Ubiquitin ligase regulation of tissue-resident T cell and anti-tumor activity

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PROJECT SUMMARY In malignancies, CD8+ T cells can recognize and eliminate tumor cells, but often fail to cure disease due to their progressive loss of antitumor function resulting from chronic activation in the immunosuppressive tumor microenvironment. In response to infection in healthy tissues, T cells differentiate into tissue-resident memory cells (TRM), and after clearance of antigen can remain lodged in tissues to survey and provide protection from reinfection. When TRM-like T cells are found in cancer patient tumors, improved responses to immunotherapy and better patient outcomes are observed. However, whether TRM-like TIL represent ‘progenitors’ of exhausted TIL, or are a separate cell state outside the exhaustion spectrum is still unclear. To better understand the relationship among TRM-like TIL, exhaustion states, and TRM memory cells, we directly compared TRM from acute viral infection and exhausted TIL from tumors to find transcriptional differences between these distinct T cell states. Focusing on genes highly expressed by TRM that may mediate their enhanced functions in tissues, we asked which of those were downregulated as T cells became terminally exhausted, coincident with loss of function. This approach identified numerous genes related to protein regulation, including multiple under-characterized E3 ubiquitin ligases. Protein regulation by the ubiquitin proteosome system is an essential biological process for homeostasis, crucial for cell differentiation and function, and has been previously shown to be important for memory T cell identity. Correlated with our preliminary data, we found that exhausted TIL have an excess of unfolded proteins in their cytosol, and when we enforced expression of the identified E3 ubiquitin ligases in tumor-specific T cells, it allowed for better tumor control and improved mouse survival. Therefore, we propose to explore the relationship between protein homeostasis and TRM, exhaustion, and TRM-like TIL cell fates. Aim 1 seeks to understand if the identified E3 ubiquitin ligases influence exhaustion or TRM cell fate by using mouse models of cancer to enforce expression or knock out these ligases and study exhaustion T cell fate, or to enforce expression or knock out the ligases in acute viral infection and study TRM cell fate. Aim 2 seeks to identify the protein-interaction targets of these E3 ubiquitin ligases by in vitro BioID proximity labeling assay and mass spectrometry, then verify the targets in vivo TIL and determine if expression of these ligases in TIL can decrease unfolded protein abundance. Understanding the relationship between T cell exhaustion and TRM can provide vital new insights into the biology of these two differentiated T cell populations and inform efforts to manipulate T cell fates towards TRM-like TIL to benefit cancer immunotherapy.