Understanding the Role of Circulating and Tissue-Resident T cells in Cancer and Autoimmunity

Abstract

T cells have long been regarded as essential contributors in cancer surveillance and autoimmune disease, due to their vast abilities to coordinate, execute and monitor the adaptive immune response. Although many studies have focused on the important contributions of circulating memory T cells in cancer, there is a large knowledge gap in the development and functions of the recently characterized tissue-resident memory T cell population in the tumor. In addition, while significant strides have been made in understanding the pathogenesis of certain types of cancer, other types are less well understood. In this dissertation, I seek to understand the roles that tissue-resident memory T cells play in cancer by using high-throughput technologies to understand the clonal relationship of T cells in different tissues and to elucidate their tumor protective mechanisms at the single cell level. In a less characterized model of glioma, I also seek to expand our knowledge of the role of circulating effector T cells and to apply these findings to cancer immunotherapy with a novel form of adoptive T cell transfer.Tissue resident memory T cells (TRMs) develop after initial virus encounter and rapidly clear the pathogen. In the tumor environment, the association between increased TRMs in the tumor and prolonged patient survival has been well documented; however, TRM development and direct functions in tumorigenesis remain elusive. To address this, we used a murine breast cancer model and tracked TRM development in the tumor and in the contralateral distant mammary mucosa tissue. Single-cell RNA-sequencing of both intratumor and distant mucosa TRMs revealed two phenotypically distinct populations of TRMs representing their active and quiescent state. We found that TRMs in different tissue compartments shared the same TCR clonotypes and transcriptomes with a subset of intratumoral effector/effector memory T cells (TEff/EMs), clarifying their developmental ontogeny. At the mechanistic level, we showed that tumor production of CXCL16 maintains CXCR6+ TEff/EMs in the tumor, while the CXCR6- population egressed the tumor to form distant TRMs. We found that releasing CXCR6 mediated retention in the primary tumor led to superior control against lung metastases, indicating a potential direct role of TRMs in protection against tumor metastasis. Furthering our understanding of the circulating T cell response in gliomagenesis, we focused on mutant IDH1 gliomas. Despite the presence of this mutation in most low grade gliomas, there are still many remaining questions about the immune landscape during tumor formation and a lack of therapeutic targets. Using novel compound genetic mouse models that recapitulate the hallmark features of mutant IDH1 glioma, we performed high throughput TCR repertoire sequencing in mutant IDH1 versus WT IDH1 gliomas. Surprisingly, the glioma genotypes showed little differences in T cell infiltration and expansion. Extensive in vitro profiling experiments confirmed this, showing that the metabolite produced by mutant IDH1 tumors, D-2HG, had little effect on the skewing of the immune response. We developed an engineered T Cell Receptor (TCR-T) adoptive cell transfer based approach to identify and clone mutant IDH1 expressing T cells. We hope this collection of T cells will be useful in the immunotherapy of gliomas. Finally, we synthesized and biologically evaluated novel immune-suppressive therapies for the treatment of autoimmune diseases. While treatment options for autoimmune diseases have increased over the past several years, they are limited in their clinical efficacy by high drug toxicity and lack of selectivity. Thus, we sought new immunomodulatory agents with lower toxicity. Our previous work identified subglutinol A as a natural agent that exerts immune-suppressive effects on activated T cells. To provide guiding principles in future therapeutic development and to specifically define the structural requirements of subglutinols that exert their immunomodulatory activity, we prepared and evaluated the immunomodulatory activities of several subglutinol analogs. Though in vitro studies of structure-activity relationship, we identified a new subglutinol analog with reduced structural complexity. It will serve as a potential lead compound for future autoimmune drug development. This new subglutinol A compound, when compared to its parent compound, effectively suppressed inflammatory IFN and IL-17A cytokine production and has reduced T cell toxicity. Using a mouse model of experimental autoimmune encephalitis (EAE), we found that in vivo treatment of this new analog did not ameliorate the symptoms of disease, although it significantly increased the percentage of inflammatory neutrophils. These results suggest that, while not effective in EAE, this compound has potential as a novel therapy in diseases where promoting an influx of inflammatory neutrophils is beneficial.