Abstract B04: The use of whole genome methylation scanning to define genes preferentially suppressed in African American Prostate Cancer

Abstract

Abstract Background: The incidence of prostate cancer (PCa) is approximately 60% higher, and the mortality rate is 2 to 3 times greater, among African American men (AA) resident in the U.S. compared with American men with a European background (EA). Men of West African ancestry from the Caribbean and South America share similar incidence and mortality to AAs, suggesting a possible genetic and/or epigenetic contribution to these outcomes. We previously carried out a sensitive expression analysis comparing the expression of both tumor and tumor-adjacent stroma of AA and EA patients by Paired T-tests for matched (age, stage, grade, tumor content, stroma content) patients (1). Remarkably, 92% of expression differences between AA and EA occurred in the stroma component and of these 97% were in the direction of lower expression in AA compared to EA patients. The downregulated genes were dominated by immune regulatory and extracellular matrix genes. This suggests the possibility that decreased immune and inflammatory processes in tumor-adjacent stroma may be responsible for the aggressive nature of prostate cancer in AA patients (1). We have begun to test this possibility by examining whether the down regulated genes are methylated. Methods: Whole Genome FFPE Methylation and Transcriptome Profiling. We used archived FFPE samples where there is a potential to examine many patients. We are in the early methods-development stage of this project. One AA and two EA prostate cancer cases were matched for age, time to relapse/survival and Gleason score. A Norgen kit was used to obtain both DNA and RNA from the same sample. Methylated regions in each case were captured by methylated DNA ChIP using the human Methyl-CpG Binding Domain-2 (hMBD2) protein MBD2 then DNA purification followed by NGS. The transcriptome of tumor stroma was obtained using the TruSeq RNA access kit which is based on capture oligonucleotides to each exon to enrich RNA of coding regions. The method works for low amounts of highly degraded RNA isolated from low quality samples. The kit includes > 425,000 probes each constructed against NCBI377 hg19 reference genome, covering 98.3% of the RefSeq exome. The probes capture >210,000 targets, spanning 21,415 genes. Results: Our preliminary data show that one AA tumor-adjacent stroma has a greater number of hypermethylated regions than in tumor-adjacent stroma of two matched EA patients. Genome-wide methylation analysis revealed 5217 sites of significant (p < 0.001) hypermethylation in AA compared to EA, and 988 other sites of hypermethylation in EA compared AA PCa cases, indicating a marked increase in methylation in this one AA PCa case compared to the two EA cases. Within coding DNA the major classes of methylated genes included immune regulatory, interferon stimulated genes, and genes of the extracellular matrix. Our studies provide the first joint methylation and transcriptome analysis of PCa patients using FFPE samples and support the possibility that epigenetic alterations might be responsible for deficiencies in tumor immunity in AA PCa. Reference: Kinseth M, A., Z. Jia, et al., 2014. Int. J. Cancer 134: 81-91. DOI: 10.1002/ijc.28326. Citation Format: Farah Rahmatpanah, Kathleen McGuire, Michael Lilly, Michael McClelland, Dan Mercola. The use of whole genome methylation scanning to define genes preferentially suppressed in African American Prostate Cancer. [abstract]. In: Proceedings of the Ninth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2016 Sep 25-28; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2017;26(2 Suppl):Abstract nr B04.