Chloroquinoxaline sulfonamide (chlorosulfaquinoxaline, CQS, NSC 339004) is active against murine ... more Chloroquinoxaline sulfonamide (chlorosulfaquinoxaline, CQS, NSC 339004) is active against murine and human solid tumors. On the basis of its structural similarity to the topoisomerase II-specific drug XK469, CQS was tested and found to be both a topoisomerase-II␣ and a topoisomerase-II poison. Topoisomerase II poisoning by CQS is essentially undetectable in assays using the common protein denaturant SDS, but easily detectable with strong chaotropic protein denaturants. The finding that detection of topoisomerase poisoning can be so dependent on the protein denaturant used in the assay has implications for drug discovery efforts and for our understanding of topoisomerase poisons.
Polymerase with 3&amp... more Polymerase with 3' to 5'exonulcease plays an important role in the maintenance of in vivo DNA replication fidelity. In order to develop more reliable SNP assays, we revisit the underlying molecular mechanisms by which DNA polymerases with 3' exonucleases maintain high fidelity of DNA replication. In addition to mismatch removal by proofreading, we recently discovered a premature termination of polymerization by a new mechanism of OFF-switch. This novel ON/OFF switch turns off DNA polymerization from mismatched primers and turns on DNA polymerization from matched primers. Two SNP assays were developed based on the proofreading and the newly identified OFF-switch respectively: terminal labeled primer extension and the ON/OFF switch operated SNP assay. These two new methods are well adapted to conventional techniques such as electrophoresis, real time PCR, microplates, and microarray. Application of these reliable SNP assays will greatly facilitate genetic and biomedical studies in the post-genome era.
Proceedings of the National Academy of Sciences of the United States of America, Nov 1, 1999
XK469 (NSC 697887) is a synthetic quinoxaline phenoxypropionic acid derivative that possesses unu... more XK469 (NSC 697887) is a synthetic quinoxaline phenoxypropionic acid derivative that possesses unusual solid tumor selectivity and activity against multidrug-resistant cancer cells. We report here that XK469 and its S(-) and R(+)-isomers induce reversible protein-DNA crosslinks in mammalian cells. Under protein denaturing conditions, the protein-DNA crosslinks are rendered irreversible and stable to DNA banding by CsCl gradient ultracentrifugation. Several lines of evidence indicate that the primary target of XK469 is topoisomerase IIβ . Preferential targeting of topoisomerase IIβ may explain the solid tumor selectivity of XK469 and its analogs because solid tumors, unlike leukemias, often have large populations of cells in the G1/G0 phases of the cell cycle in which topoisomerase IIβ is high whereas topoisomerase IIα , the primary target of many leukemia selective drugs, is low.
Molecular medicine (Cambridge, Mass.), Jan 13, 2015
Piwi-interacting RNAs (piRNAs) are a distinct group of small non-coding RNAs (sncRNAs) that silen... more Piwi-interacting RNAs (piRNAs) are a distinct group of small non-coding RNAs (sncRNAs) that silence transposable genetic elements to protect genome integrity. Due to their limited expression in gonads and sequence diversity, piRNAs remain the most mysterious class of small RNAs. Studies have shown piRNAs are present in somatic cells and dysregulated in gastric, breast and liver cancers. By deep sequencing 24 frozen benign kidney and clear cell renal cell carcinoma (ccRCC) specimens and using the publically available piRNA database, we found 26,991 piRNAs present in human kidney tissue. Among 920 piRNAs that at least had two copies in one specimen, 19 were differentially expressed in benign kidney and ccRCC tissues, and 46 were associated with metastasis. Among the metastasis-related piRNAs, we found 3 piRNAs, piR-32051, piR-39894 and piR-43607, to be derived from the same piRNA cluster at chromosome 17. We confirmed the 3 selected piRNAs not to be miRNAs or miRNA-like sncRNAs. We fu...
CHAPTER 8 Mutation Discovery Using High-Throughput Mutation Screening Technology KAI LI, HANLIN G... more CHAPTER 8 Mutation Discovery Using High-Throughput Mutation Screening Technology KAI LI, HANLIN GAO, HONG-GUANG XIE, WANPING SUN, and JIA ZHANG ... Accumulating evidencehas well documented that genetic diseases and cancers are caused by gene mutations ...
