Date of Award

9-7-2023

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Immunology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type

Dissertation

Abstract

The immune system plays a critical role in maintaining tissue homeostasis and defending against pathogens. Recent discoveries have highlighted the significance of tissue-resident memory T cells (TRM) and Innate Lymphoid Cells (ILCs) in tissue immunity. TRM exhibit memory-like properties, persist long-term in various tissues, and express markers such as CD69, CD103, and transcription factors like Hobit and Blimp-1. Similarly, ILCs, considered the innate counterparts of T cells, are abundant at barrier organs and mucosal sites, sharing similar markers and transcriptional factors with TRM, and rapidly responding to insults. Unraveling the heterogeneity and function of tissue-resident lymphocytes is crucial for understanding immune responses. Here, we focused on elucidating the heterogeneity of T cells within the human small intestine (SI) and the challenges associated with characterizing human ILC1s. Firstly, we characterized T cells in the SI of both healthy individuals and patients with Crohn's disease (CD). Utilizing cutting-edge single-cell profiling techniques, we characterized T cells isolated from the intestinal epithelium layer (IEL) and lamina propria (LP) from the terminal ileum of either healthy or CD patients. We discovered unique T cell subsets, including NKp30+γδT cells expressing RORγt and producing IL-26 upon NKp30 engagement within the IEL. Comparative analyses between inflamed and non-inflamed regions of CD patients and healthy controls revealed altered spatial distribution of T cell subsets, suggesting potential links between transmural inflammation and changes in IEL and LP T cell populations. Secondly, we aimed to characterize Innate Lymphoid Cells (ILCs) within human tissues, specifically focusing on ILC1s. Unlike their well-characterized mouse counterparts, human ILC1s lack definitive markers, posing challenges in their distinction from other ILC subsets, especially NK cells. Leveraging single-cell RNA sequencing (scRNAseq) and flow cytometry validation, we explored the heterogeneity and functional diversity of human NKs and ILC1s. Our study identified distinct populations of ILC1s with varying abundance and characteristics across different tissues. For instance, intraepithelial ILC1s in the tonsil expressed the EOMES transcript, while the intestinal epithelium contained both mature EOMES–ILC1s expressing PRDM1 and immature TCF1+ILC1s. Additionally, the lung harbored ZNF683+ILC1s emerging from a fibrotic environment, and a minor population of immature TCF7+EOMES–ZNF683+ILC1s was observed in the blood. Furthermore, novel clusters of NK cells were identified through scRNAseq analysis. Collectively, these findings provide valuable insights into the heterogeneity, functional profiles, and spatial distribution of T cells and ILCs within human tissues. The observed alterations in T cell subsets in CD pathogenesis and the characterization of distinct NK and ILC1 populations across tissues open new avenues for understanding tissue-specific immunity and immune dysregulation in disease settings. This research significantly contributes to our knowledge of tissue-resident lymphocytes and their implications in immune responses and disease pathogenesis.

Language

English (en)

Chair and Committee

Marco Colonna

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