in 1 ml of PBS. Add, and dissolve in this solution, 2
of distilled water. This solution can be mg RNase A (the final concentration of PI
stored at 0-4 "C for weeks. and RNase should be 20 ug/ml and 0.2
• prepare 1% formaldehyde solution in PBS. mg/ml, respectively). This solution should
This solution should also be made fresh. be made fresh.
Method
1. Deposit the cells on the microscope slide, preferably by cytocentri-
fugation. To attach cells by cytocentrifugation add 300 ul of cell sus-
pension in tissue culture medium (with serum) containing approxi-
mately 20000 cells into a cytospin (e.g. Shandon Scientific, Pittsburgh,
PA) chamber. Cytocentrifuge at 1000 r.p.m. (~1 l0g) for 6 min.
2. Without allowing the cytospun cells to dry completely,fix them by im-
mersing the slides in a Coplin jar containing 1% formaldehyde in PBS,
on ice for 15 min.
3. Transfer the slides into Coplin jars containing 70% ethanol. The cells
may be stored in ethanol for several days.
4. After fixation, rinse the slides in PBS for 5 min. Stain the cells with the
working solution of PI for 20 min at room temperature. Mount the cells
under a coverslip in the working solution of PI and seal the preparation
with melted paraffin or nail polish. Measure the cellular red fluor-
escence (>600 nm; integrated fluorescence and maximal pixel) by
LSC, illuminating the cells at 488 nm.
Identification of apoptotic cells by LSC based on the highest pixel value for
DNA-associated fluorescence, as shown in Figure 1, is done in conjunction
with DNA content analysis. Thus, DNA ploidy and/or the cell cycle position
of apoptotic and non-apoptotic cells, can be determined at the same time as
the estimate of the apoptotic index. Furthermore, the staining procedure is
simple and can be combined with analysis of other constituents of the cell
when the latter are probed with fluorochromes of another colour. The dis-
advantage of this approach is that it cannot discriminate between mitotic and
apoptotic cells. Also, early Gl (post-mitotic) cells may have high fluorescence
intensity of the maximal pixel (31). The distinction between apoptotic and
mitotic cells is critical during treatment with agents such as taxol or other
mitotic blockers, i.e. when mitotic cells undergo apoptosis. However, visual
examination of the cells, or analysis of other morphometric features, such as
nuclear to cytoplasm ratio, nuclear or cell area, forward light scatter, etc., as
offered by LSC, can be helpful in these instances.
60
Several cytometric methods designed to identify apoptotic cells, or to study
molecular or metabolic events associated with apoptosis, probe the cells that
have vital functions preserved and therefore cannot be fixed prior to analysis.
Analysis of plasma membrane transport function (e.g. 9,32), detection of phos-
phatidylserine on the plasma membrane (5, 10; see Chapter 7), or probing the
mitochondrial metabolism (7, 8; see Chapter 8) all require unfixed cells. Sus-
pensions of live cells in appropriately prepared reaction media are generally
used when such analyses are done by flow cytometry. In the case of LSC, how-
ever, the measured cells have to be attached to a microscope slide to be re-
located for morphological examination, additionally probed by another fluoro-
chrome(s), or stained with a light-absorbing dye for analysis by light microscopy.
Two different approaches can be used to attach live cells to microscope
slides. The first involves direct cell culturing on microscope slides or cover-
slips. Culture vessels are commercially available that have a microscope slide
for the bottom of the chamber (e.g. 'Chamberslide', Nunc, Inc., Naperville,
II). The cells growing in these chambers spread and attach to the slide surface.
Chambers made on glass rather than plastic slides are preferred as the latter
often have high autofluorescence. Alternatively, the cells can be grown on
coverslips, which then can be inverted over shallow wells on the microscope
slides for analysis by LSC. This mode of attaching cells to slides is, of course,
applicable only to cells that normally grow on the surface of flasks, e.g. cells of
epithelial or fibroblast lineage, macrophages/monocytes, etc. It should be
stressed, however, that because the cells detach during late stages of
apoptosis, many apoptotic cells may be selectively lost if the analysis is limited
to the attached cells only.
Cells that grow in suspension can be attached to glass slides by electrostatic
forces. This is done by incubating them on microscope slides in the absence of
any serum or serum proteins (27-29, 33). A short (15-20 min) incubation of
the cell suspension in PBS, at room temperature and 100% humidity, in
shallow wells on the microscope slides, is generally adequate to attach the
cells to the slide surface. The live cells thus attached can be subjected to
surface immmunophenotyping (33), viability tests, or intracellular enzyme
kinetics assays (27-29). Following fixation, e.g. in formaldehyde, the electro-
statically attached cells become firmly attached by the fixative. When such
preparations are restained, a large majority of the cells (>95%) is found to be
still attached and can be relocated by LSC (33). However, as in the case of cell
growth on glass, the late apoptotic cells have a tendency not to attach, or may
detach after the initial attachment.
3. Light-scattering properties of apoptotic and

necrotic cells
Intersection of a cell with the light of the laser beam in a flow cytometer leads
to light scatter, and analysis of the signal of the scattered light reveals
61
information about cell size and structure (34). The possibility of the analysis
of light scattered in the forward and at right angles ('side scatter'; 90°)
directions is a built-in feature of every commercially available flow cytometer
utilizing laser illumination, and is a routine measurement, either alone or in
conjunction with the measurement of cell fluorescence. Forward light scatter
correlates well with cell size, whereas side scatter bears information on the
cell light refractive and reflective properties and reveals optical inhomogene-
ity of the cell structure, such as that resulting from condensation of the
cytoplasm or nucleus, granularity, etc. Side scatter, however, cannot be
measured by LSC.
As a consequence of cell shrinkage, a decrease in forward light scatter is
observed at a relatively early stage of apoptosis (Figure 2). Initially, there is
little change in side scatter during apoptosis, though in some cell systems an
increase in intensity of the side scatter signal is seen, reflecting, perhaps,
chromatin and cytoplasm condensation and nuclear fragmentation. When
apoptosis is more advanced and the cells become small, the intensity of the
side scatter decreases, just as the forward scatter. Late apoptotic cells are thus
characterized by a markedly diminished intensity for both the forward and
Figure2. Light scattering properties of apoptotic cells. To induce apoptosis HL60 cells
were treated with CRT for 3 h (16, 17). Their light scattering properties were measured by
FACScan (Becton Dickinson, San Jose, CA). The heterogeneity of apoptotic cells is
reflected by the large variability in the scattered light. The early apoptotic cells (Ap) have
diminished forward scatter but show no change in side scatter.The cells that are more
advanced in apoptosis have both the forward and side scatter greatly decreased.
62
side scatter signals. In contrast to apoptosis, cell swelling, which occurs early
during cell necrosis, is detected by a transient increase in forward light scatter.
Rupture of the plasma membrane and leakage of the cytosol during subse-
quent steps of necrosis correlates with a marked decrease in the intensity of
both forward and side scatter signals.
Because there is a great variability in the light scattering properties of
individual cells, an exponential scale (logarithmic amplifiers) should be used
during scatter measurements. Analysis of light scatter is often combined with
other assays, most frequently with surface immunofluorescence (e.g. to
identify the phenotype of the dying cell), or with another marker of apoptosis.
It should be mentioned, however, that the light scatter changes alone are not a
very specific marker of apoptosis or necrosis. Mechanically broken cells,
isolated nuclei, cell debris, and individual apoptotic bodies may also have
diminished light scattering properties. Therefore, the analysis of light scatter
should be combined with measurements that can provide a more definite
identification of apoptotic or necrotic cells.
4. Analysis of mitochondrial transmembrane

potential (Au m )
Decrease in Aum is one of the early events of apoptosis (7, 8, 11, see also
Chapter 8). Several types of membrane-permeable lipophilic cationic
fluorochromes can serve as probes of Aum in flow or laser-scanning cytometry.
When live cells are incubated in their presence the probes accumulate in
mitochondria and the extent of their uptake, measured by the intensity of the
cellular fluorescence, is considered to reflect Au m . Rhodamine 123 (Rhl23)
and 3,3'-dihexiloxa-dicarbocyanine [DiOC6 (3)] are the fluorochromes most
frequently used thus far to probe Aum (7, 8, 11, 35). A combination of Rhl23
and propidium iodide (PI) was originally proposed as a cell viability assay
discriminating between live cells that stain with Rhl23 only (green
fluorescence), dead or dying cells whose plasma membrane integrity was
compromised (cells with damaged plasma membrane, late apoptotic, and
necrotic cells) that stain only with PI (red fluorescence), and early apoptotic
cells that show somewhat increased stainability with PI but also stain with
Rhl23 (35). The specificity of Rhl23 and DiOC6 (3) as mitochondrial probes
is greater when these fluorochromes are used at low concentration. Still
another probe of Aum is the J-aggregate-forming lipophilic cationic
fluorochrome 5,5',6,6'-tetrachloro-1,1',3,3'-tetrathylbenzimidazolcarbocyanine
iodide (JC-1) (7). Its binding to mitochondria is detected by the shift in
colour of fluorescence from green, which is characteristic of its monomeric
form, to orange, which reflects its aggregation in mitochondria, driven by the
transmembrane potential (7).
63
Protocol 2. Measurement of mitochondrial transmembrane

potential
Reagents and stock solutions
• 3,3'-dihexiloxa-dicarbocyanine [DiOC6 (3)], • stock solution of JC-1: dissolve 1 mg JC-1
rhodamine 123 and/or 5,5',6,6'-tetrachloro- in 1 ml DMSO
1,1',3,3'- • stock solution of PI: dissolve 1 mg PI in 1 ml
tetraethylbenzimidazolcarbocyanine iodide distilled water
(JC-1) (Molecular Probes) Each of the above stock solutions is stable
• PI (Molecular Probes) and can be stored at 0-4°C in the dark for
• stock solution of Rh123: dissolve 0.1 mg of weeks.
Rh123 in 1 ml distilled water • working solution of Di06 (3): add 5.0 ul of
• stock solution of DiOC6 (3): dissolve 5 ug of the stock solution of Di06 (3) and 5 ul of the
DiOC6 (3) in 1.0 ml ethanol stock solution of PI into 1 ml PBS
Methods
A. Staining with Rh 123 and PI and analysis by flow cytometry
1. Add 1.0 ul of Rh123 stock solution to approximately 106 cells sus-
pended in 1 ml of tissue culture medium (or HBSS) and incubate for 10
min at 37°C in the dark.
2. Add 20 ul of the PI stock solution and keep for 5 min at room
temperature in the dark.
3. Analyse cells by flow cytometry.
• use excitation in blue light (e.g. 488 nm line of the argon ion laser)
• use light scattering to trigger cell measurement
• measure green (Rh123) fluorescence at 530±20 nm
• measure red (PI) fluorescence at >600 nm
Analysis by LSC
To be analysed by LSC the cells have to be first attached to a microscope
slide, then incubated with Rh123 and PI. To attach the cells:
1. Rinse the cells to be free of serum (or bovine serum albumin) and
resuspend them in PBS to have 2 X 105-106 cells/ml.
2. Take 50 ul of this suspension and deposit it within a shallow well on the
microscope slide. The slides with wells can be made by preparing a
strip of Parafilm 'M' (American National Can, Greenwich, CT) of the size
of the slide, cutting a hole 2.0 cm x 0.5 cm in the middle of this strip,
placing the strip on the microscope slide and heating the slide on a
warm plate until the Parafilm starts to melt. Alternatively, the well can
be made by drawing a border with a hydrophobic marker ('Isolator',
Shandon Scientific, Pittsburgh, PA). The cell suspension is placed
within the well on a slide and is maintained at room temperature at
100% humidity for 10 min to allow the cells to attach electrostatically to
the slide surface.
64
3. The cells thus attached are then incubated for 10 min with Rh123 and
then with PI as described above for cells in suspension. A coverslip is
then placed over the well and using illumination at 488 nm the cells'
green and red fluorescence is measured by LSC.
4. If desired, the cells, while still attached to the slide after the measure-
ment, can be fixed (e.g. in formaldehyde or ethanol) for subsequent
staining with other dye(s) and/or visual inspection or measurement,
following their relocation ('merge') on the slide.
B. Staining with DiOCe (3) and PI and analysis by flow cytometry

1. Suspend the cell pellet (~106 cells) in a working solution of DiOC6 (3).
2. Incubate for 15 min at room temperature in the dark.
3. Measure the cells' green and red fluorescence as described above for
Rh123 and PI.
Analysis by LSC
Follow the procedure as described above for Rh123 and PI, except that
after attaching the cells to the microscope slide incubate them with the
working solution of DiOC6 (3) for 15 min.
C. Staining with JC-1 and analysis by flow cytometry
1. Suspend the cell pellet (~106 cells) in 1 ml of tissue culture medium
with 10% serum.
2. Add 10 ul of the stock solution of JC-1. Vortex cells intensely during
addition of JC-1 and for the next 20 sec.
3. Incubate cells for 10 min at room temperature in the dark.
4. Measure the cells' fluorescence by flow cytometry.
• excite fluorescence with blue light (488 nm line of argon laser)
• measure green fluorescence at 530±20 nm
• measure orange fluorescence at 570±20 or above (long pass filter)
570 nm
Analysis by LSC
1. Prepare the cells and incubate them with JC-1 in suspension as
described above in steps 1-3.
2. Place 50 ul of this suspension into a well on the microscope slide.
Cover with a coverslip.
3. Analyse cells by LSC.
• use excitation in blue light (488 nm)
• use forward scattering as a contouring (triggering) parameter
• measure green fluorescence at 530±20 nm
• measure orange fluorescence at 570±20 or above (long pass filter)
570 nm
65
The decrease in Aum which occurs during apoptosis can be measured by
different markers, as discussed above, and shown in Figure 3. A combination
of PI and DiOC6 (3) identifies non-apoptotic cells that stain only green, early
apoptotic cells whose green fluorescence is markedly diminished, and late
apoptotic or necrotic cells that stain with PI showing red fluorescence. Like-
wise, a combination of Rhl23 and PI labels live non-apoptotic cells green,
early apoptotic cells dim green, and late apoptotic and necrotic cells red. The
change in binding of JC-1 is manifested by a loss of orange fluorescence,
which represents the aggregate binding of this dye in mitochondria. Green
fluorescence of JC-1 also decreases during apoptosis, although to a lesser
degree than orange. Because still another mitochondrial probe, nonyl acridine
orange, reports mitochondrial mass but is not sensitive to Aum (7) it is possible
Figure 3. Decrease of mitochondrial transmembrane potential during apoptosis

measured by LSC. Apoptosis of U-937 cells was induced by their incubation with 5 ng/ml
TNF-a combined with with 5 ug/ml of cycloheximide for 3 h; the cells were then
incubated with DiOC6 (3) and PI as described in Protocol 2. HL60 cells were treated with
0.15 uM CpT for 4 h to induce apoptosis and then stained with JC-1 as described in
Protocol 2. The drop in mitochondrial transmembrane potential (Aum), which character-
izes apoptotic cells, is reflected by a decrease in intensity of the green fluorescence of
DiOC6 (Si-stained cells (CHX, top right panel) and loss of orange fluorescence of JC-1
stained cells (bottom right panel). Note that very few cells stain with PI (red fluorescence).
66
to analyse both the mitochondrial mass and Aum in the same cells. Although
apoptotic cells are sometimes more flattened on the slides and may have a
greater diameter, their forward light scatter is diminished compared with the
non-apoptotic cells.
5. Detection of apoptotic cells exposing

phosphatidylserine on plasma membrane
In live, non-apoptotic cells phospholipids of the plasma membrane are asym-
metrically distributed between the inner and outer leaflets of the membrane.
Thus, while phosphatidylcholine and sphingomyelin are exposed on the
external leaflet of the lipid bilayer, phosphatidylserine is almost exclusively
located on the inner surface. Early during apoptosis this asymmetry is broken
and phosphatidylserine becomes exposed on the outside of the plasma mem-
brane (5,10, see also Chapter 7). Because the anticoagulant protein annexin V
binds with high affinity to negatively charged phospholipids like phos-
phatidylserine, the fluoresceinated annexin V has found an application as a
marker of apoptotic cells, in particular for their detection by flow cytometry
(5). In the course of apoptosis the cells become reactive with annexin V after
the onset of chromatin condensation but prior to the loss of plasma
membrane ability to exclude cationic dyes such as PI. Therefore, by staining
cells with a combination of fluorescein-conjugated annexin V and PI, it is
possible to detect unaffected, non-apoptotic cells (annexin V negative/Pi
negative), early apoptotic cells (annexin V positive/Pi negative), and late
apoptotic or necrotic cells (PI positive) by flow or laser-scanning cytometry.
Protocol 3. Measurement of changes in plasma membane
Reagents
• dissolve fluorescein-conjugated annexin V • PI stock solution: dissolve 1 mg PI in 1 ml
[1:1 stoichiometric complex, available from distilled water. The solution is stable for
BRAND Applications, The Netherlands (cat. months when stored in the dark at 0-4°C.
no. A-700)] in binding buffer [10 mM Hepes
(W-2-hydroxyethylpiperazine-W-2-ethane-
sulfonic acid)-NaOH, pH. 7.4, 140 mM NaCI,
2.5 mM CaCI2] at concentration of 1.0 ug/ml
This solution has to be prepared fresh prior
to use.
Method
1. Suspend 105-106 cells in 1 ml of fluorescein-conjugated annexin V in
binding buffer for 5 min.
2. Add PI solution to the cell suspension prior to analysis to have a final
PI concentration of 1.0 ug/ml.
67
• use excitation in blue light (e.g. 488 nm line of the argon ion laser)
• light scattering (forward vs. side) may be used to trigger cell
measurements
• measure green fluorescein-annexin V fluorescence at 530±20 nm
• measure red (PI) fluorescence at >600 nm
4. Cell analysis by LSC. To be analysed by LSC the cells should be
stained in suspension, as described above, then placed on a micro-
scopic slide under a coverslip for fluorescence measurement. Alterna-
tively, the cells should be initially attached electrostatically to a
microscope slide, as described above (see Section 2) and then sub-
jected to staining with fluoresceinated annexin V and PI. It is critical
that cells should not dry or be mechanically damaged during the
attachment and staining procedure.
Live, non-apoptotic cells have low green (fluorescein) fluorescence and

little or no red PI fluorescence. Cells undergoing apoptosis stain green but
continue to be negative for PI staining; such cells often have low forward and
high side scatter (Figure 4). Isolated nuclei, or cells with damaged membranes
should stain rapidly and brightly with PI. Note that cells with damaged
membranes may also be positive for annexin V since phosphatidylserine on
the inside of the plasma membrane is available to the ligand. Thus, damaged
cells may be PI positive/annexin V negative or PI positive/annexin V positive.
Any procedure which affects the integrity of the membrane will allow access
of annexin V to the inner leaflet of plasma membrane, resulting in cells which
will be scored as positive for apoptosis. The use of proteolytic enzymes to
disrupt cell clumps or to remove adherent cells from culture walls was reported
to affect the binding of fluoresceinated annexin V. As a result, care should be
exercised in the use of such preparatory procedures. Longer incubation times
will also allow cells which still maintain membrane integrity to become positive
for PI since this dye will enter intact cells, although very slowly. Therefore, if
flow cytometric analysis is not performed quickly after staining, do not add PI
until 5 min before measurement. Apoptosis, itself, is an ongoing process. As a
result, cells stained with fluorescein-annexin V should not be kept for
prolonged lengths of time (>1 h) prior to measurement.
6. Detection of apoptotic cells based on their

fractional DNA content
Activation of an endonuclease causes DNA fragmentation (see Chapter 3)
and such DNA can be extracted from the cells following their fixation and
permeabilization such that less DNA in apoptotic cells stains with any DNA
68
Figure 4. The distinction between live, early apoptotic, and late apoptotic/necrotic cells
by LSC after their staining with fluoresceinated annexin V and PI as described in Protocol
3. Apoptosis of HL60 cells was induced by their incubation with 0.15 uM of CPT for 3 h as
described (16, 17), (A)The live, non-apoptotic cells neither stain with annexin V-FITC nor
with PI, (B) Early apoptotic cells stain with fluorescein but exclude PI while (C) late
apoptotic and necrotic cells stain with both dyes. The representative cells from the
sectors A, B, or C of the contour map were relocated, viewed under blue light incident
illumination, and their colour pictures were converted to grey scale.
fiuorochrome (12, 13). The degree of DNA degradation varies depending on

the stage of apoplosis, the ecll type, and often the nature of the apoptosis-
inducing agent. Hence, the extractability of DNA during the staining procedure
also varies. It has been noted that a high molarity phosphate-citrate buffer
enhances extraction of the fragmented DNA (36), This approach can be used to
control the extent of DNA extraction from apoptotic cells to the desired level
and to obtain their optimal separation by flow cytometry, as described in
Protocol 4,
Protocol 4. Detection of fractional DNA content

Reagents
• DNA staining solution: dissolve 200 ug of PI • DNA extraction buffer: mix 192 ml of 0.2 M
in 10 ml of PBS and add 2 mg of DNase-free Ma2HPO4 with 8 ml of 0.1 M citric acid; pH
RNase A (boil RNase for 5 min if it is not 7.8
DNase free] Prepare fresh staining solution
before each use
Method
1. Fix the cells in suspension in 70% ethanol by adding 1 ml of cells
suspended in PBS (1-5 x I06 cells) into 9 ml of 70% ethanol in a tube
on ice. Cells can be stored in fixative at -20°C for several weeks.
69
2. Centrifuge cells (200 g, 3 min), decant ethanol, suspend cells in 10 ml
of PBS, and centrifuge (300 g, 5 min).
3. Suspend cells in 0.5 ml PBS, into which you may add 0.2-1.0 ml of the
DNA extraction buffer.
4. Incubate at room temperature for 5 min, centrifuge.
5. Suspend the cell pellet in 1 ml of DNA staining solution.
6. Incubate the cells for 30 min at room temperature.
7. Analyse the cells by flow cytometry.
• use 488 nm laser line (or a mercury arc lamp with a BG12 filter) for
excitation
• measure red fluorescence (>600 nm) and forward light scatter
Alternative methods
Cellular DNA may be stained with other fluorochromes instead of PI, and
other cell constituents may be counterstained in addition to DNA. The
following is the procedure used to stain DNA with 4.6-diamidino-2-
phenylindole (DAPI).
1. After step 4 above, suspend the cell pellet in 1 ml of a staining solution
which contains DAPI (Molecular Probes) at a final concentration
1 ug/ml in PBS. Keep on ice for 20 min.
• use excitation with UV light (e.g. 351 nm line from an argon ion
laser, or mercury lamp with a UG1 filter)
• measure the blue fluorescence of DAPI in a band from 460 to 500 nm
Cell analysis by LSC

To be analysed by LSC the cells should be fixed, rinsed with phosphate-
citrate buffer, and stained in suspension, as described above, then placed
on microscopic slides under a coverslip for measurement. Alternatively,
the cells may be cytocentrifuged, smeared, or attached electrostatically to
a microscope slide (see Section 2). To attach cells to a microscope slide
by cytocentrifugation follow the steps as below:
1. Add 300 ul of cell suspension in tissue culture medium (with serum)
containing approximately 20000 cells into a cytospin (e.g. Shandon
Scientific) chamber. Cytocentrifuge at 1000 r.p.m. (~110 g) for 6 min.
2. Without allowing the cytospun cells to dry completely, fix them by
immersing the slides in a Coplin jar containing 70% ethanol. The cells
can be stored in ethanol for several days. After fixation, rinse the slides
in phosphate-citrate buffer, stain the cells with PI as described above
for cell suspensions, and measure their fluorescence by LSC.
70
Figure 5. Detection of apoptotic cells with fractional DNA content based on cellular DNA
content analysis. To induce apoptosis the cells were treated with DNA topoisomerase II
inhibitor, fostriecin, as described (37). The cells were then fixed in 70% ethanol, stained
with PI and their fluorescence was measured by flow cytometry (FACScan), as described
in Protocol 4. The population of apoptotic cells is represented by the sub-G1 peak (Ap).
Apoptotic cells have a decreased PI (or DAPI) fluorescence and dimin-

ished forward light scatter compared with the cells in the main peak (Gl)
(Figure 5). It should be emphasized that the degree of extraction of low MW
DNA from apoptotic cells, and consequently the content of DNA remaining
in the cell for flow cytometric analysis, may vary dramatically depending on
the degree of DNA degradation (duration of apoptosis), the number of cell
washings, the pH, and the molarity of the washing and staining buffers.
Therefore, in Protocol 4, step 3, add less or no extraction buffer (e.g. 0-0.2 ml)
if DNA degradation in apoptotic cells is extensive (late apoptosis), and more
(up to 1.0 ml) if DNA is not markedly degraded (early apoptosis) and there
are problems with separating apoptotic cells from Gl cells due to their
overlap on DNA content frequency histograms.
7. Identification of apoptotic cells based on the

presence of DNA strand breaks
DNA fragmentation during apoptosis generates a large number of DNA
strand breaks. The 3'-OH termini in the strand breaks can be detected by
attaching a fluorochrome to them. This is generally done by using, directly or
indirectly (e.g. via biotin or digoxygenin), fluorochrome-labelled deoxynucleo-
tides in a reaction preferentially catalysed by exogenous TdT, as originally
71
described in refs 14 and 16 and discussed in Chapter 2. Of all the markers of
DNA strand breaks, BrdUTP appears to be the most advantageous with
respect to sensitivity, low cost, and simplicity of the reaction (17). This
deoxynucleotide, once incorporated into DNA strand breaks, is detected by
an FITC-conjugated anti-BrdU antibody. It should be stressed that detection
of DNA strand breaks requires cell pre-fixation with a cross-linking agent such
as formaldehyde, which, unlike ethanol, prevents the extraction of small
sections of the fragmented DNA. Thus, despite cell permeabilization (with
ethanol) and the subsequent cell washings during the procedure, the DNA
content of early apoptotic cells (and with it the number of DNA strand breaks)
is not markedly diminished compared with unfixed cells.
Protocol 5. Detection of DNA strand breaks
Reagents
• prepare fixatives—1st fixative: 1% • BrdUTP stock solution: BrdUTP (Sigma) 2
methanol-free formaldehyde (available mM (100 nmoles in 50 ul) in 50 mM
from Polysciences Inc., Warrington, PA) in Tris-HCI, pH 7.5
PBS, pH 7.4; 2nd fixative: 70% ethanol • FITC-conjugated anti-BrdU mAb solution
• the TdT reaction buffer (5 x) contains: (per 100 ul of PBS): 0.3 ug of anti-BrdU
potassium (or sodium) cacodylate, 1 M; FITC-conjugated mAb (available from
Tris-HCI, 125 mM, pH 6.6; bovine serum Becton Dickinson); 0.3% Triton X-100; 1%
albumin (BSA), 1.25 mg/ml BSA
. cobalt chloride (CoCI2), 10 mM • rinsing buffer. Dissolve in PBS: Triton X-
• TdT in storage buffer, 25 units in 1 ul 100, 0.1% (v/v); BSA, 5 mg/ml
The buffer, TdT, and CoCI2 are available from . PI staining buffer. Dissolve in PBS: PI, 5
Boehringer Mannheim, Indianapolis, IN. u/ml; DNase-free RNase A, 200 ug/ml
Method
1. Fix cells in suspension in 1% formaldehyde for 15 min on ice.
2. Centrifuge (300 g, 5 min), resuspend the cell pellet in 5 ml PBS, centri-
fuge (300 g, 5 min), resuspend the cells (approximately 106 cells) in
0.5 ml of PBS.
3. Add the above 0.5 ml aliquot of cell suspension into 5 ml of ice-cold
70% ethanol. The cells can be stored in ethanol, at -20°C for several
weeks.
4. Centrifuge (200 g, 3 min), remove ethanol, resuspend cells in 5 ml
PBS, centrifuge (300 g, 5 min).
5. Resuspend the pellet (not more than 106 cells) in 50 ul of a solution
which contains:
• 10 ul of the reaction buffer
• 2.0 ul of BrdUTP stock solution
• 0.5 ul (12.5 units) of TdT in storage buffer
• 5 ul of CoCI2 solution
• 33.5 ul distilled H,O
72
6. Incubate cells in this solution for 40 min at 37°C (alternatively,
incubation can be carried at 22-24°C overnight).
7. Add 1.5 ml of the rinsing buffer, centrifuge (300 g, 5 min).
8. Resuspend cells in 100 ul of FITC-conjugated anti-BrdU mAb solution.
9. Incubate at room temperature for 1 h or at 4°C overnight. Add 2 ml of
rinsing buffer, centrifuge (300 g, 5 min).
10. Resuspend the cell pellet in 1 ml of PI staining solution containing
RNase.
11. Incubate for 30 min at room temperature in the dark.
• illuminate with blue light (488 nm laser line or BG12 excitation
filter)
• measure green fluorescence of FITC-anti-BrdU mAb at 530±20 nm
• measure red fluorescence of PI at >600 nm
Commercial kits
Phoenix Flow Systems and PharMingen Inc., (San Diego, CA, USA) pro-
vide kits to identify apoptotic cells based either on a single-step procedure
utilizing TdT and FITC-conjugated dUTP (APO-DIRECT™) or TdT and
BrdUTP, as described above (APO-BRDU™). A description of the method,
which is nearly identical to the above, is included with the kit. Another kit
(ApopTag™), based on two-step DNA strand break labelling with
digoxygenin-16-dUTP by TdT, is provided by ONCOR Inc., (Gaithersburg,
MD, USA).
Analysis of DNA strand breaks by laser-scanning cytometry (LSC)

1. Add 300 ul| of cell suspension in tissue culture medium (with serum)
containing approximately 20000 cells into a cytospin chamber. Cyto-
centrifuge at 1000 r.p.m. (~110 g) for 6 min.
2. Without allowing the cytospins to dry completely, pre-fix cells in 1%
formaldehyde in PBS for 15 min on ice.
3. Transfer the slides to 70% ethanol and fix for at least 1 h; the cells can
be stored in ethanol for several days.
4-9. Follow steps 4-9 above, as described for flow cytometry. Small
volumes (50-100 ul) of the respective buffers, rinses, or staining
solutions are carefully layered on the cytospin area of the slides held
horizontally. At appropriate times these solutions are removed with a
Pasteur pipette (or vacuum suction pipette). Small pieces (2.5 cm x
2.5 cm) of thin polyethylene foil may be layered on slides atop the
drops to prevent drying. The incubations should be carried out in a
moist atmosphere to prevent drying at any step of the reaction.
73
10. Rinse the slide in PBS and mount the cells under a coverslip in a drop
of the PI staining solution containing RNase A. If the preparations are
to be stored for a longer period of time (hours, days, at 4°C), the
coverslips are mounted in a drop of a mixture of glycerol and PI
staining solution (9:1).
11. Measure cell fluorescence on LSC.
• excite fluorescence with 488 nm laser line
• measure green fluorescence of FITC-anti-BrdU mAb at 530±20 nm
• measure red fluorescence of PI at >600 nm
Identification of apoptotic cells is based on their intense labelling with

FITC-anti-BrdU mAb, which frequently requires use of an exponential scale
(logarithmic photomultipliers) for data acquisition and display (Figure 6).
Simultaneous measurement of DNA content makes it possible to identify
the cell cycle position of both cells in apoptotic and non-apoptotic popula-
tions.
Figure 6. DNA strand break labelling in apoptotic cells. To induce apoptosis HL60 cells
were treated with CPT for 3 h as described (16, 17). DNA strand breaks were labelled with
BrdUTP and cellular DNA was counterstained with PI, as described in Protocol 5, Cellular
fluorescence was measured by flow cytometry (FACScan). Note that, preferentially, S
phase cells are undergoing apoptosis.
74
8. Identification of apoptotic cells based on the

increased DNA sensitivity to denaturation
The sensitivity of DNA in situ to denaturation is higher in the condensed
chromatin of apoptotic cells compared with DNA in the interphase nuclei of
live cells (37). There is also evidence that a fraction of DNA in apoptotic cells
is denatured, reacting with antibody against single-stranded DNA (38).
Measurement of DNA denaturability is based on the metachromatic property
of the fluorochrome acridine orange (AO) which differentially stains double-
stranded (ds) vs. denatured, single-stranded (ss) nucleic acids. In this method,
cells are briefly pre-fixed in formaldehyde followed by ethanol. RNA is then
removed by pre-incubation with RNase A and DNA is denatured in situ by
brief cell exposure to 0.1 N HC1. The cells are then stained with AO at pH 2.6;
the low pH of the staining reaction prevents DNA renaturation (37).
Apoptotic cells, having a larger fraction of DNA in the denatured form, have
more intense red and reduced green fluorescence, compared with non-
apoptotic (interphase) cells, which stain intensively green but have low red
fluorescence (Figure 7).
Compared with non-apoptotic interphase cells, apoptotic cells show in-
creased red and decreased green fluorescence (Figure 7). Because the increased
DNA sensitivity to denaturation is associated with chromatin condensation
and seems to be unrelated to the presence of DNA strand breaks (37) this
method may be preferable in situations of atypical apoptosis, when inter-
nucleosomal DNA degradation does not occur (19-21).
Figure 7. Detection of apoptotic cells based on the increased DNA denaturability.

Apoptosis of HL60 cells was induced by CRT, as described (37).The cells were stained
with AO after denaturation of DNA with 0.1 M HCI, as described in Protocol 6. Their
fluorescence was measured by flow cytometry (FACScan). Apoptotic cells (Ap) are
characterized by the increased red fluorescence and lowered green fluorescence.
75
Protocol 6. Identification of apoptotic cells by DNA denaturation

Reagents
Stock solutions, buffers:
• stock solution of AO: dissolve 1 mg of AO • fixatives: (a) 1% methanol-free formaldehyde
(Molecular Probes, Inc.) in 1 ml of distilled dissolved in PBS, pH 7.4; (b) 70% ethanol
water (AO stock solution is stable for . HCI, 0.1 M
several months when stored at 4°C and in • AO staining solution: (a) mix 90 ml of 0.1 M
the dark) citric acid with 10 ml of 0.2 M Na2HPO4; the
• RNase stock solution: dissolve 1 mg of final pH is 2.6; (b) add 0.6 ml of the AO
RNase A in 1 ml of distilled water (use stock solution (1 mg/ml) to 100 ml of this
DNase-free RNase). Less pure preparations buffer; the final AO concentration is 6
require 2-3 min heating at 100°C to M.ug/ml. This solution is stable for several
inactivate DNase. weeks when stored in the dark, at 4°C.
Method
1. Rinse the cells with PBS and suspend 106-107 cells in 1 ml of PBS.
2. Fix the cells by transferring 1 ml of the above cell suspension into a
tube containing 9 ml of 1% formaldehyde in PBS, on ice. After 15 min,
centrifuge (300 g, 5 min).
3. Suspend the cell pellet in 10 ml of PBS, centrifuge (300 g, 5 min).
4. Suspend the cell pellet in 1 ml of PBS, transfer this suspension with a
Pasteur pipette into a tube containing 9 ml of 70% ethanol, on ice.
Samples can be stored in ethanol at 4°C for a minimum of 4 h to up to
several weeks.
5. Centrifuge (200 g, 3 min) and suspend the cell pellet (106-107 cells) in
1 ml of PBS.
6. Add 0.2 ml of RNase A stock solution. Incubate at 37°C for 30 min.
7. Centrifuge and resuspend cells in 1 ml of PBS.
8. Withdraw a 0.2 ml aliquot of cell suspension in PBS and transfer it to
a small (e.g. 5 ml volume) tube.
9. Add 0.5 ml of 0.1 M HCI, at room temperature.
10. After 30 sec, add 2.0 ml of AO solution, also at room temperature
(Important: do not use cold solutions in steps 9 and 10).
11. Transfer this suspension to the flow cytometer and measure cell
fluorescence.
• AO is excited with blue light; use the 457 (preferred) or 488 nm
laser lines, or BG12 excitation filter
• measure the green fluorescence at 530±20 nm
• measure red fluorescence with a long pass filter at >640 nm
76
9. General comments
The selection of a particular method depends on the cell system, the nature of
the inducer of cell death, the mode of cell death, the information that is being
sought (e.g. specificity of apoptosis with respect to the cell cycle phase or
DNA ploidy), and the technical restrictions (e.g. the need for sample trans-
portation, type of flow cytometer available, etc.). Positive identification of
apoptotic cells is not always easy. The most specific methods appear to be
those based on detection of DNA strand breaks. The number of DNA strand
breaks in apoptotic cells is so large that the intensity of their labelling seems
to be an adequate marker for their identification (14). The situation, however,
is complicated in the instances of apoptosis where internucleosomal DNA
degradation does not occur (19-21). The number of DNA strand breaks in
such atypical apoptotic cells may be inadequate for their identification by this
method. Conversely, false-positive identification of apoptotic cells can take
place when internucleosomal DNA degradation accompanies cell necrosis.
Apoptosis can be recognized with greater certainty when more than a single
viability assay is used. The assays may include simultaneous assessment of
plasma membrane integrity, exposure of phosphatidylserine to fluoresceinated
annexin V, mitochondrial transmembrane potential, DNA denaturability,
and/or DNA fragmentation . For example, preservation of plasma membrane
integrity combined with chromatin condensation and extensive DNA break-
age is a more specific marker of apoptosis than each of these features alone.
However, regardless of the assay used to identify apoptosis, the mode of cell
death should be positively identified by inspection of cells by light or electron
microscopy. Morphological changes during apoptosis have a very specific
pattern (24) and should be the deciding factor in situations where ambiguity
arises regarding the mechanism of cell death.
There are characteristic features of LSC distinguishing it from flow cyto-
metry which offer some advantages and even unique technical possibilities in
its use in the analysis of cell death. The major advantage of LSC is that cells
may be relocated after they are measured, and examined visually or by image
analysis. This can confirm the mode of cell death, which, as discussed above, is
not possible based on measurement of a single cell attribute. This feature of
LSC is useful, for example, in recognizing non-apoptotic phagocytic cells that
have ingested apoptotic bodies of neighbouring cells (2). Such phagocytes
could be erroneously identified as apoptotic cells by flow cytometry. The
possibility of relocating once measured cells on the slide also enables one to
perform additional examinations after bleaching and restaining with other
fluorochrome(s) or absorbing dyes (39). Since the slides can be stored
indefinitely, the same cells can be re-examined in the future using new probes.
Since the data, including the cell position on the slide, are stored in list-mode
fashion, the measurements performed at different time points on the same
cells can be correlated with each other.
77
Although imaging by LSC is at a lower resolution compared with classical
image analysis, LSC offers the possibility of extracting morphometric features
from the examined cell that are not available by flow cytometry. The charac-
teristic condensation of chromatin resulting in hyperchromicity of DNA in
apoptotic cells, revealed by high maximal pixel values, provides a marker
identifying apoptotic cells (30; Figure 2). Cell and nuclear area are measured
by the number of pixels recording cytoplasmic (e.g. protein) and nuclear
(DNA) fluorescence, and the nucleus to cytoplasm ratio can be calculated and
can be a valuable parameter of morphological changes that occur during
apoptosis.
The duration of apoptosis is usually short (1-6 h) and variable depending
on cell type, inducer of apoptosis, in vitro vs. in vivo conditions, etc. Both
prolongation and increased frequency of apoptosis are reflected by the in-
creased apoptotic index . One has to be careful, therefore, in interpreting data
that show an increased apoptotic index as representing increased frequency of
apoptosis. Likewise, the 'time window' through which a particular flow cyto-
metric method sees this kinetic event, and thus can identify the apoptotic cell,
also varies. Hence, the apoptotic index in the same cell population detected
by different methods may not be identical. Quantitative estimation of cell
death in cell populations requires a simultaneous measure of the absolute
number of live cells, in addition to quantitation of apoptosis or necrosis (40).
Acknowledgements
This work was supported by NCI grant CA RO1 28704, the Chemotherapy
Foundation and 'This Close' Foundation for Cancer Research. Elzbieta
Bedner, the recipient of an Alfred Jurzykowski Foundation fellowship, was
on leave from the Department of Pathology, Pomeranian School of Medicine,
Szczecin, Poland.
References
1. Darzynkiewicz, Z., Bruno, S., Del Bino, G., Gorczyca, W., Hotz, M.A., Lassota,
P., and Traganos, F. (1992). Cytometry, 13,795-808.
2. Darzynkiewicz, Z., Juan, G., Li, X., Gorczyca, W., Murakami, T., and Traganos, F.
(1997). Cytometry, 27,1-20.
3. Frey, T. (1995). Cytometry, 21, 265-274.
4. Ormerod, M.G. (1998). Leukemia, 12,1013-1025.
5. van Engeland, M., Nieland, L.J.W., Ramaekers, F.C.S., Schutte, B., and
Reutelingsperger, P.M. (1998). Cytometry, 31,1-9.
6. Telford, W.G., King, L.E., and Fraker, P.J. (1994). J. Immunol. Meth., 172,1-16.
7. Cossarizza, A., Ceccarelli, D., and Masini, A. (1996). Exp. Cell Res., 222, 84-94.
8. Zamzani, N., Brenner, C., Marzo, I., Susin, S.A., and Kroemer, G. (1998).
Oncogens, 16, 2265-2282.
78
9. Ormerod, M.G., Collins, M.K.L., Rodriguez-Tarduchy, G., and Robertson, D.
(1992). J. Immunol. Meth., 153,57-66,.
10. Koopman, G., Reutelingsperger, C.P.M., Kuijten, G.A.M., Keehnen, R.M.J., Pals,
S.T., and van Oers, M.H.J. (1994). Blood, 84,1415-1420.
11. Petit, P.X., LeCoeur, H., Zorn, E., Dauguet, C., Mignotte, B., and Gougeon,
M.L.J. (1995). Cell Biol, 130,157-165.
12. Nicoletti, I., Migliorati, G., Pagliacci, M.C., Grignani, F., and Riccardi, C. (1991).
J. Immunol. Meth., 139,271-280.
13. Umansky, S.R., Korol', B.R., and Nelipovich, P.A. (1981). Biochim. Biophys.
Acta, 655,281-290.
14. Gorczyca, W., Bruno, S., Darzynkiewicz, R., Gong, J., and Darzynkiewicz, Z.
(1992). Int. J.OncoL, 1,639-648.
15. Gold, R., Schmied, M., Rothe, G., Zischler, H., Breitschopf, H., Wekerle, H., and
Lassman, H. (1993). J. Histochem. Cytochem., 41,1023-1030.
16. Gorczyca, W., Gong, J., and Darzynkiewicz, Z. (1993). Cancer Res., 52, 1945-
1951.
17. Li, X. and Darzynkiewicz, Z. (1995). Cell Prolif., 28, 571-579.
18. Li, X., Melamed, M.R., and Darzynkiewicz, Z. (1996). Exp. Cell Res., 222,28-37.
19. Catchpoole, D.R. and Stewart, B.W. (1993). Cancer Res., 53,4287-4296.
20. Ormerod, M.G., O'Neill, C.F., Robertson, D., and Harrap, K.R. (1994). Exp. Cell
Res., 211,231-237.
21. Zamai, L., Falcieri, E., Marhefka, G., and Vitale, M. (1996). Cytometry, 23,
303-311.
22. Hara, S., Halicka, H.D., Bruno, S., Gong, J., Traganos, F., and Darzynkiewicz, Z.
(1996). Exp Cell Res., 232,372-384.
23. Arends, M.J., Morris, R.G., and Wyllie, A.M. (1990). Am. J. Pathol., 136, 593-608.
24. Kerr, J.F.R., Wyllie, A.H., and Curie, A.R. (1972). Br. J. Cancer, 26,239-257.
25. Kamentsky, L.A., Burger, D.E., Gershman, R.J., Kamentsky, L.D., and Luther, E.
(1997). Acta Cytol., 41,123-143.
26. Kamentsky, L.A., and Kamentsky, L.D. (1991). Cytometry, 12,381-387.
27. Bedner, E., Burfeind, P., Gorczyca, W., Melamed, M.R., and Darzynkiewicz, Z.
(1997). Cytometry, 29,191-196.
28. Bedner, E., Melamed, M.R., and Darzynkiewicz, Z. (1998). Cytometry, 33,1-9.
29. Bedner, E., Burfeind, P., Hsieh, T-C., Wu, J.M., Augero-Rosenfeld, M., Melamed,
M.R., Horowitz, H.W., Wormser, G.P., and Darzynkiewicz, Z. (1998). Cytometry,
33,47-55.
30. Furuya, T., Kamada, T., Murakami, T., Kurose, A., and Sasaki, K. (1997).
Cytometry, 29,173-177.
31. Luther, E. and Kamentsky, L.A. (1996). Cytometry, 23,272-278.
32. Schmid, I., Uttenbogaart, C.H., and Giorgi, J.V. (1994). Cytometry, 15,12-20.
33. Clatch, R.J., Foreman, J.R., and Walloch, J.L. (1998). Cytometry, 34, 3-16.
34. Salzman, G.C., Singham, S.B, Johnston, R.G., and Bohren, C.F. (1990). In Flow
cytometry and sorting (ed. M.R. Melamed, T. Lindmo, and M.L. Mendelsohn),
pp. 81-107. Wiley-Liss, New York.
35. Darzynkiewicz, Z., Traganos, F., Staiano-Coico, L., Kapuscinski, J., and Melamed,
M.R. (1982). Cancer Res., 42,799-806.
36. Gong, J., Traganos, F., and Darzynkiewicz, Z. (1994). Anal. Biochem., 218,
314-319.
79
37. Hotz, M.A.,Gong J., Traganos, F., and Darzynkiewicz, Z. (1994). Cytometry, 15,
237-244.
38. Frankfurt, O.S., Byrnes, J.J., Seckinger, D., and Sugarbaker, E.V. (1993). Oncol.
Res., 5, 37-42.
39 Li, X., and Darzynkiewicz, Z. (1999) Exp. Cell Res., 249; 404-412.
40. Darzynkiewicz, Z., Bedner, E., Traganos, F., and Murakami, T. (1998). Human
Cell., 11, 3-12.
80
Cell-mediated cytotoxicity and cell
death receptors
JAVIER NAVAL and ALBERTO ANEL
1. Overview of pathways for cell-mediated

cytotoxicity
T cell-mediated cytotoxicity in short time assays (3-4 h) is achieved through
two main mechanisms. A first mechanism, Ca2+ dependent, requires the action
of the pore-forming protein perform and a subfamily of serine proteases
named granzymes or fragmentins (1). The second mechanism, which is Ca2+
independent for its execution, requires the expression of Fas (Apo-l/CD95)
at the target cell surface (2), and of the Fas ligand (FasL) at the effector cell
surface (3). The fact that the residual cytotoxic activity detected in T cells
from perform knock-out mice could be attributed solely to Fas-based cyto-
toxicity underscored the importance of these two lytic mechanisms (4)
Perform and granzymes are only expressed in specialized killer cells like
cytotoxic T lymphocytes (CTL) or natural-killer (NK) cells, where they are
stored in secretory granules (5, 6). After the recognition by CTL or NK cells
of a virus-infected or a tumour cell, these granules are secreted and the
perforin-mediated entry of granzymes into the cytoplasm causes the rapid
lysis of target cells (4, 7). Although also implicated in CTL- and NK-induced
lysis, the main physiological role of Fas-based cytotoxicity may be the control
of peripheral tolerance (8, 9). The implication of Fas-based cytotoxicity in
activation-induced cell death (AICD) of T cell hybridomas (10) and of normal
T cell blasts (11) has been clearly demonstrated. It has been suggested that
tumour necrosis factor-a (TNF) mediates AICD of CD8+ T cells in the
absence of Fas expression, while the Fas/FasL system would be the main
cause for AICD of CD4+ T cells (12). These results suggest that T cells able to
secrete TNF could use this cytokine for the lysis of target cells expressing TNF
receptors. It should be noted, however, that TNF-induced toxicity is usually
detected only after long incubation times (48-72 h) (12).
1.1 Fas-based cytotoxicity

1.1.1 Induction of FasL expression in CTL
The expression of FasL in CTL is not constitutive and a strong activation
signal through the T cell antigen receptor (TCR) is needed (13). This can also
be achieved using a combination of the phorbol ester PMA, which activates
efficiently protein kinase C (PKC), and the calcium ionophore ionomycin (2).
The induction of FasL expression in CTL can be prevented by protein
tyrosine kinase inhibitors, and by cyclosporin A, presumably through the
inhibition of calcineurin phosphatase (13). Hence, although the execution of
Fas-based cytotoxicity occurs in the absence of extracellular Ca2+, the TCR-
induced FasL expression is dependent on Ca2+ (14). It was later demonstrated
that TCR-induced, but not PMA/ionomycin-induced, FasL expression in CTL
was dependent on phosphatidylinositol 3-kinase activity (15), and that the
transcriptional regulation of FasL expression was dependent on the activation
of the transcription factor NF-AT (16), according to the observed inhibition
by cyclosporin A.
1.1.2 Mechanism for Fas-induced apoptosis
Fas (Apo-l/CD95) is a type I transmembrane glycoprotein belonging to the
TNF receptor superfamily. Fas is expressed in some thymocyte subsets,
activated and tumour T and B cells, and in several non-immune tissues. Fas
induces apoptosis when cross-linked with agonist mAbs or by its natural
ligand, FasL (17). Fas and the TNF receptor share a cytoplasmic domain
needed to induce apoptosis that has been termed the 'death domain' (18).
A great deal of research effort has demonstrated the implication of intra-
cellular cysteine-proteases with Asp specificity of the interleukin-l(3-converting
enzyme (ICE) family, later named as caspases, in apoptosis (see Chapter 10),
and in particular in Fas-induced cell death (reviewed in refs 19 and 20)).
Using the peptide inhibitor, Ac-DEVD-CHO, which inhibits, preferentially,
caspases of the CPP32 (caspase-3) subfamily (21), it has been shown that
these caspases play a key role in cytotoxicity exerted by anti-Fas mAbs (22),
and by FasL-expressing T cell effectors (23). The finding that activation of
CPP32-like caspases plays a pivotal role in many types of apoptotic process
has led to the proposal that these caspases constitute the apoptotic
executioner (24).
The connection between Fas ligation and the activation of the apoptotic
executioner has recently been unveiled. Aggregation of Fas through agonist
antibodies or by its physiological ligand induces the recruitment to the cross-
linked receptors and, through their respective death domains, of a molecule
termed FADD (Fas-associated death domain) (25). In addition to the death
domain, which allows its interaction with the aggregated receptors, FADD
also contains a 'death effector domain' that mediates the recruitment of
another molecule composed of two death effector domains and a caspase
82
5: Celt-mediated cytotoxicity and cell death receptors
domain, named FLICE, MACH, Mch5, or caspase-8 (26-28). The recruitment
of this molecule induces activation of its protease activity, resulting in the
cleavage and activation of CPP32-like proteases, the apoptotic executioner.
An alternative pathway implicated in the activation of CPP32-like caspases is
the release of pro-apoptotic proteins (cytochrome c and the apoptosis-inducing
factor, AIF) from mitochondria in the first stages of apoptosis (29, 30). This
process takes place through the assembly of a complex that also includes Apaf-
1, the mammalian homologue of Ced-4, and caspase-9, which in turn, activates
caspase-3 (31) (see also Chapter 1, Fig. 6). Both processes, 'direct' activation of
caspase-3 through caspase-8 recruitment to the aggregated receptor and
'indirect' activation of caspase-3 through mitochondrial activation of caspase-9,
are not mutually exclusive. In fact, it has recently been demonstrated that the
relative importance of one over the other depends on the nature of the cells
undergoing apoptosis (32).
1.2 Perforin/granzyme-based cytotoxicity

1.2.1 Perform and granzymes
The insertion of perform into the plasma membrane of target cells facilitates
the entry of granzymes inside the cell cytoplasm (5, 33). Granzymes, in turn,
activate programmed cell death (34). At least 10 different serine proteases are
expressed in CTL and/or NK cells, granzyme A and granzyme B being the
major components of lytic granules and the main contributors to cytotoxicity
(6, 34, 35). Although granzyme B is a serine protease, it shares with caspases
an unusual substrate specificity characterized by the requirement of an Asp
residue at the P1 position. Granzyme A, on the contrary, has a tryptase-like
specificity (34), suggesting functional versatility of the system. This versatility
has been evidenced in granzyme A-knock-out mice, where cell-mediated
cytotoxicity is normal (36), and in granzyme B-knock-out mice, where
although cell-mediated cytotoxicity is blocked at short incubation times (4 h),
it is completely recovered at longer times (16 h) (37).
1.2.2 Mechanism for perforin/granzymes-induced apoptosis
A possible connection between granzyme-induced cell death and caspase
activation has been demonstrated, since it was observed that purified
granzyme B cleaves and activates caspase-3 (38) or its close homologue
caspase-7 (39). It was later demonstrated that in short-term assays (3-4 h), the
peptide inhibitors Ac-DEVD-CHO (40) and Z-VAD-fmk (41) prevented
nuclear apoptosis induced by CTL on Fas-negative targets, as measured by
the [125I]iododeoxyuridine release assay and nuclear staining. These studies
clearly implicated caspases in perforin/granzyme-based cytotoxicity exerted
by CTL. However, caspase inhibitors did not prevent cell lysis under the same
or similar experimental conditions, as measured by the 51Cr release assay
(41, 42) or membrane manifestations of apoptosis, like phosphatidylserine
exposure (41). In addition, the inhibition of CTL-induced nuclear apoptosis
83
Javier Naval and Alberto Ann!
Figure 1. Schematic representation of the known biochemical mechanisms for apoptosis

induction by CTL on target cells (see Section 1 for details),
by Ac-DEVD-CHO observed in 3-4 h assays was no longer observed in 6-16

h assays. The combination of Ac-DEVD-CIIO and an inhibitor of gran/.yme
A, inhibited nuclear apoptosis at any time-point tested (40). Altogether, these
data indicate that: (i) granzyme B induces the nuclear manifestations of
apoptosis through a mechanism mediated by caspases; (ii) gran/yme B
induces cytoplasmic apoptotic manifestations leading to cell lysis through a
caspase-independent mechanism; and (iii) all the manifestations of granzyme
A-induced apoptosis, nuclear and cytoplasmic, seem to proceed through a
caspase-independent mechanism. A summary of all these considerations is
shown in Figure 1.
2. Standard methods for the evaluation of cell-

mediated cytotoxicity
2.1 Chromium release assay
Perhaps the most simple, cheap, and effective technique for in vitro cyto-
toxicity tests is the one based on target cell labelling with Na251CrO4. This is
probably still the most widely used method and is commonly referred to as
'the chromium (51Cr) release assay'. Radioactive chromate passes through the
cell membrane by an unknown mechanism and is bound mainly to cyto-
84
5: Cell-mediated cytotoxicity and cell death receptors
plasmic proteins. Since 51Cr is a -/-emitter, no special preparation of cell

samples is needed for radioactive determination. This technique was first used
to evaluate the effect of radiation on thymocytes (43) and complement-
mediated cytotoxicity (44), and was subsequently applied to the study of cell-
mediated cytotoxicity (45). This method measures lysis of target cells, so both
apoptotic and non-apoptotic deaths are detected.
Protocol 1. Chromium-51 release assay
Safety recommendations
Chromium-51 is a medium-energy y-radiation emitter and it must be
manipulated according to the corresponding national regulations for use
of radioactive materials. The researcher must wear appropriate protective
clothing (laboratory coat, surgical gloves) and dosimeter. Stock, concen-
trated solutions of Na251CrO4 must be conveniently shielded (half-value
layer: 3 mm lead, approximately). On the other hand, the manipulation of
51
Cr does not require any other special precaution, since in the form of
chromate it is not absorbed by any organ in the body.

