肿瘤表观基因组学、生物芯片和生物信息学
|
摘要
肿瘤的分子生物学研究一直是生命科学和医学研究的热点,随着科学技术的发展,高通量的分析方法在分子生物学研究中的广泛应用,使其成为肿瘤研究的一种高效手段,同时表观基因组学和生物信息学也促进了肿瘤学的发展,本文就表观基因组学、生物芯片和生物信息学方法在肿瘤研究中的应用进行综述,并对未来的发展和展望进行了讨论。
The molecular biology remains a hotspot of life and medical sciences. With the development of scientific technology, the widely application of high-throughput analysis method in molecular biology research makes itself a powerful approach. Meanwhile, epigenomics and bioinformatics also promote the advance of cancer science. This paper summarized the application of epigenomics, biochip and bioinformatics in cancer researches, and discussed the development and perspectives of cancer researches in the future.
The molecular biology remains a hotspot of life and medical sciences. With the development of scientific technology, the widely application of high-throughput analysis method in molecular biology research makes itself a powerful approach. Meanwhile, epigenomics and bioinformatics also promote the advance of cancer science. This paper summarized the application of epigenomics, biochip and bioinformatics in cancer researches, and discussed the development and perspectives of cancer researches in the future.
引文
[1]Hendrich B,Bird A.Mammalian met hylt ransferases and methyl-GpG-binding domains:proteins in DNA methylation[J].Curri Top Microbiol Immuol,2000,249:55-74.
[2]张海元,刘娟.肿瘤相关基因的表观遗传修饰研究进展[J].长江大学学报(医学卷),2007,4(2):202-204.
[3]Jones P A,Baylin S B.The fundamental role of epigenetic events in cancer[J].Nat Rev Genet,2002,3(6):415-428.
[4]Ordway J M,Budiman M A,Korshunova Y,et al.Identifica-tion of novel high-frequency DNA methylation changes in breast cancer[J].PLoS ONE,2007,2(12):e1314
[5]Keshet I,Schlesinger Y,Farkash S,et al.Evidence for an in-structive mechanism of de novo methylation in cancer cells[J].Nat Genet,2006,38(2):149-153.
[6]Gebhard C,Schwarzfischer L,Pham T H,et al.Genome-wide profiling of CpG methylation identifies novel targets of aberrant hy-permethylation in myeloid leukemia.Cancer Res,2006,66(12):6118-6128.
[7]Yu J,Zhang H Y,Ma Z Z,et al.Methylation profiling of twenty four genes and the concordant methylation behaviours of nineteen genes that may contribute to hepatocellular carcinogenesis.Cell Res,2003,13(5):319-333.
[8]Yang H J,Liu V W,Wang Y,et al.Differential DNA methyla-tion profiles in gynecological cancers and correlation with clinico-pathological data[J].BMC Cancer,2006,6:212.
[9]Schones D E and Zhao K.Genome-wide approaches to studying chromatin modifications[J].Nat Rev Genet,2008,9:179-191.
[10]Bock C,Kuster G V,Halachev K,et al.Web-based analysis of(epi-)genome data using EpiGRAPH and Galaxy[J].Methods Mol Biol,2010,628:275-296.
[11]Jinhua Xu,Dezheng Huo,Yinghua Chen,et al.CpG island methylation affects accessibility of the proximal BRCA1promoter to transcription factors[J].Breast Cancer Research and Treat-ment,2010,120(3):593-601.
[12]Christian Muchardt,Brigitte Bourachot,Christophe Rachez,et al.HP1proteins from silencing to activation of inducible promot-ers[J].Genomic Med.,2008,2:147-148.
[13]Van Lint C,Emiliani S,Verdin E.The expression of a small frac-tion of cellular genes is changed in responses to histone hyper-acetylation[J].Gene Expr,1996,5:245-253.
[14]Lindemann R K,Johnstone R W.histone deacetylase inhibitors:promising candidates for chemotherapeutic drugs[J].Gene Ther Mol Biol,2004,8:61-74.
