Integrative analysis of DNA methylation in discordant twins unveils distinct architectures of systemic sclerosis subsets

Abstract

Background Systemic sclerosis (SSc) is a rare autoimmune fibrosing disease with an incompletely understood genetic and non-genetic etiology. Defining its etiology is important to allow the development of effective predictive, preventative, and therapeutic strategies. We conducted this epigenomic study to investigate the contributions of DNA methylation to the etiology of SSc while minimizing confounding due to genetic heterogeneity. Methods Genomic methylation in whole blood from 27 twin pairs discordant for SSc was assayed over 450 K CpG sites. In silico integration with reported differentially methylated cytosines, differentially expressed genes, and regulatory annotation was conducted to validate and interpret the results. Results A total of 153 unique cytosines in limited cutaneous SSc (lcSSc) and 266 distinct sites in diffuse cutaneous SSc (dcSSc) showed suggestive differential methylation levels in affected twins. Integration with available data revealed 76 CpGs that were also differentially methylated in blood cells from lupus patients, suggesting their role as potential epigenetic blood biomarkers of autoimmunity. It also revealed 27 genes with concomitant differential expression in blood from SSc patients, including IFI44L and RSAD2 . Regulatory annotation revealed that dcSSc-associated CpGs (but not lcSSc) are enriched at Encyclopedia of DNA Elements-, Roadmap-, and BLUEPRINT-derived regulatory regions, supporting their potential role in disease presentation. Notably, the predominant enrichment of regulatory regions in monocytes and macrophages is consistent with the role of these cells in fibrosis, suggesting that the observed cellular dysregulation might be, at least partly, due to altered epigenetic mechanisms of these cells in dcSSc. Conclusions These data implicate epigenetic changes in the pathogenesis of SSc and suggest functional mechanisms in SSc etiology. Electronic supplementary material The online version of this article (10.1186/s13148-019-0652-y) contains supplementary material, which is available to authorized users.

Identification and Validation of Key Genes Associated With Systemic Sclerosis-Related Pulmonary Hypertension

“…Several studies have demonstrated that RSAD2 showed hypomethylation and overexpression in blood from SSc patients ( Tan et al, 2006 ; Bos et al, 2009 ; Assassi et al, 2010 ; Bodewes et al, 2018 ). Consistent with a more recent study that investigated the contributions of DNA methylation to the pathogenesis of SSc, a subset of 27 genes with concomitant differential expression was detected in whole blood from 27 twin pairs discordant for SSc, including RSAD2 ( Ramos et al, 2019 ). Both IFIT2 and IFIT3 are the members of the IFIT family and are induced by type I interferon ( Daffis et al, 2010 ).…”

“…SSc, systemic sclerosis; PAH, pulmonary arterial hypertension; HCs, healthy controls; mRNA, messenger RNA; WGCNA, weighted gene co-expression network analysis. of SSc, a subset of 27 genes with concomitant differential expression was detected in whole blood from 27 twin pairs discordant for SSc, including RSAD2 (Ramos et al, 2019). Both IFIT2 and IFIT3 are the members of the IFIT family and are induced by type I interferon (Daffis et al, 2010).…”

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

“…First, although we are the first to analyze patterns of DNA methylation in dermal fibroblasts in African Americans, the sample size is modest. Nevertheless, with 15 SSc patients, it is comparable to previous genome-wide DNA methylation analyses focused on skin fibroblasts (n = 12 SSc patients), 14 whole blood (n = 27 SSc patients), 15 and CD4+ T cells (n = 9 patients), 16 which included primarily individuals of European ancestry. Second, we were not able to collect a new independent cohort of African Americans to validate the results.…”

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

Twin Registries Moving Forward and Meeting the Future: A Review

“…For example, it is known that parental imprinting is modulated through epigenetic changes and is widespread across the genome (Baran et al, 2015;Zink et al, 2018) with subsequent strong effect on health and disease (Begemann et al, 2018). Epigenetic investigations in phenotypically discordant MZ twins have been able to show that aberrant imprinting in Beckwith-Wiedemann syndrome (Weksberg et al, 2002), Silver-Russell syndrome (Riess et al, 2016) and others can exist.…”