Apoorva Uboveja, Baixue Yang, Raquel Buj, Amandine Amalric, Hui Wang, Naveen Kumar Tangudu, Aidan R. Cole, Julie A. Disharoon, Richard Fang, Evan Levasseur, Miho Naruse, Zhentai Huang, Emily Megill, Daniel S. Kantner, Adam Chatoff, Hafsah Ahmad, Mariola M. Marcinkiewicz, Sarah Graff, Ellen De Pieri, Andrea Andress Huacachino, Frank P. Vendetti, Jeff Danielson, Erika S. Dahl, Jennifer L Pennise, Esther Elishaev, Alison Jaccard, Lauren Borho, Miriam D. Post, K M Cooper, Francesmary Modugno, Nadine Hempel, Wayne Stallaert, Christopher J. Bakkenist, Simone Sidoli, Kathryn E. Wellen, Benjamin G. Bitler, David T. Long, Nathaniel W. Snyder, Katherine M. Aird
Homologous recombination (HR) deficiency increases sensitivity to DNA-damaging agents that are commonly used to treat cancer1. In HR-proficient cancers, the metabolic mechanisms that drive response or resistance to DNA-damaging agents remain unclear. Here we have identified that depletion of α-ketoglutarate (αKG) sensitizes HR-proficient cells to DNA-damaging agents by metabolic regulation of histone acetylation. αKG is required for the activity of αKG-dependent dioxygenases2 (αKGDDs), and previous work has focused almost exclusively on the demethylase functions of αKGDD. Using a targeted CRISPR knockout library consisting of 64 αKGDDs, we discovered that trimethyllysine hydroxylase epsilon (TMLHE), the first and rate-limiting enzyme in de novo carnitine synthesis, is necessary for the survival of HR-proficient cells in the presence of DNA-damaging agents. Unexpectedly, αKG-mediated TMLHE-dependent carnitine synthesis was required for histone acetylation and was non-redundant with other nucleo-cytosolic acetyl-CoA-generating pathways. The increase in histone acetylation by means of the αKG–carnitine axis promoted HR-mediated DNA repair through site-specific histone acetylation. Finally, we observed a positive correlation between TMLHE and histone acetylation in patient samples and found that high TMLHE or acetylcarnitine correlates with worse progression-free survival in patients treated with DNA-damaging agents. This study demonstrates for the first time, to our knowledge, that αKG affects site-specific histone acetylation and provides a mechanism of HR proficiency through carnitine synthesis. Moreover, these data provide a metabolic avenue for inducing HR deficiency and promoting sensitivity to DNA-damaging agents. The metabolite αKG promotes carnitine synthesis and increases site-specific histone acetylation, thereby promoting homologous recombination-mediated DNA repair, which has potential implications for chemoresistant cancers.