A major challenge in cancer research field is to define molecular features that distinguish cance... more A major challenge in cancer research field is to define molecular features that distinguish cancer stem cells from normal stem cells. In this study, we compared microRNA (miRNA) expression profiles in human glioblastoma stem cells and normal neural stem cells using combined microarray and deep sequencing analyses. These studies allowed us to identify a set of 10 miRNAs that are considerably up-regulated or down-regulated in glioblastoma stem cells. Among them, 5 miRNAs were further confirmed to have altered expression in three independent lines of glioblastoma stem cells by real-time RT-PCR analysis. Moreover, two of the miRNAs with increased expression in glioblastoma stem cells also exhibited elevated expression in glioblastoma patient tissues examined, while two miRNAs with decreased expression in glioblastoma stem cells displayed reduced expression in tumor tissues. Furthermore, we identified two oncogenes, NRAS and PIM3, as downstream targets of miR-124, one of the down-regulated miRNAs; and a tumor suppressor, CSMD1, as a downstream target of miR-10a and miR-10b, two of the up-regulated miRNAs. In summary, this study led to the identification of a set of miRNAs that are differentially expressed in glioblastoma stem cells and normal neural stem cells. Characterizing the role of these miRNAs in glioblastoma stem cells may lead to the development of miRNA-based therapies that specifically target tumor stem cells, but spare normal stem cells.
The two known antineoplastic quinoxaline topoisomerase II poisons, XK469 (NSC 697887) and CQS (ch... more The two known antineoplastic quinoxaline topoisomerase II poisons, XK469 (NSC 697887) and CQS (chloroquinoxaline sulfonamide, NSC 339004), were compared for DNA cleavage site specificity, using purified human topoisomerase II␣ and human topoisomerase II. The DNA cleavage intensity pattern for topoisomerase II␣ poisoning by CQS closely resembled that of VM-26, despite the lack of any apparent common pharmacophore. In contrast, the topoisomerase II␣ DNA cleavage intensity patterns of XK469 and CQS were very different from one another despite the similar overall structures of the two drugs. This suggests that the differences in DNA site specificity of topoisomerase II poisoning by XK469 and CQS may be caused by differences in their geometry, side chains, or electronic
Strand asymmetries in DNA evolution, including indel and single nucleotide substitutions, were re... more Strand asymmetries in DNA evolution, including indel and single nucleotide substitutions, were reported in prokaryotes. Recently, an excess of G>A over C>T substitutions in hemophilia B patients was recognized in our molecular diagnostic practices. Further analysis demonstrated biased point mutations between sense and antisense strands when unique changes in factor IX were counted. Similar mutation spectra of factor IX and the HGMD prompted us to speculate that the excess of G>A over C>T may be present in genes other than factor IX. Data from nine genes (each has ≥ 100 missense mutations) retrieved from HGMD, international factor IX database, and Dr. Sommer's lab database in the City of Hope National Medical Center, Duarte, CA, USA were analyzed for their point mutation spectra. Similar to factor IX, all genes selected in this study have biased G>A over C>T unique mutations when nonsense mutations were excluded. The biased missense point mutations were recently convincingly documented by the statistic data of categorized missense mutation in HGMD. The consistence of the genetic observation and the genomic data from HGMD strongly indicate that biased point mutations, possibly a phenotypic selection, are more widespread than previously thought. The biased mutations have immediate clinical impact in molecular diagnostics.
Thymic tumors are epithelial tumors of the thymus for which multimodal therapies are often ineffe... more Thymic tumors are epithelial tumors of the thymus for which multimodal therapies are often ineffective because of a lack of standardized regimens. Due to the low incidence, the molecular pathology and genomic abnormalities of thymic epithelial tumors are largely unknown. In this study, we report our comprehensively genomic study on a case of metastatic thymic tumor. Using next generation deep DNA sequencing technology, we sequenced 190 segments of 46 cancer genes of the cancer genome to cover 739 COSMIC mutations in 604 loci. Among these sequenced cancer genes, we identified that three low frequency (∼10% of cells) mutations in the TP53 gene (c.782+1G > T), ALK gene (c.3551C > T), and RET gene (c.2651A > T). To the best of our knowledge, this is the first study to show those mutations in thymic tumor. Of note, our study further indicates comprehensive molecular analysis may facilitate development of novel diagnostic and therapeutic strategies for thymic tumors.