• tissue culture facilities • V-shaped 96-well microtitre plates
• effector and target cells • sterile Na251CrO4 in aqueous solution (from
• complete culture medium (e.g. RPMI 1640 Amersham, MEN, or ICN) (1 mCi/ml)
supplemented with heat-inactivated 5% • y-radiation counter (solid scintillation)
FCS, 5 mM Hepes, pH 7.4, and antibiotics)
A. Labelling of target cells

The protocols given are adequate for labelling of tumour target cells and
for lymphocytes from mixed lymphocyte cultures (MLC). Some examples
of commonly used murine target cells, including their MHC restriction, are
the following:
• L1210: lymphocytic leukaemia-expressing H-2d
• EL-4: thymoma-expressing H-2Kb
• RMA: lymphoma-expressing H-2Kb
• P815: monocytic leukaemia-expressing H-2d
• L929: fibrosarcoma-expressing H-2Kk (adherent cell)
Two labelling alternatives are possible.
(a) Rapid (2 h) labelling.

1. Resuspend the appropriate amount of washed, cultured targets in
non-diluted FCS at 1 x 106 cells in 100 ul.
2. Add 10 (uCi of Na251CrO4 per 1 x 106 cells and incubate at 37°C for
1 h.
85
3. Wash then by dilution and centrifugation in complete medium, re-
suspend at 1 x 106 cells/ml in complete medium, and incubate for
another hour at 37 °C.
4. Eliminate the second supernatant, wash again in complete medium,
and resuspend the cells for the experiment.
(b) Overnight labelling

1. Resuspend around 2 x 10s target cells in 5 ml of complete medium,
place the suspension in a 25 cm2 culture flask, and add 200-300 uCi of
Na251Cr04.
2. Incubate overnight at 37°C in a C02 incubator, and then wash twice
with RPMI 1640.
3. Resuspend the cells in complete medium for the experiment.
B Cytotoxicity test
1. The manipulation during the cytotoxicity tests can be done under non-
sterile conditions. Resuspend the labelled target cells at 105 cells/ml
and add 100 ul per well of 96-well plates, so that 104 labelled target
cells are used per experimental point. Make points at least in triplicate.
2. Wash and resuspend the effector cells in complete medium. Several
effector to target (E:T) ratios should be used. In the case of CTL clones,
E:T ratios that should give a good lysis are between 1:1 and 10:1. In the
case of primary mixed lymphocyte cultures (MLC), the E:T ratios
recommended are between 20:1 and 100:1. Resuspend the effector
cells at the maximum cell density to be used in a given experimental
point. Then, plate 100 ul on the wells already containing the labelled
target cells, previously having made the corresponding dilutions of the
effectors with complete medium to obtain the E:T ratios chosen.
3. Include at least triplicates of (i) labelled target cells alone resuspended
in 200 ul of complete medium; and <ii) labelled target cells alone in
100 ul of complete medium where 100 ul of 1% Triton X-100 or 2 N HCI
are added to estimate, respectively, the spontaneous release and total
labelling of the targets.
4. Centrifuge the plate at 400 g at room temperature for 1 min to favour
cell-cell contact. Incubate at 37°C in a cell incubator for the time
chosen. Usually, 4 h cytotoxicity tests are performed, but longer times
can also be used, provided that spontaneous release of the label from
the targets does not increase above 20% of the total labelling. If
spontaneous release in the experimental conditions used is greater
than 30%, the assay is not reliable.
86
5. At the end of the incubations, centrifuge the plates at 400 g during 5min
and harvest 100 ul aliquots of each supernatant by using a multichannel
pipette. Transfer the aliquots directly to small RT-15 plastic tubes (Bibby
Sterilin), seal them with molten paraffin wax, and determine the
radioactivity associated with the supernatants in the y-counter.
6. Calculate the specific 51Cr release at the different E:T ratios as follows:
% of lysis = % of specific 51Cr release =
(cpm sample-cpm spontaneous release)
(cpm maximum release-cpm spontaneous release)
2.2 [125I]Iododeoxyuridine (125IUdR) release assay

125
IUdR competes with thymidine for incorporation during DNA synthesis
because the iodine atom is sterically similar to the methyl group of thymidine.
So 125IUdR is incorporated into DNA and, when the target cell is killed by
effector cells, 125IUdR is released in the form of DNA fragments that are not
re-utilized. Since this event is a nuclear marker of apoptosis, 125IUdR release
is the method of choice to analyse nuclear apoptosis during cell-mediated
cytotoxicity. This method was initially used by comparing it with 51Cr release
to distinguish CTL-induced death from lysis induced by antibody plus
complement, which is not associated with DNA fragmentation (46,47).
Protocol 2. [125l]lododeoxyuridine (125IUdR) release assay
Precautions
125
I is a low-energy y- emitter, and is more easily shielded (half-value
layer: 0.02 mm lead) than 51Cr. The same precautions as indicated for 51Cr
manipulation should be used here (Protocol 1). The incorporation of 125I
into the thyroid by inhalation is its main biological risk. However, since
125
IUdR is not volatile, special precautions are not needed for its
manipulation.

• tissue culture facilities • sterile 126IUdR (from Amersham, NEN, or
» effector and target cells ICN) (1 mCi/ml)
• sterile 1.5 ml Eppendorf cones • hypotonic lysis buffer: 0.5% Triton X-100 in
• culture medium (e.g. RPMI 1640 20 mM Tris, 1 mM EDTA, pH 7.5
supplemented with heat-inactivated 5% • -y-counter (solid scintillation counter)
PCS, 5 mM Hepes, pH 7.4, and antibiotics)
A. Labelling of target cells

1. It is convenient for target tumour cells to be in an exponential phase of
growth when labelling with 125IUdR.
87
2. Resuspend the washed target cells in complete medium at 5 x 105
cells/ml.
3. Add 10-15 nCi of 125IUdR per ml and incubate in a C02 incubator at
37°C for 2-3 h. Then, wash the cells twice with RPMI 1640 and
resuspend in complete medium for the experiment.
B. Cytotoxicity test
1. Resuspend the labelled target cells at 1 x 105 cells/ml and add 100 ul
to a 1.5 ml Eppendorf tube, so that 104 labelled target cells are used
per experimental point. Each experimental point should be made in
triplicate at least.
2. Wash and resuspend the effector cells in complete medium. The same
considerations about E:T ratios indicated for the 51Cr release assay
(Protocol 1) apply here. Resuspend the effector cells at the maximum
cell density to be used in a given experimental point. Then, add 100 ul
into the tubes already containing the labelled target cells, having
previously made the corresponding dilutions of the effectors with
complete medium to obtain the E:T ratios chosen.
3. Include duplicates, at least, of labelled target cells alone, resuspended
in 200 ul of complete medium to estimate the spontaneous release of
the label from the targets.
4. Centrifuge the Eppendorf tubes at 400 g at room temperature for 2 min
to favour cell-cell contact. Incubate at 37°C in a cell incubator for the
time chosen. Usually, 4 h cytotoxicity tests are performed, but longer
times can also be used, provided that spontaneous release of the label
from the targets is not greater than 20% of the total labelling.
5. Centrifuge the tubes at 400 g for 5 min, harvest carefully the whole
supernatant, and save it for counting.
6. Lyse the cells by adding 500 ul of ice-cold lysis buffer, followed by
brief vortexing, and incubation on ice for 20 min. Centrifuge the
lysates at 12000 g for 10 min at 4°C in a minifuge, collect the super-
natants containing fragmented DNA and cut off (with scissors or
blade) the bottom of the tube that contains non-fragmented DNA.
7. Determine the radioactivity associated with each sample in a y-
counter, including the incubation medium, the supernatant of the
lysate, and the DNA pellet.
8. Calculate the specific 125IUdR release at the different E:T ratios as
follows:
% DNA fragmentation = % of specific 125IUdR release =
(cpm sample-cpm spontaneous)
x 100
(cpm total-cpm spontaneous)
88
cpm sample = (cpm in the incubation medium + cpm in the cell
lysate) of the sample
cpm spontaneous = (cpm in the incubation medium + cpm in the cell
lysate) spontaneous
cpm total = (cpm in the incubation medium + cpm in the cell lysate +
cpm in the DNA pellet) of the sample
2.3 The JAM test

This method measures, using target cells labelled with [3H]thymidine and a
conventional cell-harvester, the intact DNA that remains associated with
living target cells. This allows for the estimation of the DNA amount that has
undergone fragmentation during cell-mediated cytotoxicity (48). Hence, the
JAM test detects DNA fragmentation induced by effector cells on the
labelled targets and the data obtained can be considered equivalent to those
obtained using the 125IUdR release assay.
Protocol 3. [3H]Thymidine-labelled DNA retention by living

cells
Precautions
3
H radioactivity is a low-energy (3-radiation emitter. Conventional plastic
and glass containers and surgical gloves protect quite well from this type
of radiation. On the other hand, due to its low energy, tritium p-particles
must be detected in a liquid scintillation counter, making the sample
preparation slightly more laborious. This method is fast, sensitive, and
easy to perform if an automated cell-harvester is available, but it
generates more radioactive waste.

• tissue culture facilities « sterile [3Hlmethylthymidine (from Amer-
• effector and target cells sham, NEN, or ICN) (1 mCi/ml)
• sterile round-bottom, 96-well plates • automated cell-harvester
• culture medium (e.g. RPMI 1640 supple- • scintillation vials and liquid scintillation
mented with heat-inactivated 5% PCS, 5 fluid
mM Hepes, pH 7.4, and antibiotics) • p-counter (liquid scintillation counter)
A Labelling of target cells

1. It is very convenient if the target cells to be in an exponential phase of
growth when labelling with [3H]thymidine.
2. The day before the assay, resuspend the target cells into fresh
medium and add 1 ml to the wells of a 24-well tissue culture plate at
3-5 x 105 cells/ml.
89
3. To label, add [3H]thymidine to a final concentration of 5 uCi/ml to the
cultures and incubate under the same culture conditions for 4-6 h.
After the incubation, wash the cells twice with RPMI 1640 and
resuspend in complete medium for the experiment.
B Cytotoxicity test
1. Resuspend labelled target cells at 105 cells/ml and add 100 (ul per well,
so that 104 labelled target cells are used per experimental point. Each
experimental point should be made in triplicate at least.
2. Wash and resuspend the effector cells in complete medium. The same
considerations about E:T ratios indicated for the previously described
assays also apply here. Resuspend the effector cells so that 100 ul
contains the maximum effector number to be used in a given experi-
mental point. Add 100 JJL! of the corresponding dilution of effector cells
to the labelled target cells, in order to obtain the desired E:T ratios.
3. Include at least triplicates of labelled target cells alone, resuspended in
200 ul of complete medium to estimate the spontaneous release of
label from the targets. To calculate the total labelling, a triplicate of
labelled target cells can be directly placed into scintillation vials.
4. Centrifuge the plates at 400 g at room temperature for 2 min to favour
cell-cell contact. Incubate at 37°C in a CO2 incubator for the time
chosen (1-4 h).
5. At the end of the incubations, aspirate the cells and medium from the
plate wells on to fibre glass filters using an automated cell-harvester.
6. Wash the filters, dry, and count them in a liquid scintillation counter.
7. Calculate the percentage of DNA fragmentation at the different E.T
ratios as follows:
% specific DNA fragmentation =
(spontaneous cpm-sample cpm)
x 100
spontaneous cpm
spontaneous cpm = cpm from retained labelled DNA in the absence
of killers
sample cpm = cpm from retained labelled DNA in the presence of
killers
Although the total incorporation (total labelling of target cells in the
absence of effector cells) is not needed for the calculation of specific
DNA loss, it does need to be measured in each assay, to be sure that
the DNA retained in the absence of killers ('spontaneous cpm') is
roughly the same as the total labelling.
90
2.4 BLT-esterase release assay

One of the consequences of CTL activation through the antigen receptor or
by the combination of phorbol esters and calcium ionophores is the exocytosis
of cytoplasmic granules containing perform and granzymes. The presence of
these proteins in the supernatant of stimulated CTL can be detected by a
colorimetric method termed the BLT-esterase release assay (49). Trypsin-
type serine esterases are detected in fact in these assay, granzyme A being
predominant in CTL or NK cells.
Protocol 4. BLT-esterase release assay

• tissue culture facilities • benzyloxycarbonyl-L-lysine thiobenzyl ester
• effector and target cells (BLT) (from Sigma or Calbiochem) and
• culture medium (e.g. RPMI 1640 supple- dithiobis-(2-nitrobenzoic) acid (DTNB)
mented with heat-inactivated 5% FCS, 5 (from Sigma). BLT powder should be
mM Hepes, pH 7.4, and antibiotics) stored at -20°C inside a desiccator, while
DTNB can be stored at room temperature.
• flat and round-bottomed 96-well plates
• ELISA plate reader
Assay
1. Wash and resuspend the effector cells in complete medium. Stimulate
the cells with the appropriate stimulus. The stimuli could vary: anti-
TCR/CD3 antibodies, phorbol esters plus calcium ionophores,
alloantigen-bearing target cells, etc. If target cells are chosen as
stimulants, several effector to target (E:T) ratios may be used. In this
case, the E:T ratios recommended are 1:1, 1:2, and 1:3, increasing the
number of targets, not of effectors, to optimize granule release from
the CTL In this case, resuspend effector cells in complete medium at
2 x 106 cells/ml and add 50 Ul of the suspension (1 x 105 cells) into the
wells of a round-bottomed 96-well plate. Resuspend the target cells so
that 50 uJ contains the maximum target cell number to be used in a
given experimental point and then make the corresponding dilutions
with complete medium. Plate 50 uJ of the target cell suspensions on
the wells that already contain the CTL, in order to obtain the E:T ratios
chosen.
2. Include at least triplicates of (i) effector cells alone resuspended in
100 ul of complete medium; and (ii) effector cells alone in 50 ul of
complete medium where 50 ul of 1% Triton X-100 are added to
estimate, respectively, the spontaneous release and total CTL content
of BLT-esterase.
3. Centrifuge the plate at 400 g at room temperature for 2 min to favour
cell-cell contact. Incubate at 37°C in a cell incubator during 3-4 h.
91
4. At the end of the incubations, centrifuge the plate at 400 g for 10 min,
harvest carefully 30 ul of the supernatants, and plate them on the wells
of a clean, flat-bottomed, 96-well plate. Make a triplicate blank with
30 ul of fresh culture medium.
5. During the last centrifugation, prepare the BLT reagent by dissolving
4 mg of BLT and 4 mg of DTNB in 50 ml of phosphate-buffered saline,
pH 7.4, by gently shaking and vortexing. Add 150 ul of the reagent to
each well of the plate and incubate at 37°C. The BLT reagent is of
limited stability and can only be used for 3 or 4 h after preparation.
6. Read the intensity of the yellow colour formed using an ELISA plate
reader at 405-415 nm, depending on the filters available, subtracting
automatically the blank values from the sample values. It is recom-
mended that absorbances be read after different incubation times, for
example a first reading at 15 min, followed by measurements at 30
min, 45 min, and 1 h.
7. Calculate the specific esterase release at the different E:T ratios as
follows:
% of specific BLT-esterase release =
2.5 Estimation of target cell nuclear fragmentation using

fluorescent dyes
Apoptosis is associated with chromatin condensation and nuclear fragmenta-
tion. By using fluorescent dyes that label the DNA, these morphological
nuclear changes can be detected by using fluorescence microscopy (see
Chapters 2 and 4 for a more detailed discussion). We will describe here briefly
a method based on p-phenylenediamine (PPDA) labelling (23), but other
fluorescent dyes, like Hoechst 33342, have been successfully used (41) [we
recommend chapter 2 and the work of Nakajima et al. (50) where the use of
Hoechst 33342 is described]. PPDA is currently used as solution in pure
glycerol as a mounting, anti-fading reagent, but when prepared in oxidized
glycerol, it gives a fluorescent adduct which stains nuclei.
92
Protocols. Estimation of target cell nuclear fragmentation by

PPDA staining
Contrary to other nuclear fluorochromes, the yellow to orange PPDA

fluorescence can be visualized with the same filter arrangement as for
FITC, the most commonly used.

• tissue culture facilities • sterile Eppendorf cones
• effector and target cells • PPDA mounting medium: 10 mg PPDA
• culture medium (e.g. RPMI 1640 supple- dissolved in 1 ml PBS, pH 7.4, and then
mented with heat-inactivated 5% PCS, 5 mixed with 9 ml of oxidized glycerol.
mM Hepes, pH 7.4, and antibiotics) Neutralize if necessary with 1 M NaOH. To
prepare oxidized glycerol, treat 10 ml
• 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl- glycerol with 100 (Ul H2O2 (33%, 110 vols),
tetrazolium bromide (MTT) aliquot, and store for 1 day in a crystal-clear
• 1% paraformaldehyde in PBS (fixation tube, exposed to sunlight at room
buffer) temperature. Once prepared, store the
• round cover glasses (13 mm diameter) pre- PPDA reagent until use in the dark at-20°C.
viously treated for 20 min with a 0.1 mg/ml • fluorescence microscope (excitation filter:
solution of poly-L-lysine (Sigma) in water 450-490 nm)
Assay
1. PPDA staining is done after the fixation of cells, and so target cells can
be previously incubated with MTT to distinguish them from effector
cells. For that, incubate target cells with MTT at 0.2 mg/ml in complete
medium for 3-4 h under normal culture conditions. Formazan crystals
will appear inside the cells, in the form of microspikes, that can be
visualized in the microscope under white light. These spikes do not
interfere with the cytotoxic assay.
2. Wash the target cells and resuspend in complete medium at 1 x 106
cells/ml. Add 100 ul to Eppendorf tubes so that 1 x 105 target cells are
used per experimental point.
3. Wash and resuspend the effector cells in complete medium. Several
E:T ratios can be used but it is recommended not to go over a 5:1 ratio,
since the presence of too many effectors in the images could hinder
the finding of apoptotic target cells.
4. Include a control with target cells alone resuspended in 200 |xl of
complete medium to check for spontaneous apoptosis during the
assay.
5. Centrifuge the Eppendorf tubes at 400 g at room temperature for 5 min
to favour cell-cell contact. Incubate at 37°C in a CO2 incubator for the
time required.
6. At the end of incubations, centrifuge the tubes at 400 g for 10 min and
93
discard supernatants. Wash the cells with RPMI 1640 and fix in 1%
paraformaldehyde in PBS, pH 7.4, at room temperature for 15 min.
7. Place the poly-L-lysine pre-treated, round cover glasses into wells of
24-well plates and drop upon the fixed cell suspensions. Centrifuge the
plates for 5 min at 200 g to fix the cells to the glass cover.
8. Wash (twice) the cover glasses containing the fixed cells with PBS, air-
dry, and finally place each cover glass over a drop (20 ul) of PPDA
reagent previously added to glass slides.
9. Visualize fluorescent-labelled nuclei using a fluorescence microscope.
Non-apoptotic cells will predominate (effectors), but they can be easily
distinguished from targets using normal illumination by the absence
of formazan crystals. In non-apoptotic cells, nuclei are stained uni-
formly, giving an orange-red fluorescence of medium intensity.
Apoptotic nuclei are characterized by chromatin condensation, which
gives a much brighter yellow PPDA fluorescence, accompanied by the
characteristic chromatin condensation and nuclear fragmentation. The
number of apoptotic cells can be evaluated by counting different fields
and photographing.
2.6 Activation-induced cell death (AICD)

The so-called AICD refers to the process by which an overactivated T cell
kills itself or its neighbours. This process occurs physiologically during
peripheral T cell deletion and is important for the termination of the immune
response and the prevention of autoimmune attack. AICD is known to be
mediated by the interactions between FasL/Fas, APO2L/DR4, TNF/TNFR,
and possibly other uncharacterized molecules (51). AICD may be induced in
vitro by incubation of T cell blasts, leukaemic or hybridoma cells with mito-
genic lectins [phytohaemagglutinin (PHA), concanavalin A], phorbol esters,
or anti-TCR/CD3 antibodies. The peculiarity of the process lies in the fact
that effector cells are also the target cells and, therefore, the classical
methods for evaluating cell-mediated cytotoxicity using radioisotopes (51Cr,
125
IUdR) are not applicable. For this type of assay it is recommended that a
suitable dye-reduction method is used (e.g. the MTT assay; see ref. 52) to
analyse cell death induced by a given stimulus. If bystander killing needs to
be evaluated, a cytotoxicity assay using the methods described in Protocols 1
and 2 should be performed. In this case, stimulated T cells should be used as
effectors, while non-stimulated T cells of the same type should be used as
targets.
94
3. Separate studies of Fas- and perforin/granzyme-

based cytotoxicity
3.1 Fas-based cytotoxicity in the absence of
perforin/granzyme contribution
One of the best ways to study Fas-based cytotoxicity in the absence of the
perforin/granzyme contribution is using cytolytic effector cells that are
defective in the perforin/granzyme system, while keeping intact their ability to
induce FasL expression. This was first done in the laboratory of Dr Pierre
Golstein (Marseille, France) by serial subcloning from the cytolytic hybrid-
oma PC60 to generate dlOS, dllS, and d!2S cells (2). These cells were able to
kill Fas-expressing cells once activated with a combination of PMA plus
ionomycin whether in the presence or absence of extracellular calcium. They
were later used in the laboratory of Dr Shikegazu Nagata (Osaka, Japan) to
clone FasL (3).
Another approach has been to isolate effector cells from perform knock-
out mice. In these mice, the whole perforin/granzyme system is defective,
while FasL expression is normal (1,4).
However, normal effector cells, harbouring all the cytotoxicity mechanisms
mentioned, can also be used to study Fas-based cytotoxicity in the absence of
a perforin/granzyme contribution, or vice versa. This allows a good estimation
of the relative contribution of each cytotoxicity mechanism in a given experi-
mental system. We will describe suitable methods using whole functional CTL
clones (13,15).
Protocol 6. Assay of Fas-based cytotoxicity in the absence of

perforin/granzyme contribution
Reagents
• 10 ng/ml PMA • sodium carbonate/bicarbonate buffer, pH 8.0
• 600 nM ionomycin . 1 mM EGTA
• anti-TCR or anti-CD3 antibodies . 1.5mMMgCI2
Method
1. Culture CTL clones in complete culture medium supplemented with IL-
2, in 24-well plates, to a density between 3 and 6 x 105 cells/ml. Then,
stimulate the cells for Shin the same culture conditions to induce FasL
expression with one of the following stimuli:
(i) a combination of PMA and ionomycin.
(ii) anti-TCR or anti-CD3 antibodies. In the case of anti-CD3 anti-
bodies, their previous immobilization on wells of a 24-well plate
95
by overnight incubation of a 20 ug/ml antibody solution at 4°C in
sodium carbonate/bicarbonate buffer recommended,
(iii) antigen-bearing target cells. In this case, it is recommended that a
1:0.7 effector to target ratio is used, to minimize the interference
between the activating cells and the Fas-bearing target cells in the
subsequent cytotoxicity assay.
2. After stimulation, wash out the stimulating agents, and test functional
FasL expression in a cytotoxicity test on Fas-expressing target cells
using one of the protocols described above. A good system for such
an assay is the use of a cell line that does not express Fas and its
corresponding Fas transfectant. For instance, the leukaemic cell line
L1210 has been transfected with the Fas cDNA, generating an identical
cell line which expresses high Fas membrane levels and is very
sensitive to Fas-induced apoptosis (2). Then, Fas-based cytotoxicity
can be assayed using any pre-stimulated effector cell on L1210Fas
cells and using L1210 cells as a negative control. Any other system
with such characteristics can also be chosen (e.g. L929/L929Fas).
3. To avoid any hypothetical contribution of perforin/granzymes, cyto-
toxicity tests on L1210 and L1210Fas cells should be performed in the
absence of extracellular calcium. To do this, add EGTA and MgCI2 to
the medium of the cytotoxicity test. The execution of Fas-based cyto-
toxicity, once FasL is expressed, is calcium independent, while the
execution of perforin/granzyme-based cytotoxicity is entirely calcium
dependent.
3.2 Perforin/granzyme-based cytotoxicity in the absence of

FasL contribution
In this case, a suitable option would be to test the cytotoxicity of effector cells
on antigen-bearing target cells that do not express Fas. Murine L1210 cells,
which express H-2Kd, have been used by several authors to estimate perform/
granzyme-based cytotoxicity of anti-H-2Kd effectors (42, 53). However,
perforin/granzyme-based cytotoxicity exerted by effector cells of any antigen
specificity can also be tested using anti-CD3 antibody-redirected lysis on
L1210 cells (40).
Protocol 7. Anti-CD3 antibody-redirected lysis of Fas-negative

target cells
Reagents
• L1210 cells . 1 mM EGTA
• 3 ug/ml anti-CDS antibody . 1.5mMMgCI2
96
Method
1. Effector cells should be treated in the same way as in a normal
cytotoxicity assay. Targets of choice for this assay should be Fas-
negative and express Fc receptors, conditions which are met by L1210
cells. Label the target cells with 51Cr or 125IUdR, as described in
Protocols 1 and 2, and perform the assay as indicated, but including
anti-CD3 antibody in the medium of the cytotoxicity test.
2. To ensure that all the cytotoxicity observed is due to perform/
granzyme, the inclusion of a negative control with EGTA and MgCI2 in
the medium of the cytotoxicity test is recommended.
4. Use of caspase and granzyme inhibitors in cell-

mediated cytotoxicity assays
Initial studies on caspase and granzyme inhibitors were done in vitro, using
purified molecules and cell-free systems. The validation of the results
obtained concerning the possible implication of several caspases and/or
granzymes in cell-mediated cytotoxicity should come using whole-cell assays.
Several peculiarities of the inhibitors and of the assays should be kept in mind
when performing these studies, which we will briefly consider now.
Editors note: Additional cautions regarding the use of caspase inhibitors are
discussed in Chapter 10, Section 8.2.
4.1 Caspase inhibitors
inhibitors
The most frequently used caspase inhibitors are the following:
• Ac-YVAD-cmk or Ac-YVAD-CHO, specific inhibitors for caspase-1 (ICE)
(54,55)
• Ac-DEVD-fmk or Ac-DEVD-CHO, which preferentially inhibit at low
concentrations caspases of the CPP32-like subfamily, especially caspase-3
(CPP32) and caspase-7 (ICE-LAP3) (21). At higher concentrations they
may also inhibit caspase-1, caspase-8 (FLICE), and caspase-10 (Mch4) (55).
• Z-VAD-fmk, a general caspase inhibitor (56), although its ability to inhibit
caspases of the CPP32-like subfamily and caspase-2 (Ich-1) is limited (55).
• Z-VDVAD-fmk, a specific inhibitor of caspase-2, which needs a 5 amino
acid peptide to be efficiently inhibited (55). It also inhibits caspase-3,
though less efficiently than DEVD.
• Boc-D-fmk, a general caspase inhibitor (57)
Although granzyme B is also a protease with Asp specificity, peptide
fluoromethylketones inhibit caspases but not granzymes. To inhibit serine
proteases, the more reactive peptide chloromethylketones are needed (57).
Several biotechnological companies sell these peptides, among them
97
Bachem (Bubendorf, Switzerland), Neosystem Laboratoire (Strasbourg,
France), and Enzyme System Products (Dublin, California).
Protocol 8. Use of caspase inhibitors in whole-cell cytotoxicity

assays
Method
1. Stock solutions of peptide caspase inhibitors are normally prepared in
DMSO and stored at-20°C. Recommended concentrations of the stocks
range between 100 and 300 mM. Peptides are better stored lyophilized
at 4°C.
2. In many cases, a pre-incubation of target cells with peptide caspase
inhibitors is needed to ensure enough incorporation by the cells. Z-
VAD-fmk, Z-VDVAD-fmk, and Boc-D-fmk are effective at concentrations
between 20 and 100 uM and 1 h of pre-incubation is recommended.
Ac-DEVD-CHO has three lateral carboxyl chains, hindering its passage
through the cell membrane. Therefore, in spite of being a very efficient
caspase-3 inhibitor in vitro (Ki <1 nM), high concentrations (between
300 and 600 (uM) and pre-incubation times of 3 h are needed to
guarantee that the inhibitory intracellular concentration is reached.
Some biotechnological companies have solved this permeability
problem by methylation of the carboxylic side chains, e.g. the
commercially available Ac-DEVD-fmk. In this case, the efficient con-
centration to be used and the time of pre-incubation recommended is
similar to that of Z-VAD-fmk.
3. Another consideration should be made when using this type of
inhibitor, and especially the non-methylated Ac-DEVD-CHO, regarding
the effector to target ratio. If there is a great excess of effector cells,
then the inhibitor will be taken up by the effectors, greatly reducing the
actual peptide concentration in the medium and, consequently,
lowering its intracellular concentration inside the targets. For example,
no effect of Ac-DEVD-CHO is observed on Fas-based cytotoxicity when
using an E:T ratio of 10:1, while it is completely inhibited at an E:T ratio
of 5:1 (23). Hence, E:T ratios from 1:1 to 5:1, but not greater, should be
used in this type of experiment.
4. When using any inhibitor in a cytotoxicity assay, the possible increase
in spontaneous release of the label from target cells induced by the
inhibitor itself should be carefully controlled. Each experimental point
where an inhibitor is included should be accompanied by a spon-
taneous release control of target cells alone, incubated with the
inhibitor at the same concentration as in the assay. If the spontaneous
release induced by the inhibitor alone is greater than 30% of the total
98
labelling, then this inhibitor cannot be used in such an assay. In our
hands, peptide caspase inhibitors do not induce increases in spon-
taneous release either of 51Cr or 125IUdR, even at high concentrations
(up to 1 mM) and long incubation times (up to 16 h).
5. Bearing in mind these considerations, perform any of the cytotoxicity
tests described in Protocols 1 and 2 in the presence of peptide caspase
inhibitors.
4.2 Granzyme inhibitors

The chemistry of granzymes has been extensively studied in the laboratory of
Dr James Powers (Atlanta, Georgia) in collaboration with several other
groups (see ref. 58). For example, the BLT-esterase release method described
in Section 2.4 is one of the applications of these studies. As discussed above,
peptide inhibitors of serine proteases should be chloromethylketones. How-
ever, these compounds, because of their high reactivity, could inhibit other
cellular proteases. For this reason, several other chemical inhibitors, mainly
isocoumarin derivatives, have been developed.
• For granzyme B, the most specific peptide inhibitor described is Z-AAD-
cmk, which does not inhibit granzyme A or related proteases (6). In the
case of isocoumarins, 3,4-dichloroisocoumarin (DCI) has been described to
inhibit granzyme B much more efficiently than granzyme A (around 50-fold
difference in Kfi (59).
• Granzyme A, unlike granzyme B, is a trypsin-like protease. In a cytotoxicity
assay, it can be considered that the major targets for these inhibitors are
trypsin-like granzymes, granzyme A being the predominant one. The most
specific peptide inhibitor for trypsin-like proteases is d-FPR-cmk, which
does not inhibit granzyme B (6). On the other hand, 7-( phenyl-ureido)-4-
chloro-3-(2-isothioureidoethoxy)-isocoumarin, abbreviated as IGA, is the
most potent isocoumarin described for granzyme A inhibition (60,61).
Z-AAD-cmk and d-FPR-cmk are sold by Enzyme System Products
(Dublin, California) and DCI is sold by many chemical companies (e.g.
Sigma).
Protocol 9. Use of granzyme inhibitors in whole-cell cytotoxicity

assays
Method
1. Stock solutions of peptide and iosocumarin granzyme inhibitors are
usually prepared in DMSO and stored at-20°C.
2. Pre-incubation of inhibitors with target cells is not needed in this case
99
since the inhibitors exhibit sufficient permeability through the cell
membrane. The effective concentrations for DCI, IGA, and Z-AAD-cmk
are between 20 and 50 jjiM.
3. The considerations of effector to target ratios in Protocol 8 also apply
here. Hence, E:T ratios from 1:1 to 5:1, but not greater, should be used
in this type of experiment.
4. The possible increase in spontaneous release of the label from target
cells induced by the inhibitor itself should be carefully controlled. If the
spontaneous release induced by the inhibitor alone is greater than
30% of the total labelling, then this inhibitor cannot be used in such an
assay. In our hands, Z-AAD-cmk, DCI and IGA do not induce an
increase in the spontaneous release in 125IUdR release assays at the
concentrations mentioned, even when using long incubation times (up
to 16 h). However, these inhibitors do induce spontaneous 51Cr release
in long-term assays. These inhibitors can only be used at the indicated
concentrations in short-term assays (3-5 h), and the particular con-
ditions of incubation with each target cell used need to be carefully
optimized.
5. Bearing in mind these considerations, perform any of the cytotoxicity
tests described above in the presence of the described granzyme
inhibitors.
Acknowledgements
We would like to acknowledge the high-quality scientists from whom we
learned the techniques described above, and who transmitted to us their
passion for cell-mediated cytotoxicity. In chronological order, thanks to Alan
Kleinfeld, Anne O'Rourke, Matt Mescher, Michel Buferne, Claude Boyer,
Anne-Marie Schmitt-Verhulst, and Pierre Golstein.
References
1. Kagi, D., Ledermann, B., Bilrki, K., Seller, P., Odermatt, B., Olsen, K. J., Podack,
E. R., Zinkernagel, R. M. and Hengartner, H. (1994). Nature, 369, 31.
2. Rouvier, E., Luciani, M. F. and Golstein, P. (1993). Journal of Experimental
Medicine, 177,195.
3. Suda, T., Takahashi, T., Golstein, P. and Nagata, S. (1993). Cell, 75,1169.
4. Kagi, D., Vignaux, F., Ledermann, B., Biirki, K., Depraetere, V., Nagata, S.,
Hengartner, H. and Golstein, P. (1994). Science, 265, 528.
5. Henkart, P. A., Millard, P., Reynolds, C. W. and Henkart, M. P. (1984). Journal of
Experimental Medicine, 160, 75.
100
6. Shi, L., Kam, C. M., Powers, J. C, Aebersold, R. and Greenberg, A. H. (1992).
Journal of Experimental Medicine, 176,1521.
7. Van den Broek, M. F., Kagi, D., Ossendorp, F., Toes, R., Vamvakas, S., Lutz, W.
K., Melief, C. J. M., Zinkernagel, R. M. and Hengartner, H. (1996). Journal of
Experimental Medicine, 184,1781.
8. Russell, J. H., Rush, B., Weaver, C. and Wang, R. (1993). Proceedings of the
National Academy of Sciences USA, 90, 4409.
9. Vignaux, F. and Golstein, P. (1994). European Journal of Immunology, 24,923.
10. Dhein, J., Walczak, H., Baumler, C., Debatin, K. M. and Krammer, P. H. (1995).
Nature, 373,438.
11. Alderson, M. R., Tough, T. W., Davis-Smith, T., Braddy, S., Falk, B., Schooley,
K. A., Goodwin, R. G., Smith, C. A., Ramsdell, F. and Lynch, D. H. (1995).
Journal of Experimental Medicine, 181,71.
12. Zheng, L., Fisher, G., Miller, R. E., Peschon, J., Lynch, D. H. and Lenardo, M. J.
(1995). Nature, 377,348.
13. Anel, A., Buferne, M., Boyer, C., Schmitt-Verhulst, A. M. and Golstein, P. (1994).
European Journal of Immunology, 24,2469.
14. Vignaux, F., Vivier, E., Malissen, B., Depraetere, V., Nagata, S. and Golstein, P.
(1995). Journal of Experimental Medicine, 181,781.
15. Anel, A., Simon, A. K., Auphan, N., Buferne, M., Boyer, C., Golstein, P. and
Schmitt-Verhulst, A. M. (1995). European Journal of Immunology, 25,3381.
16. Latinis, K. M., Carr, L. L., Peterson, E. J., Norian, L. A., Eliason, S. L. and
Koretzky, G. A. (1997). Journal of Immunology, 158,4602.
17. Nagata, S. and Golstein, P. (1995). Science, 267,1449.
18. Tartaglia, L. A., Ayres, T. M., Wong, G. H. W. and Goeddel, D. V. (1993). Cell,
74, 845.
19. Nagata, S. (1997) Cell, 88,355.
20. Nicholson, D. W. and Thornberry, N. A. (1997). Trends in Biochemical Sciences,
22,299.
21. Nicholson, D. W., Ali, A., Thornberry, N. A., Vaillancourt, J. P., Ding, C. K.,
Gallant, M., Gareau, Y., Griffin, P. R. et al. (1995). Nature, 376,37.
22. Schlegel, J., Peters, L, Orrenius, S., Miller, D. K., Thornberry, N. A., Yamin, T. T.
and Nicholson, D. W. (1996). Journal of Biological Chemistry, 271,1841.
23. Anel, A., Gamen, S., Alava, M. A., Schmitt-Verhulst, A. M., Pineiro, A. and
Naval, J. (1996). International Immunology, 8,1173.
24. Henkart, P. A. (1996). Immunity, 4,195.
25. Chinnaiyan, A. M., O'Rourke, K., Tewari, M. and Dixit, V. M. (1995). Cell, 81,505.
26. Muzio, M., Chinnayian, A. M., Kischkel, F. C., O'Rourke, K., Shevchenko, A., Ni,
J., Scaffidi, C., Bretz, J. D., Zhang, M., Gentz, R., Mann, M., Krammer, P. H.,
Peter, M. E. and Dixit, V. M. (1996). Cell, 85,817.
27. Boldin, M. P., Goncharov, T. M., Goltsev, Y. V. and Wallach, D. (1996). Cell, 85,
803.
28. Fernandes-Alnemri, T., Armstrong, R. C., Krebs, J., Srinivasula, S. M., Wang, L.,
Bullrich, F., Fritz, L. C., Trapani, J. A., Tomaselli, K. J., Litwack, G. and Alnemri,
E. S. (1996). Proceedings of the National Academy of Sciences USA, 93, 7464.
29. Susin, S. A., Zamzami, N., Castedo, M., Hirsch, T., Marchetti, P., Macho, A.,
Daugas, E., Geuskens, M. and Kroemer, G. (1996). Journal of Experimental
Medicine, 184,1331.
101
30. Liu, X., Kim, C. N., Yang, J. and Wang, X. (1996). Cell, 86,147.
31. Li, P., Nijhawan, D., Budihardjo, I., Srinivasula, S. M., Ahmad, M., Alnemri, E. S.
and Wang, X. (1997). Cell, 91,479.
32. Scaffidi, C., Fulda, S., Srinivasan, A., Friesen, C., Li, F., Tomaselli, K. J., Debatin,
K. M., Krammer, P. H. and Peter, M. E. (1998). EMBO Journal, 17,1675.
33. Liu, C. C., Walsh, C. M. and Young, J. D. E. (1995). Immunology Today, 16,194.
34. Smyth, M. J. and Trapani, J. A. (1995). Immunology Today, 16,202.
35. Pasternack, M. S. and Eisen, H. N. (1985). Nature, 314, 743.
36. Ebnet, K., Hausmann, M., Lehmann-Grube, F., Mullbacher, A., Kopf, M.,
Lamers, M. and Simon, M. M. (1995). EMBO Journal, 14,4230.
37. Heusel, J. W., Wesselschmidt, R. L., Shresta, S., Russell, J. H. and Ley, T. J.
(1994). Cell, 76, 977.
38. Darmon, A.J., Nicholson, D.W. and Bleackley, R.C. (1995). Nature, 377,446.
39. Gu, Y., Sarnecki, C., Fleming, M. A., Lippke, J. A., Bleackley, R. C. and Su, M. S.
S. (1996). Journal of Biological Chemistry, 271,10816.
40. Anel, A., Gamen, S., Alava, M. A., Schmitt-Verhulst, A. M., Pineiro, A. and
Naval, J. (1997). Journal of Immunology, 158,1999.
41. Sarin, A., Williams, M. S., Alexander-Miller, M. A., Berzofsky, J. A., Zacharchuk,
C. M. and Henkart, P. A. (1997). Immunity, 6,209.
42. Darmon, A. J., Ley, T. J., Nicholson, D. W. and Bleackley, C. R. (1996). Journal of
Biological Chemistry, 271, 21709.
43. Scaife, J. F. and Vittorio, P. V. (1964). Canadian Journal of Biochemistry, 42, 503.
44. Sanderson, A. R. (1964). British Journal Experimental Pathology, 45, 398.
45. Holm, G. and Perlham, P. (1967). Immunology, 12, 525.
46. Oldman, R. K. and Herberman, R. B. (1973). Journal of Immunology, 111, 1862.
47. Russell, J. H., Masakowski, V. R. and Dobos, C. B. (1980). Journal of
Immunology, 124,1100.
48. Matzinger, P. (1991). Journal of Immunological Methods, 145,185.
49. Takayama, H., Trenn, G., Humphrey, W., Bluestone, J. A., Henkart, P. A. and
Sitkovsky, M. V. (1987). Journal of Immunology, 138,566.
50. Nakajima, H., Lichtenfels, R., Martin, R. and Henkart, P. A. (1995). In Tech-
niques in apoptosis: a user's guide (ed. T.G. Cotter and S.J. Martin), pp. 175-190.
Portland Press, London.
51. Ashkenazi, A. and Dixit, V. M. (1998). Science, 281,1305.
52. Skehan, P. (1999). In Cell growth, differentiation, and senescence: a practical
approach (ed. G.P. Studzinski). Oxford University Press, Oxford.
53. Simon, M. M., Hausmann, M., Tran, T., Ebnet, K., Tschopp, J., Thahla, R. and
Miillbacher, A. (1997). Journal of Experimental Medicine, 186,1781.
54. Thornberry, N. A., Bull, H. G., Calaycay, J. R., Chapman, K. T., Howard, A. D.,
Kostura, M. J. et al. (1992). Nature, 356, 768.
55. Talanian, R. V., Quinlan, C., Trautz, S., Hackett, M. C., Mankovich, J. A., Banach,
D., Ghayur, T., Brady, K. D. and Wong, W. W. (1997). Journal of Biological
Chemistry, 272,9677.
56. Pronk, G.J., Ramer, K., Amiri, P. and Williams, L.T. (1996). Science, 271, 808.
57. Sarin, A., Wu, M. L. and Henkart, P. A. (1996). Journal of Experimental Medicine,
184, 2445.
58. Powers, J. C. and Kam, C. M. (1994). In Methods in enzymology (ed. A. J.
Barrett), Vol. 244, p. 442. Acadaemic Press, New York.
102
59. Odake, S., Kam, C. M., Narasimhan, L., Poe, M., Blake, J. T., Krahenbuhl, O.,
Tschopp, J. and Powers, J. C. (1991). Biochemistry, 30, 2217.
60. Kam, C. M., Kerrigan, J. E., Plaskon, R. R., Duffy, E. J., Lollar, P., Suddath, F. L.
and Powers, J. C. (1994). Journal of Medicinal Chemistry, 37,1298.
61. Beresford, P. J., Kam, C. M., Powers, J. C. and Lieberman, J. (1997). Proceedings
of the National Academy of Sciences USA, 94,9285.
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6
Sphingolipids as messengers of cell

death
GARY M. JENKINS and YUSUF A. HANNUN
1. Introduction
This chapter discusses the most commonly used methods for the study of
sphingolipids in their role as messengers of cell death. A basic review of
Sphingolipids and the role they play in apoptosis is given. The rest of the
chapter outlines the methods used for the study of sphingolipids and the
enzymes relevant to the sphingomyelin (SM) cycle. Each method is described
with full experimental details, and emphasis is given to one or two protocols
used for the study of each class of sphingolipids and relevant enzymes.
2. Sphingolipids and their role in apoptosis

2.1 Overview of sphingolipids
Mammalian cells have four major classes of sphingolipids, which are the
sphingoid backbones, ceramides, sphingomyelins, and glycosphingolipids
(Figure 1). Sphingoid backbones are the basic building blocks of sphingolipids
formed by the condensation of serine and palmitoyl CoA. Mammalian cells
have two predominant forms of sphingoid backbones, which are sphingosine
and dihydrosphingosine, each composed of an 18 carbon backbone. The
addition of an N-linked fatty acid to the sphingoid backbone creates cera-
mides. The fatty acid in mammalian cells is usually a 16-24 carbon structure
and can be attached to either sphingosine or dihydrosphingosine. Recent
research indicates that dihydroceramide is formed first by acylation of
dihydrosphingosine and then desaturated to form ceramide (1). Next, an
addition of a phosphatidylcholine-derived phosphocholine creates the
sphingomyelins. Mammalian cells can have a wide variety of sphingomyelins
depending on the ceramides present. The final and predominant class of
sphingolipids are the glycosphingolipids formed by various additions of sugar
groups to the ceramides.
GaryM. Jenkins and YusufA. Hannun
Figure 1. Examples of each class of sphingolipids in mammalian cells. The classes

represented are, in order from top to bottom, sphingoid backbones, ceramides,
sphingomyelins, and glycosphingolipids.
2.2 Role of sphingolipids in apoptosis

