Reversing tumor immunoediting by inhibiting DNA methylation

Abstract

Cancer cells use DNA hypermethylation to downregulate tumor suppressor genes and important immune-related genes to escape immune surveillance. However, not much is known about which genes are modified by DNA methylation during tumor editing. I hypothesized that DNA methylation during tumor editing suppresses multiple innate immune pathways to enable tumors to evade anti-tumor immune responses and that inhibiting DNA methylation would derepress innate immune genes and make tumors more susceptible to immune control or immunotherapy. To test this hypothesis, I used RNA sequencing, ATAC sequencing, and qRT-PCR to compare gene expression and immune responses of B16 melanoma and 4T1 triple-negative breast cancer cells that were untreated or treated with a DNMT inhibitor, decitabine (DAC). DAC treatment derepressed multiple innate immunity and cell death pathway genes. DAC-upregulated genes in the tumors were highly enriched for key genes in multiple innate immune pathways, including the interferon response, necroptosis, and pyroptosis. DAC treatment also strongly suppressed tumor growth and increased antitumor immunity in vivo. I also compared the in vivo anti-tumor effect of DAC, which suppresses DNA methylation in all cells with a tumor-selective DNMT inhibitor, EpCAM aptamer-siRNA chimeras (AsiCs) to knock down Dnmt1 and Dnmt3b, in the 4T1E breast cancer model. Both strategies suppressed tumor growth and promoted antitumor immunity, but DAC was slightly, but significantly, more effective because it increased T cell differentiation of tumor-infiltrating lymphocytes to the resident memory subtype and

that arose spontaneously in a genetically engineered mouse bearing doxycycline-inducible mammary expression of a mutated Her2 oncogene. Genes suppressed during tumor growth overlapped with genes derepressed by DAC. This study suggests that tumors edit and repress multiple innate immune pathways to survive immune selection pressure. Thus, therapeutic strategies to inhibit DNA demethylation or activate innate immunity might make immunologically cold tumors sensitive to immune control and be effective on their own or enhance the responses to checkpoint inhibitor immunotherapy.