Research Article
Functional Profiling: From Microarrays via Cell-Based Assays
to Novel Tumor Relevant Modulators of
the Cell Cycle
1
1
2
1
1
Dorit Arlt, Wolfgang Huber, Urban Liebel, Christian Schmidt, Meher Majety,
1
1
1
1
Mamatha Sauermann, Heiko Rosenfelder, Stephanie Bechtel, Alexander Mehrle,
1
1
1
2
Detlev Bannasch, Ingo Schupp, Markus Seiler, Jeremy C. Simpson,
1
1
1
1
Florian Hahne, Petra Moosmayer, Markus Ruschhaupt, Birgit Guilleaume,
1
2
1
Ruth Wellenreuther, Rainer Pepperkok, Holger Sültmann,
1
1
Annemarie Poustka, and Stefan Wiemann
Division of Molecular Genome Analysis, German Cancer Research Center and 2Cell Biology and
Cell Biophysics Programme, European Molecular Biology
Laboratory, Heidelberg, Germany
1
Abstract
Cancer transcription microarray studies commonly deliver
long lists of ‘‘candidate’’ genes that are putatively associated
with the respective disease. For many of these genes, no
functional information, even less their relevance in pathologic conditions, is established as they were identified in
large-scale genomics approaches. Strategies and tools are
thus needed to distinguish genes and proteins with mere
tumor association from those causally related to cancer.
Here, we describe a functional profiling approach, where we
analyzed 103 previously uncharacterized genes in cancer
relevant assays that probed their effects on DNA replication
(cell proliferation). The genes had previously been identified
as differentially expressed in genome-wide microarray
studies of tumors. Using an automated high-throughput
assay with single-cell resolution, we discovered seven
activators and nine repressors of DNA replication. These
were further characterized for effects on extracellular signalregulated kinase 1/2 (ERK1/2) signaling (G1-S transition) and
anchorage-independent growth (tumorigenicity). One activator and one inhibitor protein of ERK1/2 activation and three
repressors of anchorage-independent growth were identified.
Data from tumor and functional profiling make these
proteins novel prime candidates for further in-depth study
of their roles in cancer development and progression. We
have established a novel functional profiling strategy that
links genomics to cell biology and showed its potential for
discerning cancer relevant modulators of the cell cycle in the
candidate lists from microarray studies. (Cancer Res 2005;
65(17): 7733-42)
Note: Supplementary data for this article are available at Cancer Research Online
(http://cancerres.aacrjournals.org/).
D. Arlt and W. Huber contributed equally to this work.
W. Huber is currently at the European Bioinformatics Institute, Cambridge CB10
1SD, England.
Requests for reprints: Annemarie Poustka, Division of Molecular Genome
Analysis, German Cancer Research Center, Im Neuenheimer Feld 580 69120
Heidelberg, Germany. Phone: 49-6221-42-4646; Fax: 49-6221-42-3454; E-mail:
a.poustka@dkfz.de.
I2005 American Association for Cancer Research.
doi:10.1158/0008-5472.CAN-05-0642
www.aacrjournals.org
Introduction
Proliferation of mammalian cells requires that DNA replication is
strictly regulated and done with high fidelity. The commitment of
cells to enter the S phase is the primary decision point at which
they control their division. Alterations in expression and activity of
proteins that are involved in this process can cause unrestrained
growth and are prerequisite for the development and progression
of cancer (1). In this line, tumor-associated changes in mRNA
transcription are frequently examined in tumor microarray studies.
Whereas such analyses typically identify hundreds or thousands of
genes (2–4), often, the function of the encoded proteins is unknown
and their role in the disease process is not well understood (5).
Long lists of differentially expressed genes reflect the complex
interplay of biological processes that are involved in cancer (e.g.,
inflammation, angiogenesis, metabolism, as well as cell cycle
control, and apoptosis; refs. 6–9). The distinction between
causative changes in gene expression from secondary effects
remains a key challenge.
We adopted the idea of functional profiling (10), developed a
cancer relevant automated high-throughput assay, and applied it
to genes that were associated with cancer by whole genome
microarray analysis (11, 12). This identified novel proteins that
modified the rate of DNA replication in mammalian cells, this
being the first direct indication of a causative relation to
oncogenic processes. We refined the functional profiles for 16
candidate genes and proteins with assays that probed other cell
cycle– and cancer-related processes, extracellular signal-regulated
kinase 1/2 (ERK1/2) signaling, and anchorage-independent
growth. Functional profiling distinguished causative from secondary effects and is therefore able to bridge the gap between
whole genome tumor microarray studies and single candidate
analysis.
Materials and Methods
Selection of novel full-length cDNAs. Tumors of the brain, breast,
kidney, and gastrointestinal stroma were screened for cancer-associated
changes in mRNA transcription using a 31,500-element whole transcriptome cDNA array (11, 12). Genes with differential expression
between normal and tumor samples or between tumor types were
selected by a two-sample t test. From these, we selected 103 open
7733
Cancer Res 2005; 65: (17). September 1, 2005
Cancer Research
reading frames (ORF) based on the availability of full-length cDNAs for
the cell-based bromodeoxyuridine (BrdUrd) incorporation assay. The
cDNAs had been isolated from libraries of human fetal brain (library
DKFZp564), human fetal kidney (DKFZp566), human amygdala
(DKFZp761), human uterus (DKFZp586), and human testis (DKFZp434;
ref. 13). ORFs were cloned and sequence validated in Gateway (14)
vectors, then shuttled into NH2-terminal cyan fluorescent protein (CFP)
and COOH-terminal yellow fluorescent protein (YFP) to produce
mammalian expression constructs under control of the cytomegalovirus
promoter (15). Subcellular localization of proteins was determined as
described (15). Initial annotation of protein sequences was done with
automated tools (16).
