Cell type-specific genetic regulation of gene expression across human tissues

Abstract

The Genotype-Tissue Expression (GTEx) project has identified expression and splicing quantitative trait loci in cis (QTLs) for the majority of genes across a wide range of human tissues. However, the functional characterization of these QTLs has been limited by the heterogeneous cellular composition of GTEx tissue samples. We mapped interactions between computational estimates of cell type abundance and genotype to identify cell type-interaction QTLs for seven cell types and show that cell type-interaction expression QTLs (eQTLs) provide finer resolution to tissue specificity than bulk tissue cis-eQTLs. Analyses of genetic associations with 87 complex traits show a contribution from cell type-interaction QTLs and enables the discovery of hundreds of previously unidentified colocalized loci that are masked in bulk tissue.

Fig. 1.. Study design of mapping cell type ieQTLs and isQTLs in GTEx v8 project.

(A) Illustration of 43 cell type-tissue pairs included in the GTEx v8 project. See (1) for the full list of tissues included in the GTEx v8 project; two brain regions (frontal cortex and cerebellum) were sampled in replicates. Cell types with median xCell enrichment score > 0.1 within a tissue were used (fig. S2). (B) Schematic representation of a cell type interaction eQTL and sQTL. RNA-seq coverage is depicted in gray, blue, and red, representing different genotypes. Differences in coverage between genotypes, corresponding to a QTL effect, are only observed with high cell type enrichment. The scatter plot illustrates the regression model used to identify iQTLs, where the dots represent individual samples. (C) Example cell type ieQTL and isQTL. The CNTN1 eQTL effect in not sun-exposed skin is associated with keratinocyte abundance (p = 4.1 × 10⁻¹⁹; left panel). The TNFRSF1A sQTL effect in whole blood is associated with neutrophil abundance but is only detected in samples with lower neutrophil abundances (p = 6.7 × 10⁻⁷⁸; right panel). Each data point represents an individual and is colored by genotype. Cell type enrichment scores and gene expression were inverse normal transformed, and intron excision ratios were standardized. The regression lines from the interaction model illustrate how the QTL effect is modulated by cell type enrichment.

Fig. 2.. Cell type ieQTL and isQTL discovery.

(A) Number of cell type ieQTLs (left panel) and isQTLs (right panel) discovered in each cell type-tissue combination at FDR < 5%. Bar labels show the number of ieQTLs and isQTLs, respectively. See Fig. 1A for the legend of tissue colors. (B) Proportion of cell type ieQTLs that validated in ASE data. Validation was defined as ieQTLs for which the Pearson correlation between allelic fold-change (aFC) estimates from ASE and cell type estimates was nominally significant (P < 0.05). Tissue abbreviations are provided in table S2. Bar labels indicate the number of ieQTLs with validation/number of ieQTLs tested.

Fig. 3.. Cell type ieQTLs contribute to cis-eQTL tissue specificity.

(A) Coefficients from logistic regression models of cis-eQTL tissue sharing, where epithelial cell ieQTL status is one of the predictors: All significant top cis-eQTLs per tissue were annotated based on if they were also a significant ieQTL for a given cell type. The coefficients represent the log(odds ratio) that an eQTL is active in a replication tissue given a predictor. Chromatin states were defined using matched Epigenomics Roadmap tissues and the 15-state ChromHMM (37). Genomic annotations, conservation, and overlaps with Ensembl regulatory build TF, CTCF, and DHS peaks are also included. Bars represent the 95% confidence interval. (B) Proportion of cell type ieQTL-genes (ieGenes) among tissue-specific and tissue-shared eGenes. An eGene is considered tissue-specific if its eQTL had a MASH local false sign rate (LFSR, equivalent to FDR) < 0.05 only in the cell type ieQTL tissue (or tissue type) otherwise it is considered tissue-shared. Results of all 43 cell type-tissue combinations are shown. See Fig. 1A for the legend of tissue colors. (C+D) Tissue activity of cell type ieQTLs and eQTLs, where a cell type ieQTL and eQTL was considered active in a tissue if it had an LFSR < 0.05 (left panel). Pairwise tissue-sharing of ieQTLs (middle panel) or lead standard cis-eQTLs (right panel) respectively. The color-coded sharing signal is the proportion of significant QTLs (LFSR < 0.05) that are shared in magnitude (within a factor of 2) and sign between two tissues.

Fig. 4.. Cell type iQTLs are enriched for GWAS signals.

(A) Distribution of adjusted GWAS fold-enrichment of 23×87 (top panel) and 7×87 (bottom panel) tissue-trait combinations using the most significant iQTL or standard QTL per eGene/sGene. (B) Adjusted GWAS fold-enrichments of 87 GWAS traits among iQTLs on the x-axis and standard QTLs on the y-axis. Filled circles indicate significant GWAS enrichment among iQTLs at P < 0.05 (Bonferroni-corrected). Colors represent GWAS categories of the 87 GWAS traits (see table S3).

Fig. 5.. Cell type iQTLs improve GWAS-QTL matching.

(A) Proportion of cell type ieQTLs (left panel) or isQTLs (right panel) with evidence of colocalization using COLOC posterior probabilities (PP4 > 0.5), for ieQTLs and isQTL at FDR < 0.4. Color saturation indicates if a trait colocalized with the cell type iQTL only (dark), the cis-QTL only (light) or both QTLs (medium). Bar labels indicate the number of cell type iQTLs with evidence of colocalization (either as iQTL or cis-QTL)/number of iQTLs tested. (B) Summary of all QTL-trait colocalizations from (A). (C) Association p-values in the DHX58 locus for an asthma GWAS (top), standard heart left ventricle cis-eQTL (middle) and myocyte ieQTL (bottom), and in the KREMEN1 locus for a birth weight GWAS (top), standard subcutaneous adipose cis-eQTL (middle), and adipocyte ieQTL (bottom). (D) Association p-values in the CDHR5 locus for an eosinophil count GWAS (top), standard small intestine terminal ileum cis-sQTL (middle) and epithelial cell isQTL (bottom), and in the ATP5SL locus for a standing height GWAS (top), standard heart left ventricle cis-sQTL (middle), and myocyte isQTL (bottom).