Tu194 - Delineating Target Genes for Autoimmune Disease-associated Enhancer Variants Using 3D Genomics

Katharina Lambert, PhD – Post Doctoral Research Associate, Buckner lab, Benaroya Research Institute; Megan Tatum – Research Technician III, Buckner lab, Benaroya Research Institute; Meenakshi Dunga – Research Technician III, Cerosaletti Lab, Benaroya Research Institute; Stephanie Battle, PhD – Research Scientist, Hawkins lab, University of Washington; Eryn Weston – research scientist 2, Hawkins lab, University of Washington; Karen Cerosaletti, PhD – Center Director of Translational Science, Cerosaletti Lab, Benaroya Research Institute; Jane Buckner, MD – President, Buckner Lab, Benaroya Research institute; David Hawkins, PhD – Associate Professor, Medical Genetics, Genome Science, University of Washington

Abstract Text: To demonstrate that autoimmune-associated enhancer variants have a functional impact, we first prioritized GWAS and proxy variants for rheumatoid arthritis (RA), type 1 diabetes (T1D), allergy, and asthma by overlapping them with disease-relevant cell type enhancer marks H3K4me1 (Th0, Th1, Th2, and Th17), resulting in approximately 8150 enhancer variants. Next, we generated Hi-C maps for the Th1, Th2, and Th17 cell types and captured enhancer regions of interest, recovering approximately 80% of the targeted region and allowing us to assigned target genes for 70% targeted T1D enhancers, 78% of targeted RA enhancers, 67% targeted asthma enhancers and 70% of targeted allergy enhancers. Our results validate known eQTL target genes, and also identify cell type-specific regulatory interactions, including interactions with genes important for maintaining cellular specificity. In order to validate regulatory loops, we have performed CRISPRi for a subset of enhancers in different T cell types. To determine functional enhancer variants, we performed massively parallel reporter assays (MPRA) for a subset of the prioritized variants. Here we tested 1435 Th1 enhancer variants and 2375 Th2 enhancer variants in their respective cell types. At 5% FDR, 53 enhancer variants show significant allelic activity in Th1 cells, and 91 variants show significant allelic activity in Th2 cells. By combining capture Hi-C target genes with MPRA activity and CRISPRi validations, we have identified putative causal variants and novel target genes for autoimmune disease-associated enhancer variants.