The role of sphingolipids in the process of apoptosis is centred on the sphingo-
myelin (SM) cycle (Figure 2). The inducers of the sphingomyelin cycle include
many agents that induce apoptosis and/or growth arrest in cells, and examples
are: cytokines such as TNF-a, interleukin-1, and y-interferon; Fas ligand; 1,25-
dihydroxyvitamin D3; and environmental stresses such as ultraviolet
radiation, serum withdrawal, and chemotherapeutic agents (2).
The initial finding pointing to sphingolipids in apoptosis was the observa-
tion that ceramide was often cytotoxic to U937 cells, resulting in DNA frag-
mentation (3), while closely related compounds such as dihydroceramide and
diacylglycerol did not induce DNA fragmentation. Furthermore, recent studies
have shown that ceramide acts as a lipid mediator in cells and has, for targets,
a ceramide-activated protein kinase and a ceramide-activated protein phos-
phatase. Downstream of these effects are the caspases, Raf-1 and the ERKs
(2, 4) (Figure 2). The generation of ceramide is thought to be from the
hydrolysis of SM by the neutral sphingomyelinase (n-SMase) (5) and/or acid
106
6: Sphingolipids as messengers of cell death
Figure 2. Overview of the role of the sphingomyelin cycle in apoptosis. A stress signal
activates sphingomyelinase (SMase) which cleaves sphingomyelin (SM), forming
ceramide. Ceramide can induce a ceramide-activated protein phosphatase (CAPP) and/or
a ceramide-activated protein kinase (CAPK). CAPP effects can be blocked by Bcl-2 or PKC
and leads to activation of caspases, and apoptosis. CAPK works through a different
pathway, activating Raf-1 and then the extracellular signal regulated kinases (ERKs).
sphingomyelinase (a-SMase). Furthermore, the overexpression of Bcl-2, a

known protector against apoptosis, has been able to protect cells from
ceramide-induced apoptosis. Therefore, the study of sphingolipids in the
process of apoptosis has become an important field.
2.3 Strategies and considerations in evaluating

sphingolipids
Efficient study of sphingolipids in cellular responses entails several basic con-
siderations. The selection of appropriate time points is one of these consider-
ations. Time points should be selected to be relevant to when the biology to
be studied is observed. Often this means time points in the range of hours in
many cases of sphingolipids in apoptosis; however, shorter time points can be
107
informative for quick changes in sphingolipids. Another basic consideration is
the use of time-matched controls from which to compare values from treated
samples.
The analysis of various sphingolipid levels requires an initial step for ex-
traction of lipids followed by mild base hydrolysis, which helps by removing
most of the glycerolipids whose ester bonds are sensitive to this form of
hydrolysis. Quantitation of specific sphingolipids can then be performed using
specific and specialized assays. Finally, the levels of sphingolipids are adjusted
to either total lipid levels or to cell number.
The starting point for analysis of sphingolipids in apoptosis is the measure-
ment of ceramide levels. When analysing ceramide levels using the diacyl-
glycerol kinase assay, care should be exercised in using the enzyme in a
quantitative range and not a catalytic range. The reason for starting with
ceramide levels is twofold. First, ceramide has been correlated with many
cellular events such as differentiation, stress responses, and apoptosis (2).
Secondly, changes of ceramide levels are often found in response to stress. An
increase in ceramides can result from many pathways, including hydrolysis of
sphingomyelin or glycoceramides, inhibition of sphingomyelin synthase or
ceramidase, and/or enhancement of de novo synthesis of ceramides. There-
fore, once an increase in ceramide is found, further analysis of sphingolipids
becomes relevant. The measurement of sphingomyelin can show whether the
increase in ceramide levels is from its hydrolysis or another source. Sphingo-
myelin hydrolysis has been implicated in some ceramide increases, as repre-
sented by the SM cycle (2). Sphingoid backbone levels have not been
implicated to the same extent as sphingomyelin and ceramide levels. Enhance-
ment of sphingolipid turnover studies can be gained by analysis of the SMases
and SM synthase. Changes in the activity of these enzymes reflect either an
induction in enzyme amounts and/or some poorly defined form of post-
translational modification. Neither the acid/neutral SMase assay or SM
synthase assay will detect reversible allosteric regulation of the enzymes.
Together, the above analyses allow for an initial in depth look at the possible
role of sphingolipids in a given cellular response.
3. Extraction of sphingolipids and normalization by

lipid phosphate
3.1 Extraction of sphingosines, ceramides, and
sphingomyelins
Extraction of sphingosines, ceramides, and sphingomyelins is most easily
accomplished via two commonly used methods. The most prevalent is the
method of Bligh and Dyer (6). Also of use is the Folch extraction (7). The two
methods rely upon the hydrophobic/organic nature of the sphingolipids to
separate them from other cellular components (Figure 3). The resulting
108
Figures. Illustration of the phase break induced in the Bligh and Dyer extraction by the
addition of water and chloroform. To obtain clear phases allow to sit or spin in a table-top
centrifuge at 2000 g. The organic phase may be collected by first aspirating the aqueous
phase, then collecting it, or by directly taking the organic phase.
extract can be used for analysis of Sphingolipids using various protocols and
these measurements can be normalized to lipid phosphate.
Protocol 1. Extraction of Sphingolipids by the method of Bligh

and Dyer (6)
Reagents
• PBS • methanol
• chloroform/methanol (1:2 pre-mixed) • dry nitrogen
Method
1. Grow 2-5 x 106 cells per sample to be analysed. Treat as desired.
Adherent cells need to be suspended.
2. Pellet cells by table-top centrifugation of 500 g for 5 min.
3. Aspirate off the media or wash PBS from the pellet.
4. Resuspend the cell pellet in 3 ml of chloroform/methanol (1:2 pre-
mixed) and vortex until an even suspension is gained.
5. Add 0.8 ml of water and vortex. Transfer the resuspended cells to a
glass screw-cap tube and set on the bench for 30 min or overnight at
4°C for best extraction. If there is a phase break at this point it can be
corrected by the addition of 0.5 ml of methanol. A premature phase
break can hinder proper extraction.
6. Pellet cellular debris via table-top centrifugation at 2000 g for 5 min.
Transfer liquid material to a fresh tube and discard cellular debris.
7. Add 1 ml of chloroform and 1 ml of water and vortex. These additions
will induce a break of the liquid material into an organic (lower) and
aqueous (upper) phases (Figure 3). Allow 15-30 min for the phases to
separate and then centrifuge for 5 min at 2000 gto obtain clean phase
separation.
109
Gary M. Jenkins and YusufA. Hannun
8. One may now collect the lower organic phase directly or aspirate the
aqueous phase and then collect the organic phase.
9. The extracted lipids should be in the 2 ml of chloroform and should
be dried down via a speed vacuum apparatus or under a stream of
dry nitrogen.
10. The dried down lipids should now be resuspended in chloroform with
one aliquot designated for phosphate measurement (usually one-
third) and another aliquot for the experimental measurement desired
(usually one-third; the last third is a back-up).
Protocol 2. Extraction of sphingolipids by the method of Folch

Reagents
• chloroform • dry nitrogen
• methanol
Method
1. Grow 2-5 x 106 cells per sample to be analysed. Treat as desired.
Adherent cells need to be suspended.
2. Pellet cells by table-top centrifugation of 500 gfor 5 min.
3. Aspirate off the media or wash liquid from the pellet.
4. Add 1 ml of methanol to the pellet, vortex, and transfer to a glass
screw-cap tube.
5. Add 2 ml of chloroform to the above and vortex. Make sure that the
cell pellet is completely resuspended. For best extraction, let samples
sit on the bench for 30 min or at 4°C overnight.
6. Pellet cellular debris via table-top centrifugation at 2000 g for 5 min.
Transfer liquid material to a fresh tube and discard cellular debris.
7. Add 0.8 ml of water and vortex. This addition should induce a phase
break in the samples to an organic (lower) and aqueous (upper)
phases.
dry nitrogen.
10. The dried down lipids should now be resuspended in chloroform with
one aliquot designated for phosphate measurement (usually one-
third) and another aliquot for the experimental measurement desired
(usually one-third; the last third is a back-up).
110
Once the extraction and aliquoting of lipids is accomplished the actual
analysis of each sphingolipid class can begin. Storage of the lipids should be as
either a powder or in chloroform at -20 °C. As noted in step 10 of either
protocol, you should end up with three tubes, each containing one-third of
your extract. Both methods are useful for the extraction of the three classes of
sphingolipids, but are not efficient for sphingoid phosphates.
3.2 Alkaline hydrolysis of sphingolipids

Analysis of sphingoid backbones and sphingomyelins requires an additional
step of refinement. This step is a mild alkaline hydrolysis, which is useful for
hydrolysing most glycerolipids, leaving the resistant sphingolipids. Mild
alkaline hydrolysis is not used for ceramide measurement when there is
additional interest in diacylglycerol, which is sensitive to the procedure. Thus,
one can quickly and easily purify the organic lipid extract to one containing
mainly sphingolipids.
Protocol 3. Mild alkaline hydrolysis of lipids
Reagents
• chloroform • methanol
. 2 N KOH
Method
1. Resuspend dried down lipids from either the Bligh and Dyer (Protocol 7)
or Folch (Protocol 2) extractions in 2 ml of chloroform.
2. Add 0.2 ml of KOH in methanol to the tubes and vortex vigorously.
3. Incubate in a shaking water bath at 37°C for 1 h.
4. Immediately add 0.2 ml of 2 N HCI in methanol to neutralize the
KOH.
5. Now add 0.6 ml of methanol and 0.4 ml of water and vortex to break
the solution into an organic (lower) and aqueous (upper) phases. The
lower phase contains the alkaline-resistant sphingolipids, while the
upper has the other hydrolysed lipids.
6. Aspirate off the upper, aqueous phase. Wash the organic phase with
1 ml of pH-neutral water (make neutral by use of 50 n,l of 1 N NH4OH
per 15 ml of distilled water). Vortex after adding the water and let the
samples set for 15 min. Spin at 2000 g in a table-top centrifuge to
clarify the phase break then aspirate off the aqueous phase. Repeat
wash as above.
7. Dry down the organic phase under nitrogen or by a speed vacuum.
3.3 Lipid phosphate measurement for normalization of

experimental samples
The comparison of control versus treated samples is of utmost importance in
the analysis of in vivo sphingolipids. Therefore, a method to ensure consist-
ency between samples is necessary. The most commonly used is that of lipid
phosphate measurement taken directly from the aforementioned sphingolipid
extraction methods. Furthermore, lipid phosphate can be used to more
accurately quantitate sphingolipid samples. This method normalizes for any
variance in cell number and extraction efficiency, since lipid phosphate should
not vary much between cells. The method relies upon a standard curve
analysis and uses a colorimetric assay of phosphate that has been ashed.
Protocol 4. Measurement of lipid phosphate
Reagents
. 1 mM NaH2PO4 • 0.9% w/v ammonium molybdate
. ashing buffer: H2O:10 N H2S04:70% HCIO4 • 10% w/v L-ascorbic acid
(40:9:1)
Method
1. Prepare a standard curve of phosphates in duplicate. Put 0, 3, 5, 7, 10,
12, 15, 20, and 30 ul of NaH2P04 (1 nmol. per ul) in labelled tubes.
2. Dry down by speed vacuum or dry nitrogen the aliquots from either
extraction above. Use the same style of glass tube for both the
standards and the samples to ensure consistent ashing.
3. Add 0.6 ml of ashing buffer and vortex.
4. Place samples in a heating block at 160°C overnight. Approximately
100 ul should be left in the tube after incubation.
5. Add 0.9 ml of water and mix after allowing the samples to cool.
6. Now add 0.5 ml of ammonium molybdate and add 0.2 ml of L-ascorbic
acid. Mix tubes very vigorously.
7. Incubate at 45°C for 30 min.
8. Read samples on a spectrophotometer at 820 nm in 0.8 ml cuvettes. First
construct the standard curve then use it to get the experimental values.
The number obtained from the phosphate measurement now becomes the
denominator for the samples. This means that results are expressed as pico-
moles of sphingolipids/nanomoles of lipid phosphate. This will be accom-
plished by comparing the value of the third obtained above to the value of the
measurement obtained in the experimental third of sphingolipids. However,
phosphate levels should be used to normalize sphingolipids for comparison of
cells from a given cell line and not for comparison between cell lines. Cell lines
112
can have very different lipid phosphate levels per cell. Therefore, analysis
should be limited to time-matched controls with a change in only one variable.
4. Analysis of sphingoid backbones

4.1 HPLC on sphingoid backbones
The measurement of sphingoid backbones is most prevalently done by derivat-
ization and separation via high performance liquid chromatography (HPLC)
(8). This method of analysis requires a mild alkaline hydrolysis of the lipids.
The sphingoids are then derivatized on their free amine group (only available
on the sphingoid backbones) with orf/zo-phthaldialdehyde (o-PA), a fluor-
escent compound. The samples are then injected and separated on HPLC,
yielding a peak area for each sphingoid. The sensitivity of this system is around
5 pmol. This method allows for the separation of sphingoid backbones by their
saturation, chain length, and, to a certain extent, stereochemistry (Figure 4d).
Figure 4. (a) HPLC chart of sphingolipid standards as follows: peak 1, L-threo sphingosine
(11.6 min); peak 2, o-erythro sphingosine (12.3 min); peak 3, L-threo dihydrosphingosine
(15.2 min); peak 4, o-erythro dihydrosphingosine (16.9 min); peak 5, C20 sphingosine (29.5
min). (b) HPLC chart of sphingoid backbones extracted from MOLT4 cells. Peak 1 is
sphingosine (12.3 min), peak 2 is D -erythro dihydrosphingosine (16.5 min), and peak 3 is
the internal standard C20 sphingosine (29.2 min). The front peak on each chart is un-
reacted o-PA. Times given are the retention times, which can change with each run due to
variation in columns, different back pressures, and slight differences in the running buffer.
113
Stereoisomers can be separated on a reverse phase column, but diastereomers
require a chiral column. A further way of comparison available for this
analysis is the use of an internal standard. An internal standard should ideally
be a non-endogenous sphingoid backbone. Addition of the internal standard
allows for comparison of samples within each experiment. 200 pmol of
internal standard need to be added to every sample by step 5 of either the
Folch (Protocol 2) or Bligh and Dyer (Protocol 1) extraction given above. In
addition to the internal standard, the running of samples of specific sphingoid
backbones is wise owing to possible shifts in retention times. Retention times
shift because of the different reverse phase CIS columns used, back pressure
changes, minor variances in the solvent systems, and type of HPLC system.
Knowing the exact retention time of known standards allows for the selection
of the proper peaks from mammalian samples (Figure 4b) from the back-
ground peaks.
Protocol 5. HPLC analysis of sphingoid backbones
Reagents
• D-erythro sphingosine and D,L-erythro • p-mercaptoethanol
dihydrosphingosine (Sigma) . 100% ethanol
. 5%o-PA • running buffer: 90% methanol, 10% 5 mM
. 3% K-borate buffer (pH 10.5 by addition of potassium phosphate, pH 7.0
KOH pellets to boric acid solution)
Method
1. Prepare 100-200 pmol of known standards of D-erythro sphingosine
and D,u-erythro dihydrosphingosine for derivatization. These stand-
ards are useful for defining retention times within an HPLC run. If
necessary a standard curve of values can be constructed with known
standards of the D -erythro sphingosine.
2. On the day of running the samples on HPLC, one should make up the
o-PA reagent fresh. This requires 9.9 ml of 3 % K-borate buffer, 5 ul of
p-mercaptoethanol and 0.1 ml of 5% o-PA in 100% ethanol (for
example, weigh out over 5 mg of o-PA and resuspend in 20 times the
volume of weighed material in uJ, i.e. 8.6 mg would be resuspended in
172 ul of ethanol).
3. In order to derivatize dried down lipids from the alkaline hydrolysis
procedure (Protocol 3) they must be resuspended in 50 ul of methanol
and then reacted with 50 ul of the freshly made o-PA solution. The
samples should be incubated for at least 5 min in the dark as the
reagent is light sensitive (note: samples should be kept in the dark
throughout the HPLC run).
4. Add 0.2-0.5 ml of the running buffer to each tube.
114
5. Detection on HPLC is at an emission wavelength of 455 nm with
excitation wavelength of 345 nm using a fluorescence detector.
6. Samples can now be injected on a reverse phase C18 column with a
flow of 1 ml/min.
The quantitation of sphingoid backbones can either be done as a ratio to the

internal standard and then normalized to phosphate, or in absolute amounts
with the suggested external standard curve then normalized to phosphate.
The case of using the ratio of experimental lipid over internal standard is done
by simply dividing the peak area of experimental lipid by the peak area of the
known standard. This gives a number that takes into consideration the extrac-
tion efficiency throughout the procedure and, once normalized to lipid phos-
phate, can be easily compared between control and treated samples. The reason
for this is that the ratio does not change throughout experimental manipula-
tions such as injections and quantitative transfers. Use of the external stand-
ard curve involves more manipulation. First, the peak area must be converted
into picomoles via the standard curve generated. Next, one should determine
the factors of how much sample was finally injected on the HPLC of the
original third used. Therefore, one must account for extraction efficiency
using the internal standard, amount injected over total amount, and any loss
of sample through the quantitative transfer from the alkaline hydrolysis pro-
cedure. Once all these factors are accounted for one needs to calculate the
true picomoles of each sphingoid backbone in each sample third and then
normalize it to lipid phosphate. The absolute numbers can now be compared
between control and treated samples.
5. Analysis of ceramides
Quantitation of ceramides and diacylglycerol (DAG) is accomplished most
commonly by phosphorylation by the diacylglycerol kinase (DGK) method
(9, 10). For the analysis of ceramides one should not use base hydrolysis
because this procedure would hydrolyse the DAG. The basis of the assay
is the 32P-labelling of the ceramides using a tracer of hot y-ATP which
the kinase uses to phosphorylate the lipids. Once phosphorylated the lipids
are re-extracted and then run out on thin layer chromatography (TLC) plates
(Figure 5). Detection is done either by film or phosphoimager. Quantitation
can be handled either by using Image Quant or by scraping the spots from
the plate and doing scintillation counting. The protocol below uses Image
Quant analysis to avoid the hazards of scraping (silica and dispersion of
radiation).
115
Gary M. Jenkins and Yusuf A. Ilannun
Figure 5. TLC of ceramide (CER) and diacylglycerol (DAGJ post-DGK phosphorylation.

Lanes are as follows: lane 1, 160 pmol standards of type III ceramide (Sigma) and
diacylglycerol; lanes 2-13, MOLT4 samples; lane 14, 320 pmol standards of type |1| ceramide
and diacylglycerol; and lane 15, 640 pmol standards of type |1| ceramide and diacylglycerol.
Protocol 6. DGK of ceramides and DAG

Reagents
• ceramide (type III from Sigma) . chloroform/methane I (1:2]
. DAG • reaction mix: 103 mM imidazole, 17.9 MgCIz
« B-octyl glucoside, BOG/dioleoylphos- 2.86 mM dittliothreitol, 1.43 mM EGTA,
phatidylglycerol, DOPG (7.5%:2E mM 71.4 mM LiCI, 71.4 ug/ml DAG kinase, and 0.57
mixed micelle] rnM diathylenetriamine pentaacetic acid.
. 10 mM ATP
Method
1. Construct a standard curve of both ceramide and DAG, including
a blank. The range of standards should be 40, 80, 160, 320, 640, and
116
1280 pmol. Combining the standards of ceramide and DAG into one
tube per pmol amount helps to limit the assay size and the number of
lanes to be spotted.
2. Dry down the standards and add to dried samples from either of the
aforementioned extraction procedures (Protocols 1 and 2}
3. Resuspend the lipids with BOG/DOPG and vortex vigorously. If lipids
do not go into solution, then sonicate and revortex.
4. Add 70 ul of reaction mixture to each sample and vortex well.
5. To start the reaction add 10 ul of ATP with an activity of 4.5 uCi per
tube.
6. Allow reaction to proceed for 30 min at room temperature.
7. Stop the reaction with the addition of 3 ml of chloroform/methanol
and vortex.
8. Add 1 ml of chloroform, 1.7 ml of water, and vortex to induce a phase
break (Bligh and Dyer extraction conditions; Protocol 1).
9. Let samples sit briefly, then spin at 2000 g for 5 min to clarify phases.
10. Carefully aspirate off the upper phase (contains around 90% of the
radiation) and collect 1.2-1.5 ml of the lower phase. Dry down the
collected lipids via dry nitrogen or a speed vacuum.
11. Resuspend in 50 ul of chloroform and spot half on TLC plates
(Whatman Silica 60A plates).
12. Develop plates in a TLC chamber containing the following solvent
system: chloroform/acetone/methanol/acetic acid:water (10:4:3:2:1).
Allow tank to equilibrate before running plates.
13. Expose plate to film overnight to obtain an image or directly go to an
imager cassette with the phosphor screen and scan in using a phos-
phoimager. The resulting scan from the imager may be quantified
using Image Quant.
The final quantitation of the ceramides and DAGs can be done after either
counts per minute or band intensity have been determined. The actual pico-
moles should be obtained from the specific activity of ATP and, therefore,
complete conversion of lipids by the kinase is required. Alternatively, quanti-
tation of the mass may be obtained from the standard curve. Since the
standard curve is internal and has been through all the experimental manipu-
lations as have the samples, one can directly label them as their starting
amounts. The standard curve is also a control for the assay in that it will show
whether the assay is in the range of complete phosphorylation, and how well
the assay was executed, by its linearity. Once conversion to picomoles has
been done this number is for the whole third one started with and can be
117
GaryM. Jenkins and Yusuf A. Hannun
directly normalized to the third used for lipid phosphate. The minimal change
in ceramide usually considered significant is a 50% increase or more and often
a rise of twofold or more over basal.
6. Analysis of sphingomyelins
Presented in this section are two methods for the analysis of sphingomyelin.
The first method is one of radiolabelling the sphingomyelin pool with tritiated
choline, extracting the lipids, performing alkaline hydrolysis, and then meas-
uring total sphingomyelin by counts released by incubation with bacterial
sphingomyelinase (11) from Streptomyces (Sigma). The advantage of this
method is the number of samples that may be analysed quickly; however, the
method does not allow for analysis of particular sphingomyelins. The second
method follows the same initial work-up as the first but then separates the
sphingomyelins via HPLC (12) and fractions are collected and then counted.
The advantage of this method is specific types of sphingomyelins (Figure 6)
can be followed, but each sample takes a long time to run and count.
To quantitate the results one must calculate total cpms in each tube. Since
we took 400 \y\ of the 800 jjul upper phase (the upper phase is everything
except chloroform), multiply the cpms by two. This value can now be
Figures. HPLC profiles of brain sphingomyelins. Peak 1 is 16:0 fatty acyl SM (24 min),
peak 2 is 18:0 fatty acyl SM (31 min), peak 3 is 20:0 fatty acyl SM (47 min), peak 4 is a
combination of 22:0 fatty acyl SM and 24:1 unsaturated fatty acyl SM (68 min), and peak 5
is 24:0 fatty acyl SM (85 min).
118
normalized to the phosphate value obtained above. Total sphingomyelin
levels often decrease up to 30% with certain treatments.
Protocol 7. Bacterial sphingomyelinase on total SM
Reagents
• TMT buffer: 0.19 M Tris-HCI, pH 7.5, 12 mM • bacterial SMase: 2 units/ml in 10 mM
MgCI2, and 0.2% Triton X-100 Tris-HCI, pH 7.5
• chloroform/methanol (2:1)
Method
1. Suspend samples to be tested in 50 ul of TMT buffer and vortex
vigorously.
2. Sonicate the samples for three one-minute bursts, vortex after each
sonication then rest for 1 min between each sonication.
3. Pre-incubate the samples at 37°C for 5 min.
4. Add 50 n.1 of bacterial Smase to each tube and allow the reaction to
proceed for 30 min at 37°C.
5. Stop the reaction with 1.5 ml of chloroform/methanol and vortex.
6. Add 0.2 ml of water to induce a phase break in the sample and vortex.
7. Spin tubes at 2000 gtfor 5 min to clarify phases.
8. Collect 400 ul of the upper phase for scintillation counting. (Remem-
ber, the cells were labelled with precursors to the polar head group
and once incorporated will be released to the aqueous phase by
enzyme cleavage.)
Protocol 8. HPLC on SM
Method
1. Prepare a known standard of radiolabelled SM for a control run.
2. Take samples post-extraction and alkaline hydrolysis and resuspend
them in methanol.
3. Inject samples on to a C18 reverse phase column at a flow rate of
1 ml/min in a running system of 98% methanol, 2% 5 mM potassium
phosphate, pH 7.0.
4. Count by either fraction collecting and scintillation counting or a flow
through detector.
After counting each fraction a chart can be prepared for each sample. The
charts of a treated versus non-treated sample can now be directly compared to
119
see which specific SM species is changing. This comparison will allow analysis
of each peak for changes in a specific sphingomyelin type.
7. Measurement of SMase and SM synthase activities

Further investigation of sphingolipid involvement in apoptosis can be gained
by the analysis of the two key enzymes in the SM cycle. The most prominently
measured enzymes are the sphingomyelinases, both acid and neutral. Basic-
ally, protein is extracted and incubated with radiolabelled substrate. The
sphingomyelinase assay measures either an increase in enzyme levels and/or a
post-translational modification activating or inactivating the enzyme, and not
allosteric regulation in vivo. An enzyme of emerging importance is the SM
synthase (13). The analysis of SM synthase activity is again accomplished by
incubation under the proper conditions with radiolabelled ceramide. Again,
the SM synthase assay can measure only increases in enzyme levels and/or
post-translational modifications which regulate enzyme activity, and not other
factors of control. These two enzyme assays can strengthen data on changes in
the sphingolipids in a cell.
Protocol 9. Measurement of sphingomyelinase activity

. PBS « assay buffer: 0.2M Tris-HCI, pH 7.4, 5mM
• lysis buffer: 25 mM Tris-HCI, pH 7.4/5 mM MgCI2, and 0.2% Triton X-100 for neutral
EDTA, 20 ug/ml chymostatin, leupeptin, SMase or 0.2M NaAC, pH 5.0, and 0.2%
antipain and pepstatin, and 1 mM Triton X-100 for acid Smase
phenylmethylsulfonyl fluoride (PMSF) • nitrogen bomb
• chloroform/methanol (2:1)
Method
1. Pellet 5 X 107 cells at 200 g in a table-top centrifuge at 4°C.
2. Resuspend in ice-cold PBS and then repellet as above.
3. Resuspend the cells in 0.5 ml lysis buffer.
4. Load cells into a nitrogen bomb on ice to perform nitrogen cavitation.
5. Assemble the nitrogen bomb, apply 350-500 psi of N2 and let it sit on
ice for 30 min.
6. Carefully open the outlet valve and allow cell homogenate to flow
dropwise into a pre-chilled, 15 ml centrifuge tube.
7. Spin the homogenate at 1000 g for 10 min at 4°C.
8. Collect the supernatant (one can keep a crude homogenate for further
analysis at this point).
9. Centrifuge the supernatant at 100000 grfor 1 h at 4°C.
10. Collect the supernatant from high speed spin (cytosol).
120
11. Resuspend the pellet in 0.5 ml of lysis buffer (membrane).
12. Determine protein concentrations via your favourite assay (e.g.
Biorad).
13. Prepare the substrate. Each sample should have 4 x 105 dpm of
labelled SM in 10 nmols of cold SM. Dry lipids down under nitrogen,
then resuspend in appropriate amount of assay buffer. Vortex vigor-
ously and sonicate if needed to completely solubilize the lipids.
14. Put 20-100 ug of cvtosol or membrane protein into each tube. Use
lysis buffer to bring the volume up to 100 (xl. Set up blanks for each
assay containing only 100 ul of lysis buffer.
15. To all tubes add 100 ul of SM substrate in the appropriate buffer.
16. Mix gently and incubate for 30 min at 37°C.
17. Add 1.5 ml of chloroform/methanol (2:1) to stop the reaction and
vortex.
18. Add 0.4 ml of water to break the phases and vortex.
19. Centrifuge at 2000 g for 5 min in a table-top centrifuge to clarify the
phases.
20. Take 400 ul of the upper phase and do scintillation counting. Remem-
ber to count 100 n-l of substrate for total activity.
One has counted 400 of 900 ul, so one must determine total cpms
hydrolysed from each sample. Now subtract the matching blank tube
prepared for each assay. The number now obtained can be normalized to the
amount of protein used in the assay.
Protocol 10. Measurement of sphingomyelin synthase activity

. PBS • incubation buffer: 50 mM Tris-HCI, pH 7.4,
• lysis buffer: 25 mM Tris-HCI, pH 7.4, 5 mM 25 mM KCI, and 0.5 mM EDTA
EDTA, 1 mM phenylmethylsulfonyl fluoride, • 20 nmoles [14C]C6 ceramide (9 X 103
and 20 ug/ml of chymostatin, leupeptin, cpm/nmole)
antipain, and pepstatin • 27 gauge 0.5 inch needle
• fatty acid-free BSA • TLC plates
Method
1. Collect 1 x 107 cells via centrifugation at 500 g on a table-top
centrifuge.
2. Wash cells with PBS and then repellet as above.
3. Suspend cells in approximately 0.8 ml of ice-cold lysis buffer.
4. Homogenize the cells by 10-15 passages through a 27 gauge 0.5 inch
needle.
121
Gary M. Jenkins and YusufA. Hannun
5. Centrifuge homogenates for 10 min at 1000 g at 4°C to remove
cellular debris and unbroken cells (One can keep part of this fraction
as a crude homogenate).
6. Transfer the supernatant and spin at 100000 g for 1 h at 4°C.
7. Collect the supernatant from high speed spin (cytosol).
8. Resuspend the pellet (membrane) in 0.4-0.5 ml of incubation buffer.
9. Determine protein concentrations via your favourite assay (e.g.
Biorad).
10. Put 150 ug of protein from the above into a final volume of 0.5 ml
incubation buffer. Set up blanks for each assay containing only 0.5 ml
of incubation buffer.
11. Pre-incubate samples for 10 min at 37°C.
12. Start the reaction with the addition of [14C]C6 ceramide as an equi-
molar complex with fatty acid-free bovine serum albumin.
13. Allow the reaction to proceed for up to 15 min at 37°C.
14. Stop the reaction with 3 ml of chloroform/methanol (1:2), 0.2 ml of
water, vortex, and keep on ice.
15. Add 1 ml of chloroform, 1 ml of water, and vortex. These additions
induce a phase break. Allow the phase to clarify for 30 min, then
centrifuge at 2000 g in a table-top centrifuge for 5 min to obtain clear
phases.
dry nitrogen.
18. Resuspend in 50 ul of chloroform/methanol (1:2) and spot half onTLC
plates (Whatman Silica 60A plates).
19. Take a small amount of the resuspended lipid and count to ensure
similar cpms for each tube.
20. Develop the plates in a TLC chamber containing the following solvent
system: chloroform/methanol/15 mM anhydrous CaCI2 (60:35:8).
Allow tank to equilibrate overnight before running plates.
21. The [14C]C6-SM band on the TLC plates is detected by auto-
radiography.
22. Scrape the band from the plate and do scintillation counting to yield
cpms.
122
One has counted only half of the sample since this is what has been spotted.
Subtract the matching blank tube prepared for each sample. Now multiply the
obtained number by two as this will give you total cpms produced in each
assay tube. The number now obtained can be normalized to the amount of
protein used in the assay. Increased SM synthase activity should be reflected
in a decrease of cellular ceramide levels.
Acknowledgements
This work was partly supported by NIH grant GM-43825.
References
1. Michel, C., van Echten-Deckert, G., Rother, J., Sandhoff, K., Wang, E., and
Merrill, A. E. (1997). Journal of Biological Chemistry, 272,22432.
2. Perry, D., Obeid, L., and Hannun, Y. A. (1996). Trends in Cardiovascular
Medicine, 6,158.
3. Obeid, L. M., Linardic, C. M., Karolak, L. A., and Hannun, Y. A. (1993). Science,
259,1769.
4. Kolesnick, R. and Fuks, Z. (1995). Journal of Experimental Medicine, 181, 949.
5. Liu, B. and Hannun, Y. A. (1997). Journal of Biological Chemistry, 272,6281.
6. Bligh, E. G. and Dyer, W. J. (1959). Canadian Journal of Biochemical Physiology,
37, 911.
7. Folch, J., Lees, M., and Sloane Stanley, G. H. (1957). Journal of Biological
Chemistry, 226,497.
8. Merrill, A. H., Jr., Wang, E., Muffins, R. E., Jamison, W. C., Nimkar, S., and
Liotta, D. C. (1988). Analytical Biochemistry, 171,373.
9. Preiss, J., Loomis, C. R., Bishop, W. R., Stein, R., Niedel, J. E., and Bell, R. M.
(1986). Journal of Biological Chemistry, 261, 8597.
10. Van Veldhoven, P. P., Bishop, W. R., and Bell, R. M. (1989). Analytical
Biochemistry, 183 177.
11. Jayadev, S., Linardic, C., and Hannun, Y. A. (1994). Journal of Biological
Chemistry, 269 5757.
12. Jungalwala, F. B., Hayssen, V., Pasquini, J. M., and McCluer, R. H. (1979).
Journal of Lipid Research, 20, 579.
13. Luberto, C. and Hannun, Y. A. (1998). Journal of Biological Chemistry, 73,14550.
123
7
Cytochemical detection of
cytoskeletal and micleoskeletal
changes during apoptosis
MANON VAN ENGELAND, BERT SCHUTTE,
ANTON H. N. HOPMAN, FRANS C. S. RAMAEKERS, and
CHRIS P. M. REUTELINGSPERGER
1. Introduction
Apoptosis is an evolutionarily conserved form of physiological cell death by
which redundant and damaged cells are eliminated during embryonic develop-
ment and tissue homeostasis. In diseased tissue the process may be disturbed in
such a way that accumulation of cells or increased cell loss may occur. Rapid
elimination of the dying cell, without evoking an inflammatory response, is
accomplished by disintegration of the cell into apoptotic bodies, which will
then be phagocytosed (1). During this process, in which the plasma membrane
remains intact, cleavage of cytoskeletal and nucleoskeletal proteins occurs by
caspases, a family of cysteine proteases that cleave key proteins at conserved
aspartic amino acid residues. The cleavage of cell-cell adhesion molecules
leads to loss of contact with neighbouring cells (2), proteolysis of nuclear pro-
teins facilitates nuclear disassembly (3), and the reorganization of actin
filaments plays a role in the formation of apoptotic bodies (4). Proteolysis of
fodrin may play a role in the loss of plasma membrane lipid asymmetry,
resulting in exposure of phosphatidylserine (PS) at the outer leaflet of the cell
membrane (5). Apoptosis can be detected on the basis of the characteristic
morphological changes, such as chromatin aggregation and formation of
apoptotic bodies. Furthermore, techniques have been developed which are
based on apoptosis-specific biochemical changes (e.g. DNA fragmentation),
expression of apoptosis-associated proteins, proteolysis of apoptosis-specific
substrates, generation of apoptosis-specific neo-epitopes, or exposure of specific
phospholipids at the outer plasma membrane. However, the individual tech-
niques detect specific events in the process of apoptosis and therefore every
technique has its limitations. In this chapter we describe methods to study
changes in cyto- and nucleoskeletal proteins during apoptosis by means of
immunocytochemistry. For detection of apoptotic cells the annexin V affinity
Manon van Engeland et al.
assay and the TUNEL assay is used. The applications and limitations of the
detection systems will be discussed.
2. Cyto- and nucleoskeletal changes during apoptosis

2.1 General
Apoptotic cells show characteristic morphological changes, such as loss of
contact with neighbouring cells and with the substratum to which they adhere,
nuclear condensation, and membrane blebbing. These morphological changes
are, amongst others, the result of a dramatic reorganization of the cyto- and
nucleoskeleton of the dying cell. Therefore, it is not surprising that many of
the cyto- and nucleoskeletal components themselves are targets for the caspase
family of proteases. However, in addition to caspase cleavage, post-trans-
lational modifications of these proteins, such as (de)phosphorylation, cross-
linking, and citrullination are also reported to contribute to reorganization
and modification of cyto- and nucleoskeletal proteins during apoptosis (6).
2.2 Microfilaments and microfilament-associated proteins

Reorganization of the microfilament network is involved in membrane bleb-
bing during apoptosis. F-actin, present at the base of blebs during apoptosis
(4, 7, 8), is necessary for bleb formation and the eventual formation of
apoptotic bodies (9, 10). Whether actin itself is a direct target for caspases
remains elusive. Several groups have proposed that actin is cleaved by
caspases during apoptosis (11-14). However, Brown et al. (15) reported that
in membrane-associated actin, a component of the cytoskeleton that links
polymerized actin to the plasma membrane, cleavage occurred at a site devoid
of a consensus motif for cleavage by caspases. Song et al. (16) reported pro-
tection of actin for proteolysis in vivo. Loss of contacts between neighbouring
cells is caused by the disassembly of the cytoskeletal organization at the level
of cell-cell adhesion sites. In fact, p-catenin, a known regulator of cell-cell
adhesion, is proteolytically processed after induction of apoptosis. (3-Catenin
cleavage by caspase-3 removes the amino- and carboxy-terminal regions of
the protein. The resulting 0-catenin product is unable to bind a-catenin which
is responsible for actin filament binding and organization (17). Also, cleavage
of gelsolin (18) may be a physiological effector of morphological changes
during apoptosis. The function of gelsolin is to bind barbed ends of actin
monomers to prevent monomer exchange. Expression of the gelsolin cleavage
product in multiple cell types caused the cells to round up, detach from the
substratum, and undergo nuclear fragmentation (18).
2.3 Microtubules
Reorganization of tubulin is an integral part of the apoptotic process, indepen-
dent of the involvement of tubulin in cell division (19). During apoptosis
126
7: Cytochemicai detection of cyiu- und nuclt-ioskeletol changes
tubuliii is reorganized into visible polymeri/cd tuhulin structures (20) which
display characteristics similar to those observed following treatment with
drugs that do interact directly with tubulin (21). Disruption of the micro-
tubule architecture might influence signalling cascades. Recent studies by
Blagosklonny et at. (22) have shown that disruption of microtubular archi-
tecture leads to Raf-1 activation and Bcl-2 phosphorylation, serving a role
similar to p53 induction following DNA damage.
2.4 Intermediate filaments

Cytokeratins, the intermediate filament proteins of epithelial cells, are
necessary for the structural support of cells. During apoptosis, cytokeratin-
and vimentin-containing intermediate filaments reorganize into granular
structures (20, 23-25), as is illustrated in Figure 1, This process seems to be
governed mainly by (hypcr)phosphorylation of the cytokeratins during
apoptosis (26).
Furthermore, it has been shown that phosphorylation and dephosphoryl-
ation events also critically control cell junction assembly and stability and also
regulate the formation of the cadherin-cytoskcleton complex (27. 28), thus
influencing the adhesive properties of cells.
Recently Caulin et al. (24) and Leers et al. (25) showed that intermediate
filamcnt proteins are cleaved by caspases during apoptosis. A conserved
caspase-6 motif is found in the linker-2 region of all intermediate filament
proteins, except for the type II cytokeratins. Cytokeratin 18 has an additional
caspase cleavage site at the C-terminus. as was suggested by Caulin et al, (24)
and recently identified as the DALD motif by Leers et at. (25). The functional
significance of the co-ordinated breakdown of the cytokeratins remains
unknown. Caulin et al. (24) suggest that proteolytic cleavage of these inter-
mediate filaments, which are highly polymeri/.ed and arc relatively insoluble
Figure 1. Linear projections of slacks of confocal scanning laser microscopy images of an

apoptotic MR65 lung cancer cell after annexin V labelling, fixation, and staining with the
M30 cytodeath antibody: (a) annexin V labelling, (b) aggregated cytokeratin 18
fragments. Apoptosis was induced by 6 h exposure of the cells to 50 um roscovitine.
127
in normal aqueous solutions, is necessary for the formation of apoptotic
bodies.
2.5 Nucleoskeletal components

Nuclear events in apoptosis include DNA condensation and fragmentation,
redistribution of nuclear pores, disassembly of the nuclear lamina, and re-
distribution and proteolysis of other nuclear proteins (29). Of the nuclear
proteins proteolysed in apoptosis, several appear to be involved in DNA
repair processes and in maintaining the proper conformation of chromatin
through interactions with the nuclear matrix. Cleavage and reorganization of
these proteins may contribute to the collapse of the nucleus in apoptosis. For
example, proteolysis of lamin proteins facilitates nuclear disassembly (3).
Lamins are intermediate filament proteins which form a lamina underlying
the inner nuclear membrane. They have been shown to stabilize the nuclear
envelope and to participate in determining the organization of the interphase
nucleus (30). Two subtypes of lamins can be distinguished: i.e. the A-type
lamins, which comprise lamin A, lamin AA10, and lamin C; and the B-type
lamins, which comprise lamin Bl and lamin B2 (31). During apoptosis, lamins
are cleaved by caspase-6 at a conserved VEID (A-type lamins) or VEVD (B-
type lamins) amino acid sequence (3). Several of the nucleoskeleton proteins
proteolysed in apoptosis appear to be autoantigens (32). Cleavage and
modification of autoantigens may reveal immunocryptic epitopes that could
potentially induce autoantibody response (32).
2.6 Generation of neo-epitopes in cytoskeletal proteins

during apoptosis
Caspases are amongst the most specific endopeptidases known today. There-
fore, activation of this family of proteases results in limited proteolytic cleavage
at specific aspartate residues of the target molecules (33). A novel approach
to probe for specific proteolytic events during apoptosis is the use of anti-
bodies directed against neo-epitopes generated by caspase cleavage. This
approach has been shown to be feasible for the caspase-cleaved cytoskeletal
proteins actin and cytokeratin 18. Yang et al. (14) raised a polyclonal anti-
serum using a synthetic peptide representing the last five amino acids of the
C-terminus of the 32 kDa actin fragment produced during apoptosis. The
antiserum specifically labels apoptotic but not necrotic cells. Similarly, Leers
et al, (25) describe a monoclonal antibody specific for the liberated DALD
sequence in the C-terminus of cytokeratin 18. Also this antibody specifically
recognizes apoptotic cells and does not detect necrotic cells. Antibodies for
the in situ detection of caspase-cleaved cyto- and nucleoskeletal proteins pro-
vide simple, specific tools to evaluate the role of caspase activation in cyto-
skeletal reorganization during apoptosis. They are now in use as apoptosis
markers that can be applied to routinely processed tissues and cells.
128
7: Cytochemical detection ofcyto- and nucleoskeletal changes
3. Apoptosis detection systems

3.1 Overview
Apoptosis was originally detected because of the characteristic cell morph-
ology, which allows apoptotic cells to be distinguished from healthy and
necrotic cells. Although different cell types do not necessarily display all the
hallmarks of apoptosis, there are similar features shared by cells undergoing
apoptosis, which include shrinkage, blebbing, and chromatin condensation.
Detection techniques based on apoptosis-specific biochemical changes, such
as DNA fragmentation, exposure of phosphatidylserine (PS) at the outer
plasma membrane, and proteolysis of proteins have been developed. In the
next paragraphs, we describe protocols to study cyto-and nucleoskeletal
proteins during apoptosis using two different apoptosis detection systems, i.e.
the annexin V affinity assay to detect PS exposure and the TUNEL assay to
detect DNA fragmentation.
3.2 The annexin V affinity assay

In healthy cells, the phospholipids of the plasma membrane are distributed
asymmetrically over the two leaflets of the bilayer. Phosphatidylcholine and
sphingomyelin are the predominant species of the outer membrane leaflet and
PS is located exclusively in the inner membrane leaflet. This asymmetry is
maintained by an aminophospholipid translocase which transports the amino-
phospholipids, with preference for PS, from the outer to the inner leaflet (34).
In addition, the localization of PS to the inner membrane leaflet is maintained
by association of PS with annexins, polyainines, and membrane skeletal
proteins such as fodrin (35).
Early in apoptosis, PS is externalized to the outer membrane leaflet due to
inhibition of the aminophospholipid translocase and subsequent activation of
a scramblase (36, 37). Also, fodrin cleavage by caspase-3 and calpain may
contribute to PS externalization (38).
Exposure of PS at the outer surface of the plasma membrane serves as a
trigger for macrophages, which posses a PS receptor on their plasma mem-
brane, to engulf and digest the apoptotic cell. Exposure of PS on the plasma
membrane of the apoptotic cell seems to be a phylogenetically conserved
phenomenon which occurs in mammalian, avian, insect, and plant cells
(39-41) and can be detected in vitro and in vivo using annexin V (42).
Annexin V was first discovered by Bohn and co-workers (43) who isolated the
protein from human placenta and called it placental protein (PP4). Later, the
same protein was isolated from human umbilical cord by Reutelingsperger et
al. (44) who called it vascular anticoagulant protein a (VACa). Meanwhile,
other groups also isolated the protein and referred to it as inhibitor of blood
coagulation (IBC), endonexin II, placental anticoagulant protein I (PAP-I),
lipocortin V, 35 K calelectrin, and anchorin II (45). The function of annexin V
129
in vivo is still unknown, but from in vitro experiments it is has become clear
that it has anti-phospholipase, anti-coagulant, anti-kinase, and phospholipid-
binding activities (46). Annexin V binds PS in the presence of calcium ions.
Therefore, the availability of biotin- or fluorochrome-labelled annexin V
enables one to study PS exposure in cells undergoing apoptosis.
Protocol 1a. In vitro detection of apoptotic cells by annexin V

affinity labelling. Cells grown in suspension
analysed by flow cytometry or fluorescence
microscopy

• cell line of interest • fluorochrome-conjugated annexin V:
• apoptosis-inducing agent of interest APOPTESTtm-FITC, APOPTEST™-oregon
• annexin V-binding buffer (25 mM Hepes, green, APOPTESTTM-phycoerythrinb
125 mM NaCI, 2.5 mM CaCI2, included in • propidium iodide [PI, included in
APOPTEST™ kit)a APOPTEST™ kit, stock solution of 250 (u/ml
• flow cytometer or fluorescence microscope in PBS/RNAse A (10 mg/ml]
Method
1. Add fluorochrome-labelled annexin V (dilute according to the manu-
facturer's instructions) to the apoptotic cells (106 cells/ml) in culture
medium or in annexin V-binding buffer.c,d
2. Incubate for 3-5 min at room temperature.
3. Add PI to the cell suspension (final concentration 5 ug/ml for flow
cytometry and 1 pg/ml for fluorescence microscopy) and incubate on
ice for 15 min.e,f
4. Quantify annexin V binding by flow cytometry or place a drop of cells
on a glass slide, add a coverslip, and visualize the cells using fluor-
escence microscopy.
"All APOPTEST™ products are obtained from Nexins Research.

b
Annexin V-phycoerythrin can only be used for flow cytometry.
c
For double-labelling with PI, annexin V-oregon green or annexin V-FITC is recommended.
d'It is essential that the culture medium and the annexin V-binding buffer contain 2.5 mM
calcium, since binding of annexin V to PS is calcium dependent.
a Annexin V is able to detect PS at the outer surface of the plasma membrane. However,
annexin V also binds PS present at the cytoplasmic site of the cell membrane. Thus it will bind
necrotic cells of which the plasma membrane is permeable. Therefore, in in vitro assays, a
membrane-impermeable vital dye, such as PI, must be included in the assay to monitor plasma
membrane integrity and to discriminate between apoptotic and necrotic cells.
fUsing the annexin V/PI assay in viable cells, three populations of cells can be detected: (a)
viable cells which are annexin V negative/Pi negative; (b) apoptotic cells which are annexin V
positive/Pi negative; and (c) (secondary) necrotic cells which are annexin V positive/Pi positive.
Koopman et al. (47) were the first to describe detection of apoptotic cells in
vitro using FITC-labelled annexin V. Hapten-labelled annexin V can bind to
130
externalized PS in the outer plasma membrane leaflet of apoptotic cells. It will
not bind to normal cells because the molecule cannot trespass the phos-
pholipid bilayer. In necrotic cells, however, the inner leaflet of the plasma
membrane is available for binding, since the integrity of the plasma membrane
is lost. To discriminate between necrotic and apoptotic cells, a membrane-
impermeable DNA dye, for example propidium iodide (PI), can be included
in the assay. In this way vital, apoptotic, and necrotic cells can be discrimin-
ated on the basis of double-labelling for annexin V and PI and analysed by
flow cytometry and fluorescence microscopy.
For cells cultured in suspension, detection of PS exposure is relatively easy
(Protocol la). For adherent cells, however, the situation is more complex.
When cells are grown on glass slides, they can be analysed immediately after
annexin V labelling using a fluorescence microscope. To obtain a single-cell
suspension of adherent cells for flow cytometric analysis, cells have to be
harvested. However, enzymatic harvesting of adherent cell lines may interfere
with reliable detection of PS exposure and trypsin or ethylenediaminotetra-
acetic acid (EDTA) harvesting of cells before annexin V labelling can induce
changes in the plasma membrane, which leads to false-positive results.
Trypsin or EDTA treatment after annexin V labelling interferes with the
detection of bound annexin V, because trypsin and EDTA remove bound
annexin V by proteolysis and chelation of calcium ions, respectively. There-
fore, a method is developed (Protocol Ib) to detect PS exposure in adherent
cell lines by labelling cells as a monolayer with annexin V and by harvesting
the cells thereafter by means of scraping (48).
Protocol 1b. In vitro detection of apoptotic cells by annexin V

affinity labelling. Adherent cells analysed by flow
cytometry or fluorescence microscopy

• adherent cell line of interest, grown in a • fluorochrome-conjugated annexin V (see
culture flask or on glass slides Protocol 1a)
• apoptosis-inducing agent of interest • rubber policeman
• annexin V-binding buffer (see Protocol la) . PBS/PI/RNAse (see Protocol 1a)
Method
1. Add fluorochrome-labelled annexin V (dilute according to the manu-
facturer's instructions) to the adherent cells in the culture flask or the
cells grown on slides without washing the cells.a-c
2. Incubate for 3-5 min in the culture flask or on glass slides. Cells
labelled with annexin V-FITC or annexin V-oregon green can now be
visualized immediately after addition of PI (see step 7).
3. Collect the culture medium (this fraction contains the detached
apoptotic cells).
131
Protocol 1b. Continued
4. Wash the adherent cells three times with culture medium or annexin V-
binding buffer to remove excess annexin V, collect the rinse solution,
and pool with the collected culture medium from step 3. Pellet these
cells by centrifugation (400 g, 5 min, 4°C), discard the supernatant,
resuspend the pellet in culture medium or annexin V buffer, pellet the
cells again by centrifugation, discard the rinse medium, and repeat this
washing procedure.d
5. Detach the adherent cells in culture medium gently by scraping with a
rubber policeman, pellet the cells by centrifugation, and discard the
culture medium.6
6. Resuspend the pellet of detached cells in culture medium or annexin V
buffer and pool these cells with the cells collected in step 4. Dilute to a
final concentration of 106 cells/ml.
7. Add PI to the cell suspension (final concentration 5 ng/ml for flow
cytometry and 1 xg/ml for fluorescence microscopy) and incubate on
ice for 15 min.
8. Analyse the cells by flow cytometry or visualize cells using fluor-
escence microscopy.
* Annexin V-phycoerythrin can only be used for flow cytometry.

b
For double-labelling with PI, annexin V-oregon green or annexin V-FITC is recommended.
c
lt is essential that the culture medium and the annexin V-binding buffer contain 2.5 mM
calcium since binding of annexin V to PS is calcium dependent. The washing step is omitted to
obtain an optimal number of apoptotic cells, which would otherwise be rinsed away.
d Removal of annexin V before scraping of the adherent cells prevents annexin V binding to
internally located PS in cells that become damaged (permeable) during the scraping
procedure.
aTo avoid false-positive and false-negative results due to trypsin or EDTA treatment, annexin
V-labelled cells are harvested using a rubber policeman. This method of harvesting introduces
a fourth population of cells, i.e. damaged cells, which are annexin V negative and PI positive.
To study PS exposure and cyto- and nucleoskeletal reorganizations in

apoptosis simultaneously, using annexin V and immunocytochemistry, cells
have to be permeabilized for antibodies to enter the cell and to detect their
epitopes. Therefore a method (Protocol 2) is developed in which the cells are
fixed after labelling with annexin V (20).
In some circumstances the annexin V affinity assay cannot be used to detect
apoptotic cells. In frozen and paraffin-embedded tissue sections, for example,
annexin V also detects PS at the inner plasma membrane leaflet. Therefore,
another apoptosis detection system has to be chosen to study cyto- and
nucleoskeletal changes in tissue sections. In tissue sections the TUNEL (49)
and (50) DNA end-labelling procedures are often used to detect apoptotic
cells. The methods described below can be applied to tissue sections as well as
cells in culture.
132
7; Cytochemical detection ofcyto- and nucleoskeletal changes
Protocol 2. Combined annexin V labelling and nucleo- and

cytoskeletal protein immunostaining of cells analysed
by flow cytometry or fluorescence microscopy

