Deciphering the role of microbiome-fibroblast crosstalk in intestinal immune development, homeostasis and inflammation

The microbiome plays an essential role in intestinal immune development, homeostasis and inflammatory bowel diseases (IBD), however, our understanding of the underlying mechanisms by which it regulates these processes remains incomplete. Intestinal fibroblasts (iFB) are a heterogeneous population of tissue-resident cells increasingly recognized for their role in immune regulation. In preliminary studies, the host group and a collaborator found that human and mouse iFB express distinct arrays of microbial sensors and immune mediators and that iFB transcription is altered in germ-free mice. In my proposed project, I will combine state-of-the-art high dimensional flow cytometry, single cell (sc)RNA-seq, CITE-seq, spatial transcriptomics and bioinformatics analysis with animal models and analysis of human intestinal datasets to test the hypothesis that microbiome-iFB crosstalk plays a key role in intestinal immune system development, homeostasis and inflammation. Microbiome impact on iFB and intestinal immune system development will be assessed throughout the weaning period by treating mice with broad-spectrum antibiotics and/or antifungals. The importance of direct iFB-microbiome sensing for immune homeostasis and inflammation will be assessed as above as well as in dextran sulphate sodium (DSS)-induced colitis model in mice whose FB are deficient in either the Toll-like receptor signaling adaptor Myd88 or the C-type lectin receptor-Syk mediated antifungal response adaptor CARD9. Finally, translational aspects will be assessed through extensive bioinformatics analysis of iFB scRNA-seq datasets to map microbial sensor expression in human iFB subsets, evidence of downstream signaling through such sensors and their alterations in IBD. Collectively, this project uses a multi-systems approach to obtain novel insights into the importance of microbiome-iFB interactions in intestinal immune system homeostasis and disease with potential relevance for IBD management.