Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer

详细信息    查看全文

• 作者：Holger Heyn ; Enrique Vidal ; Humberto J. Ferreira ; Miguel Vizoso…
• 关键词：Super ; enhancer ; DNA methylation ; Epigenomics ; Cancer
• 刊名：Genome Biology
• 出版年：2016
• 出版时间：December 2016
• 年：2016
• 卷：17
• 期：1
• 全文大小：3,758 KB
• 参考文献：1.Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, et al. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat Genet. 2013;45:1198–206.CrossRef PubMed PubMedCentral
  2.Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, et al. Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci U S A. 2005;102:10604–9.CrossRef PubMed PubMedCentral
  3.Rideout 3rd WM, Eggan K, Jaenisch R. Nuclear cloning and epigenetic reprogramming of the genome. Science. 2001;293:1093–8.CrossRef PubMed
  4.Baylin SB, Jones PA. A decade of exploring the cancer epigenome - biological and translational implications. Nat Rev Cancer. 2011;11:726–34.CrossRef PubMed PubMedCentral
  5.Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet. 2011;44:40–6.CrossRef PubMed PubMedCentral
  6.Hansen KD. Increased methylation variation in epigenetic domains across cancer types. Nat Genet. 2011;43:768–75.CrossRef PubMed PubMedCentral
  7.Heyn H, Li N, Ferreira HJ, Moran S, Pisano DG, Gomez A, et al. Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A. 2012;109:10522–7.CrossRef PubMed PubMedCentral
  8.Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell. 2013;153:307–19.CrossRef PubMed PubMedCentral
  9.Stamatoyannopoulos JA, Clegg CH, Li Q. Sheltering of gamma-globin expression from position effects requires both an upstream locus control region and a regulatory element 3’ to the A gamma-globin gene. Mol Cell Biol. 1997;17:240–7.CrossRef PubMed PubMedCentral
  10.Talbot D, Collis P, Antoniou M, Vidal M, Grosveld F, Greaves DR. A dominant control region from the human beta-globin locus conferring integration site-independent gene expression. Nature. 1989;338:352–5.CrossRef PubMed
  11.Hnisz D, Abraham BJ, Lee TI, Lau A, Saint-André V, Sigova AA, et al. Super-enhancers in the control of cell identity and disease. Cell. 2013;155:934-947.
  12.Chapuy B, McKeown MR, Lin CY, Monti S, Roemer MGM, Qi J, et al. Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma. Cancer Cell. 2013;24:777–90.CrossRef PubMed PubMedCentral
  13.Lovén J, Hoke HA, Lin CY, Lau A, Orlando DA, Vakoc CR, et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell. 2013;153:320–34.CrossRef PubMed PubMedCentral
  14.Mansour MR, Abraham BJ, Anders L, Berezovskaya A, Gutierrez A, Durbin AD, et al. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element. Science. 2014;346:1373-1377.
  15.Chipumuro E, Marco E, Christensen CL, Kwiatkowski N, Zhang T, Hatheway CM, et al. CDK7 inhibition suppresses super-enhancer-linked oncogenic transcription in MYCN-driven cancer. Cell. 2014;159:1126–39.CrossRef PubMed PubMedCentral
  16.Network CGA. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490:61–70.CrossRef
  17.Network CGA. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487:330–7.CrossRef
  18.Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014;511:543–50.CrossRef
  19.Consortium TEP. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57–74.CrossRef
  20.Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Schöler A, et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature. 2011;480:490–5.PubMed
  21.Feldmann A, Ivanek R, Murr R, Gaidatzis D, Burger L, Schübeler D. Transcription factor occupancy can mediate active turnover of DNA methylation at regulatory regions. PLoS Genet. 2013;9:e1003994.CrossRef PubMed PubMedCentral
  22.Molaro A, Hodges E, Fang F, Song Q, McCombie WR, Hannon GJ, et al. Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell. 2011;146:1029–41.CrossRef PubMed PubMedCentral
  23.Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, et al. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol Cell. 2011;44:17–28.CrossRef PubMed PubMedCentral
  24.Schlesinger F, Smith AD, Gingeras TR, Hannon GJ, Hodges E. De novo DNA demethylation and non-coding transcription define active intergenic regulatory elements. Genome Res. 2013;23:1601-1614.
  25.Wiench M, John S, Baek S, Johnson TA, Sung M-H, Escobar T, et al. DNA methylation status predicts cell type-specific enhancer activity. EMBO J. 2011;30:3028–39.CrossRef PubMed PubMedCentral
  26.Aran D, Sabato S, Hellman A. DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes. Genome Biol. 2013;14:R21.CrossRef PubMed PubMedCentral
