Interactions between the microbiota and host transcription factor HNF4A in the intestinal epithelium regulate intestinal inflammation throughout the lifespan

Abstract

The inflammatory bowel diseases (IBD) occur in genetically susceptible individuals that mount inappropriate immune responses to their microbiota leading to chronic intestinal inflammation. The natural history of IBD progression includes early subclinical stages of disease occurring before disease is diagnosed in the clinic. There is evidence in first degree relatives of IBD patients and members of the general population who go on to develop IBD, that these stages are characterized by increased gut barrier permeability, increased levels of inflammation biomarkers, detection of microbiota-specific antibodies in sera, and changes in microbiota composition. Mouse models can be a useful tool in studying disease dynamics during these early stages. The transcription factor Hepatocyte nuclear factor 4 alpha (HNF4A) has been associated with human IBD, and deletion of Hnf4a in intestinal epithelial cells (IEC) in mice (Hnf4aΔIEC) leads to spontaneous colonic inflammation by 6-12 months of age. However, early stages of disease in this mouse model were not well defined, and the role of microbiota in promoting disease was also unclear. Here I tested if pathology in Hnf4aΔIEC mice begins earlier in life and if microbiota contribute to that process, as well as later inflammatory stages of disease. Longitudinal analysis revealed that Hnf4aΔIEC mice reared in specific pathogen-free (SPF) conditions develop episodically elevated fecal lipocalin 2 (Lcn2) and episodic loose stools beginning by 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 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 months, 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. I conclude that HNF4A functions in IEC to shape composition of the gut microbiota, and protect against episodic inflammation induced by microbiota throughout the lifespan. Lastly, I discuss future directions for this work, including using single cell RNA sequencing of the colonic epithelium to identify genes regulated by HNF4A in distinct colonic epithelial cell types, gnotobiotic studies using the strain of Akkermansia muciniphila we isolated to test the hypothesis that it can promote disease in Hnf4aΔIEC mice, testing clinically relevant disease triggers using this mouse IBD model, and further immune cell profiling.