The mechanisms of pathogen sensing and immune effector induction in intestinal epithelial cells are not
completely understood. Disruption in the mechanisms of pathogen sensing and immune homeostasis in
intestinal epithelial cells can lead to dysbiosis and inflammation, as well as susceptibility to bacterial infection.
Key insights into intestinal epithelial cell immunity and host-pathogen interactions have been made using the
nematode C. elegans. Nematodes mount innate immune defenses against bacterial infection via conserved
immune pathways, but the mechanisms of pathogen detection are unknown in this organism. In nematodes,
the family of nuclear hormone receptors (NHRs) has dramatically expanded compared to other metazoans.
NHRs are ligand-gated transcription factors that sense endogenous and exogenous signals to induce adaptive
transcriptional responses. The C. elegans genome encodes 274 NHRs, of which 260 are homologs of human
HNF4a. HNF4a is a key NHR involved in inflammatory bowel disease, though the mechanism through which
HNF4a mediates inflammatory bowel disease in humans is unknown. The central hypothesis of this proposal is
that C. elegans HNF4a homologs are an ancient family of pathogen sensors whose evolutionary expansion in
C. elegans was driven by their function in detecting diverse pathogens. The following key findings support this
hypothesis: (i) The nuclear hormone receptor, NHR-86/HNF4a, senses the cellular environment and activates
C. elegans intestinal immune defenses; (ii) NHR-86/HNF4a is required for pathogen resistance and immune
response towards the gram positive human pathogen E. faecalis; and (iii) A different C. elegans HNF4a
homolog is required for pathogen defense and immune effector regulation against the gram negative pathogen
P. aeruginosa. In this proposal, Aim 1 will define the role of C. elegans NHR-86/HNF4a in pathogen detection
and immune effector induction during E. faecalis infection using a combination of transcriptomics, ChIP-
sequencing, tissue-specific rescue and genetic epistasis. Aim 2 will characterize the function of a separate C.
elegans HNF4a homolog in pathogen sensing during P. aeruginosa infection. The approach includes:
transcriptomics, global NHR binding site identification, tissue specific rescue, and P. aeruginosa genetics.
Collectively, these studies will characterize a fundamentally new paradigm of immune activation, which will
solve a major conundrum of how pathogens are sensed in C. elegans. These findings will also establish NHRs
as evolutionarily ancient pathogen sensors. Ultimately, the expectation is that detailed dissection of this
mechanism will shed light on the role of HNF4a in mammalian pathogen sensing and inflammatory bowel