The comparative methylome analysis of tumor microenvironment from African American and Non- White Hispanic American prostate cancer

We investigated differences in DNA methylation in tumor-adjacent stroma (TAS) of African Americans (AA) (n=17) and European Americans (EA) (n=15) to uncover differences that might contribute to a higher rate of aggressive prostate cancer (PCa) in AA men. We performed methyl binding domain sequencing (MBD-seq) on dissected FFPE tumor-adjacent stroma of both cohorts. To further investigate the tumor microenvironment methylome between AA and EA cohorts, we prepared carcinoma associated fibroblasts (CAFs) from fresh prostatectomy tissue of 3 AA and 4 EA patients. Prostate cancer tissues were examined to confirm the location of tumor and a 1-2 mm cube of tumor-adjacent stroma was removed. Frozen stocks of passages 1 to 6 primary cultures were prepared. At passage 6, a portion of the cells were placed in serum-free medium and incubated for 1 day. CAFs were cultured in the presence of PBS or low-dose (0.5 µM) 5AzaC . CAFs were treated with 5AzaC for 1 day, followed by culture for 10 days in drug-free medium. To investigate DNA methylation differences in TAS, PCa FFPE tissues from AA and EA cohorts were collected using IRB-approved protocols at the Baylor College of Medicine (BCM). Fresh prostatectomy tissue was obtained from Medical University of South Carolina (MUSC) to develop the cultured CAFs. Patient and clinical information was provided to study members as de-identified data elements.