Chromatin Profiling Reveals Regulatory Network Shifts and a Protective Role for Hepatocyte Nuclear Factor 4α during Colitis

Abstract

h Transcriptional regulatory mechanisms likely contribute to the etiology of inflammatory bowel disease (IBD), as genetic variants associated with the disease are disproportionately found at regulatory elements. However, the transcription factors regulating colonic inflammation are unclear. To identify these transcription factors, we mapped epigenomic changes in the colonic epithelium upon inflammation. Epigenetic marks at transcriptional regulatory elements responded dynamically to inflammation and indicated a shift in epithelial transcriptional factor networks. Active enhancer chromatin structure at regulatory regions bound by the transcription factor hepatocyte nuclear factor 4␣ (HNF4A) was reduced during colitis. In agreement, upon an inflammatory stimulus, HNF4A was downregulated and showed a reduced ability to bind chromatin. Genetic variants that confer a predisposition to IBD map to HNF4A binding sites in the human colon cell line CaCo2, suggesting impaired HNF4A binding could underlie genetic susceptibility to IBD. Despite reduced HNF4A binding during inflammation, a temporal knockout model revealed HNF4A still actively protects against inflammatory phenotypes and promotes immune regulatory gene expression in the inflamed colonic epithelium. These findings highlight the potential for HNF4A agonists as IBD therapeutics.T he colonic epithelium is an integral component in inflammatory bowel disease (IBD) pathology, as compromised epithelial integrity permits increased interaction between the gut immune system and luminal antigens. However, the colonic epithelium is not merely a passive barrier against luminal microbes; active epithelial roles include antigen presentation, adaptive and innate immune regulation, and antimicrobial peptide production, among others (1-3). A detailed molecular understanding of the epithelium's role in IBD and how the epithelium responds to an inflammatory insult could offer therapeutic alternatives or innovations to current treatments.Transcriptional regulatory networks serve as the interface between the extracellular environment and genome regulation. Defining how the regulatory networks of the epithelium respond to inflammation could provide important insights into the role of the epithelium in IBD. Transcriptional regulatory networks can be inferred from a cell's epigenome, which is a collection of epigenomic marks, typically a histone posttranslational modification that is associated with a particular genome function. Transcriptional enhancer epigenomic marks are strong predictors of cellular identity and gene expression (4, 5). Nucleosomes containing histone 3, lysine 27 acetylation (H3K27ac) can be used to identify regions that have distal regulatory activity (transcriptional enhancers), flank chromatin-accessible transcription factor binding regions, and are predictive of active transcription in a conditionspecific manner (4, 6, 7). Changes in H3K27ac levels and DNA accessibility predict changes in transcription factor occupancy (8, 9); dynamic enhancer chromatin structur...

Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha

“…DSS-induced colitis results in reduced HNF4A protein levels and altered cellular localization (Chahar et al 2014); however, our results indicate the microbiota neither reduce HNF4A protein levels nor impact its nuclear localization in jejunal IECs 2 wk after colonization (Supplemental Fig. S6H,I).…”

“…HNF4A has been shown to play key roles in anti-oxidative and anti-inflammatory defense mechanisms (Marcil et al 2010), so aberrant microbial suppression could promote an inflammatory state. HNF4A target genes are down-regulated in human IBD (Arijs et al 2009;Haberman et al 2014) and mouse experimental colitis (Chahar et al 2014), and the HNF4A target APOA1 has been shown to be protective against intestinal inflammation in mice (Gkouskou et al 2016). We speculate that the genes governed by this novel microbiota-HNF4A axis may include additional anti-and pro-inflammatory factors that could provide new targets for IBD therapy.…”

Systematic analysis of chromatin interactions at disease associated loci links novel candidate genes to inflammatory bowel disease

“… IL10RA : The IL10-receptor consists of the two subunits IL10RA and IL10RB. Sequence variants in genes encoding these two subunits are known to cause severe very early onset IBD in a monogenic fashion [32]. While the association of IL10RB with the complex form of IBD was reported by GWASs, the link with IL10RA was so far missing. SMAD5: SMAD5 is a downstream effector in BMP signaling.…”

Differential Effects of Hepatocyte Nuclear Factor 4α Isoforms on Tumor Growth and T-Cell Factor 4/AP-1 Interactions in Human Colorectal Cancer Cells

“…4A). Wound healing was another common category, consistent with HNF4␣ playing a role in protecting the colonic epithelium from inflammatory bowel disease (10,11,13,27,78). In contrast, HNF4␣2 specifically upregulated genes involved in cell death and response to extracellular stimuli, while the only category of genes upregulated only by HNF4␣8 was cell adhesion, although several of those genes actually promote cell growth (Fig.…”