Antineoplastic bis(dioxopiperazine)s, such as meso-2,3-bis(2,6-dioxopiperazin-4-yl)butane (ICRF-1... more Antineoplastic bis(dioxopiperazine)s, such as meso-2,3-bis(2,6-dioxopiperazin-4-yl)butane (ICRF-193), are widely believed to be only catalytic inhibitors of topoisomerase II. However, topoisomerase inhibitors have little or no antineoplastic activity unless they are topoisomerase poisons, a special subclass of topoisomerasetargeting drugs that stabilize topoisomerase-DNA strand passing intermediates and thus cause the topoisomerase to become a cytotoxic DNA-damaging agent.
Although the exact oncogenetic mechanisms in this schwannomatosis family remain to be elucidated,... more Although the exact oncogenetic mechanisms in this schwannomatosis family remain to be elucidated, our data strongly indicate a probable role of COQ6 mutation and CoQ10 deficiency in the development of familial schwannomatosis.
Abstract: The changes in physical and chemical characteristics derived from genetic alteration ar... more Abstract: The changes in physical and chemical characteristics derived from genetic alteration are the basis for the development of mutation assays. Among the ever-increasing number of mutation assays available, most are variants of allele-specific primer extension ...
Purpose: Atypical teratoid/rhabdoid tumors (AT/RT) are highly aggressive pediatric malignancies c... more Purpose: Atypical teratoid/rhabdoid tumors (AT/RT) are highly aggressive pediatric malignancies characterized by biallelic inactivation of the SMARCB1 tumor suppressor gene. We searched for novel genomic aberrations by investigating the copy number and expression alterations of let-7a3/let-7b micro-RNA (miRNA) and correlated these with expression of high-mobility group AT-hook 2 (HMGA2) oncoprotein, a target of let-7 miRNA family, in 18 AT/RT samples to elucidate potential roles of HMGA2 in the pathogenesis of AT/RT.
Fibroblast growth factor (FGF) receptor (FGFR) substrate 2 (FRS2) is an adaptor protein that play... more Fibroblast growth factor (FGF) receptor (FGFR) substrate 2 (FRS2) is an adaptor protein that plays a critical role in FGFR signaling. FRS2 is located on chromosome 12q13-15 that is frequently amplified in liposarcomas. The significance of FRS2 and FGFR signaling in high-grade liposarcomas is unknown. Herein, we first comparatively examined the amplification and expression of FRS2 with CDK4 and MDM2 in dedifferentiated liposarcoma (DDLS) and undifferentiated high-grade pleomorphic sarcoma (UHGPS). Amplification and expression of the three genes were identified in 90% to 100% (9-11 of 11) of DDLS, whereas that of FRS2, CDK4, and MDM2 were observed in 55% (41 of 75), 48% (36 of 75), and 44% (33/75) of clinically diagnosed UHGPS, suggesting that these "UHGPS" may represent DDLS despite lacking histologic evidence of lipoblasts. Immunohistochemical analysis of phosphorylated FRS2 protein indicated that the FGFR/FRS2 signaling axis was generally activated in about 75% of FRS2positive high-grade liposarcomas. Moreover, we found that FRS2 and FGFRs proteins are highly expressed and functional in three high-grade liposarcoma cell lines: FU-DDLS-1, LiSa-2, and SW872. Importantly, the FGFR selective inhibitor NVP-BGJ-398 significantly inhibited the growth of FU-DDLS-1 and LiSa-2 cells with a concomitant suppression of FGFR signal transduction. Attenuation of FRS2 protein in FU-DDLS-1 and LiSa-2 cell lines decreased the phosphorylated extracellular signal-regulated kinase 1/2 and AKT and repressed cell proliferation. These findings indicate that analysis of FRS2 in combination with CDK4 and MDM2 will more accurately characterize pathologic features of high-grade liposarcomas. Activated FGFR/FRS2 signaling may play a functional role in the development of high-grade liposarcomas, therefore, serve as a potential therapeutic target.
Cancer-secreted microRNAs (miRNAs) are emerging mediators of cancer-host crosstalk. Here we show ... more Cancer-secreted microRNAs (miRNAs) are emerging mediators of cancer-host crosstalk. Here we show that miR-105, which is characteristically expressed and secreted by metastatic breast cancer cells, is a potent regulator of migration through targeting the tight junction protein ZO-1. In endothelial monolayers, exosome-mediated transfer of cancer-secreted miR-105 efficiently destroys tight junctions and the integrity of these natural barriers against metastasis. Overexpression of miR-105 in nonmetastatic cancer cells induces metastasis and vascular permeability in distant organs, whereas inhibition of miR-105 in highly metastatic tumors alleviates these effects. miR-105 can be detected in the circulation at the premetastatic stage, and its levels in the blood and tumor are associated with ZO-1 expression and metastatic progression in early-stage breast cancer.
