Identification of diagnostic markers in colorectal cancer via integrative epigenomics and genomics data

Oncology Reports

Volumn 34, Issue 1, 2015, Pages 22-32

  Kok Sin, Teow ^a   Mokhtar, Norfilza Mohd ^a   Hassan, Nur Zarina Ali ^a   Sagap, Ismail ^a   Rose, Isa Mohamed ^a   Harun, Roslan ^b   Jamal, Rahman ^a  

^a UNIVERSITI KEBANGSAAN MALAYSIA   (Malaysia)

^b DEPARTMENT OF PHARMACOLOGY   (Malaysia)

Author keywords

Colorectal cancer; CpG loci; DNA methylation; Epigenetics; Gene expression

Indexed keywords

CELL ADHESION MOLECULE; CONTACTIN 1; JUNCTIONAL ADHESION MOLECULE B; TRANSCRIPTOME; TUMOR MARKER;

ADULT; ARTICLE; CANCER PROGNOSIS; CNTN1 GENE; COLON CARCINOGENESIS; COLORECTAL CANCER; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; DOWN REGULATION; EPIGENETICS; FEMALE; GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC ASSOCIATION; GENOMICS; HUMAN; HUMAN CELL; HUMAN TISSUE; ITGA8 GENE; JAM2 GENE; MAJOR CLINICAL STUDY; MALE; METHYLATION SPECIFIC MULTIPLEX LIGATION DEPENDENT PROBE AMPLIFICATION; MICROARRAY ANALYSIS; MIDDLE AGED; MULTIPLEX LIGATION DEPENDENT PROBE AMPLIFICATION; NCAM1 GENE; PRIORITY JOURNAL; PROMOTER REGION; UPREGULATION; BIOSYNTHESIS; CARCINOGENESIS; COLORECTAL TUMOR; GENETICS; PATHOLOGY;

BIOMARKERS, TUMOR; CARCINOGENESIS; COLORECTAL NEOPLASMS; CPG ISLANDS; DNA METHYLATION; EPIGENOMICS; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOMICS; HUMANS; PROMOTER REGIONS, GENETIC;

EID: 84930027328     PISSN: 1021335X     EISSN: 17912431     Source Type: Journal    
DOI: 10.3892/or.2015.3993     Document Type: Article

References (64)

