The identification of specific methylation patterns across different cancers

PLoS ONE

Volumn 10, Issue 3, 2015, Pages

  Zhang, Chunlong ^a   Zhao, Hongyan ^a   Li, Jie ^a   Liu, Hongbo ^a   Wang, Fang ^a   Wei, Yanjun ^a   Su, Jianzhong ^a   Zhang, Dongwei ^b   Liu, Tiefu ^a   Zhang, Yan ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

^b THE SECOND AFFILIATED HOSPITAL OF HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MONOCYTE CHEMOTACTIC PROTEIN 2; SOMATOMEDIN C; TUMOR MARKER;

ACTG2 GENE; ACVR1 GENE; ARTICLE; BREAST CANCER; CCL8 GENE; COLON ADENOCARCINOMA; COLON CANCER; CONTROLLED STUDY; CYGB GENE; DNA METHYLATION; DNA METHYLATION CORRELATION NETWORK; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE REGULATORY NETWORK; GPSM1 GENE; GYPC GENE; HCK GENE; HIGH RISK POPULATION; HUMAN; HUMAN TISSUE; IGF1 GENE; KIDNEY CARCINOMA; LOW RISK POPULATION; LUNG ADENOCARCINOMA; MAGEA8 GENE; MAP3K14 GENE; NEOPLASM; ONCOGENE; OR51B4 GENE; PCDHB15 GENE; PROTEIN PROTEIN INTERACTION; PRRT1 GENE; PTN GENE; RECTUM CARCINOMA; SALL1 GENE; SALL3 GENE; SQUAMOUS CELL LUNG CARCINOMA; TMEFF2 GENE; WBSCR17 GENE; ZBTB32 GENE; BIOLOGY; CLUSTER ANALYSIS; EPIGENETICS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; METABOLISM; MORTALITY; NUCLEIC ACID DATABASE; PROGNOSIS; PROTEIN ANALYSIS;

CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; DNA METHYLATION; EPIGENESIS, GENETIC; EPIGENOMICS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; HUMANS; NEOPLASMS; PROGNOSIS; PROTEIN INTERACTION MAPPING; PROTEIN INTERACTION MAPS;

EID: 84924942532     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0120361     Document Type: Article

References (69)