• biotin-conjugated annexin V (APOPTEST""- . PBS
biotin) or Oregon green-conjugated annexin . PBS/BSA(1%, Sigma)
V (APOPTEST™-oregon green) • fluorochrome-conjugated secondary anti-
• binding buffer (see Protocol 1a) body, e.g. phycoerythrin- or Texas Red-
• primary antibody directed against the anti- conjugated rabbit anti-mouse antibody
gen of interest, e.g. mouse monoclonal anti- • PBS/PI/RNAse (see Protocol 1a) or PBS/4',6-
body directed against actin or cytokeratin diamino-2-phenyl indole (DAPI, 0.5 ug/ml)
Method
1. Depending on the cell line, use Protocol la or Protocol 1b (steps 1-2
and 1-6, respectively) to label cells with annexin V. In this case, use
annexin V-oregon green or annexin V-biotin.a,b
2. In the case of cells in suspension or adherent cells harvested for flow
cytometry, pellet the cells by centrifugation (400 g, 5 min, 4°C), re-
suspend the cells in binding buffer, pellet again, and discard the
binding buffer.0
3. Fix the cells in methanol for 5 min at -20°C.d
4. Pellet the cells by centrifugation, discard the methanol, and re-
suspend the cells in PBS.
5. Pellet the cells by centrifugation, discard the PBS, and resuspend the
cells in PBS/BSA(1%).
6. Incubate the cells with the (appropriately diluted) primary antibody
for 60 min at room temperature.
7. Pellet the cells by centrifugation, discard the PBS/BSA, and resuspend
the cells in PBS/BSA, repeat once more.
8. Incubate the cells with the (appropriately diluted) secondary anti-
body and in the case of annexin V-biotin labelling, incubate with
fluorochrome-conjugated avidin (e.g. FITC-conjugated avidin) for 60
min at room temperature.e,f
9. Pellet the cells, discard the PBS/BSA, and resuspend the cells in
PBS/BSA, repeat once.
10. Prepare a cell suspension in PBS/BSA of 106 cells/ml.
11. For flow cytometry: counterstain cells with PI (final concentration
1 (xg/ml) and incubate on ice for 15 min.9/ h For fluorescence micro-
scopy: counterstain cells with PBS/DAPI.
133
12. Analyse cells by flow cytometry (see Figure 2) or place a drop of cells
on a glass slide, add a coverslip, and visualize the cells by fluor-
escence microscopy (see Figure 1).
"The fluorescent properties of FITC are impaired by methanol fixation, therefore the use of
annexin V-oregon green (low photobleaching and pH insensitivity) or annexin V-biotin is
recommended.
bAPOPTEST™-biotin, product B700 is recommended in in vitro experiments.
gIt is possible to stain adherent cells grown on glass slides simultaneously for PS exposure
and cyto-and nucleoskeletal proteins. However, it is recommended to harvest adherent cells
(Protocol 1b, steps 3-6) after annexin V labelling, because fixation and repeated washing
procedures during immunocytochemistry often lead to detachment and subsequent loss of
apoptotic cells.
d
Be aware of the fact that cyto- and nucleoskeletal proteins (or fragments) can be lost from
apoptotic cells using methanol fixation due to increased solubility of the protein or fragments
of proteins.
* Use two different fluorochromes to detect annexin V and antibody binding.
'A phycoerythrin-conjugated secondary antibody is recommended for flow cytomatry.
g After fixation of cells, PI cannot be used to discriminate between apoptotic and necrotic cells
by membrane permeability. In these cells PI indicates DNA content of the cells.
"The concentration PI has to be decreased in a multiparameter flow cytometric analysis
compared with a single colour analysis because of the spectral overlap between the red
colours phycoerythrin and PI.
Figure 2. Flow cytograms of (a) control and (b) apoptotic MR65 lung cancer cells after
annexin V labelling, fixation, and staining with a lamin B1 antibody. Quadrant settings
were based on the negative control, (a) In the control culture only a few annexin V
positive cells (spontaneously apoptotic cells) are observed. The majority of the cells are
positive for lamin B1 and negative for annexin V. (b) After induction of apoptosis with
roscovitine, part of the cells becomes annexin V positive. The lamin immunofluorescence
of these cells is decreased.
134
3.3 Detection of apoptosis using the TUNEL assay

DNA fragmentation is considered to be a key event in apoptosis and can be
detected as a typical DNA ladder on agarose gels. However, this method does
not provide information regarding apoptosis in individual cells and cannot be
used to evaluate apoptosis in relation to histological localization. This can be
achieved by enzymatic in situ labelling of 3'-OH ends of fragmented DNA.
For incorporation of labelled nucleotides into DNA strand breaks, terminal
deoxynucleotidyl transferase (TdT) can be used. This method is known as the
TUNEL (TdT-mediated conjugated dUTP nick end-labelling) assay (49). If
DNA polymerase I is used to incorporate the nucleotides the method is
known as the ISNT (in situ nick translation) assay (50). The disadvantage of
these methods is that late necrotic cells, showing DNA degradation, will also
be labelled. In Protocol 3 a method is described to combine the TUNEL assay
and immunostaining of cyto-and nucleoskeletal proteins in cell lines, while in
Protocol 4 a method is described to combine the TUNEL assay and the
immunocytochemical staining of cyto-and nucleoskeletal proteins in paraffin-
embedded tissue.
Protocol 3. Combined detection of DNA fragmentation (TUNEL)

and cyto- and nucleoskeletal changes in apoptotic
cells using flow cytometry or fluorescence
microscopy of cell lines

» cell line of interest in suspension (for flow • fluorochrome-labelled secondary antibody
cytometry) or cytocentrifuged on to glass (e.g. Texas Red or phycoerythrin-con-
slides (for fluorescence microscopy)8 jugated rabbit anti-mouse antibody)b
• in situ cell death detection kit, fluorescein . 4 X SSC
(Boehringer Mannheim), including TdT en- . PBS/BSA(1%, Sigma)
zyme, FITC-labelled 11-deoxyuridine triphos- . PBS/PI/RNAse [stock solution of 250 (ig/ml
phate (dUTP-FITC), and TdT reaction buffer PI in PBS/RNAse (10 mg/ml)] for flow
containing nucleotide mixture. cytometry or PBS/4',6-diamino-2-phenyl
• primary antibody directed against the anti- indole (DAPI, final concentration 0.5 ug/ml)
gen of interest (e.g. a mouse monoclonal for immunocytochemistry
antibody raised against lamin or cyto- • flow cytometer or fluorescence microscope
keratin)
Method
1. Fix the cells or slides in cold methanol (-20°C) for 5 min.
2. Rinse twice with PBS.
3. Prepare the TUNEL reaction mix according to the manufacturers
instructions.
4. Incubate with the TUNEL reaction mix for 60 min at 37 °C in a humid-
ified atmosphere in the dark. In this step, incorporation of FITC-dUTP
to 3'-OH DNA fragments by the enzyme TdT is achieved.
135
5. Rinse in 4 x SSC.
6. Rinse twice in PBS/BSA.
7. Incubate cells with the primary antibody for 60 min at room
temperature in the dark.
8. Rinse twice with PBS/BSA.
9. Incubate with a fluorochrome (non-FITC)-conjugated secondary anti-
body to visualize the antibody of interest for 60 min at room
temperature in the dark.c
10. Rinse twice with PBS/BSA.
11. For flow cytometry: add PI to the cells (final concentration 1 ug/ml)
and incubate on ice for 15 min.d For fluorescence microscopy: add
DAPI to the cells (final concentration 0.5 p-g/ml).
12. Analyse cells by flow cytometry (see Figure 3) or fluorescence micro-
scopy.
aIt is recommended to harvest adherent cells (Protocol 1b, steps 3-6) after annexin V labelling,
because fixation and repeated washing procedures during incorporation of dUTP and immuno-
cytochemistry often lead to detachment and subsequent loss of apoptotic cells from the slide.
b
For flow cytometry, a phycoerythrin-conjugated secondary antibody is recommended. For
fluorescence microscopy, a Texas Red-conjugated secondary antibody is recommended.
c
Because the dUTP is conjugated with FITC, use a non-FITC-conjugated secondary antibody.
d
The concentration of PI has to be decreased in a multiparameter flow cytometric analysis
compared with a single colour analysis because of the overlap between the red colours.
Figures. Flow cytograms of (a) control and (b) apoptotic MR65 lung cancer cells after
TUNEL reaction and staining of cells with the M30 cytodeath antibody. Quadrant settings
were based on the negative control, (a) In the control culture the majority of the cells are
TUNEL negative and M30 negative, (b) After induction of apoptosis a fraction of the cells
has become M30 positive, indicating cleavage of cytokeratin 18 by caspases. The M30
positive cells are partly positive and partly negative for TUNEL reaction.
136
The use of fluorescence microscopy on paraffin-embedded tissue is often

hampered by a high autofluorescence background present in the tissue
section. Therefore a protocol (Protocol 4) is described to study DNA
fragmentation and cyto- and nucleoskeletal changes simultaneously using
brightfield microscopy.
Protocol 4. Combined detection of DNA fragmentation (TUNED

and cyto-and nucleoskeletal changes in apoptotic
cells using brightfield microscopy on paraffin-
embedded tissue

• 3-5 |i.m thick paraffin-embedded tissue • chromogenic substrate for alkaline phos-
sections mounted on to glass slides phatase reaction (e.g. N-ASMX-phosphate/
• xylene new fuchsin)
. ethanol series (absolute, 95%, 90%, 80%, • primary antibody directed to the antigen of
70%, diluted in distilled water) interest, e.g. monoclonal mouse antibody
• 0.3% H2O2/methanol M30 cytodeath (Boehringer Mannheim),
directed against caspase-cleaved cyto-
• proteinase K (Sigma, final concentration 20 keratin 18 fragment
M-g/ml in 10 mM Tris-HCI, pH 7.4-8.0)
• peroxidase-conjugated secondary antibody,
• in situ cell death detection kit, alkaline e.g. peroxidase-conjugated rabbit anti-
phosphatase (Boehringer Mannheim), mouse antibody
including TdT enzyme, FITC-labelled 11-
deoxyuridine triphosphate (dUTP-FITC), • chromogenic substrate for peroxidase reac-
TdT reaction buffer containing nucleotide tion [e.g. diaminobenzidine tetrachloride
mixture, alkaline phosphatase-conjugated (DAB), Sigma]
sheep anti-FITC antibody • haematoxylin
. PBS • mounting medium for light microscopy
. PBS/BSA (1%) (e.g. Aquamount, BDH)
Method
1. Deparaffinize and rehydrate tissue section using xylene and descend-
ing ethanol series.
2. Rinse slides in PBS.
3. Block endogenous peroxidase activity by incubating slides with 0.3%
H2O2/methanol.
5. Incubate slides with proteinase K (final concentration 20 (xg/ml) for
15minat37°C. a
7. Prepare the TUNEL reaction mix according to the manufacturer's
instructions.
8. Incubate slides with 50 uJ TUNEL reaction mix for 60 min at 37°C in a
humidified chamber. In this step, incorporation of FITC-dUTP to 3'-
OH DNA fragments by the enzyme TdT is achieved.b
9. Rinse slides with 4 x SSC buffer.
137
10. Rinse slides with PBS.
11. Incubate slides with 50 ul alkaline phosphatase-labelled converter
antibody directed against FITC for 30 min at 37°C in a humidified
chamber.
12. Rinse slides three times with PBS.
13. Detect alkaline phosphatase activity by precipitating chromogenic
substrates, e.g. N-ASMX-phosphate/new fuchsin.c
14. Rinse slides in distilled water.
15. Rinse slides in PBS/BSA.
16. Incubate with the primary antibody for 60 min at room temperature in
a humidified chamber.
17. Rinse slides three times with PBS.
18. Incubate with the peroxidase-conjugated secondary antibody for 60
min at room temperature in a humidified chamber.
19. Rinse three times with PBS.
20. Detect peroxidase activity by precipitating chromogenic substrates,
e.g. DAB.
21. Rinse slides in distilled water.
22. Counterstain slides with hematoxyline.
23. Embed slides in an aqueous mounting medium for light microscopy.
24. Analyse slides with a brightfield microscope.
'Concentration, time, and temperature of the pre-treatment steps have to be optimized for
each type of tissue and for each type of antibody. The described conditions are the conditions
optimized for the M30 antibody, directed against a caspase-cleaved cytokeratin 18 fragment.
Use of other antibodies directed against cyto-and nucleoskeletal proteins may need specific
adaptations of the protocol concerning epitope recognition.
bAt this stage samples can be visualized under a fluorescence microscope.
cFor more information on chromogenic substrates that can be combined, see Speel ef al. (51).
References
1. Wyllie, A.M. (1993). fir. J. Cancer, 67, 205.
2. Herren, B., Levkau, B., Raines, E.W. and Ross, R. (1998). Mol. Biol. Cell, 6,1589.
3. Rao, L., Perez, D. and White, E. (1996). J. Cell Biol., 135,1441.
4. Laster, S.M. and MacKenzie, J.M. (1996). Microsc. Res. Tech., 34,272.
5. Martin S.J., Reutelingsperger, C.P.M., McGahon, A.J., Rader, J.A., van Schie,
R.C., LaFace, D.M. and Green, D.R. (1995). J. Exp. Med., 182,1545.
6. Utz, P.J. and Anderson, P. (1998). Arthritis Rheum., 41,1152.
7. Pitzer, F., Dantes, A., Fuchs, T., Baumeister, W. and Amsterdam, A. (1996).
FEES Lett., 394, 47.
138
8. Vemuri, G.S., Zhang, J., Huang, R., Keen, J.H. and Rittenhouse, S.E. (1996).
Biochem. J., 314,805.
9. Cotter, T.G., Lennon, S.V., Glynn, J.M. and Green, D.R. (1992). Cancer Res., 52,
997.
10. Levee, M.G., Dabrowska, M.I., Lelli, J.L. and Hinshaw, D.B. (1996). Am. J. Physiol.,
271,C1981.
11. Mashima, T., Naito, M., Fujita, N., Noguchi, K. and Tsuruo, T. (1995). Biochem.
Biophys. Res. Commun., 217,1185.
12. Kayalar, C., Ord, T., Testa, M. P., Zhong, L.T. and Bredesen, D.E. (1996). Proc.
Natl. Acad. Sci. USA, 93,2234.
13. McCarthy, N.J., Whyte, M.K.B, Gilbert, C.S. and Evan, G.I. (1997). J. Cell Biol.,
136,215.
14. Yang, F., Sun, X., Beech, W., Teter, B., Wu, S., Sigel, J., Vinters, H.V., Frautschy,
S.A. and Cole, G.M. (1998). Am. J. Pathol, 152, 379.
15. Brown, S.B., Bailey, K. and Savill, J. (1997). Biochem. J., 323,233.
16. Song, Q., Wei, T., Lees-Miller, S., Alnemri, E., Walters, D. and Lavin, M.F.
(1997). Proc. Natl. Acad. Sci. USA, 94,157.
17. Brancolini, C., Lazarevic, D., Rodriguez, J. and Schneider, C. (1997). J. Cell. Biol.,
139, 759.
18. Kothakota, S., Azuma, T., Reinhard, C., Klippel, A., Tang, J., Chu, K., McGarry,
T.J., Kirschner, M.W., Koths, K., Kwiatkowski, D.J. and Williams, L.T. (1997).
Science, 278,294.
19. Pittman, S.M., Strickland, D. and Ireland, C.M. (1994). Exp. Cell Res., 215,263.
20. van Engeland, M., Kuijpers, H.J.H., Ramaekers, F.C.S., Reutelingsperger, C.P.M.
and Schutte, B. (1997). Exp. Cell Res., 235,421.
21. Ireland, C.M. and Pittman, S.M. (1995). Biochem. Pharmacol, 49,1491.
22. Blagosklonny, M.V., Giannakakou, P., el-Deiry, W.S., Kingston, D.G., Higgs, P.I.,
Neckers, L.and Fojo, T. (1997). Cancer Res., 57,130.
23. Tinnemans, M.M.F.J., Lenders, M.H.J.H., ten Velde, G.P.M., Ramaekers, F.C.S.
and Schutte, B. (1995). Eur. J. Cell Biol, 68,35.
24. Caulin, C., Salvesen, G.S. and Oshima, R.G. (1997). J. Cell Biol., 138,1379.
25. Leers, M.P.G., Kolgen, W., Bjorklund, V., Bergman, T., Tribbick, G., Persson, B.,
Bjorklund, P., Ramaekers, F.C.S., Bjorklund, B., Nap, M., Jornvall, H. and
Schutte, B. (1999). J. Pathol, 187,567.
26. Liao, J., Ku, N.O. and Omary, M.B. (1997). /. Biol Chem., 272,17565.
27. Serres, M., Grangeasse, C., Haftek, M., Durocher, Y., Duclos, B. and Schmitt, D.
(1997). Exp. Cell Res., 231,163.
28. Aberle, H., Bauer, A., Stappert, J., Kispert, A. and Kemler, R. (1997). EMBO J.,
16,3797.
29. Earnshaw, W.C. (1995). Curr. Opin. Cell Biol, 7,337.
30. Moir, R.D. and Goldman R.D. (1993). Curr. Opin. Cell. Biol, S, 408.
31. Moir R.D., Spann. T.P. Goldman, R.D. (1995). Int. Rev.Cytol, 162B, 141.
32. Casiano, C.A., Martin, S.J., Green, D.R. and Tan, E.M. (1996). J. Exp. Med., 184,
765.
33. Salvesen, G.S. and Dixit, V.M. (1997). Cell, 91,443.
34. Diaz, C. and Schroit, A.J. (1996). /. Membr. Biol, 151,1.
35. Fadok, V.A., Bratton, D.L., Frasch, S.C., Warner, M.L. and Henson, P.M. (1998).
Cell Death Differ., 5,551.
139
36. Zwaal, R.F.A. and Schroit, AJ. (1997). Blood, 89,1121.
37. Verhoven, B., Schlegel, R.A., Williamson, P. (1995). J. Exp. Med., 182,1597.
38. Vanags D.M., Porn Ares, M.I., Coppola, S., Burgess, D.H. and Orrenius, S.
(1996). J. Biol. Chem., 271,31075.
39. Fadok, V.A., Voelker, D.R., Campbell, P.A., Cohen, J.J., Bratton, D.L. and
Henson, P.M. (1992). J. Immunol, 148, 2207.
40. van den Eijnde, S.M., Boshart, L., Reutelingsperger, C.P.M., de Zeeuw, C.I.,
Vermeij-Keers, C. (1997). Cell Death Differ., 4, 311.
41. O'Brien, I.E.W., Reutelingsperger, C.P.M. and Holdaway, K.M. (1997).
Cytometry, 29, 28.
42. van Engeland, M, Nieland, L.J.W., Ramaekers, F.C.S., Schutte, B. and
Reutelingsperger C.P.M. (1998). Cytometry, 31,1.
43. Inaba, N., Sato, N., Ijichi, M., Fukazawa, I., Nito, A., Takamizawa, H., Luben, G.,
Bohn, H. (1984). Tumour Biol., 5,75.
44. Reutelingsperger, C.P.M, Hornstra, G. and Hemker, H.C. (1985). Eur. J.
Biochem., 151, 625.
45. van Heerde, W.L., Degroot, P.G. and Reutelingsperger, C.P.M. (1995). Thromb.
Haemost., 73,172.
46. Reutelingsperger, C.P.M. and van Heerde, W.L. (1997). Cell. Mol. Life Sci., 53,
527.
47. Koopman, G., Reutelingsperger, C.P.M., Kuijten, G.A.M., Keehnen, R.M.J., Pals,
S.T. and van Oers, M.H.J. (1994). Blood, 84,1415.
48. van Engeland, M., Ramaekers, F.C.S., Schutte, B. and Reutelingsperger, C.P.M.
(1996). Cytometry, 24,131.
49. Gavrieli, Y., Sherman, Y. and Ben-Sasson, S.A. (1992). /. Cell. Biol., 119,493.
50. Wijsman, J.H., Jonker R.R., Keijzer, R., van de Velde, C.J.H., Cornelisse, C.J. van
Dierendonck, J.H. (1993). /. Histochem. Cytochem., 41,7
51. Speel, E.J.M., Ramaekers, F.C.S. and Hopman, A.H.N. (1995). Histochem. /., 27,
833.
140
8
Metabolic alterations associated

with apoptosis
ANA P. COSTA-PEREIRA and THOMAS G. COTTER
1. Introduction
Apoptosis is an active form of cell death, induced both by endogenous and
exogenous stimuli, which occurs under physiological conditions (1, 2).
Morphologically, it is characterized by cellular features such as membrane
blebbing, cell shrinkage, and chromatin condensation (3). Intracellular events
include various types of DNA fragmentation (4), cytoskeletal alterations, and
protease activation (reviewed in ref. 5).
Oxidative stress is believed to play a key role in the process of apoptosis.
Indeed, accumulation of oxidized proteins and lipids (6), rapid production of
reactive oxygen intermediates (ROI), and alterations of the cellular redox (7,
8), as well as disruption of the transmembrane potential (Aiym) (9), have all
been reported to be common metabolic alterations during the apoptosis of a
variety of cell types. Oxidative stress is also seen in a number of pathological
conditions (reviewed in ref. 10). The degeneration of neural cells observed
during the progression of Alzheimer's, Parkinson's, and other neuro-
degenerative diseases have been linked to the cumulative damage caused by
oxidative stress. The levels of glutathione (GSH), a major component of the
intracellular antioxidant defence, have been shown to be decreased in HIV-
infected cells (11). In addition, in vitro studies on cells from HIV patients have
shown the decrease of several other antioxidant enzymes (12). Moreover,
tumour promotion during oncogenesis is favoured under pro-oxidant con-
ditions and several antineoplastic drugs have been demonstrated to be potent
antioxidants (13).
This chapter describes some current procedures used to analyse common
intracellular metabolic alterations which are of importance in apoptosis, namely
the disruption of Ay m , generation of ROI (e.g. peroxide and superoxide
anion), alteration of glutathione levels and its oxidative state, and catalase
levels.
Ana P. Costa-Pereira find Thomas C. Cotter
2. Detection of changes in the mitochondrial

transmembrane potential
Emerging evidence suggests a key role for mitochondria during apoptosis
induced by a diverse range of stimuli. Mitochondria not only function as
integrators of different pro-apoptolic pathways, but also constitute the target
of a number of anti-apoptotic molecules. Discontinuity of the outer mito-
Figurel. Depending on the membrane polarization, JC-1 fluorescent probe can form
monomers (FL-1) or J-aggregates (FL-2). Hence, ^ym depolarization can be monitored by
measuring the fluorescence in FL-1 and/or FL-2. (a) ^ym was measured in untreated
DU145 prostate cancer cells (shaded line) and in cells treated with camptothecin (100
rig/ml, 24 h) (solid line), as described in Protocol 7. An increase in fluorescence (FL-1) is
indicative of membrane depolarization. [bl Treatment of HL60 cells (human
promyelocytic leukaemia cell line) with 5.0 ug/ml camptothecin for 6 h causes a
significant decrease in the fluorescence measured in FL-2 (seen as a shift to the bottom
left panel in the contour plot), which is also indicative of ^ym disruption.
142
8: Metabolic alterations associated with apoptosis
chondrial membrane results, in some instances, in redistribution of cytochrome
c from the intermembrane space to the cytosol, followed by subsequent inner
mitochondrial membrane depolarization.
Disruption of ^ym is believed to occur through permeability transition
(FT), which can be activated in response to a variety of pro-apoptotic signal
transduction molecules. The mitochondrial PT pore is a megachannel thought
to be directly regulated by the Bcl-2/Bax complex (14). Opening of the PT
pore, following PT, allows the release of solutes 1.5 kDa and smaller, and
subsequent disruption of ^ym. As a consequence of intermembrane protein
release, caspases and nucleases are released (14). Importantly, inhibitors of
PT also inhibit apoptosis in several models of apoptosis, suggesting that dis-
ruption of mitochondrial function is of key importance to the apoptotic
process (9).
The cell-permeant fluorescent probe 5,5',6,6'-tetrachloro-l,l',3,3'-tetraethyl-
benzimidazolylcarbocyanine iodide (JC-1) can be employed to monitor
changes in ^ym in cells, by flow cytometry. In the presence of a high A^m JC-1
forms what are termed J-aggregates which fluoresce strongly at 590 nm (FL-
2). Reduced ^ym results in an increased FL-1 signal and/or in a reduced FL-2
signal in JC-1-stained cells (see Figure 1). This method allows subpopulations
of cells with different mitochondrial properties to be identified (15).
Protocol 1. Measurement of mitochondrial transmembrane

potential (^ym) using JC-1

• JC-1 (Molecular Probes), made as a • FACScan flow cytometer (e.g. Becton
5 mg/ml stock in DMSO (Sigma). Protect Dickinson), with an excitation source of
from light and store at -20°C 488 nm
Method
1. Plate the cells in a standard 24-well plate at a density of 5 x 105/ml.
2. Treat the cells with the apoptosis-inducing agents either before, after,
or during the incubation period, depending on the time point at which
^ym is to be measured.
3. Transfer the sample into a standard FACS tube.
4. Incubate the cells with 5 ug/ml JC-1 for 15 min at 37°C, in the dark.
5. Collect the fluorescence emission through a 530/30 band pass filter
(FL-1) and through a 585/42 band pass filter (FL-2), both on a log scale,
using a FACScan flow cytometer (see Figure 7). For each sample,
collect 5000-10000 events.
143
3. Detection of intracellular reactive oxygen

intermediates (ROI)
Oxidative stress has been suggested as a possible common mediator of
apoptosis in response to a number of stimuli (6, 8). Apoptosis can be induced
by several agents that are known to cause oxidative stress, or it can be caused
directly by the addition of oxidants (7). Accordingly, addition of antioxidants
has been shown to block apoptosis induced by a variety of agents and to
function at an early stage in the apoptotic process (6). Interestingly. Bcl-2 has
been shown to act as an antioxidant (16, 17).
The formation of ROI results from the reduction of oxygen. These ROI
include hydrogen peroxide (H 2 O 2 ), superoxide anion (O 2 . - ), and hydroxyl
radical (OH . ) (reviewed in ref. 10). Both superoxide and hydrogen peroxide
are relatively unreactive compared with hydroxyl radicals, which can cause
damage to most biological molecules. Possible sources of intracellular ROI
include the depiction of cellular antioxidants such as GSH, disruption of
mitochondrial respiration, and the activation of oxidant-producing enzymes
such as NADPH oxidase.
Free radicals can activate tyrosine kinases (18). induce calcium release (19),
cause sphingomyclin hydrolysis with consequent ceramide production (20),
increase proteolytic degradation of proteins (21), and affect a varicty of
redox-sensitive targets such as transcription factors (22). Hence, oxidative
stress can lead to the activation of other signal transduction pathways.
The fluorescent probes 2',7'-dichlorofluorescin diacetate (DCFH/DA) and
dihydroethidium (DHH) may be used for the measurement of intracellular
Figure2. Peroxide levels were assessed in untreated HL60 cells (shaded line) and in cells
treated with 5 ug/ml camptothecin for 15 min (dotted line), or cells treated with 1 mM
H202 (broken line) for 30 min, as described in Protocol 2, After treatment with
camptothecin or with H2O2 there is an increase in peroxide production which can be seen
as a shift to the right in relative fluorescence (FL-1).
144
Figure 3. Superoxide levels were assessed in heat-shocked (43°C, 1 h) HL60 cells (dotted
line) and in non-heat-shocked cells (shaded line), as described in Protocol 2, Heat shock
caused an increase in superoxide anion levels in HL60 which can be seen as a shift to the
right in relative fluorescence (FL-2).
peroxide and superoxide anion levels, respectively. Both probes can be used
in a flow cytometer with a 15 milliwatt, air-cooled, argon ion laser. DCFH/DA
is cell permeant and is non-fluorescent until the acetate groups are removed
by cellular esterase activity and a peroxide group is subsequently en-
countered. Hydrolysed, oxidized DFCH/DA fluoresces at 529 nm (FL-1, log
scale) (sec Figure 2) and is unable to leave the cell, thus allowing the
measurement of intracellular peroxides by flow cytometry.
DHE is also cell permeant and is oxidized to ethidium by superoxide anion.
Once oxidized, ethidium is free to intercalate with DNA in the nucleus,
whereupon it emits fluorescence at 605 nm (FL-2; log scale) (see Figure 3).
Protocol 2. Measurement of intracellular peroxide levels

• DCFH/DA (Molecular Probes) prepared as a . FACScan flow cytometer (e.g. Becton
5 mM stock in DMSO (Sigmal. Protect from Dickinson), with an excitation source of
light and store at -20°C 4BB nm
Method
peroxide levels are to be assessed,a
4. Incubate the cells with 5 uM DCFH/DA, for 1 h at 37 °C, in the dark.
145
5. Assess the peroxide levels using a FACScan flow cytometer with
excitation and emission settings of 488 nm and 530 nm, respectively
(FL-1, log scale) (see Figure 2). For each sample collect 5000-10000
events.
aAs a positive control for peroxide production, cells can be treated with 1 mM H202 for 30-60
min.
Protocol 3. Assessment of intracellular superoxide anion

• DHE (Molecular Probes) prepared as a 10 • FACScan flow cytometer (e.g. Becton
mM stock in DMSO (Sigma). Protect from Dickinson), with an excitation source of
light and store at -20°C 488 nm
Method
1. Plate the cells in a standard 2 4-we 11 plate at a density of 5 x 105/ml.
the levels of superoxide anion are to be assessed.
4. Incubate the cells with 10 uM DHE, for 15 min at 37°C, in the dark.
5. Assess the superoxide levels using a FACScan flow cytometer with
excitation and emission settings of 488 nm and 600 nm, respectively
(FL-2; log scale) (see Figure 3). For each sample collect 5000-10000
events.
4. Determination of glutathione levels and its

oxidative state
Disruption of critically important oxidants can impair the redox status of the
cell, leading to oxidative stress. The oxidative changes reported range from
decreased levels of reduced glutathione (23, 24), a-tocopherol (23), and
protein thiols (23), to downregulation of primary antioxidant defence enzymes
such as catalase, manganese superoxide dismutase (MnSOD), Cu/Zn super-
oxide dismutase (Cu/ZnSOD), and thioredoxin (25).
GSH plays a central role in defending cells against radicals and electro-
philes (26). The protective role of GSH consists of four components, namely
chemical reaction with intracellular targets, enzymatic reduction of peroxides
146
to prevent their conversion into more reactive species, enzymatic detoxification
of electrophiles, and maintenance of the redox state of cellular thiols.
The response of cells to certain anti-tumour drugs and to ionizing radiation
can be modulated by alteration of intracellular GSH concentration (27).
Indeed, GSH has been implicated in the resistance of certain cell lines to
oxygen radicals, various toxins, alkylating agents, and other chemosensitizers
(28). In addition, GSH levels have been shown to be greater in many neo-
plasms compared with normal tissue, thus suggesting that resistance to
apoptosis may involve altered levels of GSH (29). Moreover, it has recently
been shown (30) that Fas ligation results in a rapid and specific efflux of GSH.
Severe depletion of GSH will lower the reducing capacity of a cell, enhancing
oxidative stress independent of any increase in the production of ROI.
There are a number of methods (e.g. chemical, enzymatic, chromato-
graphic, fluorimetric) which can be used to measure GSH and/or glutathione
disulfide (GSSG). Techniques that assay GSH concentration in a cell extract
measure an average concentration, usually expressed as nmol/106 cells or on
a per mg protein basis. Such measurements are not accurate if there is hetero-
geneity in the population with respect to the GSH content/cell (27). Solid
tumours are very heterogeneous in many aspects and, in fact, micro-
environmental factors known to be highly heterogeneous in solid tumours are
known to influence cellular GSH content (31). In such cases, flow cytometric
analysis using monochlorobimane (mBCl) provides more accurate and
informative data (described on p. 151).
GSH can be assayed using an enzymatic procedure, which involves its
sequential oxidation by 5,5'-dithio-bis(2-nitrobenzoic acid) (DTNB) and
reduction by NADPH in the presence of glutathione reductase. The DTNB-
glutathione reductase recycling procedure was first described by Tietze (32),
and later modified by Griffith (33). GSH is oxidized by DTNB to stoichio-
metrically give GSSG and 5-thio-2-nitrobenzoic acid (TNB) (see eqn 1).
GSSG is then reduced to GSH by glutathione reductase and NADPH (see
eqn 2). The rate of TNB formation can be followed spectrophotometrically
(at 412 nm, or 405 nm) and it is proportional to the sum of GSH and GSSG
present. The assay can also be monitored at 340 nm (NADPH).
One of the advantages of the enzymatic assay is its ability to measure

extremely low GSH levels provided that there is enough starting material. It is
also a specific and reliable procedure. It is critical, however, to set up
appropriate standards, as the method depends on an accurate standard
curve.
Because GSSG is normally present at very low concentrations compared
with GSH, the determination of GSSG is often difficult. The above assay can
be made specific for GSSG by masking any GSH present with N-ethyl-
147
maleimide (NEM) (32). Although this procedure is effective, residual NEM
must be removed as it is a potential inhibitor of glutathione reductase. This
process is not only time consuming but also a potential source of error (33).
The method described by Griffith (33) uses 2-vinylpyridine (2-VP), a reagent
which does not inhibit glutathione reductase and thus need not to be
removed. The GSH present in solutions of pH >5.5 is readily derivatized by
adding 2 ul neat 2-VP/100 ul solution and mixing the solution for 1 min.
Depending on the final pH, GSH (up to at least 15 mM) will be fully
derivatized after 20-60 min at 25 °C. Acid solutions must be at least partially
neutralized (e.g. with triethanolamine, which is very soluble and, due to its
pKa, is unlikely to increase the pH to the point where auto-oxidation is rapid)
before the reaction of GSH and 2-VP. In some circumstances the 2-VP added
is sufficient to raise the pH.
Protocol 4. DTNB-glutathione reductase recycling assay for GSH

andGSSG
Reagentsa
• PBS • NADPH (Sigma), prepared fresh as a 0.3
• 5-sulfosalicylic acid (SSA) (Sigma) mM stock solution, in stock buffer
• stock buffer: 125 mM sodium phosphate, • glutathione reductase (Sigma). The yeast
6.3 mM Na4EDTA, pH 7.5 enzyme is diluted to 50 U/ml in stock buffer
.
• DTNB (Sigma), is prepared in stock buffer GSH standards (from 100 mM stock
as a 6 mM stock solution solution), are diluted daily in 3% (w/v) SSA
Method
1. Harvest the cells (5 x 106) from culture by centrifugation (200 g, 5
min).
2. Wash the cells by resuspending in 4 ml of PBS and centrifuging as
described in step 1.
3. Lyse the cells in 1.2 ml water.
4. Mix 900 ul lysate with 100 ul 30% (w/v) SSA, and incubate for 15 min
on ice.
5. Centrifuge the sample at 12000 g for 2 min.
6. In a 1 cm light path cuvette, mix 700 ul of NADPH solution (0.21 mM),
100 ul of DTNB (0.6 mM) solution, and 100 ul GSH sample" (or water)
to give a final volume of 1 ml.
7. Equilibrate the cuvette to 30°C (e.g. water bath or incubator), for 15
min.
8. To initiate the assay, add 10 ul glutathione reductase (0.5 U/ml) and
follow the formation of TNB by monitoring the absorbance at 412 nm,
until it exceeds 2.0.c
148
9. Determine the amount of GSH from a standard curve in which the GSH
equivalents are plotted against the rate of change in X\412. Express the
level of GSH as GSH equivalents (e.g. nmol/106 cells).
' All solutions are stable for two weeks at 0°C, although the NADPH solution forms a precipitate
which must be dissolved by warming to room temperature.
6
As a blank, use a sample lacking GSH.
"The linear portion of the curve is usually between 1 and 2 absorbance units.
Protocol 5. DTNB-glutathione reductase recycling assay for

GSSG
Reagents3
• PBS • DTNB (Sigma), is prepared in stock buffer
• SSA, prepared as a 30% (w/v) solution as a 6 mM stock solution
• Z-VP (Sigma), used undiluted and stored at • NADPH (Sigma), prepared fresh as a 0.3
-20°C. Replace 2-VP if it becomes viscous mM stock solution, in stock buffer
or brownish • glutathione reductase (Sigma). The yeast
• triethanolamine (Sigma), used undiluted enzyme is diluted to 50 U/ml in stock buffer
• stock buffer: 125 mM sodium phosphate, • GSSG standards (e.g. 50 mM stock)
6.3 mM NaiEDTA, pH 7.5 (Sigma), are diluted daily in 3% (w/v) SSA
Method
1. Harvest the cells (5 x 10s) from culture by centrifugation (200 g, 5
min).
3. Lyse the cells in 1.2 ml water.
4. Mix 900 ul lysate with 100 ul 30% (w/v) SSA, and incubate for 15 min
on ice.
5. Centrifuge the sample at 12000 g for 2 min.
6. Add 2 ul of 2-VP to a 100 ul SSA supernatant aliquot'with gentle
agitation.b,c
7. Add 6 ul (45 (umol) of neat triethanolamine to the side of the test tube,
above the liquid level, and agitate the tube vigorously.d
8. Check the pH and make sure it is between 6 and 7.e
9. Allow the samples to stand at room temperature for 60 min.
10. In a 1 cm light path cuvette, mix 700 ul of NADPH solution (0.21 mM),
100 ul of DTNB (0.6 mM) solution, GSSG sample (108 ul), and 92 ul
water to give a final volume of 1 ml.
11. Equilibrate the cuvette to 30°C (e.g. water bath or incubator), for 15
min.
149
12. To initiate the assay, add 10 ul glutathione reductase (0.5 U/ml) and
follow the formation of TNB by monitoring the absorbance at 412 nm,
until it exceeds 2.0.
13. Determine the amount of GSSG from a standard curve.
"All solutions are stable for two weeks at 0°C, although the NADPH solution forms a
precipitate which must be dissolved by warming to room temperature.
'The derivatization procedure should be carried out in a fume hood, as 2-VP has a low vapour
pressure and frequent exposure to it might be irritating.
c
Run a blank containing 2-VP, but no GSSG.
d
Since triethanolamine gives a small interference with the assay, the standards should contain
an amount of amine equivalent to the samples.
"If the pH inadvertently exceeds 7, redo derivatization on a new sample using less
triethanolamine.
Several fluorescent reagents have been developed for determining cellular

levels of GSH. However, no probe is without drawbacks in quantitative
studies of live cells. The high (up to 10 mM) but variable levels of intracellular
GSH make kinetic measurements under saturating substrate conditions diffi-
cult (34, 35). The fluorescent reagents designed to measure GSH may react
with other intracellular thiols, including proteins in GSH-depleted cells (36).
Monochlorobimane (mBCl) is a reagent that reacts non-enzymatically with
GSH. It is cell-permeant and non-fluorescent until conjugated. The fluor-
escent adduct formed between mBCl and GSH can be detected by cytofluoro-
Figure4. GSH levels were mesured in untreated Jurkat cells and in cells treated with 200
ng/ml anti-Fas IgM, for various periods of time. Following anti-Fas treatment there is a
decrease in cellular GSH content, which was measured as described in Protocols. The data
(from triplicate samples) represent mean %GSH±SE of each sample in relation to the
control/untreated sample (100% GSH) and results shown are representative of three
independent experiments.
150
metry, or by flow cytometry using 50 milliwatt UV excitation and emission
integrated above 425 nm. While mBCl will react non-specifically with many
different thiols, preferential derivatization of GSH can be achieved by using a
low concentration of mBCl (short time incubation), as the reaction with GSH
is catalysed by GST and the non-enzymatic reaction is very slow (27).
Although the cytofluorimetric assay is not quantitative, it will allow the
comparison of relative GSH content in different samples (e.g. GSH content in
cancer cells before and after treatment with a particular chemotherapeutic
drug) (see Figure 4). In addition, the assay is reliable, easy, and rapid to
perform.
Protocol 6. GSH determination with monochlorobimane (mBCl)

by cytofluorometry

• mBCl (Molecular Probes), prepared as 10 . PBS
mM stock in ethanol. Protect from light and • cytofluorimeter (e.g. SLM-AMINCO)
store at-20 °C
Method
1. Harvest 1 x 106 and centrifuge at 200 gfor 5 min at room temperature.
3. Resuspend the pelleted cells in 2 ml of PBS.
4. Incubate the cells with 50 uM of mBCl for 15 min at room temperature,
in the dark.a
5. Read the fluorescence of the sample with excitation set at 395 nm and
fluorescence emission set at 482 nm (see Figure 4).
a
As a blank use 2 ml of PBS incubated with 50 uM mBCl for 15 min at room temperature.
The flow cytometric method was first described by Rice et al. (31). It was
shown that the GSH-bismane adduct, quantitated by HPLC, was formed with
similar kinetics to the appearance of cellular fluorescence, as quantitated by
flow cytometry. In addition, analysis of GSH by flow cytometry showed a
strong correlation with parallel GSH analysis by an enzymatic method over a
wide range of values for intracellular GSH. Hence, derivatization of cellular
GSH with mBCl allows measurement of single-cell GSH content by flow
cytometry. The kinetics of the reaction should be determined for each cell
type to be sure that the reaction goes to completion, and the stoichiometry of
the reaction should also be taken into account (27). For example, if the GSH
content of 106 cells is 10 nmol, then at least 10 uM mBCl would be required to
derivatize cellular GSH at a density of 106 cells/ml, and the concentration of
151
Ana P. Costa-Pereim and Thomas G. Cotter
mBCl would change as derivatization progresses. The assay does not require
large numbers of cells but may not be applicable to all cell types (e.g. cells
with low levels of glutathione S-transferase (GST). Although the assay may
not discriminate very low GSH levels, it will reveal subpopulations and the
fractions of cells contained in each, as well as their relative GSH contents.
Protocol 7. Flow cytometric analysis of GSH using

monochlorobimane (mBCl)

• mBCl (Molecular Probes), prepared as 10 • flow cytometer equipped with a 50
mM stock in ethanol. Protect from light and milliwatt UV excitation and emission
store at -20°C integrated above 425 nm
Method
1. Harvest 1 x 106/ml cells into a standard FACS test tube.
2. Stain the cells with 40 uM mBCl at room temperature for 5 min and
immediately transfer the cells to ice.
3. Read samples using a flow cytometer with excitation emission
integrated above 425 nm. For each sample collect 5000-10000 events.
DL-buthionine-S,R-sulfoximine (BSO) is a specific inhibitor of GSH syn-

thesis, which has been shown to dramatically reduce GSH levels (28) (see
Figure 5). The disruption of antioxidant mechanisms in cells can impair the
Figures.5.GSH levels can be artificially reduced by treating HL60 cells with 100 ug/ml BSO
(see Protocol 8) for various periods of time. GSH levels were assessed as described in
Protocol 6. The data (from triplicate samples) represent mean %GSH±SE and the results
shown are representative of three independent experiments.
152
redox status of the cell, leading to oxidative stress and subsequent apoptosis.
For instance, hormone-mediated apoptosis in prostate tissue is preceded by
an increase in GST expression (37). McGowan et al. (38) have shown that
artificial depletion of GSH significantly increased the levels of peroxide in
leukaemic cells and caused subsequent apoptosis.
Protocol 8. Reduction of glutathione levels in cell lines with DL-

buthionine-S,R-surfoximine (BSO), a specific inhibitor
of GSH synthesis
Reagents
• BSO (Sigma) freshly prepared as a 1 mg/ml stock in cell culture media (e.g. RPMI640)
Method
2. Incubate the cells, at 37°C, with varying concentrations of BSO (e.g.
100 ug/ml), for various time intervals (e.g. 18-24 h), in order to deter-
mine the optimal concentration of BSO.
3. Assess the levels of GSH as previously described (see Protocols 4, 6 or
7, and Figure 5).
5. Measurement of catalase in cells undergoing

apoptosis
Catalase has a dual function: (a) dismutation of hydrogen peroxide (H2O2) to
oxygen and water (catalytic activity) (see eqn 3) and (b) oxidation of
hydrogen donors such as methanol, ethanol, formic acid, and phenols, with
the decomposition of 1 mol of peroxide (peroxidic activity) (see eqn 4) (39).
Because the kinetics of catalase do not obey a normal pattern, measure-

ments of the enzyme activity at substrate saturation, or determination of the
KS is virtually impossible (40). It is not possible to saturate the enzyme with
substrate within the physiological range; however, at H2O2 concentrations
above 0.1 M there is a rapid inactivation of catalase. Hence, to avoid a rapid
decrease in the initial rate of the reaction, the spectrophotometric assay
described below [which is fundamentally that of Aebi (40)] must be carried
out at low H2O2 concentration. The decomposition of H2O2 can be followed
directly by the decrease in the absorbance measured at 240 nm in a spectro-
photometer. It follows initially (0-30 sec) a first-order reaction, with H2O2
153
concentration between 0.01-0.05 M. The decrease in absorbance per unit time
is a measure of catalase activity. Owing to the abnormal kinetics it is not
possible to define international catalase units. Thus, one unit of catalase is
defined as the amount of enzyme that catalyses the decomposition of 1 (xrnol
H2O2/min. The calculation of activity (U/ml) can be determined using eqn 5:
activity = (Ay4240/t)/e x assay volume X 1000/sample volume (5)
where AA240/t is the decrease in the absorbance at 240 nm measured spectro-
photometrically over a period of time and e is the extinction coefficient of
catalase (40 mM-1cm-1). The specific activity of the enzyme can be obtained
by dividing the activity by the protein concentration in the sample (U/mg
protein).
Protocol 9. Measurement of catalase in cells
Reagents
• Assay buffer: 50 mM phosphate buffer • H2O2 (BDH) is diluted prior to the assay with
pH7.0 assay buffer to 30 mM
Method
1. Harvest by centrifugation (200 g, 5 min) 6-10 x 106 cells.
2. Resuspend the cells in ~600 uJ assay buffer and freeze the cells at
-20°C, until the experiment is carried out.
3. Thaw the cells at room temperature and refreeze at -70°C.
4. Freeze-thaw the cells twice more, as described in step 3.a
5. Centrifuge the cells at 200 g for 5 min.
6. In a 1 cm light path cuvette, mix 1 ml assay buffer and 500 ul super-
natant.
7. To initiate the reaction add 1 ml H2O2 to the cuvette and monitor the
absorbance at 240 nm over 30 sec.b
aOnce diluted, catalase is not a very stable enzyme, therefore the assay should be carried out
within 10 min of the final freeze-thaw procedure.
bThe blank should contain 2 ml assay buffer and 500 ul supernatant.
Acknowledgements
This work has been supported by the Foundation for Science and Technology
(Fundagao para a Cidncia e a Tecnologia), Lisbon, Portugal and the Health
Research Board of Ireland. The authors would like to thank Emma Creagh
and George Royle for many helpful discussions.
154
References
1. Kerr, J.F.R., Wyllie, A.M. and Currie, A.R. (1972). fir. /. Cancer, 26,239.
2. Wyllie, A.H., Kerr, J.F.R. and Currie, A.R. (1980). Int. Rev. Cytol., 68,251.
3. Cohen, J.J., Duke, R.C., Fadok, V.A. and Sellins, K.S. (1992). Anna. Rev.
Immunol., 10,267.
4. Bortner, C.D., Oldenburg, N.B.E. and Cidlowski, J.A. (1995). Trends Cell Biol., 5,
21.
5. Martin, S.J. and Green, D.R. (1995). Cell, 82,349.
6. Buttke, T.M. and Sandstrom, P.A. (1994). Immunol. Today, 15,7.
7. Lennon, S.V., Martin, S.J. and Cotter, T.G. (1991). Cell Prolif., 24, 203.
8. McGowan, A.J., Ruiz-Ruiz, M.C., Gorman, A.M., Lopez-Rivas, A. and Cotter,
T.G. (1996). FEES Lett., 392,299.
9. Kroemer, G. (1997). Cell Death Differ., 4,443.
10. Gorman, A.M., McGowan, A.J., O'Neill, C. and Cotter, T.G. (1996). J. Neurol.
ScL, 139,45.
11. Staal, F.J.T., Ela, S.W., Roederer, M., Anderson, M.T. and Herzenberg, L.A.
(1992). The Lancet, 2,1294.
12. Briehl, M.M. and Baker, A.F. (1996). Cell Death Differ., 3,63.
13. Cerrutti, P.A. (1985). Science, 227, 375.
14. Kroemer, G. (1998). Cell Death Differ., 5, 547.
15. Salvioli, S., Ardizzoni, A., Franceschi, C. and Cossarizza, A. (1997). FEBS Lett.,
411,77.
16. Hockenbery, D.M., Oltvai, Z.N., Yin, X.M., Milliman, C.L. and Korsmeyer, S.J.
(1993). Cell, 75,241.
17. Zhong, L.T., Sarafian, T., Kane, D.J., Charles, A.C., Mah, S.P., Edwards, R.H. and
Bredesen, D.E. (1993). Proc. Natl. Acad. Sci., 90,4533.
18. Bauskin, A.R., Alkalay, I. and Ben-Neriah, Y. (1991). Cell, 66, 685.
19. Richter, C. (1993). FEBS Lett., 325,104.
20. Jayadev, S., Linnardic, C.M. and Hannun, Y.A. (1994). J. Biol. Chem., 269,5757.
21. Grune, T., Reinheckel, T., Joshi, M. and Davies, K.J.A. (1995). J. Biol. Chem.,
270,2344.
22. Schreck, R., Rieber, P. and Baeuerle, P.A. (1991). EMBO J., 10,2247.
23. Slater, A.F.G., Nobel, C.S.I., Maellaro, E., Bustamante, J., Kimland, M. and
Orrenius, S. (1995). Biochem. J., 306,771.
24. Beaver, J.P. and Waring, P.A. (1995). Eur. J. Cell Biol., 68,47.
25. Briehl, M.M., Cotgreave, LA. and Powis, G. (1995). Cell Death Differ., 2,41.
26. Bump, E.A., Yu, N.Y., Taylor, Y.C., Brown, J.M., Travis, E.L. and Boyd, M.R.
(1983). In Radioprotectors and anticarcinogens (ed. M.G. Simic and O.F.
Nygaard), p. 297. Academic Press, New York.
27. Shrieve, D.C., Bump, E.A. and Rice, G.C. (1988). /. Biol. Chem., 263,4107.
28. Green, J.A., Vistica, D.T., Young, R.C., Hamilton, T.C., Rogan, A.M. and Ozols,
R.F. (1984). Cancer Res., 44,5427.
29. Hamilton, T.C., Winker, M.A., Louie, K.G., Batist, G., Behrens, B.C., Tsuruo, T.,
Grotzinger, K.R., McKoy, W.M., Young, R.C. and Ozols, R.F. (1986). Int. J.
Radiat. Oncol. Biol. Phys., 12,1175.
30. Van den Dobbelsteen, D.J., Nobel, C.S.I., Schlegel, J., Cotgreave, LA., Orrenius,
S. and Slater, A.F.G. (1996). J. Biol. Chem., 271,15420.
155
31. Rice, G.C., Bump, B.A., Shrieve, D.C., Lee, W. and Kovacs, M. (1986). Cancer
Res., 46, 6105.
32. Tietze, F. (1969). Anal. Biochem., 27, 502.
33. Griffith, O.W. (1980). Anal. Biochem., 106, 207.
34. Van der Ven, A., Mier, P., Peters, W.H., Dolstra, H., Van Erp, P.E., Koopmans,
P.P. and Van der Meer, J.W. (1994). Anal. Biochem., 217,41.
35. Hedley, D.W. and Chow, S. (1994). Cytometry, 15,349.
36. Nair, S., Singgh, S.V. and Krishan, A. (1991). Cytometry, 12, 366.
37. Jung, K., Seidel, B., Rudolph, B., Lein, M., Cronaeur, M.V., Henke, W., Hampel,
G., Schnorr, D. and Loening, S.A. (1997). Free Radic. Biol. Med., 23,127.
38. McGowan, A.J., Bowie, A.G., O'Neill, L.A.J. and Cotter, T.G. (1998). Exp. Cell
Res., 238, 248.
39. Chance, B. (1947). Acta Chem. Scand., 1,236.
40. Aebi, H. (1984). In Methods in enzymology (ed. L. Packer), Vol. 105, p. 121.
Academic Press, London.
156
9
Methods of measuring Bcl-2 family

proteins and their functions
JOHN C. REED, ZHIHUA XIE, SHINICHI KITADA,
JUAN M. ZAPATA, QUNLI XU, SHARON SCHENDEL,
MARYLA KRAJEWSKA, and STANISLAW KRAJEWSKI
1. Introduction
Bcl-2 family proteins play critical roles in the regulation of programmed cell
death and apoptosis (reviewed in refs 1-4). Changes in the levels or
bioactivities of these proteins are associated with a variety of physiological
processes where cell death occurs, including fetal development, haemato-
poietic and immune cell differentiation, oogenesis, mammary gland involution,
and normal cell turnover in the epidermis, gut, and several other tissues.
Moreover, pathological alterations in the expression of Bcl-2 family proteins
have been documented in cancer, autoimmunity, immunodeficiency, heart
failure, stroke, and other diseases (reviewed in refs 5-9). Consequently,
methods for assessing the relative levels and bioactivities of Bcl-2 family
proteins can be of interest to scientists in a board range of disciplines.
Here, we describe some of the methods routinely employed in our
laboratory for this purpose. Many of the techniques described are specifically
intended for analysis of the Bcl-2 (anti-apoptotic) or Bax (pro-apoptotic)
proteins or mRNAs, but can be modified readily for applications to other
members of the Bcl-2 family.
2. Immunoblot analysis
The analysis of Bcl-2 family proteins by immunoblotting involves: (a) lysis of
cells or processing of tissues for extraction and recovery of intact proteins; (b)
SDS-PAGE separation of proteins and transfer to either nitrocellulose or
nylon membranes; and (c) detection of antigens using antibody-based
methods. In addition, the reprobing of blots with additional antibodies is
often an important consideration. Here, we describe methods which have
provided successful for extraction of Bcl-2 family proteins from cultured cells
and tissues, and for immunodetection of these proteins once immobilized on
John C. Reed et al.
membranes. A procedure developed in our laboratory which permits multiple
reprobings of blots is also described (10).
2.1 Cell lysis and tissue processing procedures
2.1.1 Cultured cells
Protocol 1.
Method
1. (a) Suspension cells are collected by centrifugation from culture
medium, (b) For adherent cells, remove the culture medium com-
pletely from the culture dish. Add 5 ml of PBS and shake gently to
wash cells. Then remove PBS completely. Add 5 ml of ice-cold PBS
containing PMSF and scrape off with the aid of a rubber policeman (do
not trypsinize adherent cells). Transfer cells to a 15 ml centrifuge tube
and centrifuge at 500 g for 5 min.
2. Remove the supernatant carefully from cell pellets and add 1.5 ml of
ice-cold PBS/PMSF. Pipette cells gently to resuspend and transfer the
cells to a 1.5 ml microcentrifuge tube.
3. Centrifuge at 500 g for 0.5-1 min with a swinging bucket rotor at 4°C.
4. Remove the supernatant carefully and add either TEN-T solution
(described on p. 160) or RIPA buffer with protease inhibitors. Pipette to
resuspend the cell pellet. The volume of lysis solution depends on the
cell numbers harvested. We usually add 200 ul of TEN-T solution to 1 x
107 cultured cells.
5. Keep on ice for 15 min. Then centrifuge at 10000 g for 20 min. at 4°C
(in the cold).
6. Recover supernatant and store at -80°C.
2.1.2 Tissues
Tissue specimens are either frozen in liquid nitrogen (N2) and tissue powder is
prepared by crushing in a mortar and pestle in N2 followed by solubilization
with a lysis buffer, or fresh tissue pieces are mechanically homogenized and
sonicated in lysis buffers.
Fresh tissues
Protocol 2.
Method
1. Cut the tissue sample with scalpel blades into small pieces and
transfer them to 1.5 ml Eppendorf tube.
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9: Methods of measuring Bcl-2 family proteins
2. Immediately add RIPAa lysis buffer to the tissue and homogenize using
a motor-driven pestle (e.g. KONTES Scientific Glassware/Instruments,
Vineland, NJb). The volume of lysis buffer depends on the volume of
sample harvested. We usually add lysis buffer at a 5:1 ratio of buffer to
tissue volume (5 vol. RIPA buffer:1 vol. tissue).
3. Incubate on ice for 15 min.
4. Centrifuge 800-1600 g for 20 min at 4°C to pellet debris.
5. Recover the supernatant and store at -80°C.
* An alternative to RIPA solutions is to use a modified Laemmli solution. Resuspend tissues in
boiling 1 x Laemmli buffer lacking bromophenol blue dye and 2-mercaptoethanol at a 5:1 ratio
of buffer to tissue volume. Homogenize and centrifuge at 800-1600 g for 20 min at room
temperature (SDS will precipitate at 4°C). Store the supernatant at -20°C.
''Alternatively, disrupt tissue using a probe sonicator. A 25 |J.m probe and ~4 cycles of 0.5
minutes each typically works well. (Avoid heating lysates).
Frozen tissues
Frozen tissue specimens may either be derived from tissue samples that were
placed directly in liquid nitrogen (and stored in the same or at -80 °C) or
derived from histological specimens which were frozen in OTC compound
(outside tissue compound, Tissue Tek-II, USA, VWR) for cryosectioning. The
latter typically involves submerging in cold isopentane which is sitting in a
dry-ice-acetone bath. The frozen material is then placed into a pre-cooled
plastic mould and OTC compound is poured over the tissue, thus encasing it
in a 'plastic-like' covering. The samples are then stored at -80 °C and can be
shipped on dry-ice.
If samples are embedded in OTC, this covering must first be removed.
Place the tissue specimen in a petri dish that has been pre-cooled on dry-ice.
Working quickly, use scalpel and forceps to remove the OTC coating.
Protocol 3.
Method
1. Immediately submerge the tissue in liquid nitrogen in a pre-cooled
mortar and pestle.
2. Grind the tissue to a fine powder and transfer with the remaining
liquid N2 into a polypropylene centrifuge tube. (Caution. Do not close
the tube completely or it will blow up! Close the cap partially to
prevent tissue from bubbling out and hold in a partially closed
position with a gloved finger until 'boiling' of the liquid N2 subsides.)
3. When the liquid nitrogen has nearly all evaporated, add 1-2 volumes
(at least!) of RIPA buffer with protease inhibitors.
4. This will initially freeze. Let it thaw on ice.
5. Vortex vigorously.
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6. Sonicate (e.g. Heat-Systems Ultrasonicator using the standard 1.5 mm
diameter tip and 1-3 sec pulses and power settings of 2-4). If the
sample heats beyond ~ room temperature, put on ice and allow to
cool. Sonicate until the solution is no longer viscous and has become
clear, without residual chucks of tissue.
7. Centrifuge in a microcentrifuge (16000 g) for 20 min and transfer the
supernatant to a fresh microcentrifuge (1.5 ml) tube.
8. Store the supernatant at -80°C or keep on ice and proceed directly to
protein quantification and subsequent SDS-PAGE/immunoblot analysis.
2.1.3 Protein quantification