1. Soon MS, Soon A, Lin TY and Lin OS: Distribution of colon neoplasia in Chinese patients: Implications for endoscopic screening strategies. Eur J Gastroenterol Hepatol 20: 642-647, 2008.
2. Sung JJ, Lau JY, Goh KL and Leung WK; Asia Pacific Working Group on Colorectal Cancer: Increasing incidence of colorectal cancer in Asia: Implications for screening. Lancet Oncol 6: 871-876, 2005.
3. Yeh CC, Hsieh LL, Tang R, Chang-Chieh CR and Sung FC: Risk factors for colorectal cancer in Taiwan: A hospital-based case-control study. J Formos Med Assoc 102: 305-312, 2003.
4. Flamen P, Hoekstra OS, Homans F, Van Cutsem E, Maes A, Stroobants S, Peeters M, Penninckx F, Filez L, Bleichrodt RP, et al: Unexplained rising carcinoembryonic antigen (CEA) in the postoperative surveillance of colorectal cancer: The utility of positron emission tomography (PET). Eur J Cancer 37: 862-869, 2001.
5. Steele N, Haigh R, Knowles G and Mackean M: Carcinoembryonic antigen (CEA) testing in colorectal cancer follow up: What do patients think? Postgrad Med J 83: 612-614, 2007.
6. Duffy MJ: Carcinoembryonic antigen as a marker for colo rectal cancer: Is it clinically useful? Clin Chem 47: 624-630, 2001.
7. Leung WK, To KF, Man EP, Chan MW, Bai AH, Hui AJ, Chan FK, Lee JF and Sung JJ: Detection of epigenetic changes in fecal DNA as a molecular screening test for colorectal cancer: A feasibility study. Clin Chem 50: 2179-2182, 2004.
8. Esteller M: Epigenetics in cancer. N Engl J Med 358: 1148-1159, 2008.
9. Jones PA and Baylin SB: The epigenomics of cancer. Cell 128: 683-692, 2007.
10. Illingworth RS and Bird AP: CpG islands - 'a rough guide'. FEBS Lett 583: 1713-1720, 2009.
11. Saxonov S, Berg P and Brutlag DL: A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci USA 103: 1412-1417, 2006.
12. Baylin SB and Jones PA: A decade of exploring the cancer epigenome - biological and translational implications. Nat Rev Cancer 11: 726-734, 2011.
13. Lao VV and Grady WM: Epigenetics and colorectal cancer. Nat Rev Gastroenterol Hepatol 8: 686-700, 2011.
14. Hinoue T, Weisenberger DJ, Lange CP, Shen H, Byun HM, Van Den Berg D, Malik S, Pan F, Noushmehr H, van Dijk CM, et al: Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res 22: 271-282, 2012.
15. Bird A: DNA methylation patterns and epigenetic memory. Genes Dev 16: 6-21, 2002.
16. Ballestar E and Esteller M: Methyl-CpG-binding proteins in cancer: Blaming the DNA methylation messenger. Biochem Cell Biol 83: 374-384, 2005.
17. Coppede F: Epigenetic biomarkers of colorectal cancer: Focus on DNA methylation. Cancer Lett 342: 238-247, 2011.
18. Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, et al: DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38: 1378-1385, 2006.
19. Lofton-Day C, Model F, Devos T, Tetzner R, Distler J, Schuster M, Song X, Lesche R, Liebenberg V, Ebert M, et al: DNA methylation biomarkers for blood-based colorectal cancer screening. Clin Chem 54: 414-423, 2008.
20. Ahlquist T, Lind GE, Costa VL, Meling GI, Vatn M, Hoff GS, Rognum TO, Skotheim RI, Thiis-Evensen E and Lothe RA: Gene methylation profiles of normal mucosa, and benign and malignant colorectal tumors identify early onset markers. Mol Cancer 7: 94, 2008.
21. Ang PW, Loh M, Liem N, Lim PL, Grieu F, Vaithilingam A, Platell C, Yong WP, Iacopetta B and Soong R: Comprehensive profiling of DNA methylation in colorectal cancer reveals subgroups with distinct clinicopathological and molecular features. BMC Cancer 10: 227, 2010.
22. Zhang H, Song YC and Dang CX: Detection of hypermethylated spastic paraplegia-20 in stool samples of patients with colorectal cancer. Int J Med Sci 10: 230-234, 2013.
23. Kibriya MG, Raza M, Jasmine F, Roy S, Paul-Brutus R, Rahaman R, Dodsworth C, Rakibuz-Zaman M, Kamal M and Ahsan H: A genome-wide DNA methylation study in colorectal carcinoma. BMC Med Genomics 4: 50, 2011.
24. Derks S, Postma C, Carvalho B, van den Bosch SM, Moerkerk PT, Herman JG, Weijenberg MP, de Bruïne AP, Meijer GA and van Engeland M: 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. Carcinogenesis 29: 434-439, 2008.