Automated cell-based assay to assess DNA replication. Expression
plasmids were isolated in a 96-well format using a MultiProbe IIex-Robot
(Perkin-Elmer, Wellesley, MA) and Montage Plasmid Miniprep96 Kits
(Millipore, Bedford, MA). DNA masterplates were generated with a final
concentration of 27.5 ng/AL and a total volume of 80 AL per well. Cells
(10,000; NIH 3T3 cells: ATCC CRL-1658) were transfected (Effectene, Qiagen,
Hilden, Germany) using 100 ng plasmid DNA per well in an array of 12
chamber slides (MWG Biotech, Ebersberg, Germany) to mimic a 96-well
plate. Each CFP and YFP expression construct was included in duplicate.
Control cDNAs (CFP-cyclin A, cyclin A-YFP as positive controls for
activating, CFP subunit A of phosphatase 2, subunit A of phosphatase 2YFP as positive controls for repressing effects on DNA replication; CFP and
YFP served as negative controls) were placed at fixed positions within the
plate. After 24 hours, cells were incubated in presence of 1 mmol/L BrdUrd
for 6 hours before fixation with 4% paraformaldehyde. Transfection, BrdUrd
immunostaining with a mouse anti-BrdUrd primary antibody (Roche
Diagnostics, Penzberg, Germany), incubation with a Cy5-labeled goat antimouse secondary antibody (Molecular Probes, Karlsruhe, Germany), and
4V,6-diamidino-2-phenyindole (DAPI) staining were done using a MultiProbe robot.
Image acquisition and analysis. A fully automated high-content
screening microscope (17) was used to measure on average 19 frames
from each well. The image frames consisted of three color channels (CFP/
YFP, Cy5, and DAPI) each at 1,280 1,024 pixels at 12-bit resolution. Images
were analyzed by an automated segmentation and quantification algorithm
that we implemented in Labview (National Instruments, http://ni.com).
Within-well analysis. The data from one well were modeled as
Between-well analysis. To obtain a ranking of the proteins, we
compared the set of z scores from the replicate wells for each ORF to the
overall distribution of z scores via the two-sided Wilcoxon test. We
considered an effect significant when P < 0.05. Multiple testing adjustment
for control of the false discovery rate was done following Benjamini and
Hochberg (19).
We provide software for statistical procedures and visualizations through
the package prada , which is part of the bioinformatics platform
Bioconductor (http://www.bioconductor.org).
Assay for quantification of anchorage-independent growth. Flatbottomed 96-well plates were coated with poly(2-hydroxylethyl methacrylate) [poly(HEMA), 120 mg/mL of 95% ethanol] as described (20). Kidney
clear cell carcinoma cells Caki-1 (ATCC HTB-46) and Caki-2 (ATCC HTB47) cells were cultured in RPMI 1640 with 1% penicillin/streptomycin, 1 %
L-glutamine, 1% nonessential amino acids, and 10% fetal bovine serum
(Life Technologies, Gaithersburg, MD) and transfected with Lipofectamine
2000 (Invitrogen, Karlsruhe, Germany) according to the manufacturer’s
instructions. Proteins found to activate DNA replication were transfected
into Caki-2 cells to measure their potential to stimulate anchorageindependent growth of this cell line. Repressors of DNA replication were
analyzed in Caki-1 cells for their potential to reduce anchorageindependent growth. Twenty-four hours after transfection, 3,500 Caki-1
or Caki-2 cells were spread in each well of the poly(HEMA)-coated plates
in a total volume of 200 AL RPMI 1640. Medium was exchanged after
bi ¼ mðti Þ þ uf ðiÞ þ jdi þ ei
where bi , ti , and di are the BrdUrd, transfection, and DAPI intensities,
respectively, for cell i; m is a smooth regression function, f(i) is the frame
in which cell i was found; uf is the background for the fth frame; n is a
spectral crosstalk coefficient; and ei is a noise term. We introduced the
correction terms uf and ndi to address empirically observed systematic effects:
effects: uf accounts for the different baseline levels of the fluorescence
intensities in different frames and n for spectral overlap from the DAPI
signal into the CFP detection channel. A separate coefficient n was fitted
for each 96-well plate to account for apparent long-time drift of the
equipment. Values for n were between 0 and 0.06. Spectral overlap
between DAPI and YFP was negligible. The smooth local regression
function m, its derivative mV, and confidence bands for mV were fitted
using the R package locfit (18). A constant bandwidth a = 1 was used
throughout. To determine the intensity t * that corresponds to very
weakly expressing cells we calculated the midpoint of the shorth, which
is the shortest interval that contains half of the ti . As a measure of the
effect, we used the z score, which is the ratio of the estimated slope and
its SE.
z¼
m̂Vðt Þ
r̂mV ðt Þ
Cancer Res 2005; 65: (17). September 1, 2005
Figure 1. Schematic representation of the experimental and analysis workflow
in functional profiling. Lists from whole genome tumor microarray studies
(11, 12), and a full-length ORF collection (13, 15) were intersected to select
103 previously uncharacterized proteins for the functional profiling assays.
Data were analyzed only from those expression constructs (NH2-terminal CFP
or COOH-terminal YFP) annotated as expressing correctly localizing proteins.
Statistical analysis determined 16 proteins with significant effect on DNA
replication, which were analyzed in further assays (ERK1/2 activation and
anchorage-independent growth). Quantitative reverse transcription-PCR
(qRT-PCR ) analysis (Taqman) compared gene expression between two
cancer cell lines which differ in anchorage-independent growth. Finally, data
were integrated to annotate the novel cancer-relevant candidate genes and
proteins.
7734
www.aacrjournals.org
Functional Profiling Identifies Cancer-Relevant Genes
Figure 2. Within-well analysis of protein
overexpression and the effects on DNA replication.
A, cells were fixed and stained with DAPI (left) to
allow for automatic identification (nuclei boxed ).
