Single-cell eQTL mapping identifies cell type specific genetic control of autoimmune disease [Genotype_data]
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ABSTRACT:
PROVIDER: PRJNA807390 | ENA |
REPOSITORIES: ENA
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Project description:Single-cell eQTL mapping identifies cell type specific genetic control of autoimmune disease
| PRJNA807386 | ENA
Project description:Single-cell eQTL mapping identifies cell type specific genetic control of autoimmune disease [scRNAseq_data]
| PRJNA807049 | ENA
Project description:The human immune system displays remarkable variation between individuals, leading to differences in susceptibility to autoimmune disease. We present single cell RNA sequence data from 1,267,768 peripheral blood mononuclear cells from 982 healthy human subjects. For 14 cell types, we identified 26,597 independent cis-expression quantitative trait loci (eQTLs) and 990 trans-eQTL, with the majority showing cell type specific effects on gene expression. We subsequently show how eQTLs have dynamic allelic effects in B cells transitioning from naïve to memory states and demonstrate how commonly segregating alleles lead to inter-individual variation in immune function. Finally, utilizing a Mendelian randomization approach, we identify the causal route by which 305 risk loci contribute to autoimmune disease at the cellular level. This work brings together genetic epidemiology with scRNA-seq to uncover drivers of inter-individual variation in the immune system.
2022-04-08 | GSE196829 | GEO
Project description:The human immune system displays remarkable variation between individuals, leading to differences in susceptibility to autoimmune disease. We present single cell RNA sequence data from 1,267,768 peripheral blood mononuclear cells from 982 healthy human subjects. For 14 cell types, we identified 26,597 independent cis-expression quantitative trait loci (eQTLs) and 990 trans-eQTL, with the majority showing cell type specific effects on gene expression. We subsequently show how eQTLs have dynamic allelic effects in B cells transitioning from naïve to memory states and demonstrate how commonly segregating alleles lead to inter-individual variation in immune function. Finally, utilizing a Mendelian randomization approach, we identify the causal route by which 305 risk loci contribute to autoimmune disease at the cellular level. This work brings together genetic epidemiology with scRNA-seq to uncover drivers of inter-individual variation in the immune system.
2022-04-08 | GSE196735 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2022-04-08 | GSE196830 | GEO
Project description:Genome-wide association studies (GWAS) have boosted our knowledge of genetic risk variants in autoimmune diseases (AIDs). Most of the risk variants are located within or near genes with immunological functions, and the majority is found to be non-coding, pointing towards a regulatory role. We have performed a cis expression quantitative trait locus (eQTL) screen to investigate whether single nucleotide polymorphisms (SNPs) associated with AIDs influence gene expression in thymus. Genotyping was performed using the Immunochip and 353 AID associated SNPs were tested against expression of surrounding genes (+/- 1 Mb) from human thymic tissue (N=42). We identified eight genes where the expression was associated with AID risk SNPs at a study-wide level of significance (P < 2.57x10-5). Five genes (FCRL3, RNASET2, C2orf74, SIRPG and SYS1) displayed cis eQTL signals also in other tissues, while for two loci (NPIPB8 and LOC388814), the eQTL signal appear to be thymus-specific. Since many AID risk variants from GWAS have been subsequently fine-mapped in recent Immunochip projects, we explored the overlap between these novel AID risk variants and the thymic eQTL regions. Moreover, we examined the functional annotation of the seven expression altering SNPs (eSNPs). Our study reveals autoimmune risk variants that act as eQTLs in thymus. We have highlighted functional variants within these genetic regions that potentially can represent causal autoimmune risk variants. Total RNA from 42 human thymic samples were obtained from children undergoing cardiac surgery.
2016-01-21 | E-GEOD-77052 | biostudies-arrayexpress
Project description:Mapping of expression quantitative trait loci (eQTL) is a powerful means for elucidating the genetic architecture of gene regulation. Yet, eQTL mapping has not been applied towards investigating the regulation architecture of genes involved in the process of population divergence, ultimately leading to speciation events. Here, we conducted an eQTL mapping experiment to compare the genetic architecture of transcript regulation in adaptive traits differentiating the recently evolved limnetic (dwarf) and benthic (normal) species pairs of lake whitefish. The eQTL were mapped in three data sets derived from a F1 hybrid-dwarf backcrossed family: the entire set of 66 genotyped individuals, and the two sexes treated separately. We identified strikingly more eQTL in the female dataset (174), compared to both male (54) and combined (33) data sets. The majority of these genes were not differentially expressed between male and female progeny of the backcross family, thus providing evidence for a strong pleiotropic sex-linked effect in transcriptomic regulation. The subtelomeric region of a linkage group segregating in females encompassed more than 50% of all eQTL, which exhibited the most pronounced additive effects. We also conducted a direct comparison of transcriptomic profiles between pure dwarf and normal progeny reared in controlled conditions. We detected 34 differentially expressed transcripts associated with eQTL segregating only in sex-specific data-sets, and mostly belonging to functional groups that differentiate dwarf and normal whitefish in natural populations. Therefore, these eQTL are not related to inter-individual variation, but instead to the adaptive and historical genetic divergence between dwarf and normal whitefish. This study exemplifies how the integration of genetic and transcriptomic data offers a strong means for dissecting the functional genomic response to selection by separating mapping family specific effects from genetic factors under selection, potentially involved in the phenotypic divergence of natural populations. Keywords: eQTL mapping
2008-09-01 | GSE11378 | GEO
Project description:Inappropriate activation or inadequate regulation of CD4+ and CD8+ T cells may contribute to the initiation and progression of multiple autoimmune and inflammatory diseases. Studies on disease-associated genetic polymorphisms have highlighted the importance of biological context for many regulatory variants, which is particularly relevant in understanding the genetic regulation of the immune system and its cellular phenotypes. Here we show cell type-specific regulation of transcript levels of genes associated with several autoimmune diseases in CD4+ and CD8+ T cells including a trans-acting regulatory locus at chr12q13.2 containing the rs1131017 SNP in the RPS26 gene. Most remarkably, we identify a common missense variant in IL27, associated with type 1 diabetes that results in decreased functional activity of the protein and reduced expression levels of downstream IRF1 and STAT1 in CD4+ T cells only. Altogether, our results indicate that eQTL mapping in purified T cells provides novel functional insights into polymorphisms and pathways associated with autoimmune diseases.
2017-02-23 | GSE78840 | GEO
Project description:Single-Cell Transcriptomics Identifies Brain Endothelium Inflammatory Networks in Experimental Autoimmune Encephalomyelitis
| PRJNA820021 | ENA
Project description:The functional interpretation of GWAS remains challenging due to the cell-type dependent influences of genetic variants. Here, we generated comprehensive maps of expression quantitative trait loci (eQTL) for 659 microdissected human kidney samples and identified cell-type eQTLs by mapping interactions between cell type abundance and genotype. By partitioning heritability using stratified LD-score regression to integrate GWAS with scRNA-seq and snATAC-seq data, we prioritized proximal tubules in kidney function and endothelial cells and distal tubule segments in blood pressure pathogenesis. Bayesian colocalization analysis nominated more than 200 genes for kidney function and hypertension. Our study clarifies the mechanism of commonly used antihypertensive and renal protective drugs and identifies drug repurposing opportunities for kidney disease.
2021-05-10 | GSE172008 | GEO