OP03 Mapping the observable IBDverse: Using massive-scale single-cell RNA sequencing of gut and blood samples to nominate genes, cell types and pathways driving IBD susceptibility
Authors: Harris B , Alegbe T , Ramirez-Navaro L , Tutert M , Krzak M , Ozols M , Ghouraba M , Strickland M , Wana N , Hu M , Ostermayer J , McIntyre R , Cotobal Martin C , Fachal L , Jones G R , Raine T , Anderson C 
Published: January 2025

Background

Genome-wide association studies (GWAS) have identified 370 loci associated with inflammatory bowel disease (IBD) susceptibility1. The majority of these are driven by non-coding variants, thought to dysregulate the expression of a nearby gene. The dysregulated disease effector gene, and the operative cell-type(s) is often unknown. Previous efforts to nominate effector genes have relied on identifying expression quantitative trait loci (eQTL) and expression-linked genes (eGenes). However, gene expression is often derived from healthy individuals, a single, non-primary site, and measured using bulk RNA sequencing. This likely misses cell-, site-, or disease-specific genetic effects, and has nominated disease effector genes for only a minority of IBD loci.

Methods

To better characterise the universe of IBD effector genes, we created IBDverse - the largest collection of single-cell RNAseq data from the terminal ileum (TI, nCD=119, nHealthy=243), rectum (nHealthy=275) and blood (nCD=95) - a total of &gt;2.4 million high quality transcriptomes from 732 samples across 396 individuals. After grouping cells into different cell types, we mapped genetic variants associated with gene expression changes. Disease effector genes were nominated by identifying expression-linked genetic effects likely driven by the same causal variant as an IBD GWAS signal, as determined by colocalisation analysis2.

Results

Across all tissues, we identify 102 transcriptionally distinct cell types (Fig 1), and genetic effects associated with the expression of &gt;17,000 genes. For 507 genes, the genetic association for their expression was strongly associated with genetic effects for IBD susceptibility, suggesting them to be drivers of disease risk. Remarkably, this doubles the previous best efforts to nominate disease effector genes3, doing so at &gt;52% of IBD susceptibility loci.

As well as their nomination, this study also helps contextualise disease effector expression variation. Disease effector genes were detectable in only a single tissue or cell annotation in &gt;40% of cases, highlighting the need for high resolution data obtained across multiple tissues. We also find the first evidence for upregulation of RASGRP1, a gene previously correlated with exacerbated colitis in mice4, to drive Crohn’s disease susceptibility. As this is identified in a subset of tissue-resident memory T cells, and only from the TI, this also suggests this cell type and tissue as governing this effect.

Conclusion

This study serves as a step change in the understanding of cellular heterogeneity of these tissues, provides a compendium of genetic regulatory effects across constituent cell types, and quantifies the relevance of these to IBD susceptibility.

References

Liu et al., (2023). Nat. Genetics. ‘Genetic architecture of the inflammatory bowel diseases across East Asian and European ancestries’

Giambartolemi et al., (2014) PLOS Genetics. ‘Bayesian test for colocalisation between pairs of genetic association studies using summary statistics’

Panousis et al., (2024) Nat. Comms (in press).

Wang et al., (2022) Nat. Comms. ‘RasGRP1 promotes the acute inflammatory response and restricts inflammation-associated cancer cell growth’