Biochemical and Biophysical Research Communications, 2001
Topoisomerase II knockout mouse cells (؊/؊) were found to have only slight resistance to m-AMSA... more Topoisomerase II knockout mouse cells (؊/؊) were found to have only slight resistance to m-AMSA, a dual topoisomerase II␣-II poison, as compared to wild-type cells (؉/؉) during 1 h or 3 day exposures to the drug. In contrast, the ؊/؊ cells were greater than threefold resistant to XK469, a selective topoisomerase II poison during three day drug exposures (؉/؉ IC 50 ؍ 175 M, ؊/؊ IC 50 ؍ 581 M). Short term (1 h) exposure to XK469 was not cytotoxic to either ؊/؊ or ؉/؉ cells, suggesting that anticancer therapy with XK469 may be more efficacious if systemic levels can be prolonged. During studies on topoisomerase activity in nuclear extracts of the ؉/؉ and ؊/؊ cells, we found evidence that XK469 is a weak topoisomerase I catalytic inhibitor. The high IC 50 for topoisomerase I inhibition (2 mM) suggests that topoisomerase I is not a significant target for XK469 cytotoxicity.
Very virulent (vv) infectious bursal disease virus (IBDV) Gx strain with high pathogenicity was a... more Very virulent (vv) infectious bursal disease virus (IBDV) Gx strain with high pathogenicity was attenuated through replication in specific-pathogen-free (SPF) chicken embryos and in chicken embryo fibroblast (CEF) cell cultures. The changes in VP2 nucleotide and the deduced amino acid sequences were obtained during attenuation of vvIBDV in CEF culture. Sequence analysis of selected passages from numbers 0 to 20 in CEFs (designated here Gx to CEF-20) showed that no changes were detectable in the VP2 gene before CEF-7. There were a few changes in the nucleotide sequence of the VP2 gene but no amino acid substitutions at CEF-8. The virus of CEF-9 was an intermediate with some amino acid changes that possibly were related to virulence. CEF-10 virus had become similar to CU-1 strain. The VP2 gene sequence remained the same from CEF-10 to CEF-20. The results of pathogenicity tests showed that the mortalities of Gx, CEF-5, CEF-8, and CEF-9 in 4-wk-old SPF chickens were 64%, 60%, 60%, and 32%, respectively; whereas CEF-10, CEF-15, and CEF-20 were nonpathogenic. Virus neutralization tests with Gx strain showed that the antigenicities are similar from Gx to CEF-20.
Indels in evolutionary studies are rapidly decayed obeying a power law. The present study analyze... more Indels in evolutionary studies are rapidly decayed obeying a power law. The present study analyzed the length distribution of small insertions and deletions associated with human diseases and confirmed that the decay pattern of these small mutations is similar to that of indels when the mutation datasets are large enough. The describable decay pattern of somatic mutations may have application in the evaluation of varied penetrance of different mutations and in association study of gene mutation with carcinogenesis.
The CLN6 gene that causes variant late-infantile neuronal ceroid lipofuscinosis (vLINCL), a reces... more The CLN6 gene that causes variant late-infantile neuronal ceroid lipofuscinosis (vLINCL), a recessively inherited neurodegenerative disease that features blindness, seizures, and cognitive decline, maps to 15q21-23. We have used multiallele markers spanning this ∼4-Mb candidate interval to reveal a core haplotype, shared in Costa Rican families with vLINCL but not in a Venezuelan kindred, that highlighted a region likely to contain the CLN6 defect. Systematic comparison of genes from the minimal region uncovered a novel candidate, FLJ20561, that exhibited DNA sequence changes specific to the different disease chromosomes: a GrT transversion in exon 3, introducing a stop codon on the Costa Rican haplotype, and a codon deletion in exon 5, eliminating a conserved tyrosine residue on the Venezuelan chromosome. Furthermore, sequencing of the murine homologue in the nclf mouse, which manifests recessive NCL-like disease, disclosed a third lesion-an extra base pair in exon 4, producing a frameshift truncation on the nclf chromosome. Thus, the novel ∼36-kD CLN6-gene product augments an intriguing set of unrelated membrane-spanning proteins, whose deficiency causes NCL in mouse and man.
