Integrative genomic analysis identifies epigenetic marks that mediate genetic risk for epithelial ovarian cancer
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Siegel R, Naishadham D, Jemal A: Cancer statistics, 2013. CA Cancer J Clin. 2013, 63 (1): 11-30. 10.3322/caac.21166.
Bodurka-Bevers D, Sun CC, Gershenson DM: Pharmacoeconomic considerations in treating ovarian cancer. Pharmacoeconomics. 2000, 17 (2): 133-150. 10.2165/00019053-200017020-00003.
Mariotto AB, Yabroff KR, Shao Y, Feuer EJ, Brown ML: Projections of the cost of cancer care in the United States: 2010-2020. J Natl Cancer Inst. 2011, 103 (2): 117-128. 10.1093/jnci/djq495.
Cicek MS, Koestler DC, Fridley BL, Kalli KR, Armasu SM, Larson MC, Wang C, Winham SJ, Vierkant RA, Rider DN, et al: Epigenome-wide ovarian cancer analysis identifies a methylation profile differentiating clear-cell histology with epigenetic silencing of the HERG K + channel. Hum Mol Genet. 2013, 22 (15): 3038-3047. 10.1093/hmg/ddt160.
Bauerschlag DO, Ammerpohl O, Brautigam K, Schem C, Lin Q, Weigel MT, Hilpert F, Arnold N, Maass N, Meinhold-Heerlein I, et al: Progression-free survival in ovarian cancer is reflected in epigenetic DNA methylation profiles. Oncology. 2011, 80 (1–2): 12-20.
Watts GS, Futscher BW, Holtan N, Degeest K, Domann FE, Rose SL: DNA methylation changes in ovarian cancer are cumulative with disease progression and identify tumor stage. BMC Med Genomics. 2008, 1: 47-10.1186/1755-8794-1-47.
Shen H, Fridley BL, Song H, Lawrenson K, Cunningham JM, Ramus SJ, Cicek MS, Tyrer J, Stram D, Larson MC, et al: Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancer. Nat Commun. 2013, 4: 1628.
Langevin SM, Koestler DC, Christensen BC, Butler RA, Wiencke JK, Nelson HH, Houseman EA, Marsit CJ, Kelsey KT: Peripheral blood DNA methylation profiles are indicative of head and neck squamous cell carcinoma: an epigenome-wide association study. Epigenetics. 2012, 7 (3): 291-299. 10.4161/epi.7.3.19134.
Marsit CJ, Koestler DC, Christensen BC, Karagas MR, Houseman EA, Kelsey KT: DNA methylation array analysis identifies profiles of blood-derived DNA methylation associated with bladder cancer. J Clin Oncol. 2011, 29 (9): 1133-1139. 10.1200/JCO.2010.31.3577.
Pedersen KS, Bamlet WR, Oberg AL, de Andrade M, Matsumoto ME, Tang H, Thibodeau SN, Petersen GM, Wang L: Leukocyte DNA methylation signature differentiates pancreatic cancer patients from healthy controls. PLoS One. 2011, 6 (3): e18223-10.1371/journal.pone.0018223.
Wang L, Aakre JA, Jiang R, Marks RS, Wu Y, Chen J, Thibodeau SN, Pankratz VS, Yang P: Methylation markers for small cell lung cancer in peripheral blood leukocyte DNA. J Thorac Oncol. 2010, 5 (6): 778-785. 10.1097/JTO.0b013e3181d6e0b3.
Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Gayther SA, Apostolidou S, Jones A, Lechner M, Beck S, Jacobs IJ, et al: An epigenetic signature in peripheral blood predicts active ovarian cancer. PLoS One. 2009, 4 (12): e8274-10.1371/journal.pone.0008274.
Houseman EA, Accomando WP, Koestler DC, Christensen BC, Marsit CJ, Nelson HH, Wiencke JK, Kelsey KT: DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinforma. 2012, 13 (1): 86-10.1186/1471-2105-13-86.