25. Mo Q, Wang S, Seshan VE, Olshen AB, Schultz N, Sander C, Powers RS, Ladanyi M and Shen R: Pattern discovery and cancer gene identification in integrated cancer genomic data. Proc Natl Acad Sci USA 110: 4245-4250, 2013.
26. Cancer Genome Atlas Network: Comprehensive molecular characterization of human colon and rectal cancer. Nature 487: 330-337, 2012.
27. Ramalho-Carvalho J, Pires M, Lisboa S, Graça I, Rocha P, Barros-Silva JD, Savva-Bordalo J, Maurício J, Resende M, Teixeira MR, et al: Altered expression of MGMT in high-grade gliomas results from the combined effect of epigenetic and genetic aberrations. PLoS One 8: e58206, 2013.
28. Ali Hassan NZ, Mokhtar NM, Kok Sin T, Mohamed Rose I, Sagap I, Harun R and Jamal R: Integrated analysis of copy number variation and genome-wide expression profiling in colorectal cancer tissues. PLoS One 9: e92553, 2014.
29. Kim YH, Lee HC, Kim SY, Yeom YI, Ryu KJ, Min BH, Kim DH, Son HJ, Rhee PL, Kim JJ, et al: Epigenomic analysis of aberrantly methylated genes in colorectal cancer identifies genes commonly affected by epigenetic alterations. Ann Surg Oncol 18: 2338-2347, 2011.
30. Lin SY, Yeh KT, Chen WT, Chen HC, Chen ST and Chang JG: Promoter CpG methylation of caveolin-1 in sporadic colorectal cancer. Anticancer Res 24 (3a): 1645-1650, 2004.
31. Wang DR and Tang D: Hypermethylated SFRP2 gene in fecal DNA is a high potential biomarker for colorectal cancer noninvasive screening. World J Gastroenterol 14: 524-531, 2008.
32. Oster B, Thorsen K, Lamy P, Wojdacz TK, Hansen LL, Birkenkamp-Demtröder K, Sørensen KD, Laurberg S, Orntoft TF and Andersen CL: Identification and validation of highly frequent CpG island hypermethylation in colorectal adenomas and carcinomas. Int J Cancer 129: 2855-2866, 2011.
33. Lind GE, Raiborg C, Danielsen SA, Rognum TO, Thiis-Evensen E, Hoff G, Nesbakken A, Stenmark H and Lothe RA: SPG20, a novel biomarker for early detection of colorectal cancer, encodes a regulator of cytokinesis. Oncogene 30: 3967-3978, 2011.
34. Mori Y, Cai K, Cheng Y, Wang S, Paun B, Hamilton JP, Jin Z, Sato F, Berki AT, Kan T, et al: A genome-wide search identifies epigenetic silencing of somatostatin, tachykinin-1, and 5 other genes in colon cancer. Gastroenterology 131: 797-808, 2006.
35. Chen WF, Gao WD, Li QL, Zhou PH, Xu MD and Yao LQ: SLIT2 inhibits cell migration in colorectal cancer through the AKT-GSK3β signaling pathway. Int J Colorectal Dis 28: 933-940, 2013.
36. Jacinto FV, Ballestar E, Ropero S and Esteller M: Discovery of epigenetically silenced genes by methylated DNA immunoprecipitation in colon cancer cells. Cancer Res 67: 11481-11486, 2007.
37. Lind GE, Kleivi K, Meling GI, Teixeira MR, Thiis-Evensen E, Rognum TO and Lothe RA: ADAMTS1, CRABP1, and NR3C1 identified as epigenetically deregulated genes in colorectal tumorigenesis. Cell Oncol 28: 259-272, 2006.
38. Zou H, Harrington JJ, Shire AM, Rego RL, Wang L, Campbell ME, Oberg AL and Ahlquist DA: Highly methylated genes in colorectal neoplasia: Implications for screening. Cancer Epidemiol Biomarkers Prev 16: 2686-2696, 2007.
39. Syeed N, Hussain F, Husain SA and Siddiqi MA: 5′-CpG island promoter hypermethylation of the CAV-1 gene in breast cancer patients of Kashmir. Asian Pac J Cancer Prev 13: 371-375, 2012.
40. Sen M, Ozdemir O, Turan M, Arici S, Yildiz F, Koksal B and Goze F: Epigenetic inactivation of tumor suppressor SFRP2 and point mutation in KRAS proto-oncogene in fistula-associated mucinous type anal adenocarcinoma: Report of two cases. Intern Med 49: 1637-1640, 2010.
41. Lee SM, Park JY and Kim DS: Methylation of TMEFF2 gene in tissue and serum DNA from patients with non-small cell lung cancer. Mol Cells 34: 171-176, 2012.
42. Jin Z, Mori Y, Hamilton JP, Olaru A, Sato F, Yang J, Ito T, Kan T, Agarwal R and Meltzer SJ: Hypermethylation of the somatostatin promoter is a common, early event in human esophageal carcino-genesis. Cancer 112: 43-49, 2008.
43. Beggs AD, Jones A, Shepherd N, Arnaout A, Finlayson C, Abulafi AM, Morton DG, Matthews GM, Hodgson SV and Tomlinson IP: Loss of expression and promoter methylation of SLIT2 are associated with sessile serrated adenoma formation. PLoS Genet 9: e1003488, 2013.
