Broadening our understanding of genetic risk for scleroderma/systemic sclerosis by querying the chromatin architecture surrounding the risk haplotypes

Abstract

Background Genetic variants in the human leukocyte antigen (HLA) locus contribute to the risk for developing scleroderma/systemic sclerosis (SSc). However, there are other replicated loci that also contribute to genetic risk for SSc, and it is unknown whether genetic risk in these non-HLA loci acts primarily on the vasculature, immune system, fibroblasts, or other relevant cell types. We used the Cistrome database to investigate the epigenetic landscapes surrounding 11 replicated SSc associated loci to determine whether SNPs in these loci may affect regulatory elements and whether they are likely to impact a specific cell type. Methods We mapped 11 replicated SNPs to haplotypes and sought to determine whether there was significant enrichment for H3K27ac and H3K4me1 marks, epigenetic signatures of enhancer function, on these haplotypes. We queried pathologically relevant cell types: B cells, endothelial cells, fibroblasts, monocytes, and T cells. We then identified the topologically associated domains (TADs) that encompass the SSc risk haplotypes in primary T cells to identify the full range of genes that may be influenced by SSc causal SNPs. We used gene ontology analyses of the genes within the TADs to gain insight into immunologic functions that might be affected by SSc causal SNPs. Results The SSc-associated haplotypes were enriched (p value < 0.01) for H3K4me1/H3K27ac marks in monocytes. Enrichment of one of the two histone marks was found in B cells, fibroblasts, and T cells. No enrichment was identified in endothelial cells. Ontological analyses of genes within the TADs encompassing the risk haplotypes showed enrichment for regulation of transcription, protein binding, activation of T lymphocytes, and proliferation of immune cells. Conclusions The 11 non-HLA SSc risk haplotypes queried are highly enriched for H3K4me1/H3K27ac-marked regulatory elements in a broad range of immune cells and fibroblasts. Furthermore, in immune cells, the risk haplotypes belong to larger chromatin structures encompassing genes that regulate a wide array of immune processes associated with SSc pathogenesis. Though importance of the vasculature in the pathobiology of SSc is widely accepted, we were unable to find evidence for genetic influences on endothelial cell function in these regions.

Analysis of chromatin data supports a role for CD14+ monocytes/macrophages in mediating genetic risk for juvenile idiopathic arthritis

“…We used the BedTools software to assess for enrichment in CD14+ human monocytes, following the method described by Poppenberg et al. ( 22 ). Briefly, we mined publicly available CD14+ H3K4me1 and H3K27ac ChIPseq using the Cistrome database…”

“…We therefore adapted the method described by Poppenberg et al. ( 22 ) to identify TAD structures that encompass the JIA risk haplotypes in monocytes. In brief, we first analyzed a publicly available HiC data set ( 26 ) using Juicebox software ( 27 ) following the method described by Kessler et al.…”

Analysis of Chromatin Data Supports a Role For CD14+ Monocytes/Macrophages in Mediating Genetic Risk for Juvenile Idiopathic Arthritis

“…Enrichment analysis: H3K4me1/H3K27ac ChIPseq data -We investigated the presence of potential enhancers within the JIA risk regions by defining enrichment (compared to genome background) for H3K4me1 and H3K27ac histone marks from publicly available ChIPseq data. We used the BedTools software to assess for enrichment in CD14+ human monocytes, following the method described by Poppenberg et al (22) Briefly, we mined publicly available CD14+ H3K4me1 and H3K27ac ChIPseq using the Cistrome database (http://cistrome.org/db/#/ ). We first queried a single data set for each H3K4me1 (GEO accession #GSM1003535) and H3K27ac (GEO accession #GSM2818004).…”

“…For example, Gasperini et al (25) showed that, on a genome-wide CRISPRi screen, 71% of enhancers regulate genes within the same TAD. We therefore adapted the method described by Poppenberg et al (22) to identify TAD structures that encompass the JIA risk haplotypes in monocytes. In brief, we first analyzed a publicly available HiC data set (26) using Juicebox software (27) following the method described by Kessler et al (8) to identify interacting regions in the monocyte THP-1 cell line.…”

Functional genomics in primary T cells and monocytes identifies mechanisms by which genetic susceptibility loci influence systemic sclerosis risk

“…Interestingly, many of the different genes assigned to SSc GWAS loci are related to T cell activation and macrophages regulation pathways (11,12), and are shared among immune-mediated diseases, which may be of interest in the drug repositioning of rare diseases like SSc, where there are no specific available treatments (13). However, the majority of single nucleotide polymorphisms (SNPs) associated with SSc map to non-coding regions of the genome that are enriched in enhancer elements, which are often cell-type specific (14,15). These regulatory elements can interact with genes often located hundreds of kilobases away, bypassing in many cases nearby genes (16).…”