Fluorescence intensities were recorded for each
cell in the YFP channel and indicate the level of
cyclin A-YFP expression (middle ). Cy5
fluorescence in the nucleus is proportional to the
level of BrdUrd incorporation (right). B, histogram
of the YFP fluorescence intensities (arbitrary units)
from 1,025 cells. The vertical grey line indicates
the midpoint of the shorth t * that is an estimator
of the mode of the distribution. C, scatterplot of
expression level versus BrdUrd incorporation.
The control population of nonexpressing cells (left),
showing a considerable intrinsic variation in their
BrdUrd-Cy5 signal. A systematic trend was
observed for the population of expressing cells
towards the right end of the plot: the higher the
expression level, the more cells had incorporated
BrdUrd. This is visualized by the local regression
curve, which was calculated based on the data of
nonexpressing and weakly overexpressing cells
only, not regarding cells with signal intensities
>100. As expected, the slope was indicative of
cyclin A being an activator of DNA replication.
D, visual overview of the protein effects from
a whole 96-well plate. Z scores for positive
(activators) and negative (repressors) slopes are
indicated in red and blue color, respectively. Data
from well A2 (arrowhead ) are shown in (A-C ).
4 days of culture. Measurement of cell growth was done as described by
Fukazawa et al. (20).
Results and Discussion
Assay automation. We designed a functional profiling strategy
that took genes that had been associated with cancer by
microarray studies and screened the encoded proteins in tumor
relevant assays (Fig. 1). ORFs of previously uncharacterized genes
were subcloned from publicly available full-length cDNA resources
(13, 21) into expression vectors (15) and transfected into NIH 3T3
cells to overexpress the encoded proteins. All ORFs were fused
to NH2-terminal CFP or COOH-terminal YFP variants of the green
fluorescent protein (GFP), and their expression was monitored
by automated microscopy. The protein localization at the
subcellular level was visually inspected for all constructs (15,
22). This information was used in the subsequent assays, only
data obtained with the relevant expression constructs were
considered (Fig. 1).
A DNA replication assay was fully automated with help of liquid
handling robots and customized statistics software. Transient trans-
www.aacrjournals.org
fections were carried out in 96-well plates; analysis of protein
overexpression and induced effects was 24 hours later. We applied
automated high-content screening microscopy (17, 23) to achieve a
single-cell resolution (Fig. 2) and traced individual cells within their
microenvironmentofthewell.Werestrictedouranalysistocellshaving
small levels of protein expression to minimize the perturbation of the
cellular system. Whereas we cannot completely rule out nonphysiologic effects that might be induced by even minor increases in protein
content, our strategy is superior to other approaches, like plate reader
assays and RNA interference, where a correlation of protein levels with
effects is not possible at a single-cell resolution. Additionally, we could
simultaneously identify activators and repressors of DNA replication
(i.e., potential oncogenes and tumor suppressor genes; Figs. 2 and 3).
Cyclin A and phosphatase 2A were used in the assay set up and in every
screening plate as positive controls for activation and repression,
respectively.
DNA replication was quantified by monitoring the rate of
BrdUrd incorporation with help of a Cy5-labeled antibody. In
addition, cells were stained with DAPI to facilitate autofocus of the
microscope and to aid the image segmentation algorithm with the
cell finding. Thus, three fluorescence intensities (GFP/YFP, Cy5,
7735
Cancer Res 2005; 65: (17). September 1, 2005
Cancer Research
Figure 3. Between-well analysis to
validate activating and repressing effects
on DNA replication through replicate
experiments. A, scatterplots from
individual wells were produced to show
activating or repressing effects. The z
scores of 9.51 and 4.56 indicate the
protein DKFZp434C2415 to be a
repressor. B, we summarized and
compared the results from multiple wells
for the same protein through histograms
of the z scores for both tag orientations.
The plot shows the z scores calculated
for individual wells, separately for
NH2-terminal CFP-fusions (gray ) and for
COOH-terminal YFP-fusions (black ).
P = 3.4 105 is indication that the
measured effect is significant. C, box plot
of the z score values were produced for
the seven activators (red ) and nine
repressors of DNA replication (blue )
identified in the screen. Columns, means;
bars, SE. Outliers (o).
and DAPI) were recorded for each cell. The effect of the candidate
proteins’ expression on DNA replication was determined by local
regression of the Cy5 signal (BrdUrd) on the GFP/YFP signal
(expression). For each well, this resulted in an estimated regression
slope and a z score that is the estimate standardized by its SE.
Data from replicate wells per protein were summarized by the
Wilcoxon statistic and P value for the comparison of their z scores
to the overall distribution of z scores. This resulted in a ranking
of the proteins for effect strength and a list of 16 proteins with
Ps < 0.05.
Assay performance. The results of all microscopic frames
(19 on average) from within one well were combined, taking into
the account disturbance factors as spectral overlaps and framespecific background values. One such frame is shown in Fig. 2A.
The intracellular amount of recombinant protein varied over a
broad range. The majority of cells were either untransfected (cells
left of the midpoint of the shorth in Fig. 2B) or expressed the
protein at low levels (right of the midpoint of the shorth). Few
cells strongly expressed the recombinant protein with signal
intensities of >100 in the YFP channel. A scatterplot of expression
level versus BrdUrd incorporation is shown in Fig. 2C. Even the
population of nonexpressing cells showed a considerable intrinsic
variation in DNA replication as reflected by varying BrdUrd-Cy5
signals. A systematic trend was observed, however, for the
population of cyclin A–expressing cells towards the right end of
Cancer Res 2005; 65: (17). September 1, 2005
the plot: the higher the expression level, the more cells had
incorporated BrdUrd during the experiment. This trend is
visualized by the local regression curve in Fig. 1C. This curve
was calculated based on the data of nonexpressing and weakly
overexpressing cells. Strongly overexpressing cells (e.g., signal
intensity >100 in Fig. 2B-C) were downweighed as in these the level
of recombinant protein could induce nonphysiologic effects (e.g.,
apoptosis). A z score was calculated as a summary of the data for
the cells within one well.
