Extrinsic and intrinsic regulation of intestinal stem cell injury and regeneration Restricted; Files & ToC

Abstract

The intestinal epithelium must sustain digestion, nutrient absorption, and host defense while renewing itself every few days, a task maintained by intestinal stem cells (ISCs). When ISCs are depleted, often through chemotherapy or radiation-induced injury, the intestine mounts a highly plastic response in which recent descendants and progenitors transiently reacquire stem-like competence to rebuild the tissue. How extrinsic context and intrinsic chromatin regulation jointly govern this intestinal injury response remains incompletely defined. This dissertation addresses both dimensions. First, I show that colonization with the  eukaryotic commensal Tritrichomonas muris (Tmu) heightens doxorubicin (DXR)-induced intestinal injury. Even prior to DXR, Tmu-colonized mice exhibit elevated inflammatory tone, reduced tight-junction gene expression, and altered bacterial community composition. After DXR, these features associate with increased epithelial apoptosis, consistent with a two-hit model in which baseline barrier perturbation and microbiome remodeling amplify chemotoxic injury. These findings highlight neglected contributors to mucositis beyond bacteria and demonstrate how housing-specific microbiota can shift phenotypes and complicate cross-study comparison. Secondly, I define a role for the DNA demethylase Tet1 in epithelial plasticity after targeted ablation of Lgr5⁺ active ISCs (aISCs). Using an inducible, epithelium-specific Tet1 knockout combined with the Lgr5-2A-DTR model, I profiled FACS-sorted  Sox9^EGFP compartments by RNA-seq and ATAC-seq. Despite minimal global changes in chromatin accessibility, Tet1 loss produced compartment-specific transcriptional perturbations, most prominently in Sox9^low cells consistent with facultative ISCs (fISCs), that point to greater activation of fISC programs alongside elevated lineage programs in the absence of Tet1. Inferred transcription-factor occupancy also shifted, implicating perturbations across multiple levels of chromatin organization. Together, these data support a model in which Tet1 buffers responses to regenerative cues and decommissions lineage identity to permit unbiased reconstitution of the ISC pool, potentially through coordination of DNA-modification states and higher-order chromatin features rather than wholesale accessibility remodeling. Overall, this dissertation advances an integrated framework in which intestinal regeneration emerges from the interplay between extrinsic context and intrinsic regulatory factors.

Table of Contents

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About this Dissertation

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School	Laney Graduate School
Department	Biological and Biomedical Sciences
Subfield / Discipline	Genetics and Molecular Biology
Degree	Ph.D.
Submission	Dissertation
Language	English
Research Field	Biology, Bioinformatics Biology, Molecular Biology, Genetics
Keyword	Stem cells Regeneration Intestine Chromatin Microbiome
Committee Chair / Thesis Advisor	Adam Gracz, Emory University
Committee Members	Christopher Scharer, Emory University Bing Yao, Emory University Roger Deal, Emory University Kenneth Moberg, Emory University

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