  27.Taberlay PC, Statham AL, Kelly TK, Clark SJ, Jones PA. Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer. Genome Res. 2014;24:1421–32.CrossRef PubMed PubMedCentral
  28.Blattler A, Yao L, Witt H, Guo Y, Nicolet CM, Berman BP, et al. Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biol. 2014;15:469.CrossRef PubMed PubMedCentral
  29.Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012;148:84–98.CrossRef PubMed PubMedCentral
  30.Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, et al. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res. 2012;22:246–58.CrossRef PubMed PubMedCentral
  31.Rubio-Perez C, Tamborero D, Schroeder MP, Antolín AA, Deu-Pons J, Perez-Llamas C, et al. In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities. Cancer Cell. 2015;27:382–96.CrossRef PubMed
  32.Hon GC, Song C-X, Du T, Jin F, Selvaraj S, Lee AY, et al. 5mC Oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation. Mol Cell. 2014;56:286-297.
  33.Stewart SK, Morris TJ, Guilhamon P, Bulstrode H, Bachman M, Balasubramanian S, et al. oxBS-450 K: A method for analysing hydroxymethylation using 450 K BeadChips. Methods. 2015;72:9-15.
  34.Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13:484–92.CrossRef PubMed
  35.Byers LA, Diao L, Wang J, Saintigny P, Girard L, Peyton M, et al. An epithelial-mesenchymal transition gene signature predicts resistance to EGFR and PI3K inhibitors and identifies Axl as a therapeutic target for overcoming EGFR inhibitor resistance. Clin Cancer Res Off J Am Assoc Cancer Res. 2013;19:279–90.CrossRef
  36.Fernandez AF, Assenov Y, Martin-Subero JI, Balint B, Siebert R, Taniguchi H, et al. A DNA methylation fingerprint of 1628 human samples. Genome Res. 2012;22:407-419.
  37.Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144:646–74.CrossRef PubMed
  38.Wang K, Yuen ST, Xu J, Lee SP, Yan HHN, Shi ST, et al. Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer. Nat Genet. 2014;46:573–82.CrossRef PubMed
  39.Bieller A, Pasche B, Frank S, Gläser B, Kunz J, Witt K, et al. Isolation and characterization of the human forkhead gene FOXQ1. DNA Cell Biol. 2001;20:555–61.CrossRef PubMed
  40.Cheng Y, Lotan R. Molecular cloning and characterization of a novel retinoic acid-inducible gene that encodes a putative G protein-coupled receptor. J Biol Chem. 1998;273:35008–15.CrossRef PubMed
  41.Jeong M, Sun D, Luo M, Huang Y, Challen GA, Rodriguez B, et al. Large conserved domains of low DNA methylation maintained by Dnmt3a. Nat Genet. 2014;46:17–23.CrossRef PubMed PubMedCentral
  42.Hovestadt V, Jones DTW, Picelli S, Wang W, Kool M, Northcott PA, et al. Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing. Nature. 2014;510:537–41.CrossRef PubMed
  43.Anastas JN, Moon RT. WNT signalling pathways as therapeutic targets in cancer. Nat Rev Cancer. 2012;13:11–26.CrossRef
  44.Wu Z-Q, Brabletz T, Fearon E, Willis AL, Hu CY, Li X-Y, et al. Canonical Wnt suppressor, Axin2, promotes colon carcinoma oncogenic activity. Proc Natl Acad Sci U S A. 2012;109:11312–7.CrossRef PubMed PubMedCentral
  45.Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinforma Oxf Engl. 2011;27:1571–2.CrossRef
  46.Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinforma Oxf Engl. 2009;25:2078–9.CrossRef
  47.Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinforma Oxf Engl. 2010;26:841–2.CrossRef
  48.Li H. Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinforma Oxf Engl. 2011;27:718–9.CrossRef
  49.R Development Core Team. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing; 2009.
  50.Hansen KD, Langmead B, Irizarry RA. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol. 2012;13:R83.CrossRef PubMed PubMedCentral
  51.Haider S, Ballester B, Smedley D, Zhang J, Rice P, Kasprzyk A. BioMart Central Portal--unified access to biological data. Nucleic Acids Res. 2009;37(Web Server issue):W23–7.CrossRef PubMed PubMedCentral
  52.Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012;22:1760–74.CrossRef PubMed PubMedCentral
  53.Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinforma Oxf Engl. 2009;25:1105–11.CrossRef
  54.Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, et al. Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays. Bioinforma Oxf Engl. 2014;30:1363-1369.
  55.Morris TJ, Butcher LM, Feber A, Teschendorff AE, Chakravarthy AR, Wojdacz TK, et al. ChAMP: 450 k Chip Analysis Methylation Pipeline. Bioinforma Oxf Engl. 2014;30:428–30.CrossRef
  56.Leek JT, Storey JD. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet. 2007;3:e161.CrossRef PubMedCentral
  
