The oncometabolite D-2-hydroxyglutarate promotes DNA hypermethylation at lineage-specific enhancers controlling microglial activation in IDHmut gliomas

Laurenge, A.; Pugliese, P.; Richard, Q.; Mathon, B.; Jouannet, S.; Hayat, Y.; Scuderi, S.; Marijon, P.; Labreche, K.; Alentorn, A.; Verreault, M.; Idbaih, A.; Birzu, C.; Huillard, E.; Pottier, N.; Aurore Desmons, A. D.; Fayache, I.; Kaas, G. A.; Kingsley, P. J.; Marnett, L. J.; Duplus, E.; El-Habr, E.; Salas, L. A.; Mokhtari, K.; Tran, S.; Touat, M.; Bielle, F.; Suva, M. L.; Iavarone, A.; Ceccarelli, M.; Mallat, M.; Sanson, M.; Castro-Vega, L. J.

doi:10.1101/2024.08.23.608811

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bioRxiv · 10.1101/2024.08.23.608811

The oncometabolite D-2-hydroxyglutarate promotes DNA hypermethylation at lineage-specific enhancers controlling microglial activation in IDHmut gliomas

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Abstract

Tumor-associated microglia and macrophages (TAMs), the most abundant myeloid populations in gliomas, shape immune responses through transcriptional programs influenced by the tumor microenvironment. Although these programs differ according to tumor IDH status, the underlying epigenetic mechanisms remain poorly understood. Here, we uncover widespread DNA hypermethylation in the myeloid compartment of IDH-mutant gliomas, predominantly at distal enhancers enriched for motifs of core microglial transcription factors (TFs). This remodeled enhancer landscape strongly correlated with reduced activity of TF regulons and coordinated repression of immunomodulatory programs that normally support microglial activation. Using primary human microglia, we show that prolonged exposure to the oncometabolite D-2-hydroxyglutarate (D-2HG) reduces TET activity and increases 5mC/5hmC ratios near TF-binding motifs within enhancers affected ex vivo. Consistent with these epigenetic alterations, D-2HG-treated microglia exhibited transcriptional signatures compatible with blunted proinflammatory responses, whereas pharmacological inhibition of mutant IDH in patients partially restored microglial immune reactivity. Altogether, our findings reveal a chronic D-2HG-driven epigenetic priming mechanism that promotes a hyporesponsive microglial state, providing a rationale for the immunologically cold phenotype of IDH-mutant gliomas and offering insight into how IDH-targeted therapies may reshape microglial immune responses.

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Laurenge, A., Pugliese, P., Richard, Q., Mathon, B., Jouannet, S., Hayat, Y., Scuderi, S., Marijon, P., Labreche, K., Alentorn, A., Verreault, M., Idbaih, A., Birzu, C., Huillard, E., Pottier, N., Aurore Desmons, A. D., Fayache, I., Kaas, G. A., Kingsley, P. J., Marnett, L. J., Duplus, E., El-Habr, E., Salas, L. A., Mokhtari, K., Tran, S., Touat, M., Bielle, F., Suva, M. L., Iavarone, A., Ceccarelli, M., Mallat, M., Sanson, M., Castro-Vega, L. J.. 2024-08-23. The oncometabolite D-2-hydroxyglutarate promotes DNA hypermethylation at lineage-specific enhancers controlling microglial activation in IDHmut gliomas. https://doi.org/10.1101/2024.08.23.608811

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