Atlas of Promoter-Enhancer Interactions in Human ILC3s Links Crohn’s Disease-Associated Variants with Established and Newly Implicated Target Genes

Valeriya Malysheva – University of Antwerp; Helen Ray-Jones – University of Antwerp; Rachel Brown – Ohio State University; Mikhail Spivakov – Imperial College London; Stephen Waggoner – Cincinnati Children's Hospital

Abstract Text: Type 3 innate lymphoid cells (ILC3s) are tissue-resident lymphocytes that maintain homeostasis and regulate inflammation at mucosal barriers. To gain insight into the cis-regulatory circuitries underlying ILC3 function, we used high-resolution Promotor Capture Hi-C to map interactions between promotors and distal regulatory elements in primary human ILC3s. We found that promoter-interacting regions in ILC3s are enriched for genetic variants associated with multiple autoimmune diseases. Given the established role of ILC3s in Crohn’s disease, we devised a Bayesian approach incorporating multivariate fine-mapping to link Crohn’s-associated genetic variants with their putative target genes. This algorithm identified 33 previously known and 56 newly implicated genes expressed by human ILC3s that increase risk for Crohn’s Disease.

One noteworthy candidate gene, Cln3, encodes a ubiquitously expressed transmembrane lysosomal protein. Loss-of-function mutations in Cln3 cause the pediatric neurodegenerative disorder Batten disease. Although extensive research has explored the role of Cln3 in the nervous system, our study is the first to implicate Cln3 in an immune-mediated disease. Therefore, we aimed to experimentally define the ILC3-specific functions of Cln3 and uncover the mechanisms by which Cln3 dysfunction increases Crohn’s Disease risk. We developed CRISPR-dCas9 interference and activation systems in mouse ILC3s to precisely modulate expression of Cln3. Functional studies suggest that Cln3 maintains ILC3 homeostasis through regulating autophagy, managing oxidative stress, and modulating inflammatory pathways. Our ongoing research aims to rigorously define the function Cln3 in ILC3 biology, with the potential to reveal common mechanisms underpinning diverse neurodegenerative and inflammatory diseases.