Chloroquinoxaline sulfonamide (chlorosulfaquinoxaline, CQS, NSC 339004) is active against murine ... more Chloroquinoxaline sulfonamide (chlorosulfaquinoxaline, CQS, NSC 339004) is active against murine and human solid tumors. On the basis of its structural similarity to the topoisomerase II-specific drug XK469, CQS was tested and found to be both a topoisomerase-II␣ and a topoisomerase-II poison. Topoisomerase II poisoning by CQS is essentially undetectable in assays using the common protein denaturant SDS, but easily detectable with strong chaotropic protein denaturants. The finding that detection of topoisomerase poisoning can be so dependent on the protein denaturant used in the assay has implications for drug discovery efforts and for our understanding of topoisomerase poisons.
Polymerase with 3&amp... more Polymerase with 3' to 5'exonulcease plays an important role in the maintenance of in vivo DNA replication fidelity. In order to develop more reliable SNP assays, we revisit the underlying molecular mechanisms by which DNA polymerases with 3' exonucleases maintain high fidelity of DNA replication. In addition to mismatch removal by proofreading, we recently discovered a premature termination of polymerization by a new mechanism of OFF-switch. This novel ON/OFF switch turns off DNA polymerization from mismatched primers and turns on DNA polymerization from matched primers. Two SNP assays were developed based on the proofreading and the newly identified OFF-switch respectively: terminal labeled primer extension and the ON/OFF switch operated SNP assay. These two new methods are well adapted to conventional techniques such as electrophoresis, real time PCR, microplates, and microarray. Application of these reliable SNP assays will greatly facilitate genetic and biomedical studies in the post-genome era.
Proceedings of the National Academy of Sciences of the United States of America, Nov 1, 1999
XK469 (NSC 697887) is a synthetic quinoxaline phenoxypropionic acid derivative that possesses unu... more XK469 (NSC 697887) is a synthetic quinoxaline phenoxypropionic acid derivative that possesses unusual solid tumor selectivity and activity against multidrug-resistant cancer cells. We report here that XK469 and its S(-) and R(+)-isomers induce reversible protein-DNA crosslinks in mammalian cells. Under protein denaturing conditions, the protein-DNA crosslinks are rendered irreversible and stable to DNA banding by CsCl gradient ultracentrifugation. Several lines of evidence indicate that the primary target of XK469 is topoisomerase IIβ . Preferential targeting of topoisomerase IIβ may explain the solid tumor selectivity of XK469 and its analogs because solid tumors, unlike leukemias, often have large populations of cells in the G1/G0 phases of the cell cycle in which topoisomerase IIβ is high whereas topoisomerase IIα , the primary target of many leukemia selective drugs, is low.
Molecular medicine (Cambridge, Mass.), Jan 13, 2015
Piwi-interacting RNAs (piRNAs) are a distinct group of small non-coding RNAs (sncRNAs) that silen... more Piwi-interacting RNAs (piRNAs) are a distinct group of small non-coding RNAs (sncRNAs) that silence transposable genetic elements to protect genome integrity. Due to their limited expression in gonads and sequence diversity, piRNAs remain the most mysterious class of small RNAs. Studies have shown piRNAs are present in somatic cells and dysregulated in gastric, breast and liver cancers. By deep sequencing 24 frozen benign kidney and clear cell renal cell carcinoma (ccRCC) specimens and using the publically available piRNA database, we found 26,991 piRNAs present in human kidney tissue. Among 920 piRNAs that at least had two copies in one specimen, 19 were differentially expressed in benign kidney and ccRCC tissues, and 46 were associated with metastasis. Among the metastasis-related piRNAs, we found 3 piRNAs, piR-32051, piR-39894 and piR-43607, to be derived from the same piRNA cluster at chromosome 17. We confirmed the 3 selected piRNAs not to be miRNAs or miRNA-like sncRNAs. We fu...
CHAPTER 8 Mutation Discovery Using High-Throughput Mutation Screening Technology KAI LI, HANLIN G... more CHAPTER 8 Mutation Discovery Using High-Throughput Mutation Screening Technology KAI LI, HANLIN GAO, HONG-GUANG XIE, WANPING SUN, and JIA ZHANG ... Accumulating evidencehas well documented that genetic diseases and cancers are caused by gene mutations ...
