αKG-mediated carnitine synthesis promotes homologous recombination via histone acetylation

Uboveja, A.; Huang, Z.; Buj, R.; Amalric, A.; Wang, H.; Tangudu, N. K.; Cole, A. R.; Megill, E.; Kantner, D.; Chatoff, A.; Ahmad, H.; Marcinkiewicz, M. M.; Disharoon, J. A.; Graff, S.; Dahl, E. S.; Hempel, N.; Stallaert, W.; Sidoli, S.; Bitler, B. G.; Long, D. T.; Snyder, N. W.; Aird, K. M.

doi:10.1101/2024.02.06.578742

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bioRxiv · 10.1101/2024.02.06.578742

αKG-mediated carnitine synthesis promotes homologous recombination via histone acetylation

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Abstract

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 (KG) sensitizes HR-proficient cells to DNA damaging agents by metabolic regulation of histone acetylation. KG is required for the activity of KG-dependent dioxygenases (KGDDs), and prior work has shown that changes in KGDD affect demethylases. Using a targeted CRISPR knockout library consisting of 64 KGDDs, 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, KG-mediated TMLHE-dependent carnitine synthesis was required for histone acetylation, while histone methylation was affected but dispensable. The increase in histone acetylation via KG-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 KG directly influencing histone acetylation via carnitine synthesis and provide a metabolic avenue to induce HR-deficiency and sensitivity to DNA damaging agents.

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Uboveja, A., Huang, Z., Buj, R., Amalric, A., Wang, H., Tangudu, N. K., Cole, A. R., Megill, E., Kantner, D., Chatoff, A., Ahmad, H., Marcinkiewicz, M. M., Disharoon, J. A., Graff, S., Dahl, E. S., Hempel, N., Stallaert, W., Sidoli, S., Bitler, B. G., Long, D. T., Snyder, N. W., Aird, K. M.. 2024-02-07. αKG-mediated carnitine synthesis promotes homologous recombination via histone acetylation. https://doi.org/10.1101/2024.02.06.578742

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