EZH2 Inhibition Induces Endogenous Retroviral Elements and Primes Immunogenicity in Mesenchymal Small Cell Lung Cancer

Abstract

Small cell lung cancer (SCLC) is characterized by heterogeneous mesenchymal and neuroendocrine cell states. In particular, aggressive mesenchymal subclones in SCLC harbor characteristic cytokine profiles and activation of innate immune signaling pathways. Recent work has shown that exposure of mesenchymal SCLC tumor cells to IFN-γ leads to production of double-stranded RNA (dsRNA) through transcription of a novel subclass of endogenous retroviruses (ERVs) located in the 3’ UTR of IFN-γ-inducible genes, with this subclass being termed SPARCS (Stimulated 3 Prime Antisense Retroviral Coding Sequences). However, the mechanism of SPARCS de-repression or the consequences of SPARCS dsRNA production for immune signaling and response to immunotherapy in mesenchymal subclones remained unclear. Chromatin profiling using ATAC-seq and ChIP-seq demonstrated increased accessibility of SPARCS loci marked by loss of H3K27 trimethylation in SCLC mesenchymal subclones, suggesting core regulation by the histone methyltransferase EZH2. Neuroendocrine SCLC cells treated with EZH2 inhibition displayed activated SPARCS expression, phenotypic changes suggestive of a mesenchymal state transition, and secretion of mesenchymal-associated cytokines with important roles in immune cell recruitment. EZH2 inhibition also induced endogenous production of IFN-γ and upregulation of antigen presentation machinery, suggesting the development of increased immunogenicity in this state. In addition, SPARCS-high samples across tumor types displayed loss of EZH2, highlighting the potential role of EZH2 in ERV regulation across tumor types. Taken together, these suggest that mesenchymal-associated alterations in histone demethylation lead to induction of ERVs and priming of immunogenicity in SCLC tumor subclones, identifying unique points of intervention which may have important consequences for immunotherapy in small cell lung cancer and other tumors.