Effect of tumor editing on antitumor immunity - Project Summary Immunotherapy has revolutionized cancer therapy, but most solid cancers do not respond. Thus, immunotherapy needs to be improved. Developing cancers undergo tumor editing to evade immune surveillance. Because most editing occurs before cancers are detected, surprisingly little is known about what genes are edited. Studies of immune editing have examined candidate genes in antigen processing and presentation but have largely ignored genes active in innate immunity, which plays a critical role in self:non-self or normal cell:tumor discrimination and in inducing and amplifying adaptive immunity. Genome-wide studies of tumor immune editing have not previously been done. Our first goal is to identify genome-wide changes in gene expression early in tumorigenesis in a variety of cancers by taking advantage of genetically engineered mouse models (GEMM) of cancer to capture and compare early vs late spontaneously arising tumors, using scRNA-seq, spatial transcriptomics and multiplexed flow cytometry and immunofluorescence microscopy to identify the genes/pathways whose expression is suppressed during early tumorigenesis. We will also identify changes in gene expression in the tumor and metastatic niche in the transition from dormancy at tissue sites of colonization to macrometastases. Comparing both tumor and infiltrating immune cell gene expression, cell subset abundance, cell-cell communications and spatial organization will provide a detailed picture of how tumor editing leads to immune exhaustion and evasion of immune surveillance and identify the genes, pathways, and processes that are suppressed. Preliminary data suggest that early tumor editing is highly focused on genes involved in both adaptive and innate immunity, including interferon, inflammasome/pyroptosis, necroptosis, and inflammatory cytokine pathways, which are epigenetically repressed. The dominant genes/pathways edited in GEMM will also be examined in human cancers, comparing gene expression and immune cell infiltration in carcinoma in situ with advanced carcinomas. Reversing immune editing could potentially convert immunologically cold tumors into immune responsive tumors. Epigenetic repression of gene expression by DNA hypermethylation of promoters is a major mechanism of gene repression that is prominent during tumor editing. Our next goal is to determine how much DNA hypermethylation and other epigenetic changes contributes to tumor editing and whether inhibiting DNA methylation or other epigenetic modifications that maintain heterochromatin can reignite protective immunity or induce responsiveness to checkpoint inhibition. Another goal is to investigate in more detail the role of suppression of specific innate immune pathways in the tumor and in specific immune cell subtypes in tumor resistance to immune control. We will determine whether activating specific innate immune pathways, repressed during tumor editing, using small molecule activators or inhibitors or tumor-targeted RNA-based gene knockdown, knockout or mRNA expression, can induce immune responsiveness in immunologically cold tumors. These studies will identify novel drug targets that could potentially reverse editing and restore tumor immunity.
