Comparative and integrative analysis of transcriptomic and epigenomic-wide DNA methylation changes in African American prostate cancer

References

• DeSantis CE, Siegel RL, Sauer AG, et al. Cancer statistics for African Americans, 2016: progress and opportunities in reducing racial disparities. CA Cancer J Clin. 2016;66(4):290–14.
   PubMed Web of Science ®Google Scholar
• Ward E, Jemal A, Cokkinides V, et al. Cancer disparities by race/ethnicity and socioeconomic status. CA Cancer J Clin. 2004;54(2):78–93.
   PubMed Web of Science ®Google Scholar
• Hoffman RM, Gilliland FD, Eley JW, et al. Racial and ethnic differences in advanced-stage prostate cancer: the prostate cancer outcomes study. J Natl Cancer Inst. 2001;93(5):388–395.
   PubMed Web of Science ®Google Scholar
• Mahal BA, Aizer AA, Ziehr DR, et al. Trends in disparate treatment of African American men with localized prostate cancer across National Comprehensive cancer network risk groups. Urology. 2014;84(2):386–392.
   PubMed Web of Science ®Google Scholar
• Mahal BA, Berman RA, Taplin ME, et al. Prostate cancer-specific mortality across gleason scores in black vs nonblack men. JAMA. 2018;320(23):2479–2481.
   PubMed Web of Science ®Google Scholar
• Baca SC, Prandi D, Lawrence MS, et al. Punctuated evolution of prostate cancer genomes. Cell. 2013;153(3):666–677.
   PubMed Web of Science ®Google Scholar
• Barbieri CE, Demichelis F, Rubin MA. Molecular genetics of prostate cancer: emerging appreciation of genetic complexity. Histopathology. 2012;60(1):187–198.
   PubMed Web of Science ®Google Scholar
• Berger MF, Lawrence MS, Demichelis F, et al. The genomic complexity of primary human prostate cancer. Nature. 2011;470(7333):214–220.
   PubMed Web of Science ®Google Scholar
• Taylor BS, Schultz N, Hieronymus H, et al. Integrative genomic profiling of human prostate cancer. Cancer Cell. 2010;18(1):11–22. [published Online First: 20100624].
   PubMed Web of Science ®Google Scholar
• Hieronymus H, Schultz N, Gopalan A, et al. Copy number alteration burden predicts prostate cancer relapse. Proc Natl Acad Sci U S A. 2014;111(30):11139–11144. [published Online First: 20140714].
   PubMed Web of Science ®Google Scholar
• Barbieri CE, Baca SC, Lawrence MS, et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet. 2012;44(6):685–689. [published Online First: 20120520].
   PubMed Web of Science ®Google Scholar
• Tomlins SA, Bjartell A, Chinnaiyan AM, et al. ETS gene fusions in prostate cancer: from discovery to daily clinical practice. Eur Urol. 2009;56(2):275–286. [published Online First: 20090424].
   PubMed Web of Science ®Google Scholar
• Carter HB, Albertsen PC, Barry MJ, et al. Early detection of prostate cancer: AUA Guideline. J Urol. 2013;190(2):419–426. [published Online First: 20130506].
   PubMed Web of Science ®Google Scholar
• Khani F, Mosquera JM, Park K, et al. Evidence for molecular differences in prostate cancer between African American and Caucasian men. Clin Cancer Res. 2014;20(18):4925–4934.
   PubMed Web of Science ®Google Scholar
• Shivapurkar N, Gazdar AF. DNA methylation based biomarkers in non-invasive cancer screening. Curr Mol Med. 2010;10(2):123–132.
   PubMed Web of Science ®Google Scholar
• Bree KK, Hensley PJ, Pettaway CA. Germline Predisposition to prostate cancer in diverse populations. Urol Clin North Am. 2021;48(3):411–423.
   PubMed Web of Science ®Google Scholar
• Borno ST, Fischer A, Kerick M, et al. Genome-wide DNA methylation events in TMPRSS2-ERG fusion-negative prostate cancers implicate an EZH2-dependent mechanism with miR-26a hypermethylation. Cancer Discov. 2012;2(11):1024–1035.
   PubMed Web of Science ®Google Scholar
• Mahapatra S, Klee EW, Young CY, et al. Global methylation profiling for risk prediction of prostate cancer. Clin Cancer Res. 2012;18(10):2882–2895.
   PubMed Web of Science ®Google Scholar
• Herman JG, Baylin SB. Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med. 2003;349(21):2042–2054.
   PubMed Web of Science ®Google Scholar
• Baylin SB, Jones PA. A decade of exploring the cancer epigenome - biological and translational implications. Nat Rev Cancer. 2011;11(10):726–734. [published Online First: 20110923].
