HETEROGENEITY AND PLASTICITY OF THE NAÏVE CD4+ T CELL COMPARTMENT

Author

Alia Sajani, Dartmouth CollegeFollow

Date of Award

Spring 4-12-2024

Document Type

Thesis (Ph.D.)

Department or Program

Microbiology and Immunology

First Advisor

Randolph Noelle

Second Advisor

Mary Jo Turk

Abstract

Recent studies have illuminated unexpected heterogeneity in the naïve T cell compartment. Using single cell RNA sequencing of mouse naïve CD4⁺ T cells, we identified 5 unique transcriptional subsets within the naïve CD4⁺ T cell compartment. These include a quiescence cluster (T^Q) marked by Klf2, Klf6, Jun and Btg2, a memory-like cluster (T^MEM) marked by Ccr7, Il7r and Tcf7, a TCR reactive cluster (T^TCR) marked by Cd5, Cd6 and Nr4a1, an IFN responsive cluster (T^IFN) marked by Stat1, Irf7 and Ifit1 and an undifferentiated cluster (T^UND) marked by cytoskeletal genes like Act1g. We also identified conservation of these naïve CD4⁺ T cell subsets in mice and human, and were able to identify these naïve CD4⁺ T cell subsets in two publicly available datasets. These clusters emerge in the thymus, at the single positive T cell developmental stage, and are maintained in recent thymic emigrants and mature conventional CD4⁺ T cells in the periphery. Pseudotime analysis indicates that T^IFN is the most terminally differentiated naïve CD4⁺ T cell subset. Additionally, we examined how immune contexts such as microbiome, inflammation, tonic signaling and cytokine experience impact homeostatic stability and plasticity of the naïve CD4⁺ T cell compartment. To assess the functional relevance and biases in differentiation fates of the identified naïve T cell subsets, we utilized GFP reporter mice that express transcriptional factors unique to each cluster, specifically Mx1-GFP, Nur77-GFP and KLF2-GFP. We isolated GFP^HI and GFP^LO naïve CD4⁺ T cells from each reporter strain and showed that upon TCR activation and culture in T helper conditions, T^IFN and T^Q are biased towards Th1 and Th17 fates, while T^TCR is an overall hyporesponsive subset of naïve CD4⁺ T cells. Upon examination of human naïve CD4⁺ T cells in health and in the autoimmune disease lupus, we show that T^IFN expands in disease, and this expansion is correlated with disease severity as measured by SLEDAI score. Finally, in autoimmune disease, naïve CD4⁺ T cells lose their homeostatic stability, suggesting that bystander naïve T cells are shaped by their surroundings.

Recommended Citation

Sajani, Alia, "HETEROGENEITY AND PLASTICITY OF THE NAÏVE CD4+ T CELL COMPARTMENT" (2024). Dartmouth College Ph.D Dissertations. 236.
https://digitalcommons.dartmouth.edu/dissertations/236