Differentiation of CD8 T cells during chronic viral infection Restricted; Files Only

Chang, Daniel Yunmin (Summer 2021)

Permanent URL: https://etd.library.emory.edu/concern/etds/s7526d822?locale=en


CD8 T cells play a vital role in immunity against pathogens. After vaccination or clearance of an acute infection, long-lived memory T cells are generated and provide long-term immunity. However, if the antigen persists such as during chronic viral infections and cancer, CD8 T cells adapt to upregulate inhibitory receptor contributing to their dysfunction. Recently, our lab has discovered a novel subset of stem-like CD8 T cells residing in the T cell zones of lymphoid tissues that give rise to exhausted subsets in a chronic antigen setting. These PD-1+ TCF1+ cells are normally quiescent but provide the proliferative burst after PD-1 blockade. My work aims to establish the TCR relationship between the stem-like and the exhausted CD8 T cells at homeostasis and after immunotherapy, and second, study the fate and phenotype of these subsets after the clearance of chronic antigen stimulation. 

First, we investigated the progenitor-progeny relationship between the stem-like and exhausted CD8 T cells during chronic viral infection. At the late time point of infection, almost all the repertoires of exhausted cells were shared with stem-like cells which were composed of only a handful of dominant clonotypes. This suggested that the stem-like CD8 T cells act as quiescent resource cells that maintain the T cell response during chronic viral infection. We then compared the repertoire in the context of an acute infection. In contrast, the repertoire during and after an acute infection was rich and broad while the repertoire during the chronic viral infection started broad but shrank in diversity at the later time point. The emergence of dominant clonotypes raised questions about the heterogeneity within clonotypes. Single-cell analyses elucidated potential heterogeneity in phenotype between the dominant and sub-dominant clonotypes. Because the stem-like CD8 T cells are crucial target of PD-1 blockade, we studied the changes of the TCR repertoire after PD-1 monotherapy, in combination with TLR7 agonist, and in combination with low-dose IL-2. PD-1 blockade alone did not have a significant impact on the TCR repertoire but in combination with TLR7 agonist, improved the repertoire to be more diverse. Interestingly, the IL-2 combination therapy biased the repertoire to one or two dominant clonotypes. These results suggest that the dendritic cells play an important role in differentiating stem-like CD8 T cells and cell intrinsic expression of CD25, the high affinity receptor of IL-2, may be driving the clonal bias during IL-2 combination therapy. 

We still do not know if memory after the clearance of chronic viral infection is generated. Antigen-specific CD8 T cells one year after the chronic viral infection was characterized. Similar to the canonical memory cells, TCF1+ CD127+ CD62L+ cells were observed long after the clearance of chronic viral infection. These chronic memory cells were transcriptionally distinct from the central memory cells found after an acute infection and resembled the stem-like CD8 T cells found during the chronic infection. To study the ontology of these cells after the chronic viral infection, the stem-like CD8 T cells were parked into an antigen-free environment. Interestingly, the stem-like CD8 T cells maintained TCF1 and upregulated CD127 and CD62L. Functionally, the chronic memory cells had superior recall potential against rechallenge with the chronic virus. 

We conclude that the differentiation of dominant stem-like CD8 T cell clones into exhausted CD8 T cells maintain the T cell response during the chronic viral infection. Importantly, these quiescent cells differentiate into antigen-independent memory cells that are persistent and able to provide recall response upon antigen rechallenge. Together, our data have implications to act as a potential biomarker of response to PD-1 blockade and its combination and change our paradigm about the generation of memory cells after the clearance of chronic antigen stimulation which is clinically relevant for patients with cancer or chronic viral infection on therapy.

Table of Contents

Table of Contents


Chapter 1: Introduction

1.1       T cell exhaustion

1.2       Imprinting in T cell exhaustion:

1.3       Checkpoint blockade

1.4       Summary

Chapter 2: T cell receptor diversity and lineage relationship between virus-specific CD8 T cell subsets during chronic LCMV infection





LCMV-specific TCR repertoires show substantial overlap between stem-like and exhausted CD8 T cells within mice

LCMV-specific TCR repertoires are private amongst inbred mice

Dominant clonotypes within the exhausted subset are shared with the stem-like population

Virus-specific TCR repertoire diversity contracts during chronic viral infection

Comparison of TCR repertoire diversity between acute and chronic viral infection models


Materials and Methods

Mice and Virus

Flow cytometry, Cell Sorting, gDNA isolation, and TCRβ sequencing

TCR repertoire analysis

Data Analysis


Chapter 3: Defining cell intrinsic mechanisms of clonal bias


Longitudinal analysis of TCR repertoire during chronic viral infection

Single cell analyses of phenotype and TCR repertoire early during chronic viral infection

Single cell analyses of phenotype and TCR repertoire late during chronic viral infection

Chapter 4: The effects of immunotherapies on antigen-specific CD8 TCR repertoire


Effect of PD-1 monotherapy on LCMV-specific CD8 TCR repertoire

Effect of PD-1 combination therapy on LCMV-specific CD8 TCR repertoire

Chapter 5: Phenotype, fate, and function of antigen-specific CD8 T cells after the cessation of chronic antigen stimulation


Development of antigen-specific CD8 T cells with expression of canonical memory markers after chronic viral clearance

Unique gene expression signatures are observed between acute and chronic memory subsets

Differentiation of stem-like CD8 T cells into chronic memory cells after antigen withdrawal

CD62L+ chronic memory subset has similar recall potential as the acute central memory subset against an acute infection

CD62L+ chronic memory subset has superior recall potential upon rechallenge after chronic LCMV

Chapter 6: Discussion


TCR relationship between the stem-like and exhausted CD8 T cell subsets

Effect of immunotherapy on TCR repertoire

Development of antigen-independent memory cells after chronic viral infection


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