• 作者单位：Holger Heyn (1)
  Enrique Vidal (1)
  Humberto J. Ferreira (1)
  Miguel Vizoso (1)
  Sergi Sayols (1)
  Antonio Gomez (1)
  Sebastian Moran (1)
  Raquel Boque-Sastre (1)
  Sonia Guil (1)
  Anna Martinez-Cardus (1)
  Charles Y. Lin (2) (3) (4)
  Romina Royo (5)
  Jose V. Sanchez-Mut (1)
  Ramon Martinez (6)
  Marta Gut (7)
  David Torrents (5) (8)
  Modesto Orozco (10) (5) (9)
  Ivo Gut (7)
  Richard A. Young (11) (2)
  Manel Esteller (1) (12) (8)
  
  1. Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain
  2. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA, 02142, USA
  3. Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
  4. Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA, 02115, USA
  5. Joint Biomedical Research Institute-Barcelona Supercomputing Center (IRB-BSC) Program in Computational Biology, Baldiri Reixac 10-12, 08028, Barcelona, Catalonia, Spain
  6. Department of Neurosurgery, University of Goettingen, Robert Koch. Str. 40, 37075, Goettingen, Germany
  7. Centre Nacional d’Anàlisi Genòmica, Barcelona, Catalonia, Spain
  8. Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain
  10. Department of Biochemistry and Molecular Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain
  9. Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10-12, 08028, Barcelona, Catalonia, Spain
  11. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
  12. Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036, Barcelona, Catalonia, Spain
  
• 刊物主题：Animal Genetics and Genomics; Human Genetics; Plant Genetics & Genomics; Microbial Genetics and Genomics; Fungus Genetics; Bioinformatics;
• 出版者：BioMed Central
• ISSN：1465-6906

文摘

Background One of the hallmarks of cancer is the disruption of gene expression patterns. Many molecular lesions contribute to this phenotype, and the importance of aberrant DNA methylation profiles is increasingly recognized. Much of the research effort in this area has examined proximal promoter regions and epigenetic alterations at other loci are not well characterized.