Koestler DC, Marsit CJ, Christensen BC, Accomando W, Langevin SM, Houseman EA, Nelson HH, Karagas MR, Wiencke JK, Kelsey KT: Peripheral blood immune cell methylation profiles are associated with nonhematopoietic cancers. Cancer Epidemiol Biomarkers Prev. 2012, 21 (8): 1293-1302. 10.1158/1055-9965.EPI-12-0361.
Reinius LE, Acevedo N, Joerink M, Pershagen G, Dahlen SE, Greco D, Soderhall C, Scheynius A, Kere J: Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility. PLoS One. 2012, 7 (7): e41361-10.1371/journal.pone.0041361.
Liu Y, Aryee MJ, Padyukov L, Fallin MD, Hesselberg E, Runarsson A, Reinius L, Acevedo N, Taub M, Ronninger M, et al: Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Nat Biotechnol. 2013, 31 (2): 142-147. 10.1038/nbt.2487.
Lin PC, Giannopoulou EG, Park K, Mosquera JM, Sboner A, Tewari AK, Garraway LA, Beltran H, Rubin MA, Elemento O: Epigenomic alterations in localized and advanced prostate cancer. Neoplasia. 2013, 15 (4): 373-383.
Baylin SB, Jones PA: A decade of exploring the cancer epigenome - biological and translational implications. Nat Rev Cancer. 2011, 11 (10): 726-734. 10.1038/nrc3130.
Bolton KL, Tyrer J, Song H, Ramus SJ, Notaridou M, Jones C, Sher T, Gentry-Maharaj A, Wozniak E, Tsai YY, et al: Common variants at 19p13 are associated with susceptibility to ovarian cancer. Nat Genet. 2010, 42 (10): 880-884. 10.1038/ng.666.
Goode EL, Chenevix-Trench G, Song H, Ramus SJ, Notaridou M, Lawrenson K, Widschwendter M, Vierkant RA, Larson MC, Kjaer SK, et al: A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24. Nat Genet. 2010, 42 (10): 874-879. 10.1038/ng.668.
Song H, Ramus SJ, Tyrer J, Bolton KL, Gentry-Maharaj A, Wozniak E, Anton-Culver H, Chang-Claude J, Cramer DW, DiCioccio R, et al: A genome-wide association study identifies a new ovarian cancer susceptibility locus on 9p22.2. Nat Genet. 2009, 41 (9): 996-1000. 10.1038/ng.424.
Pharoah PD, Tsai YY, Ramus SJ, Phelan CM, Goode EL, Lawrenson K, Buckley M, Fridley BL, Tyrer JP, Shen H, et al: GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer. Nat Genet. 2013, 45 (4)): 362-370. 370e361-362
Bojesen SE, Pooley KA, Johnatty SE, Beesley J, Michailidou K, Tyrer JP, Edwards SL, Pickett HA, Shen HC, Smart CE, et al: Multiple independent variants at the TERT locus are associated with telomere length and risks of breast and ovarian cancer. Nat Genet. 2013, 45 (4): 371-384. 10.1038/ng.2566. 384e371-372
Permuth-Wey J, Lawrenson K, Shen HC, Velkova A, Tyrer JP, Chen Z, Lin HY, Chen YA, Tsai YY, Qu X, et al: Identification and molecular characterization of a new ovarian cancer susceptibility locus at 17q21.31. Nat Commun. 2013, 4: 1627.
Painter JN, Anderson CA, Nyholt DR, Macgregor S, Lin J, Lee SH, Lambert A, Zhao ZZ, Roseman F, Guo Q, et al: Genome-wide association study identifies a locus at 7p15.2 associated with endometriosis. Nat Genet. 2011, 43 (1): 51-54. 10.1038/ng.731.
Cedar H, Bergman Y: Programming of DNA methylation patterns. Annu Rev Biochem. 2012, 81: 97-117. 10.1146/annurev-biochem-052610-091920.
Permuth-Wey J, Kim D, Tsai YY, Lin HY, Chen YA, Barnholtz-Sloan J, Birrer MJ, Bloom G, Chanock SJ, Chen Z, et al: LIN28B Polymorphisms influence susceptibility to epithelial ovarian cancer. Cancer Res. 2011, 71 (11): 3896-3903. 10.1158/0008-5472.CAN-10-4167.
