Celiac and inflammatory bowel diseases: functional post-GWAS approach

ABSTRACT Celiac disease (CeD) is one of the most prevalent yet understudied gastrointestinal disorders in the U.S., and there is a critical need to understand genotype-phenotype relationships and underlying mechanisms, to improve patient care. Likewise inflammatory bowel disease (IBD; comprising ulcerative colitis and Crohn’s disease), another prevalent autoimmune/inflammatory disorder, presents stubborn challenges including a wide range of severity and poorly predictable treatment responses. Genomics-based precision medicine for these diseases will benefit from new approaches that can go beyond genome-wide association study (GWAS) data to better stratify patients for disease risk, severity, and treatment response. Genotype-dependent allele-specific DNA methylation (ASM), a focus of our lab (Tycko; HMH-CDI), can be a useful “post-GWAS” tool. Our work has suggested that ASM differentially methylated regions (ASM DMRs) are footprints of allele-specific transcription factor (TF) binding, and thus can act as signposts for functional regulatory SNPs (rSNPs) under GWAS peaks, with direct relevance to CeD and IBD. To apply this approach to a key target cell type in CeD and CD/IBD, namely the intestinal epithelial cell (IEC), as well as immune cell types, we are collaborating in multi-PI format with Hamilton and her colleagues at CHOP, who have extensive expertise in biological and clinical aspects of these diseases. Our project, bolstered by new and extensive preliminary data, combines genomic + epigenomic mapping with mechanistic studies in cell lines and primary human IEC organoids, to define which polymorphic TF binding motifs, and which transcriptional pathways and external environmental signals have roles in CeD and CD/IBD. First, to map ASM DMRs under a greater number of CeD and IBD GWAS peaks and identify tissue-specific ASM in these regions, we will generate whole-genome bisulfite sequencing data (WGBS; methyl-seq) from key cell types, with a major focus on IECs. Second, to test polymorphic TF binding motifs as the underlying mechanism leading to ASM at CeD and IBD risk loci, we will carry out site-directed mutagenesis in human cell lines using CRISPR-Cas9 and assess the effects on ASM and allele-specific gene expression. Third, to ask whether external factors in the cellular microenvironment, converging on cellular TF levels, are reflected in changes in the strength of ASM at CeD and IBD risk loci, we will manipulate IECs from organoid cultures using a series of disease-relevant external stimuli and identify changes in ASM strength that correlate with changes in expression of cognate TFs. We expect that our research will elucidate disease-specific and cell type-specific transcriptional and epigenetic pathways that are both genotype-dependent and sensitive to acute and chronic effects of the cellular environment, with implications for future precision medicine approaches that can go beyond GWAS and polygenic risk scores to incorporate gene-environment interactions – leading to improved disease prevention and treatment.