   PubMed Web of Science ®Google Scholar
• Lin X, Tascilar M, Lee WH, et al. GSTP1 CpG island hypermethylation is responsible for the absence of GSTP1 expression in human prostate cancer cells. Am J Pathol. 2001;159(5):1815–1826.
   PubMed Web of Science ®Google Scholar
• Woodson K, O’Reilly KJ, Hanson JC, et al. The usefulness of the detection of GSTP1 methylation in urine as a biomarker in the diagnosis of prostate cancer. J Urol. 2008;179(2):508–511. discussion 11-2.
   PubMed Web of Science ®Google Scholar
• Jeronimo C, Henrique R, Hoque MO, et al. A quantitative promoter methylation profile of prostate cancer. Clin Cancer Res. 2004;10(24):8472–8478.
   PubMed Web of Science ®Google Scholar
• Locke WJ, Guanzon D, Ma C, et al. DNA methylation cancer biomarkers: translation to the clinic. Front Genet. 2019;10:1150. [published Online First: 20191114].
   PubMed Web of Science ®Google Scholar
• Massie CE, Mills IG, Lynch AG. The importance of DNA methylation in prostate cancer development. J Steroid Biochem Mol Biol. 2017;166:1–15. [published Online First: 20160424].
   PubMed Web of Science ®Google Scholar
• Lee WH, Morton RA, Epstein JI, et al. Cytidine methylation of regulatory sequences near the pi-class glutathione S-transferase gene accompanies human prostatic carcinogenesis. Proc Natl Acad Sci U S A. 1994;91(24):11733–11737.
   PubMed Web of Science ®Google Scholar
• Mian OY, Khattab MH, Hedayati M, et al. GSTP1 Loss results in accumulation of oxidative DNA base damage and promotes prostate cancer cell survival following exposure to protracted oxidative stress. Prostate. 2016;76(2):199–206. [published Online First: 20151008].
   PubMed Web of Science ®Google Scholar
• Geybels MS, Zhao S, Wong CJ, et al. Epigenomic profiling of DNA methylation in paired prostate cancer versus adjacent benign tissue. Prostate. 2015;75(16):1941–1950. [published Online First: 20150918].
   PubMed Web of Science ®Google Scholar
• Kobayashi Y, Absher DM, Gulzar ZG, et al. DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer. Genome Res. 2011;21(7):1017–1027. [published Online First: 20110426].
   PubMed Web of Science ®Google Scholar
• Partin AW, Van Neste L, Klein EA, et al. Clinical validation of an epigenetic assay to predict negative histopathological results in repeat prostate biopsies. J Urol. 2014;192(4):1081–1087. [published Online First: 20140418].
   PubMed Web of Science ®Google Scholar
• Partin AW, Criekinge WA, Trock BJ, et al. Clinical evaluation of an epigenetic assay to predict missed cancer in prostate biopsy specimens. Trans Am Clin Climatol Assoc. 2016;127:313–327.
   PubMedGoogle Scholar
• Woodson K, Hayes R, Wideroff L, et al. Hypermethylation of GSTP1, CD44, and E-cadherin genes in prostate cancer among US blacks and whites. Prostate. 2003;55(3):199–205.
   PubMed Web of Science ®Google Scholar
• Woodson K, Hanson J, Tangrea J. A survey of gene-specific methylation in human prostate cancer among black and white men. Cancer Lett. 2004;205(2):181–188.
   PubMed Web of Science ®Google Scholar
• Enokida H, Shiina H, Urakami S, et al. Ethnic group-related differences in CpG hypermethylation of the GSTP1 gene promoter among African-American, Caucasian and Asian patients with prostate cancer. Int J Cancer. 2005;116(2):174–181.
   PubMed Web of Science ®Google Scholar
• Das PM, Ramachandran K, Vanwert J, et al. Methylation mediated silencing of TMS1/ASC gene in prostate cancer. Mol Cancer. 2006;5:28. [published Online First: 20060718].
   PubMed Web of Science ®Google Scholar
• Kwabi-Addo B, Wang S, Chung W, et al. Identification of differentially methylated genes in normal prostate tissues from African American and Caucasian men. Clin Cancer Res. 2010;16(14):3539–3547. [published Online First: 20100706].
   PubMed Web of Science ®Google Scholar
• Tang D, Kryvenko ON, Mitrache N, et al. Methylation of the RARB gene increases prostate cancer risk in black Americans. J Urol. 2013;190(1):317–324. [published Online First: 20130130].
   PubMed Web of Science ®Google Scholar
• Sharad S, Ravindranath L, Haffner MC, et al. Methylation of the PMEPA1 gene, a negative regulator of the androgen receptor in prostate cancer. Epigenetics. 2014;9(6):918–927. [published Online First: 20140402].