44. Senchenko VN, Krasnov GS, Dmitriev AA, Kudryavtseva AV, Anedchenko EA, Braga EA, Pronina IV, Kondratieva TT, Ivanov SV, Zabarovsky ER, et al: Differential expression of CHL1 gene during development of major human cancers. PLoS One 6: e15612, 2011.
45. Cai LY, Abe M, Izumi S, Imura M, Yasugi T and Ushijima T: Identification of PRTFDC1 silencing and aberrant promoter methylation of GPR150, ITGA8 and HOXD11 in ovarian cancers. Life Sci 80: 1458-1465, 2007.
46. Bovolenta P, Esteve P, Ruiz JM, Cisneros E and Lopez-Rios J: Beyond Wnt inhibition: New functions of secreted Frizzled-related proteins in development and disease. J Cell Sci 121: 737-746, 2008.
47. MacDonald BT, Tamai K and He X: Wnt/beta-catenin signaling: Components, mechanisms, and diseases. Dev Cell 17: 9-26, 2009.
48. Qi J, Zhu YQ, Luo J and Tao WH: Hypermethylation and expression regulation of secreted frizzled-related protein genes in colorectal tumor. World J Gastroenterol 12: 7113-7117, 2006.
49. Bakowska JC, Jupille H, Fatheddin P, Puertollano R and Blackstone C: Troyer syndrome protein spartin is mono-ubiquitinated and functions in EGF receptor trafficking. Mol Biol Cell 18: 1683-1692, 2007.
50. Hooper C, Puttamadappa SS, Loring Z, Shekhtman A and Bakowska JC: Spartin activates atrophin-1-interacting protein 4 (AIP4) E3 ubiquitin ligase and promotes ubiquitination of adipophilin on lipid droplets. BMC Biol 8: 72, 2010.
51. Urdinguio RG, Sanchez-Mut JV and Esteller M: Epigenetic mechanisms in neurological diseases: Genes, syndromes, and therapies. Lancet Neurol 8: 1056-1072, 2009.
52. White WM, Brost B, Sun Z, Rose C, Craici I, Wagner SJ, Turner ST and Garovic VD: Genome-wide methylation profiling demonstrates hypermethylation in maternal leukocyte DNA in preeclamptic compared to normotensive pregnancies. Hypertens Pregnancy 32: 257-269, 2013.
53. Shen J, Wang S, Zhang YJ, Kappil M, Wu HC, Kibriya MG, Wang Q, Jasmine F, Ahsan H, Lee PH, et al: Genome-wide DNA methylation profiles in hepatocellular carcinoma. Hepatology 55: 1799-1808, 2012.
54. Stahl JM, Sharma A, Cheung M, Zimmerman M, Cheng JQ, Bosenberg MW, Kester M, Sandirasegarane L and Robertson GP: Deregulated Akt3 activity promotes development of malignant melanoma. Cancer Res 64: 7002-7010, 2004.
55. Mure H, Matsuzaki K, Kitazato KT, Mizobuchi Y, Kuwayama K, Kageji T and Nagahiro S: Akt2 and Akt3 play a pivotal role in malignant gliomas. Neuro Oncol 12: 221-232, 2010.
56. Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Soldà G, Simons C, et al: Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18: 1433-1445, 2008.
57. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, et al: Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 106: 11667-11672, 2009.
58. Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, Song JJ, Kingston RE, Borowsky M and Lee JT: Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell 40: 939-953, 2010.
59. Amaral PP, Clark MB, Gascoigne DK, Dinger ME and Mattick JS: lncRNAdb: A reference database for long noncoding RNAs. Nucleic Acids Res 39: D146-D151, 2011.
60. Kibler K, Svetz J, Nguyen TL, Shaw C and Shaulsky G: A cell-adhesion pathway regulates intercellular communication during Dictyostelium development. Dev Biol 264: 506-521, 2003.
61. Juliano RL: Signal transduction by cell adhesion receptors and the cytoskeleton: Functions of integrins, cadherins, selectins, and immunoglobulin-superfamily members. Annu Rev Pharmacol Toxicol 42: 283-323, 2002.
62. Beckman M: CAMs are stopping cancer in its metastatic tracks. J Natl Cancer Inst 98: 576-577, 2006.
63. Conacci-Sorrell ME, Ben-Yedidia T, Shtutman M, Feinstein E, Einat P and Ben-Ze'ev A: Nr-CAM is a target gene of the beta-catenin/LEF-1 pathway in melanoma and colon cancer and its expression enhances motility and confers tumorigenesis. Genes Dev 16: 2058-2072, 2002.
64. Li S, Jo YS, Lee JH, Min JK, Lee ES, Park T, Kim JM and Hong HJ: L1 cell adhesion molecule is a novel independent poor prognostic factor of extrahepatic cholangiocarcinoma. Clin Cancer Res 15: 7345-7351, 2009.