A major challenge in cancer research field is to define molecular features that distinguish cance... more A major challenge in cancer research field is to define molecular features that distinguish cancer stem cells from normal stem cells. In this study, we compared microRNA (miRNA) expression profiles in human glioblastoma stem cells and normal neural stem cells using combined microarray and deep sequencing analyses. These studies allowed us to identify a set of 10 miRNAs that are considerably up-regulated or down-regulated in glioblastoma stem cells. Among them, 5 miRNAs were further confirmed to have altered expression in three independent lines of glioblastoma stem cells by real-time RT-PCR analysis. Moreover, two of the miRNAs with increased expression in glioblastoma stem cells also exhibited elevated expression in glioblastoma patient tissues examined, while two miRNAs with decreased expression in glioblastoma stem cells displayed reduced expression in tumor tissues. Furthermore, we identified two oncogenes, NRAS and PIM3, as downstream targets of miR-124, one of the down-regulated miRNAs; and a tumor suppressor, CSMD1, as a downstream target of miR-10a and miR-10b, two of the up-regulated miRNAs. In summary, this study led to the identification of a set of miRNAs that are differentially expressed in glioblastoma stem cells and normal neural stem cells. Characterizing the role of these miRNAs in glioblastoma stem cells may lead to the development of miRNA-based therapies that specifically target tumor stem cells, but spare normal stem cells.
The two known antineoplastic quinoxaline topoisomerase II poisons, XK469 (NSC 697887) and CQS (ch... more The two known antineoplastic quinoxaline topoisomerase II poisons, XK469 (NSC 697887) and CQS (chloroquinoxaline sulfonamide, NSC 339004), were compared for DNA cleavage site specificity, using purified human topoisomerase II␣ and human topoisomerase II. The DNA cleavage intensity pattern for topoisomerase II␣ poisoning by CQS closely resembled that of VM-26, despite the lack of any apparent common pharmacophore. In contrast, the topoisomerase II␣ DNA cleavage intensity patterns of XK469 and CQS were very different from one another despite the similar overall structures of the two drugs. This suggests that the differences in DNA site specificity of topoisomerase II poisoning by XK469 and CQS may be caused by differences in their geometry, side chains, or electronic
Strand asymmetries in DNA evolution, including indel and single nucleotide substitutions, were re... more Strand asymmetries in DNA evolution, including indel and single nucleotide substitutions, were reported in prokaryotes. Recently, an excess of G>A over C>T substitutions in hemophilia B patients was recognized in our molecular diagnostic practices. Further analysis demonstrated biased point mutations between sense and antisense strands when unique changes in factor IX were counted. Similar mutation spectra of factor IX and the HGMD prompted us to speculate that the excess of G>A over C>T may be present in genes other than factor IX. Data from nine genes (each has ≥ 100 missense mutations) retrieved from HGMD, international factor IX database, and Dr. Sommer's lab database in the City of Hope National Medical Center, Duarte, CA, USA were analyzed for their point mutation spectra. Similar to factor IX, all genes selected in this study have biased G>A over C>T unique mutations when nonsense mutations were excluded. The biased missense point mutations were recently convincingly documented by the statistic data of categorized missense mutation in HGMD. The consistence of the genetic observation and the genomic data from HGMD strongly indicate that biased point mutations, possibly a phenotypic selection, are more widespread than previously thought. The biased mutations have immediate clinical impact in molecular diagnostics.
Thymic tumors are epithelial tumors of the thymus for which multimodal therapies are often ineffe... more Thymic tumors are epithelial tumors of the thymus for which multimodal therapies are often ineffective because of a lack of standardized regimens. Due to the low incidence, the molecular pathology and genomic abnormalities of thymic epithelial tumors are largely unknown. In this study, we report our comprehensively genomic study on a case of metastatic thymic tumor. Using next generation deep DNA sequencing technology, we sequenced 190 segments of 46 cancer genes of the cancer genome to cover 739 COSMIC mutations in 604 loci. Among these sequenced cancer genes, we identified that three low frequency (∼10% of cells) mutations in the TP53 gene (c.782+1G > T), ALK gene (c.3551C > T), and RET gene (c.2651A > T). To the best of our knowledge, this is the first study to show those mutations in thymic tumor. Of note, our study further indicates comprehensive molecular analysis may facilitate development of novel diagnostic and therapeutic strategies for thymic tumors.
