Validation study of genes with hypermethylated promoter regions associated with prostate cancer recurrence

Cancer Epidemiology Biomarkers and Prevention

Volumn 23, Issue 7, 2014, Pages 1331-1339

  Stott Miller, Marni ^a   Zhao, Shanshan ^a   Wright, Jonathan L ^a,b   Kolb, Suzanne ^a   Bibikova, Marina ^d   Klotzle, Brandy ^d   Ostrander, Elaine A ^e   Fan, Jian Bing ^d   Feng, Ziding ^a,c   Stanford, Janet L ^a,c  

^a Fred Hutchinson Cancer Research Center   (United States)

^b UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

^d ILLUMINA INC   (United States)

^e NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROSTATE SPECIFIC ANTIGEN; EPHX3 PROTEIN, HUMAN; EPOXIDE HYDROLASE; HOMEODOMAIN PROTEIN; HOXA4 PROTEIN, HUMAN;

ABHD9 GENE; ADULT; ADVANCED CANCER; AGED; APC GENE; ARTICLE; ASC GENE; CANCER LOCALIZATION; CANCER PATIENT; CANCER RECURRENCE; CANCER SURVIVAL; CANCER TISSUE; CD44 GENE; CDH13 GENE; CONTROLLED STUDY; CPG ISLAND; DNA EXTRACTION; DNA METHYLATION; FOLLOW UP; GENE; GENETIC LINKAGE; GENETIC SELECTION; GLEASON SCORE; GPR7 GENE; GSTP1 GENE; HEALTH SURVEY; HOXD3 GENE; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; MALE; MDR1 GENE; MEDICAL RECORD REVIEW; ONCOGENE; PITX2 GENE; PRIORITY JOURNAL; PROMOTER REGION; PROSTATE CANCER; PROSTATECTOMY; PTGS2 GENE; RARBETA GENE; RASSF1A GENE; RECURRENCE FREE SURVIVAL; RUNX3 GENE; VALIDATION STUDY; DNA MICROARRAY; GENETICS; MIDDLE AGED; PATHOLOGY; PROSTATE TUMOR; TUMOR RECURRENCE;

AGED; DNA METHYLATION; EPOXIDE HYDROLASES; HOMEODOMAIN PROTEINS; HUMANS; MALE; MIDDLE AGED; NEOPLASM RECURRENCE, LOCAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; PROSTATIC NEOPLASMS;

EID: 84903948240     PISSN: 10559965     EISSN: None     Source Type: Journal    
DOI: 10.1158/1055-9965.EPI-13-1000     Document Type: Article

References (52)

