Targeting mitochondrial RNA processors enhances epigenetic therapy in lung cancer

Abstract

DNA-demethylating agents, such as decitabine (DAC) inhibit DNA methyltransferases (DNMTs), causing reactivation of genes that are epigenetically silenced via methylation of their promoters. Indeed, DAC induces antitumor effects by upregulating the expression of tumor suppressor genes in cancer cells. While effective in myelodysplastic syndrome and acute myeloid leukemia patients, DAC shows limited effects in solid tumors despite the strong induction of tumor suppressor genes. Here, we find that DAC treatment upregulates mitochondrial RNA (mtRNA) expression in lung adenocarcinoma cells that do not respond to DAC. Increased mtRNA level results in the subsequent elevation in the mitochondrial-encoded OXPHOS proteins and ATP synthesis. We further employ the CRISPR-Cas9 system to knockout (KO) 13 key regulators of the mtRNA life cycle. We find that the KO of mtRNA polymerase (POLRMT) significantly enhances the antitumor effects of DAC. By blocking mtRNA transcription through POLRMT KO, the DAC-mediated elevation in ATP production is suppressed, leading to increased cytotoxicity. We verify using a small molecular POLRMT inhibitor that suppressing mtRNA expression enhances DAC cytotoxicity in lung cancer cells. Notably, HCT116 cells that show good response to DAC do not exhibit mtRNA elevation upon drug treatment. Our study unveils the insensitivity to DNA-demethylating agents through enhanced mitochondrial transcription and suggests targeting mitochondria RNA as a potential combinatorial strategy for epigenetic therapy.