Background/Purpose: The etiology and mechanisms underlying the wide variation in disease heterogeneity and severity in systemic sclerosis (SSc) remain unknown. To assess the role of DNA methylation in SSc risk and clinical heterogeneity while controlling for genetic background, we performed a genome-wide DNA methylation analysis in whole blood and skin fibroblasts of twin pairs discordant for SSc. We also performed gene expression analysis from the same fibroblasts to investigate the relationship between the DNA methylation changes and mRNA expression levels.

Methods: Genome-wide methylation was assessed on approximately 480,000 CpG sites using genomic DNA isolated from 1) whole blood from 20 twin pairs discordant for limited cutaneous SSc (lcSSc) and 10 twin pairs discordant for diffuse cutaneous SSc (dcSSc), and 2) skin fibroblasts cultured from dermal punch biopsies of 7 twin pairs discordant for dcSSc and 5 twin pairs discordant for lcSSc. Total RNA was extracted from fibroblasts in passage 3 for gene expression profiling of 47,000 transcripts. An efficiency analysis was performed with caGEDA to determine best normalization and feature selection methods and to identify differentially methylated probes and differential gene expression between unaffected and affected twins. Ingenuity Pathway Analysis was used for pathway analysis.

Results: A total of 68 CpGs were differentially methylated in whole blood from patients with SSc compared with their healthy twin. In the disease subsets, 206 and 409 CpGs were differentially methylated in the twin pairs discordant for lcSSc and dcSSc, respectively. Only 1% of differentially methylated genes were common between both subsets. In the dermal fibroblasts, 103 CpGs were differentially methylated in patients with SSc compared with their healthy twin. In the disease subsets, 110 and 220 CpGs were differentially methylated in lcSSc and dcSSc, respectively. 7% of differentially methylated genes were common between both subsets. In each disease subset, less than 2% of differentially methylated genes were observed in blood and fibroblasts. Despite the enrichment of different pathways and biological functions in each cell type and disease subset, most of these pathways can be placed into broader categories implicating an overall involvement of cancer functions. On the other hand, gene expression data from fibroblasts revealed 20% of genes shared between disease subsets. There were common and unique pathways enriched in disease subsets, also implicating an involvement of cancer functions. There were no genes simultaneously differentially methylated and expressed in either disease subset.

Conclusion: The distinct methylation patterns observed in blood and fibroblasts between lcSSc and dcSSc corroborate a similar observation reported in skin fibroblasts and suggest that subset-specific epigenetic signatures may be, at least in part, responsible for the clinical heterogeneity of the disease. These data also support a role for DNA methylation differences in mediating susceptibility to SSc.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/genome-wide-dna-methylation-analysis-in-blood-and-dermal-fibroblasts-from-twin-pairs-discordant-for-systemic-sclerosis/