Deciphering the genomic architecture of systemic sclerosis

Abstract

Systemic sclerosis (SSc) is a complex rheumatic autoimmune disease (AD) with an important genetic and environmental component, characterized by the triad of pathological hallmarks: extensive fibrosis of skin and internal organs, vascular damage, and altered immune response (including the presence of autoantibodies). SSc shows a wide range of phenotypical manifestations and heterogeneous clinical characteristics, making it difficult to treat. The present PhD dissertation is focused on the study of the genetic component of SSc. To date, more than 25 loci have been firmly associated to SSc by genome-wide association studies (GWAS). Nevertheless, most of these studies have been performed in Caucasian population. In order to extent the knowledge of the genetic component of SSc, we performed a GWAS in the Iranian and Turkish populations, confirming previous associations both within the human leukocyte antigen (HLA) region, by performing an extensive study of this locus, and outside this region, such as IRF5-TNPO3 and NFKB1. We also identified a suggestive association within the GOT1-NKX2.3 locus, suggesting NKX2.3 as a potential candidate gene in SSc. In addition, we also studied the shared genetic component between SSc and other immune-mediated disorders through cross-disease meta-GWAS approach. Using this strategy, we found four new loci shared with Crohn’s disease (STAT3, IRF1, IL12RB2, and ZBTB9-BAK1), and identified the IL-12/IL-23 signaling as one of a most common relevant pathway for both diseases. Furthermore, we analyzed the genetic component shared among four systemic seropositive rheumatic diseases (SSc, rheumatoid arthritis, systemic lupus erythematosus and idiopathic inflammatory myopathy) identifying 26 genome-wide significant common loci for at least two conditions, of which NAB1, DGKQ, KPNA4-ARL14, LIMK1, and PRR12 had not been reported before, as well as determining that the type I IFN signalling pathway and its regulation play a more prominent role in these disorders. However, one of the main limitations of GWAS is the difficulty to identify true causal genes, variants and cell types. Thus, we performed functional genomics studies including expression quantitative trait locus (eQTL) analysis and chromosome conformation capture studies (promoter capture Hi-C, pCHi-C) in order to provide a mechanistic link between non-coding SSc-associated variants and their target genes. Through the integration of GWAS and RNA-seq data we performed the first eQTL analysis in SSc, revealing that more than half of the eGenes detected were associated with the most important SSc hallmarks and highlighting the crucial role of the apoptotic process in SSc. On the other hand, pCHi-C analysis performed in CD4+ T cells and CD14+ monocytes from SSc patients and healthy controls, revealed cell-type specific interactions between SSc-associated loci and previously confirmed causal genes, such as IRF8 in CD14+ monocytes, and CD247 and STAT4 in CD4+ T cells, as well as new potential candidate genes, especially CXCR5, which plays an important role in the differentiation of follicular helper T cells and has been associated with other ADs. Finally, drug repurposing analyses performed throughout the different conducted studies identified more than 20 drug target genes already targeted in similar immune-mediated diseases, thus contributing to the potential repositioning of different drugs for its use in systemic sclerosis treatment.