Comprehensive Identification of Differentially Methylated Regions Associated with Systemic Sclerosis in Dermal Fibroblasts from African-American Patients

Paula S. Ramos^1,2, Willian da Silveira³, E. Starr Hazard³, Ilia Atanelishvili⁴, Robert C. Wilson⁵, Jim C. Oates¹, Galina S. Bogatkevich⁴ and Gary Hardiman^1,2,3, ¹Department of Medicine, Medical University of South Carolina, Charleston, SC, ²Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, ³Center for Genomic Medicine, Medical University of South Carolina, Charleston, SC, ⁴Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, SC, ⁵Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC

Meeting: 2017 ACR/ARHP Annual Meeting

Date of first publication: September 18, 2017

Keywords: African-Americans, DNA Methylation, Genome, skin fibrosis and systemic sclerosis

Session Information

Date: Monday, November 6, 2017

Title: Genetics, Genomics and Proteomics Poster II

Session Type: ACR Poster Session B

Session Time: 9:00AM-11:00AM

Background/Purpose: The etiology and reasons underlying the ethnic disparities in systemic sclerosis (SSc) remain unknown. African-Americans are disproportionally affected by SSc, yet dramatically underrepresented in research. The role of DNA methylation in disease risk remains unclear. This analysis was conducted to comprehensive identify differentially methylated loci associated with SSc in AA.

Methods: Genomic DNA was isolated from cultured dermal fibroblasts isolated from 15 AA SSc cases and 15 AA controls. All patients met the 2013 ACR/EULAR classification criteria for SSc, most (93%) presenting with diffuse cutaneous SSc. DNA methylation patterns were profiled through reduced representation bisulfite sequencing (RRBS). Alignment and methylation calling were performed using Bismarck v0.16.3 and the GRCh37/hg19 reference genome. Data was filtered, normalized, and analyzed with RnBeads v1.6.1. Differential methylation analysis was conducted on CpG, promoter, gene and system level.

Results: We generated DNA methylation data for over 5 million CpGs in each sample with at least 40x coverage in promoter and CpG islands. Using the Combined Score approach implemented in RnBeads, a total of 97 CpG islands, 197 genes and 112 promoters showed significant differential enrichment in methylation levels between cases and controls. The top differentially methylated loci include, among others, the promoter of SERPINA1 (a protease inhibitor of elastase, plasmin, thrombin and trypsin) and SERPINA3, SERPINA4, SERPINA5, SERPINA11 and SERPINA13P. The SERPIN superfamily is characterized by its function as chaperone proteins and its roles in inflammation and immune function. Enrichment analysis revealed that both hypo- and hypermethylated genes and their promoter regions were enriched for differentiation and immune-related gene ontology terms (hypomethylated regions: IL2-mediated signaling pathway, P=5E-3; and mesenchymal cell differentiation, P=3E-4; hypermethylated regions: type I IFN signaling pathway, P=8E-4; and positive regulation of cell differentiation, P=1E-3).

Conclusion: We observed dramatic DNA methylation differences between cases and controls. Interestingly, most of the dysregulated genes can be placed in immune pathways, supporting the role of immune dysregulation in triggering the fibrosis characteristic of SSc. These add to previous reports of mostly European-Americans that report an enrichment of extracellular matrix-receptor interaction and focal adhesion genes. These data support a role for DNA methylation differences in mediating susceptibility to SSc in AA, and a potentially stronger immune-driven etiology in AA.

Disclosure: P. S. Ramos, None; W. da Silveira, None; E. S. Hazard, None; I. Atanelishvili, None; R. C. Wilson, None; J. C. Oates, None; G. S. Bogatkevich, NIH/NIAMS P60 AR062755, 2,Scleroderma Foundation, 2; G. Hardiman, None.

To cite this abstract in AMA style:

Ramos PS, da Silveira W, Hazard ES, Atanelishvili I, Wilson RC, Oates JC, Bogatkevich GS, Hardiman G. Comprehensive Identification of Differentially Methylated Regions Associated with Systemic Sclerosis in Dermal Fibroblasts from African-American Patients [abstract]. Arthritis Rheumatol. 2017; 69 (suppl 10). https://acrabstracts.org/abstract/comprehensive-identification-of-differentially-methylated-regions-associated-with-systemic-sclerosis-in-dermal-fibroblasts-from-african-american-patients/. Accessed .

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