Methylation correlates with suppressed expression of immunomodulatory genes in the tumor‐adjacent stroma of African American Prostate Cancer compared patients of European American ancestory

Abstract

BackgroundThe 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.Studies from our lab have indicated that stroma of tumor‐bearing prostate has thousands of significant RNA expression changes compared to normal tissue which correlate with age, grade, and outcome. These important properties of stroma have been exploited to develop biomarker panels (classifiers) from tumor‐associated stroma that reliably distinguish normal prostate from tumor‐bearing prostate or distinguish good outcome from bad outcome for individual patients. Our studies have identified hundreds of significant differences in gene expression in AA versus EA stroma (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. Altered immune/inflammatory processes in tumor‐adjacent stroma may be responsible for the aggressive nature of prostate cancer in AA patients (1).It is possible that differences in DNA methylation in specific genes of immune/inflammatory pathways could contribute, at least in part, to the generally more aggressive behavior of AA compared to EA PCa through suppressing immune response elements.MethodsThe methylation and expression status of tumor‐adjacent stroma was determined using archived FFPE samples from one AA and two EA prostate cancer cases using ChIP protocols for methylated CpG on a whole genome (NGS) basis. The AA and EA cases were matched for age, time to relapse/survival and Gleason score. Differentially methylated regions in each case were identified using methyl‐CpG binding domain of the human MBD2 protein combined with NGS. Transcriptome of tumor stroma was generated using the same exact cases. For the analysis of NGS data (Chip‐ Seq and RNA‐Seq) we used Strand NGS package.ResultsGenome‐wide methylation analysis revealed 4399 sites of significant (p < 0.001) hypermethylation in AA versus EA, and 899 sites of hypermethylation in EA versus AA PCa cases. Pathway analysis of 259 genes that were both methylated in this study and, simultaneously down regulated for RNA expression in tumor stroma of AA compared to EA identified by expression analysis of previous microarray data (1) showed significant enrichment (p < 0.05) of immune related pathways such as interleukins (IL) ‐17, ‐5, ‐11, ‐9 and microRNA targeted genes in leukocytes and lymphocytes, B‐cell receptor signaling and interferon type1 response pathways.ConclusionOur studies provide the first whole gene methylation analysis of PCa FFPE patients and provide insights into the global methylome of the tumor microenvironment of PCa in two different races. 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. The fact that many of the stroma‐associated hyper methylated and suppressed genes in AA PCa patients are associated with immune/‐inflammatory response pathways implies that epigenetic alterations might be responsible for deficiencies in tumor immunity in AA PCa.Kinseth et al (2014). Int J Cancer 134, 81–91.Support or Funding InformationNCI 1 U01 CA152738‐01 (PI: Mercola/C. Lee – Co‐Pis); 09/01/10–8/31/16. “The Prostate Cancer Tumor Microenvironment Exhibits Differentially Expressed Genes Useful for Diagnosis”DOD CDMRP (McClelland) 09/15/15–09/14/18Health disparities in African Americans Role: Principal Investigator. Major Goal: Studies of prostate stroma for prognosis.