To quantify the total protein concentration in lysates, we use the bicinchoninic
acid (BCA) protein assay reagent (PIERCE) for Triton X-100-solubilized
RIPA lysates (11) and for Laemmli lysates, provided fi-mercaptoethanol has
been withheld until ready to boil, and load samples in gels.
Use the Coomassie protein assay reagent (PIERCE) for Laemmli lysates
because SDS interferes with the BCA method.
2.1.4 Lysis solutions
TEN-T solution. This solution is generally reliable for extraction of Bcl-2
family protein from most cultured cells. A modified version is useful for co-
immunoprecipitation experiments in which 0.2-1 % (v/v) NP-40 is substituted
for Triton X-100. Phosphatase inhibitors are optional, depending on whether
experiments entail assessment of phosphorylation of Bcl-2 family proteins.
150 mM NaCl
1% Triton X-100
10 mM Tris (pH 7.4)
5 mM EDTA (pH 8.0)
Make from autoclaved solutions. Store at room temperature but add
protease inhibitors fresh each time to the aliquot of the solution needed for
your experiments.
RIPA solution. This lysis solution reliably extracts Bcl-2 family proteins for
cultured cells and many tissues, including frozen tissues. It can be stored at
room temperature and protease inhibitors are added immediately prior to
use. Phosphatase inhibitors are optional, depending on whether the experi-
ments entail assessment of phosphorylation of Bcl-2 family proteins.
10 mM Tris (pH 7.4)
150 mM NaCl
1% Triton X-100
160
1% deoxycholate
0.1% SDS
5 mM EDTA
Laemmli solution. Ensures vigorous extraction of proteins from tissue
specimens.
6.25 ml of 0.5 M Tris (pH 6.6)
11.25 ml of 10% SDS
5 ml of glycerol
Bring volume to 45 ml
Store at room temperature
When used as a loading solution for SDS-PAGE, the solution is typically
prepared at 2 X concentration and mixed with an equal volume of sample
lysate. In this case, BPB (bromophenol blue; 5 mg per 45 ml) is added and
10% 2-mercaptoethanol is included fresh each time to the portion needed.
Protease inhibitors. Table 1 lists the protease inhibitors.
Phosphatase inhibitors (final concentrations).
10 mM sodium (3-glycerophosphate (pH 7.4)
1 mM Na3VO4 (sodium orthovanadate)
SmMNaF
2 mM Na4P2O7 (pyrophosphate)
50 mM 4-nitrophenyl phosphate
1 uM microcystin-LR
2.2 Immunoblotting procedure

The methods for SDS-PAGE separation and transfer of Bcl-2 family proteins
to membranes are not unusual, and thus detailed protocols are not provided
here. We have, however, devised an immunoblotting method which permits
sequential detection of multiple antigens on a single protein blot without
Table 1. Protease inhibitors
Protease inhibitor Stock solution Solvent Dilution

PMSF (phenylmethyl- 100 mM Methanol 1:100
sulfonyl fluoride)
Aprotinin (Sigma, cat. no. A-6279) 28TIU/ml PBS 1:100
Leupeptin 5 mg/ml PBS 1:100
Benzamidine 100 mM PBS 1:100
Pepstatin 0.7 mg/ml Methanol 1:1000
All of these are stored at -20°C in 1 ml aliquots, except aprotinin solution which is stored at 4°C.
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stripping off prior antibodies (10). The procedure is described here. It has
worked well in our hands for detection of multiple members of the Bcl-2
family of proteins, using antibodies generated in our laboratory or from
commercial sources.
The multiple antigen detection (MAD) procedure utilizes horseradish
peroxidase (HRPase)-based detection with a chemiluminescent substrate.
After detection by enhanced chemiluminescence (ECL) with exposure to X-
ray film, the antigen-antibody complexes on the blot are treated with a
chromogenic substrate [either 3,3'-diaminobenzidine (DAB) or the "SG"
substrate (Vector Labs, Inc.)] which renders the antigen-antibody-HRPase
complexes unreactive in subsequent reprobings of the same membrane with
additional antibodies using the same detection method. Because no stripping
is involved, immobilized proteins are not lost from the membrane, thus
allowing for multiple sequential reprobings of the same membrane with
different primary antibodies (>12) and retention of strong signal intensities
for sequential antibody probings.
2.2.1 Multiple antigen detection (MAD) procedure
SDS-PAGE is typically performed using 12% gels, loading either 50-100 or
10-25 ug of total protein per lane, depending on whether one is using a
standard size gel (e.g. 10 cm X 14 cm) or a minigel (4 cm X 6 cm). Cell lysates
should be mixed with an equal volume of 2 X Laemmli buffer containing 10%
2-mercaptoethanol (Sigma Inc.) and boiled for 5 min prior to loading in
gels. Proteins are transferred from gels to either nitrocellulose membranes
(0.45 um; Biorad) or PVDV nylon membranes (Amersham Life Sci) using
Tris-glycine buffer [25 mM Tris (pH 8.3), 192 mM glycine, 20% methanol,
0.01 % SDS]. Typically, we transfer at 280 mA for 2 h when working with
minigels and at 350 mA for 3.5 h when preparing standard-size gels.
Protocol 4.
Method
11. Wash the blot for 5 min in modified PBS (mPBS) solution using at
least 0.5 ml per cm2 blot.
All incubation steps described here should be performed with gentle agita-
tion on a rotating or rocking platform shaker at room temperature (unless
an overnight incubation is involved, in which case 4°C should be used).
12. Transfer the nitrocellulose membranes to —0.25-0.5 ml/cm2 pre-
blocking solution (TN-TBM) with optional 1% normal goat serum and
incubate for 1 h at room temperature.
13. Decant off the pre-blocking solution and save (can be stored at-20°C
and reused —10 times).
162
14. Incubate the blot overnight at 4°C in -0.25 ml/cm2 TN-TBM (see *,
p. 165, 2.2.3) containing 0.2% normal goat serum (or serum from
whatever species the secondary antibody was raised in) and primary
antibody at an empirically determined appropriate dilution [most
high-titre rabbit polyclonals can be used at ~1:1000-1:5000 (v/v),
whereas monoclonals are employed at ~0.1-1.0 ug/ml].
For antisera raised using ovalbumin as the carrier protein, also add
50 ug/ml of ovalbumin (Sigma, Inc.) to the TN-TBM.
15. Decant off the primary antibody solution and save (with high-titre
polyclonal antisera, this solution can be stored at -20°C and reused
typically ~5-10 times).
16. Rinse the blot briefly in mPBS and then wash three times for 30 min
each with >0.5 ml/cm2 of mPBS.
17. Incubate the blot for 2 h to overnight in -0.25-0.5 ml/cm2 of TN-TBM
containing 0.2% goat serum (or other appropriate non-immune
serum from the same species as the source of the secondary
antibody), and secondary antibody.
The secondary antibody detection method can involve use of either
HRPase-conjugated anti-lg as a single-step reagent, or biotinylated anti-lg
with subsequent incubation with HRPase-avidin-biotin complex (ABC)
reagent. For HRPase-conjugated anti-lg, we use affinity-purified reagents
at 1:3000 (v/v) (-0.65 fig/ml) for goat anti-rabbit Ig and goat anti-mouse Ig
and at 1:3000 (v/v) (-0.2 ug/ml) for sheep anti-mouse Ig. For avidin-
biotin-based detection, we typically employ biotinylated goat anti-rabbit
IgG at 1-1.5 ug/ml, anti-mouse IgG at 0.6-1.0 ug/ml, or anti-mouse IgM at
0.6-1.0 gu/ml.
18. Decant off the secondary antibody solution and save at-20°C (can be
reused —2-5 times), rinse the blots once with PBS, and wash three
times for 30 min each in =0.5 ml/cm2 of mPBS.
19. If using the avidin-biotin method, prepare HRPase-ABC reagent by
dispensing two drops of Vector Labs solution A into 5 ml 0.1 M Tris
(pH 8.2), mixing, and then adding two drops of the manufacturer's
solution B, and allowing the complex to form for 1 h. Incubate the
washed blot in 0.25-0.5 ml/cm2 of HRPase-ABC solution for 45 min to
1 h. Save the ABC solution at -20°C (can be reused ~10 times).
10. Rinse in PBS and wash the blot three times for 10-30 minutes each in
mPBS.
11. Antibody detection is then accomplished using a chemiluminescent
substrate reagent (Amersham, Inc.) with exposure to X-ray film
(Eastman-Kodak, Inc., XOMAT-AR) according to the manufacturer's
instructions. Eliminate excess fluid from the membrane prior to ECL,
then place the blot into a plastic bag and add just enough ECL reagent
to ensure complete coverage of the blot surface. Immediately expose
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John C. Reed et al.
to X-ray film in the dark. Exposure times vary widely, from a few
seconds to 5 minutes. We typically develop after 15-30 sees initially,
and then adjust the exposure time based on this result.
12. Rinse the blot in PBS for 3 min, and add 0.25 ml/cm2 'activated' SG
chromogenic substrate (Vector Labs, Inc.). For this purpose, the SG
substrate is prepared by dispensing three drops of Vector SG sub-
strate into 15 ml of PBS, mixing well, and then adding three drops of
H2O2 (0.5%) and mixing. DAB is also suitable but tends to cause more
damage to blots and thus reduces the number of reprobings possible.
It is important to designate containers in the laboratory for SG substrate
use and not to use these for ECL. The SG substrate is very difficult to
wash off plastic and will compete with ECL reactions. (Bleach, however,
can remove most SG substrate from plastic containers.)
13. Incubate for 15-30 min.
14. Discard the substrate solution and wash the blot twice for 15 min
each in mPBS.
15. Transfer the blot to a clear (non-SG) container and resume at step 4 to
apply another primary antibody. Alternatively, cover the blot in plastic
wrap while moist and store at -80°C between pieces of cardboard
held together with rubber bands.
" Non-specific bands. If non-specific antibody reactivity is seen on blots, an additional step can
be added to the procedure which minimizes non-specific background. This involves first
incubating the blot with secondary antibody alone at step 4, instead of applying the primary
antibody, and then proceeding through the protocol (steps 8-10 and then steps 12-15). Even
better results are typically obtained by performing a pre-screen using pre-immune serum or a
negative control monoclonal antibody in substitution for the desired primary antibody (at step
4), followed by secondary antibody (steps 4-10 and then steps 12-15). In these cases, the pre-
screen ing development of the blot need not include use of the ECL substrate (skip step 11).
Instead, proceed directly to colorimetric (SG or DAB) 'burn-out' of the non-specific bands
detected by pre-immune or secondary antibodies. After the pre-screening has been
accomplished, the protocol can be resumed at step 4, now using the desired primary antibody;
however, it is sometimes useful to repeat the pre-blocking (step 2) before addition of primary
antibody. Moreover, for best results, the secondary antibody solution, which has been pre-
adsorbed on the blot during pre-screening, should be reused when probing the same blot with
the desired primary antibodies. This blot pre-treatment with secondary antibody can
substantially reduce the background in ECL-based detection procedures.
b
Primary antibody sequence. The membrane will become progressively darker with repeated
cycles of antibody probing and SG substrate treatment. Most epitopes appear to withstand this
problem, but some do not. We therefore empirically determine which primary antibodies
produce weaker signals (either because the litre is low, the affinity is low, or the antigenic
epitope is labile) and perform the immunodetections using those antibody reagents first,
followed by more robust antibodies.
c
Overlapping bands. The quenching of HRPase using SG or DAB substrates creates an
insoluble, coloured precipitate on the membrane. The effected area (bands) on the membrane,
therefore, is typically unavailable for subsequent rounds of ECL-based immunodetection.
Thus, if two proteins co-migrate in SDS-PAGE, it may prove difficult to detect them using this
method. For the same reason, one cannot use this method using two or more antibodies that
react with different epitopes on the same protein.
164
2.2.2 Materials
The chromogenic HRPase substrate SG (cat. no. SK-4700), avidin-biotin
complex (ABC) with HRPase (cat. no. PK-6100), biotinylated goat anti-
rabbit IgG (cat. no. BA-1000), horse anti-mouse IgG (cat. no. BA2080), and
goat anti-mouse IgM (cat. no. BA-2020) can be purchased from Vector Labs,
Inc. (Burlingame, CA). HRPase-conjugated goat anti-rabbit IgG (cat. no.
172-1013) and goat anti-mouse IgG (cat. no. 170-6520) from Biorad, Inc.
(Richmond, CA). HRPase-conjugated sheep anti-mouse Ig can be obtained
from Amersham, Inc. (cat. no. NA-931) (Buckinghamshire, England). The
ECL Western blotting detection reagent (cat. no. RPN2106; Amersham Inc.)
is prepared according to the manufacturer's instructions. The chromogen,
3,3'-diaminobenzidine (DAB) can be purchased from Sigma, Inc. (St. Louis,
MO; cat. no. D-5637) and dissolved at 0.5 mg/ml in 0.1 M Tris (pH 8.2).
Immediately before use, 0.1 ml of 1% H202 is added to 10 ml of DAB solution
followed by filtration through a 0.45 um filter (Acrodisk; Millipore, Inc.).
3-Amino-9-ethylcarbasole (AEC) (Sigma, Inc.; cat. no. A-5754) is dissolved
first at 25 mg per 1 ml of W,Af-dimethyl formamide and then added to 50 ml of
acetic acid buffer (0.1 M; pH 5.5) and filtered through Whatmann 3MM
paper. Immediately before use, 25 jxl of 30% H2O2 is added to 50 ml of the
AEC-containing solution. The chromogen 3,3',5,5'-tetramethylbenzidene
(TMB) can be purchased as a solution from Promega, Inc. (cat. no. W4121).
Primary antibodies employed for these studies include rabbit polyclonal
antisera generated against synthetic peptides corresponding to sequences in
the human (h) Bcl-2, hBax, hBcl-X, hMcl-1, and hBak proteins, mouse (m)
Bax, or monoclonal antibodies to hBAD (12-19). Our antibodies are avail-
able commercially from various vendors (PharMingen; Chemicon; DAKO;
Stratagene). Comparable antisera specific for these and other Bcl-2 family
proteins are also available from a variety other vendors.
2.2.3 Solutions
Sodium acetate buffer (0.2 M, pH 5.5) is prepared by combining 150 ml of 0.2
M glacial acetic acid and 350 ml of 0.2 M sodium acetate.
Modified phosphate-buffered saline (mPBS) is 120 mM NaCl, 11.5 mM
NaH2PO4, 30 mM K2HPO4 (pH 7.5) and should be prepared fresh each week.
TN-TBM solution is 10 mM Tris (pH 7.7), 150 mM NaCl, 0.01 % (v/v)*
Triton X-100, 2% (w/v) bovine serum albumin (BSA) fraction V (Sigma, cat.
no. A-6793), and 5% skimmed milk (Difco Labs, cat. no. 0032-17-3), with
either 0.01% NaN3 or 0.01% thimerosal.
3. Detection of Bcl-2 family proteins by flow

cytometry (FAGS)
Bcl-2 family proteins are intracellular antigens and thus their detection by in-
direct immunofluorescence and subsequent analysis by flow cytometry (FACS)
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John C. Reed et al.
requires permeabilization of the cells using non-ionic detergents. Procedures
are described here specifically for FACS analysis of Bcl-2 but are readily
adapted to detection of other Bcl-2 family members by adjustment of the choice
and amount of primary antibody employed. The immunodetection of Bcl-2 or
other Bcl-2 family proteins can be combined with traditional cell-surface
marker analysis, as well as with DNA content analysis or TUNEL assays for
detecting cells with fragmented DNA, in two- or three-colour FACS assays.
3.1 Indirect immunofluorescence procedure
Protocol 5.
Method
11. Wash the cells three times with ice-cold PBS.
12. Aliquot 2.5 x 106 cells per 12 mm x 75 mm polystyrene centrifuge
tube and fix for 10 min on ice in PBS containing 2% para-
formaldehyde (2 ml).
13. Add 0.1 ml of 1% Triton X-100 (in PBS) and incubate on ice for 10 min.
14. Wash three times with 3 ml ice-cold PBS. [Washes consist of centrifug-
ation at 1100 r.p.m. in a Sorval or IEC table-top (-350 g) with swing-
ing bucket rotor for 5 minutes. Then decant quickly the supernatant
and tap the tube once while holding upside down to knock-out excess
fluid. This leaves -100-200 \d of PBS after each wash.]
15. Decant the supernatant and resuspend the cell pellet in the residual
PBS (-100-200 ml). Add 10 ul of pre-blocking solution [PBS con-
taining 10 mg/ml human IgG (Cappel, Inc.)] and incubate on ice for
10 minutes.
16. Add 1.25-10 JJL! of PBS containing anti-Bcl-2 or other monoclonal
antibody (typically 0.25-2 ug of antibody is appropriate) and incubate
on ice for 30 min.
As controls, the same amount of a control immunoglobulin which is
matched for species (mouse, rat, hamster), isotype (lgG, IgM), and subclass
(lgG1, lgG2a, lgG2b) is added in a similar mannerto a duplicate cell sample.
17. Wash the cells with 3 ml of ice-cold PBS, three times.
18. After the last wash, decant the supernatant and resuspend the cell
pellet in residual PBS (-100-200 ul).
19. Add secondary antibody:
(a) 20 ul of PE-conjugated rat anti-mouse IgGl (6.25 (ug/ml) with 2%
gelatin and 0.1% sodium azide (Becton Dickinson) in PBS.
or
(b) 100 ul of 1:100 dilution in PBS of FITC-conjugated goat anti-
hamster IgG (H+L) at 1.4 mg/ml (Jackson ImmunoResearch
Laboratories, Inc., West Grove, PA.).
166
10. Following incubation with the secondary antibody on ice for 30 min,
wash the cells again with 3 ml of ice-cold PBS, three times.
11. Fix the cells in 0.5 ml of 1% formaldehyde in PBS (use methanol-free
formaldehyde: purchased from Polysciences, Inc., Warrington, PA, as
a 10% formaldehyde ultrapure EM grade).
12. Analyse within a few days by FACS, keeping at 4°C and protected
from light. (Actually, when fixed in formaldehyde and stored in the
dark, these can be analysed up to 1 month later). There is no need to
wash out formaldehyde before FACS analysis.
3.2 Antibodies
1. Bcl-2 monodonals. The most widely used monoclonal antibodies for
detecting human Bcl-2 protein are MablOO and Mabl24, both mouse IgG1,
which are available from DAKO, Inc. (20). The 4D7 monoclonal (21),
available from PharMingen, Inc., is also a mouse IgGj and is suitable for
FACS analysis. The 6C8 antibody is a hamster IgG2a (22) (PharMingen,
Inc.). For FACS-based detection of mouse Bcl-2 protein, we have used the
3F11 monoclonal with success (23,24), a hamster IgG2a (PharMingen, Inc.).
2. Control antibodies. As controls, the same amount of mouse IgGj (in the
case of DAKO antibody or 4D7 antibody) or hamster IgG2a (in the case of
6C8) are added to duplicate cell samples.
• mouse IgGj negative control (Dako, Inc., cat. no. 931)
• hamster IgG isotype standard (Pharmingen, Inc., cat. no. 11091D)
3. Primary antibody optimization. For optimal results, the amount of primary
antibody employed should be titered for each type of cell undergoing
FACS analysis. Using too much can reduce the signal/noise ratio. For
example, based on titration experiments performed using leukaemic B
cells from patients with chronic lymphocytic leukaemia (B-CLL), we have
determined that 0.32-0.65 u,g per sample of anti-Bcl-2 antibody MablOO
(DAKO, Inc.) is optimal for FACS quantification of Bcl-2 protein levels,
whereas 0.32 u.g was optimal for the anti-Bcl-2 antibody 4D7 (PharMingen,
Inc.). Note that these concentrations are 5-10 times less than those
recommended by the manufacturers.
4. Northern blot analysis of BCL-2 mRNA

Reproducible detection of BCL-2 mRNA can be challenging, particularly in
human tissues and cells, because the mRNA is subject to several alternative
splicing events, differential termination/polyadenylation site selection, and
variable transcription initiation site usage. This results in several mRNA
species, most of which contain an intact open reading frame for the Bcl-2
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John C. Reed et al.
protein, but which vary in length and thus fail to form a tight band upon
agarose gel electrophoresis and subsequent analysis by Northern blotting.
Partly for this reason, as well as because BCL-2 is a relatively low abundance
mRNA in many tissues, it is often necessary to use polyA-selected mRNA.
In humans, BCL-2 transcripts vary in size from 5.5 to 8.5 kb. In addition,
shorter transcripts of 3.0-3.5 kb can also be seen which contain an open
reading frame for a shorter protein, Bcl-2-p and which arise through an
alternative splicing mechanism (25). The Bcl-2-p protein, however, is rarely if
ever seen in cells, suggesting either that it is an unstable protein or that these
shorter transcripts are inefficiently translated. In mice, bcl-2 mRNAs are
generally -7.5 kb (full-length Bcl-2) and -2.5 kb (Bcl-2-p) (26).
The 5' portions of the BCL-2 gene are GC-rich, and thus hybridization
probes derived from this portion of the gene or from cDNAs corresponding to
this region are difficult to work with. Background is typically high and cross-
hybridization to the 28S rRNA band is problematic. Probes derived from the
3'-untranslated region (3'-UTR) of BCL-2 cDNAs or the corresponding exon
from the BCL-2 gene are preferred and generally give clean results under
standard high stringency conditions. In fact, using 32P-labelled hybridization
probes from the 3'-UTR, it is often possible to hybridize at usual conditions of
stringency in the presence of 50% formaldehyde at 42 °C, and then to wash at
relatively low stringency. This results in Northern blot results that are
sufficiently free of background but in which the BCL-2 bands are stronger,
thereby improving signal to noise ratios.
4.1 General guidelines for RNA blotting

The methods for preparation of RNA, gel electrophoresis, and transfer to
nylon membranes can be found in any basic textbook on molecular biological
methods. In general, however, we obtain best results using RNA prepared
by the guanidinium thiocyanate-phenol-chloroform extraction method of
Chomczynski and Sacchi (27). We also prefer formaldehyde gels as opposed
to glyoxyl and have enjoyed good success with Gene Screen nylon membranes
(DuPont, Inc.), though certainly nylon membranes made by other manu-
facturers should be adequate. The transfer is done in 10 X SSC. A brief
alkaline treatment (5-15 min) prior to transfer can improve the transfer
efficiency but also reduces the signal in many cases and thus we do not
routinely employ it. To encourage transfer of the relatively large BCL-2
mRNAs, we typically use a 0.8% agarose gel and allow the electrophoresis to
proceed until the bromophenol blue marker has run off the gel. This brings
the BCL-2 mRNA down towards the centre of the gel and probably ensures
better subsequent transfer. We also transfer for a full 24 h and change the
blotting papers several times during the transfer, replenishing the transfer
solution as needed. A T75 cm2 tissue-culture flask, filled with water, and
placed on its side makes a good weight for placement on top of the paper
168
towels during transfers. We do not have experience with the recently
described downward capillary transfer technique (28), which has been
claimed to improve transfer efficiencies. In the past, we have added ethidium
bromide (7.5 ug) directly to the RNA sample during loading into the gel, but
recent reports that ethidium impairs transfer suggest that this may not be a
good practice (29). Adding the ethidium directly, however, allows one to
assess the integrity of the RNA and requires no destaining prior to photo-
graphing the gel. We do, however, limit the exposure of the ethidium-stained
RNA gels to < 3 secs during the photography, to minimize damage. After
transfer in 10 X SSC, the membrane is rinsed briefly in 2 X SSC, placed on
3M paper wetted in 2 X SSC, and UV cross-linked (1200 joules), then dried
on 3M paper and baked in a vacuum oven at 80 °C for 1 h.
4.2 Pre-hybridization and hybridization procedures

Use RNase precautions and RNase-free solutions prepared using diethyl
pyrocarbonate (DEP)-treated dH2O.
Protocol 6.
Method
11. Float the dry membrane, RNA side up, on DEP-treated dH2O. When
completely wetted, submerge the filter.
12. Place into a heat-sealable plastic bag.
13. Pipette 10 ml of pre-hybridization/hybridization solution into the bag.
14. Heat-seal the bag, then cut a corner off, and careful expel all bubbles.
Seal.
15. Pre-hybridize submerged in a 42°C water bath with gentle shaking for
6 h up to overnight. Occasionally, massage the bag to ensure uniform
distribution of solution.
16. Cut a corner of the bag and expel the pre-hybridization solution.
17. Pipette into the bag 10 ml of pre-warmed (42°C) hybridization
solution containing 106 cpm per ml of 32P-labelled DMA probe.
18. Carefully expel bubbles, catching any radioactive fluid on paper
towels. Heat-seal the bag and test for leaks.
19. Incubate in the 42°C bath overnight with gentle shaking. Occasionally
massage the bag to mix the solution.
10. Expel radioactive hybridization solution into an appropriate con-
tainer. Remove the blot and wash for 20 min at room temperature in
2 x SSC/0.1% SDS (200-250 ml per blot) with shaking.
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John C. Reed et al.
11. Wash at 68°C in pre-warmed 2 X SSC/0.1 % SDS for 15 min with
vigorous agitation.
12. Rinse briefly (3-5 minutes) in 2 X SSC (room temperature) to remove
excess SDS.
13. Dry the membrane briefly, RNA side up, on 3M paper but leave
slightly damp.
14. Cover in plastic wrap and expose to X-ray film using intensifying
screens at-80°C.
15. If the background is high, re-wet the membrane in 2 X SSC and wash
at 68°C for 15-30 min in 1 x SSC/0.1% SDS. Expose to film. If the
background is still high, try successive washes (with exposures to
film in between) using 0.5 x and then 0.1 x SSC with 0.1 % SDS.
4.3 Solutions
All ingredients are made from RNase-free solutions. Refer to any standard
textbook on molecular biology for details on the preparation of the stock
solutions required (30). Sodium-heparin is purchased from Sigma Chem-
icals, Inc., dissolved in DEP-treated water, and stored in 0.5 ml aliquots at
-20 °C.
Make the pre-hybridization/hybridization solution fresh each time,
preparing enough solution for both the pre-hybridization and hybridization.
After pre-warming to 42 °C, remove half for hybridization, and store at
4°C until ready to perform the hybridization (if doing overnight pre-
hybridization), then pre-warm to 42°C again. The denatured DNA should be
added to both the pre-hybridization and hybridization solution just before
use.
Per 50 ml
Formamide (deionized) 25ml
1 M Tris-base (pH 7.4) 2.5ml
5 M NaCl 10ml
50% dextran sulfate 10ml
10% SDS 5ml
50 X Denhardt's solution 1ml
50 mg/ml Na-heparin 0.5ml
Sheared or sonicated salmon sperm DNA at 10 mg/ml in TE buffer is boiled
for 10 min, quick-cooled on ice for 5 min, and 0.25 ml added per 10 ml.
DNA probes are radiolabelled by the random primer method, purified by
centrifugation through Sephadex G50, and boiled in TE buffer for 10 min,
170
then cooled on ice for 5 min before addition to hybridization buffer. The
unused probe can be stored at -20°C and used for up to 2 weeks in many
cases. The specific activity of probes should be ~109 cpm/jjig.
5. Reverse transcriptase-polymerase chain reaction

(RT-PCR)
An alternative to Northern blotting for detecting and estimating relative
amounts of BCL-2 mRNA is RT-PCR. If performed in a semi-quantitative
fashion, this technique can allow for monitoring of fluctuations in BCL-2
mRNA levels within cells and requires far fewer cells than Northern blotting
experiments. We have used the RT-PCR approach, for example, to monitor
the effects of antisense oligonucleotides targeted against the human BCL-2
mRNA, which induce an RNAse-H-like degradation of mRNAs, as well as
for assessing the effects of p53 on bcl-2 mRNA levels in murine leukaemia
cells (31-33).
Total RNA can be prepared by either the guanidinium isothiocyanate pro-
cedure described above (27) or using a commercially available, streamlined
version of the method involving the TRIzol™ reagent (BRL/Gibco, Inc.). In
some cases, it may be advisable to check 1 u.g of the RNA in a minigel
(formaldehyde-containing) to assess integrity of the 28S and 18S rRNA
bands, assess whether contaminating DNA is present, and verify the
quantification results (i.e. the starting amount is approximately the same for
all samples).
The procedure described below involves use of a recombinant version of
Moloney Virus-derived RTase, Superscript™ (BRL/Gibco, Inc.) for the
cDNA synthesis and Taq DNA polymerase (Perkin-Elmer, Inc.) for the
PCR, but other RTases and heat-stable DNA polymerases may also be
suitable.
It is important to also perform RT-PCR for the same sample of RNA using
a control set of primers. For mouse, we typically target p2-microglobulin
mRNA, whereas for human GADPH is used. The primer sequences for
amplification of these control mRNAs are also provided. Of course, a variety
of other control mRNAs could be equally, or even more, appropriate,
depending on the particular cells of interest. The value of the control RT-
PCR is that it permits the bcl-2 results to be normalized relative to a control
that should (in most circumstances) not vary.
The procedures described here are designed specifically for detection of
bcl-2 RNAs but can be adapted through use of alternative amplification
primers for any of the Bcl-2 family proteins.
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John C. Reed et al.
5.1 cDNA synthesis
Protocol 7.
Method
1. Pipette 5 ug of total RNA into a 0.5 ml microcentrifuge tube and bring
the total volume to 24.5 ul using DEP-treated water.
2. Briefly heat (95°C, 3 min) and then quickly cool on ice.
3. Add the following reagents.
5 X first strand buffer (GIBCO-BRL), 20 nl
RNAsin (Promega) 20 units, 0.5 ul
random hexamers (62.5 A26o units/ml), 4 ul
dNTPs (2.5 mM each), 40 ul
0.1 M DTT, 10 nl
Superscript™ reverse transcriptase (GIBCO-BRL) (200 units), 1 JJL!
4. Incubate at 37°C for 1 h.
5. Heat at 95°C for 5 min to terminate reactions.
5.2 PCR amplication
Protocol 8.
Method
1. To a 0.5 ml microcentrifuge, add 8-10 ul of the cDNA reaction mixture
from above.
2. Add the following reagents.
DEP-treated water, 75-77 ul
10 x reaction buffer (Perkin-Elmer Cetus),a 10 ul
forward primer (25 pmol/ml), 2 ul
reverse primer (25 pmol/ml), 2 ul
dNTPs (2.5 mM each), 2.4 ul
Tag polymerase (5 units/ml), 0.5 ul
Final concentration is 25 mM TAPS [pH 9.3], 50 mM KCI, 2 mM MgCI2,
1 mM B-mercaptoethanol.
3. Overlay with 50 ul mineral oil and heat to 94°C for 7 min (alternatively,
Taq can be omitted until after the heat denaturation, then pipetted
under the mineral oil layer into the aqueous solution).
172
4. Amplify bc/-2cDNA using the following PCR cycling conditions:
Mouse bcl-2:
94 °C, 30 sec
57 °C, 30 sec
72°C, 3 min (this should be 8 minforthe last cycle)
Human BCL-2:
94°Cfor 1 min
72 °C for 1 min, where the 72°C step is lengthened by 8 sec per cycle
(A final extension at 72°C is performed for 10 min after the last cycle)
The number of cycles for obtaining results within the linear portion of the
reaction varies between cells and tissue types. In general, 25-30 cycles
has been appropriate for mouse and 25-20 for human, but a range of
cycle numbers should be examined in pilot experiments, e.g. 15, 20, 25,
30, 35 cycles.
The two cycle profiles for mouse and human BCL-2 were independently
arrived at by separate workers in the laboratory and have proved to be
empirically successful in our hands. No efforts have been made to test the
interconvertibility of these cycling profiles for mouse and human BCL-2.
5.3 Southern blot analysis of PCR products
Protocol 9.
Method
1. Prepare a 3% agarose gel using 3:1 ratio of NuSieve agarose to
agarose (FMC Bioproducts, Inc.; Rockland, ME).
2. Mix 20 ml of the RT-PCR reaction product with 10 |J of TAE electro-
phoresis buffer. Add 6 nl of 6 x loading dye #3 (30) and heat at 68°C
for 10 min, followed by quick cooling on ice for 5 min.
3. Load samples into the wells of the gel and perform electrophoresis at
~30 volts/cm until the bromophenol blue marker has run ~2/3 to 3/4
the length of the gel.
4. If using unlabelled DNA markers, briefly stain gel with ethidium and
photograph with UVtransillurnination (add 50 ul of 10 mg/ml ethidium
bromide to ~500 ml of TAE, using the old electrophoresis buffer). The
expected PCR product for the human is 318 bp; and for the mouse
575 bp.
5. Transfer the size-fractionated DNA to GeneScreen Plus™ nylon
membranes (New England Nuclear/DuPont, Inc.) using 0.4 N NaOH as
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John C. Reed et al.
the transfer buffer. Alternatively a solution of 0.1 N NaCI and 0.1 N
NaOH can be used to transfer to Zeta-Probe membranes (Biorad,
Inc.).
6. If using Gene Screen Plus membranes, no baking or UV cross-linking
is required. The filters are merely, rinsed in 2 x SSC for 5-10 min to
neutralize NaOH, before proceeding to pre-hybridization.
For Zeta-Probe or similar nylon membranes, neutralize the filter for 10
min in 2 x SSC, and UV cross-link (1200 joules).
7. For the mouse bcl-2. we hybridize overnight at 57°C with ~10 pmoles
of 32P-end-labelled internal oligonucleotide probe in 5 x SSPE (1 x
SSPE=0.15 M NaCI/0.01 M NaH2P04, pH 7.0/1 mM EDTA), 0.6 % SDS,
50 n-g/ml heat-denatured salmon sperm DNA. Washes of the filter
are then performed in 5 x SSPE and 0.1 % SDS at 57°C for 20 min
(twice).
8. For the human BCL-2, the procedure we have used entails hybrid-
ization with 10 pmoles of 32P-end-labelled oligonucleotide probe in 5 x
SSC containing 0.1% SDS, 5 x Denhardt's (30), and 100 |xg/ml salmon
sperm overnight at 50°C.
Washes are performed with 5 x SSC and 0.1% SDS twice for 10 min at
room temperature, followed by exposure to X-ray film [Kodak XAR
film (Eastman-Kodak, Rochester, NY)] overnight at -80°C with
intensifying screens.
These two alternative approaches have not been compared side-by-side
to determine whether one is superior to the other, but both have
reproducibly yielded excellent results in our hands.
5.4 Primers and probes for PCR

5.4.1. Mouse bcl-2
Forward primer: 5'-TGCACCTGAGCGCCTTCAC-3'
Reverse primer: 5'-TAGCTGATTCGACCATTTGCCTGA-3'
Oligonucleotide internal probe: 5'-CCAGGAGAAATCAAACAAAGG-
3'(expected size of the PCR product is 575 bp) {Oligonucleotides are end-
labelled with [32P]-yATP using T4 polynucleotide kinase. Unincorporated
[32P]ATP is separated from the probe using either ethanol precipitations
in the presence of carrier tRNA, DEAE-cellulose minicolumns
(Whatman DE-52), or molecular sieve chromatography [centrifuge
through Bio-spin 6 minicolumns (BIORAD, Inc.) (exclusion limit 6000
daltons or ~5 bases)].}
174
5.4.2 Human BCL-2 primers and probes

Forward primer: 5'-CGA CGA CTT CTC CCG CCG CTA CCG C-3'
Reverse primer: 5'-CCG CAT GCT GGG GCC GTA CAG TTC C-3'
Oligonucleotide internal probe: 5'-GGC GAT GTT GTC CAC CAG GGG
CGA C-3' { Oligonucleotides are end-labelled with [32P]ÂTP using T4
polynucleotide kinase. Unincorporated [32P]ATP is separated from the
probe using either ethanol precipitations in the presence of carrier tRNA,
DEAE-cellulose minicolumns (Whatman DE-52), or molecular sieve
chromatography [centrifuge through Bio-spin 6 minicolumns (BIORAD,
Inc.) (exclusion limit 6000 daltons or ~5 bases)].}
5.4.3 Mouse p2-microglobulin (for internal control)

Forward primer: 5'-ATGGCTCGCTCGGTGACCCTAG-3'
Reverse primer: 5'-TCATGATGCTTGATCACATGTCTCG-3'
Oligonucleotide internal probe: 5'-GCTACGTAACACAGTTCCAC-3'
(expected size of the PCR product is 373 bp)
5.4.4 Human GADPH

Forward primer: 5'-CCA CCC ATG GCA AAT TCC ATG GCA-3'
Reverse primer: 5'-TCT AGA CGG CAG GTC AGO TCC ACC-3'
Hybridization Oligonucleotide probe: 5'-CAA CAC AGA CCC ACC CAG
AGC CCT CCT GCC CTC CTT CCG CGG GGG C-3' (expected PCR
product is 598 bp in length)
For GAPDH, the thermocycler profile is as follows:
Heat samples at 94 °C for 7 min.
Cycle=94°C for 1 min, 55°C for 1 min, 72°C for 1 min (The numbers of cycles
of PCR must be empirically adjusted to find the linear-range for your cells
(30,25,20 and 15 cycles.)
Perform a final extension at 72 °C for 10 min prior to termination reactions
Analyse one-fifth of the PCR product
6. Immunohistochemical detection of Bcl-2 family

proteins in tissues
The approach we prefer for immunohistochemical detection of Bcl-2 protein
is to employ sections derived from paraffin-embedded tissues (Figure 7). This
yields morphology which is far superior to cryostat sections and permits use of
175
Figure!. Imntunohistochemical analysis of Bcl-2 family protein in tissue sections.
Examples are provided of immunohistochemicsl analysis of Bcl-2 (A-CI, Mcl-1 (D-FI, and
Bcl-X iG-ll in lymph nodes. Photomicrographs are presented at low (first column),
medium (second column}, and high {third column) magnification. Immunodctection was
accomplished by a diaminobenîdine method (brown] and nuclei were counterstained
with haematoxylin (blue). The tissue sections highlight the different patterns of Bcl-2
family protein expression in the germinal centre (GO lymphocytes of the lyrnphoid
follicles and the surrounding mantle zone region and interfollicular zones. (A-C) Bel 2
staining is found primarily in the mantle zone lymphocytes surrounding the germinal
centres and in occassional cells in the interfollicular regions. (D-F) Mcl-1 immnostaining
is strongest in germinal centre lymphocytes. IG-D Bcl-X staining is found primarily in
plasma cells and occassional activated lymphocytes.
17K
archival clinical material. A critical aspect of the procedure is either fixation
of the tissues in an acidic fixative or, if fixed in a neutral solution, subsequent
treatment with an acidic solution. The lower pH somehow reveals the
epitopes that are recognized by all of the currently available commercial
antibodies, thus markedly improving sensitivity. This same approach has also
yielded superior results for antibodies raised against other members of the
Bcl-2 protein family, such as Bcl-X, Mcl-1, and Bax (12-19). Several colori-
metric or fluorescence-based detection systems can theoretically be employed
for visualization of the antibodies, but most of our experience is with
horseradish peroxidase (HRPase)-based colorimetric detection methods.
6.1 Procedures for tissue preparation, embedding, and

sectioning
6.1.1 Fixation
Tissues should be quickly fixed with acidic based solutions such as Bouin's
solution (Sigma Chemicals Inc.; cat. no. HT10-1-128) by immersion or if
possible from animals, by perfusion with 2% paraformaldehyde in PBS or 4%
neutral-buffered formalin and subsequent post-fixation in Bouin's solution.
(Bouin's is an acidic fixative and thus will cause DNA nicking. Do not use
Bouin's if planning to do in situ detection of DNA fragmentation.)
However, very satisfactory immunostaining can often be achieved using
routine archival material that was fixed in 10% buffered formalin and then
embedded in paraffin. Thus, if such material is available, it is worth a try.
Protocol 10. Immersion method
Method
1. If tissues are derived from animals that were not perfused or from
human autopsy specimens, put excised tissues/organs into fixative for
3-5 h {Bouin's) or overnight (10% neutral-buffered formalin) in intact
form, then cut in half to allow for better infiltration of fixative if a large
organ (e.g. liver, heart, muscle, spleen). Cutting is generally not
required for mouse lymph nodes or thymus because the tissues are
small. [For brain tissue, fix intact overnight (even if using Bouin's),
then cut the next day.]
2. Let the tissues fix for an additional 3-5 days, depending on the size of
the tissues (e.g. mouse/rat for 3 days vs. human autopsy for 5 days).
Typically, the fixation is done in plastic beakers/jars.
If tissues are derived from perfused animals (see below), the post-
fixation time can be reduced to 1-2 days and the formalin is only 4%
instead of the usual 10%. Post-fixations in Bouin's solution are at usual
full strength.
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John C. Reed et al.
3. Place tissues into cassettes for paraffin embedding. Label with a
'superfrost' marking pen which is resistant to alcohols and xylenes. It
may be necessary to cut the tissues smaller with a scalpel to get them
to fit. However, do not let the tissue pieces dry out at any point. Also,
orient the tissues in the direction you will want them cut, then instruct
the histotechnician to organize the tissues in the paraffin molds in the
same fashion as they appear in the cassettes. (The bottom of the
cassette is the cutting surface.)
4. Submerge the cassettes for a few hours in 50% EtOH/PBS and then
proceed to dehydrations using an automatic tissue processor.3 Alterna-
tively, if fixed tissues will not go directly to embedding, dump out the
fixative and replace with PBS. Change the PBS solution twice over the
next day or so and store the fixed tissues in PBS at 4°C. These fixed
tissues should be good for at least a few weeks, but add azide if keep-
ing longer or if shipping unembedded tissues at room temperature.
'Our tissue processor is a Shandon, Inc. (model Citadel). This must be optimized for your own
processor, but the conditions we use are: (a) 50% ethanol/PBS for 1 h; (b) 70% ethanol/water
for 1 h; (c) 95% ethanol for 1 h; (d) 95% ethanol for 1 h again; (e) 100% ethanol for 1 h; (f) 100%
ethanol for 1 h again; (g) xylene or xylene substitute (Hemo-De from Fisher, cat no. 15-182-
507A or Histosol from National Diagnostics, cat. no. HS-100) for 1 h; (h) repeat xylene or xylene
substitute for 1 h; (i) paraffin at 57-61 °C for 1.5 h; (j) repeat paraffin at 57-61 °C for 1.5 h. Note
that isopropanol can be substituted for ethanol in all of these steps.
Protocol 11. Perfusion method
For paraffin immunocytochemistry, the optimal solution composition

should be either: 4% formaldehyde, buffered with PBS to pH 7.4-7.6 (4%
formaldehyde/PBS) or 2% paraformaldehyde in PBS. The approximate
volume required for perfusion by cardiac puncture is 100 ml per mouse
and 200-300 ml per rat. An i.v. infusion system with a volving system and
manometer is required, equipped with appropriate tubing and a 16-18
gauge needle attached for cardiac punctures.
Method
1. Animals are first placed into deep anaesthesia, usually using
Nembutal.
2. Lift the skin over the mid-epigastric region and make an incision with
scissors. Spread open the hole with the scissor blades and cut horizont-
ally to reveal the diaphragmatic muscle. Carefully cut the diaphragm
178
away from its attachments. Cut the ribs and lift the sternum, revealing
the heart. Insert the needle, hooked to the infusion bottle containing
PBS without fixative into the left ventricle. Immediately cut a small hole
in the right atrium or ventricle with scissors to relieve pressure. Start
the flow of PBS into the left ventricle with pressure set at 100-120
mmHg. (The animal should be in a pan to catch the fluid that will drain
from the right side of the heart.) Continue infusion of PBS at 100-120
mmHg until essentially all blood has been removed from the
vasculature: i.e. the flow from the right ventricle is clear PBS and not
blood.
3. Switch to the fixative infusion bottle and infuse fixative until the body
of the animal becomes stiff (about 10 min for mice and 15-20 min for
rats).
4. Discontinue the infusion, and excise the tissues of interest.
5. Place the tissue into post-fixative which is either the same formalin
solution used for perfusion or Bouin's solution.
6. If sufficient material is available, it is often advisable to split it into two
portions. Post-fix one of the pieces in Bouin's solution, which is
generally the better fixative for Bcl-2 protein family immunocyto-
chemistry (Sigma Dgn.; cat. no. HT10-1-128). Post-fix the second piece
in 4% buffered formalin for immunostaining with other antibodies or
for DNA fragmentation analysis by the TdT end-labelling method (34).
(Bouin's solution fixation results in non-specific DNA breaks.)
"Tissue processing and paraffin embedding is accomplished as in Protocol 10 above.
6.1.2 Paraffin embedding