1. Sutherland JE, Costa M. Epigenetics and the environment. Ann N Y Acad Sci. 2003; 983: 151-160. PMID: 12724220
2. Delgado-Cruzata L, Wu HC, Perrin M, Liao Y, Kappil MA, Ferris JS, et al. Global DNA methylation levels in white blood cell DNA from sisters discordant for breast cancer from the New York site of the Breast Cancer Family Registry. Epigenetics. 2012; 7: 868-874. doi: 10.4161/epi.20830 PMID: 22705975
3. Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res. 2013; 23: 555-567. doi: 10.1101/gr. 147942.112 PMID: 23325432
4. Choo KB. Epigenetics in disease and cancer. Malays J Pathol. 2011; 33: 61-70. PMID: 22299205
5. Deng J, Liang H, Zhang R, Ying G, Xie X, Yu J, et al. Methylated CpG site count of dapper homolog 1 (DACT1) promoter prediction the poor survival of gastric cancer. Am J Cancer Res. 2014; 4: 518-527. PMID: 25232493
6. Nakamura J, Tanaka T, Kitajima Y, Noshiro H, Miyazaki K. Methylation-mediated gene silencing as biomarkers of gastric cancer: A review. World J Gastroenterol. 2014; 20: 11991-12006. doi: 10.3748/wjg. v20.i34.11991 PMID: 25232236
7. Gokul G, Khosla S. DNA methylation and cancer. Subcell Biochem. 2013; 61: 597-625. doi: 10.1007/ 978-94-007-4525-4-26 PMID: 23150269
8. Kang C, Song JJ, Lee J, Kim MY. Epigenetics: an emerging player in gastric cancer. World J Gastroenterol. 2014; 20: 6433-6447. doi: 10.3748/wjg.v20.i21.6433 PMID: 24914365
9. Davis CD, Uthus EO. DNA methylation, cancer susceptibility, and nutrient interactions. Exp Biol Med (Maywood). 2004; 229: 988-995. PMID: 15522834
10. Kawano H, Saeki H, Kitao H, Tsuda Y, Otsu H, Ando K, et al. Chromosomal Instability Associated with Global DNA Hypomethylation is Associated with the Initiation and Progression of Esophageal Squamous Cell Carcinoma. Ann Surg Oncol 21 Suppl: . 2014; 4: 696-702.
11. The Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature. 2012; 490: 61-70. doi: 10.1038/nature11412 PMID: 23000897
12. van den Broek AJ, de Ruiter K, van 't Veer LJ, Tollenaar RA, van Leeuwen FE, Verhoef S, et al. Evaluation of the Dutch BRCA1/2 clinical genetic center referral criteria in an unselected early breast cancer population. Eur J Hum Genet. 2014.
13. Mahon KL, Qu W, Devaney J, Paul C, Castillo L, Wykes RJ, et al. Methylated Glutathione S-transferase 1 (mGSTP1) is a potential plasma free DNA epigenetic marker of prognosis and response to chemotherapy in castrate-resistant prostate cancer. Br J Cancer. 2014.
14. Varisli L. Identification of new genes downregulated in prostate cancer and investigation of their effects on prognosis. Genet Test Mol Biomarkers. 2013; 17: 562-566. doi: 10.1089/gtmb.2012.0524 PMID: 23621580
15. Barchitta M, Quattrocchi A, Maugeri A, Vinciguerra M, Agodi A. LINE-1 hypomethylation in blood and tissue samples as an epigenetic marker for cancer risk: a systematic review and meta-analysis. PLoS One. 2014; 9: e109478. doi: 10.1371/journal.pone.0109478 PMID: 25275447
16. Li YX, Lu Y, Li CY, Yuan P, Lin SS.Role of CDH1 promoter methylation in colorectal carcinogenesis: a meta-analysis. DNA Cell Biol. 2014; 33: 455-462. doi: 10.1089/dna.2013.2291 PMID: 24684676
17. Oh JH, Rhyu MG, Jung SH, Choi SW, Kim SI, Hong SJ. Slow overmethylation of housekeeping genes in the body mucosa is associated with the risk for gastric cancer. Cancer Prev Res (Phila). 2014; 7: 585-595. doi: 10.1158/1940-6207.CAPR-13-0320 PMID: 24654229
18. Asiaf A, Ahmad ST, Aziz SA, Malik AA, Rasool Z, Masood A, et al. Loss of Expression and Aberrant Methylation of the CDH1 (E-cadherin) Gene in Breast Cancer Patients from Kashmir. Asian Pac J Cancer Prev. 2014; 15: 6397-6403. PMID: 25124632
19. Li G, Liu Y, Yin H, Zhang X, Mo X, Tang J, et al. E-cadherin gene promoter hypermethylation may contribute to the risk of bladder cancer among Asian populations. Gene. 2013.
20. Litovkin K, Joniau S, Lerut E, Laenen A, Gevaert O, Spahn M, et al. Methylation of PITX2, HOXD3, RASSF1 and TDRD1 predicts biochemical recurrence in high-risk prostate cancer. J Cancer Res Clin Oncol. 2014.
21. Daniunaite K, Jarmalaite S, Kalinauskaite N, Petroska D, Laurinavicius A, Lazutka JR, et al. Prognostic value of RASSF1 promoter methylation in prostate cancer. J Urol. 2014.
22. Guerrero-Setas D, Perez-Janices N, Blanco-Fernandez L, Ojer A, Cambra K, Berdasco M, et al. RASSF2 hypermethylation is present and related to shorter survival in squamous cervical cancer. Mod Pathol. 2013; 26: 1111-1122. doi: 10.1038/modpathol.2013.32 PMID: 23542458
