Whole-genome bisulfite sequencing in systemic sclerosis provides novel targets to understand disease pathogenesis

Lu, Tianyuan; Klein, Kathleen; Colmegna, Inés; Lora, Maximilien; Greenwood, Celia; Hudson, Marie

doi:10.21203/rs.2.12858/v1

Cited by 6 publications

(9 citation statements)

References 31 publications

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“…Analysis of functional categories of the identified DMPs, DMRs and DEGs revealed the enrichment of numerous relevant pathways, in which many were in accordance to previous studies, including circadian signalling, Rho protein signalling, thyroid hormone secretion, T cell activation and cytokine-mediated responses 50,51 , however, we were able to identify several novel pathways, including several cytokine receptor-propagated pathways, MHC complex assembly, T cell polarization and NF-κB signalling pathway, amonst others. Given the association of the HLA loci with SSc disease, as observed by previous genetic studies 5,52 , aberrant methylation of these loci may have implications in regards to correct function of the MHC complex.…”

Section: Discussionsupporting

confidence: 89%

Epigenomics and Transcriptomics of Systemic Sclerosis CD4+ T cells reveal Long Range Dysregulation of Key Inflammatory Pathways mediated by disease-associated Susceptibility Loci

Ortíz

Andrés-León

et al. 2020

Preprint

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System 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. In this study, we obtained DNA methylation and expression profiles of CD4+ T cells from 48 SSc patients and 16 healthy controls. Consequently, we identified 9112 and 3929 differentially methylated CpGs positions (DMPs) and differentially expressed genes (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 promoter capture Hi-C data, we confirmed that 212 CD4+ T cel specific pairs of DMP-DEG physically interact involving CTCF. Finally, utilizing SSc GWAS data, we identified four important SSc-associated susceptibility loci, TNIP1 (rs3792783), GSDMB (rs9303277), IL12RB1 (rs2305743) and CSK (rs1378942) , that physically interact with DMP-DEG pairs cg17239269-ANXA6, cg19458020-CCR7, cg10808810-JUND and cg11062629-ULK3 respectively. Overall, our study reveals a solid link between genetic, epigenetic and transcriptional deregulation in CD4+ T cells of SSc patients, providing a novel integrated view of SSc pathogenic determinants.

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Section: Discussionsupporting

confidence: 89%

Epigenomics and Transcriptomics of Systemic Sclerosis CD4+ T cells reveal Long Range Dysregulation of Key Inflammatory Pathways mediated by disease-associated Susceptibility Loci

Ortíz

Andrés-León

et al. 2020

Preprint

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“…Analysis of functional categories of the identified DMPs, DMRs, and DEGs revealed the enrichment of numerous relevant pathways, in which many were in accordance to previous studies, including circadian signaling, Rho protein signaling, thyroid hormone secretion, T cell activation, and cytokine-mediated responses [70,71]; however, we were able to identify several novel pathways, including several cytokine receptor-propagated pathways, MHC complex assembly, T cell polarization, and NF-κB signaling pathway, among others. Interestingly, several of these deregulated pathways were enriched in both hyper-and hypomethylated DMP/DMR datasets.…”

Section: Discussionsupporting

confidence: 87%

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

Ortiz-Fernández

Andrés-León

et al. 2020

Genome Med

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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.

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“…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.…”

Section: Discussionsupporting

confidence: 68%

“…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. 19…”

Section: Introductionmentioning

confidence: 99%

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

Frost

Silveira

Hazard

et al. 2020

Preprint

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Objective. The etiology and reasons underlying the ethnic disparities in systemic sclerosis (SSc) remain unknown. African Americans are disproportionally affected by SSc, yet underrepresented in research. The aim of this study was to comprehensively investigate the association of DNA methylation levels with SSc in dermal fibroblasts from patients of African ancestry. Methods. Reduced representation bisulfite sequencing (RRBS) was performed on primary cultured dermal fibroblasts from 15 SSc patients and 15 controls of African ancestry, and over 3.8 million CpG sites were tested for differential methylation patterns between cases and controls. Gene set enrichment (GSEA) and gene ontology (GO) analyses were computed to elucidate the underlying biological processes. Quantitative PCR (qPCR) was performed to assess correlations between DNA methylation changes and gene expression levels of top candidate genes. Results. Skin fibroblasts from African American patients exhibited widespread reduced DNA methylation. Differentially methylated CpG sites were most enriched in introns and intergenic regions, while depleted in 5′ UTR, promoters, and CpG islands. Seventeen genes and eleven promoters showed significant differential methylation, mostly in non-coding RNA genes and pseudogenes. GSEA and GO enrichment analysis revealed enrichment of immune, metabolism, cell development, and cell signaling pathways, including those related to interferon signaling and mesenchymal differentiation. The hypomethylation of DLX5 and TMEM140 was accompanied by these genes′ overexpression, while for the lncRNA MGC12916, it was accompanied by its under-expression in patients. Conclusion. These data show that differential methylation occurs in dermal fibroblasts from African American patients with SSc and identifies novel coding and non-coding genes.

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Whole-genome bisulfite sequencing in systemic sclerosis provides novel targets to understand disease pathogenesis

Abstract: Background Systemic sclerosis (SSc) is a rare autoimmune connective tissue disease whose

Cited by 6 publications

References 31 publications

Epigenomics and Transcriptomics of Systemic Sclerosis CD4+ T cells reveal Long Range Dysregulation of Key Inflammatory Pathways mediated by disease-associated Susceptibility Loci

Epigenomics and Transcriptomics of Systemic Sclerosis CD4+ T cells reveal Long Range Dysregulation of Key Inflammatory Pathways mediated by disease-associated Susceptibility Loci

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

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

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