Differential DNA methylation landscape in skin fibroblasts from African Americans with systemic sclerosis

ABSTRACT Objective The etiology and reasons underlying the ethnic disparities in systemic sclerosis (SSc) remain unknown. African Americans are disproportionally affected by SSc, yet underrepresented in research. The aim of this study was to comprehensively investigate the association of DNA methylation levels with SSc in dermal fibroblasts from patients of African ancestry. Methods Reduced representation bisulfite sequencing (RRBS) was performed on primary cultured dermal fibroblasts from 15 SSc patients and 15 controls of African ancestry, and over 3.8 million CpG sites were tested for differential methylation patterns between cases and controls. Gene set enrichment (GSEA) and gene ontology (GO) analyses were computed to elucidate the underlying biological processes. Quantitative PCR (qPCR) was performed to assess correlations between DNA methylation changes and gene expression levels of top candidate genes. Results Skin fibroblasts from African American patients exhibited widespread reduced DNA methylation. Differentially methylated CpG sites were most enriched in introns and intergenic regions, while depleted in 5’ UTR, promoters, and CpG islands. Seventeen genes and eleven promoters showed significant differential methylation, mostly in non-coding RNA genes and pseudogenes. GSEA and GO enrichment analysis revealed enrichment of immune, metabolism, cell development, and cell signaling pathways, including those related to interferon signaling and mesenchymal differentiation. The hypomethylation of DLX5 and TMEM140 was accompanied by these genes’ overexpression, while for the IncRNA MGC12916 , it was accompanied by its under-expression in patients. Conclusion These data show that differential methylation occurs in dermal fibroblasts from African American patients with SSc and identifies novel coding and non-coding genes.