Alpha-ketoglutarate -mediated carnitine synthesis promotes homologous recombination via histone acetylation

Homologous recombination (HR) deficiency enhances sensitivity to DNA damaging agents commonly used to treat cancer. In HR-proficient cancers, metabolic mechanisms driving response or resistance to DNA damaging agents remain unclear. Here we identified that depletion of alpha-ketoglutarate (aKG) sensitizes HR-proficient cells to DNA damaging agents by metabolic regulation of histone acetylation. aKG is required for the activity of aKG-dependent dioxygenases (aKGDDs), and prior work has shown that changes in aKGDD affect demethylases. Using a targeted CRISPR knockout library consisting of 64 aKGDDs, we discovered that Trimethyllysine Hydroxylase Epsilon (TMLHE), the first and rate-limiting enzyme in de novo carnitine synthesis, is necessary for proliferation of HR-proficient cells in the presence of DNA damaging agents. Unexpectedly, aKG-mediated TMLHE-dependent carnitine synthesis was required for histone acetylation, while histone methylation was affected but dispensable. The increase in histone acetylation via aKG-dependent carnitine synthesis promoted HR-mediated DNA repair through site- and substrate-specific histone acetylation. These data demonstrate for the first time that HR-proficiency is mediated through aKG directly influencing histone acetylation via carnitine synthesis and provide a metabolic avenue to induce HR-deficiency and sensitivity to DNA damaging agents. Overall design: We used Ovcar8 high grade serous cancer cells with CCNE1 overexpression and knocked down TMLHE using 2 independent shRNAs. All samples were done in triplicate. Comparative gene expression profiling analysis for CCNE1 overexpression vs. control and shTMLHE vs. CCNE1 overexpression.