To obtain a visual overview of the protein effects from a 96well experiment, we produced plate plots (Fig. 2D). Z scores for
positive (activators) and negative (repressors) slopes are indicated
in color. The red color for cyclin A is indicative of this protein
to be an activator of DNA replication. Interactive versions of
the plate plots are provided in the web supplement (http://
www.dkfz.de/mga/home/fctassay/sphase). Scatterplots similar to
and including the one shown in Fig. 2C can be viewed by
mouse clicking on a well. To assess statistical significance, we
compared the results from multiple wells for the same protein
through histograms of the z scores for both tag orientations
(Fig. 3).
Candidate selection. We selected 103 genes (Fig. 1; Table S1)
for a cellular screen based on the following criteria: (i) their
transcripts were contained in a set of 396 differentially expressed
genes from genome-wide tumor microarray studies (11, 12); (ii)
7736
www.aacrjournals.org
Functional Profiling Identifies Cancer-Relevant Genes
the encoded proteins had no public functional annotation, other
than from high-throughput projects such as microarray analysis;
(iii) we had determined the subcellular localization of the
proteins (15, 22). This provided an initial piece of information
that connected the proteins to their respective cellular environment and thus limited their potential for protein interactions.
In addition, use of full-length proteins ensured that all motifs
determining, for example, protein localization, activity, and
regulation were present.
DNA replication assay and functional profiling. Analyzing
the 103 proteins in the BrdUrd incorporation assay, cells were
detected in 2,462 of 2,880 wells. Fluorescence intensities were
recorded for CFP/YFP, Cy5 (BrdUrd), and DAPI signals
individually, resulting in 3 46,221 images. A total of
2,251,739 cells were analyzed, giving over 6.75 million data
points. Sixteen of the 103 proteins showed a significant effect on
the passage through the S phase (individual P < 0.05; false discovery rate <0.16). Seven of these were activators and nine were
repressors of BrdUrd incorporation and thus of DNA replication
(Fig. 3; Table 1). The 16 proteins were then examined for a
possible effect on ERK1/2 activation, to measure effects on G1-S
transition (24). There we found one activating and one inhibiting
protein (Fig. S1; Table 1). Repressors of DNA replication were
further subjected to a poly(HEMA) growth assay to test their
potential to modulate anchorage-independent cell proliferation.
Three proteins were positive in this assay (Fig. 4; Table 1). We
annotated all 16 genes and proteins using tumor microarray
results from Oncomine (ref. 25; Table S1). Taqman RNA
quantification was done in two kidney cancer cell lines (Caki-1
and Caki-2) to refine analysis of the poly(HEMA) assay and was
included in the annotation as well as protein and domain
classifications from Source (26) and Interpro (ref. 27; Table S1).
Together, this integrated data set provided us with candidates
for detailed and ongoing studies. In the following, four such
genes will be described to show the synergy that is achieved
with the functional profiling strategy.
Cancer-relevant cell cycle modulators. The protein encoded
by cDNA DKFZp434P2235, an activator of passage through the
S phase, localizes to the plasma membrane. The corresponding
gene has been independently reported as PRC17 oncogene (28).
Pei et al. found it amplified in 15% of prostate cancers and highly
overexpressed in about half of metastatic prostate tumors. We
found the transcription of the PRC17 (DKFZp434P2235) gene upregulated in kidney tumors (Table 1). The gene is also expressed
in the kidney carcinoma cell line Caki-1, which shows anchorageindependent growth but not in Caki-2 which does not (Figs. S2
and S3). The encoded protein interacts with Rab5 and activates
its GTPase activity (28). Pei et al. discuss that expression of
PRC17 could affect the amount of inactive Rab5, which should
inhibit receptor endocytosis and result in prolonged growth
factor signaling. This hypothesis is consistent with our finding
that the overexpressed DKFZp434P2235 protein promotes DNA
synthesis in the S phase (Fig. 3). Whereas the PRC17 oncogene
takes one candidate from our list of truly novel genes, the
discovery of this protein in the DNA replication assay shows the
power of our integrated approach to identify proteins with
cancer relevance.
The gene for DKFZp566A0646 was found down-regulated in
kidney tumors (Table 1) and to have a lower expression in Caki-1
compared with Caki-2 cells (Fig. S2). The overexpressed protein
inhibited DNA synthesis in the S phase (Fig. 3) and blocked
www.aacrjournals.org
anchorage-independent growth of Caki-1 cells (Fig. 4). These
findings suggest a repressing effect on tumorigenicity in vitro.
The protein encoded by cDNA DKFZp566A0646 contains a
domain common to the Rab subfamily of Ras small GTPases
(IPR003579). The function of its orthologous protein p34 in rat is
not established; however, in a yeast two-hybrid screen, it was
shown to be a binding partner for the g and a subunits of the
AP1 and AP2 complexes, respectively (29). These adaptor complexes participate in intracellular clathrin-coated vesicle trafficking. We found that Rab5 as well as its effector early endosome
antigen-1 (EEA-1) are down-regulated in kidney tumors (11).
Together with the up-regulation of the Rab5 GTPase-activating
enzyme PRC17, this would imply reduced receptor internalization through endocytosis. In addition, Rab GDP-dissociation
inhibitor a (GDIa) was found up-regulated and Rab11b downregulated in kidney tumors, supporting the hypothesis that
endocytosis is inhibited in kidney cancer. Changing expression
levels of Rab genes have also been described for other cancer
types (30–32).