[15]Cameron E E,Bachman K,Myohanen S,et al.Synergy of dem-ethylation and histone deacetylase inhibition in the re-expression of gene silenced in cancer[J].Nat Genet,1999,21:103-107.
[16]Zhe WG,Lakshmanan R R,Beal M D,et al.DNA methyl-transferase inhibition enhanced apoptosis induced by histone deacetylase inhibition[J].Cancer Res,2001,61:1327-1333.
[17]Berger S L,Felsenfeld G.Chromatin goes global[J].Mol Cell,2001,8:263-268.
[18]Strahl B D,Allis C D.The language of covalent histone modifi-cations[J].Nature,2000,403:41-45.
[19]Roberts C W,Leroux M M,Fleming M D,Orkin S H.Highly penetrant,rapid tumorigenesis through conditional inversion of the tumor suppressor gene Snf5[J].Cancer Cell,2002,2:415-425.
[20]Raj Chari,Kelsie L.Thu,Ian M.Wilson,et al.Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer[J].Cancer and Metastasis Reviews,2010,29(1):73-93.
[21]Hacia J G,Brody L C,Chee M S,et al.Detection of heterozv-gous mutations in BBf.AI using high density oligonucleotide ar-rays and two-colour fluorescence analysis[J].Nat Genet,1996,14(4):441-447.
[22]H.Mika,T.Toshihiro,H.Yoichi,K.Masako,T.Toshihisa and N.Yusuke,Nucl.Acids Res.,2002,30(1):158-162.
[23]Wang DG,Fan JB,Siao CJ,et al.Large-scale identification,mapping and genotyping of single-nucleotide polymorph-isms in the human genome[J].Science,1998,280(5366):1077-1082.
[24]Welford S M,Cregg J,Chen E,et al.Detection of differentially ex-pressed genes in primary tumor tissues using representa-tional differences analysis coupled to microarray hyhridizalion[J].Nu-cleic Acids Res,1998,26(12):3059-3065.
[25]Yang G P,Ross D T,Kuang W W,et al.Combining SSH and cD-NA microarrays for rapid identificalion of differentially expressed genes[J].Nucleic Acids Res,1999,27(6):1517-1523.
[26]Lueking A,Horn M,Eickhoff H,et al.Protein microarrays forgene expression and antibody screening[J].Ana1Biochem,1999,270(1):103-111.
[27]MacBealh G,Schreiber S L.Printing proteins as microarrays high-throughput function determination[J].Science,2000,289:1760-1763.
[28]M.Bizzarri,A.Cucina,F.Conti,et al.Beyond the Oncogene Paradigm:Understanding Complexity in Cancerogenesis[J].Acta Biotheor,2008,56:173–196.
[29]徐兴兴,常文军,翟羽佳,等.PPP4R1基因与肿瘤相关性的生物信息学预测及在胃癌组织中的初步验证[J].第二军医大学学报,2009,30(3):275-278.
[30]Swanson DR.Fish oil,Raynaud’s syndrome,and undiscovered public knowledge[J].Perspect Biol Med,1986,30(1):7-18.
[31]李铁求,冯春琼,邹亚光,等.基于文献挖掘的雄激素非依赖型前列腺癌特异表达基因的生物信息学分析[J].中华男科学杂志,2009,15(12):1102–1107.
[32]Bult C J,Krupke D M,N?f D,Sundberg J P,Eppig J T.Web-based access to mouse models of human cancers:the Mouse Tumor Biology(MTB)Database[J].Nucleic Acids Res,2001,29(1):95-97.
[33]Strausberg R L,Simpson A J,Wooster R.Sequence-based cancer genomics:progress,lessons and opportunities[J].Nat Rev Genet,2003,4(6):409-418.
[34]Olivier M,Eeles R,Hollstein M,Khan M A,Harris C C,Hainaut P.The IARC TP53database:new online mutation anal-ysis and recommendations to users[J].Hum Mutat,2002,19(6):607-614.
