Increased stromal ERV methylation in African American compared to European American prostate cancer patients: Enrichment on chromosome 19

Background : African American (AA) men experience worse prostate cancer (PCa) outcomes than European American (EA) men, including higher PSA levels, larger tumors, earlier onset, and more aggressive disease progression. These disparities persist even after accounting for healthcare access and socioeconomic factors, suggesting underlying biological contributors. Endogenous retroviruses (ERVs), normally silenced through DNA methylation, have emerged as regulators of anti-tumor immune activity and as effective prognostic markers in PCa. Despite constituting 8% of the human, ERVs' role in the tumor microenvironment remains incompletely understood. In our previous study, pathways associated with anti-tumor immune activity were significantly more methylated and silenced in AA PCa patients in the tumor-adjacent stroma (TAS) compared to EA patients, indicating potential epigenetic differences that may contribute to observed disparities. Methods : We performed methyl-binding domain sequencing (MBD-seq) and RNA sequencing (RNA-seq) on TAS tissue from 17 AA and 15 EA PCa patients. Two custom bioinformatic pipelines were developed: one for ERV methylation analysis and another for ERV expression analysis. For methylation, sequencing reads were mapped to ERVs curated from the Human Endogenous Retrovirus Database (HERVd) to quantify locus-specific methylation. For expression, RNA-seq data were aligned to the same database to assess ERV expression profiles. ERV methylation patterns and their chromosomal distribution were visualized using chromoMap. Results: In tumor-adjacent stroma, African American patients demonstrated significantly higher global ERV methylation with lower expression, while European American patients exhibited reduced methylation with elevated transcriptional activity (p<0.05). ChromoMap and statistical analysis revealed non-random chromosomal distribution of methylated ERVs, with the most significant ancestry-related differences on chromosome 19 (AA: 2.09 vs. EA: 1.76, p<10⁻¹⁵⁹), which harbored the highest methylation levels, consistent with its enrichment for repetitive elements and ERV sequences. Chromosome Y showed no significant difference (p=0.148), potentially due to constitutive heterochromatin status across ancestries. Conclusion : In TAS, enhanced ERV silencing through hypermethylation in AA patients may represent a potential epigenetic mechanism contributing to disease aggressiveness through altered immune response genes. Conversely, hypomethylated and transcriptionally active ERVs in EA patients may enhance antitumor immune signaling, potentially explaining distinct clinical outcomes between populations.