   PubMed Web of Science ®Google Scholar
• Devaney JM, Wang S, Furbert-Harris P, et al. Genome-wide differentially methylated genes in prostate cancer tissues from African-American and Caucasian men. Epigenetics. 2015;10(4):319–328. [published Online First: 20150411].
   PubMed Web of Science ®Google Scholar
• Ittmann M, Wieczorek R, Heller P, et al. Alterations in the p53 and MDM-2 genes are infrequent in clinically localized, stage B prostate adenocarcinomas. Am J Pathol. 1994;145(2):287–293.
   PubMed Web of Science ®Google Scholar
• Zhang L, Wang J, Wang Y, et al. MNX1 is oncogenically upregulated in African-American prostate cancer. Cancer Res. 2016;76(21):6290–6298.
   PubMed Web of Science ®Google Scholar
• Creighton CJ, Nagaraja AK, Hanash SM, et al. A bioinformatics tool for linking gene expression profiling results with public databases of microRNA target predictions. RNA. 2008;14(11):2290–2296. [published Online First: 20080923].
   PubMed Web of Science ®Google Scholar
• Saldanha AJ. Java Treeview–extensible visualization of microarray data. Bioinformatics. 2004;20(17):3246–3248. [published Online First: 20040604].
   PubMed Web of Science ®Google Scholar
• Cancer Genome Atlas Research Network. The molecular taxonomy of primary prostate cancer. Cell. 2015;163:1011–1025.
   PubMed Web of Science ®Google Scholar
• Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13(7):484–492. [published Online First: 20120529].
   PubMed Web of Science ®Google Scholar
• Baylin SB, Herman JG, Graff JR, et al. Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv Cancer Res. 1998;72:141–196.
   PubMed Web of Science ®Google Scholar
• Stopsack KH, Nandakumar S, Arora K, et al. Differences in prostate cancer genomes by self-reported race: contributions of genetic ancestry, modifiable cancer risk factors, and clinical factors. Clin Cancer Res. 2021. DOI:10.1158/1078-0432.CCR-21-2577. [published Online First: 20211019].
   Web of Science ®Google Scholar
• Martin DN, Starks AM, Ambs S. Biological determinants of health disparities in prostate cancer. Curr Opin Oncol. 2013;25(3):235–241.
   PubMed Web of Science ®Google Scholar
• Lara OD, Wang Y, Asare A, et al. Pan-cancer clinical and molecular analysis of racial disparities. Cancer. 2020;126(4):800–807. [published Online First: 20191115].
   PubMed Web of Science ®Google Scholar
• Wang BD, Ceniccola K, Yang Q, et al. Identification and functional validation of reciprocal microRNA-mRNA pairings in African American prostate cancer disparities. Clin Cancer Res. 2015;21(21):4970–4984. [published Online First: 20150618].
   PubMed Web of Science ®Google Scholar
• Spratt DE, Chan T, Waldron L, et al. Racial/Ethnic Disparities in Genomic Sequencing. JAMA Oncol. 2016;2(8):1070–1074.
   PubMed Web of Science ®Google Scholar
• Fan X, Shao L, Fang H, et al. Cross-platform comparison of microarray-based multiple-class prediction. PLoS One. 2011;6(1):e16067. [published Online First: 20110111].
   PubMed Web of Science ®Google Scholar
• Yauk CL, Berndt ML, Williams A, et al. Comprehensive comparison of six microarray technologies. Nucleic Acids Res. 2004;32(15):e124. [published Online First: 20040827].
   PubMed Web of Science ®Google Scholar
• Lorincz MC, Dickerson DR, Schmitt M, et al. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat Struct Mol Biol. 2004;11(11):1068–1075. [published Online First: 20041003].
   PubMed Web of Science ®Google Scholar
• Kornblihtt AR. Chromatin, transcript elongation and alternative splicing. Nat Struct Mol Biol. 2006;13(1):5–7.
   PubMed Web of Science ®Google Scholar
• Suzuki MM, Bird A. DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet. 2008;9(6):465–476.
   PubMed Web of Science ®Google Scholar
• Sahu B, Laakso M, Pihlajamaa P, et al. FoxA1 specifies unique androgen and glucocorticoid receptor binding events in prostate cancer cells. Cancer Res. 2013;73(5):1570–1580. [published Online First: 20121226].
   PubMed Web of Science ®Google Scholar
• Arora VK, Schenkein E, Murali R, et al. Glucocorticoid receptor confers resistance to antiandrogens by bypassing androgen receptor blockade. Cell. 2013;155(6):1309–1322.
   PubMed Web of Science ®Google Scholar
• Tang H, Qiao J, Fu YX. Immunotherapy and tumor microenvironment. Cancer Lett. 2016;370(1):85–90. [published Online First: 20151019].
   PubMed Web of Science ®Google Scholar