There exist fundamental gaps in our understanding of the transcriptional regulatory pathways through which microbiota and inflammation alter gene expression in the intestinal epithelium, and how those pathways promote and might predict intestinal homeostasis. Our long-term goal is to understand the evolutionarily-conserved mechanisms underlying host-microbe interactions in the intestine and how they contribute to human diseases. The overall objectives of this project are to identify conserved transcriptional regulatory pathways mediating intestinal epithelial cell (IEC) responses to microbiota and inflammation, and determine if their activity can be used as phenotypic indicators in human inflammatory bowel disease (IBD). Our preliminary studies in human, mouse, and zebrafish IECs have uncovered striking conservation of transcriptional signatures and regulatory mechanisms, predicting central conserved roles for transcription factors (TF) implicated in human IBD including HNF4A and ELF3. We recently made the key discovery that HNF4A is a novel mediator of IEC transcriptional responses to microbiota in zebrafish and mice. Mechanistic studies in zebrafish and mice revealed that HNF4A is a positive regulator of microbially-suppressed genes, and that microbiota broadly suppress HNF4A activity in IECs. Further, our results show that intestinal suppression of HNF4A target genes is a prevalent feature of human, mouse, and zebrafish models of IBD, and indicate that HNF4A constrains inflammatory responses to microbiota and suppresses a conserved IBD-like gene expression signature. Finally, we identified DNA enhancer elements in mouse IECs that are regulated by microbiota colonization, and leverage those results to implicate ELF3 as a potential integrator of inflammatory and microbial signals in IECs. We will test the central hypothesis that microbiota promote intestinal inflammation by coordinately suppressing anti-inflammatory HNF4A activity and activating ELF3 and other pro-inflammatory transcriptional pathways.
In Specific Aim 1, we will identify host signaling mechanisms mediating microbial suppression of HNF4A activity in IECs.
In Specific Aim 2, we will define the roles of ELF3 and broader transcriptional pathways in IEC responses to microbiota and inflammation, and test if IBD phenotypes are associated with distinct signatures of ELF3 and HNF4A activity. The expected outcomes will vertically advance the field in several ways. First, they will generate a foundational mechanistic understanding of how gut microbes regulate the activity of HNF4A and ELF3, conserved TFs with critical roles in intestinal inflammation. Second, they will provide much-needed insights into the transcriptional regulatory networks utilized by IECs to integrate microbial and inflammatory stimuli, and how those networks are deranged in human IBD. These outcomes are expected to have a significant impact because they will vertically advance our understanding of the IEC transcriptional programs that integrate responses to microbiota and inflammation, which can be expected to lead to new diagnostic, prognostic, and therapeutic approaches for human IBD.

Public Health Relevance

The proposed research is relevant to public health because the discovery of mechanisms by which microorganisms and inflammation influence intestinal gene expression is expected to lead to increased understanding and new treatments for the human inflammatory bowel diseases. The proposed research is therefore relevant to the part of NIH?s mission that pertains to developing fundamental new knowledge that will enhance health and reduce disease burdens.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Research Program Projects (P01)
Project #
Application #
Study Section
Special Emphasis Panel (ZDK1)
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of North Carolina Chapel Hill
Chapel Hill
United States
Zip Code
Cronan, Mark R; Matty, Molly A; Rosenberg, Allison F et al. (2018) An explant technique for high-resolution imaging and manipulation of mycobacterial granulomas. Nat Methods 15:1098-1107
Ellermann, Melissa; Sartor, R Balfour (2018) Intestinal bacterial biofilms modulate mucosal immune responses. J Immunol Sci 2:13-18
Pushalkar, Smruti; Hundeyin, Mautin; Daley, Donnele et al. (2018) The Pancreatic Cancer Microbiome Promotes Oncogenesis by Induction of Innate and Adaptive Immune Suppression. Cancer Discov 8:403-416
Truax, Agnieszka D; Chen, Liang; Tam, Jason W et al. (2018) The Inhibitory Innate Immune Sensor NLRP12 Maintains a Threshold against Obesity by Regulating Gut Microbiota Homeostasis. Cell Host Microbe 24:364-378.e6
Vázquez-Baeza, Yoshiki; Gonzalez, Antonio; Xu, Zhenjiang Zech et al. (2018) Guiding longitudinal sampling in IBD cohorts. Gut 67:1743-1745
Ho, G-T; Aird, R E; Liu, B et al. (2018) MDR1 deficiency impairs mitochondrial homeostasis and promotes intestinal inflammation. Mucosal Immunol 11:120-130
Keith, Benjamin P; Barrow, Jasmine B; Toyonaga, Takahiko et al. (2018) Colonic epithelial miR-31 associates with the development of Crohn's phenotypes. JCI Insight 3:
Huang, Juin-Hua; Liu, Chu-Yu; Wu, Sheng-Yang et al. (2018) NLRX1 Facilitates Histoplasma capsulatum-Induced LC3-Associated Phagocytosis for Cytokine Production in Macrophages. Front Immunol 9:2761
Weiser, Matthew; Simon, Jeremy M; Kochar, Bharati et al. (2018) Molecular classification of Crohn's disease reveals two clinically relevant subtypes. Gut 67:36-42
Sartor, R Balfour; Wu, Gary D (2017) Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches. Gastroenterology 152:327-339.e4

Showing the most recent 10 out of 35 publications