Chelala C, Khan A, Lemoine NR: SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms. Bioinformatics. 2009, 25 (5): 655-661. 10.1093/bioinformatics/btn653.
Dayem Ullah AZ, Lemoine NR, Chelala C: SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update). Nucleic Acids Res. 2012, 40 (Web Server issue): W65-W70.
Dayem Ullah AZ, Lemoine NR, Chelala C: A practical guide for the functional annotation of genetic variations using SNPnexus. Brief Bioinform. 2013, 14 (4): 437-447. 10.1093/bib/bbt004.
Yang HH, Hu N, Wang C, Ding T, Dunn BK, Goldstein AM, Taylor PR, Lee MP: Influence of genetic background and tissue types on global DNA methylation patterns. PLoS One. 2010, 5 (2): e9355-10.1371/journal.pone.0009355.
Harper KN, Peters BA, Gamble MV: Batch effects and pathway analysis: two potential perils in cancer studies involving DNA methylation array analysis. Cancer Epidemiol Biomarkers Prev. 2013, 22 (6): 1052-1060. 10.1158/1055-9965.EPI-13-0114.
Du P, Zhang X, Huang CC, Jafari N, Kibbe WA, Hou L, Lin SM: Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinforma. 2010, 11: 587-10.1186/1471-2105-11-587.
Kuan PF, Wang S, Zhou X, Chu H: A statistical framework for Illumina DNA methylation arrays. Bioinformatics. 2010, 26 (22): 2849-2855. 10.1093/bioinformatics/btq553.
Johnson WE, Li C, Rabinovic A: Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007, 8 (1): 118-127. 10.1093/biostatistics/kxj037.
Chen C, Grennan K, Badner J, Zhang D, Gershon E, Jin L, Liu C: Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods. PLoS One. 2011, 6 (2).
Kupfer P, Guthke R, Pohlers D, Huber R, Koczan D, Kinne RW: Batch correction of microarray data substantially improves the identification of genes differentially expressed in rheumatoid arthritis and osteoarthritis. BMC Med Genomics. 2012, 5: 23-10.1186/1755-8794-5-23.
Dedeurwaerder S, Defrance M, Bizet M, Calonne E, Bontempi G, Fuks F: A comprehensive overview of infinium HumanMethylation450 data processing. Brief Bioinform. 2013
Morris TJ, Butcher LM, Feber A, Teschendorff AE, Chakravarthy AR, Wojdacz TK, Beck S: ChAMP: 450k chip analysis methylation pipeline. Bioinformatics. 2013
Wilhelm-Benartzi CS, Koestler DC, Karagas MR, Flanagan JM, Christensen BC, Kelsey KT, Marsit CJ, Houseman EA, Brown R: Review of processing and analysis methods for DNA methylation array data. Br J Cancer. 2013, 109 (6): 1394-1402. 10.1038/bjc.2013.496.
Bishara S, Griffin M, Cargill A, Bali A, Gore ME, Kaye SB, Shepherd JH, Van Trappen PO: Pre-treatment white blood cell subtypes as prognostic indicators in ovarian cancer. Eur J Obstet Gynecol Reprod Biol. 2008, 138 (1): 71-75. 10.1016/j.ejogrb.2007.05.012.
Cho H, Hur HW, Kim SW, Kim SH, Kim JH, Kim YT, Lee K: Pre-treatment neutrophil to lymphocyte ratio is elevated in epithelial ovarian cancer and predicts survival after treatment. Cancer Immunol Immunother. 2009, 58 (1): 15-23. 10.1007/s00262-008-0516-3.
den Ouden M, Ubachs JM, Stoot JE, van Wersch JW: Whole blood cell counts and leucocyte differentials in patients with benign or malignant ovarian tumours. Eur J Obstet Gynecol Reprod Biol. 1997, 72 (1): 73-77. 10.1016/S0301-2115(96)02662-0.
Koestler DC, Christensen B, Karagas MR, Marsit CJ, Langevin SM, Kelsey KT, Wiencke JK, Houseman EA: Blood-based profiles of DNA methylation predict the underlying distribution of cell types: a validation analysis. Epigenetics. 2013, 8 (8).