Antineoplastic bis(dioxopiperazine)s, such as meso-2,3-bis(2,6-dioxopiperazin-4-yl)butane (ICRF-1... more Antineoplastic bis(dioxopiperazine)s, such as meso-2,3-bis(2,6-dioxopiperazin-4-yl)butane (ICRF-193), are widely believed to be only catalytic inhibitors of topoisomerase II. However, topoisomerase inhibitors have little or no antineoplastic activity unless they are topoisomerase poisons, a special subclass of topoisomerasetargeting drugs that stabilize topoisomerase-DNA strand passing intermediates and thus cause the topoisomerase to become a cytotoxic DNA-damaging agent.
Although the exact oncogenetic mechanisms in this schwannomatosis family remain to be elucidated,... more Although the exact oncogenetic mechanisms in this schwannomatosis family remain to be elucidated, our data strongly indicate a probable role of COQ6 mutation and CoQ10 deficiency in the development of familial schwannomatosis.
Abstract: The changes in physical and chemical characteristics derived from genetic alteration ar... more Abstract: The changes in physical and chemical characteristics derived from genetic alteration are the basis for the development of mutation assays. Among the ever-increasing number of mutation assays available, most are variants of allele-specific primer extension ...
Purpose: Atypical teratoid/rhabdoid tumors (AT/RT) are highly aggressive pediatric malignancies c... more Purpose: Atypical teratoid/rhabdoid tumors (AT/RT) are highly aggressive pediatric malignancies characterized by biallelic inactivation of the SMARCB1 tumor suppressor gene. We searched for novel genomic aberrations by investigating the copy number and expression alterations of let-7a3/let-7b micro-RNA (miRNA) and correlated these with expression of high-mobility group AT-hook 2 (HMGA2) oncoprotein, a target of let-7 miRNA family, in 18 AT/RT samples to elucidate potential roles of HMGA2 in the pathogenesis of AT/RT.
Fibroblast growth factor (FGF) receptor (FGFR) substrate 2 (FRS2) is an adaptor protein that play... more Fibroblast growth factor (FGF) receptor (FGFR) substrate 2 (FRS2) is an adaptor protein that plays a critical role in FGFR signaling. FRS2 is located on chromosome 12q13-15 that is frequently amplified in liposarcomas. The significance of FRS2 and FGFR signaling in high-grade liposarcomas is unknown. Herein, we first comparatively examined the amplification and expression of FRS2 with CDK4 and MDM2 in dedifferentiated liposarcoma (DDLS) and undifferentiated high-grade pleomorphic sarcoma (UHGPS). Amplification and expression of the three genes were identified in 90% to 100% (9-11 of 11) of DDLS, whereas that of FRS2, CDK4, and MDM2 were observed in 55% (41 of 75), 48% (36 of 75), and 44% (33/75) of clinically diagnosed UHGPS, suggesting that these "UHGPS" may represent DDLS despite lacking histologic evidence of lipoblasts. Immunohistochemical analysis of phosphorylated FRS2 protein indicated that the FGFR/FRS2 signaling axis was generally activated in about 75% of FRS2positive high-grade liposarcomas. Moreover, we found that FRS2 and FGFRs proteins are highly expressed and functional in three high-grade liposarcoma cell lines: FU-DDLS-1, LiSa-2, and SW872. Importantly, the FGFR selective inhibitor NVP-BGJ-398 significantly inhibited the growth of FU-DDLS-1 and LiSa-2 cells with a concomitant suppression of FGFR signal transduction. Attenuation of FRS2 protein in FU-DDLS-1 and LiSa-2 cell lines decreased the phosphorylated extracellular signal-regulated kinase 1/2 and AKT and repressed cell proliferation. These findings indicate that analysis of FRS2 in combination with CDK4 and MDM2 will more accurately characterize pathologic features of high-grade liposarcomas. Activated FGFR/FRS2 signaling may play a functional role in the development of high-grade liposarcomas, therefore, serve as a potential therapeutic target.
Cancer-secreted microRNAs (miRNAs) are emerging mediators of cancer-host crosstalk. Here we show ... more Cancer-secreted microRNAs (miRNAs) are emerging mediators of cancer-host crosstalk. Here we show that miR-105, which is characteristically expressed and secreted by metastatic breast cancer cells, is a potent regulator of migration through targeting the tight junction protein ZO-1. In endothelial monolayers, exosome-mediated transfer of cancer-secreted miR-105 efficiently destroys tight junctions and the integrity of these natural barriers against metastasis. Overexpression of miR-105 in nonmetastatic cancer cells induces metastasis and vascular permeability in distant organs, whereas inhibition of miR-105 in highly metastatic tumors alleviates these effects. miR-105 can be detected in the circulation at the premetastatic stage, and its levels in the blood and tumor are associated with ZO-1 expression and metastatic progression in early-stage breast cancer.