1. Siegel R, Naishadham D, Jemal A. Cancer statistics, 2013. CA Cancer J Clin 2013;63: 11-0.
2. Isaacs JT, Yang SS, Warner HR. Prostate cancer: an age-old problem. The underlying molecular, cellular, and immunological factors in cancer. New York: Plenum Press; 1993. p. 167-84.
3. Sakr WA, Haas GP, Cassin BF, Pontes JE, Crissman JD. The frequency of carcinoma and intraepithelial neoplasia of the prostate in young male patients. J Urol 1993;150: 379-5.
4. Siegel R, Ward E, Brawley O, Jemal A. Cancer statistics, 2011: the impact of eliminating socioeconomic and racial disparities on premature cancer deaths. CA Cancer J Clin 2011;61: 212-6.
5. Herman JG, Baylin SB. Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med 2003;349: 2042-4.
6. Baylin SB, Herman JG. DNA hypermethylation in tumorigenesis: epigenetics joins genetics. Trends Genet 2000;16: 168-74.
7. Chiam K, Ricciardelli C, Bianco-Miotto T. Epigenetic biomarkers in prostate cancer: current and future uses. Cancer Lett 2012;342: 248-6.
8. Mahapatra S, Klee EW, Young CY, Sun Z, Jimenez RE, Klee GG, et al. Global methylation profiling for risk prediction of prostate cancer. Clin Cancer Res 2012;18: 2882-95.
9. Kobayashi Y, Absher DM, Gulzar ZG, Young SR, McKenney JK, Peehl DM, et al. DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer. Genome Res 2011;21: 1017-7.
10. Cottrell S, Jung K, Kristiansen G, Eltze E, Semjonow A, Ittmann M, et al. Discovery and validation of 3 novel DNA methylation markers of prostate cancer prognosis. J Urol 2007;177: 1753-8.
11. Richiardi L, Fiano V, Vizzini L, De Marco L, Delsedime L, Akre O, et al. Promoter methylation in APC, RUNX3, and GSTP1 and mortality in prostate cancer patients. J Clin Oncol 2009;27: 3161-8.
12. Weiss G, Cottrell S, Distler J, Schatz P, Kristiansen G, Ittmann M, et al. DNA methylation of the PITX2 gene promoter region is a strong independent prognostic marker of biochemical recurrence in patients with prostate cancer after radical prostatectomy. J Urol 2009;181: 1678-5.
13. Alumkal JJ, Zhang Z, Humphreys EB, Bennett C, Mangold LA, Carducci MA, et al. Effect of DNA methylation on identification of aggressive prostate cancer. Urology 2008;72: 1234-9.
14. Kron KJ, Liu L, Pethe VV, Demetrashvili N, Nesbitt ME, Trachtenberg J, et al. DNA methylation of HOXD3 as a marker of prostate cancer progression. Lab Invest 2010;90: 1060-7.
15. Bastian PJ, Ellinger J, Wellmann A, Wernert N, Heukamp LC, Muller SC, et al. Diagnostic and prognostic information in prostate cancer with the help of a small set of hypermethylated gene loci. Clin Cancer Res 2005;11: 4097-6.
16. Rosenbaum E, Hoque MO, Cohen Y, Zahurak M, Eisenberger MA, Epstein JI, et al. Promoter hypermethylation as an independent prognostic factor for relapse in patients with prostate cancer following radical prostatectomy. Clin Cancer Res 2005;11: 8321-5.
17. Bastian PJ, Ellinger J, Heukamp LC, Kahl P, Muller SC, von Rucker A. Prognostic value of CpG island hypermethylation at PTGS2, RARbeta, EDNRB, and other gene loci in patients undergoing radical prostatectomy. Eur Urol 2007;51: 665-74.
18. Liu L, Kron KJ, Pethe VV, Demetrashvili N, Nesbitt ME, Trachtenberg J, et al. Association of tissue promoter methylation levels of APC, TGFbeta2, HOXD3, and RASSF1A with prostate cancer progression. Int J Cancer 2011;129: 2454-62.
19. Henrique R, Ribeiro FR, Fonseca D, Hoque MO, Carvalho AL, Costa VL, et al. High promoter methylation levels of APC predict poor prognosis in sextant biopsies from prostate cancer patients. Clin Cancer Res 2007;13: 6122-9.
20. Woodson K, O'Reilly KJ, Ward DE, Walter J, Hanson J, Walk EL, et al. CD44 and PTGS2 methylation are independent prognostic markers for biochemical recurrence among prostate cancer patients with clinically localized disease. Epigenetics 2006;1: 183-6.
21. Kito H, Suzuki H, Ichikawa T, Sekita N, Kamiya N, Akakura K, et al. Hypermethylation of the CD44 gene is associated with progression and metastasis of human prostate cancer. Prostate 2001;49: 110-5.
22. Banez LL, Sun L, van Leenders GJ, Wheeler TM, Bangma CH, Freedland SJ, et al. Multicenter clinical validation of PITX2 methylation as a prostate specific antigen recurrence predictor in patients with postradical prostatectomy prostate cancer. J Urol 2010;184: 149-6.
23. Enokida H, Shiina H, Igawa M, Ogishima T, Kawakami T, Bassett WW, et al. CpG hypermethylation of MDR1 gene contributes to the pathogenesis and progression of human prostate cancer. Cancer Res 2004;64: 5956-62.
24. Maruyama R, Toyooka S, Toyooka KO, Virmani AK, Zochbauer-Muller S, Farinas AJ, et al. Aberrant promoter methylation profile of prostate cancers and its relationship to clinicopathological features. Clin Cancer Res 2002;8: 514-9.
