To date, genome-wide association studies (GWAS) have identified 418 independent genetic risk loci contributing to inflammatory bowel disease (IBD) and its two subtypes: ulcerative colitis (UC) and Crohn’s disease (CD) (PMID:37156999). Deciphering disease mechanisms from these data is an outstanding challenge. Like other complex diseases, the majority of IBD risk variants are noncoding. If causal, they likely alter transcription factor (TF) binding, gene regulatory control loci (e.g., promoters, enhancers) and gene expression in particular cell types and contexts (e.g., age, disease).

To identify potential cell types, contexts and molecular mechanisms mediating IBD genetic risk, we built a novel resource: multiome-seq (tandem single-nuclei (sn)RNA-seq and chromatin accessibility (snATAC)-seq) of intestinal tissue from IBD patients (Fig. 1). From the snATAC-seq data, we generated a first-time atlas of chromatin accessibility (putative regulatory elements) for diverse intestinal cell types in the context of IBD.

For cell types/contexts mediating genetic risk, we reasoned that accessible chromatin will co-localize with genetic disease risk loci. Thus, we systematically tested for significant co-localization of our chromatin accessibility maps and risk variants for 1353 GWAS traits (Fig. 2A) (PMID:29662164). Globally, genetic risk variants for autoimmune diseases are enriched in accessible chromatin of immune populations, while other traits (e.g., colorectal cancer, metabolic phenotypes) are enriched in epithelial and stromal populations. Accessible chromatin maps of CD4+ T cell populations had the most significant enrichment of IBD, UC and CD risk variants. CD8+ T cells and DCs, followed by macrophages, were also significantly enriched in IBD risk loci. These enrichments were mirrored but dramatically reduced in blood-derived CD4+ T cells, CD8+ T cells and DCs of healthy control donors, highlighting the importance of tissue and disease context in deciphering genetic risk variants. In Fig. 2B, we visualize underlying data for the risk locus containing RORA, where an accessible region, unique to CD4+ T cells from inflamed tissue, overlapped an IBD risk variant; further resolution pinpoints the putative enhancer to T follicular helper (Tfh) cells. Altered regulation of at this risk locus in Tfh could promote Tfh development by repression of RORA, a Th17 regulator. Increased circulating Tfh is associated with disease activity in UC patients (PMID:32117258).

Future work includes prediction of gene regulatory mechanisms from these data (altered TF binding (PMID:36719906), gene regulatory and cell-cell communication networks (PMID:36945549)) and making predictions and underlying data web-accessible and interactively explorable to the community.

$Figure 1. Multiome-seq was generated for 36 inflamed or non-inflamed terminal ileal and rectal biopsies of pediatric patients with CD (n=17) or UC (n=9), responsive or refractory to anti-TNFα therapy as defined by endoscopic healing. Quality control of the data yielded 258k nuclei for construction of accessible chromatin maps of intestinal cell types. DC = dendritic cell; TA = transit amplifying epithelial cell; NK cell = natural killer cell; ILC = innate lymphoid cells; CD4+TM = CD4+ memory T cell; CD4+Teff = CD4+ T effector cell; Treg = regulatory T cell; Tfh = T follicular helper cell.$

Figure 1. Multiome-seq was generated for 36 inflamed or non-inflamed terminal ileal and rectal biopsies of pediatric patients with CD (n=17) or UC (n=9), responsive or refractory to anti-TNFα therapy as defined by endoscopic healing. Quality control of the data yielded 258k nuclei for construction of accessible chromatin maps of intestinal cell types. DC = dendritic cell; TA = transit amplifying epithelial cell; NK cell = natural killer cell; ILC = innate lymphoid cells; CD4⁺TM = CD4⁺ memory T cell; CD4⁺Teff = CD4⁺ T effector cell; Treg = regulatory T cell; Tfh = T follicular helper cell.

<b>Figure 2.</b> <b>(A)</b> Chromatin accessibility maps, resolved by cell type, tissue and inflammatory status, were systematically tested for co-localization with curated genetic risk variants for 1,353 GWAS phenotypes. Enrichments for selected phenotypes are shown. To better visualize relative enrichments across cell types and context, the enrichment values (-log<sub>10</sub>(P<sub>adj</sub>)) are Z-scored. <b>(B)</b> Underlying chromatin accessibility data for a single IBD risk locus at <i>RORA</i>, in which an accessible chromatin region, unique to the inflamed intestinal Treg/Tfh population overlapped an IBD risk variant (left). Further resolution of this population pinpoints the putative enhancer in the <i>RORA</i> locus to T follicular helper (Tfh) cells (top right), while linked <i>RORA</i> transcript expression (bottom right) correlates with accessibility.

Figure 2. (A) Chromatin accessibility maps, resolved by cell type, tissue and inflammatory status, were systematically tested for co-localization with curated genetic risk variants for 1,353 GWAS phenotypes. Enrichments for selected phenotypes are shown. To better visualize relative enrichments across cell types and context, the enrichment values (-log₁₀(P_adj)) are Z-scored. (B) Underlying chromatin accessibility data for a single IBD risk locus at RORA, in which an accessible chromatin region, unique to the inflamed intestinal Treg/Tfh population overlapped an IBD risk variant (left). Further resolution of this population pinpoints the putative enhancer in the RORA locus to T follicular helper (Tfh) cells (top right), while linked RORA transcript expression (bottom right) correlates with accessibility.

Emily Miraldi

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