Biochemical and Biophysical Research Communications, 2001
Topoisomerase II knockout mouse cells (؊/؊) were found to have only slight resistance to m-AMSA... more Topoisomerase II knockout mouse cells (؊/؊) were found to have only slight resistance to m-AMSA, a dual topoisomerase II␣-II poison, as compared to wild-type cells (؉/؉) during 1 h or 3 day exposures to the drug. In contrast, the ؊/؊ cells were greater than threefold resistant to XK469, a selective topoisomerase II poison during three day drug exposures (؉/؉ IC 50 ؍ 175 M, ؊/؊ IC 50 ؍ 581 M). Short term (1 h) exposure to XK469 was not cytotoxic to either ؊/؊ or ؉/؉ cells, suggesting that anticancer therapy with XK469 may be more efficacious if systemic levels can be prolonged. During studies on topoisomerase activity in nuclear extracts of the ؉/؉ and ؊/؊ cells, we found evidence that XK469 is a weak topoisomerase I catalytic inhibitor. The high IC 50 for topoisomerase I inhibition (2 mM) suggests that topoisomerase I is not a significant target for XK469 cytotoxicity.
Very virulent (vv) infectious bursal disease virus (IBDV) Gx strain with high pathogenicity was a... more Very virulent (vv) infectious bursal disease virus (IBDV) Gx strain with high pathogenicity was attenuated through replication in specific-pathogen-free (SPF) chicken embryos and in chicken embryo fibroblast (CEF) cell cultures. The changes in VP2 nucleotide and the deduced amino acid sequences were obtained during attenuation of vvIBDV in CEF culture. Sequence analysis of selected passages from numbers 0 to 20 in CEFs (designated here Gx to CEF-20) showed that no changes were detectable in the VP2 gene before CEF-7. There were a few changes in the nucleotide sequence of the VP2 gene but no amino acid substitutions at CEF-8. The virus of CEF-9 was an intermediate with some amino acid changes that possibly were related to virulence. CEF-10 virus had become similar to CU-1 strain. The VP2 gene sequence remained the same from CEF-10 to CEF-20. The results of pathogenicity tests showed that the mortalities of Gx, CEF-5, CEF-8, and CEF-9 in 4-wk-old SPF chickens were 64%, 60%, 60%, and 32%, respectively; whereas CEF-10, CEF-15, and CEF-20 were nonpathogenic. Virus neutralization tests with Gx strain showed that the antigenicities are similar from Gx to CEF-20.
Indels in evolutionary studies are rapidly decayed obeying a power law. The present study analyze... more Indels in evolutionary studies are rapidly decayed obeying a power law. The present study analyzed the length distribution of small insertions and deletions associated with human diseases and confirmed that the decay pattern of these small mutations is similar to that of indels when the mutation datasets are large enough. The describable decay pattern of somatic mutations may have application in the evaluation of varied penetrance of different mutations and in association study of gene mutation with carcinogenesis.
The CLN6 gene that causes variant late-infantile neuronal ceroid lipofuscinosis (vLINCL), a reces... more The CLN6 gene that causes variant late-infantile neuronal ceroid lipofuscinosis (vLINCL), a recessively inherited neurodegenerative disease that features blindness, seizures, and cognitive decline, maps to 15q21-23. We have used multiallele markers spanning this ∼4-Mb candidate interval to reveal a core haplotype, shared in Costa Rican families with vLINCL but not in a Venezuelan kindred, that highlighted a region likely to contain the CLN6 defect. Systematic comparison of genes from the minimal region uncovered a novel candidate, FLJ20561, that exhibited DNA sequence changes specific to the different disease chromosomes: a GrT transversion in exon 3, introducing a stop codon on the Costa Rican haplotype, and a codon deletion in exon 5, eliminating a conserved tyrosine residue on the Venezuelan chromosome. Furthermore, sequencing of the murine homologue in the nclf mouse, which manifests recessive NCL-like disease, disclosed a third lesion-an extra base pair in exon 4, producing a frameshift truncation on the nclf chromosome. Thus, the novel ∼36-kD CLN6-gene product augments an intriguing set of unrelated membrane-spanning proteins, whose deficiency causes NCL in mouse and man.
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Papers by Hanlin Gao