The protein encoded by cDNA DKFZp564D152 has 36%
identity over 186 residues with the SET protein of Drosophila
melanogaster (SOURCE; ref. 26), which belongs to the
nucleosome assembly protein (NAP) family. The NAP family
is a group of histone chaperone-like proteins that are known
to be regulators of transcriptional control (33). Nucleosome
assembly and disassembly are essential processes in the S
phase of the cell cycle. In proliferating cells, the synthesis of
histones during the S phase is coupled to DNA synthesis. This
ensures the packing of chromatin. The protein NAP-1 is
thought to be a cell cycle regulator and interacts with
Kap114p (34). That protein is a member of the karyopherin/
importin family, which executes the nuclear import of histone
2A and histone 2B. The activating effect of the DKFZp564D152
protein on DNA replication (Fig. 3), in conjunction with its
nuclear and cytoplasmic localization support the assumption
that it might be involved in cytoplasmic-nuclear transfer of
histones.
The protein encoded by DKFZp434C2415 was found to repress
DNA replication in the S phase (Fig. 3). However, it had a
significant activating effect on ERK1/2 activation in serum starved
as well as in stimulated cells (Table 1; Fig. S1). The protein was
recently described as UBA5, which is an E1-like enzyme in the
ubiquitin degradation pathway (35). Ubiquitin activating enzymes
regulate the rate of ubiquitin conjugation and ubiquitin mediated
protein degradation, which are essential control mechanisms in
the transition from G1 to S phase. Several studies show that cell
cycle regulating proteins are directly targeted for ubiquitinmediated destruction through ERK1/2 (36, 37). Thus, DKFZp434C2415 could regulate ERK1/2 activity through ubiquitin
mediated degradation of, for example, phosphatases, the activated
ERK1/2 would then mark cell cycle–regulating proteins for
degradation.
The DKFZp566F123 protein was identified as a BTB/POZ
zinc finger protein (POK protein). The BTB/POZ domain
(IPR000210) mediates protein/protein interaction, whereas the
C2H2 zinc finger (IPR007087) is a DNA-binding domain.
DKFZp566F123 shares closest homology to the transcriptional
repressor BCL-6. The latter protein is involved in hematopoiesis, oncogenesis, and immune response (38) and multiple roles
in cell survival and differentiation are described (39). Zhang
7737
Cancer Res 2005; 65: (17). September 1, 2005
Cancer Research
Table 1. Summary of the results for the 16 candidate proteins
Clone ID
Genbank
accession no.
Localization
NH2-terminal tag
Localization
COOH-terminal tag
S-phase
effect
DKFZp564D152
AL136629
Cytoplasm and nucleus
Cytoplasm and nucleus
+
0.0012
DKFZp434P2235
AL136860
AL136869
Golgi and plasma
membrane
Nucleus
+
DKFZp434J0450
Golgi and plasma
membrane
Nucleus
DKFZp564I1216
AL136600
Cytoplasm and nucleus
DKFZp434G0326
AL136820
DKFZp564F2122
S-phase
P
ERK1/2
effect
ERK1/2
P
HEMA
effect
Tumor
profiling
NE
NA
0.0021
NE
NA
+
7.9e5
NE
NA
Up in kidn
GIST tu
Up in kidn
versus
Down in k
versus
Endoplasmic reticulum
+
0.014
NE
NA
Down in k
Cytoplasm
Cytoplasm
+
0.0025
ND
NA
Different i
AL136604
Cytoskeleton and
microtubules
Cytoskeleton and
microtubules
+
0.0088
NE
NA
NA
DKFZp564C182
DKFZp434I0515
AL136628
AL136761
Cytoplasm
Cytoplasm and nucleus
Golgi
Cytoplasm and nucleus
+
0.022
6e6
NE
NA
NE
ND
Down in k
versus
DKFZp566A0646
AL136715
Cytoplasm
Cytoplasm
0.0038
NE
Down in k
versus
DKFZp434C2415
AL136757
Cytoplasm
Cytoplasm
3.4e5
+
NE
Up in kidn
versus
DKFZp566I133
AL136711
Endoplasmic reticulum
NA
0.015
NE
Up in kidn
versus
DKFZp434G1415
AL136759
Nucleus
Nucleus
7.9e7
NE
DKFZp566K013
AL136712
Mitochondria
Mitochondria
8e5
NE
NE
Different i
multifo
oligode
Different i
stage II
DKFZp564I0123
AL136615
Cytoplasm
Cytoplasm
3.4e4
NE
NE
NA
DKFZp566F123
AL050276
Nucleus
Nucleus
9.3e4
NE
NE
DKFZp761G2023
AL136570
Nucleus
Nucleus
0.035
NE
NE
Up in GIS
versus
Different i
multifo
oligode
0.02
1e4
NOTE: Localization data were taken from http://www.LIFEdb.de (50) and are given for both orientations of the tag relative to the ORF. Wrongly
localizing fusion proteins are indicated in gray. Measured effects on the S phase are given with direction (+, activators; , repressors), and P
value of the calculated z score All proteins were analyzed for effects on ERK1/2 activation. Activators of ERK1/2 phosphorylation are marked
with +, repressors with . Proteins having no effect on ERK1/2 phosphorylation are marked with NE. Proteins repressing DNA replication were
tested for effects on anchorage-independent growth [poly(HEMA) assay] in the Caki-1 cell line (Fig. 4).