Do not overheat or overdehydrate the samples. Keep the temperature of the
paraffin no higher than 65 °C. We use the 56-60 °C melting-temperature
paraffin from Surgipath, Inc. (cat. no. El-600) or equivalent. (Note: The two
pieces fixed differently can be embedded in the same paraffin block under the
same patient/experiment number. For example, we have adopted the con-
vention of placing the Bouin's-fixed piece at the top and the formalin-fixed
piece at the bottom of the slide.)
6.1.3 Sectioning
Paraffin sections 3-5 p,m are prepared and mounted on poly-L-lysine coated
slides or Fisher-Superfrost-plus slides (generally 50-200 slides can be
obtained per block, but of course it depends on the size and thickness of the
tissue specimen).
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John C. Reed et al.
If the paraffin samples are small, 2 or 3 separate patient samples or
experimental animal samples can be placed adjacent to each other on the
same glass slide so as to minimize the labour of immunostaining.
6.1.4 Solutions
Modified PBS.
NaCl 7 g/litre
NaH2PO4 (X H20) 1.38 g/litre
K2HPO4/anhydrous 5.44 g/litre
adjust pH to 7.4-7.6
4% Neutral-buffered formalin/PBS.
add 108 ml of 37% formaldehyde
bring volume to 1 litre using modified PBS
readjust pH to 7.4-7.6 with 10 N NaOH
10% Neutral-buffered formalin/PBS
first make 2 X PBS solution by combining the salts described above into 0.5
litres instead of 1 litre. Then mix:
500 ml of 2 X PBS
270 ml of 37% formaldehyde
230 ml of dH2O
adjust pH to 7.4-7.6. with 10 N NaOH
6.2 Pre-staining sample preparation
Protocol 12. Deparafinization procedure
Method
1. Pre-warm the slides in an oven at 55°C for 1-3 days. This enforces
attachment of the tissue to coated slides. (If you receive your slides
from an outside source, check whether this has already been done.)
The slides should be placed into a Wheaton glass slide rack for this
procedure.
Any oven can be used for this. A standard vacuum oven found in most
molecular biology laboratories is suitable. We typically hook to house
vacuum line and turn on the vacuum, which helps to keep the
temperature constant (~15 mmHg).
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9: Methods of measuring Bc1-2 family proteins
2. Remove the slides from the oven. Then pre-warm the oven to 65°C
before reinserting.
3. Melt the paraffin at 65°C for 20 min (the drops of paraffin should be
seen at the bottom of the slides).
4. Set up three separate glass containers (Wheaton/Fisher, cat. no. 08-
812) containing xylene or xylene substitute (such as Hemo-D from
Fisher Scientific, cat. no, 15-182-507A) and transfer the slides while still
in the glass slide rack sequentially to each jar for 2 min each. Agitate
the slides up and down a few times during each transfer before
submerging for 2 min, then agitate up and down before transferring to
the next container of xylene. Shake off drops before transferring to the
next solution.
5. Immerse slides in 100% ethanol for 15 sec.
6. Place into 3% H202 in methanol for 30-45 min.
7. Next, transfer to 95% ethanol for 20 sec.
8. Then transfer to 70% ethanol for 20 sec.
9. dH20 for 1 min.
From this point on, keep the slides moist. DO NOT let them dry out.
Protocol 13. Antigen retrieval (acid treatment)
Microwaving in acidic solutions is used to enhance antigen reactivity.a
Method
1. Transfer slides to four polyethylene Coplin 'jars' (Fisher Scientific, Inc.;
cat. no. 08-815-10) and place these jars at the four corners of a plastic
box. Each container should have 10 glass slides. Insert 'blank' glass
slides if your experiment involves fewer than 40 slides.
2. Add acidic solution (pH 5.5-6.0) into the containers until the slides are
just covered. Also put tap water into the plastic box until the bottom is
covered.
3. If your microwave does not have a rotating stand, after each pulse of
microwaves change the positions of the flasks (it is convenient to
simply move the container clockwise or counter-clockwise so that
each of the coplin jars will have occupied all four corners of a square
by the end of the procedure). Also gently agitate each container after
each heating to ensure uniform heating of the fluid
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John C. Reed et al.
4. For our oven (General Electric; model JE1453H-001), we heat as
follows:
Power setting Time (min) Desired temperature (°C)
7 1
6 1
5 2 85
6 1
5 0.5 90-95
In general, however, the goal is to bring the solution in which the
slides are submerged close to a boil (~90-95°C) without boiling. (If
boiling does occur for a few seconds, however, it is usually not
deleterious.) Once brought to a temperature of 90-95°C, the sample
need not be held at this temperature. Simply let cool it to room
temperature.
5. Let the containers cool at room temperature for 15 min.
6. Wash twice in PBS (pH 7.4-7.6} for 5 min each.
a Microwaving should be performed at a slightly acidic pH. The dH20 at our institution has a pH
of ~6.0 and we therefore use it directly. Alternatives include 10 mM citrate buffer at pH 6.0 or
50 mM acetate buffer at pH 5.5. These conditions should be optimized for your particular
microwave and water source.
Protocol 14. Alternative antigen retrieval protocol
An alternative to microwaving is to treat the slides with more acidic

solutions without heating. Though results are superior with microwaving,
some tissue sections can detach from the glass microscope slides during
microwaving (depending on how they were prepared) and therefore this
alternative procedure is also provided here.
Method
1. Incubate slides in 0.02 M citrate buffer (pH 3.2) for 2 h.
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6.3 Immunostaining
Protocol 15. Immunostaining procedure
Materials
• primary antibodies. Polyclonal rabbit anti- • flat-tipped forceps
sera to Bcl-2 family proteins or mono- • reagents for avidin-biotin complex prep-
clonals derived from mouse or hamster aration (Vector Lab. ABC-Kit Standard; cat.
• glass dishes with removable horizontal tray no:PK-6100)
that holds slides (20 slides capacity; • secondary antibodies. Biotinylated goat
Fisher/Wheaton, cat. no 08-812) anti-rabbit IgG (Vector Labs, cat no: BA-
• closed humidity chamber; prepared from 1000) or biotinylated horse anti-mouse IgG
plastic boxes with plastic pipettes (10 ml) (Vector Labs, cat no: BA-2000) or bio-
fixed at the bottom with superglue. Put tap tinylated sheep anti-hamster IgG (Vector
water in the bottom of the box Labs, cat no: BA-9100)
Method
This procedure is optimized for final detection of antibodies using an
avidin-biotin complex reagent and diaminobenzidine colorimetric re-
action involving horseradish peroxidase. Other detection methods may
require some modifications. Perform all of the following steps in a
humidity chamber at room temperature.
Do not let the slides dry at any point. Keep covered with sufficient volume
of various reagents (~500 ul per slide).
1. Pre-block by incubating in slides in either 0.1 M Tris (pH 7.6-7.8) or
TSK [Tris/sodium chloride/potassium chloride (pH 7.6-7.8)] with 2%
BSA, 1% normal goat, and 0.05% Triton X-100 for 1 h.a,b
2. (a) Decant the pre-blocking solution and incubate with 0.4-0.6 ml of
primary polyclonal antibody diluted typically 1:800 to 1:2000 in
either 0.1 M Tris or TSK containing BSA and Triton X-100. Alterna-
tively, 3-10 ug/ml of anti-Bcl-2 murine monoclonal antibody or
2 ug/ml of anti-Bcl-2 hamster monoclonal antibody in either 0.1 M
Tris-BT or TSK-BT may be used. Incubate overnight at room
temperature.c
(b) A negative control slide(s) should also be prepared using pre-
immune serum of the same rabbit or, alternatively, normal rabbit
serum. Use isotype- and subclass-matched control monoclonals
when using anti-Bcl-2 monoclonals (Dako, Inc., Santa Barbara, CA). If
no negative control antibodies are available, perform immunostain-
ing using only the secondary antibody, without a primary antibody.
(c) An excellent control entails pre-adsorbing the antibody with ex-
cess antigen (peptide or recombinant Bcl-2 protein). For peptides,
we typically add 10 ul of antiserum to 1 ml of TSK-BT and 10 ul of
a solution containing the appropriate Bcl-2 peptide at 1 mg/1 ml.
The antigen and antibody are incubated at 37°C for 2 h before use.
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John C. Reed et al.
3. The next day, wash slides three times in PBS for 5 min each using
plastic Coplin jars. Agitate gently to wash. Do not put slides with
different antibodies (or even different dilutions of antibodies) together
in the same washing container.
4. Incubate with ~0.5 ml of secondary antibody for 1 h in a humidity
chamber.
(a) For polyclonal antisera: 3-5 ug/ml of biotinylated antibody from
goat anti-rabbit immunoglobulins (Vector Lab.; cat. no. BA-1000)
in 0.1 M Tris-BT or TSK-BT, with 0.5% normal serum.d (Usually
5 ug/ml is used.)
(b) For mouse monoclonals: 2.7 ug/ml of biotinylated horse anti-
mouse IgG (Vector Labs, Inc.; cat. no. BA-2000) in either 0.1 M
Tris-BT or TSK-BT with 0.5% normal serum.d
(c) For hamster monoclonals: 2.5-2.7 ug/ml of biotinylated sheep
anti-hamster IgG (Vector Labs, Inc.; cat. no. BA-9100) in either
0.1 M Tris-BT or TSK-BT with 0.5% normal human serum.
5. Wash three times for 5 min each in PBS. (Keep slides separated into
different Coplin jars if they received different secondary antibodies
and/or different dilutions).
6. Incubate slides in a humidity chamber for 45 min in ~0.5 ml each of
avidin-biotin complex reagent containing horseradish peroxidase
(HRPase) (Vector Labs.; Vectastain Kit, cat. no. PK-6100). [This solution
must be prepared in 0.1 M Tris (pH 7.4-7.8) 1 h before use!]
7. Wash with PBS three times for 5 min each. (All slides can be washed
together at this point, regardless of primary or secondary antibodies
or the dilutions of antibodies, with the exception that we generally
take the additional precaution of washing separately any negative
control slides, e.g. those that received pre-immune serum or peptide-
adsorbed antibodies, etc.)
8. Develop the reaction product for 10-20 minutes in a humidity chamber
by covering slides in DAB solution containing H2O2, as described
below. (This solution must be prepared freshly each time!)
9. Wash slides in dH20 using plastic Coplin jars three times for 5 min each.
a
We generally use 0.1 Tris (pH 7.6-7.8) but if high background is a problem, try TSK. The high
salt concentration eliminates much non-specific immunostaining.
b
The use of goat serum assumes that the secondary antibody employed is derived from goat. If a
different species is employed for secondary antibody production (horse, sheep, donkey, rabbit),
then 1% of normal serum from that species should be used instead of normal goat serum.
c
If non-specific immunostaining is seen with polyclonal antisera raised against synthetic
peptides, pre-adsorption of the antibody with the same protein used as a carrier (ovalbumin,
KLH) can be helpful. The optimal amount of murine monoclonal depends on the quality of
fixation, etc., but usually ~10 mg/ml for Mab124 and ~2 mg/ml for 407.
d
Include 0.05-0.1% normal serum from the same species that the tissue sections are derived
from, e.g. if immunostaining human tissue then add human serum.
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6.4 Counterstaining and mounting
Protocol 16.
Perform all steps using glass slide racks. Counterstaining with methyl
green may be preferred to haematoxylin when studying lymphocytes
because of the scant cytoplasm (high nuclei/cytosolic ratio). However,
methyl green will fade with time, especially if not kept in the dark.
Generally, it is wise to photograph such slides within 2 weeks.
Method
1. Rinse slides in tap water for 1 min.
2. Submerge slides in haematoxylin Counterstaining solution (Mayer's
Hematoxylin; Sigma, Inc., cat. no. MH5128) for 20 sec to as much as
5-15 min. (The optimal time depends on the source of haematoxylin
and how fresh the solution is; it will take longer after many uses.)
Alternatively, methly green can be used for Counterstaining.a
3. Rinse slides in tap water for 1 min.
4. Place slides, still in the slide racks, into ~200 ml of tap water
containing 5-7 ml of NH4OH (28-30%; Aldrich Chemicals, Inc., cat. no.
1336-21-6) for 15-20 sec.
5. Rinse in tap water again.
6. Rinse in dH20 for 1 min.
7. Dehydrate samples by submerging for 15-30 sec each in sequence
into 70% EtOH, then 95% EtOH, then 100% EtOH, followed by three
treatments with xylene or a xylene substitute.
8. Place a drop of acrytol mounting media (Surgipath; cat. no. MM-160)
on to the slide over the tissue or cells, and apply a coverslip.
9. Let dry at room temperature for a few hours, while lying flat with the
tissue.side up.
a(a) Counterstain in methyl green in a glass Coplin jar for 10 min at room temperature. (If the
methyl green solution has be reused several times, increase the Counterstaining time to 15-25
min.) (b) Wash three times in three changes of distilled water in a Coplin jar, dipping the slide
3-5 times each in the first and second washes, followed by 15 sec without agitation for the
third wash. (c) Wash in three changes of 100% butanol in a Coplin jar, dipping the slide 10
times each in the first and second washes, followed by 10 sec with out agitation/dipping for the
last wash. (d) Dehydrate in three changes of xylene for 2 min for each of the first two washes
and for 5 min on the last wash. (e) Mount.
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John C. Reed et al.
6.5 Solutions
1. Modified PBS
• sodium chloride, 7 g
• sodium phosphate (NaH2PO4.H20), 1.38 g
• potassium phosphate, dibasic, anhydrous (K2HPO4), 5.44 g
• bring volume to 1 litre with dH2O and adjust pH to 7.6 with 10 N NaOH.
2. 0.02 M Citrate buffer
• solution A: 0.01 M citric acid (MW 192.1), monohydrate (Sigma, C-0759),
0.192 g in 100 ml dH20
• solution B: 0.01 M citric acid (MW 294.1), trisodium salt (Sigma, C-8532),
0.294 g in 100 ml dH20
• combine 87.4 ml of A and 12.6 ml of B.
• adjust pH to 3.2 using concentrated HC1
3. 0.1 M Tris
• Trisma base 12.1 g
• add dH20 to ~950 ml
• adjust pH to 7.6-7.8 with HC1
• bring total volume to 1 litre
4. TSK
• Trisma (Sigma) base 12.1 g=100 mM final
• sodium chloride 32.0 g=550 mM final
• potassium chloride 0.8 g=10 mM final
• add dH20 to 950 ml and adjust to pH 7.6-7.8 with HC1
• adjust total volume to 1 litre
5. TSK-BT
• 2 g BSA (crystalline powder)
• add TSK to 100 ml
• add 0.05 ml Triton X-100
6. Diaminobenzidine/H202 solution
Caution. DAB is a carcinogen. Use precautions and dispose of properly.
• dissolve diaminobenzidine in 0.1 M Tris (pH 8.1) at 0.5 mg/ml [3,3'-
diaminobenzidine from Sigma powder (cat. no. D-5637) or in tablet form
(D-5905)]. The final pH should be ~7.6-7.8
• add 41 ml of 30% H202 per 50 ml of DAB solution
• load into a 60 cm3 syringe
186
• attach a 0.45 mm filter disk
• filter the DAB on to the glass slides
• H202 should be purchased anew every 2-4 weeks
• do not add the H202 to the DAB solution until just before applying on to the
slides
7. Methyl green counter stain
• add 1 g methyl green dye to 200 ml 50 mM acetate buffer (pH 5.5) in a glass
container
• add ~50 ml chloroform and shake vigorously
• allow layers to separate
• discard bottom (chloroform) layer
• repeat chloroform extractions until all traces of methyl violet (purple
colour) have disappeared
• allow the methyl green staining solution to stand in an open flask overnight
so that any residual chloroform evaporates
• if crystals remain, filter through Whatman 3MM paper
• the solution is stable for several months at room temperature
• methyl green can be reused several times. Filter through Whatman 3MM
paper or equivalent
8. Acetic acid solution
• prepare a 0.2 M acetic acid solution using glacial acetic acid (Fisher Sci.,
Inc.; cat. no. A38-212). Add 11.55 ml glacial acetic acid to 988.45 ml dH2O.
• prepare a 0.2 M sodium acetate solution. Dissolve 27.2 g sodium acetate
(Sigma; cat. no. S-8625) into 1 litre dH2O.
9. 10 mM Citric acid (pH 6.0)
• dissolve 2.1 g citric acid (anhydrous) (MW 192) in 1 litre of dH2O
• adjust pH to 6.0 with ~13 ml of N NaOH
The deparaffinization solutions (xylene, EtOH, citrate buffer) may be used
for 2-4 weeks, depending upon the frequency of experimental procedures.
The 2% H202 in methanol should be freshly prepared every two weeks. PBS
should be prepared fresh each week. DAB should be made fresh each time.
7. Immunohistochemical detection of Bcl-2 protein in

cultured cells
The overall procedure for immunostaining cultured cells is similar to that
used for tissue sections in paraffin. The fixative solutions are more dilute
and/or are used for only a short time, owing to the rapid penetration. Because
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John C. Reed et al.
most tissue culture medium contains biotin, which can cause non-specific stain-
ing when using avidin-biotin-based detection methods, an alkaline phosphatase
detection system or Peroxidase Anti-Peroxidase Complex (PAP) (35) can be
employed as an alternative to DAB. The sensitivity with these methods, how-
ever, is generally less than with DAB and therefore DAB should be tried first.
7.1 Procedures
7.1.1 Adherent cells
Prior to seeding the cells into 100 mm plastic culture dishes, put autoclaved
microscope coverslips on the bottom of Petri dishes (four coverslips per 100
mm dish) and let the cells adhere and grow on them to the desired density.
Protocol 17.
Method
1. Place coverslips with cell side up into a plastic petri dish (~10 cover-
slips per dish).
2. Add 4% buffered formalin (4% formaldehyde/PBS) or Bouin's solution
and incubate for 5 min.
3. Remove coverslips using forceps and dip into a container of PBS.
Agitate for a few seconds in PBS.
4. Transfer for a few seconds to a second container of PBS and agitate
for a few seconds.
5. Air-dry the coverslips with cell side up in a Petri containing dry
Whatman filter paper.
6. Apply one or two drops of acrytol mounting medium to the bottom of
the coverslip and place with cell side up on to a glass microscope
slide. Let dry for 1 h or longer. If desired, each coverslip can be divided
into four pieces with a diamond pencil. This permits more antibody
staining conditions to be tried from a small number of cells.
7. The fixed and dried slides can be stored at 4°C for several months, or
you may precede to immunostaining.
7.1.2 Suspension cells
Protocol 18.
Method
11. Take 5-10 ml cells from tissue culture or ~0.2 ml of whole blood.
12. Add an equal volume of PBS, and mix.
188
13. Spin down at 1500 r.p.m. for 5-10 minutes (~400 g).
14. Discard the supernatant.
15. Wash once with ~10 ml PBS. Then aspirate supernatant off.
16. Add 500 ml of Bouin's solution or 4% formaldehyde/PBS.
17. Incubate at room temperature for 3-5 min.
18. Spin down at 1500 r.p.m. for 10 min.
19. Aspirate off fixative and wash 3-5 times in PBS.
10. Resuspend the cells in ~0.5 ml PBS containing 0.01% NaN3 and store
at 4°C.
11. Prepare poly-L-lysine-coated slides; put one drop of solution (Sigma
Chemicals, Inc.; cat. no. 1010) on the slide, smear the drop with a
gloved finger tip, and let it polymerize at 37°C for 1-3 h.
12. Mix the fixed cell suspension before applying to the slides.
13. Place a drop on the coated slides and gently spread the drop with a
pipette tip over an area of ~2 cm diameter. Up to three drops can be
placed on the slide and spread over a larger area.
14. Dry at 37°C for a couple of hours.
15. Store in slide boxes or proceed to imrnunostaining procedure.
7.2 Immunostaining
Protocol 19.
Method
1. Rinse slides in PBS for 5 min.
2. Incubate for 30 min in 0.03% H202 in PBS.
3. Wash for 5 min in PBS.
4. Incubate for 5 min in PBS containing 0.1% glycine.
6. Pre-block and incubate with primary antibodies as described in
Protocol 17, steps 1-3.
7. Incubate with secondary antibody (differs depending on whether
using avidin-biotin-HRPase/DAB method described above versus
alkaline phosphatase or PAP method for detection; see Protocols 20
and 21).
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John C. Reed et al.
Protocol 20. Alkaline phosphatase method

Method
1. Add ~0.5 ml of alkaline phosphatase (AP)-conjugated antibody to
slides and Incubate for 1 h in a humidity chamber.
AP-conjugated swine anti-rabbit IgG is used for detection of rabbit anti-
bcl-2 polyclonals. Dilute 1:25 to 1:50 in 0.1 M Tris (pH 7.6-7.8) containing
2% BSA and 0.05% Triton X-100 (final conc. 10-20 mg/ml) (Dako, Inc.; cat.
no. D306).
AP-conjugated goat anti-mouse IgG is used for detection of mouse mono-
clonals and is diluted in the same way (final conc. 32-64 mg/ml) (Dako,
Inc.; cat. no. D486).
2. Wash three times in PBS (5 min each).
3. Add AP-substrate solution (NBT/BCIP) and incubate for 30 min.
4. Stop reactions by washing in PBS containing 20 mM EDTA.
5. Counterstain with methyl green and mount as described above in
Protocol 16.
Protocol 21. PAP method

Method
1. Add 0.5 ml of either swine anti-rabbit IgG (Dako, Inc.; cat. no. Z196)
diluted 1:50 (final conc. 62 mg/ml) in 0.1 M Tris (pH 7.6-7.8) contain-
ing 2% BSA and 0.05% Triton X-100 (for detection of rabbit
polyclonals), or rabbit anti-mouse IgG (Dako, Inc.; cat. no. Z259)
diluted 1:50 in the same way (final conc. 60 mg/ml) for detection of
mouse monoclonals.
2. Incubate for 1 h, then wash three times with PBS.
3. Add 0.5 ml per slide of 1:200 (~40 mg/ml) PAP complex (rabbit or
mouse) in 0.1 M Tris-BT and incubate for 1 h.
4. Wash three times with PBS.
5. Cover slides with DAB/H202 solution (described above in Section 6.5)
and incubate for 10-20 min.
6. Wash three times in dH20.
7. Counterstain and mount as described above in Protocol 16.
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7.3 Solutions
NBT/BCIP (make fresh each time)
• dissolve 0.5 g NBT (nitroblue tetrazolium) in 10 ml of 70% dimethyl-
formamide (DMF) (NBT is stored in desiccator at 4°C before use)
• dissolve 0.5 g BCIP (bromochloroindolyl phosphate) in 10 ml of 100%
dimethyl formamide (DMF) (BCIP is stored in desiccator at -20°C before
use)
• prepare TNM solution: 0.1 M Tris (pH 9.5), 0.1 M NaCl, 5 mM MgCl2
• then, just prior to use, add 66 ul of NBT stock solution to 10 ml of TNM.
Mix.
• add 33 ul of BCIP stock. Mix.
• use within 1 h
Note. The NBT and BCIP stock solutions were stable at 4°C for ~1 year.
PAP complex
• HRPase in a soluble complex with either rabbit anti-HRPase or mouse anti-
HRPase can be purchased from Dako, Inc.
• dilute 1:200, final conc. 40 ug/ml, in 0.1 M Tris (pH 7.6-7.8) containing 2%
BSA and 0.05% Triton X-100.
8. Production of recombinant Bcl-2 family proteins in

bacteria
Biochemical and functional analysis of Bcl-2 family proteins can be accom-
plished using recombinant proteins produced in bacteria (E. coli). We have
used such proteins for: (a) analysis of dimerization amongst Bcl-2 family
proteins by surface plasmon resonance and other methods; (b) circular
dichroism studies of protein secondary structure regulation; (c) investigations
of ion channel activity of Bcl-2 family proteins; (d) microinjection into cells;
(e) studies of the effects of Bcl-2 family proteins on isolated mitochondria;
and (f) as immunogens for antibody generation (36-39). Procedures are
described here for production of recombinant Bcl-2, Bcl-XL, Bax, and Bid. In
the cases of Bcl-2, Bcl-XL, and Bax, the cDNAs encoding these proteins have
been engineered to introduce a stop codon just prior the carboxyl-terminal
~20 amino acids which constitute hydrophobic membrane-anchoring domains
in these proteins (36-38). This is necessary to obtain soluble proteins.
To facilitate the purification, these Bcl-2 family proteins are produced with
either GST or His6 tags fused to their N-terminus or C-terminus. In general,
we have obtained better results with GST tagging of these proteins, compared
with His6 tagging. The GST versions of these recombinant proteins generally
have better solubility and there are some advantages to glutathione-
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John C. Reed et al.
Sepharose affinity chromatography compared with Ni-chelation resins. How-
ever, the disadvantage of using GST fusion proteins is that enzymatic cleavage
to remove the GST-tag can be problematic, leading to some accidental
cleavage of the desired final product as well (e.g. Bid, Bax). The GST moiety
can be left on the proteins for some types of assays, but not all. For example,
the presence of a GST-tag at the N-terminus of Bc1-2 or Bcl-XL has been
shown to preclude their interaction with some others types of proteins. How-
ever, the presence of the GST-tag may also carry advantages, such as reduced
toxicity to E. coli, which we have observed for GST-Bax compared with
His6-Bax, thus making it possible to produce 80-100 mg Bax fusion protein
from as little as one litre of bacterial culture.
We describe below protocols to express and purify several of the commonly
studied members in Bcl-2 family proteins. Generally, 5-10 mg of purified
protein can be obtained from 1 litre culture in approximately one week.
8.1 Human Bcl-2

Both GST- and His6-tagged versions of huBc1-2 (lacking the C-terminal
membrane-anchoring domain) can be produced with large yields in bacteria.
For GST-Bc1-2 (1-218), we use XL-1 blue cells (Stratagene, Inc.) expressing
the proteins from a pGEX vector (Pharmacia). For His6-Bcl-2, we use BL21
(DE3) cells, expressing the protein from a pET vector (Novagen, Inc.).
Bcl-2 is notoriously insoluble at neutral pH. However, at pH 3.5,
recombinant soluble Bcl-2 protein can be concentrated up to 10-15 mg per ml
without detergents. Thus, the procedures described here are for preparation
of Bcl-2 in acidic solution. The solubility of Bcl-2 at neutral pH is limited to
~50 mg per ml in PBS. High concentrations of glycerol (40%) afford little
benefit at neutral pH for increasing solubility but will slow down protein
aggregation. In the presence of high concentrations of non-ionic detergents
(4% v/v), the concentration of Bcl-2 can reach to 1-2 mg per ml. However, the
presence of detergent is not desirable for many experiments.
Protocol 22. GST-Bcl-2 (1-218) protein
Method
11. Inoculate a colony of XL-1 blue cells carrying the pGEX-4T1-Bcl-2 (1-
218) plasmids into 1 litre of Luria-Bertani (LB) medium containing 100
mg/mlampicillin and grown at 37°C overnight with moderate agitation.
12. Dilute the culture by half in fresh LB medium containing 100 mg/ml
ampicillin and allow to cool to room temperature for 1 h.
13. Induce GST-Bcl-2 protein production by addition of 0.4 M IPTG
(isopropylthio-B-D-galactoside) to medium at 25°C from 6 h to over-
night.
192
14. Recover cells by centrifugation using a Sorvall GSA rotor at 4000 g for
10 min. Store cells at -20°C until use. The expression level is moni-
tored by SDS-PAGE (100 ml of the culture is resuspended in 25 ml
Laemmli-SDS sample buffer, and 12.5 ml is loaded into a 15%
SDS-PAGE minigel to verify protein induction: 1 mg induced band
equates to ~20 mg/l protein).
15. Resuspend cells in 50 ml of 50 mM Tris, pH 8.0, 150 mM NaCI, 1%
Tween, 0.1% 2-mercaptoethonal, 5 mM EDTA, complete protease
inhibitor set (Boerhinger 1697498), 1mM PMSF. Lyse cells with 0.5
mg/ml lysozyme at room temperature for 0.5 h.
16. Sonicate on ice until viscosity is minimal.
17. Centrifuge samples at 27500 g for 10 min and collect both
supernatant and pellet.
18. To purify the soluble GST-Bcl-2 found in the supernatant, incubate
the cell lysate with glutathionine resin (Pharmacia) at 4°C overnight.
Samples should be tumbled gently during incubation in a 50 ml
polypropylene centrifuge tube.
19. Pack beads in a column and wash it with 20 mM Tris, pH 8.0, 150 mM
NaCI, 0.1% Tween, 0.1% 2-mercaptoethanol until the OD280 (optical
density at 280 nm) is less than 0.01.
10. Wash beads again with 10 vols of the same buffer without detergent.
11. Elute GST-Bcl-2 with 2 vols of washing buffer containing 20 mM
glutathionine. Alternatively, the beads are collected and resuspended
into a 50% (v/v) slurry in washing buffer containing 20 mM gluta-
thionine in a 50 ml polypropylene centrifuge tube, incubated at 4°C
for 1 h, and the supernatant containing eluted GST-Bcl-2 is collected
after centrifugation at 760 g for 5 min.
Protocol 23. His6-Bcl-2 (1-218)
Method
11. Inoculate a single colony of cells into 1 litre of LB medium containing
100 mg/ml ampicillin and grow at 37°C overnight in a 2 litre Erlenmeyer
flask with vigorous agitation.
ampicillin and allow to cool to room temperature (RT) for 1 h.
13. Induce HiS6-Bcl-2 protein production using 1 mM IPTG for 6 h at RT,
with vigorous agitation.
14. Recover cells by centrifugation in a GSA rotor at 4000 g for 10 min.
Store cells at -20°C until use. The expression level can be monitored
by SDS-PAGE (see Protocol 22).
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John C. Reed et al.
15. Resuspend cells in 50 ml of 50 mM phosphate buffer, pH 8.0, 150 mM
NaCI, 1% Tween, complete protease inhibitor set (Boerhinger
1697498), 1mM PMSF. Lyse cells with 0.5 mg/ml lysozyme at room
temperature for 0.5 h.
17. Centrifuge samples at 27 500 g for 10 min and collect the pellet.
18. Wash the pellet by resuspending and then centrifuging three times in
200 ml of 50 mM phosphate buffer, pH 8.0, 150 mM NaCI, 1% Tween
to remove soluble contaminant proteins.
19. Resuspended pellet in 10 ml water by sonication. Add 8 M GuHCI and
1 M phosphate stock solution to give final concentrations of 6 M
GuHCI, 50 mM phosphate. Adjust pH to 6.8 with NaOH.
10. Centrifuge at 27 500 g for 10 min and collect supernatant.
11. Add nickel resin at ~6-8 mg His6-Bcl-2 per 1 ml resin. Add imidazole
at 25 mM final concentration. Adjust the pH to 6.8.
12. Incubate at 4°C from 3 h to overnight.
13. Pack beads in a column and wash it with 50 mM phosphate buffer, pH
6.8, 4M GuHCI, 25 mM imidazole until OD280 is less than 0.01.
14. Elute His6-Bcl-2 protein with 2 X resin volume of 0.2 M acetic acid,
4 M GuHCI.
15. Dialyse the eluted HiS6-Bcl-2 against 100 X volumes of cold 25 mM
acetic acid, 1mM EDTA, 0.1% 2-mercaptoethonal at 4°C for 4 h, three
times.
16. Store protein at -20°C until use.
17. The eluted sample is generally >90% pure. It can be further purified
by gel filtration under denaturing conditions (4 M GuHCI) or, after
refolding (step 15), by ion-exchange chromatography using acidic pH
solution (Mono S HR10/10 at pH 4.5) (Pharmacia).
8.2 Human Bcl-XL protein

The expression and purification of human Bcl-XL protein is not difficult. Both
GST-Bcl-XL and His6-Bcl-XL can be expressed as soluble proteins under
standard conditions. Bcl-XL is stable during thrombin digestion. Following
affinity chromatography using glutathione-Sepharose or Ni-chelation resin,
Bcl-XL can be further purified using Mono Q ion-exchange chromatography,
typically producing a sharp peak at ~250 mM NaCI at pH 8.0. Recombinant
Bcl-XL protein is soluble in both neutral and acidic solutions. At pH 4.0,
concentrations of 2-3 mg per ml of Bcl-XL protein can be obtained in the
194
presence of 150 mM NaCl. Bcl-XL exits as monomeric protein at both neutral
and acidic pH (37).
For storage of Bcl-XL, samples are dialysed against 20 mM Tris, pH 8.0, 150
mM NaCl, 1mM EDTA. 0.1% 2-mercaptoethanol, and kept at 1 mg per ml at
4°C. If frozen, at least some of the Bcl-XL protein will precipitate out of
solution.
Protocol 24. GST-BCI-XL (1-211)/Bcl-XL protein
Method
1. Inoculate a colony of XL-1 blue cells carrying the pGEX-4T1-Bcl-XL (1-
211) plasmid into 1 litre of LB medium containing 100 mg/ml
ampicillin and grown at 37°C overnight with moderate agitation.
3. Induce GST-Bcl-XL protein production by addition of 0.4 M IPTG to
the medium at 25°C from 6 h to overnight.
Store cells at -20°C until use. The expression level is monitored by
SDS-PAGE (see Protocol 22) (1 mg of induced band equates to
~20 mg/l protein).
5. Resuspend cells in 50 ml of 50 mM Tris, pH 8.0, 150 mM NaCl, 1%
inhibitor set (Boerhinger 1697498), 1 mM PMSF. Lyse cells with
0.5 mg/ml lysozyme at room temperature for 0.5 h.
7. Centrifuge samples at 27 500 g for 10 min and collect the supernatant.
8. Incubate the cell lysate with glutathionine resin (Pharmacia) at 4°C
overnight. The amount of resin is based on the expression level in
step 4 (use ~2-4 mg recombinant protein per 1 ml beads). Samples
should be tumbled gently during incubation in a 50 ml polypropylene
centrifuge tube at 4°C.
9. Pack beads in a column and wash with 20 mM Tris, pH 8.0, 150 mM
NaCl, 0.1% Tween, 0.1% 2-mercaptoethanol until OD280 is less than
0.01.
10. Wash the beads again with 10 vols of the same buffer without
detergent.
11. Elute GST-Bcl-XL with 2 vols of washing buffer containing 20 mM
glutathionine. Alternatively, beads are collected and resuspended
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John C. Reed et al.
for 1 h, and the supernatant containing eluted GST-Bcl-XL is collected
after centrifugation at 760 g for 5 min.
12. If the GST group will be removed by proteolysis, incubate the resin
after step 9 (above) with thrombin (Boerhinger) at 4°C in 20 mM Tris,
pH 8.0, 150 mM NaCI, 0.1% 2-mercaptoethanol, 0.1% Tween, 2.5 mM
CaCI2, overnight. For 50 ml of 50% slurry, 23 mg thrombin is typically
used.
13. Dialyse the eluted Bcl-XL against 100 X vols of 10 mM Tris-HCI, pH 8.0,
1 mM EDTA, 0.1% 2-mercaptoethonal at 4°C for 3 h. Inject into a
Mono Q column (Pharmacia, HR10/10) that has been equilibrated with
dialysis buffer, using a 2 ml/min flow rate. Wash the column with
50 ml of the same buffer at 2 ml/min. Elute Bcl-XL with a linear
gradient of 0-500 mM NaCI in 60 min at 2 ml/min. Collect the samples
in 1.5 ml fractions and monitor purity on 15% SDS-PAGE.
14. Pool pure fractions and store at 4°C at a concentration of 1 mg/ml.
Protocol 25. His6-Bcl-XL protein
Method
11. Inoculate a single colony of cells into 1 litre of LB medium containing
100 mg/ml ampicillin and grow at 37°C overnight in a 2 litre
Erlenmeyer flask with vigorous agitation.
13. Induce HiS6-Bcl-XL protein production using 1 mM IPTG for 6 h at RT,
with vigorous agitation.
SDS-PAGE (see Protocol 22).
15. Resuspend the cell pellet in 50 ml of 50 mM phosphate buffer, pH 8.0,
150 mM NaCI, 1% Tween, complete protease inhibitor set (Boerhinger
1697498), 1 mM PMSF. Lyse cells with 0.5 mg/ml lysozyme at room
temperature for 0.5 h.
18. Add nickel resin ~6-8 mg His6-Bcl-XL per 1 ml resin) in 50 mM
phosphate buffer, pH 6.8, 150 mM NaCI, 1% Tween, 25 mM imidazole.
Adjust the pH to 6.8. Incubate at 4°C from 3 h to overnight.
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19. Pack beads into a column and wash with 50 mM phosphate buffer,
pH 6.8, 150 mM NaCI, 0.1% Tween, 25 mM imidazole until OD280 is
less than 0.01.
10. Elute His6-Bcl-XL protein with 2 vols of washing buffer containing
250 mM imidazole.
11. Dialyse the eluted His6-Bcl-XL against 100 vols of 10 mM Tris-HCI,
pH 8.0, 1 mM EDTA, 0.1% 2-mercaptoethonal at 4°C for 3 h. Inject into
a Mono Q column (Pharmacia, HR10/10) that was equilibrated with
dialysis buffer, at 2 ml/min flow rate. Wash with 50 ml of the same
buffer at 2 ml/min. Elute Bcl-XL with a linear gradient of 0-500 mM
NaCI in 60 min at 2 ml/min. Collect the samples in 1.5 ml fractions and
monitor purity on 15% SDS-PAGE.
12. Pool pure fractions and store at 4°C at a concentration of ~1 mg/ml.
8.3 Mouse Bax protein

Bax is a pro-apoptotic protein which is also toxic to E. coli (40). This toxicity
limits the expression of Bax in E. coli. The protocol developed in our
laboratory takes advantage of the leakiness of the trc promoter within pGEX
plasmids to achieve a slow gradual induction, using low concentrations of
IPTG and modifications of sugar levels in media. Also, the presence of a GST
tag at the N-terminus of Bax can reduce the toxicity of the recombinant
protein in bacteria. We have not successfully produced large amounts of
His6-Bax.
We have observed that, after cleavage and removal of GST, the recom-
binant Bax protein will non-specifically stick to GST resin unless ~0.1%(v/v)
non-ionic detergent is added. The concentration of purified Bax is limited to
=0.2 mg per ml in the absence of detergent.
About half of the expressed GST-Bax protein is found in the insoluble
pellet, probably associated with cell membrane debris. Non-ionic detergent
does not increase the solubility of this pool of Bax. Bax protein found in the
insoluble pellet, however, can be recovered through solubilization and
refolding. The washed pellet is solubilized in 6 M GuHCl, 50 mM phosphate
buffer, pH 7.0, 0.1% 2-mercaptoethonal. The supernatant is then diluted 30-
fold into ice-cold refolding buffer (50 mM phosphate-buffer, pH 7.0, 0.1% 2-
mercaptoethonal, 150 mM NaCI, 0.1% Tween-20, 1m EDTA) with vigorous
stirring, then placed on ice for 16 h. After clarification by centrifugation, the
diluted refolding mixture is mixed with GST-resin. This rapid dilution of
GuHCl appears to be preferable to dialysis-based approaches to refolding,
since when solubilized GST-Bax in GuHCl is dialysed against refolding buffer,
most of GST-Bax protein appears as a high molecular weight aggregate.
A problem associated with the purification of Bax is that Bax can become
cleaved during proteolytic removal of GST tag. Initially, we attempted an
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John C. Reed et al.
approach where GST-Bax was eluted and concentrated, then digested with
thrombin. However, we found that most Bax is degraded under these con-
ditions. Thus, digestion is performed directly on GST beads at 4°C for 24 h.
Under these conditions, about 20% of Bax still becomes truncated near its N-
terminus. If a homogeneous N-truncated Bax preparation is desirable, the
eluted Bax protein from GST beads can be kept at 4°C for 1 week, which
typically results in complete conversion of the Bax protein.
When chromatographed on Mono Q, Bax co-elutes at 350 mM NaCl in a
broad peak. Although this ion-exchange step does not separate these
proteins, it does separate Bax from contaminating thrombin and residual GST
protein, and it can be used to remove detergents which have been employed
in previous steps.
Purified GST-Bax, Bax, and truncated Bax all elute as high molecular
weight complexes in gel filtration columns, migrating at ~430-280 kDa. These
complexes can withstand up to 4 M urea and up to 1 M NaSCN, as well as
alkaline solutions to pH 9.5. In this regard, it has been reported that Bax may
form heptamers (41). At low pH, Bax precipitates out of solution unless
diluted into detergent-containing solutions or provided with membranes for
insertion.
Protocol 26. GST-Bax (1-171) protein
Method
11. Inoculate a colony of XL-1 blue cells carrying the pGEX-4T1-Bax (1-
171) plasmid into 1 litre of terrific broth medium supplemented with
1-2% glycerol containing 0.5 mg/ml cabenicillin, and grown at 37°C
overnight with moderate agitation.
12. Allow the culture to cool to room temperature for 1 h, and add 10 mM
IPTG.
13. Grow at room temperature for another 24 h with moderate agitation.
14. Recover cells by centrifugation in a GSA rotor at 5000 r.p.m. for 10
min. Store cells at-20°C until use. The expression level is monitored
by SDS-PAGE (see Protocol 22).
15. Resuspend cells in 50 ml of 50 mM Tris, pH 8.0, 150 mM NaCl, 1%
inhibitor set (Boerhinger 1697498), 1 mM PMSF. Lyse cells with
0.5 mg/ml lysozyme at room temperature for 0.5 h.
Also, save the pellet if planning to attempt solubilization in 6 M GuHCI
and refolding as described above.
198
18. Incubate cell lysate with glutathionine resin (Pharmacia) at 4°C
overnight, The amount of resin is based on the expression level as
determined above. Using ~2-4 mg proteins per 1 ml beads. Samples
should be tumbled gently during incubation in a 50 ml polypropylene
centrifuge tube.
NaCI, 0.1% Tween, 0.1% 2-mercaptoethanol until OD280 is less than
0.01.
11. Elute GST-Bax with 2 vols of washing buffer containing 20 mM
glutathionine. Alternatively, beads can be collected and resuspended
for 1 h, and the supernatant containing eluted GST-Bax is collected
after centrifugation at 2000 r.p.m. for 5 min.
pH 8.0, 150 mM NaCI, 0.1% 2-mercaptoethanol, 0.1% Tween, 2.5 mM
CaCI2 overnight. For 50 ml of 50% slurry, 23 mg thrombin is used.
Elute Bax with 2 x resin volumes of the same buffer.
13. Dialyse the eluted Bax protein against 100 vols of 10 mM Tris-HCI,
pH 8.0, 1 mM EDTA, 0.1% 2-mercaptoethonal at 4°C for 3 h. Inject into
a Mono Q column (Pharmacia, HR10/10) that has been equilibrated
with dialysis buffer, using a 2 ml/min flow rate. Wash the column with
50 ml of same buffer at 2 ml/min. Elute Bax with a linear gradient of
0-500 mM NaCI in 60 min at 2 ml/min. Collect the samples in 1.5 ml
fractures and monitor purity on 15% SDS-PAGE.
14. Pool pure fractions and store at -20°C at a concentration of
~0.2 mg/ml.
8.4 Human Bid protein

The expression of Bid in bacteria is easily achieved. The recombinant BID
protein is highly soluble at both neutral and acidic pH (37). The only problem
associated with purification of Bid is that it is susceptible to digestion by
thrombin. Therefore, performing partial digestions of GST-Bid is advised to
reduce the degradation of Bid by thrombin. We typically digest GST-Bid
under the same conditions as those described above for other Bcl-2 family
proteins, except the digestion is stopped after 1-2 hours by addition of PMSF.
The eluted protein is then dialysed against 50 mM acetate buffer, pH 4.8,
1 mM EDTA, 0.1% 2-mercaptoethonal, and Mono S ion-exchange chromato-
graphy is performed. Bid elutes at very low salt concentrations (~50 mM
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John C. Reed et al.
NaCl), whereas the degraded contaminant elutes at high concentrations of
salt. The recombinant purified Bid protein exists as monomeric protein at
neutral and acidic pH (37).
Protocol 27. GST-Bid/Bid protein
Method
11. Inoculate a colony of XL-1 blue cells carrying the pGEX-4T1-Bid
plasmid into 1 litre of terrific broth medium supplemented with 1-2%
glycerol and containing 0.5 mg/ml cabenicillin. Grown at 37°C
overnight with moderate agitation.
12. Allow the culture to cool to room temperature for 1 h. Add 0.4 mM
IPTG and grow at room temperature for 6 h with moderate agitation.
SDS-PAGE (see Protocol 22).
14. Resuspend the cell pellet in 50 ml of 50 mM Tris, pH 8.0, 150 mM
NaCl, 1% Tween, 0.1% 2-mercaptoethonal, 5 mM EDTA, complete
protease inhibitor set (Boerhinger 1697498), 1 mM PMSF. Lyse cells
with 0.5 mg/ml lysozyme at room temperature for 0.5 h.
16. Centrifuge samples at 27 500 g for 10 min. Collect the supernatant
and discard the pellet.
17. Incubate the cell lysate with glutathionine resin (Pharmacia) at 4°C
overnight. The amount of resin is based on the expression level. Use
~2-4 mg protein per 1 ml beads). Samples should be tumbled gently
during incubation in a 50 ml polypropylene centrifuge tube.
NaCl, 0.1% Tween, 0.1% 2-mercaptoethanol until OD280 is less than
0.01.
10. Elute GST-Bid with 2 x resin volumes of washing buffer containing
20 mM glutathionine. Alternatively, beads are collected and resus-
pended into a 50% (v/v) slurry in washing buffer containing 20 mM
glutathionine in a 50 ml polypropylene centrifuge tube, incubated at
4°C for 1 h, and the supernatant containing eluted GST-Bid is
collected after centrifugation at 760 g for 5 min.
pH 8.0, 150 mM NaCl, 0.1% 2-mercaptoethanol, 0.1% Tween, 2.5 mM
200
CaCI2 for 2 h, and stop the reaction by adding 1 mM PMSF and 5 mM
EDTA. For 50 ml of 50% slurry, 23 mg thrombin is used. Elute Bid with
2 x resin volumes of the same buffer.
12. Dialyse the eluted Bid against 100 vols of 50 mM acetate buffer, pH
4.8, 1mM EDTA, 0.1% 2-mercaptoethonal at 4°C overnight. Inject into
a Mono S column (Pharmacia, HR10/10) that has been equilibrated
with dialysis buffer using a 2 ml/min flow rate. Wash with 50 ml of the
same buffer at 2 ml/min. Elute Bid with a linear gradient of 0-500 mM
NaCI in 60 min at 2 ml/min. Collect the samples in 1.5 ml and monitor
purity on 15% SDS-PAGE.
13. Pool pure fractions and store at -20°C at a concentration of ~1 mg/ml.
9. Measurements of pore formation by Bc1-2 family

proteins
One of the biochemical activities ascribed to some members of the Bcl-2
family of proteins is ion-channel activity (reviewed in ref. 42). The deter-
mination of the three-dimensional structure of Bcl-XL (43) showed that this
protein shares striking similarities with the previously determined structures
of the pore-forming domains of the bacterial toxins diphtheria (44) and
colicins A, E1, and Ia (45-47). These bacterial proteins share the same unique
ability in that they can exist either as soluble or membrane-inserted proteins.
They are able to achieve this large change in character by burying two, long,
predominantly hydrophobic a-helices within a shell of amphipathic helices.
Under appropriate conditions, the outer amphipathic a helices splay away,
freeing the central hydrophobic a helical hairpin to insert into the membrane
bilayer which initiates channel formation.
Bcl-XL consists of a bundle of seven a helices, arranged in three layers. The
outer two layers of amphipathic helices shield between them two long central
a-helices, each ~20 amino acids in length with a bias towards hydrophobic
residues (43). The two central a helices are of sufficient length to span the
hydrophobic cross-section of a membrane bilayer. The structural similarity
between Bcl-XL and the pore-forming domains of the bacterial toxins suggests
that the Bcl-2 protein family may possess pore-forming potential as well.
Indeed, several studies have shown that Bcl-2, Bcl-XL, and Bax exhibit
channel-forming activity in vitro (36, 48-50).
The following section describes methods for examining Bcl-2 protein family
channel formation on a macroscopic level. Macroscopic level measurements
have the advantage in that in order for channel activity to be detected, a
majority of the protein molecules must participate in channel formation.
However, the methods described do not yield information about channel
formation on a single-channel basis, particularly in terms of conductivity and
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John C. Reed et al.
ion selectivity. For quantifying these characteristics, planar bilayer measure-
ments are more appropriate. Explanation of this technique may be found in
several reviews, including refs 51 and 52.
9.1 Liposome preparation

9.1.1 Lipids
Two lipid sources are Avanti Polar Lipids (Birmingham, AL) and Sigma (St.
Louis, MO). The lipids are supplied either in powder or chloroform suspen-
sions. In either case, the contact with air of these lipid stocks should be kept to
a minimum to prevent lipid oxidation.
The lipids may be either synthetic or purified from a natural source, such as
the soybean lipid, asolectin. The latter is a mosaic of lipids, and in the case of
colicin El, higher activity is often observed over liposomes produced from
synthetic lipids (53). The synthetic lipids allow greater control over vesicle
composition, particularly the ratio of charged to uncharged lipids.
Studies of both bacterial toxins and the Bc1-2 protein family have utilized
lipid vesicles that contain at least 10 mol% negatively charged lipids. The
negatively charged lipid most commonly used has a glycerol moiety at its
headgroup, although phosphatidylserine carries a negative charge as well. In
the case of colicin El, the net negative charge of the vesicle is important for
the tight binding of the protein to the membrane surface (54). Presumably,
this requirement may be applied to the Bcl-2 protein family as well.
9.1.2 Lipid purification

Synthetic lipid stocks are of sufficient purity to be used as supplied. Further
purification of asolectin is often performed. The following purification
procedure is a modification of that described previously (55).
Protocol 28.
Method
1. 10 g asolectin is added to 100 ml acetone and stirred overnight.
2. The mixture is centrifuged at 5000 g for 10 min at room temperature.
3. The supernatant is discarded, the pellet dissolved in 40 ml anhydrous
ether, and the mixture centrifuged for 10 min at 5000 g, at room
temperature.
4. The ether is evaporated on a rotary evaporator device.
5. The dried lipid is dissolved in ~80 ml chloroform.
6. The lipid concentration is determined by a phosphate analysis (56).
202
9.1.3 Liposome production

