Prevalent cross-cell type QTL trans-regulatory genetic effects impacting innate lymphoid cells in the small intestine

Tissue function in homeostasis and disease arise from coordinated interactions between different cell types and can vary between individuals in a population, in part due to the impact of genetic variants. In barrier tissues such as the gut, innate lymphoid cells (ILCs) play critical roles in maintaining tissue homeostasis and immunity, but the genetic basis and associated regulatory circuitry affecting tissue ILCs remain largely unknown. Here, we systematically mapped the regulatory functions of genetic variants across 273,370 gut ILCs profiled by single cell RNA-seq from 274 diversity outbred (DO) mice. Computational analysis identified quantitative trait loci (QTL) impacting ILCs at three levels: cell subtype-specific mRNA expression (local and distal), cell subset proportions, and ILC gene expression programs (in trans), of which we experimentally validated a pivotal role for the transcription factor Rbpj in regulating ILC3s. All three classes of ILC QTL display polygenic inheritance signatures and broadly overlap with QTL affecting peripheral cytokine levels that we measured in another 261 DO mice. Strikingly, nearly half of trans-QTL affecting ILC traits did not overlap (within a 50-kb window) genes expressed in ILCs, and such loci were enriched for genes expressed by non-ILCs especially enteric neurons and intestinal glia. This suggests that such loci may act instead across cell type boundaries and allowed us to recover causal trans-cell type regulatory circuits in the tissue, including loci encoding multiple neuron-expressed peptides, epithelial-cell expressed Sox9, and phagocyte-expressed Ccl17. Finally, human orthologs of genes in QTL impacting gene expression and cell proportions are enriched for autoimmune disease risk heritability, suggesting their relevance to human disease. Our findings highlight how the impact of genetic variants may propagate to maintain tissue homeostasis and show a path to understand causality in tissue biology using quantitative genetics.