Cancer Res 2005; 65: (17). September 1, 2005
7738
www.aacrjournals.org
Functional Profiling Identifies Cancer-Relevant Genes
Table 1. Summary of the results for the 16 candidate proteins (Cont’d)
Tumor profiling
Oncomine
Annotation (Source; InterPro)
Up in kidney tumors versus normal,
up in GIST tumors versus normal
Up in kidney tumors versus normal
Up in lung (Bhattacharjee), down in liver (Chen),
down in multiple tumors (Ramaswamy)
Not differential in one study
TSPY-like 1, IPR002164 NAP
Down in kidney tumors
versus normal
Up in lung (Bhattacharjee), up in endometrium
(Risinger), up in breast cancer with bad
prognosis (van’t Veer), down in melanoma
(Segal), down in prostate (Singh)
Up in liver (Chen), up in metastatic prostate cancers
(Ramaswamy), up in breast cancer with bad
prognosis (van’t Veer)
Up in breast adenocarcinoma: grade 3 versus
grade 1 (van’t Veer)
Down in kidney tumors
versus normal
Different in glioblastomas
multiforme versus
oligodendrogliomas
NA
ND
Down in kidney tumors
versus normal
Down in kidney tumors
versus normal
Up in kidney tumors
versus normal
Up in kidney tumors
versus normal
Different in glioblastomas
multiforme versus
oligodendrogliomas
Different in brain tumors
stage III versus stage IV
Down in breast adenocarcinoma: metastasis within
5 y of diagnosis versus no metastasis; grade
3 versus grade 1 (van’t Veer)
Not differentially expressed in four studies
Not probed in any of the studies
Up in liver (Chen), lung (Garber), down in kidney
(Higgins), up in breast cancer with bad prognosis
(van’t Veer)
Up in lung (Garber), down in pancreas (Iacobuzio)
Up in liver (Chen), prostate (Luo, Dhanasekaran),
lung (Garber), renal (Higgins), and in multiple
tumors (Ramaswamy); down in pancreas
(Iacobuzio)
Not differentially expressed in three studies
Down in CNS (Khatua, astrocytoma; Nutt, glioma;
Ramaswamy, Multicancer)
NA
Up in lung (Bhattacharjee), up in salivary adenoid
cystic carcinoma (Frierson)
Up in GIST tumors
versus normal
Different in glioblastomas multiforme
versus oligodendrogliomas
Down in prostate in three different studies
(La Tulippe, Luo JH, Welsh)
Down in high-grade breast tumors (van’t Veer)
TBC1 domain family, member 3,
IPR000195 RabGAP/TBC domain
RecQ protein-like 5, no InterPro-hits
Transmembrane protein 9; IPR004153
CXCXC repeat
Hypothetical protein, IPR000379 esterase/
lipase/thioesterase
Spermatogenesis associated 7, no InterPro-hits
Hypothetical protein, no InterPro-hits
Radial spokehead-like 1, IPR001156 Peptidase
S60, transferin lactoferrin, IPR006802 Radial
spokehead-like protein
Hypothetical protein, IPR003579 Ras small
GTPase, Rab type
Ubiquitin-activating enzyme estrone-domain
containing 1, IPR000594 UBA/THIF-type
NAD/FAD binding fold, IPR000205
NAD-binding site, IPR006140 D-isomer
specific 2-hydroxyacid dehydrogenase,
NAD-binding, IPR009036 Molybdenum
cofactor biosynthesis
Likely homologue of rat vacuole
membrane protein 1, no InterPro-hits
Hypothetical protein, IPR001656
tRNA pseudouridine synthase D, TruD
Dynamin-related protein DNM1,
IPR000375 Dynamin central region/
IPR001401 Dynamin/IPR001849
Pleckstrin-like/IPR003130 Dynamin
GTPase effector
Protein activator of the IFN-induced protein
kinase, IPR000999 Ribonuclease III family/
IPR001159 double-stranded RNA binding
(DsRBD) domain
Zinc finger protein 288, IPR000210 BTB/POZ
domain/IPR007087 Zn-finger, C2H2 type
LIM homeobox 6, IPR001356 Homeobox/
IPR001781 Zn-binding protein, LIM/
IPR003350 Homeodomain protein CUT
NOTE: Proteins reducing growth of Caki-1 carcinoma cells are marked with , proteins having no effect when overexpressed are marked with
NE. Tumor profiling results were extracted from Boer et al. (11) and Sultmann et al. (12). The individual studies mentioned in the Oncomine (25)
column are referenced in http://www.oncomine.org. Protein annotations are from the Source (26) and InterPro (27) databases. The complete data
for the 103 proteins analyzed is in Table S1.
Abbreviations: NA, not analyzed; ND, no detectable expression.
www.aacrjournals.org
7739
Cancer Res 2005; 65: (17). September 1, 2005
Cancer Research
Figure 4. Screening of repressors of DNA proliferation for their effect on anchorage-independent growth of Caki-1 kidney carcinoma cells. A, growth curves of
transiently transfected Caki-1 cells growing in poly(HEMA)-coated plates (transfection efficiency, 90%). MTT reduction (OD ) was measured from days 1 to 6.
B, inhibition of anchorage independent growth. While YFP-transfected Caki-1 cells retained their potential to grow on poly(HEMA) substrate, cells overexpressing
proteins from cDNAs DKFZp566A0646, DKFZp566I133, and DKFZp434G1415 did not survive in this assay.
et al. hypothesize that the protein encoded by DKFZp566F123
might also be involved in these biological processes and we
found that overexpression of this protein has indeed a
repressing effect on passage through the S phase (Fig. 3).
Thus, we postulate that DKFZp566F123 is a transcriptional repressor that regulates the expression of proteins that are essential
for control of cell cycle progression, and its down-regulation
would lead to enhanced cell growth. Also for other POK
proteins (e.g., the tumor suppressor HIC1; ref. 40), it has been
shown that their inactivation is associated with cell transformation (39).
Conclusions
We have developed a fully automated cell-based assay that is
designed to identify modulators of DNA replication. It has a
Cancer Res 2005; 65: (17). September 1, 2005
single-cell resolution with exceptionally high sensitivity and
specificity. The assay was applied to narrow down a list of cancer associated genes from microarray studies, identifying novel
candidate modulators of the cell cycle. Here we selectively
discerned proteins based on their property to affect a specific
activity of cells (DNA replication); however, this transfection
screen is adaptable for analyzing diverse cellular pathways and
processes.
The endogenous expression of genes in tumor and normal cells
in many cases correlated with the outcome of the DNA
replication assay. For example, the gene encoding cDNA DKFZp434I0515 was found down-regulated in kidney tumor profiling,
whereas it is expressed in normal kidney. Gene expression was
not detectable in Caki-1 and Caki-2 cells. The encoded protein
had repressing effects on DNA replication. Such correlation
should however not be regarded obligatory (41), because cellular
effects of endogenous and overexpressed proteins may be tissue
7740
www.aacrjournals.org
Functional Profiling Identifies Cancer-Relevant Genes
and cell type specific that are tuned by cellular regulatory
networks.