For solute efflux to be measured, the liposomes must be large (> 0.1 mm
diameter) and unilamellar, i.e. having only a single membrane bilayer. To
produce such vesicles, the following procedure, a modification of that outlined
in Peterson and Cramer (57) is employed.
Protocol 29.
Method
1. The appropriate amount of lipid is measured. Typically, a liposome
suspension having the final concentration of 10 mg/ml lipid is used, of
which ~80 and 20% are neutral and negatively charged lipids, re-
spectively. This ratio can be varied. If powdered lipid stocks are used,
the lipid powder is first dissolved in chloroform. The chloroform lipid
suspension should be placed in a Pyrex tube.
2. The chloroform is evaporated under a stream of either nitrogen or
argon while vortexing. Use of a vortex ensures an even distribution of
the lipid film. Be certain that no pockets of chloroform are entrapped
under a thin layer of dried lipid, as inadequate removal of organic
solvents will affect liposome formation. The lipid film is further dried
under vacuum for at least two hours to remove any remaining trace of
organic solvent.
3. The lipid is then resuspended in buffer to the desired final concentra-
tion (typically 10 mg/ml). The buffer utilized in this laboratory is 10 mM
DMG (dimethyl glutaric acid), 100 mM KCI, 2 mM Ca(N03)2, pH 5.0,
although Hepes or phosphate buffers can be employed. The sus-
pension is vortexed under a stream of N2 for at least 5 min to flush out
any air from the tube. The tube is then sealed with at least two layers
of Parafilm, the top layer being somewhat lose.
4. The tube is placed in a sonicator bath (Branson). For best results, the
bath should be cleaned well and allowed to run for 30 min prior to lipid
sonication. The tube should be placed in a visible 'node' with the liquid
meniscus even with the water level. Continue sonication until the
solution has been converted from opaque to completely clear. The
lipid suspension is now composed of small unilamellar vesicles
(SUVs).
5. To convert the SUVs to large unilamellar vesicles (LUV) several freeze-
thaw cycles are employed. The suspension is frozen as rapidly as
possible in a dry-ice ethanol bath or liquid nitrogen. The frozen solution
is allowed to thaw slowly to room temperature. Repeat with at least four
additional freeze-thaw cycles. The solution should again be opaque.
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John C. Reed et al.
9.2 Channel activity measurements

9.2.1 Electrode set-up
Changes in chloride concentration are followed with a chloride-specific
electrode (Orion 94-17B) coupled to a double junction reference electrode
(Orion 90-02). The electrode signal is output to a pH meter or other suitable
voltmeter attached to a strip chart recorder. The meter utilized in this
laboratory was built according to the method of Cramer and colleagues (57)
which allows for expansion of the scale and readings of very small con-
centration changes. In addition to chloride efflux, channels formed by the Bc1-
2 protein family will also permit passage of K+, and a K+-sensitive electrode
(Orion 93-19) may be easily substituted for the chloride electrode.
9.2.2 Extravesicular buffer and protein buffers
The buffer commonly used for chloride efflux measurements in this laboratory
is that described in Peterson and Cramer (57). The buffer composition is 10
mM DMG, 100 mM choline nitrate, 2 mM Ca(NO3)2. Choline nitrate is formed
from choline bicarbonate (Sigma) and nitric acid. The buffer is degassed for at
least 1 h and titrated to the appropriate pH with NaOH. Other chloride-free
buffers are also suitable for measurement, provided their ionic strength is
similar to that used for vesicle preparation.
The protein sample should be in a buffer that is chloride free, if possible,
and should also lack any compounds which would interfere with electrode
response. B-Mercaptoethanol has been found to especially perturb electrode
response (S. L. Schendel and J. C. Reed, unpublished results).
9.2.3 Ion efflux measurement
Extravesicular buffer (15 ml) is placed in a disposable plastic beaker (Fisher).
Use of such inexpensive beakers removes the need for tedious washing
between trials. Approximately 75-100 ml of the liposome suspension is
pipetted into the beaker and the electrode allowed to equilibrate until a stable
baseline is achieved. The solution should be stirred at medium speed at all
times and no bubbles should adhere to the electrode tips. Once the baseline
has stabilized, 2 ml of a 70 mM methanol stock of the K+-specific ionophore
valinomycin is added to the beaker. Valinomycin induces the formation of a
Nernst diffusion potential of ~135 mV, negative inside. The ionophore may
be omitted if no membrane potential is desired. The electrode is again
allowed to equilibrate following valinomycin addition. The Bc1-2 family pro-
tein is then added to a concentration that will induce release of 50-80% of the
total encapsulated Cl- and induce a response having a slope between 30 and
60° which facilitates accurate calculation of the efflux rate. After the protein-
induced efflux has levelled off, Triton X-100 is added to the beaker to a final
concentration of 0.1%. This detergent addition lyses the vesicles and releases
any residual chloride, allowing the total amount of chloride encapsulated to
204
be determined. Examples of chloride-efflux induced by Bcl-2 family proteins, as
measured by these methods, can be found in previous publications (36, 38, 48).
At the end of the measurements, a calibration curve is produced by
additions of known amounts of KC1. The KC1 is added in the presence of an
aliquot of liposomes, so that the background Cl~ concentration is similar. KC1
is added in progressively increasing amounts until the chart recorder
deflection equals the maximum observed by Triton X-100 lysis of the vesicles.
For colicin molecules, where the molecularity of the channel is known to be
1 (58), a specific Cl~ efflux rate can be calculated by determining the ratio of
colicin-induced Cl~ release to the total encapsulated Cl-. This value is then
divided by the number of colicin molecules present (assuming that each
molecule forms one channel) and the quotient divided by the time taken for
the efflux to occur. Since the molecularity of the Bcl-2 protein family channels
is still unclear, this rate calculation is not as straightforward. For purposes of
comparison between trials, this laboratory simply determines the slope of the
initial response.
10. Methods of assaying Bcl-2 and Bax family protein

function in yeast
Bcl-2 family proteins play an evolutionarily conserved role in regulating the
life and death of the cell. Certain pro-apoptotic members of the Bcl-2 family,
Bax and Bak, have intrinsic cytotoxic activities in that they not only induce or
sensitize mammalian cells to undergo apoptosis but also display a lethal
phenotype when ectopically expressed in two yeast species Saccharomyces
cerevisiae and S. pombe (59-65). Furthermore, the anti-apoptotic Bcl-2 and
Bcl-XL proteins can protect yeast against Bax-mediated lethality, suggesting
that the death-regulatory functions of these Bcl-2 family proteins are well
preserved in yeast. These observations provide the opportunity to study the
function of Bcl-2 family proteins in genetically tractable yeast and to apply
classical yeast genetics and functional cloning approaches to the dissection of
programmed cell death pathway regulated by Bcl-2 family proteins. We
describe here methods used in our laboratory to assess cytotoxic and cytopro-
tective functions of Bcl-2 family proteins in the budding yeast 5. cerevisiae.
10.1 Plasmid considerations

A variety of expression vectors are available to express foreign genes in
5. cerevisiae. Two major issues require consideration when choosing a yeast
vector for expressing Bax or other Bcl-2 family members in these organisms.
First, Bax needs to accumulate to high levels to cause cell death, thus a strong
promoter should be employed. Secondly, vectors with appropriate selectable
markers should be chosen depending on the yeast strain used. Two general
types of promoters are used to achieve high level gene expression in S.
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John C. Reed et al.
cerevisiae: (a) constitutive and (b) conditional promoters. Promoters of the
alcohol dehydrogenase (ADH1) and glyceraldehyde-3-phosphate dehydro-
genase (GPD or GAP) genes are commonly employed strong constitutive
promoters. When expressing the bax gene under the control of either the
ADH1 or GPD promoter, the diminished number of transformed colonies
can be employed as an indicator of the lethality caused by Bax. A parallel
transformation with an 'empty' vector is included as a control. This assay,
however, has limitations in interpreting the data, because reductions in
transforming activity can be a result of cell cycle arrest, cell death, or even
some contaminants in DNA that affect transformation efficiency. For this
reason, we prefer a regulatable expression system over a constitutive system.
Several conditional promoters have been employed for expressing
heterologous genes in yeast; the most commonly used is a hybrid promoter
combining the UAS (upstream activating sequence) from the GAL1/GAL10
gene and the basal promoter from the CYC1 gene, these are often referred to
as the GAL1 or GAL10 promoters. The GAL promoter is regulated by the
availability of carbon sources in the growth medium: transcription is
repressed when yeast are grown in glucose-containing medium; derepressed
when yeast are grown in raffinose-containing medium; and dramatically
induced when yeast are grown in galactose-containing medium. Under
optimal conditions, inductions as high as a 1000-fold can be achieved when
yeast are grown in medium which contains galactose but lacks glucose. The
optimal time for inducing transcription from the GAL promoter is strain
dependent and thus should be determined empirically. In general, however,
we perform assays at 18-24 h after placing cells in galactose-containing
medium. The induction can be monitored by immunoblot analysis using
antibodies directed against the heterologous protein of interest.
Basic machinery for transcription and translation is highly conserved from
yeast to mammals; therefore, a mammalian cDNA, with minor engineering,
often expresses well in yeast. By employing a yeast promoter, transcription
initiation of the heterologous gene should proceed efficiently. Most expression
vectors also include a yeast transcription terminator, such as the terminator for
the CYC1 gene, to ensure production of correctly sized mRNAs and to
improve transcription efficiency. Translation initiation in mammalian cells
occurs most efficiently within the context of preferred sequences flanking the
AUG initiation codon, commonly referred to as a Kozak sequence (66). AUG
codons that deviate from the Kozak consensus often translate inefficiently. No
well-defined equivalent of the Kozak sequence exists in yeast. To achieve
efficient translation initiation, it is required that the initiation codon within
heterologous cDNAs represents the first AUG from the 5'-end. In addition, it
is preferable to eliminate as much of the 5'-untranslated sequences from the
introduced cDNA as possible, since translation can be hindered if the 5'-
untranslated region of the mRNA has the potential to form secondary
structures or contains a high GC content (67).
206
For our experiments, we employed the GAL promoter-containing vector
YEp5l for expressing Bax in S. cerevisiae. YEp5l is a high copy number yeast
plasmid bearing the LEU2 gene as a selectable marker. We cloned bax cDNA
into YEp5l using the SalI site in the polylinker (i.e. the restriction site closest
to the GAL10 promoter), thus keeping the length of the resulting 5'-
untranslated region to a minimum (61).
A variety of yeast expression vectors containing either the GAL regulat-
able promoter or the ADH1 and GPD constitutive promoters are available
from American Type Culture Collection (ATCC, Manassas, VA) (68, 69).
10.2 Saccharomyces cerevisiae strains

Once constructed, the expression plasmid is transformed into an appropriate
yeast strain following standard transformation procedures, as described below.
In principle, any laboratory strain with appropriate auxotrophic mutations
corresponding to the selectable marker on the expression plasmid can be used
as a host strain for expressing Bax. In practice, however, strain background
variations may affect the sensitivity of yeast to Bax. We have tested the effect
of Bax in a few haploid strains. Some strains, such as BF264-15Dau (70), were
found to be relatively more sensitive to Bax, suggesting that strain differences
do matter. Thus, it is advisable to test yeast stains from different origins, so
that the most sensitive ones can be employed. A second factor to consider
when selecting a yeast strain is the availability of auxotrophic markers. URA3,
LEU2, HIS3, and TRP1 are the four commonly used auxotrophic markers for
5. cerevisiae. Strains with multiple auxotrophic markers provide greater flexi-
bility, especially in cases where the effects of more than one protein are to be
tested. Some commonly used laboratory yeast strains contain these auxo-
trophic mutations, including W303a or a (genotype: MAT a/or a leu2-3 112
his3-11,15 try1-1 ura3-1 can1-100 ade2-l) and EGY48 (genotype: MATa
leu2-3 112 his3-11,15 trp1-1 ura3-l 6LexAop-LEU2). Yeast strains can be
obtained from the Yeast Genetic Stock Center at ATCC.
10.3 Media and growth conditions

We routinely culture yeast in YPD-rich medium. Once a plasmid is intro-
duced, yeast should be grown in synthetic drop-out medium to select for the
plasmid. For example, after transforming YEp51-Bax into yeast, transform-
ants are initially selected and subsequently maintained on synthetic drop-out
medium lacking leucine (SD-Leu) and supplemented with glucose to repress
Bax expression. We observed that the amount of nutrients in the medium can
also affect the sensitivity of yeast to pro-apoptotic proteins. In general, we
find that yeast are more sensitive to Bax when cultured in medium with mini-
mal nutrients. For this reason, Burkholder's Minimal Medium (BMM)
medium (71) may be useful for detecting a more striking lethal effect of Bax
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John C. Reed et al.
in yeast. The preparation of commonly used media is listed below (see refs 72
and 73 for detailed descriptions of S. cerevisiae media).
Protocol 30. YPD medium
Method
1. To a 2 litre flask, add 10 g Bacto-yeast extract and 20 g Bacto-peptone.
Include 20 g of agar when making YPD plates.
2. Bring the volume to 900 ml with distilled H20.
3. Following autoclaving, add 100 ml of filter-sterilized 20% glucose
(dextrose) stock.
4. When making plates, let the medium cool to 65°C and then pour into
Petri dishes. 1 litre of medium should yield about 50 100 mm diameter
plates.
Protocol 31. SD medium
There are three steps to the preparation of SD medium.
Method
1. Prepare the following amino acid and supplement stocks in distilled
H20: 4 mg/ml each of adenine, L-histidine-HCI, L-arginine-HCI, L-
methionine, L-leucine, L-isoleucine, L-lysine-HCI, phenylalanine,
aspartic acid, and valine; 2 mg/ml of uracil. Sterilize by autoclaving. 4
mg/ml each of L-tryptophan, L-tyrosine, and L-threonine and sterilize by
filtration. Store at room temperature.
2. To a 2-litre Erlenmeyer flask, add 6.7 g yeast nitrogen base without
amino acids, and 10 ml each of the above amino acid stocks and 20 ml
of uracil, leaving out the three heat-sensitive amino acids (tryptophan,
tyrosine, and threonine). Omit the amino acid(s) that will be used
for selection of the plasmid(s). Add 20 g of agar when making
solid medium. Bring the volume to 870 ml with distilled H2O and
autoclave.
3. Cool the solution to about 80°C, then add 10 ml each of the three heat-
sensitive amino acids and 100 ml of filter-sterilized sugar stocks (either
20% glucose or 20% galactose; we often supplement galactose
medium with 1% raffinose). SD plates are prepared similarly as
described for YPD plates above.
208
Protocol 32. BMM medium
Method
1. Prepare the following stock solutions in distilled H2O.
Mineral stocks (10000 X)
(a) To a 100-ml Erlenmeyer flask, add 30 mg H3BO3, 50 mg
MnSO4.7H20, 150 mg ZnS04.7H2O, and 20 mg CaS04.5 H2O. Bring
the volume to 50 ml with dH20.
(b) To a 100-ml Erlenmeyer flask, add 100 mg Na2MoO4.2H20. Bring
the volume to 50 ml with dH20.
(c) To a 100-ml Erlenmeyer flask, add 125 mg FeCI3.6H2O. Bring the
volume to 50 ml with dH20.
(d) Do not autoclave. Store at 4°C.
Vitamin stock (WOO x)
To a 250-ml Erlenmeyer flask, add 20 mg thiamine, 20 mg pyridoxine,
20 mg nicotinic acid, 20 mg pantothenic acid, 0.2 mg biotin, and 1 g inositol,
add H2O to 100 ml. Filter sterilize and store at 4°C.
2. To a 2-litre Erlenmeyer flask, add 1.5 g KH2P04, 500 mg MgS04.7H2O,
330 mg CaCI2.2H2O, 100 mg Kl, 2 g asparagine. 100 ml each of mineral
stocks (a), (b), and (c) (10000 x) and 10 ml each required amino acids
(the ones that yeast can not make) except the heat-sensitive ones
(amino acid stocks are made as described for SD medium). Include
20 g agar when making solid medium. Bring the volume to 900 ml with
dH2O and autoclave.
3. Following autoclaving and cooling to about 80°C, add 1 ml vitamin
stock (1000 x), 10 ml each of heat-sensitive amino acids and 100 ml of
appropriate carbon source (from 20% glucose or galactose stock as
described for SD medium). BMM plates are made similarly as
described for YPD or SD plates.
10.4 Transformation of S. cerevisiae by the LiOAc method

Plasmid DNA can be introduced into yeast by several different means. We
routinely transform 5. cerevisiae using the LiOAc method (74). The trans-
formation efficiency achieved with this method can be influenced by multiple
factors. Strain background, cell density at the time of transformation, the
quality of the plasmid DNA and carrier DNA used for transformations, and
the length of heat-shock can all play some role in influencing the final out-
come. When using the protocol below, the transformation efficiency we
routinely obtain is103-104transformants/ ug DNA.
209
John C. Reed et al.
Protocol 33.
Method
1. Inoculate a single colony into 50 ml YPD or SD medium in a 250-ml
Erlenmeyer flask and grow yeast to a mid-exponential phase
(OD600=0.8) at 30°C in an incubator-shaker set at 250 rpm.
2. Harvest cells by centrifugation (5 min at 1000 g) and wash once in 50
ml distilled H20.
3. Collect cells by centrifugation as above. Wash cells in 10 ml LiOAc
solution (0.1 M LiOAc, 10 mM Tris-HCI, pH 8.0, 1 mM Na2EDTA) and
resuspend the cell pellet in 0.5 ml (1/100 of initial culture volume)
LiOAc solution. Cells can be stored in LiOAc at 4°C for up to one week
and transformation can be performed at a later time, but with reduced
efficiency.
4. Aliquot 100 MI cell suspension into each microfuge tube and add 5 mI
10 mg/ml carrier DNA (sheared single-strand salmon sperm DNA;
Sigma) and 1 mg plasmid DNA to each aliquot. Keep the total volume
of DNA below 10 ml.
5. Add 0.7 ml PEG solution [40% polyethylene glycol (PEG 3300-4000),
0.1 M LiOAc, 10 mM Tris-HCI, pH 8.0, 1 mM Na2EDTA, pH 8.0] to the
cell DNA mixture, vortex vigorously, and incubate at 30°C for 45 min
with constant shaking.
6. Heat-shock in a 42°C water bath for 5-15 min. Centrifuge in a
microcentrifuge at 1000 g for 5 min and resuspend the cells in 200 ml
TE buffer (10 mM Tris-HCI, pH 8.0, 1 mM Na2EDTA, pH 8.0).
7. Spread the transformation mixture on SD solid plates lacking amino
acids required for selection of the plasmid and place the plates in a
30°C incubator (VWR Scientific Products).
8. Colonies should appear in 2-4 days.
10.5 Assay for Bax-induced lethality in S. cerevisiae

When YEp51-Bax is introduced into an appropriate yeast strain, the effect of
Bax on yeast growth can be easily observed by plate tests. Yeast containing
YEp51-Bax are maintained on glucose-containing SD-Leu plates. A single
colony can be streaked on galactose-containing SD-Leu plates to induce Bax
expression side by side with a control streak from a colony containing YEp51
lacking Bax ('empty'). This test of growth inhibition can also be performed by
standard replica-plating, although it is less sensitive than streaking. The
drastically reduced growth rate observed on galactose medium which induces
the bax gene indicates that the gene product is either cytotoxic to yeast or
210
induces cell cycle arrest. Two assays can be employed to distinguish between
these possibilities: the clonogenic (or colony formation) assay and the vital
dye exclusion assay.
10.5.1 Clonogenic assay

The rationale for this assay is that if inducing Bax expression (by culturing in
galactose medium) induces cell death there will be few colonies formed when
spreading these dead cells on glucose plates since death is irreversible. On the
other hand, if Bax simply causes cell cycle arrest (a reversible process), cells
should be able to re-enter the cell cycle and to proliferate when shifted back
to permissive conditions (glucose medium) where Bax expression is shut off.
1. Inoculate a single colony of yeast bearing YEp51-Bax into 5 ml liquid
SD-Leu medium and culture at 30°C in an incubator-shaker (Lab-line
Instruments Inc., Melrose Park, IL) set at 250 r.p.m. to a mid-exponential
phase (OD600=0.4-0.6).
2. Cells are harvested by centrifugation at 1000 g for 5 min and washed three
times in sterilized H2O or PBS at room temperature to remove residual
glucose.
3. After the final wash, cells are resuspended in 5 ml galactose-containing
SD-Leu liquid medium for continuous culturing. At different times
thereafter, cell densities are determined by measuring OD600, (OD600 of 1
equals about 3 X 107 cells/ml). Cells are then diluted and about 103 cells are
spread on glucose-containing SD-Leu plates.
10.5.2 Vital dye exclusion assay

Cell viability can also be determined by the vital dye exclusion assay. Dead
cells have lost plasma membrane integrity and as a result cannot exclude dyes
and thus are stained. For example, trypan blue can be used to stain yeast. The
ability of cells to exclude trypan blue indicates that they are still alive. Thus, if
yeast failed to grow on galactose plates but still excludes trypan blue, then
presumably this is the result of a problem with the cell cycle rather than cell
death. On the other hand, inability to exclude trypan blue (cells are thus
stained blue) indicates that the gene introduced is lethal to yeast. The
percentage of blue cells can also be employed as an indicator of the potency of
the killing. Other vital dyes, such as methylene blue and erythrosine B, have
also been employed (62).
1. Grow YEp51-Bax-containing yeast and transfer to galactose-containing
medium as described above for the clonogenic assay.
2. At different times after inducing Bax expression in galactose-containing
liquid medium, remove 20 ml of the yeast culture and mix with 20 ml of 0.4
% of trypan blue solution in PBS (Sigma). The numbers of dead (blue) and
live (no colour) cells are determined using a haemocytometer (Hausser
211
John C. Reed et al.
Scientific, Horsham, PA) under a light microscope and the percentage of
dead cells is calculated. The existence of cell wall on yeast does not
interfere with trypan blue assays.
When the death gene introduced is under the control of a constitutive
promoter, e.g. the ADH1 or GPD promoter, no transformants or far fewer
transformants will form after introducing the expression plasmids into yeast
and plating on selective drop-out medium, which selects for the introduced
plasmid. An 'empty' vector should also be transformed in parallel as a control.
In this assay, however, one will not be able to tell the difference between
growth arrest and cell death. One way to circumvent this, is to introduce, for
example, ADH1—Bax-bearing plasmid into a strain already containing an
anti-apoptotic gene under the control of a conditional promoter, e.g. GAL-
bc1-2. When cells are cultured in galactose-containing medium, expression of
the anti-apoptotic gene will protect yeast cells from the cytotoxic effect of the
introduced bax gene. After transformants are formed on galactose plates,
these can be streaked or patched on glucose-containing plates where expres-
sion of the anti-apoptotic bc1-2 gene is shut off, and thus the effect of the bax
gene is revealed. In this case, streaking or patching in parallel to a glucose
plate provides a control for any non-specific growth failures due to unforeseen
technical problems.
11. Summary
The methods described here provide a broad range of techniques for scientists
interested in studying the expression and function of Bcl-2 family proteins.
Though alternative approaches are possible, the protocols presented here
have proved robust and reproducible when used by multiple investigators in
our laboratory. We welcome feedback from others who attempt these
methods or who make further modifications and improvements in the future.
Acknowledgements
We thank T. Brown for manuscript preparation and E. Smith for artwork.
References
1. Reed, J. (1998) Oncogene 17, 3225-3236
2. Zamzami, N., Brenner, C., Marzo, Susin, S., and Kroemer, G. (1998) Oncogene 16,
2265-2282
3. Chao, D.T., and Korsmeyer, S. J. (1998) Annu. Rev. Immunol. 16, 395-419
4. Adams, J., and Cory S. (1998) SCIENCE 281, 1322-1326
5. Reed, J. C. (1996) Behring Inst. Mitt. 97, 72-100
6. Reed, J. C. (1997) in Vitamins and Hormones (Litwack, G., ed) Vol. 53, pp. 99-138,
Academic Press, San Diego
7. Reed, J. (1998) Heart Failure Rev. 3, 15-26
8. Thompson, C. B. (1995) SCIENCE 267, 1456-1462
9. Strasser, A., Huang, D. C. S., and Vaux, D. L. (1997) Biochim. Biophys. Acta 1333,
F151-F178
212
10. Krajewski, S., Zapata, J. M., and Reed, J. C. (1996) Anal. Biochem. 236, 221-228
11. Smith, P., Krohn, R., Hermanson, G., Mallia, K., Gartner, F., Prozenzano, M., Fujimoto,
E., Goeke, N., Olson, B., and Klenk, D. (1985) Anal. Biochem. 150, 76-85
12. Krajewski, S., Bodrug, S., Gascoyne, R., Berean, K., Krajewska, M., and Reed, J. C.
(1994) Am. J. Pathol. 145, 515-525
13. Krajewski, S., Krajewska, M., Shabaik, A., Wang, H.-G., Irie, S., Fong, L., and Reed,
J. C. (1994) Cancer Res. 54, 5501-5507
14. Krajewski, S., Krajewska, M., Shabaik, A., Miyashita, T., Wang, H.-G., and Reed, J. C.
(1994) Am. J. Pathol. 145, 1323-1333
15. Krajewski, S., Bodrug, S., Krajewska, M., Shabaik, A., Gascoyne, R., Berean, K., and
Reed, J. C. (1995) Am. J. Pathol. 146, 1309-1319
16. Krajewski, S., Blomvqvist, C., Franssila, K., Krajewska, M., Wasenius, V.-M.,
Niskanen, E., and Reed, J. C. (1995) Cancer Res. 55, 4471-4478
17. Krajewski, S., Mai, J. K., Krajewska, M., Sikorska, M., Mossakowski, M. J., and Reed,
J. C. (1995) J. Neurosci. 15, 6364-6376
18. Krajewski, S., Krajewska, M., and Reed, J. C. (1996) Cancer Res. 56, 2849-2855
19. Kitada, S., Krajewska, M., Zhang, X., Scudiero, D., Zapata, J. M., Wang, H. G., Shabaik,
A., Tudor, G., Krajewski, S., Myers, T. G., Johnson, G. S., Sausville, E. A., and Reed,
J. C. (1998) Am. J. Pathol. 152(1), 51-61
20. Pezzella, F., Tse, A., Cordell, J., Pulford, K., Gatter, K., and Mason, D. (1990) Am. J.
Pathol. 137, 225
21. Reed, J. C., Tanaka, S., Cuddy, M., Cho, D., Smith, J., Kallen, R., Saragovi, H. U., and
Torigoe, T. (1992) Anal. Biochem. 205(1), 70-76
22. Hockenbery, D. M., Zutter, M., Hickey, W., Nahm, M., and Korsmeyer, S. J. (1991)
Proc. Natl. Acad. Sci. USA 88, 6961-6965
23. Novack, D. V., and Korsmeyer, S. J. (1994) Am. J. Pathol. 145, 61-73
24. Broome, H. E., Dargan, C. M., Bessent, E. F., Krajewski, S., and Reed, J. C. (1995)
Immunol. 84, 375-382
25. Tsujimoto, Y., and Croce, C. (1986) Proc. Natl .Acad. Sci. USA 83, 5214-5218
26. Negrini, M., Silini, E., Kozak, C., Tsujimoto, Y., and Croce, C. M. (1987) Cell 49, 455-463
27. Chomczynski, P., and Sacchi, N. (1987) Anal. Biochem. 162, 156-159
28. Chomczynski, P. (1992) Anal. Biochem. 201, 134-139
29. Ogretmen, B., Ratajczak, H., Kats, A., Stark, B. C., and Gendel, S. M. (1993) Biotech-
niques 14, 932-935
30. Maniatis, T., Fritsch, E. F., and Sambrook, J. (1982) Molecular Cloning, 0 Ed., Cold
Spring Harbor Laboratory, Cold Spring Harbor
31. Kitada, S., Miyashita, T., Tanaka, S., and Reed, J. C. (1993) Antisense Res. Dev. 3,
157-169
32. Kitada, S., Takayama, S., DeRiel, K., Tanaka, S., and Reed, J. C. (1994) Antisense Res.
Dev. 4, 71-79
33. Miyashita, T., Krajewski, S., Krajewska, M., Wang, H. G., Lin, H. K., Hoffman, B.,
Lieberman, D., and Reed, J. C. (1994) Oncogene 9, 1799-1805
34. Wijsman, J.H., Jonker, R.R., Keijzer, R., van de Velde, C.J.H., Cornelisse, C.J., and
van Dierendock, J.H. (1993) J. Histochem. Cytochem. 41, 7-12
35. Sternberger, L. A., Hardy Jr., P. H., Cuculis, J. J., and Meyer, H. G. (1970) J.
Histochem. Cytochem. 18, 315-320
36. Schendel, S. L., Xie, Z., Montal, M. O., Matsuyama, S., Montal, M., and Reed, J. C.
(1997) Proc. Natl. Acad. Sci. USA 94, 5113-5118
37. Xie, Z., Schendel, S., Matsuyama, S., and Reed, J. C. (1998) Biochemistry 37,
6410-6418
38. Matsuyama, S., Schendel, S., Xie, Z., and Reed, J. (1998) J. Biol. Chem 273,
30995-31001
39. Marzo, L, Brenner, C., Zamzami, N., Jurgensmeier, J. M., Susin, S. A., Vieira, H. L. A.,
Prevost, M.-C., Xie, Z., Matsuyama, S., Reed, J. C., and Kroemer, G. (1998) SCIENCE
281, 2027-2031
40. Asoh, S., Nishimaki, K., Nanbu-Wakao, R., and Ohta, S. (1998) J. Biol. Chem. 273(18),
11384-11391
213
John C. Reed et al.
41. Lewis, S., Bethell, S., Patel, S., Martinou, J.-C., and Antonsson, B. (1998) Protein Expr.
Purif. 13, 120-126
42. Schendel, S., Montal, M., and Reed, J. C. (1998) Cell Death Differ. 5(5), 372-380
43. Muchmore, S. W., Sattler, M., Liang, H., Meadows, R. P., Harlan, J. E., Yoon, H. S.,
Nettesheim, D., Changs, B. S., Thompson, C. B., Wong, S., Ng, S., and Fesik, S. W.
(1996) NATURE 381, 335-341
44. Choe, S., Bennett, M. J., Fujii, G., Curmi, P. M. G., Kantardjieff, K. A., Collier, R. J.,
and Eisenberg, D. (1992) NATURE 357, 216-221
45. Parker, M. W., Postma, J. P. M., Pattus, F., Tucker, A. D., and Tsernoglou, D. (1992)
J. Mol. Biol. 224, 639-657
46. Elkins, P., Bunker, A., Cramer, W. A., and Stauffacher, C. V. (1997) Structure 5, 443-458
47. Weiner, M., Freymann, S., Ghosh, P., and Stround, R. M. (1997) Nature 385, 461-464
48. Minn, A. J., Velez, P., Schendel, S. L., Liang, H., Muchmore, S. W., Fesik, S. W., Fill,
M., and Thompson, C. B. (1997) NATURE 385, 353-357
49. Antonsson, B., Conti, F., Ciavatta, A., Montessuit, S., Lewis, S., Martinou, I.,
Bernasconi, L., Bernard, A., Mermod, J.-J., Mazzei, G., Maundrell, K., Gambale, F.,
Sadoul, R., and Martinou, J.-C. (1997) SCIENCE 277, 370-372
50. Schlesinger, P., Gross, A., Yin, X.-M., Yamamoto, K., Saito, M., Waksman, G., and
Korsmeyer, S. (1997) Proc. Natl. Acad. Sci. USA 94, 11357-11362
51. Montal, M., and Mueller, P. (1972) Proc. Natl. Acad. Sci. USA 69(12), 3561-3566
52. Kagan, B. L., and Sokolov, Y. (1994) Methods in Enzymology 235, 691-705
53. Schendel, S. L., and Cramer, W. A. Unpublished results
54. Zakharov, S. D., Heymann, J. B., Zhang, Y.-L., and Cramer, W. A. (1996) Biophys. J.
70, 2774-2783
55. Kawaga, Y., and Racker, E. (1971) J. Biol. Chem. 246, 5477-5487
56. Bartlett, G. R. J. (1959) /. Biol. Chem. 234, 466-472
57. Peterson, A. A., and Cramer, W. A. (1987) J. Membr. Biol. 99, 197-204
58. Cramer, W. A., Heymann, J. B., Schendel, S. L., Deriy, B. N., Cohen, F. S., Elkins,
P. A., and Stauffacher, C. V. (1995) Annu. Rev. Biophys. Biomol. Struct. 24, 611-641
59. Sato, T., Hanada, M., Bodrug, S., Irie, S., Iwana, N., Boise, L.H., Thompson, C.B.,
Golemis, E., Fong, L., Wang, H-G., and Reed, J.C. (1994) Proc. Natl. Acad. Sci. USA 91,
9238-9242
60. Hanada, M., Aime-Sempe, C., Sato, T., and Reed, J.C. (1995) J. Biol. Chem. 270,
11962-11968
61. Zha, H., Fisk, H., Yaffe, M., Mahajan, N., Herman, B., and Reed, J.C. (1996) Mol. Cell.
Biol. 16, 6494-6508
62. Greenhalf, W., Stephan, C., and Chaudhuri, B. (1996) FEBS Lett. 380, 169-175
63. Jurgensmeier, J., Krajewski, S., Armstrong, R., Wilson, G., Oltersdorf, T., Fritz, L.,
Reed, J., and Ottilie, S. (1997) Mol. Biol. Cell 8, 325-339
64. Ink, B., Zornig, M., Baum, B., Hajibagheri, N., James, C., Chittenden, T., and Evan, G.
(1997) Mol. Biol. Cell 17(5), 2468-2474
65. Tao, W., Kurschner, C., and Morgan, J.I. (1997) /. Biol. Chem. 272(24), 15547-15552
66. Kozak, M. (1991) /. Cell. Biol. 115, 887-903
67. Hinnebusch, A. G., and Liebman, S. W. (1991) in The Molecular and Cellular Biology
of the Yeast Saccharomyces: Genome Dynamics, Protein Synthesis, and Energetics
(Broach, J. R., Pringle, J. R., and Jones, E. W., Eds.) Cold Spring Harbor Laboratory
Press, Cold Spring Harbor, NY, 627-735
68. Mumberg, D., Muller, R., and Funk, M. (1994) Nucl. Acids. Res. 22, 5767-5768
69. Mumberg, D., Muller, R., and Funk, M. (1995) Gene 156, 119-122
70. Lew, D. J., Dulic, V., and Reed, S. I. (1991) CELL 66(6), 1197-1206
71. Toh-e, A., Ueda, Y., Kakimoto, S.-L, and Oshima, Y. (1973) J. Bacteriol. 113, 727-738
72. Sherman, F. (1991) in Guide to Yeast Genetics and Molecular Biology. (Guthrie, C., and
Fink, G. R. Eds.), Academic Press, San Diego. 194, 3-21
73. Sherman, F., and Hicks, J. (1991) in Guide to Yeast Genetics and Molecular Biology.
(Guthrie, C, and Fink, G. R. Eds.), Academic Press, San Diego 194, 21-38
74. Ito, H., Fududa, Y., Murata, K., and Kimura, A. (1983) J. Bacteriol. 153, 163-168
214
10
Methods for detecting proteolysis

during apoptosis in intact cells
APRIL L. BLAJESKI and SCOTT H. KAUFMANN
1. Introduction
Over the past five years it has become clear that protease activation is the
single most important event that characterizes the process of apoptosis. In the
present chapter, we briefly review the evidence that proteases—particularly
caspases—play an important role in apoptosis. We then discuss various
methods that have been applied to the study of caspases and their precursors,
including immunoblotting, activity assays, and affinity labelling. We also
describe various polypeptides whose cleavage can be used as a marker for
caspase activation in situ. Finally, we outline an approach for determining
whether a particular cleavage is mediated by caspases, focusing on the
potential pitfalls in relying solely upon in vitro cleavage assays or inhibitor
studies.
2. Involvement of proteases in apoptosis

As described elsewhere in this volume, apoptosis is a morphologically and
biochemically distinct form of cell death that involves disassembly of the cell
without rupture and leakage of intracellular contents. Four important lines of
evidence support a role for caspases in the apoptotic process. First, these
proteases have been identified as the enzymes responsible for the proteolysis
of numerous nuclear and cytoplasmic proteins that are cleaved during
apoptosis (1). Second, proteolytic cleavage of certain caspase zymogens to
yield the active enzymes correlates with appearance of the apoptotic pheno-
type. Third, treatment with low molecular weight peptide-based caspase
inhibitors, as well as overexpression of endogenous caspase inhibitors (e.g.
inhibitor of apoptosis proteins), prevents apoptosis in cell-free models, in
intact cells, and in whole animals (1, 2). Finally, mice containing disruptions in
the genes for caspase-3 (3) or caspase-9 (4) have severe defects in brain
development, presumably due to the lack of extensive apoptosis that normally
occurs during ontogeny.
Table 1. Selected properties of ICE family proteases
New name Old name Molecular weighta Preferred small substratesb Commercial sources of antibodies
Pre Lg Sm
Caspase 1 ICE 45 24 14 Pharmingen, Upstate Biotechnology, Santa

20 10 YEVD/X WEHD/X Cruz Biotechnology, Oncogene Research
Products
Caspase 2 lch-lL, 48 32 14 VDVAD/X DEHD/X Pharmingen, Upstate Biotechnology, Santa
NEDD2 18 12 Cruz Biotechnology, Transduction
Laboratories, Oncogene
Caspase 3 CPP32,YAMA,Apopain 32 20 12 DMQD/X DEVD/X Chemicon, Pharmingen, Upstate
17 Biotechnology, Santa Cruz Biotechnology,
Oncogene, Transduction Laboratories
Caspase 4 Tx, lch-2, ICErelll LEVD/X (W/L)EHD/X Pharmingen, Oncogene
Caspase 5 ICErellll,Ty Unknown (W/L)EHD/X
Caspase 6 Mch2 34 21 13 VEID/X VEHD/X Santa Cruz Biotechnology
18 11
Caspase 7 Mch3, CMH-1, ICE-LAP3 34 20 12 DEVD/X DEVD/X Transduction Laboratories, Santa Cruz
Biotechnology
Caspase 8 Mch5, FLICE, MACH 53 43 12 IETD/X LETD/X Pharmingen, Santa Cruz Biotechnology
55 18 11
Caspase 9 ICE-LAP6, Mch6 50 37 12 Unknown LEHD/X Pharmingen, Santa Cruz Biotechnology
Caspase 10 Mch4, FLICE-2 55 43 12 IEAD/X Unknown Santa Cruz Biotechnology
17
Caspase 13 ERICE Unknown Unknown
"Pre, Lg and Sm denote the MW of the respective caspase precursor, large subunit and small subunit. The appearance of multiple entries indicates partially
processed and fully processed large and small subunits that result from sequential cleavage at the C-terminal end of the large subunit, followed by removal of
the linker peptide from the small subunit and the prodomain from the large subunit. A blank in this column indicates that the MW of the processed forms has not
been reported.
b
The left column indicates the preferred substrate specificity reported by Talanian et al. (32), whereas the right column indicates that reported by Thornberry et
al. (12).
10: Methods for detecting proteolysis during apoptosis in intact cells
Although the preceding observations clearly implicate caspases in
apoptotic biochemical events, it is important to realize that other proteases
can also play a role. Granzyme B, a serine protease present in granules of
cytotoxic lymphocytes, can proteolytically activate certain caspase precursors
and also directly cleave certain caspase substrates in situ and in vitro (5), as
discussed in Chapter 5. The serine protease A24 and the cysteine protease
cathepsin B appear to be activated downstream of caspases in certain model
systems (1), raising the possibility that these proteases might be responsible
for some of the protein cleavages that occur during apoptosis. Calpains have
also been implicated in the apoptotic process (1, 6), as have cathepsin D and
the proteosome (2). With the exception of actin, which is thought to be
cleaved by calpains in some cell types (7), the substrates of these various
proteases during apoptosis remain to be identified. Although the present
chapter focuses on caspases, the approach outlined below should be
applicable to the study of other proteases and their potential substrates.
3. Caspase nomenclature and classification

The observation that ced-3, a gene that is essential for apoptosis in the nema-
tode Caenorhabditis elegans, encodes a polypeptide with extensive homology
to the cysteine protease interleukin-lB-converting enzyme (ICE) (8) prompted
intensive investigation into the potential role of this family of proteases in
various models of apoptosis. To date, 13 mammalian members of this family
have been described, 11 in humans (1). A list of the known human caspases,
along with their old names, molecular weights, and sequence preferences, is
found in Table 1.
All of these enzymes share several properties. First, they are cysteine-
dependent proteases that cleave polypeptides on the carboxyl side of aspart-
ate residues. This activity led to the current designation of these enzymes
as 'caspases' (9). Second, each of these enzymes is an a2B2 tetramer consist-
ing of two 17-20 kDa large subunits and two 10-12 kDa small subunits.
Finally, each of the caspases is synthesized as a zymogen that encodes a
prodomain, a large subunit, and a small subunit. Activation of these
zymogens (Figure 1) involves proteolytic cleavage between the large and
small subunits, followed by removal of the prodomain (1). Caspases
themselves and the serine protease granzyme B are currently the only
enzymes known to be capableof catalysing this activation process under
physiological conditions (10-12).
Based on either sequence homology or function (1), these enzymes can be
further divided into at least two broad categories, 'initiator' caspases and
'effector' caspases. Initiator caspases catalyse the cleavage of other caspases,
thereby initiating a caspase cascade (1, 13). The initiator caspases typically
contain long prodomains that interact with other intracellular components.
For example, the prodomains of caspases-8 and -10 contain structural motifs
217
Figure 1. Schematic representation of caspase activation. As indicated in the text,

caspases are synthesized as zymogens that contain three distinct domains. Activation
involves cleavage between the large and small subunits followed by removal of the
prodomain (1). Several of the caspases that have long prodomains serve as initiator
caspases at the apex of protease cascades initiated by death receptors or endogenous
signals (1). In contrast, the caspases with short prodomains appear to be responsible for
cleavage of most of the substrates undergoing proteolysis during apoptosis.
known as death effector domains (DEDs) that can interact with the homo-
logous domains on adaptor proteins such as FADD/MORT1 (1, 13). Likewise,
a caspase recruitment domain (CARD) found in the prodomain of caspase-9
appears to promote interactions with other cytoplasmic components (e.g. the
Apaf 1/cytochrome c complex) (14, 15). According to one current model, the
protein-protein interactions between prodomains and their interacting
partners result in the juxtaposition of multiple procaspase molecules. Because
these zymogens have low levels of intrinsic catalytic activity, this induced
proximity allows one procaspase molecule to activate a neighbouring molecule
in an 'autocatalytic' fashion (1).
Once activated, the initiator caspases are then able to cleave, and thereby
activate, caspases that contain short prodomains, i.e. procaspases-3, -6, and -7
(1, 13). These so-called effector caspases cleave a variety of substrates
throughout the cell (Table 2), thereby setting into motion the biochemical and
morphological changes that constitute the apoptotic process (1).
4. Detection of procaspases and their cleavage

products by immunoblotting
4.1 Theoretical considerations
Because of the intimate involvement of caspases in apoptosis, there has been
considerable interest in studying their activation and activity under a variety
218
Table 2. Polypeptides cleaved by caspases in apoptotic cellsa
Polypeptides Cleavage Responsible Sizes reported (kDa)

site caspase Intact Fragment(s)b
Abundant cytoplasmic proteins
Gelsolin DQTD/G 3 83 41, 39
Gas-2 SRVD/G ? 35 31
Fodrin DETD/S 3 240 150
B-Catenin ? 3 92 65
Cytokeratin 18 VEVD/A 3, 6, 7 45 29,23
Abundant nuclear proteins

LaminA VEID/N 6 69 47
Lamin B1 VEVD/S 6,73 67 45
NuMA ? 3,6 230 160, 180
HnRNP proteins C1 and C2 ? 3,7 40 ~35
70 kDa protein of U1 snRNP DGPD/G 3 70 40
mdm2 DVPD/C 3, 6,7 100 55
Proteins involved in DNA metabolism and repairc

Poly(ADP-ribose) polymerase DEVD/G 3, 7, 9 113 89, 24
DNA-PKcs DEVD/N 3 460 150
Replication factor C large subunit DEVD/G 3 140 87, 53
Topoisomerase I DDVD/Y 3 100 70
Protein kinases
Protein kinase C5 DMQD/M 3 78 40
Protein kinase C6 DEVD/K 3 78 40
Protein kinase C-related kinase 2 DITD/C 3 130 110, 100
Calcium/calmodulin-dependent protein PAPD/A 3 55 38
kinase IV
p21-activated kinase 2 SHVD/G 3, 8 65 36
PITSLRE kinase a2-1 YVPD/S 3 110 60,43
Mst1 kinase DEMD/S ? 63 34-36
Mst2 kinase DELD/S ? 63 34
Focal adhesion kinase DQTD/S 3,7 125 85, 77
VSWD/S 6
MEKK-1 DTVD/G 3 200 ~100, 120
Wee1 kinase ? 3, 7, 8 ~80 ~60
Other proteins involved in signal transduction and gene expression

Pro-interleukin-1p FEAD/G 1 31 28
YVHD/A 17.5
Pro-interleukin-16 SSTD/S 3 50 20
Pro-interleukin-18 LESD/Y 1,3 24 18, 16, 15
Ras GTPase activating protein DTVD/G 3 120 ~80, ~65
D4-GDP dissociation inhibitor DELD/S 3 28 23
Protein phosphatase 2A subunit Act DEQD/S 3 65 42
Cytosolic phospholipase A2 DELD/T 3 100 70
219
Table 2. Continued
Polypeptides Cleavage Responsible Sizes reported (kDa)

b
site caspase Intact Fragment(s)
Stat1 MELD/G 3 91,84 81

NF-kB p65 ? 3 65 55, 10
NF-KB p50 ? 3 50 35, 15
IkB DRHD/S 3 40 36
Sterol response element binding protein-1 SEPD/S 3,7 ~140 60-70
Sterol response element binding protein-2 DEPD/S 3,7 -140 60-70
Proteins involved in regulation of cell cycle and proliferationd

waf1/cip1
p21 DHVD/L 3, 7 21 1416
p27kiP1 DPSD/S 3,7 27 22
Rb retinoblastoma protein DEAD/G 3 105 100
CDC 27 ? 3 97 ~60, ~40
Proteins involved in human genetic diseases

Dentatorubral pallidalysian atrophy protein DSLD/G 3 160 145
Presenilin-1, C-terminal fragment ARQD/S ? 23 10-14
Presenilin-2, C-terminal fragment DSYD/S 3 25 20
Apoptotic regulatory proteinse

Bcl-2 DAGD/V ? 26 23
Bcl-XL HLAD/S Not 3 28 16
FLIPL LEVD/G 3,8, 10 55 43
BID LQTD/G 8 25 16
BAX FIQD/R ? 21 18
ICAD/DFF45 DEPD/S 3 45 30, 11
aFor a list of proposed biological functions of cleavage, as well as a comprehensive list of references,
see ref. 1.
bEstimated masses of caspase-generated fragments are based on mobility in SDS-polyacrylamide
gels as reported by authors of the original reports describing cleavage in intact cells. ~ sign indicates
our estimate based on published gels in cases where fragment sizes were not reported. Fragments
generated by other proteases (e.g. calpains) are not listed.
c
See also the HnRNP particle proteins C1 and C2 as well as the U1 snRNP particle 70 kDa polypeptide
in other parts of this table.
d
See also Wee1 kinase, mdm2 protein, and replication factor C in other parts of this table.
e
ln addition, all of the procaspases are caspase substrates.
of conditions. Immunoblotting provides one potential method for detecting

active caspases within cells. In principle, antibodies generated against neo-
epitopes (i.e. epitopes that are generated during the proteolytic activation of
caspases) could be utilized to selectively detect active caspases on immuno-
blots. Such antibodies are not generally available. Instead, most commercially
available anti-caspase antibodies (Table 1) have been raised against epitopes
present in either the large or small subunits of the active enzymes. These
antibodies should theoretically recognize the corresponding zymogen and
active caspase with equal affinities.
220
In applying these antibodies to the study of cells undergoing apoptosis, one
might expect that decreases in zymogen levels would be accompanied by
stoichiometric increases in active caspase species. This is not usually observed.
Although the signals for certain procaspases decrease or disappear during
apoptosis, suggesting that these zymogens have been activated, a correspond-
ing increase in the large or small subunit is not always detected by immuno-
blotting. One possible explanation for this phenomenon is a rapid degrad-
ation of caspase species once they are activated. Although this explanation
remains to be rigorously tested, the detection of active caspases by
immunoblotting remains difficult in many model systems. Accordingly, the
disappearance of the procaspase signal is commonly accepted as evidence of
caspase activation.
Despite the widespread use of anti-caspase antibodies to study caspase
activation, published data do not indicate whether the caspase zymogens are
abundant or rare polypeptide species. Data in Figure 2 indicate that 3 x 10s
K562 human leukaemia cells contain ~10 ng of procaspase-3 and procaspase-
8, with 10-fold lower levels of procaspase-6. This corresponds to ~6 x 10s,
4 X 105, and 6 X 104 molecules of procaspase-3, -8, and -6, respectively, per
cell. Based on a cell diameter of 15 mm, this translates into a concentration of
Figure 2. Estimation of procaspase levels in K562 human leukaemia cells. Samples

containing 20, 10, or 5 ng of the indicated purified recombinant caspase (lanes 1-3,
respectively) or 3 x 105, 1.5 X 105, and 0.75 x 105 K562 cells (lanes 4-6, respectively) were
subjected to SDS-PAGE, followed by immunoblotting with antibodies raised against the
indicated caspase. Closed arrowhead, caspase zymogen. TWO alternatively spliced
variants of caspase-8 are present in K562 cells. Open arrowhead, large subunit of active
caspase.
221
~3 mg/ml (100 nM) for procaspase-3 if the zymogen is uniformly distributed
throughout the cell. Additional experiments in our laboratory have revealed
that procaspase-3 levels in a panel of 60 different human cancer cell lines
range from undetectable (in a cell line with a caspase-3 gene rearrangement)
to four times as high as K562 cells. Procaspase-8 levels in the same cell lines
range from 0.5 to six times as high as K562 cells.
4.2 Practical considerations in immunoblotting for

caspases
In designing immunoblotting experiments, it is important to remember that
caspases are themselves protease substrates. Zapata et al. (16) have reported
that lysis of lymphoid cells in neutral detergents such as Triton X-100 can lead
to artefactual caspase activation by granzyme B present in cytotoxic granules.
Other serine proteases can also activate certain caspases under cell-free
conditions (17). It is, therefore, important that cells be solubilized under
conditions that prevent procaspase cleavage and activation after cell lysis. We
favour the lysis of cells under strongly denaturing conditions [e.g., in 2%
sodium dodecyl sulfate (SDS) containing 4 M urea and reducing agent (18) or
in 6 M guanidine hydrochloride containing reducing agent (19)]. If the latter
buffer is used, sample preparation involves more steps (dialysis to remove the
positively charged guanidium ions and replace them with dodecyl sulfate as
described in ref. 19), but the chances of artefactual proteolysis are diminished
by the rapidity with which guanidine denatures polypeptides. Protein levels
are then quantified by one of several methods, including the Bradford assay
(20) or the bicinchoninic acid (BCA) assay (21).
4.3 Sample preparation and immunoblotting