Millstein J, Zhang B, Zhu J, Schadt EE: Disentangling molecular relationships with a causal inference test. BMC Genet. 2009, 10: 23.
Storey JD, Tibshirani R: Statistical significance for genomewide studies. Proc Natl Acad Sci USA. 2003, 100 (16): 9440-9445. 10.1073/pnas.1530509100.
Kaminsky ZA, Tang T, Wang SC, Ptak C, Oh GH, Wong AH, Feldcamp LA, Virtanen C, Halfvarson J, Tysk C, et al: DNA methylation profiles in monozygotic and dizygotic twins. Nat Genet. 2009, 41 (2): 240-245. 10.1038/ng.286.
Cookson W, Liang L, Abecasis G, Moffatt M, Lathrop M: Mapping complex disease traits with global gene expression. Nat Rev Genet. 2009, 10 (3): 184-194. 10.1038/nrg2537.
Stranger BE, Dermitzakis ET: The genetics of regulatory variation in the human genome. Hum Genomics. 2005, 2 (2): 126-131. 10.1186/1479-7364-2-2-126.
Nica AC, Parts L, Glass D, Nisbet J, Barrett A, Sekowska M, Travers M, Potter S, Grundberg E, Small K, et al: The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet. 2011, 7 (2): e1002003-10.1371/journal.pgen.1002003.
Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, Gilad Y, Pritchard JK: DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 2011, 12 (1): R10-10.1186/gb-2011-12-1-r10.
Gibbs JR, van der Brug MP, Hernandez DG, Traynor BJ, Nalls MA, Lai SL, Arepalli S, Dillman A, Rafferty IP, Troncoso J, et al: Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet. 2010, 6 (5): e1000952-10.1371/journal.pgen.1000952.
Zhang D, Cheng L, Badner JA, Chen C, Chen Q, Luo W, Craig DW, Redman M, Gershon ES, Liu C: Genetic control of individual differences in gene-specific methylation in human brain. Am J Hum Genet. 2010, 86 (3): 411-419. 10.1016/j.ajhg.2010.02.005.
Janoueix-Lerosey I, Lequin D, Brugieres L, Ribeiro A, de Pontual L, Combaret V, Raynal V, Puisieux A, Schleiermacher G, Pierron G, et al: Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma. Nature. 2008, 455 (7215): 967-970. 10.1038/nature07398.
Webb TR, Slavish J, George RE, Look AT, Xue L, Jiang Q, Cui X, Rentrop WB, Morris SW: Anaplastic lymphoma kinase: role in cancer pathogenesis and small-molecule inhibitor development for therapy. Expert Rev Anticancer Ther. 2009, 9 (3): 331-356. 10.1586/14737140.9.3.331.
Wong DW, Leung EL, So KK, Tam IY, Sihoe AD, Cheng LC, Ho KK, Au JS, Chung LP, Pik Wong M: The EML4-ALK fusion gene is involved in various histologic types of lung cancers from nonsmokers with wild-type EGFR and KRAS. Cancer. 2009, 115 (8): 1723-1733. 10.1002/cncr.24181.
Zhang Q, Wang HY, Liu X, Bhutani G, Kantekure K, Wasik M: IL-2R common gamma-chain is epigenetically silenced by nucleophosphin-anaplastic lymphoma kinase (NPM-ALK) and acts as a tumor suppressor by targeting NPM-ALK. Proc Natl Acad Sci USA. 2011, 108 (29): 11977-82. 10.1073/pnas.1100319108.
Milne K, Kobel M, Kalloger SE, Barnes RO, Gao D, Gilks CB, Watson PH, Nelson BH: Systematic analysis of immune infiltrates in high-grade serous ovarian cancer reveals CD20, FoxP3 and TIA-1 as positive prognostic factors. PLoS One. 2009, 4 (7): e6412-10.1371/journal.pone.0006412.
Kostova N, Zlateva S, Ugrinova I, Pasheva E: The expression of HMGB1 protein and its receptor RAGE in human malignant tumors. Mol Cell Biochem. 2010, 337 (1–2): 251-258.
