Expression Quantitative Trait Locus Analysis in Systemic Sclerosis Identifies New Candidate Genes Associated With Multiple Aspects of Disease Pathology

Abstract

Objective To identify the genetic variants that affect gene expression (expression quantitative trait loci [eQTLs]) in systemic sclerosis (SSc) and to investigate their role in the pathogenesis of the disease. Methods We performed an eQTL analysis using whole‐blood sequencing data from 333 SSc patients and 524 controls and integrated them with SSc genome‐wide association study (GWAS) data. We integrated our findings from expression modeling, differential expression analysis, and transcription factor binding site enrichment with key clinical features of SSc. Results We detected 49,123 validated cis‐eQTLs from 4,539 SSc‐associated single‐nucleotide polymorphisms (SNPs) (PGWAS < 10−5). A total of 1,436 genes were within 1 Mb of the 4,539 SSc‐associated SNPs. Of those 1,436 genes, 565 were detected as having ≥1 eQTL with an SSc‐associated SNP. We developed a strategy to prioritize disease‐associated genes based on their expression variance explained by SSc eQTLs (r2 > 0.05). As a result, 233 candidates were identified, 134 (58%) of them associated with hallmarks of SSc and 105 (45%) of them differentially expressed in the blood cells, skin, or lung tissue of SSc patients. Transcription factor binding site analysis revealed enriched motifs of 24 transcription factors (5%) among SSc eQTLs, 5 of which were found to be differentially regulated in the blood cells (ELF1 and MGA), skin (KLF4 and ID4), and lungs (TBX4) of SSc patients. Ten candidate genes (4%) can be targeted by approved medications for immune‐mediated diseases, of which only 3 have been tested in clinical trials in patients with SSc. Conclusion The findings of the present study indicate a new layer to the molecular complexity of SSc, contributing to a better understanding of the pathogenesis of the disease.

Modulation of microRNome by Human Cytomegalovirus and Human Herpesvirus 6 Infection in Human Dermal Fibroblasts: Possible Significance in the Induction of Fibrosis in Systemic Sclerosis

“…However, in these cases, the action of the virus is controversial as it was found to alter their expression in the opposite direction to that observed in the SSc [ 63 , 93 ]. On the other hand, new genes and factors as well as miRNAs are going to be added to the list of those involved in fibrosis, as recently reported for ten new candidate genes for potential therapy during SSc [ 94 ], and for the newly identified miR-320a, reported to be crucial in lung fibrosis during SSc [ 95 ]. The fibrotic process usually occurs because of the activation of fibroblasts, epithelial-mesenchymal transition and excessive extracellular matrix deposition.…”

Complement component C4 structural variation and quantitative traits contribute to sex-biased vulnerability in systemic sclerosis

“…Our data confirm that C4 and HERV-K CNs are strong predictors of C4 expression levels in blood and other tissues 29 . While the major site of C4 expression is the liver 38 , it has been shown that whole blood can be used with some caution as a surrogate tissue for quantitative trait analysis 39 – 41 . In addition, local complement production by bone-marrow-derived monocytes and macrophages can restore humoral response in c4 deficient mice 42 .…”

“…1 ). Second cohort: this cohort included genome-wide genotyped data, whole blood expression data and blood serum C4 protein concentrations from 333 SSc patients and 524 healthy individuals from 9 European countries 39 . This second cohort is a subset of a larger cohort of seven immune-mediated diseases plus controls described here 60 .…”

“…Single end 50 bp stranded sequencing was performed on a HiSeq2500 Illumina within the PRECISESADS consortium 60 and processed with bcl2fastq (Illumina), Cutadapt 62 , STAR v2.5.2 (2-pass default mapping to GRCh19 63 , and RSEM v1.2.31 64 to obtain estimated counts per gene. Raw count data were normalized for quantitative trait analyzes 39 . Briefly: Three genetic principal components (PCs) were regressed out from VSN-normalized 65 raw read count data.…”

Integrative epigenomics in Sjögren´s syndrome reveals novel pathways and a strong interaction between the HLA, autoantibodies and the interferon signature

“…Therefore, these studies have not contributed to the identification of new risk variants associated with SS with regulatory function that could explain further the missing heritability of this complex disease 20 . Furthermore, the vast majority of large-scale QTL studies have been performed in healthy populations, and do not directly compare the genetic regulatory effects between cases and controls, which could very much be different as the pathological condition imposes a different environmental and cellular context in affected individuals, especially in immune-related conditions, as we have recently described in scleroderma patients 25 . In this regard, several experimental studies have shown that eQTL and meQTL effects are highly context-specific, as for example cell-type specific effects have been found when studying different blood cell types 26 – 28 , and experimental studies of ex-vivo activation of immune cells have shown that eQTLs profiles are altered upon different stimuli 29 , 30 .…”