Student Theses and Dissertations

Date of Award


Document Type


Degree Name

Doctor of Philosophy (PhD)

RU Laboratory

Mucida Laboratory


The intestine plays a crucial role in food digestion, nutrient absorption, water retention, and waste excretion. It contains the most populous immune cell reservoir in the body and is continuously exposed to a large and diverse number of diet- and microbiota- derived antigens. The highly stimulating luminal environment is separated from the core of the body, the lamina propria (LP), by just a single layer of epithelial cells. The intestinal immune system is thus tasked with being able to tolerate innocuous stimuli while mounting an effective response against potential pathogens in a controlled manner. To ensure appropriate balance between tolerance and resistance, T cells undergo tissue adaptation upon migrating from the gut-draining mesenteric lymph nodes (mLN) to the intestinal lamina propria and epithelium (IE). We sought to elucidate the transcriptional mechanisms and T cell receptor (TCR) signaling requirements of CD4+ T cell plasticity and adaptation in the intestinal tissues. Within the intestine, peripherally induced Foxp3+ regulatory T cells (iTregs), which are instrumental in limiting inflammatory responses to non-self antigen, are located primarily in the lamina propria. However, CD8aa-expressing intraepithelial CD4+ T cells (CD4- IELs), which also exhibit anti-inflammatory properties and depend on similar environmental cues, reside in the epithelium. Using intravital microscopy, we find distinct cell dynamics of intestinal Tregs and CD4-IELs. We addressed the molecular imprinting of the gut epithelium on T cells by integrating mouse genetics with single-cell RNAsequencing analyses. Transcriptionally, CD4+ T cells from mLN, LP and IE segregate based on the intestinal layer they occupy; trajectory analysis suggests a stepwise loss of CD4-programming and acquisition of an intraepithelial profile as CD4+ T cells adapt to the epithelium and convert to CD4-IELs. We found that upon migration to the epithelium, Tregs can lose Foxp3 expression and convert to CD4-IELs in a microbiota-dependent fashion, an effect in part attributed to loss of the CD4 lineage-defining transcription factor ThPOK. Treg fate-mapping coupled with RNA- and ATAC-sequencing revealed that the Treg program shuts down before an intraepithelial program becomes fully accessible at the epithelium. Ablation of Thpok results in premature acquisition of an IEL profile by mLN Tregs, partially recapitulating epithelium imprinting. Furthermore, we demonstrate that iTregs and CD4-IELs perform complementary roles in the regulation of intestinal inflammation in response to dietary antigen. To uncover the specific role of the T cell receptor in the process of CD4-IEL development, we combined in vivo fate-mapping and gene ablation models with single cell TCRsequencing. Single-cell TCR repertoire and transcriptomic analysis of intraepithelial CD4+ T cells revealed different extents of clonal expansion and TCR overlap between cell states; fully differentiated CD4-IELs from regulatory or conventional CD4+ T cells were the least diverse. Conditional deletion of TCR on differentiating CD4+ T cells or of MHCII on intestinal epithelial cells prevented CD4-IEL differentiation. However, TCR ablation on developed CD4-IELs did not affect their accumulation. Overall, our results reveal an inter- and intra-tissue specialization of anti-inflammatory CD4+ T cells shaped by discrete niches of the intestine. We uncovered the stepwise molecular mechanisms and TCR-signaling requirements for T cells to adapt to the intestinal epithelium. We found that the coordinated replacement of the circulating lymphocyte program with site–specific transcriptional and chromatin changes is necessary for tissue imprinting. Furthermore, our results indicate that local recognition of possibly a limited set of antigens is an essential signal for the differentiation and adaptation of T cells to the epithelium. Taken together, the work presented in this thesis demonstrates that a combination of genetic, TCR, and environmental triggers is crucial in driving T cell plasticity and adaptation to the tissues within the intestine.


A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy

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