Development of the inflammatory bowel diseases (IBD) has been linked to altered homeostatic relationships between the intestine and the microbiota it harbors. However early preclinical stages of IBD remain poorly understood, especially with respect to host-microbiota interactions. The nuclear receptor transcription factor Hepatocyte nuclear factor 4 alpha (HNF4A) has important roles in intestinal epithelial cell (IEC) physiology, and our recent studies in zebrafish and mice revealed that HNF4A activity in IEC is suppressed by intestinal microbiota. Variants at HNF4A have been associated with human IBD, and IEC-specific knockout of Hnf4a in mice ( Hnf4a ΔIEC ) leads to spontaneous colonic inflammation by 6-12 months. We hypothesized that intestinal pathology in Hnf4a ΔIEC mice may begin earlier in life and that microbiota may contribute to that process. Longitudinal analysis revealed that Hnf4a ΔIEC mice reared in specific pathogen-free (SPF) conditions develop fecal lipocalin 2 (LCN2) flares and episodic loose stools beginning as early as 4-5 weeks of age. Lifetime cumulative LCN2 levels correlated with histopathological features of colitis at 12 months of age. Antibiotic and gnotobiotic tests showed that these phenotypes in Hnf4a ΔIEC mice were dependent on the presence of microbiota. Fecal 16S rRNA gene sequencing in an SPF cohort of Hnf4a ΔIEC mice and controls at 12 months of age disclosed that genotype was a significant contributor to alterations in microbiota composition. Longitudinal analysis in a subset of inflamed Hnf4a ΔIEC and wild-type mice revealed that microbial community differences emerged at early life stages when fecal LCN2 flares first arose. These microbiota differences included a salient increase in the relative abundance of Akkermansia muciniphila in a subset of Hnf4a ΔIEC mice. We isolated an A. muciniphila strain from an aged, inflamed Hnf4a ΔIEC mouse, and its genome sequence revealed it to be a member of a new Akkermansia phylogroup with genetic features distinct from the known phylogroups. We conclude that HNF4A functions in IEC throughout the lifespan to protect against episodic flares of inflammation induced by microbiota while also shaping microbiota assembly. These results establish Hnf4a ΔIEC mice as a useful model for investigating preclinical pathology and host-microbiota interactions that precede overt IBD onset. NIH P01-DK094779 This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

The inflammatory bowel diseases (IBD) occur in genetically susceptible individuals who mount inappropriate immune responses to their microbiota leading to chronic intestinal inflammation. Whereas IBD clinical presentation is well described, how interactions between microbiota and host genotype impact early subclinical stages of the disease remains unclear. The transcription factor hepatocyte nuclear factor 4 alpha (HNF4A) has been associated with human IBD, and deletion of Hnf4a in intestinal epithelial cells (IECs) in mice (Hnf4aΔIEC) leads to spontaneous colonic inflammation by 6-12 mo of age. Here, we tested if pathology in Hnf4aΔIEC mice begins earlier in life and if microbiota contribute to that process. Longitudinal analysis revealed that Hnf4aΔIEC mice reared in specific pathogen-free (SPF) conditions develop episodic elevated fecal lipocalin 2 (Lcn2) and loose stools beginning by 4-5 wk of age. Lifetime cumulative Lcn2 levels correlated with histopathological features of colitis at 12 mo. Antibiotic and gnotobiotic tests showed that these phenotypes in Hnf4aΔIEC mice were dependent on microbiota. Fecal 16S rRNA gene sequencing in SPF Hnf4aΔIEC and control mice disclosed that genotype significantly contributed to differences in microbiota composition by 12 mo, and longitudinal analysis of the Hnf4aΔIEC mice with the highest lifetime cumulative Lcn2 revealed that microbial community differences emerged early in life when elevated fecal Lcn2 was first detected. These microbiota differences included enrichment of a novel phylogroup of Akkermansia muciniphila in Hnf4aΔIEC mice. We conclude that HNF4A functions in IEC to shape composition of the gut microbiota and protect against episodic inflammation induced by microbiota throughout the lifespan. IMPORTANCE The inflammatory bowel diseases (IBD), characterized by chronic inflammation of the intestine, affect millions of people around the world. Although significant advances have been made in the clinical management of IBD, the early subclinical stages of IBD are not well defined and are difficult to study in humans. This work explores the subclinical stages of disease in mice lacking the IBD-associated transcription factor HNF4A in the intestinal epithelium. Whereas these mice do not develop overt disease until late in adulthood, we find that they display episodic intestinal inflammation, loose stools, and microbiota changes beginning in very early life stages. Using germ-free and antibiotic-treatment experiments, we reveal that intestinal inflammation in these mice was dependent on the presence of microbiota. These results suggest that interactions between host genotype and microbiota can drive early subclinical pathologies that precede the overt onset of IBD and describe a mouse model to explore those important processes.

As inflammatory bowel diseases (IBD) develop, the host’s homeostatic relationship with their microbiota changes. Early “preclinical” stages of colitis are relatively understudied, especially with respect to host-microbiota interactions. Intestinal epithelial cells (IECs) serve as the primary host interface for host-microbiota interactions, and their functions are achieved through specific transcriptional regulatory programs. Hepatocyte nuclear factor 4 alpha (HNF4A) is a nuclear receptor transcription factor known to regulate IEC development, barrier function, and metabolism.