Depending on the outcome of the initial DNA replication screen
additional assays were carried out with protein subsets to further
characterize the candidates. Whereas it is clear that the described
high-throughput assays do not uncover all molecular and cellular
functions of the respective proteins, they effectively bridge the gap
between gene lists from tumor microarray studies and the capacity
of single gene and protein analysis that is needed to comprehensively characterize a pathway with traditional biochemistry and cell
biology methodologies.
This concept holds the potential for clustering genes based
on their functional profiles (42) and epistatic analyses, to
quantitatively elucidate complex genetic networks. Quantitative
cell-based analysis offers an advantage by permitting the
detection of gene functions that are associated with subtle,
possibly buffered effects. These are basis for the complex
interactions of multiple processes that are involved in the onset
and progression of most diseases (43). Combined with the
References
1. Hanahan D, Weinberg RA. The hallmarks of cancer.
Cell 2000;100:57–70.
2. van ’t Veer LJ, Dai H, van de Vijver MJ, et al. Gene
expression profiling predicts clinical outcome of breast
cancer. Nature 2002;415:530–6.
3. Perou CM, Sorlie T, Eisen MB, et al. Molecular portraits
of human breast tumours. Nature 2000;406:747–52.
4. Alizadeh AA, Eisen MB, Davis RE, et al. Distinct types
of diffuse large B-cell lymphoma identified by gene
expression profiling. Nature 2000;403:503–11.
5. Ramaswamy S, Tamayo P, Rifkin R, et al. Multiclass
cancer diagnosis using tumor gene expression
signatures. Proc Natl Acad Sci U S A 2001;98:
15149–54.
6. Bissell MJ, Radisky D. Putting tumours in context. Nat
Rev Cancer 2001;1:46–54.
7. Besson A, Assoian RK, Roberts JM. Regulation of the
cytoskeleton: an oncogenic function for CDK inhibitors?
Nat Rev Cancer 2004;4:948–55.
8. Sherr CJ. Principles of tumor suppression. Cell 2004;
116:235–46.
9. Balkwill F. Cancer and the chemokine network. Nat
Rev Cancer 2004;4:540–50.
10. Giaever G, Chu AM, Ni L, et al. Functional profiling of
the Saccharomyces cerevisiae genome. Nature 2002;418:
387–91.
11. Boer JM, Huber WK, Sultmann H, et al. Identification
and classification of differentially expressed genes in
renal cell carcinoma by expression profiling on a global
human 31,500-element cDNA array. Genome Res 2001;
11:1861–70.
12. Sültmann H, v. Heydebreck A, Huber W, et al. Gene
expression in kidney cancer is associated with novel
tumor subtypes, cytogenetic abnormalities and metastasis formation. Clin Cancer Res 2005;11:646–55.
13. Wiemann S, Weil B, Wellenreuther R, et al. Toward a
catalog of human genes and proteins: sequencing and
analysis of 500 novel complete protein coding human
cDNAs. Genome Res 2001;11:422–35.
14. Hartley JL, Temple GF, Brasch MA. DNA cloning
using in vitro site-specific recombination. Genome Res
2000;10:1788–95.
15. Simpson JC, Wellenreuther R, Poustka A, Pepperkok
R, Wiemann S. Systematic subcellular localization of
novel proteins identified by large scale cDNA sequencing. EMBO Rep 2000;1:287–92.
www.aacrjournals.org
mapping of protein interaction networks (44) and other largescale cancer relevant assays (45–49), this will lay the ground for
the comprehensive exploitation of genomic resources and
information and ultimately lead to an accelerated functional
understanding of the cellular systems that control health and
disease.
Acknowledgments
Received 2/3/2005; revised 6/13/2005; accepted 6/20/2005.
Grant support: National Genome Research Network grants 01GR0101 and
01GR0420 (German Cancer Research Center) and Bundesministerium für Bildung
und Forschung grants 01KW9987 and 01KW0012 (German Cancer Research Center)
and 01KW0013 (European Molecular Biology Laboratory) within the German Genome
Project.
The costs of publication of this article were defrayed in part by the payment of page
charges. This article must therefore be hereby marked advertisement in accordance
with 18 U.S.C. Section 1734 solely to indicate this fact.
We thank Claudio Schneider (LNCIB, Trieste, Italy) for kindly providing NIH 3T3
cells; Heike Wilhelm, Angelika Duda, Kerstin Hettler, and Saskia Stegmüller for
excellent technical assistance; and Jan Mollenhauer and Patricia McCabe for
discussions, suggestions, and critical reading of the article.
16. del Val C, Mehrle A, Falkenhahn M, et al. Highthroughput protein analysis integrating bioinformatics
and experimental assays. Nucleic Acids Res 2004;32:
742–8.
17. Liebel U, Starkuviene V, Erfle H, et al. A microscopebased screening platform for large-scale functional
protein analysis in intact cells. FEBS Lett 2003;554:
394–8.
18. Loader C. Local regression and likelihood. New York:
Springer Verlag; 1999.
19. Benjamini Y, Hochberg Y. Controlling the false
discovery rate: a practical and powerful approach to
multiple testing. Journal of the Royal Statistical Society
B 1995;57:289–300.
20. Fukazawa H, Mizuno S, Uehara Y. A microplate assay
for quantitation of anchorage-independent growth of
transformed cells. Anal Biochem 1995;228:83–90.
21. Strausberg RL, Feingold EA, Grouse LH, et al.
Generation and initial analysis of more than 15,000
full-length human and mouse cDNA sequences. Proc
Natl Acad Sci U S A 2002;99:16899–903.