23. Liu Z, Zhang S. Toward a systematic understanding of cancers: a survey of the pan-cancer study. Front Genet. 2014; 5: 194. doi: 10.3389/fgene.2014.00194 PMID: 25071824
24. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A. 2001; 98: 5116-5121. PMID: 11309499
25. Wu MC, Joubert BR, Kuan PF, Haberg SE, Nystad W, Peddada SD, et al. A systematic assessment of normalization approaches for the Infinium 450K methylation platform. Epigenetics. 2014; 9: 318-329. doi: 10.4161/epi.27119 PMID: 24241353
26. Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012; 487: 330-337. doi: 10.1038/nature11252 PMID: 22810696
27. Correa CR, Darby SC. Cardiac disease and second lung cancer after radiotherapy for breast cancer. Eur J Cancer 45. 2009; Suppl 1: 420-421. doi: 10.1016/S0959-8049(09)70073-5 PMID: 19775655
28. de Visser KE, Eichten A, Coussens LM. Paradoxical roles of the immune system during cancer development. Nat Rev Cancer. 2006; 6: 24-37. PMID: 16397525
29. Pu H, Horbinski C, Hensley PJ, Matuszak EA, Atkinson T, Kyprianou N. PARP-1 Regulates Epithelial-Mesenchymal-Transition (EMT) in Prostate Tumorigenesis. Carcinogenesis. 2014.
30. Guardiola M, Oliva I, Guillaumet A, Martin-Trujillo A, Rosales R, Vallve JC, et al. Tissue-specific DNA methylation profiles regulate liver-specific expression of the APOA1/C3/A4/A5 cluster and can be manipulated with demethylating agents on intestinal cells. Atherosclerosis. 2014; 237: 528-535. doi: 10. 1016/j.atherosclerosis.2014.10.029 PMID: 25463085
31. Bediaga NG, Acha-Sagredo A, Guerra I, Viguri A, Albaina C, Ruiz Diaz I, et al. DNA methylation epigenotypes in breast cancer molecular subtypes. Breast Cancer Res. 2010; 12: R77. doi: 10.1186/bcr2721 PMID: 20920229 32.
32. Murray TI, Neugut AI, Garbowski GC, Waye JD, Forde KA, Treat MR. Relationship between breast cancer and colorectal adenomatous polyps. A case-control study. Cancer. 1992; 69: 2232-2234. PMID: 1562968
33. Prasad A, Paruchuri V, Preet A, Latif F, Ganju RK. Slit-2 induces a tumor-suppressive effect by regulating beta-catenin in breast cancer cells. J Biol Chem. 2008; 283: 26624-26633. doi: 10.1074/jbc. M800679200 PMID: 18611862
34. Dallol A, Morton D, Maher ER, Latif F. SLIT2 axon guidance molecule is frequently inactivated in colorectal cancer and suppresses growth of colorectal carcinoma cells. Cancer Res. 2003; 63: 1054-1058. PMID: 12615722
35. Sadr-Nabavi A, Ramser J, Volkmann J, Naehrig J, Wiesmann F, Betz B, et al. Decreased expression of angiogenesis antagonist EFEMP1 in sporadic breast cancer is caused by aberrant promoter methylation and points to an impact of EFEMP1 as molecular biomarker. Int J Cancer. 2009; 124: 1727-1735. doi: 10.1002/ijc.24108 PMID: 19115204
36. Gallagher WM, Greene LM, Ryan MP, Sierra V, Berger A, Laurent-Puig P, et al. Human fibulin-4: analysis of its biosynthetic processing and mRNA expression in normal and tumour tissues. FEBS Lett. 2001; 489: 59-66. PMID: 11231014
37. Isserlin R, El-Badrawi RA, Bader GD. The Biomolecular Interaction Network Database in PSI-MI 2.5. Database (Oxford). 2011; baq037.
38. Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, et al. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 2011; 39: D698-704. doi: 10.1093/nar/ gkq1116 PMID: 21071413
39. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2004; 32: D449-451. PMID: 14681454
40. Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, et al. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 2003; 13: 2363-2371. PMID: 14525934
41. Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, et al. The IntAct molecular interaction database in 2010. Nucleic Acids Res. 2010; 38: D525-531. doi: 10.1093/nar/gkp878 PMID: 19850723
42. Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, Galeota E, et al. MINT, the molecular interaction database: 2012 update. Nucleic Acids Res. 2012; 40: D857-861. doi: 10.1093/nar/gkr930 PMID: 22096227
43. Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, et al. The MIPS mammalian protein-protein interaction database. Bioinformatics. 2005; 21: 832-834. PMID: 15531608
44. Beuming T, Skrabanek L, Niv MY, Mukherjee P, Weinstein H. PDZBase: a protein-protein interaction database for PDZ-domains. Bioinformatics. 2005; 21: 827-828. PMID: 15513994
45. Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, et al. Reactome: a knowledge base of biologic pathways and processes. Genome Biol. 2007; 8: R39. PMID: 17367534
46. Yu X, Wallqvist A, Reifman J. Inferring high-confidence human protein-protein interactions. BMC Bioinformatics. 2012; 13: 79. doi: 10.1186/1471-2105-13-79 PMID: 22558947
