Examining the role of epigenetic memory in intestinal regeneration

PROJECT SUMMARY Inflammation promotes regeneration of epithelial tissues, but it is also implicated in intestinal pathologies including cancer, inflammatory bowel diseases and celiac disease. Recent studies in barrier tissues (i.e. skin and airway epithelium) demonstrate that stem cells in these organs maintain a memory of inflammatory

exposure, which enhances their wound healing capacity in later injuries. Whether intestinal stem cells (ISCs) remember encounters with inflammatory stimuli, and how this affects their subsequent function, is poorly understood. Our group recently demonstrated that infection with the enteric helminth Heligmosomoides

polygyrus (Hp) generates inflammatory granulomas in the murine intestine, which alter ISC identity and induce a fetal-like transcriptional signature in granuloma-associated crypts (GACs). Furthermore, we observed that ISCs isolated from GACs maintain this fetal-like identity when cultured as organoids ex vivo, indicating that they retain

a memory of their exposure to helminth infection. The goal of this application is to investigate whether this inflammatory memory is encoded through epigenetic reprogramming of ISCs and how this process impacts their future regenerative capacity. In Aim 1, I will perturb candidate molecular regulators of inflammatory memory

identified through analysis of epigenetic datasets comparing enteroids generated from non-inflamed tissue and fetal-like spheroids generated from GACs. Next, I will examine the in vivo epigenetic landscapes of intestinal crypts from naïve, Hp-infected, and previously infected/recovered mice using the 10x genomics Multiome assay.

This will enable characterization of cell states across conditions and identification of open chromatin domains that are established during inflammation and retained after its resolution. Analysis of transcription factor motifs associated with these regions will provide additional insight into the signaling pathways that control this

phenomenon. In Aim 2, I will study the downstream effects of these epigenetic changes on ISC function. I will first test whether ISCs that had prior exposure to inflammation have increased organoid forming capacity in vitro. I will then investigate whether previously inflamed tissue has faster regeneration kinetics in vivo, by inducing a

second injury and assessing tissue morphology, proliferation, and differentiation. This study will improve our mechanistic understanding of ISC function in regeneration and provide insight into the role of inflammatory memory in intestinal homeostasis and pathology. The proposed research will be carried out under the guidance

of a multi-disciplinary co-mentorship team with expertise in ISC biology and allergic inflammation within the dynamic and collaborative environment of UCSF. The proposed research plan is integrated with a comprehensive training plan which involves building conceptual knowledge in intestinal biology and immunology,

and developing technical proficiency in the use of transgenic animal models, epigenomic assays, and bioinformatic analyses. During this fellowship, I seek to advance my mentorship, networking, and career skills to ultimately enable a successful transition to an independent investigator position at a top-tier academic institution.