22. Wiemann S, Arlt DH, Huber W, et al. From ORFeome
to biology: a functional genomics pipeline. Genome Res
2004;14:2136–44.
23. Starkuviene V, Liebel U, Simpson JC, et al. Highcontent screening microscopy identifies novel proteins
with a putative role in secretory membrane traffic.
Genome Res 2004;14:1948–56.
24. Chang F, Steelman LS, Shelton JG, et al. Regulation
of cell cycle progression and apoptosis by the Ras/
Raf/MEK/ERK pathway (Review). Int J Oncol 2003;
22:469–80.
25. Rhodes DR, Yu J, Shanker K, et al. ONCOMINE: a
cancer microarray database and integrated data-mining
platform. Neoplasia 2004;6:1–6.
26. Diehn M, Sherlock G, Binkley G, et al. SOURCE: a
unified genomic resource of functional annotations,
ontologies, and gene expression data. Nucleic Acids Res
2003;31:219–23.
27. Mulder NJ, Apweiler R, Attwood TK, et al. InterPro,
progress and status in 2005. Nucleic Acids Res 2005;33:
D201–5.
28. Pei L, Peng Y, Yang Y, et al. PRC17, a novel oncogene
encoding a Rab GTPase-activating protein, is amplified
in prostate cancer. Cancer Res 2002;62:5420–4.
29. Page LJ, Sowerby PJ, Lui WW, Robinson MS. gSynergin: an EH domain-containing protein that interacts with g-adaptin. J Cell Biol 1999;146:993–1004.
7741
30. Yao R, Wang Y, Lubet RA, You M. Differentially
expressed genes associated with mouse lung tumor
progression. Oncogene 2002;21:5814–21.
31. He H, Dai F, Yu L, et al. Identification and
characterization of nine novel human small GTPases
showing variable expressions in liver cancer tissues.
Gene Expr 2002;10:231–42.
32. Calvo A, Xiao N, Kang J, et al. Alterations in gene
expression profiles during prostate cancer progression:
functional correlations to tumorigenicity and downregulation of selenoprotein-P in mouse and human
tumors. Cancer Res 2002;62:5325–35.
33. Shikama N, Chan HM, Krstic-Demonacos M, et al.
Functional interaction between nucleosome assembly
proteins and p300/CREB-binding protein family coactivators. Mol Cell Biol 2000;20:8933–43.
34. Mosammaparast N, Ewart CS, Pemberton LF. A role
for nucleosome assembly protein 1 in the nuclear
transport of histones H2A and H2B. EMBO J 2002;21:
6527–38.
35. Komatsu M, Chiba T, Tatsumi K, et al. A novel
protein-conjugating system for Ufm1, a ubiquitin-fold
modifier. EMBO J 2004;23:1977–86.
36. Yehia G, Schlotter F, Razavi R, Alessandrini A,
Molina CA. Mitogen-activated protein kinase phosphorylates and targets inducible cAMP early repressor
to ubiquitin-mediated destruction. J Biol Chem 2001;
276:35272–9.
37. Niu H, Ye BH, Dalla-Favera R. Antigen receptor
signaling induces MAP kinase-mediated phosphorylation and degradation of the BCL-6 transcription factor.
Genes Dev 1998;12:1953–61.
38. Zhang W, Mi J, Li N, et al. Identification and
characterization of DPZF, a novel human BTB/POZ
zinc finger protein sharing homology to BCL-6. Biochem
Biophys Res Commun 2001;282:1067–73.
39. Albagli-Curiel O. Ambivalent role of BCL6 in
cell survival and transformation. Oncogene 2003;22:
507–16.
40. Pinte S, Stankovic-Valentin N, Deltour S, Rood BR,
Guerardel C, Leprince D. The tumor suppressor gene
HIC1 (hypermethylated in cancer 1) is a sequencespecific transcriptional repressor: definition of its
consensus binding sequence and analysis of its DNA
binding and prepressive properties. J Biol Chem 2004;
279:38313–24.
41. Nilsson JA, Cleveland JL. Myc pathways provoking
cell suicide and cancer. Oncogene 2003;22:9007–21.
Cancer Res 2005; 65: (17). September 1, 2005
Cancer Research
42. Piano F, Schetter AJ, Morton DG, et al. Gene
clustering based on RNAi phenotypes of ovary-enriched
genes in C. elegans . Curr Biol 2002;12:1959–64.
43. Hartman JLt, Garvik B, Hartwell L. Principles for
the buffering of genetic variation. Science 2001;291:
1001–4.
44. Li S, Armstrong CM, Bertin N, et al. A map of the
interactome network of the metazoan C. elegans .
Science 2004;303:540–3.
45. Gelman MS, Ye XK, Stull R, et al. Identification of cell
surface and secreted proteins essential for tumor cell
Cancer Res 2005; 65: (17). September 1, 2005
survival using a genetic suppressor element screen.
Oncogene 2004;23:8158–70.
46. Eustace BK, Sakurai T, Stewart JK, et al. Functional
proteomic screens reveal an essential extracellular role
for hsp90 a in cancer cell invasiveness. Nat Cell Biol
2004;6:507–14.
47. Kittler R, Putz G, Pelletier L, et al. An endoribonuclease-prepared siRNA screen in human cells identifies
genes essential for cell division. Nature 2004;432:1036–40.
48. Wan D, Gong Y, Qin W, et al. Large-scale cDNA
transfection screening for genes related to cancer
7742
development and progression. Proc Natl Acad Sci U S A
2004;101:15724–9.
49. Boutros M, Kiger AA, Armknecht S, et al. Genomewide RNAi analysis of growth and viability in Drosophila
cells. Science 2004;303:832–5.
50. Bannasch D, Mehrle A, Glatting K-H, Pepperkok
R, Poustka A, Wiemann S. LIFEdb: a database for
functional genomics experiments integrating information from external sources, and serving as a
sample tracking system. Nucleic Acids Res 2004;32:
D505–8.
www.aacrjournals.org