Sharma A, Ray R, Rajeswari MR: Overexpression of high mobility group (HMG) B1 and B2 proteins directly correlates with the progression of squamous cell carcinoma in skin. Cancer Invest. 2008, 26 (8): 843-851. 10.1080/07357900801954210.
Gnanasekar M, Thirugnanam S, Ramaswamy K: Short hairpin RNA (shRNA) constructs targeting high mobility group box-1 (HMGB1) expression leads to inhibition of prostate cancer cell survival and apoptosis. Int J Oncol. 2009, 34 (2): 425-431.
Song B, Song WG, Li ZJ, Xu ZF, Wang XW, Wang CX, Liu J: Effect of HMGB1 silencing on cell proliferation, invasion and apoptosis of MGC-803 gastric cancer cells. Cell Biochem Funct. 2011
Yao X, Zhao G, Yang H, Hong X, Bie L, Liu G: Overexpression of high-mobility group box 1 correlates with tumor progression and poor prognosis in human colorectal carcinoma. J Cancer Res Clin Oncol. 2010, 136 (5): 677-684. 10.1007/s00432-009-0706-1.
Jiao Y, Wang HC, Fan SJ: Growth suppression and radiosensitivity increase by HMGB1 in breast cancer. Acta Pharmacol Sin. 2007, 28 (12): 1957-1967. 10.1111/j.1745-7254.2007.00669.x.
Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM: Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci USA. 2004, 101 (25): 9309-9314. 10.1073/pnas.0401994101.
Wang W, Jiang H, Zhu H, Zhang H, Gong J, Zhang L, Ding Q: Overexpression of high mobility group box 1 and 2 is associated with the progression and angiogenesis of human bladder carcinoma. Oncol Lett. 2013, 5 (3): 884-888.
Ouellet V, Le Page C, Guyot MC, Lussier C, Tonin PN, Provencher DM, Mes-Masson AM: SET complex in serous epithelial ovarian cancer. Int J Cancer. 2006, 119 (9): 2119-2126. 10.1002/ijc.22054.
Yu M, Stott S, Toner M, Maheswaran S, Haber DA: Circulating tumor cells: approaches to isolation and characterization. J Cell Biol. 2011, 192 (3): 373-382. 10.1083/jcb.201010021.
Bianchi ME, Manfredi AA: High-mobility group box 1 (HMGB1) protein at the crossroads between innate and adaptive immunity. Immunol Rev. 2007, 220: 35-46. 10.1111/j.1600-065X.2007.00574.x.
Raucci A, Palumbo R, Bianchi ME: HMGB1: a signal of necrosis. Autoimmunity. 2007, 40 (4): 285-289. 10.1080/08916930701356978.
Scaffidi P, Misteli T, Bianchi ME: Release of chromatin protein HMGB1 by necrotic cells triggers inflammation. Nature. 2002, 418 (6894): 191-195. 10.1038/nature00858.
Huang MY, Wang HM, Tok TS, Chang HJ, Chang MS, Cheng TL, Wang JY, Lin SR: EVI2B, ATP2A2, S100B, TM4SF3, and OLFM4 as potential prognostic markers for postoperative Taiwanese colorectal cancer patients. DNA Cell Biol. 2012, 31 (4): 625-635. 10.1089/dna.2011.1365.
Ballarino M, Jobert L, Dembele D, de la Grange P, Auboeuf D, Tora L: TAF15 is important for cellular proliferation and regulates the expression of a subset of cell cycle genes through miRNAs. Oncogene. 2012, 32 (39): 4646-4655.
Lam LL, Emberly E, Fraser HB, Neumann SM, Chen E, Miller GE, Kobor MS: Factors underlying variable DNA methylation in a human community cohort. Proc Natl Acad Sci USA. 2012, 109 (Suppl 2): 17253-17260.
Byun HM, Nordio F, Coull BA, Tarantini L, Hou L, Bonzini M, Apostoli P, Bertazzi PA, Baccarelli A: Temporal stability of epigenetic markers: sequence characteristics and predictors of short-term DNA methylation variations. PLoS One. 2012, 7 (6): e39220-10.1371/journal.pone.0039220.