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Review

Integrated Analysis Of Genetic And Epigenetic Alterations In Cancer

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Pages 291-299 | Published online: 03 Dec 2009

Bibliography

  • Reik W , DeanW, WalterJ: Epigenetic reprogramming in mammalian development.Science293 , 1089–1093 (2001).
  • Jones PA , BaylinSB: The epigenomics of cancer.Cell128 , 683–692 (2007).
  • Ohm JE , McGarveyKM, YuX et al.: A stem cell-like chromatin pattern may predispose tumor suppressor genes to DNA hypermethylation and heritable silencing.Nat. Genet.39 , 237–242 (2007).
  • Widschwendter M , FieglH, EgleD et al.: Epigenetic stem cell signature in cancer.Nat. Genet.39 , 157–158 (2007).
  • Toyota M , IssaJP: Epigenetic changes in solid and hematopoietic tumors.Semin. Oncol.32 , 521–530 (2005).
  • Kinzler KW , VogelsteinB: Lessons from hereditary colorectal cancer.Cell87 , 159–170 (1996).
  • Nakamura Y : The role of the adenomatous polyposis coli (APC) gene in human cancers.Adv. Cancer Res.62 , 65–87 (1993).
  • Polakis P : The many ways of Wnt in cancer.Curr. Opin. Genet. Dev.17 , 45–51 (2007).
  • Smith G , CareyFA, BeattieJ et al.: Mutations in APC, Kirsten-ras, and p53 – alternative genetic pathways to colorectal cancer.Proc. Natl Acad. Sci. USA99 , 9433–9438 (2002).
  • Moslein G , TesterDJ, LindorNM et al.: Microsatellite instability and mutation analysis of hMSH2 and hMLH1 in patients with sporadic, familial and hereditary colorectal cancer.Hum. Mol. Genet.5 , 1245–1252 (1996).
  • Feinberg AP , VogelsteinB: Hypomethylation distinguishes genes of some human cancers from their normal counterparts.Nature301 , 89–92 (1983).
  • Herman JG , MerloA, MaoL et al.: Inactivation of the CDKN2/p16/MTS1 gene is frequently associated with aberrant DNA methylation in all common human cancers.Cancer Res.55 , 4525–4530 (1995).
  • Ahuja N , MohanAL, LiQ et al.: Association between CpG island methylation and microsatellite instability in colorectal cancer.Cancer Res.57 , 3370–3374 (1997).
  • Kane MF , LodaM, GaidaGM et al.: Methylation of the hMLH1 promoter correlates with lack of expression of hMLH1 in sporadic colon tumors and mismatch repair-defective human tumor cell lines.Cancer Res.57 , 808–811 (1997).
  • Esteller M , HamiltonSR, BurgerPC, BaylinSB, HermanJG: Inactivation of the DNA repair gene O6-methylguanine-DNA methyltransferase by promoter hypermethylation is a common event in primary human neoplasia.Cancer Res.59 , 793–797 (1999).
  • Devereux TR , HorikawaI, AnnaCH et al.: DNA methylation analysis of the promoter region of the human telomerase reverse transcriptase (hTERT) gene.Cancer Res.59 , 6087–6090 (1999).
  • Montero AJ , Diaz-MonteroCM, MaoL et al.: Epigenetic inactivation of EGFR by CpG island hypermethylation in cancer.Cancer Biol. Ther.5 , 1494–1501 (2006).
  • Toyota M , ShenL, Ohe-ToyotaM et al.: Aberrant methylation of the Cyclooxygenase 2 CpG island in colorectal tumors.Cancer Res.60 , 4044–4048 (2000).
  • Toyota M , HoC, AhujaN et al.: Identification of differentially methylated sequences in colorectal cancer by methylated CpG island amplification.Cancer Res.59 , 2307–2312 (1999).
  • Toyota M , AhujaN, Ohe-ToyotaM et al.: CpG island methylator phenotype in colorectal cancer.Proc. Natl Acad. Sci. USA96 , 8681–8686 (1999).
  • Toyota M , Ohe-ToyotaM, AhujaN, IssaJP: Distinct genetic profiles in colorectal tumors with or without the CpG island methylator phenotype.Proc. Natl Acad. Sci. USA97 , 710–715 (2000).
  • Shen L , ToyotaM, KondoY et al.: Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer.Proc. Natl Acad. Sci. USA104 , 18654–18659 (2007).
  • Samowitz WS , AlbertsenH, HerrickJ et al.: Evaluation of a large, population-based sample supports a CpG island methylator phenotype in colon cancer.Gastroenterology129 , 837–845 (2005).
  • Weisenberger DJ , SiegmundKD, CampanM et al.: CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer.Nat. Genet.38 , 787–793 (2006).
  • Kakar S , DengG, CunL, SahaiV, KimYS: CpG island methylation is frequently present in tubulovillous and villous adenomas and correlates with size, site, and villous component.Hum. Pathol.39 , 30–36 (2008).
  • Kambara T , SimmsLA, WhitehallVL et al.: BRAF mutation is associated with DNA methylation in serrated polyps and cancers of the colorectum.Gut53 , 1137–1144 (2004).
  • Barault L , Charon-BarraC, JoosteV et al.: Hypermethylator phenotype in sporadic colon cancer: study on a population-based series of 582 cases.Cancer Res.68 , 8541–8546 (2008).
  • Terada K , Okochi-TakadaE, Akashi-TanakaS et al.: Association between frequent CpG island methylation and HER2 amplification in human breast cancers.Carcinogenesis30 , 466–471 (2009).
  • Kusano M , ToyotaM, SuzukiH et al.: Genetic, epigenetic, and clinicopathologic features of gastric carcinomas with the CpG island methylator phenotype and an association with Epstein–Barr virus.Cancer106 , 1467–1479 (2006).
  • Issa JP : Methylation and prognosis: of molecular clocks and hypermethylator phenotypes.Clin. Cancer Res.9 , 2879–2881 (2003).
  • Bakin AV , CurranT: Role of DNA 5-methylcytosine transferase in cell transformation by fos.Science283 , 387–390 (1999).
  • Gazin C , WajapeyeeN, GobeilS, VirbasiusCM, GreenMR: An elaborate pathway required for Ras-mediated epigenetic silencing.Nature449 , 1073–1077 (2007).
  • Wajapeyee N , SerraRW, ZhuX, MahalingamM, GreenMR: Oncogenic BRAF induces senescence and apoptosis through pathways mediated by the secreted protein IGFBP7.Cell132 , 363–374 (2008).
  • Samowitz WS , SlatteryML, SweeneyC et al.: APC mutations and other genetic and epigenetic changes in colon cancer.Mol. Cancer Res.5 , 165–170 (2007).
  • Sato H , SuzukiH, ToyotaM et al.: Frequent epigenetic inactivation of DICKKOPF family genes in human gastrointestinal tumors.Carcinogenesis28 , 2459–2466 (2007).
  • Suzuki H , WatkinsDN, JairKW et al.: Epigenetic inactivation of SFRP genes allows constitutive WNT signaling in colorectal cancer.Nat. Genet.36 , 417–422 (2004).
  • Cahill DP , LengauerC, YuJ et al.: Mutations of mitotic checkpoint genes in human cancers.Nature392 , 300–303 (1998).
  • Rajagopalan H , JallepalliPV, RagoC et al.: Inactivation of hCDC4 can cause chromosomal instability.Nature428 , 77–81 (2004).
  • Goel A , NagasakaT, ArnoldCN et al.: The CpG island methylator phenotype and chromosomal instability are inversely correlated in sporadic colorectal cancer.Gastroenterology132 , 127–138 (2007).
  • Cheng YW , PincasH, BacolodMD et al.: CpG island methylator phenotype associates with low-degree chromosomal abnormalities in colorectal cancer.Clin. Cancer Res.14 , 6005–6013 (2008).
  • Derks S , PostmaC, CarvalhoB et al.: Integrated analysis of chromosomal, microsatellite and epigenetic instability in colorectal cancer identifies specific associations between promoter methylation of pivotal tumour suppressor and DNA repair genes and specific chromosomal alterations.Carcinogenesis29 , 434–439 (2008).
  • Estecio MR , GharibyanV, ShenL et al.: LINE-1 hypomethylation in cancer is highly variable and inversely correlated with microsatellite instability.PLoS ONE2 , E399(2007).
  • Rodriguez J , FrigolaJ, VendrellE et al.: Chromosomal instability correlates with genome-wide DNA demethylation in human primary colorectal cancers.Cancer Res.66 , 8462–9468 (2006).
  • Yamada Y , Jackson-GrusbyL, LinhartH et al.: Opposing effects of DNA hypomethylation on intestinal and liver carcinogenesis.Proc. Natl Acad. Sci. USA102 , 13580–13585 (2005).
  • Nishida N , NagasakaT, NishimuraT et al.: Aberrant methylation of multiple tumor suppressor genes in aging liver, chronic hepatitis, and hepatocellular carcinoma.Hepatology47 , 908–918 (2008).
  • Henken FE , WiltingSM, OvermeerRM et al.: Sequential gene promoter methylation during HPV-induced cervical carcinogenesis.Br. J. Cancer97 , 1457–1464 (2007).
  • Yasunaga J , TaniguchiY, NosakaK et al.: Identification of aberrantly methylated genes in association with adult T-cell leukemia.Cancer Res.64 , 6002–6009 (2004).
  • Etoh T , KanaiY, UshijimaS et al.: Increased DNA methyltransferase 1 (DNMT1) protein expression correlates significantly with poorer tumor differentiation and frequent DNA hypermethylation of multiple CpG islands in gastric cancers.Am. J. Pathol.164 , 689–699 (2004).
  • Maekita T , NakazawaK, MiharaM et al.: High levels of aberrant DNA methylation in Helicobacter pylori-infected gastric mucosae and its possible association with gastric cancer risk.Clin. Cancer Res.12 , 989–995 (2006).
  • Yamamoto E , ToyotaM, SuzukiH et al.: LINE-1 hypomethylation is associated with increased CpG island methylation in Helicobacter pylori-related enlarged-fold gastritis.Cancer Epidemiol. Biomarkers Prev.17 , 2555–2564 (2008).
  • Nakajima T , YamashitaS, MaekitaT et al.: The presence of a methylation fingerprint of Helicobacter pylori infection in human gastric mucosae.Int. J. Cancer124 , 905–910 (2009).
  • Zhou L , JiangW, RenC et al.: Frequent hypermethylation of RASSF1A and TSLC1, and high viral load of Epstein–Barr Virus DNA in nasopharyngeal carcinoma and matched tumor-adjacent tissues.Neoplasia7 , 809–815 (2005).
  • Tsai CN , TsaiCL, TseKP, ChangHY, ChangYS: The Epstein–Barr virus oncogene product, latent membrane protein 1, induces the downregulation of E-cadherin gene expression via activation of DNA methyltransferases.Proc. Natl Acad. Sci. USA99 , 10084–10089 (2002).
  • Tsai CL , LiHP, LuYJ et al.: Activation of DNA methyltransferase 1 by EBV LMP1 involves c-Jun NH(2)-terminal kinase signaling.Cancer Res.66 , 11668–11676 (2006).
  • Kurokawa M , HiraiH: Role of AML1/Runx1 in the pathogenesis of hematological malignancies.Cancer Sci.94 , 841–846 (2003).
  • Follows GA , TagohH, LefevreP et al.: Epigenetic consequences of AML1-ETO action at the human c-FMS locus.EMBO J.22 , 2798–2809 (2003).
  • Linggi B , Muller-TidowC, van de Locht L et al.: The t(8;21) fusion protein, AML1 ETO, specifically represses the transcription of the p14(ARF) tumor suppressor in acute myeloid leukemia. Nat. Med.8 , 743–750 (2002).
  • Pabst T , MuellerBU, HarakawaN et al.: AML1-ETO downregulates the granulocytic differentiation factor C/EBPα in t(8;21) myeloid leukemia.Nat. Med.7 , 444–451 (2001).
  • Liu S , ShenT, HuynhL et al.: Interplay of RUNX1/MTG8 and DNA methyltransferase 1 in acute myeloid leukemia.Cancer Res.65 , 1277–1284 (2005).
  • Wang J , IwasakiH, KrivtsovA et al.: Conditional MLL-CBP targets GMP and models therapy-related myeloproliferative disease.EMBO J.24 , 368–381 (2005).
  • Okada Y , FengQ, LinY et al.: hDOT1L links histone methylation to leukemogenesis.Cell121 , 167–178 (2005).
  • Cerveira N , CorreiaC, DoriaS et al.: Frequency of NUP98-NSD1 fusion transcript in childhood acute myeloid leukaemia.Leukemia17 , 2244–2247 (2003).
  • Wang GG , CaiL, PasillasMP, KampsMP: NUP98-NSD1 links H3K36 methylation to Hox-A gene activation and leukaemogenesis.Nat. Cell Biol.9 , 804–812 (2007).
  • Estecio MR , YanPS, IbrahimAE et al.: High-throughput methylation profiling by MCA coupled to CpG island microarray.Genome Res.17 , 1529–1536 (2007).
  • Jacinto FV , BallestarE, RoperoS, EstellerM: Discovery of epigenetically silenced genes by methylated DNA immunoprecipitation in colon cancer cells.Cancer Res.67 , 11481–11486 (2007).
  • Rauch T , LiH, WuX, PfeiferGP: MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells.Cancer Res.66 , 7939–7947 (2006).
  • Gao W , KondoY, ShenL et al.: Variable DNA methylation patterns associated with progression of disease in hepatocellular carcinomas.Carcinogenesis29 , 1901–1910 (2008).
  • Kuang SQ , TongWG, YangH et al.: Genome-wide identification of aberrantly methylated promoter associated CpG islands in acute lymphocytic leukemia.Leukemia22 , 1529–1538 (2008).
  • Arai E , UshijimaS, FujimotoH et al.: Genome-wide DNA methylation profiles in both precancerous conditions and clear cell renal cell carcinomas are correlated with malignant potential and patient outcome.Carcinogenesis30 , 214–221 (2009).
  • Deng J , ShoemakerR, XieB et al.: Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming.Nat. Biotechnol.27 , 353–360 (2009).
  • Greenman C , StephensP, SmithR et al.: Patterns of somatic mutation in human cancer genomes.Nature446 , 153–158 (2007).
  • Sjoblom T , JonesS, WoodLD et al.: The consensus coding sequences of human breast and colorectal cancers.Science314 , 268–274 (2006).
  • Chan TA , GlocknerS, YiJM et al.: Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.PLoS Med.5 , E114 (2008).
  • Heng HH , BremerSW, StevensJB et al.: Genetic and epigenetic heterogeneity in cancer: a genome-centric perspective.J. Cell Physiol.220 , 538–547 (2009).

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