47. Greten FR, Karin M. The IKK/NF-kappaB activation pathway-a target for prevention and treatment of cancer. Cancer Lett. 2004; 206: 193-199. PMID: 15013524
48. Wang W, Zhao J, Wang H, Sun Y, Peng Z, Zhou G, et al. Programmed cell death 4 (PDCD4) mediates the sensitivity of gastric cancer cells to TRAIL-induced apoptosis by down-regulation of FLIP expression. Exp Cell Res. 2010; 316: 2456-2464. doi: 10.1016/j.yexcr.2010.05.027 PMID: 20595005
49. Wang L, Zeng Y, Liu Y, Hu X, Li S, Wang Y, et al. Fucoxanthin induces growth arrest and apoptosis in human bladder cancer T24 cells by up-regulation of p21 and down-regulation of mortalin. Acta Biochim Biophys Sin (Shanghai). 2014.
50. Soreide K, Janssen EA, Soiland H, Korner H, Baak JP. Microsatellite instability in colorectal cancer. Br J Surg. 2006; 93: 395-406. PMID: 16555243
51. Anwar S, Hall C, White J, Deakin M, Farrell W, Elder JB. Hereditary non-polyposis colorectal cancer: an updated review. Eur J Surg Oncol. 2000; 26: 635-645. PMID: 11078609
52. Abdel-Magid AF. Wnt/beta-Catenin Signaling Pathway Inhibitors: A Promising Cancer Therapy. ACS Med Chem Lett. 2014; 5: 956-957. doi: 10.1021/ml500276a PMID: 25264477
53. Vivanco I. Targeting molecular addictions in cancer. Br J Cancer. 2014.
54. Ghasemi R, Rapposelli IG, Capone E, Rossi C, Lattanzio R, Piantelli M, et al. Dual targeting of ErbB-2/ ErbB-3 results in enhanced antitumor activity in preclinical models of pancreatic cancer. Oncogenesis. 2014; 3: e117. doi: 10.1038/oncsis.2014.31 PMID: 25133484
55. Miura D, Yoneyama K, Furuhata Y, Shimizu K. Paclitaxel Enhances Antibody-dependent Cell-mediated Cytotoxicity of Trastuzumab by Rapid Recruitment of Natural Killer Cells in HER2-positive Breast Cancer. J Nippon Med Sch. 2014; 81: 211-220. PMID: 25186575
56. Armendariz BG, Del Mar Masdeu M, Soriano E, Urena JM, Burgaya F. The diverse roles and multiple forms of focal adhesion kinase in brain. Eur J Neurosci. 2014.
57. Kiga K, Fukuda-Yuzawa Y, Tanabe M, Tsuji S, Sasakawa C, Fukao T. Comprehensive Silencing of Tar-get-Sharing microRNAs is a Mechanism for SIRT1 Overexpression in Cancer. RNA Biol. 2014; e32093.
58. Antony P, Rose M, Heidenreich A, Knuchel R, Gaisa NT, Dahl E. Epigenetic inactivation of ST6GAL1 in human bladder cancer. BMC Cancer. 2014; 14: 901. doi: 10.1186/1471-2407-14-901 PMID: 25465919
59. Sakoda LC, Blackston C, Doherty JA, Ray RM, Lin MG, Stalsberg H, et al. Polymorphisms in steroid hormone biosynthesis genes and risk of breast cancer and fibrocystic breast conditions in Chinese women. Cancer Epidemiol Biomarkers Prev. 2008; 17: 1066-1073. doi: 10.1158/1055-9965.EPI-07-2680 PMID: 18483327
60. Giani C, Fierabracci P, Bonacci R, Gigliotti A, Campani D, De Negri F, et al. Relationship between breast cancer and thyroid disease: relevance of autoimmune thyroid disorders in breast malignancy. J Clin Endocrinol Metab. 1996; 81: 990-994. PMID: 8772562
61. Krupp M, Maass T, Marquardt JU, Staib F, Bauer T, Konig R, et al. The functional cancer map: a sys-tems-level synopsis of genetic deregulation in cancer. BMC Med Genomics. 2011; 4: 53. doi: 10.1186/ 1755-8794-4-53 PMID: 21718500
62. Bernatsky S, Boivin JF, Joseph L, Rajan R, Zoma A, Manzi S, et al. An international cohort study of cancer in systemic lupus erythematosus. Arthritis Rheum. 2005; 52: 1481-1490. PMID: 15880596
63. Wei Z, Li H. A Markov random field model for network-based analysis of genomic data. Bioinformatics 23. 2007; 1537-1544. PMID: 17483504
64. Schreiber G, Walter MR. Cytokine-receptor interactions as drug targets. Curr Opin Chem Biol. 2010; 14: 511-519. doi: 10.1016/j.cbpa.2010.06.165 PMID: 20619718
65. Wu BK,Mei SC, Brenner C. RFTS-deleted DNMT1 enhances tumorigenicity with focal hypermethylation and global hypomethylation. Cell Cycle. 2014; 13: 3222-3231. doi: 10.4161/15384101.2014.950886 PMID: 25485502
66. Vidigal JA, Ventura A. The biological functions of miRNAs: lessons from in vivo studies. Trends Cell Biol. 2014.
67. Gu H, Bock C, Mikkelsen TS, Jager N, Smith ZD, Tomazou E, et al. Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods. 2010; 7: 133-136. doi: 10. 1038/nmeth.1414 PMID: 20062050
68. Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, et al. High density DNA methylation array with single CpG site resolution. Genomics. 2011; 98: 288-295. doi: 10.1016/j.ygeno.2011.07.007 PMID: 21839163
69. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009; 462: 315-322. doi: 10. 1038/nature08514 PMID: 19829295