[35]Hernandez-Boussard T,Rodriguez-Tome P,Montesano R,Hainaut P.IARC p53mutation database:a relational database to compile and analyze p53mutations in human tumors and cell lines.International Agency for Research on Cancer[J].Hum Mutat,1999,14(1):1-8.
[36]刘妍,李官成.生物信息学方法大规模筛选肿瘤差异表达基因[J].西安交通大学学报(医学版),2009,30(6):694-700.
[37]Edison T L,Koichiro I,Leena U,Valere C,Guillaume B,Yi-jun R.Fusion gene discovery through transcriptome and rear-rangement mapping using ultra high throughput pair end sequen-cing strategies[J].Genomic Med,2008,2:147–148.
[2]张海元,刘娟.肿瘤相关基因的表观遗传修饰研究进展[J].长江大学学报(医学卷),2007,4(2):202-204.
[3]Jones P A,Baylin S B.The fundamental role of epigenetic events in cancer[J].Nat Rev Genet,2002,3(6):415-428.
[4]Ordway J M,Budiman M A,Korshunova Y,et al.Identifica-tion of novel high-frequency DNA methylation changes in breast cancer[J].PLoS ONE,2007,2(12):e1314
[5]Keshet I,Schlesinger Y,Farkash S,et al.Evidence for an in-structive mechanism of de novo methylation in cancer cells[J].Nat Genet,2006,38(2):149-153.
[6]Gebhard C,Schwarzfischer L,Pham T H,et al.Genome-wide profiling of CpG methylation identifies novel targets of aberrant hy-permethylation in myeloid leukemia.Cancer Res,2006,66(12):6118-6128.
[7]Yu J,Zhang H Y,Ma Z Z,et al.Methylation profiling of twenty four genes and the concordant methylation behaviours of nineteen genes that may contribute to hepatocellular carcinogenesis.Cell Res,2003,13(5):319-333.
[8]Yang H J,Liu V W,Wang Y,et al.Differential DNA methyla-tion profiles in gynecological cancers and correlation with clinico-pathological data[J].BMC Cancer,2006,6:212.
[9]Schones D E and Zhao K.Genome-wide approaches to studying chromatin modifications[J].Nat Rev Genet,2008,9:179-191.
[10]Bock C,Kuster G V,Halachev K,et al.Web-based analysis of(epi-)genome data using EpiGRAPH and Galaxy[J].Methods Mol Biol,2010,628:275-296.
[11]Jinhua Xu,Dezheng Huo,Yinghua Chen,et al.CpG island methylation affects accessibility of the proximal BRCA1promoter to transcription factors[J].Breast Cancer Research and Treat-ment,2010,120(3):593-601.
[12]Christian Muchardt,Brigitte Bourachot,Christophe Rachez,et al.HP1proteins from silencing to activation of inducible promot-ers[J].Genomic Med.,2008,2:147-148.
[13]Van Lint C,Emiliani S,Verdin E.The expression of a small frac-tion of cellular genes is changed in responses to histone hyper-acetylation[J].Gene Expr,1996,5:245-253.
[14]Lindemann R K,Johnstone R W.histone deacetylase inhibitors:promising candidates for chemotherapeutic drugs[J].Gene Ther Mol Biol,2004,8:61-74.
[15]Cameron E E,Bachman K,Myohanen S,et al.Synergy of dem-ethylation and histone deacetylase inhibition in the re-expression of gene silenced in cancer[J].Nat Genet,1999,21:103-107.
[16]Zhe WG,Lakshmanan R R,Beal M D,et al.DNA methyl-transferase inhibition enhanced apoptosis induced by histone deacetylase inhibition[J].Cancer Res,2001,61:1327-1333.
[17]Berger S L,Felsenfeld G.Chromatin goes global[J].Mol Cell,2001,8:263-268.
[18]Strahl B D,Allis C D.The language of covalent histone modifi-cations[J].Nature,2000,403:41-45.
