ArticleNature communications2025
Splicing QTL mapping in stimulated macrophages associates low-usage splice junctions with immune-mediated disease risk.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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Who cites it
8 citing papers in PubMed.
- Decoding Immune Regulation: From Genetic Variation to Mechanism Through Single-Cell Genomics.Immune network · 2026Review
- Design and interpretation of eQTL-GWAS colocalisation studies: Lessons from a large-scale evaluation.PLoS genetics · 2026Article
- Harnessing iPSC technology for population-level human disease/traits modeling -where are we?Frontiers in cell and developmental biology · 2026Review
- Mapping genetic effects on splicing in ten thousand post-mortem brain samples reveals novel mediators of neurological disease risk.medRxiv : the preprint server for health sciences · 2025Article
- Gene expression QTL mapping in stimulated iPSC-derived macrophages provides insights into common complex diseases.Nature communications · 2025Article
- A multi-omics resource of B cell activation reveals genetic mechanisms for immune-mediated diseases.medRxiv : the preprint server for health sciences · 2025Article
- Global impact of unproductive splicing on human gene expression.Nature genetics · 2024Article
- Global impact of aberrant splicing on human gene expression levels.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
16 authors.
Funding
Abstract
The majority of immune-mediated disease (IMD) risk loci are located in non-coding regions of the genome, making it difficult to decipher their functional effects in relevant physiological contexts. To assess the extent to which alternative splicing contributes to IMD risk, we mapped genetic variants associated with alternative splicing (splicing quantitative trait loci or sQTL) in macrophages exposed to a wide range of environmental stimuli. We found that genes involved in innate immune response pathways undergo extensive differential splicing in response to stimulation and detected significant sQTL effects for over 5734 genes across all stimulation conditions. We colocalised sQTL signals for over 700 genes with IMD-associated risk loci from 22 IMDs with high confidence (PP4 ≥ 0.75). Approximately half of the colocalisations implicate lowly-used splice junctions (mean usage ratio <0.1). Finally, we demonstrate how an inflammatory bowel disease (IBD) risk allele increases the usage of a lowly-used isoform of PTPN2, a negative regulator of inflammation. Together, our findings highlight the role alternative splicing plays in IMD risk, and suggest that lowly-used splicing events significantly contribute to complex disease risk.
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