Identifying Novel Strategies to Augment Anti-Melanoma Immunity

Date of Award

Spring 2022

Document Type


Degree Name

Doctor of Philosophy (PhD)


Experimental Pathology

First Advisor

Bosenberg, Marcus


Melanoma is the deadliest form of skin cancer and caused the deaths of over 7,000 people in the United States in 2021. While immunotherapies have revolutionized care and extended survival for melanoma patients, most will either not respond or eventually develop resistance to these treatment options. Therefore, there is an urgent need to improve our understanding of the biology underlying the immune response to melanoma, and indeed to all cancers. We performed a whole-genome CRISPR screen in an immunogenic mouse model of melanoma to identify tumor intrinsic-factors that modulate the anti-tumor immune response. We identified several pathways of interest, including antigen presentation, Interferon-gamma sensing, and the HUSH complex, a group of epigenetic modifiers responsible for enforcing gene suppression through deposition of H3K9me3 marks throughout the genome. To further characterize the role of the HUSH complex in melanoma, we evaluated the immune response to tumors bearing loss of Setdb1, which encodes a histone methyltransferase in the complex. We found that Setdb1-/- tumors are efficiently and durably cleared by CD8+ T cells. We additionally found that loss of Setdb1 allows for de-suppression of endogenous retroelements, leading to an induction of anti-viral expression programs, increased tumor cell immunogenicity, type-I interferon secretion and enhanced CD8+ T cell infiltration. Finally, we observed that type-I interferon signaling is required for full CD8+ T cell anti-tumor activity, and that CD8+ T cells are specific to ERV-antigens tumor antigens upregulated by Setdb1-loss. These findings will inform future studies of epigenetic regulators in melanoma, as well as add to the growing literature supporting a role for ERVs in activating an anti-tumor immune response. To further improve investigations of anti-tumor immunity and tumor microenvironments, we further describe a novel method for analysis of single-cell RNA sequencing datasets profiling the tumor microenvironment. This approach aims to solve some challenges inherent to data interpretation in scRNAseq, including the heterogeneity of the TME and transcriptomic dysregulation of tumor cells. Collectively, we hope that the findings described in this thesis will accelerate research into factors that can be therapeutically targeted to augment the anti-tumor immune response, and ultimately lead to novel treatment paradigms for improving melanoma patient outcomes through new generations of immunotherapies.

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