Once cells have been subjected to a pro-apoptotic stimulus, protein should be
harvested from a minimum of 106 cells per data point. After the protein in the
samples has been quantitated, equal amounts should be loaded into wells of
an SDS-polyacrylamide gel containing a 5-15% (w/v) acrylamide gradient.
This will allow detection of the caspases, which are low molecular weight
polypeptides, as well as their putative substrates on the same membrane.
After separation, the polypeptides are electrophoretically transferred to either
nitrocellulose or polyvinylidene fluoride (PVDF) membranes and probed as
described in Protocol 1. Figure 2 contains results obtained using this protocol.
222
10: Methods for detecting pwteolysis during apoptosis in intact cells
Protocol 1. Detection of caspases by immunoblotting
Reagents
• chemiluminescent reagents suitable for use • sources of anti-caspase antibodies are
with peroxidase-coupled secondary anti- listed in Table 1
bodies include ECL from Amersham or
SuperSignal ULTRA® from Pierce
Method
1. After transfer, block all of the non-specific binding sites on the
membrane with TSM* [10% dry milk, 10 mM Tris-HCI (pH 7.4 at room
temp), 150 mM NaCI, 100 U/ml penicillin G, 100 mg/ml streptomycin,
1 mM sodium azide] for at least 1 h. This blocking step should be
performed immediately after the transfer if PVDF membranes are
used. Nitrocellulose membranes can be dried before blocking.
2. Dilute the primary antibody in TSM* according to the manufacturer's
instructions and incubate with the membrane overnight at room
temperature. Although it is possible to incubate the membrane with
primary antibody for shorter periods of time (e.g. 1 h), this often
requires a higher concentration of antibody without any improvement
in the signal-to-noise ratio.
3. Remove the primary antibody and store it at 4°C for subsequent use.
Wash the membrane in PBS (137 mM NaCI, 2.7 mM KCI, 1.5 mM
KH2PO4, 8 mM Na2HP04, pH 7.4) containing 0.05% (w/v) Tween 20 for
3 x 15 min. If there is extensive background on the film after an initial
immunoblotting experiment, it may be helpful to use a wash buffer of
increased stringency (e.g. PBS-0.05% Tween 20 supplemented with
2 M urea or additional NaCI) in subsequent blotting experiments.
4. Wash the membrane with PBS for 2 x 5 min.
5. Dilute the secondary antibody in PBS containing 3% (w/v) dry milk
according to the supplier's instructions. Add antibody to the
membrane and incubate for 1 h at room temperature.
6. Remove the secondary antibody (discard) and wash the membrane
with PBS-0.05% Tween 20 for 2 x 5 min, 2 x 15 min, and 2 x 5 min.
7. Add detection reagent. If peroxidase-coupled secondary antibodies
are used, prepare luminescent reagents and add to the membrane
according to the manufacturer's instructions. This step will be omitted
if radioactive secondary antibodies are used.
8. Expose the membrane to X-ray film for an appropriate length of
time.
223
5. Cleavage of caspase targets

Since the initial description of selective protein degradation during apoptosis
(22), cleavage of a number of cellular polypeptides has been demonstrated in
one or more model systems (for recent reviews, see refs 1 and 23). It is
important to stress at the outset, however, that the vast majority of species
detected by one- or two-dimensional gel electrophoresis do not change during
the course of apoptosis (1, 22), indicating that the proteolytic cleavages are
selective.
There are three major goals in studying the cleavage of protease targets
during apoptosis: (a) to establish that proteases are activated in situ, (b) to
study the fate of a particular target during apoptosis, and (c) to determine the
biological effects of protease activation. Each of these goals requires a
somewhat different approach.
5.1 Establishing that proteases are activated in situ

As indicated above, blotting with anti-caspase antibodies can be utilized to
establish that caspase zymogens are cleaved during apoptosis. Unfortunately,
this approach does not establish whether the resulting caspase fragments, if
detectable, have enzymatic activity or not. One way to address this question is
to determine whether caspase substrates have been cleaved in situ.
Table 2 lists polypeptides that are known to be cleaved by caspases during
apoptosis. The criteria used to establish that each of these polypeptides is
cleaved by caspases include the following: (a) caspases cleave these poly-
peptides in vitro; (b) the fragments generated during apoptosis correspond to
the fragments generated by caspases in vitro; and (c) replacement of the P1
aspartate residue results in polypeptide species that cannot be cleaved in situ
during apoptosis. Each of the polypeptides in Table 2 meets the first two
criteria and many meet the third as well. Antibodies to several of these
polypeptides, including poly(ADP-ribose) polymerase, lamin A, lamin B1;
p21waf1/cip1, focal adhesion kinase (FAK), and ICAD/DFF45, are commercially
available. An immunoblot demonstrating cleavage of one or more of these
substrates to their signature fragments (Table 2) should be sufficient to
establish that caspases have been activated in situ. Because caspase targets,
like the caspases themselves, can be cleaved artefactually during sample
preparation, it is important to solubilize cells under appropriate conditions for
this analysis (see Section 4.2).
5.2 Establishing that a polypeptide is cleaved by caspases

Table 3 contains a list of additional polypeptides that are reportedly cleaved
as cells undergo apoptosis. These polypeptides do not currently meet the
criteria listed in the preceding section. To establish that one of these poly-
peptides (or any other polypeptide of interest) is cleaved by caspases during
224
Table 3. Other polypeptides cleaved during apoptosisa
Abundant cytoplasmic polypeptides

Plakoglobin
Adenomatous polyposis coli gene product
Endosome fusion protein rabaptin-5
Plasminogen activator inhibitor-2
Vimentin
Abundant nuclear polypeptides

Lamin B receptor
Chromosome scaffold-binding protein SAF-A
Polypeptides involved in DNA metabolism and repair

Human RAD51
MCM3
DNA topoisomerase II
RNA polymerase I upstream binding factor UBF
Protein kinases
Raf 1
Akt1
c-src
Other polypeptides involved in signal transduction pathways

Adapters Cb1 and Cb1-b
Phospholipase C-y-1
14-3-3B and 14-3-3e
Polypeptides involved in regulation of cell cycle and proliferation

CDC27
Polypeptides involved in human genetic diseasesb

Huntingtin
The dentatorubropallidoluysian atrophy protein atrophin-1
The spinocerebellar atrophy type 3 protein ataxin-3
The androgen receptor (altered in spinal bulbar muscular atrophy)
Amyloid precursor protein (APP)
aIn addition to the polypeptides listed in Table 2, these polypeptides are reportedly cleaved during
apoptosis. It is important to realize that the involvement of caspases in these cleavages remains to be
established. Moreover, cleavages of some of these polypeptides occur late in apoptosis and are
incomplete. For comprehensive list of references, see ref. 1.
bCleavages of these polypeptides by purified caspases have been observed in vitro. Current evidence
suggests that the cleavage of huntingtin occurs at a different site in intact cells (reviewed in ref. 1).
Cleavages of the other polypeptides have not been demonstrated in intact cells.
apoptosis requires more than the simple demonstration that cleavage occurs
in apoptotic cells, for any one of the many proteases that are activated during
apoptosis (see Section 2) could, in principle, be responsible for a particular
cleavage. Moreover, because some of these proteases are clearly activated
downstream of caspases (24, 25), the demonstration that a 'caspase inhibitor'
inhibits cleavage also does not establish that a particular polypeptide is a
caspase substrate.
225
The first step in establishing that a particular polypeptide is a caspase
substrate in situ is to show that caspases can cleave the polypeptide in vitro.
The availability of purified recombinant caspases-3, -6, -7, and -8 (e.g.
Pharmingen, San Diego, CA) has simplified this process. The polypeptide of
interest (or a cell fraction containing the polypeptide) should be incubated
with the active caspase under cell-free conditions that are compatible with
caspase action (e.g. in the presence of 2-10 mM dithiothreitol at neutral pH).
Agents that might inhibit caspases, including sulfhydryl alkylating agents (e.g.
iodoacetamide) and peptidomimetic chloromethylketones such as TPCK and
TLCK (26), should be avoided. If possible, controls should be included to
demonstrate that the caspase is active under the conditions used to cleave the
potential substrate. After incubation, the polypeptide of interest should be
assayed for biological activity (e.g. enzyme activity) and subjected to
SDS-PAGE followed by analysis (e.g. staining of the gel or immunoblotting)
to determine whether cleavage has occurred. The actual cleavage site(s) can
be determined by subjecting the carboxyl terminal fragment(s) to automated
Edman degradation (27).
Detection of cleavage by caspases in vitro does not establish that the same
cleavage occurs in situ. At the very least, it is important to demonstrate that
fragments generated in intact cells co-migrate with fragments generated by
caspases in vitro. To take a notable example, several groups reported that
actin could be cleaved by apoptotic cell lysates or purified caspases in vitro
(28, 29). Subsequent analysis, however, suggested that actin remains intact in
many cell systems during apoptosis (30). In other cell systems, it appears that
calpains, not caspases, mediate the apoptotic cleavage of actin (7).
Although the co-migration of cleavage products generated in vitro and in
situ provides strong evidence that a caspase(s) mediates the cleavage of a
particular polypeptide during apoptosis, mutagenesis studies can strengthen
this point even further. When lamins mutated at putative P1 aspartates were
introduced into tissue culture cells, the mutated polypeptides resisted cleav-
age during subsequent apoptosis (31), providing convincing support for the
view that the cleavage site had been successfully determined. In addition, cells
containing the non-cleavable lamins exhibited a delay in apoptosis, raising the
possibility that lamin cleavage facilitates, but is not absolutely required for,
subsequent apoptotic changes in nuclear morphology.
6. Assays of caspase activity

The demonstration that certain polypeptides (including procaspases) have
been cleaved to their signature fragments (Tables 1 and 2) provides pre-
sumptive evidence that caspases might have been activated. Nonetheless, the
possibility that other proteases could catalyse cleavage of a particular poly-
peptide to fragments of similar size must always be kept in mind. Accordingly,
226
investigators commonly bolster the argument that caspases have been
activated by assaying directly for caspase activity.
6.1 Theoretical considerations of caspase activity assays

Analysis of sites that are cleaved in various substrate polypeptides (Table 2)
facilitated the development of rapid fluorogenic and chromogenic assays for
caspase activity. Because the caspases have overlapping cleavage site speci-
ficities (Table 1), these assays are not specific for individual caspases. This
potential problem is best illustrated by the data of Talanian et al. (32) who
analysed the Km and kcat of purified caspases acting on a variety of low
molecular weight substrates. This analysis revealed that caspases-3 and -7 pre-
ferred the p-nitroaniline (pNA)-coupled peptide Ac-DEVD-pNA (Km = 11
or 12 mM, respectively); caspase-1 preferred Ac-YEVD-pNA (Km = 7.3 mM);
and caspase-6 preferred Ac-VEID-pNA (Km = 30 mM). These preferences
were not, however, absolute. Caspase-3, for example, displayed a kcat /Km (a
measure of catalytic efficiency) of 21.8 X 104 for Ac-DEVD-pNA, 6.1 X 104
for Ac-VEID-pNA, and 3.9 X 104 for Ac-YEVD-pNA, indicating that
efficiencies at cleaving the various substrates differed by only a factor of 5.
Aside from the inefficient cleavage of Ac-DEVD-pNA by caspase-6, the
other caspases showed similar promiscuity. Accordingly, the cleavage of small
peptide-derived substrates in cell extracts is difficult to attribute to individual
caspases.
In addition to tetrapeptide or pentapeptide substrates, in vitro translated
proteins have also been used to assay caspase activity in vitro (33-35). The
work of Andrade et al. (5) has demonstrated the feasibility of measuring the
Km and kcat using these more relevant macromolecular substrates. Recent
data suggest that caspase cleavage preferences derived solely from the study
of tetrapeptide-based substrates might not accurately predict cleavage sites in
substrate polypeptides (36), raising the possibility that macromolecular sub-
strates might still have an important role in the study of caspases. On the
other hand, the disadvantages of radiolabelled macromolecular substrates
include the need to perform both in vitro transcription/translation reactions to
generate substrates and SDS-PAGE followed by fluorography to analyse
results. In short, this labour-intensive approach is not suitable for high
throughput screening. Accordingly, we provide a protocol for a tetrapeptide-
based assay.
6.2 Measuring caspase activity in cell lysates

The protocol for measuring caspase activity in cell lysates can be divided into
two sections, the first involving the preparation of subcellular fractions and
the second measuring the cleavage of various substrates. It is critical that the
cell lysis procedure not allow inadvertent caspase activation. To avoid release
of lysosomal and other granule proteases, which could conceivably activate
227
caspases after cell lysis (16, 17), we prefer a lysis procedure that avoids de-
tergents and thereby allows removal of sequestered proteases by differential
centrifugation.
Protocol 2. Measurement of caspase activity using fluorogenic

substrates
Reagents
• procedures for the synthesis of potential • chromogenic and fluorogenic caspase sub-
substrates are described in detail in ref. 18 strates are available from a number of
• free pNA, 7-amino-4-trifluoromethylcouarin suppliers, including Bachem Bioscience,
(AFC), or 7-amino-4-methylcoumarin (AMC) Biomol, Calbiochem, and Enzyme Systems
to construct standard curves are available Products
from Sigma
Method
Part A. Preparation of cytosol or other subcellular fractions (18)
1. Harvest adherent cells by trypsinization followed by sedimentation at
200 g for 10 min. Wash the sample twice in ice-cold PBS. All further
steps are performed at 4°C unless otherwise indicated.
2. Resuspend the pellet in a small volume of buffer A [25 mM Hepes
(pH 7.5 at 4°C), 5 mM MgCI2, 1 mM EGTA supplemented immediately
before use with 1 mM a-phenylmethylsulfonyl fluoride (PMSF), 1 mM
dithiothreitol (DTT), 10 ug/ml pepstatin A, and 10 ug/ml leupeptin].
Typically, 1 ml of buffer A is added to 1-3 x 108 cells. This yields a
cytosolic extract with a protein concentration ranging from 4 to
8 mg/ml.
3. Incubate the sample for 20 minutes, then lyse the cells with 20-30
strokes in a tight-fitting Dounce homogenizer. Mix 3-5 ul of homo-
genate with an equal volume of 0.4% (w/v) trypan blue and examine
by light microscopy. Continue homogenization until >95% of the cells
stain blue.
4. Remove the nuclei by sedimentation (800 g for 10 min or 16000 g for
3 min).
5. Supplement the supernatant with EDTA to a final concentration of
5 mM. Prepare cytosol from the post-nuclear supernatant by sedi-
mentation at 280000 gmax for 60 min in a Beckman TL-100 ultra-
centrifuge. Other fractions can be likewise be purified by differential
sedimentation (37).
6. Freeze the cytosol (280000 g supernatant) in 50 ul aliquots at -70°C.
Control experiments from our laboratory have indicated that activity
capable of cleaving Ac-DEVD-AFC is stable for at least 3 months at
-70°C.
228
Part B. Fluorogenic or chromogenic substrate cleavage assay
1. Determine the protein concentration of the cytosol or other subcellular
fraction using the method of Bradford (20) or Smith et al. (21).
2. Thaw aliquots of cytosol or subcellular fractions containing 50 mg of
cytosolic protein at 4°C. Dilute to 50 ml with ice-cold buffer A
containing 5 mM EDTA.
3. Dilute sample with 225 ml of freshly prepared buffer B [25 mM Hepes
(pH 7.5), 0.1% (w/v) 3-[(3-cholamidopropyl)dimethylammonio]-1-
propanesulfonate, 10 mM DTT, 100 U/ml aprotinin, 1 mM PMSF]
containing 100 mM substrate.
4. Incubate the reaction at 37°C. Continuous monitoring of fluorochrome
release can be utilized to examine the kinetics of product release and/or
the kinetics of enzyme inhibition if suitable equipment is available (38).
Alternatively, the reaction can be run as an end-point assay (18). In
that case, add 1.225 ml ice-cold buffer B at a fixed time point to stop
the reaction.
5. Incubate negative control reactions, containing 50 ml of buffer A and
225 ml of buffer B at 37°C and then dilute them with 1.225 ml ice-cold
buffer B in parallel with experimental samples.
6. Measure the fluorescence in a fluorometer using an excitation wave-
length of 360 nm and an emission wavelength of 475 nm. The absolute
amount of fluorochrome released is determined by measuring the
fluorescence of a panel of standards containing various amounts of
the liberated fluorophore [e.g. 0-1500 pmoles AFC].
When setting up this assay, it is important to use an appropriate substrate

concentration. If the substrate concentration is below the Km for the enzyme,
changes in the amount of product released might be due to either changes in
the number of active enzyme molecules (altered vmax) or the affinity for the
substrate (altered Km). The common interpretation that changes in the
amount of product released correspond to changes in the number of active
enzyme molecules is only valid when the reaction is run under conditions
where the substrate is saturating.
When the assay is run as an end-point assay, it is important to confirm that
product release is a linear function of the length of incubation. Important
causes of non-linearity include substrate exhaustion and enzyme instability. If
extracts are prepared as described above, the assay is linear for up to 4 h
under the specified conditions.
Although numerous substrates can be utilized for this assay, peptide
derivatives of AMC and AFC are most commonly employed because of the
high quantum yield of the liberated fluorophore. Colorimetric assays utilizing
chromogenic substrates (e.g. a peptide linked to pNA) have also been
229
developed. These colorimetric assays can easily be adapted to microtitre plate
readers, permitting their use in high throughput screening.
7. Detection of active caspases by affinity labelling

7.1 Theoretical considerations in affinity labelling
Affinity labelling provides an alternative approach for demonstrating that
caspases have been activated. This approach is based on the observation that
the catalytic cysteines in active caspases can be covalently modified by re-
action with a variety of agents (reviewed in ref. 39). Reactions with aldehydes
and nitriles are reversible, whereas reactions with chloromethyl, fluoro-
methyl, or acyloxymethyl ketones are irreversible. Coupling of these reactive
groups to suitable peptides provides potential enzyme inhibitors as well as
affinity labelling reagents.
Two reagents currently in widespread use, 7V-(acetyltyrosinylvalinyl-.NE-
biotinyllysyl) aspartic acid [(2,6-dimethylbenzoyl)oxy]methyl ketone [Figure
3; abbreviated to YVK(bio)D-aomk] and AÂ^-benzyloxycarbonylglutamyl-
A^-biotinyllysyl)aspartic acid [(2,6-dimethylbenzoyl)oxy]methyl ketone
[abbreviated to Z-EK(bio)D-aomk], will be discussed to illustrate essential
features of the affinity labelling reagents. These molecules contain peptide
sequences that direct them to caspases, acyloxymethyl ketone moieties to
permit covalent coupling to the caspase active site, and biotin groups to allow
detection of polypeptides that have been derivatized. Each of these features
plays an important role in determining the properties of these reagents.
The presence of the polypeptide moiety enhances the affinity of each reagent
for certain proteases. YVK(bio)D-aomk contains a YVKD polypeptide that
preferentially binds to caspase-1. Z-EK(bio)D-aomk contains the E-X-D
motif found in many polypeptides at sites cleaved by caspases-3, -6, and -7. At
least four amino acids (or amino acid-like moieties) to the amino terminal
side of the reactive group are required to achieve relatively high affinity to
caspases (34, 38). In both YVK(bio)D-aomk and Z-EK(bio)D-aomk, the P1
amino acid is an aspartate, a group that is absolutely required for binding to
caspases (1). Because the P2 and P3 side chains point away from the active site
of the enzyme, the bulky biotin moiety is tolerated in the P2 position (1, 40).
The group in the P4 position, on the other hand, is tightly bound to the
enzyme. The corresponding subsite on caspase-3 is positively charged and
prefers acidic amino acids, whereas the subsite on caspase-1 accommodates
bulkier groups like tyrosine. As described below, however, this selectivity is
relative rather than absolute.
The acyloxymethylketone group is employed for covalent modification of
the caspases because of its somewhat lower reactivity (and presumed greater
selectivity) than chloromethyl or fluoromethyl ketones (39, 40). When
working with purified caspases, where selectivity is less of an issue, it might be
230
Figure 3. Schematic representation of the chemical reaction involved in affinity labelling

of active caspases by YVK(bio)D-aomk (40, 42). Above, the chemical structure for
YVK(bio)D-aomk, the locations of the leaving group R, and P1-P4 residues are indicated.
possible to use affinity labelling reagents with the more reactive groups. In
whole-cell lysates, however, chloromethyl ketones exhibit relatively promis-
cuous reactivity with cysteine proteases (41) in addition to their well-
established, but more selective, reactivity with serine proteases. Likewise,
fluoromethyl ketones are used to derivatize a variety of sulfhydryl proteases.
Because of the widespread reactivity of these types of molecules with
polypeptides containing activated cysteine residues, the possibility must be
231
borne in mind that peptide-coupled acyloxymethyl ketones can potentially
react with other enzymes, not just caspases.
The presence of biotin in the affinity labelling reagent permits the detection
of polypeptides that have been covalently modified (e.g. by blotting with
streptavidin). Unfortunately, endogenous biotinylated polypeptides will also
be labelled by streptavidin (18), limiting the usefulness of this approach in
immunohistochemical studies. Reagents with different detection groups
remain to be synthesized.
7.2 Practical considerations in the use of affinity labelling

reagents
Despite the original intent to design affinity labelling reagents with some
selectivity, YVK(bio)D-aomk and Z-EK(bio)D-aomk lack selectivity for
their originally intended caspase targets under the conditions commonly
utilized. YVK(bio)D-aomk has been successfully utilized to label the caspases
that are present in extracts from apoptotic cells, including the proteases that
cleave poly(ADP-ribose) polymerase and the lamins (42); and Z-EK(bio)D-
aomk readily reacts with recombinant caspases-1 and -2 as well as caspases-3
and -6 (18). Although these reagents might show some selectivity for various
caspases during brief labelling at low ligand concentrations, prolonged
incubation with high concentrations of these reagents easily compensates for
poor affinity, as demonstrated by Margolin et al. (34).
7.3 Labelling and detecting enzymatically active caspases

The overall approach to the use of these reagents involves the preparation of
whole-cell lysates or subcellular fractions from control and apoptotic cells,
reaction with the affinity label under conditions where caspases are active,
separation of polypeptides in one- or two-dimensional polyacrylamide gels,
transfer to nitrocellulose, and reaction with peroxidase-coupled streptavidin
followed by luminol.
Protocol 3. Detection of active caspases by affinity labelling
Reagents
• affinity labelling reagents are available from Bachem Bioscience, Calbiochem, Enzyme
a limited number of suppliers, including Systems Products, and the Peptide Institute
Method
1. Each sample should contain ~1 x 108 cells. At the very least, an
experiment should contain cells treated with a pro-apoptotic stimulus
and control (non-apoptotic cells).
2. After the induction of apoptosis is complete, wash cells twice in ice-
cold serum-free isotonic buffer (e.g. PBS).
232
3. Isolate cytosol or other subcellular fractions using the techniques
described in Protocol 2 and store at -70°C in buffer A supplemented
with 5 mM EDTA.
4. Determine protein concentration in an aliquot of the subcellular
fraction using an assay that is not affected by reagents in the EDTA-
supplemented buffer A [e.g. the bichinconinic acid method <21)].
5. Perform affinity labelling by reacting 30-50 mg of cytosolic protein for
1 h at 20-22°C with 1 mM Z-EK(bio)D-aomk. The Z-EK(bio)D-aomk is
conveniently prepared as a 25 mM stock in DMSO and stored in small
aliquots at-80°C.
6. To stop the reaction, dilute the sample with 0.5 vol. 3 x concentrated
SDS sample buffer [0.15 M Tris-HCI (pH 6.8 at 20°C), 45% (w/v)
sucrose, 6 mM EDTA, 9% (w/v) SDS, 0.03% (w/v) bromophenol blue,
10% (v/v) B-mercaptoethanol] and heat to 95-100°C for 3 min.
7. Subject the samples to one-dimensional SDS-PAGE in 16% (w/v)
polyacrylamide gels. Alternatively, subject the samples to two-
dimensional isoelectric focusing/SDS-PAGE. For the latter procedure,
our collaborators have obtained highly reproducible results using
pre-cast Immobiline gels (pH 4-7, Pharmacia, Upsalla, Sweden) for
the first dimension.
8. After separation, transfer polypeptides to nitrocellulose.
9. Block unoccupied protein-binding sites with PBS containing 0.1%
(v/v) Tween-20 (PBS-T) and 5% (w/v) non-fat dry milk.
10. Visualize the labelled polypeptides by reacting with peroxidase-
coupled streptavidin in PBS-T for 3-4 h at 20-22°C. Wash blots with
PBS-T for 1 x 15 min and 4 X 5 min to remove unbound peroxidase-
coupled streptavidin.
11. Detect the bound peroxidase using enhanced chemiluminescent
detection.
12. Recombinant caspases expressed in Sf9 cells (18) can be subjected to
this analysis in parallel in order to permit identification of the labelled
polypeptide species. His6-tagged caspases (e.g. commercially avail-
able from Pharmingen, San Diego, CA) should not be used as
standards for two-dimensional analysis because the charged tag will
alter their migration.
This assay can detect pg levels of active proteases. Moreover, when utilized
in conjunction with known amounts of recombinant caspases, this assay can
identify and quantify the individual proteases that are active at particular
times during the course of programmed cell death.
Control experiments indicate that cytosol can be successfully labelled after
233
storage at -70°C for at least 3 months. As an alternative to subcellular
fractionation, whole-cell lysates prepared by freezing and thawing cells can
also be labelled using analogous techniques (43). The caspase labelling pattern
in these lysates, however, is more complicated than the pattern observed
using cytosol or nuclei, suggesting that specific caspase species might target
other subcellular compartments as well.
The recommended 20-22°C temperature for incubation with the affinity
label appears to be important. Incubation of cytosol at 37°C results in rapid
degradation of active caspase species (P.W. Mesner, Jr, L. Miguel Martins,
and S.H. Kaufmann, unpublished observations).
Two types of controls can be performed to distinguish endogenous biotinyl-
ated polypeptides from species that become biotinylated as a consequence of
reaction with Z-EK(bio)D-aomk. First, as indicated above, control (non-
apoptotic) cells can be labelled in parallel with apoptotic cells. Although some
non-apoptotic cells contain active caspase-1 (38), there is no evidence for
active caspases-3, -6, or -7 in non-apoptotic cells. Secondly, the ability of other
caspase inhibitors to prevent labelling can be assessed. For example, pre-
incubation of cell lysates with certain peptide chloromethyl or fluoromethyl
ketones will completely abolish subsequent labelling of active caspases with
Z-EK(bio)D-aomk but will not have any effect on the reaction of streptavidin
with endogenous biotinylated polypeptides (44).
It is also possible to combine affinity labelling with subsequent affinity
chromatography on avidin-agarose to purify active caspases up to 100000-
fold in a single step (33, 38, 43, 45).
8. Studying the biological effects of caspase

cleavages
A recent analysis (1) suggests that caspase-mediated cleavages play three
important roles during apoptosis. First, they turn off activities required for
cell survival, including extracellular matrix-initiated signalling pathways, DNA
repair, and RNA synthesis. Second, they turn on activities that lead to cellular
disruption. Among these are gelsolin, which disrupts the actin cytoskeleton;
the caspase-activated DNase CAD/CPAN/DFF40, which contributes to
internucleosomal DNA degradation; and a variety of protein kinases. Third,
they diminish the integrity of certain critical structural components of the cell,
including cytokeratin 18, fodrin, the lamins, and the nuclear/mitotic apparatus
protein (NuMA). Collectively, these cleavages give rise to the biochemical
and morphological changes that comprise the process of apoptosis.
Two major approaches have evolved for studying the effects of caspase
activation on this process. Each of these is briefly discussed below.
234
8.1. A molecular approach for analysis of the effects of

substrate cleavage
For polypeptides that are thought to be inactivated by caspase-mediated
cleavage, expression of non-cleavable isoforms (e.g. in which the P1 aspartate
has been mutated in vitro to an alanine) can provide some evidence for the
role of cleavage. This is illustrated by the effect of non-cleavable lamins cited
above.
For polypeptides that are thought to be activated by caspase-mediated
cleavage (e.g. kinases or other enzymes), forced expression of the putative
cleavage product can provide some insight into the biological role of the
cleavage. For example, caspase-3 cleaves protein kinase C8 between its
regulatory and catalytic domains to yield a C-terminal fragment with con-
stitutive kinase activity (46). Overexpression of this C-terminal fragment
induces apoptotic morphological changes in cells, whereas overexpression of
the full-length polypeptide does not (47). By itself, this experiment simply
demonstrates that the overexpressed C-terminal fragment is toxic to cells.
However, when combined with antisense experiments demonstrating that the
downregulation of protein kinase CS inhibits apoptosis (47), the net result is
strong evidence supporting an active role for the protein kinase Cd fragment
in apoptotic changes. A similar approach has been utilized to determine the
biological effects of other caspase-generated enzyme fragments (1).
It should be noted, however, that the preceding experiments demonstrate a
role for the caspase-generated enzyme fragment during apoptosis but do not
elucidate that role. Although caspase activation has been shown to generate a
variety of constitutively active kinase fragments (1), the substrates of these
kinases remain to be identified; and the manner in which phosphorylation of
these substrates contributes to the apoptotic process remains to be clarified.
These are questions that are potentially difficult to address using a molecular
approach.
8.2. Use of caspase inhibitors: promises and pitfalls

As an alternative to the molecular genetic approach, it is appealing to attempt
to inhibit caspase-mediated cleavages using specific inhibitors. In an ideal
world, the role of caspase-3, for example, during apoptosis could be analysed
by examining the effect of treating cells with a selective caspase-3 inhibitor.
Unfortunately, there are several problems with this approach.
First, as indicated above, multiple proteases appear to be activated
downstream of the caspases. Hence, the inhibition of a particular cleavage by
a caspase-3 inhibitor might reflect cleavage of that polypeptide by caspase-3
or by a protease activated downstream of caspase-3.
Second, currently available caspase inhibitors do not have sufficient
specificity to permit this type of analysis. For example, N-(acetylaspartyl-
235
glutamylvalinyl)-3-amino-3-formyl-propionic acid (abbreviated to Ac-
DEVD-CHO), which mimics the cleavage site in poly(ADP-ribose)
polymerase (27, 33), is a potent inhibitor of caspase-3 [Ki of 0.2-0.35 nM (5)].
However, it is not selective. Ac-DEVD-CHO also inhibits caspase-1 (Ki = 17
nM) at concentrations that overlap those required to inhibit caspase-3 family
members [Ki = 31, 1, 0.8, 60, and 12 nM for caspases-6-10, respectively (5)].
As a result, it is quite possible that Ac-DEVD-CHO inhibits a wide range of
caspases at the 50-100 mM concentrations somtimes utilized in vitro and in
vivo (48). Moreover, recent experiments indicate that inhibitors such as Ac-
DEVD-CHO and Z-VAD-fluoromethyl ketone can also inhibit non-caspase
proteases (e.g. cathepsin B) at micromolar concentrations (25). This lack of
selectivity is even more problematic with the more reactive chloromethyl
ketones.
In summary, the currently available inhibitors are not sufficiently selective
to permit the study of a particular caspase. On the contrary, recent evidence
demonstrating that these compounds directly inhibit other classes of pro-
teases, coupled with the observation that non-caspase proteases can be acti-
vated downstream of caspases, makes it difficult to support the contention
that a particular effect is mediated by caspases solely on the basis of inhibition
by these compounds. Because of this lack of specificity, investigators have
found it necessary to turn to gene disruption experiments (reviewed in ref. 1)
to assess the effect of selectively abolishing the activity of individual caspases.
Acknowledgements
We apologize to the numerous authors whose seminal contributions to this
field could not be cited because of space limitations. Work in our laboratory is
supported by R01 CA69008 and a predoctoral fellowship (to A.L.B.) from the
Mayo Foundation. We wish to thank numerous colleagues, including Bill
Earnshaw, Miguel Martins, Peter W. Mesner, Jr, Tim Kottke, Phyllis Svingen,
Guy Poirier, and Greg Gores, for provocative discussions and helpful
comments. Data shown in Figure 2 were provided by Phyllis Svingen using
antibodies kindly provided by Peter W. Mesner, Jr and John Reed. The
secretarial assistance of Deb Strauss is gratefully acknowledged.
References
1. Earnshaw, W. C., Martins, L. M., and Kaufmann, S. H. (1999). Ann. Rev.
Biochem., 68, 383.
2. Mesner, P. W. and Kaufmann, S. H. (1998). In: Apoptosis in Neurobiology:
Concepts and Methods (ed. Hannun, Y. A., and Boustany, R.-M.), p. 73, CRC
Press, Boca Ratan, FL.
3. Kuida, K., Zheng, T. S., Na, S., Kuan, C., Yang, D., Karasuyama, H., Rakic, P.,
and Flavell, R. A. (1996). Nature, 384, 368.
236
4. Kuida, K., Haydar, T. F., Kuan, C.-Y., Gu, Y., Taya, C., Karasuyama, H., Su, M.
S.-S., Rakic, P., and Flavell, R. A. (1998). Cell, 94, 325.
5. Andrade, F., Roy, S., Nicholson, D., Thornberry, N., Rosen, A., and Casciola-
Rosen, L. (1998). Immunity, 8, 451.
6. Sarin, A., Clerici, M., Blatt, S. P., Hendrix, C. W., Shearer, G. M., and Henkart,
P. A. (1994). J. Immunol., 153, 862.
7. Villa, P. G., Henzel, W. J., Sensenbrenner, M., Henderson, C. E., and Pettmann,
B. (1998). J. Cell Sci., 111, 713.
8. Yuan, J, Shaham, S., Ledoux, S., Ellis, H. M., and Horvitz, H. R. (1993). Cell, 75, 641.
9. Alnemri, E. S., Livingston, D. J., Nicholson, D. W., Salvesen, G., Thornberry, N.
A., Wong, W. W., and Yuan, J. (1996). Cell, 87, 171.
10. Greenberg, A. H. (1996). Adv. Exp. Med. Biol, 406, 219.
11. Pham, C. T. and Ley, T. J. (1997). Sem. Immunol., 9, 127.
12. Thornberry, N. A., Rano, T. A., Peterson, E. P., Rasper, D. M., Timkey, T.,
Garcia-Calvo, M., Houtzager, V. M., Nordstrom, P. A., Roy, S., Vaillancourt, J. P.,
Chapman, K. T., and Nicholson, D. W. (1997). /. Biol. Chem., 272, 17907.
13. Fraser, A. and Evan, G. (1996). Cell, 85, 781.
14. Li, P., Nijhawan, D., Budihardjo, I., Srinivasula, S. M., Ahmad, M., Alnemri, E. S.,
and Wang, X. (1997). Cell, 91, 479.
15. Deveraux, Q. L., Roy, N., Stennicke, H. R., Van Arsdale, T., Zhou, Q.,
Srinivasula, S. M., Alnemri, E. S., Salvesen, G. S., and Reed, J. C. (1998). EMBO
J., 17, 2215.
16. Zapata, J. M., Takahashi, R., Salvesen, G. S., and Reed, J. C. (1998). J. Biol.
Chem., 273, 6916.
17. Zhou, Q. and Salvesen, G. S. (1997). Biochem. J., 324, 361.
18. Martins, L. M., Kottke, T. J., Mesner, P. W., Basi, G. S., Sinha, S., Frigon, N., Jr,
Tatar, E., Tung, J. S., Bryant, K., Takahashi, A., Svingen, P. A., Madden, B. J.,
McCormick, D. J., Earnshaw, W. C., and Kaufmann, S. H. (1997). J. Biol. Chem.,
272, 7421.
19. Kaufmann, S. H., Svingen, P. A., Gore, S. D., Armstrong, D. K., Cheng, Y.-C., and
Rowinsky, E. K. (1997). Blood, 89, 2098.
20. Bradford, M. M. (1976). Anal. Biochem., 72, 248.
21. Smith, P. K., Krohn, R. I., Hermanson, G. T., Mallia, A. K., Gartner, F. H.,
Provenzano, M. D., Fujimoto, E. K., Goeke, N. M., Olson, B. J., and Klenk, D. C.
(1985). Anal. Biochem., 150, 76.
22. Kaufmann, S. H. (1989). Cancer Res., 49, 5870.
23. Tan, X. and Wang, J. Y. (1998). Trends Cell Biol., 8, 116.
24. Wright, S. C., Schellenberger, U., Wang, H., Wang, Y., and Kinder, D. H. (1998).
Biochem. Biophys. Res. Commun., 245, 797.
25. Faubion, W. A., Guicciardi, M. E., Miyoshi, H., Bronk, S. F., Roberts, P. J.,
Svingen, P. A., Kaufmann, S. H., and Gores, G. J. (1999). J. Clin. Invest. 103, 137.
26. Fernandes-Alnemri, T., Takahashi, A., Armstrong, R., Krebs, J., Fritz, L.,
Tomaselli, K. J., Wang, L., Yu, Z., Croce, C. M., Salveson, G., Earnshaw, W. C.,
Litwack, G., and Alnemri, E. S. (1995). Cancer Res., 55, 6045.
27. Lazebnik, Y. A., Kaufmann, S. H., Desnoyers, S., Poirier, G. G., and Earnshaw,
W. C. (1994). Nature, 371, 346.
28. Kayalar, C., Ord, T., Testa, M. P., Zhong, L. T., and Bredesen, D. E. (1996). Proc.
Natl. Acad. Sci., USA, 93, 2234.
237
29. Mashima, T., Naito, M., Noguchi, K., Miller, D. K., Nicholson, D. W., and Tsuruo,
T. (1997). Oncogene, 14, 1007.
30. Song, Q., Wei, T., Lees-Miller, S., Alnemri, E., Watters, D., and Lavin, M. F.
(1997). Proc. Natl. Acad. Sci. USA, 94, 157.
31. Rao, L, Perez, D., and White, E. (1996). J. Cell Biol., 135, 1441.
32. Talanian, R. V., Quinlan, C., Trautz, S., Hackett, M. C., Mankovich, J. A., Banach,
D., Ghayur, T., Brady, K. D., and Wong, W. W. (1997). J. Biol. Chem., 272, 9677.
33. Nicholson, D. W., Ali, A., Thornberry, N. A., Vaillancourt, J. P., Ding, C. K.,
Gallant, M., Gareau, Y., Griffin, P. R., Labelle, M., and Lazebnik, Y. A. (1995).
Nature, 376, 37.
34. Margolin, N., Raybuck, S. A., Wilson, K. P, Chen, W., Fox, T., Gu, Y., and
Livingston, D. J. (1997). J. Biol. Chem., 272, 7223.
35. Liu, X., Zou, H., Slaughter, C., and Wang, X. (1997). Cell, 89, 175.
36. Samejima, K., Svingen, P. A., Gasi, G. S., Kottke, T., Mesner, P. W., Jr, Stewart, L.,
Champoux, J., Kaufmann, S. H., and Earnshaw, W. C. (1999). J. Biol. Chem., 274,
4335.
37. Graham, J. M., and Rickwood, D., eds. (1997). Subcellular Fractionation: A
Practical Approach. Oxford University Press, Oxford.
38. Thornberry, N. A., Bull, H. G., Calaycay, J. R., Chapman, K. T., Howard, A. D.,
Kostura, M. J., Miller, D. K., Molineaux, S. M., Weidner, J. R., and Aunins, J.
(1992). Nature, 356, 768.
39. Thornberry, N. A. and Molineaux, S. M. (1995). Protein Sci., 4, 3.
40. Thornberry, N. A., Peterson, E. P., Zhao, J. J., Howard, A. D., Griffin, P. R., and
Chapman, K. T. (1994). Biochemistry, 33, 3934.
41. Shaw, E. (1990). Adv. Enzymol. Relat. Areas Mol. Biol., 63, 271.
42. Takahashi, A., Alnemri, E. S., Lazebnik, Y. A., Fernandes-Alnemri, T., Litwack,
G., Moir, R. D., Goldman, R. D., Poirier, G. G., Kaufmann, S. H., and Earnshaw,
W. C. (1996). Proc. Natl. Acad. Sci. USA, 93, 8395.
43. Martins, L. M., Kottke, T. J., Kaufmann, S. H., and Earnshaw, W. C. (1998).
Blood, 92, 3042.
44. Martins, L. M., Mesner, P. W., Kottke, T. J., Basi, G. S., Sinha, S., Tung, J. S.,
Svingen, P. A., Madden, B. J., Takahashi, A., McCormick, D. J., Earnshaw, W. C.,
and Kaufmann, S. H. (1997). Blood, 90, 4283.
45. Faleiro, L., Kobayashi, R., Fearnhead, H., and Lazebnik, Y. (1997). EMBO J., 16,
2271.
46. Emoto, Y., Manome, Y., Meinhardt, G., Kisaki, H., Kharbanda, S., Robertson,
M., Ghayur, T., Wong, W. W., Kamen, R., Weichselbaum, R., and Kufe, D.
(1995). EMBO J., 14, 6148.
47. Ghayur, T., Hugunin, M., Talanian, R. V., Ratnofsky, S., Quinlan, C., Emoto, Y.,
Pandey, P., Datta, R., Huang, Y., Kharbanda, S., Allen, H., Kamen, R., Wong, W.,
and Kufe, D. (1996). J. Exp. Med., 184, 2399.
48. Dubrez, L., Savoy, I., Hamman, A., and Solary, E. (1996). EMBO J., 15, 5504.
238
A1
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Perkin-Elmer-Cetus (The Perkin-Elmer Corporation), 761 Main Avenue,
Norwalk, CT 0689, USA.
Pharmacia Biotech Europe Procordia EuroCentre, Rue de la Fuse-e 62, B-
1130 Brussels, Belgium.
Pharmacia Biosystems
Pharmacia Biosystems Ltd. (Biotechnology Division), Davy Avenue,
Knowlhill, Milton Keynes MK5 8PH, UK.
Pharmacia LKB Biotechnology AB, Bjorngatan 30, S-75182 Uppsala,
Sweden.
Promega
Promega Ltd., Delta House, Enterprise Road, Chilworth Research Centre,
Southampton, UK.
Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711-5399,
USA.
241
List of suppliers
Qiagen
Qiagen Inc., do Hybaid, 111-113 Waldegrave Road, Teddington, Middlesex,
TW11 8LL, UK.
Qiagen Inc., 9259 Eton Avenue, Chatsworth, CA 91311, USA.
Schleicher and Schuell
Schleicher and Schuell Inc., Keene, NH 03431A, USA.
Schleicher and Schuell Inc., D-3354 Dassel, Germany. Schleicher and Schuell
Inc., c/o Andermann and Company Ltd.
Shandon Scientific Ltd., Chadwick Road, Astmoor, Runcorn, Cheshire WA7
1PR, UK.
Sigma Chemical Company
Sigma Chemical Company (UK), Fancy Road, Poole, Dorset BH17 7NH, UK.
Sigma Chemical Company, 3050 Spruce Street, P.O. Box 14508, St. Louis,
MO 63178-9916.
SLM-AMINCO, 810 W. Anthony Drive, Urbana, IL 61801, USA.
Sorvall DuPont Company, Biotechnology Division, P.O. Box 80022,
Wilmington, DE 19880-0022, USA.
Stratagene
Stratagene Ltd., Unit 140, Cambridge Innovation Centre, Milton Road,
Cambridge CB4 4FG, UK.
Strategene Inc., 11011 North Torrey Pines Road, La Jolla, CA 92037, USA.
United States Biochemical, P.O. Box 22400, Cleveland, OH 44122, USA.
Wellcome Reagents, Langley Court, Beckenham, Kent BR3 3BS, UK.
242
Index
NOTE: Bold numbers denote reference to c-jun 37
Figures or Tables. clonogenic assay 211
c-myc 1
acidophilic bodies 5 Councilman bodies 5
acridine orange 27, 75 CPP32 216
activation-induced cell death 81 cyclophilin (nuc 18) 43
affinity labelling 230-4 cyclosporin A 82
agarose gel electrophoresis 47-8 cytochrome c 10, 11, 12, 83, 218
AICD 81, 94 cytotoxicity test 90, 94
AIF 83
annexin V 12, 37, 127, 129-34
see also phosphatidyl serine DAPI 26
Apaf-1 83, 218 DFF 40-3, 45, 220
Apo-l/CD95 81 DNA
apopain 216 content, see also fractional content 74
apoptosis specific substrates 125, 219-20, 225 degradation 6, 135
apoptotic denaturation 75-6
bodies 6, 7, 9, 29 fractional content 68-71
cascades 6, 8, 9, 10, 11 fragmentation 41-52, 53, 89-90, 06, 125
index 33 high molecular weight 41, 43-7
nuclease 34 (AN34) 43 labelling 50-3, 87, 89
ATP 6, 8 ladders 3, 8, 12, 41, 42
autoradiography 24 metabolism and repair, proteins in 219
ploidy 57
strand breaks 71-4, 77
Bcl-2/Bax 143, 144, 157-212, 176-7, 197-9, DNase
220 I 42
function in yeast 205-12 T 42
BID, Bid 199-201, 220 Y 42
dye exclusion 211-3
calcineurin 82
calcium 82, 95, 96, 130, 144 ERICE 216
calcium ionophore 2 ethidium bromide 3
calpains 217 etoposide 42
camptothecin 42, 142
cancer therapy 1,2
CARD 218 FADD 82, 84, 218
caspases 9, 10, 11, 82, 83, 84, 106, 125, 126, Fas 81, 82-3, 84, 94, 95-6, 147
127, 128, 143, 218, 216 ligand 81,84, 106
activity 226-30 filter elution 41, 48-50
inhibitors 97-99, 235-6 FLICE 83, 84, 97, 216
substrates 125, 215, 219-20, 224-6 fodrin 126, 129
caspase-activated DNase 43
catalase 153-4
B-catenin 126 gels, overloading 15
cathepsins 217 glutathione 141, 146-53
cell culture sampling 23 granzyme 83-4, 84, 91, 95, 96-7, 217
cell cycle, proteins involved in 220 inhibitors 99-100
cell death, other forms 5-7 green fluorescent protein 37
ceramide 105, 106, 107, 108-11, 115-18, 144
channel acivity 204-5
chromatin 59-61, 92 H & E, haematoxylin and eosin 25-6, 34
circadean rhythm 33 Hoechst dyes 26-7, 92
Index
HPLC 113-15, 118-19, 151 NF-KB 220
hyaline bodies 5 northern blot analysis 167-71
Nuc 18 42,43
nuclear
ICAD 43, 220 events in apoptosis 19, 128
ICE 82, 97, 216, 217 isolation 51
immunoblot analysis 157-64, 218-23 lamins 128
immunohistochemical detection 175-91 pore protein 37
intermediate filaments 127 nucleosomes 41
ion efflux 204-5
ionomycin 82, 95
ISEL 34-7 oxidative stress 141, 144
ISNT 135
perform 83, 84, 95, 96-7

J-aggregates 142 peroxide levels 144, 145-6
JC-1 143 phosphatidylserine 61, 67-8, 125, 129-34
see also annexin V
positional scoring 30-1
K562 cells 3 PMA 82,95
p-phenelynediamine 92-4
procaspase 218
laser scanning cytometry 58-61, 64, 65, 70, 73, prodomain 218
77-8 protein kinase C 82, 219
liposome preparation 202-3 pulse field gel electrophoresis 41, 43-7
MACH 83, 216 reactive oxygen intermediates 141, 144-6

macrophages 5, 129 recombinant proteins 191-201
Mch 2, 3, 4, 5, 6 216 release assay
membrane BLT esterase 91-2
inserted proteins 201-5 chromium 84-7, 99
nuclear 128 IUdR 87, 99
plasma 67-8, 84, 125 RT-PCR 171-5
microfilaments 126
microscopy
EM 27-9, 77 scatter, light 61-3, 67, 71
fluorescent 26-7 slide preparation 20-1, 25
light 24-6, 61, 77 Southern blot analysis 14, 173-4
microtubules 126-7 staurosporine 42
mitochrondria 8, 10, 12, 13-14, 15 sub G1/G0 see DNA, fractional content
mitochondrial
DNA 8, 12-14, 15
metabolism 61 T cell antigen receptor 82
transmembrane potential 63-7, 142-3 thioninblue 26
mitotic cells 24, 60 tumor necrosis factor a 81, 94, 106
mixed lymphocyte cultures 86 receptor 82,94
morphology 2, 19-20, 20, 38, 77, 125, 142 TUNEL 12, 34-7, 42, 126, 135-8, 136
MORT 1 218
MTT 93, 94
multiple antigen detection 162-5 2-vinylpyridine 148
vitamin D3,1,25-dihydroxy 2, 106
necrosis 6, 7, 8, 12, 41, 61, 63, 77, 128, 131, 135

NEDD2 216 YAMA 216
NF-AT 82
244

Apoptosis A Practical Approach Practical Approach Series

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What are some of the techniques used to study apoptosis?

What are some of the techniques used to study apoptosis?

What are some of the proteins involved in apoptosis?

What are some of the proteins involved in apoptosis?

Apoptosis

The Practical Approach Series

See also the Practical Approach web site at http://www.oup.co.uk/PAS

Affinity Chromatography Cell Growth and Apoptosis

New Jersey G.P.S.

2. Morphological recognition of apoptotic cells 19

3. Assessment of DNA damage in apoptosis 41

4. Analysis of cell death by flow and

5. Cell-mediated cytotoxicity and cell death

6. Sphingolipids as messengers of cell death 105

7. Cytochemical detection of cytoskeletal and

8. Metabolic alterations associated with

9. Methods of measuring Bcl-2 family proteins

10. Methods of assaying Bcl-2 and Bax family protein function

10. Methods for detecting proteolysis during

1. General introduction and overview of contents

3. Distinction of apoptosis from other forms of cell

Table 1. Morphological differences and similarities between apoptosis and necrosis

Table 2. Biochemical differences and similarities between apoptosis and necrosis

5. Time course of apoptotic cascades

membrane potential, an early event in apoptosis, can be detected in a similar

Figure 5. A more detailed outline of apoptosis-signalling pathways. The mitochondria are

6.1 Procedure for the determination of the increased

Protocol 1. Analysis of cell death by comparison of mitochondrial

in a project or report may be elevated by the simple expedient of including an

1.1 Key morphological features of apoptotic cells

Figure 1. Schematic diagram of morphological changes associated with apoptosis.

2. Light and fluorescent microscopy techniques for

Protocol 1. Gelatine subbing

Protocol 2. APES subbing

2.1.2 Preparation of tissue sections

Protocol 3. Using formaldehyde-fixed, paraffin wax-embedded

Equipment and reagents

Protocol 4. Using frozen tissue sections

2.1.3 Preparation of cell culture samples

Protocol 5. Preparation of cells in suspension cultures

Protocol 6. Preparation of cells from monolayer cultures

2.2 Nuclear counterstains

Protocol 7. Rehydration of slides

Protocol 8. Haematoxylin (and eosin: H&E)

Protocol 9. Thionin blue

2.2.2 Stains for fluorescence microscopy

Protocol 10. Fluorescent stains

3. Electron microscopic techniques

Protocol 11. Preparation of cells for transmission electron

Electron microscopic (EM) evidence of apoptosis is illustarted in Figure 3.

4. Quantitation of apoptotic events

Protocol 12. Preparation of tissue for the positional scoring of

If the tissue is prepared as described in Protocol 12, slides with good

4.2 Problems in scoring apoptotic events

be 'missed', resulting in an underestimation of apoptotic frequency. The

5. In situ detection of DNA strand breaks

Protocol 13. TUNEL staining using the Oncor Apoptag® kit

N.B. The protocol described below is specifically optimized for sections of

See Oncor's web site at www.oncor.com.

Using an improved ISEL technique, Pompeiano et al. (23) have demon-