Combining population-scale single-cell transcriptomics with germline genetics to understand the biology of inflammatory bowel diseases

Inflammatory bowel diseases (IBD) are chronic, incurable diseases of the gastrointestinal tract with a high prevalence in the United Kingdom and a growing incidence worldwide. The two most common forms of IBD are Crohn’s disease (CD) and ulcerative colitis (UC). Genome-wide association studies (GWAS) have discovered over 300 regions of the genome associated with increased risk of susceptibility to CD, UC, or IBD. Simultaneously, single- cell transcriptomic studies have extensively mapped the cell types present in the mostly commonly afflicted regions - the small and large intestines. Thusfar the efforts to align these two fields have been minimal despite the large benefit to doing so. In this thesis I explored the genes, cell types and pathways driving inflammatory bowel diseases with IBD relevant single-cell datasets whilst guided by the causal anchor of germline genetics. The first results chapter describes the construction of a single-cell atlas of the terminal ileum generated from biopsies of 50 individuals with CD and 71 healthy controls. With this well-powered dataset, 49 cell types could be identified across immune, epithelial, and stromal populations. I then performed a series of transcriptomic analyses including differential gene expression, non-negative matrix factorisation, and heritability partitioning. The results highlighted antigen presentation pathways upregulated in epithelial cells from diseased biopsies whilst T cell, myeloid and B cell populations were enriched in IBD risk heritability. In the second results chapter, I used a larger version of the same single-cell ileal dataset to map expression quantitative trait loci (eQTL) - genetic variants associated with gene expression changes. I examined how these eQTL, and the genes they impact, vary across the cell types present in the terminal ileum. Then I colocalised the eQTL with GWAS to prioritise likely effector genes for dozens of IBD risk loci. Finally, I compared my findings to public data and highlight the novelty this dataset adds for interpretation of IBD. My final results chapter builds on the prior two with the addition of single-cell RNA sequencing datasets spanning two more tissues: blood and rectum. The rectum is a more relevant site for ulcerative colitis and the blood contains many immune cell types that are under-represented in the gut. I compared the findings between the three datasets and show that they complement each other for eQTL discovery and interpreting IBD GWAS. I lastly used the individual-level phenotypes to test for interaction eQTLs effects and show that these can be valuable for understanding biology too. Overall, my thesis looks at diverse scRNA-seq data generated from a large cohort and harnesses that power to provide insight into IBD biology. The datasets created will prove a valuable resource within IBD but also for other gastrointestinal diseases such as colorectal cancer, coeliac and irritable bowel syndrome.

Name dc:type.qualificationname

Doctor of Philosophy (PhD)

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2024

Author dc:creator

• Alegbe, Oluwatobi

Advisors dc:contributor.advisor

• Anderson, Carl A
• Wallace, Chris

• Complex disease
• Crohn's disease
• eQTL
• Genetics
• Inflammatory bowel disease
• Single-cell RNA-sequencing
• Ulcerative colitis

Licence

• https://www.repository.cam.ac.uk/bitstreams/58adf6bc-ed47-4fcc-b4be-87119669daf6/download
• https://www.rioxx.net/licenses/all-rights-reserved/

Language dc:language

eng

DOI dc:identifier.doi

https://doi.org/10.17863/CAM.112417

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/374319