Evaluating the impact of TP53 mutation on the epigenetic therapy viral mimicry response in the non- small cell lung cancer tumor

West Virginia University, Morgantown WV

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Abstract

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related deaths in the United States. FDA approval of immunotherapy represents a major therapeutic advance, but long-term survival remains limited, and combinatorial approaches that maximize antitumor immune responses are an urgent clinical priority. Low-dose DNA methyltransferase inhibitor (DNMTi) reverses cancer-associated hypermethylation to impart durable genome-wide expression changes in NSCLC and other cancers. This includes activation of cellular antiviral signaling via ‘viral mimicry’, wherein derepression of endogenous retroviral (ERV) sequences forms cytosolic double-stranded RNA that triggers an interferon-dependent transcriptional program. Viral mimicry is critically dependent on transcriptional alterations in mitochondrial respiration and ox-phos pathways, generating reactive oxygen species that damage and fragment mitochondrial DNA, which leaks into to the cytosol and activates Stimulator of Interferon Genes (STING). Notably, both STING activation and DNMTi viral mimicry have been linked to modulation of the tumor microenvironment (TME) towards an immune-favorable phenotype, priming for enhanced response to immune checkpoint inhibitors (ICI). The tumor suppressor TP53 is mutated in ~50% of NSCLC. Mutations are functionally categorized into DNA contact mutants, where DNA interaction is impacted, and structural mutants, where protein folding is perturbed at a local or global level. TP53 mutation is associated with a chronically inflamed immunosuppressive tumor microenvironment that correlates to non-durable ICI responses and poor survival outcomes. Our novel preliminary data indicate that TP53 mutational category may fundamentally influence cellular response to DNMTi across multiple inputs, including activation of ERV transcription, orchestration of the mitochondrial DNA damage response, and modulation of STING signaling. Our central hypothesis is that p53 plays a critical role in shaping DNMTi viral mimicry, and that the resulting TME immunophenotype is differentially modulated across the spectrum of TP53 mutations. We propose the following strategies to test this hypothesis: 1) employing a clinically relevant, technologically advanced recapitulation of the TME by co-culturing TP53-mutant patient-derived organoids with their corresponding cancer-associated fibroblasts, allowing us to model bidirectional interactions governing TME immunomodulation using single cell RNA-seq and functional cellular analyses; 2) interrogating multiple next-gen sequencing modalities to integrate p53 chromatin binding, ERV sequence annotation, and gene expression data to evaluate impact of TP53 mutation on DNMTi-induced transcriptional profiles; and 3) examining molecular mechanisms contributing to viral mimicry, with focus on the mitochondrial DNA damage response. The proposed research aims to identify opportunities for strategic therapeutic personalization by combining ICI with epigenetic drugs, addressing a major clinical need of improving treatment outcomes in NSCLC.