[19]Roberts C W,Leroux M M,Fleming M D,Orkin S H.Highly penetrant,rapid tumorigenesis through conditional inversion of the tumor suppressor gene Snf5[J].Cancer Cell,2002,2:415-425.
[20]Raj Chari,Kelsie L.Thu,Ian M.Wilson,et al.Integrating the multiple dimensions of genomic and epigenomic landscapes of cancer[J].Cancer and Metastasis Reviews,2010,29(1):73-93.
[21]Hacia J G,Brody L C,Chee M S,et al.Detection of heterozv-gous mutations in BBf.AI using high density oligonucleotide ar-rays and two-colour fluorescence analysis[J].Nat Genet,1996,14(4):441-447.
[22]H.Mika,T.Toshihiro,H.Yoichi,K.Masako,T.Toshihisa and N.Yusuke,Nucl.Acids Res.,2002,30(1):158-162.
[23]Wang DG,Fan JB,Siao CJ,et al.Large-scale identification,mapping and genotyping of single-nucleotide polymorph-isms in the human genome[J].Science,1998,280(5366):1077-1082.
[24]Welford S M,Cregg J,Chen E,et al.Detection of differentially ex-pressed genes in primary tumor tissues using representa-tional differences analysis coupled to microarray hyhridizalion[J].Nu-cleic Acids Res,1998,26(12):3059-3065.
[25]Yang G P,Ross D T,Kuang W W,et al.Combining SSH and cD-NA microarrays for rapid identificalion of differentially expressed genes[J].Nucleic Acids Res,1999,27(6):1517-1523.
[26]Lueking A,Horn M,Eickhoff H,et al.Protein microarrays forgene expression and antibody screening[J].Ana1Biochem,1999,270(1):103-111.
[27]MacBealh G,Schreiber S L.Printing proteins as microarrays high-throughput function determination[J].Science,2000,289:1760-1763.
[28]M.Bizzarri,A.Cucina,F.Conti,et al.Beyond the Oncogene Paradigm:Understanding Complexity in Cancerogenesis[J].Acta Biotheor,2008,56:173–196.
[29]徐兴兴,常文军,翟羽佳,等.PPP4R1基因与肿瘤相关性的生物信息学预测及在胃癌组织中的初步验证[J].第二军医大学学报,2009,30(3):275-278.
[30]Swanson DR.Fish oil,Raynaud’s syndrome,and undiscovered public knowledge[J].Perspect Biol Med,1986,30(1):7-18.
[31]李铁求,冯春琼,邹亚光,等.基于文献挖掘的雄激素非依赖型前列腺癌特异表达基因的生物信息学分析[J].中华男科学杂志,2009,15(12):1102–1107.
[32]Bult C J,Krupke D M,N?f D,Sundberg J P,Eppig J T.Web-based access to mouse models of human cancers:the Mouse Tumor Biology(MTB)Database[J].Nucleic Acids Res,2001,29(1):95-97.
[33]Strausberg R L,Simpson A J,Wooster R.Sequence-based cancer genomics:progress,lessons and opportunities[J].Nat Rev Genet,2003,4(6):409-418.
[34]Olivier M,Eeles R,Hollstein M,Khan M A,Harris C C,Hainaut P.The IARC TP53database:new online mutation anal-ysis and recommendations to users[J].Hum Mutat,2002,19(6):607-614.
[35]Hernandez-Boussard T,Rodriguez-Tome P,Montesano R,Hainaut P.IARC p53mutation database:a relational database to compile and analyze p53mutations in human tumors and cell lines.International Agency for Research on Cancer[J].Hum Mutat,1999,14(1):1-8.
[36]刘妍,李官成.生物信息学方法大规模筛选肿瘤差异表达基因[J].西安交通大学学报(医学版),2009,30(6):694-700.
[37]Edison T L,Koichiro I,Leena U,Valere C,Guillaume B,Yi-jun R.Fusion gene discovery through transcriptome and rear-rangement mapping using ultra high throughput pair end sequen-cing strategies[J].Genomic Med,2008,2:147–148.
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |