Robust prediction of gene regulation in colorectal cancer tissues from DNA methylation profiles

References

• Lister R, Pelizzola M, Dowen RH, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009;462(7271):315–322. doi:10.1038/nature08514. PMID:19829295
   PubMed Web of Science ®Google Scholar
• Kim MS, Lee J, Sidransky D. DNA methylation markers in colorectal cancer. Cancer Metastasis Rev. 2010;29(1):181–206. doi:10.1007/s10555-010-9207-6. PMID:20135198
   PubMed Web of Science ®Google Scholar
• Naumov VA, Generozov EV, Zaharjevskaya NB, et al. Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips. Epigenetics. 2013;8(9):921–934. doi:10.4161/epi.25577. PMID:23867710
   PubMed Web of Science ®Google Scholar
• Toyota M, Ahuja N, Ohe-Toyota M, et al. .CpG island methylator phenotype in colorectal cancer. Med Sci. 1999;96:8681–8686.
   Google Scholar
• Hinoue T, Weisenberger DJ, Lange CPE, et al. Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Cancer Res. 2011 Apr 15;71:LB–173. doi:10.1158/1538-7445.AM2011-LB-173.
   Web of Science ®Google Scholar
• Lam K, Pan K, Linnekamp JF, et al. DNA methylation based biomarkers in colorectal cancer: a systematic review. Biochim Biophys Acta – Rev Cancer. 2016;1866(1):106–120. doi:10.1016/j.bbcan.2016.07.001.
   PubMed Web of Science ®Google Scholar
• Jones PA, Baylin SB. The fundamental role of epigenetic events in cancer. Nat Rev Genet. 2002;3(6):415–428. doi:10.1038/nrg816. PMID:12042769
   PubMed Web of Science ®Google Scholar
• Ball MP, Li JB, Gao Y, et al. Targeted and genome-scale methylomics reveals gene body signatures in human cell lines. Nat Biotechnol. 2009;27(4):361–368. doi:10.1038/nbt.1533. PMID:19329998
   PubMed Web of Science ®Google Scholar
• Varley KE, Gertz J, Bowling KM, et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res. 2013 Mar 1;23(3):555–567. doi:10.1101/gr.147942.112.
   PubMed Web of Science ®Google Scholar
• Merlo a, Herman JG, Mao L, et al. 5’ CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/CDKN2/MTS1 in human cancers. Nat Med. 1995;1(7):686–692. doi:10.1038/nm0795-686. PMID:7585152
   PubMed Web of Science ®Google Scholar
• Sproul D, Kitchen RR, Nestor CE, et al. Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns. Genome Biol. 2012;13(10):R84. doi:10.1186/gb-2012-13-10-r84. PMID:23034185
   PubMed Web of Science ®Google Scholar
• Sproul D, Meehan RR. Genomic insights into cancer-associated aberrant CpG island hypermethylation. Brief Funct Genomics. 2013;12(3):174–90. doi:10.1093/bfgp/els063. PMID:23341493
   PubMed Web of Science ®Google Scholar
• Moarii M, Boeva V, Vert J, et al. Changes in correlation between promoter methylation and gene expression in cancer. BMC Genomics. 2015 Dec 28;16(1):873. doi:10.1186/s12864-015-1994-2.
   PubMedGoogle Scholar
• Ma X, Liu Z, Zhang Z, et al. Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data. BMC Bioinformatics. 2017;18(1):72. doi:10.1186/s12859-017-1490-6. PMID:28137264
   PubMedGoogle Scholar
• Ma X, Wang Y-W, Zhang MQ, et al. DNA methylation data analysis and its application to cancer research. Epigenomics. 2013;5(3):301–316. doi:10.2217/epi.13.26. PMID:23750645
   PubMed Web of Science ®Google Scholar
• Jiao Y, Widschwendter M, Teschendorff AE. A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control. Bioinformatics. 2014;30(16):2360–2366. doi:10.1093/bioinformatics/btu316. PMID:24794928
   PubMed Web of Science ®Google Scholar
• West J, Beck S, Wang X, et al. An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways. Sci Rep. 2013;3:1630. doi:10.1038/srep01630. PMID:23568264
   PubMed Web of Science ®Google Scholar
• Li J, Ching T, Huang S, et al. Using epigenomics data to predict gene expression in lung cancer. BMC Bioinformatics. 2015;16:S10. doi:10.1186/1471-2105-16-S5-S10.
   PubMed Web of Science ®Google Scholar
• Barrow TM, Klett H, Toth R, et al. Smoking is associated with hypermethylation of the APC 1A promoter in colorectal cancer: the ColoCare Study. J Pathol. 2017;243(3):366–375. doi:10.1002/path.4955. PMID:28791728
   PubMed Web of Science ®Google Scholar
• Issa J-PJ. DNA Methylation as a Therapeutic target in cancer. Clin Cancer Res. 2007 Mar 15;13(6):1634–1637. doi:10.1158/1078-0432.CCR-06-2076.
   PubMed Web of Science ®Google Scholar
• Yang X, Han H, DeCarvalho DD, et al. Gene body methylation can alter gene expression and is a therapeutic target in cancer. Cancer Cell. 2014;26(4):577–590. doi:10.1016/j.ccr.2014.07.028. PMID:25263941
   PubMed Web of Science ®Google Scholar
• Vojta A, Dobrinic P, Tadic V, et al. Repurposing the CRISPR-Cas9 system for targeted DNA methylation. Nucleic Acids Res. 2016;44(12):5615–5628. doi:10.1093/nar/gkw159. PMID:26969735
   PubMed Web of Science ®Google Scholar
• Sanz-Pamplona R, Berenguer A, Cordero D, et al. Aberrant gene expression in mucosa adjacent to tumor reveals a molecular crosstalk in colon cancer. Mol Cancer. 2014;13(1):1–19. doi:10.1186/1476-4598-13-46. PMID:24387052
   PubMedGoogle Scholar
• Sandoval J, Heyn HA, Moran S, et al. Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome. Epigenetics. 2011;6(6):692–702. doi:10.4161/epi.6.6.16196. PMID:21593595
   PubMed Web of Science ®Google Scholar
• Qu Y, Lennartsson A, Gaidzik VI, et al. Differential methylation in CN-AML preferentially targets non-CGI regions and is dictated by DNMT3A mutational status and associated with predominant hypomethylation of HOX genes. Epigenetics. 2014 Aug 6;9(8):1108–1119. doi:10.4161/epi.29315.
   PubMed Web of Science ®Google Scholar
• Kamburov A, Wierling C, Lehrach H, et al. ConsensusPathDB – A database for integrating human functional interaction networks. Nucleic Acids Res. 2009;37:623–628. doi:10.1093/nar/gkn698.
   PubMed Web of Science ®Google Scholar
• Fusco A, Fedele M. Roles of HMGA proteins in cancer. Nat Rev Cancer. 2007;7(12):899–910. doi:10.1038/nrc2271. PMID:18004397
   PubMed Web of Science ®Google Scholar
• Hon GC, Hawkins RD, Caballero OL, et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Research. 2012;22(2):246–58.
   PubMed Web of Science ®Google Scholar
• Costello JF, Frühwald MC, Smiraglia DJ, et al. Aberrant CpG-island methylation has non-random and tumour-type–specific patterns. Nat Genet. 2000;24(2):132–138. doi:10.1038/72785. PMID:10655057
   PubMed Web of Science ®Google Scholar
• Ehrlich M. DNA methylation in cancer: too much, but also too little. Oncogene. 2002;21(35):5400–5413. doi:10.1038/sj.onc.1205651. PMID:12154403
   PubMed Web of Science ®Google Scholar
• Shah SN, Cope L, Poh W, et al. HMGA1: a master regulator of tumor progression in triple-negative breast cancer cells. PLoS One. 2013;8(5):e63419. doi:10.1371/journal.pone.0063419.
   PubMed Web of Science ®Google Scholar
• Resar LMS. The high mobility group A1 Gene: transforming inflammatory signals into cancer? Cancer Res. 2010;70(2):436–439. doi:10.1158/0008-5472.CAN-09-1212. PMID:20068164
   PubMed Web of Science ®Google Scholar
• Puca F, Colamaio M, Federico A, et al. HMGA1 silencing restores normal stem cell characteristics in colon cancer stem cells by increasing p53 levels. Oncotarget. 2014;5(10):3234–3245. doi:10.18632/oncotarget.1914. PMID:24833610
   PubMed Web of Science ®Google Scholar
• Yanagisawa BL, Resar LMS. Hitting the bull's eye: targeting HMGA1 in cancer stem cells. Expert Rev Anticancer Ther. 2011;4(164):23–30.
   Google Scholar
• Liau SS, Whang E. High mobility group A: a novel biomarker and therapeutic target in pancreatic adenocarcinoma. Surgeon. 2009;7(5):297–306. doi:10.1016/S1479-666X(09)80008-5. PMID:19848064
   PubMed Web of Science ®Google Scholar
• Heerboth S, Lapinska K, Snyder N, et al. Use of epigenetic drugs in disease: an overview. Genet Epigenetics. 2014;1(6):9–19.
   Google Scholar
• Aryee MJ, Jaffe AE, Corrada-Bravo H, et al. Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics. 2014;30(10):1363–1369. doi:10.1093/bioinformatics/btu049. PMID:24478339
   PubMed Web of Science ®Google Scholar
• Teschendorff AE, Marabita F, Lechner M, et al. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics. 2013;29(2):189–196. doi:10.1093/bioinformatics/bts680. PMID:23175756
   PubMed Web of Science ®Google Scholar
• Hansen KD. IlluminaHumanMethylation450kanno.ilmn12.hg19: Annotation for Illumina's 450k methylation arrays. R package version 0.6.0. 2016.
   Google Scholar
• Bibikova M, Barnes B, Tsan C, et al. High density DNA methylation array with single CpG site resolution. Genomics. 2011;98(4):288–295. doi:10.1016/j.ygeno.2011.07.007. PMID:21839163
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Phipson B, Wu D, et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. doi:10.1093/nar/gkv007. PMID:25605792
   PubMed Web of Science ®Google Scholar
• Kuhn M. Building predictive models in R Using the caret package. J Stat Softw. 2008;28(5):1–26. doi:10.18637/jss.v028.i05. PMID:27774042
   PubMed Web of Science ®Google Scholar