Differential DNA Methylation Landscape in Skin Fibroblasts from African Americans with Systemic Sclerosis

Genes

E.Starr Hazard¹  JamesC. Oates²  Carol Feghali-Bostwick²  Ilia Atanelishvili²  GalinaS. Bogatkevich²  DeAnnaBaker Frost²  Jonathan Flume²  PaulaS. Ramos²  RobertC. Wilson³  Willianda Silveira⁴  Gary Hardiman⁴  KayleighL. Day⁵ 

[1] Computational Biology Resource Center, Medical University of South Carolina, Charleston, SC 29425, USA;Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA;Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast BT9 5DL, UK;Stevenson University, Stevenson, MD 21117, USA;

关键词: systemic sclerosis;    African American;    DNA methylation;    genome;    skin fibroblasts;   

DOI  :  10.3390/genes12020129

来源: DOAJ

【 摘 要 】

The etiology and reasons underlying the ethnic disparities in systemic sclerosis (SSc) remain unknown. African Americans are disproportionally affected by SSc and yet are 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. Reduced representation bisulfite sequencing (RRBS) was performed on primary 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. The dermal 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. Gene set enrichment analysis (GSEA) and gene ontology (GO) analyses revealed an enrichment of pathways related to interferon signaling and mesenchymal differentiation. The hypomethylation of DLX5 and TMEM140 was accompanied by these genes’ overexpression in patients but underexpression for lncRNA MGC12916. These data show that differential methylation occurs in dermal fibroblasts from African American patients with SSc and identifies novel coding and non-coding genes.

【 授权许可】

Unknown