# Microbial regulation of intestinal epithelial gene expression

> **NIH NIH R01** · DUKE UNIVERSITY · 2024 · $683,483

## Abstract

Abstract
The intestinal epithelium serves essential functions of dietary nutrient absorption and defense against microbial
infections through the coordinated regulation of gene expression. Intestinal microbiota significantly influence
gene transcription in intestinal epithelial cells (IECs), including both induction and suppression of distinct gene
sets. We have shown that many microbially-suppressed genes are under control of the host transcription factor
(TF) HNF4A and are involved in differentiation and metabolism of absorptive enterocytes. Microbially-induced
genes are predicted to be downstream of TF pathways including IRF and NFκB and include genes involved in
proliferation, inflammation, and immune defense. What remains unknown is if these distinct microbiota-induced
and microbiota-suppressed TF pathways communicate with each other and how they are balanced within IECs
to maintain intestinal homeostasis. Our preliminary studies have revealed that these two opposing TF
pathways directly communicate within IECs to promote homeostasis by regulating responses to microbes. We
find that HNF4A activity in mouse IECs is suppressed by microbiota and protects against microbiota-driven
intestinal inflammation. Using single cell RNA sequencing in wild-type gnotobiotic mice, we have uncovered
significant heterogeneity in gene expression profiles among enterocytes. For example, immune genes are
induced in enterocytes by microbiota and are negatively correlated with HNF4A-dependent genes, implying
divergent transcriptional programs. We also find that IEC-specific deletion of Hnf4a leads to induction of
immune genes and enhanced protection from enterovirus infection, further confirming a negative relationship
between HNF4A and immune programs. In accord, proteomic studies in gnotobiotic mouse IECs and pathway
manipulations in human cells revealed significant interactions between HNF4A and immune signaling pathway
components. These data support our central hypothesis that HNF4A and immune pathways represent distinct
microbiota-regulated enterocyte programs, and that HNF4A suppresses the immune program and thereby
increases vulnerability to enterovirus infection. To test this, we will define the roles of HNF4A in mediating the
impacts of microbiota on IEC gene regulatory programs and enterovirus infection. We will also identify the
molecular mechanisms by which HNF4A and immune pathways interact to regulate gene expression. The
expected outcomes will vertically advance the field in several ways. First, they will provide an in-depth
understanding of how interactions between the microbiota and HNF4A determine IEC differentiation, gene
expression, chromatin organization, and enterovirus infection. Second, they will yield unprecedented insights
into the molecular mechanisms by which HNF4A and immune pathways communicate within the same cell.
These results are expected to have a positive impact because they would provide important fundamental
knowledge about int...

## Key facts

- **NIH application ID:** 10999589
- **Project number:** 1R01DK141168-01
- **Recipient organization:** DUKE UNIVERSITY
- **Principal Investigator:** John F Rawls
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $683,483
- **Award type:** 1
- **Project period:** 2024-07-15 → 2028-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10999589

## Citation

> US National Institutes of Health, RePORTER application 10999589, Microbial regulation of intestinal epithelial gene expression (1R01DK141168-01). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10999589. Licensed CC0.

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