25. Cho NY, Kim BH, Choi M, Yoo EJ, Moon KC, Cho YM, et al. Hypermethylation of CpG island loci and hypomethylation of LINE-1 and Alu repeats in prostate adenocarcinoma and their relationship to clinicopathological features. J Pathol 2007;211: 269-77.
26. Singal R, Ferdinand L, Reis IM, Schlesselman JJ. Methylation of multiple genes in prostate cancer and the relationship with clinicopathological features of disease. Oncol Rep 2004;12: 631-7.
27. Kron K, Pethe V, Briollais L, Sadikovic B, Ozcelik H, Sunderji A, et al. Discovery of novel hypermethylated genes in prostate cancer using genomic CpG island microarrays. PLoS ONE 2009;4: e4830.
28. Stanford JL, Wicklund KG, McKnight B, Daling JR, Brawer MK. Vasectomy and risk of prostate cancer. Cancer Epidemiol Biomarkers Prev 1999;8: 881-6.
29. Agalliu I, Salinas CA, Hansten PD, Ostrander EA, Stanford JL. Statin use and risk of prostate cancer: results from a population-based epidemiologic study. Am J Epidemiol 2008;168: 250-60.
30. Fritz A, Ries L. SEER program code manual. 3rd ed. Bethesda, MD: NIH; 1998. Available from: http://seer.cancer.gov/manuals/codeman.pdf.
31. Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le J, et al. High density DNA methylation array with single CpG site resolution. Genomics 2011;98: 288-95.
32. Woodson K, Hayes R, Wideroff L, Villaruz L, Tangrea J. Hypermethylation of GSTP1, CD44, and E-cadherin genes in prostate cancer among US Blacks and Whites. Prostate 2003;55: 199-05.
33. Zhang FF, Cardarelli R, Carroll J, Fulda KG, Kaur M, Gonzalez K, et al. Significant differences in global genomic DNA methylation by gender and race/ethnicity in peripheral blood. Epigenetics 2011; 6: 623-9.
34. Hansen K, Aryee M. minfi: analyze Illumina's 450k methylation arrays. R Package Version 1.2.0.
35. R Development Core Team (2012). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-7-0. Available from: http://www.R-project. org/.
36. Maksimovic J, Gordon L, Oshlack A. SWAN: subset-quantile within array normalization for illumina infinium HumanMethylation450 Bead-Chips. Genome Biol 2012;13: R44.
37. System Controls. GenomeStudio Methylation Module v18 User Guide. 233-4.
38. Yamashita S, Tsujino Y, Moriguchi K, Tatematsu M, Ushijima T. Chemical genomic screening for methylation-silenced genes in gastric cancer cell lines using 5-Aza-0-deoxycytidine treatment and oligonucleotide microarray. Cancer Sci 2006;97: 64-71.
39. Apiou F, Flagiello D, Cillo C, Malfoy B, Poupon MF, Dutrillaux B. Fine mapping of human HOX gene clusters. Cytogenet Cell Genet 1996;73: 114-5.
40. Cillo C, Cantile M, Faiella A, Boncinelli E. Homeobox genes in normal and malignant cells. J Cell Physiol 2001;188: 161-9.
41. Ewing CM, Ray AM, Lange EM, Zuhlke KA, Robbins CM, Tembe WD, et al.Germline mutations in HOXB13 and prostate-cancer risk.NEngl J Med 2012;366: 141-9.
42. Breyer JP, Avritt TG, McReynolds KM, Dupont WD, Smith Jr. Confirmation of the HOXB13 G84E germline mutation in familial prostate cancer. Cancer Epidemiol Biomarkers Prev 2012;21: 1348-3.
43. Karlsson R, Aly M, Clements M, Zheng L, Adolfsson J, Xu J, et al. A population-based assessment of germline HOXB13 G84E mutation and prostate cancer risk. Eur Urol 2014;65: 169-76.
44. Stott-Miller M, KaryadiDM, King T,KwonEM, Kolb S, Stanford JL, et al. HOXB13 mutations in a population-based, case control study of prostate cancer. Prostate 2013;73: 634-1.
45. Xu J, Lange EM, Lu L, Zheng SL,WangZ, Thibodeau SN, et al.HOXB13 is a susceptibility gene for prostate cancer: results from the International Consortium for Prostate Cancer Genetics (ICPCG). Hum Genet 2013;132: 5-4.
46. Singh D, Febbo PG, Ross K, Jackson DG, Manola J, Ladd C, et al. Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 2002;1: 203-9.
47. Pfeifer GP, Rauch TA. DNA methylation patterns in lung carcinomas. Semin Cancer Biol 2009;19: 181-7.
48. Rauch T, Li H, Wu X, Pfeifer GP. MIRA-Assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res 2006;66: 7939-7.
49. Tommasi S, Karm DL, Wu X, Yen Y, Pfeifer GP. Methylation of homeobox genes is a frequent and early epigenetic event in breast cancer. Breast Cancer Res 2009;11: R14.
50. Irizarry RA, Ladd-Acosta C,WenB,WuZ, Montano C, Onyango P, et al. The human colon cancer methylome shows similar hypo-And hypermethylation at conserved tissue-specific GpC island shores. Nat Genet 2009;41: 178-86.
51. Timp W, Fineberg AP. Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host. Nat Rev Cancer 2013;13: 497-10.
52. Uchio EM, Aslan M, Wells CK, Calderone J, Concato J. Impact of biochemical recurrence in prostate cancer among US veterans. Arch Intern Med 2010;170: 1390-5.