Background: Biologic determinants of prostate cancer racial health disparities remain largely unknown. African American (AA) men are diagnosed with more aggressive prostate cancer than European American (EA) men despite presenting tumors with lower mutational burden, copy number alterations, and lacking ETS gene fusions. The purpose of our study is to investigate how DNA methylation alterations in the context of other molecular lesions contribute to aggressive prostate cancer in AA men.
Methods: We measured DNA methylation and gene expression in twelve radical prostatectomy specimens from AA patients treated at Roswell Park Cancer (RPCI) Institute by Infinium DNA methylation arrays and RNA-sequencing, respectively. Additional AA (n=22)/EA (n=5) patients from RPCI and AA (n=22)/EA (n=172) patients from The Cancer Genome Atlas (TCGA) were included in the clustering analysis to raise statistical power of our study. The MethylMix pipeline was applied to DNA methylation and gene expression to identify transcripts that are potentially regulated by DNA methylation.
Results: Unsupervised hierarchical clustering revealed 2 large clusters, Cluster1 (n=133) and Cluster3 (n=73). AA patients in Cluster1 presented with better overall survival (57 vs. 50 months, p=0.48) and disease-free time (47 vs. 22 months, p<0.05) compared to AA patients in Cluster3. We did not observe this difference in clinical outcomes for EA patients. Cluster3 consisted of hypomethylated CG sites belonging primarily to neurogenesis development and the Wnt/Hedgehog signaling pathways. TMPRSS2-ERG fusion status thought to drive aggressive prostate cancer was similar in all clusters. Interestingly, promoter DNA methylation of ERG gene was significantly lower at 5 CG sites (p<0.0001) and at 10 CG sites in the 5′-UTR region (p<0.0001) in fusion-positive EA patients as compared to fusion-negative EA patients. In tumors of AA patients, DNA methylation of ERG gene was significantly lower at 2 CG sites at the transcription start site (p<0.05) and at 1 CG site in the 5′-UTR region (p<0.05) in fusion-positive tumors as compared to fusion-negative tumors. Overall DNA methylation at the ERG negatively correlated with ERG gene expression (Pearson: -0.632). Furthermore, we used MethylMix algorithm that revealed DNA methylation as a potential negative regulator of genes involved in suppression of tumor invasion, glycosylation of mucin proteins, calcium sensing, and terminal differentiation specifically in AA patients. For a subset of these genes we observed altered transcript levels in AA tumor samples compared to EA tumor samples from the TCGA cohort. This included GALNT5 (-0.23 vs 0.15, p<0.05), STK39 (-0.30 vs 0.03, p<0.05), and TMEM63C (46.68 vs 22.65, p<0.05).
Conclusions: Our work reveals that there are epigenetic alterations found in prostate tumors that are specific to AA men. Moreover, this differential gene methylation may have subsequent impact on gene expression and contribute to more aggressive prostate cancer. We identified novel transcripts in AA patients that are potentially regulated by DNA methylation including ERG, GALNT5, STK39, and TMEM63C. Functional validation of these genes using prostate cancer models may provide insight into whether epigenetic regulation of these genomic loci are determinants of prostate cancer racial health disparities.
Citation Format: Swathi Ramakrishnan, Peng Xuan, Qianya Qi, Qiang Hu, Emily Ellman, Gissou Azabdaftari, Elena Pop, James Mohler, Kristopher Attwood, Yan Li, Jianmin Wang, Anna Woloszynska-Read. Epigenetic alterations as potential biologic determinants of racial health disparities [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr A003.