Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci

Abstract

Background Systemic sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the principle drivers of pathogenesis. Methods DNA samples exacted from CD4+ T cells of 48 SSc patients and 16 healthy controls were hybridized on MethylationEPIC BeadChip array. In parallel, gene expression was interrogated by hybridizing total RNA on Clariom™ S array. Downstream bioinformatics analyses were performed to identify correlating differentially methylated CpG positions (DMPs) and differentially expressed genes (DEGs), which were then confirmed utilizing previously published promoter capture Hi-C (PCHi-C) data. Results We identified 9112 and 3929 DMPs and DEGs, respectively. These DMPs and DEGs are enriched in functional categories related to inflammation and T cell biology. Furthermore, correlation analysis identified 17,500 possible DMP-DEG interaction pairs within a window of 5 Mb, and utilizing PCHi-C data, we observed that 212 CD4+ T cell-specific pairs of DMP-DEG also formed part of three-dimensional promoter-enhancer networks, potentially involving CTCF. Finally, combining PCHi-C data with SSc GWAS data, we identified four important SSc-associated susceptibility loci, TNIP1 (rs3792783), GSDMB (rs9303277), IL12RB1 (rs2305743), and CSK (rs1378942), that could potentially interact with DMP-DEG pairs cg17239269-ANXA6, cg19458020-CCR7, cg10808810-JUND, and cg11062629-ULK3, respectively. Conclusion Our study unveils a potential link between genetic, epigenetic, and transcriptional deregulation in CD4+ T cells of SSc patients, providing a novel integrated view of molecular components driving SSc pathogenesis.

Pyroptosis, metabolism, and tumor immune microenvironment

“… 106 GSDMB is increasingly expressed in multiple tissues, especially the upper gastrointestinal epithelium, 148 liver and colon epithelium, 148 airway epithelial cells, 149 neuroendocrine cells, 148 and immune cells (T cells). 45 , 115 , 150 …”

“… 106 , 112 , 149 Analogous to GSDMA, GSDMB is also linked to childhood‐onset asthma, 154 while GSDMB (rs9303277) in CD4 + T cells is an SSc‐associated susceptibility locus. 115 In addition, GSDMB is included in the Type 1 and 2 diabetes (T1D, T2D) islet expression quantitative trait loci interaction network. 114 …”

“…There are differences in the length and sequence of the linkers between the CT and NT domains of isoforms 1–4 and isoform 6, whereas there is no NT domain in isoform 5 106 . GSDMB is increasingly expressed in multiple tissues, especially the upper gastrointestinal epithelium, 148 liver and colon epithelium, 148 airway epithelial cells, 149 neuroendocrine cells, 148 and immune cells (T cells) 45,115,150 …”

“…Genome‐wide sequencing and functional genes indicate that single nucleotide polymorphisms of GSDMB are related to the increased susceptibility of ulcerative colitis and Crohn's disease, as well as asthma exacerbations and antiviral pathways 106,112,149 . Analogous to GSDMA, GSDMB is also linked to childhood‐onset asthma, 154 while GSDMB (rs9303277) in CD4 + T cells is an SSc‐associated susceptibility locus 115 . In addition, GSDMB is included in the Type 1 and 2 diabetes (T1D, T2D) islet expression quantitative trait loci interaction network 114 …”

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

“…Genetic and epigenetic studies conducted mostly in individuals of European ancestry uncovered multiple loci associated with SS [10]. A role of DNA methylation in SSc is supported by a X chromosome gene methylation analysis of peripheral blood mononuclear cells [11]; the quantification of global methylation in whole blood [12]; as well as genomewide DNA methylation analyses of dermal fibroblasts [13], whole blood [14], and CD4+ T cells [15,16]. Different ancestral populations exhibit DNA methylation differences [17][18][19][20][21][22][23][24] that are partially explained by their distinct genetic ancestry, thus environmental factors not captured by genetic ancestry are significant contributors to the variation in methylation [19].…”