AEBP2-Directed H3K27me2 Defines a Specific Vulnerability in EZH2-mutant Lymphoma

Angelov, D.; Nolan, J.; Holland, G.; Nimmo, D.; Davies, M.; Monger, C.; Dillon, E.; Mucha, M.; Wang, C.; Gannon, D.; Lagan, E.; Malcolm, A.; Yang, L.; Chen, A.; Vandenberghe, E.; Flaus, A.; Chen, D.; Brien, G.; Conway, E.; Bracken, A. P.

doi:10.1101/2025.10.14.682307

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bioRxiv · 10.1101/2025.10.14.682307

AEBP2-Directed H3K27me2 Defines a Specific Vulnerability in EZH2-mutant Lymphoma

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Abstract

The catalytic subunit of Polycomb Repressive Complex 2 (PRC2), EZH2, is recurrently mutated in 25% of diffuse large B-cell lymphomas (DLBCL), causing increased H3K27me3 and decreased H3K27me2 levels. EZH2 inhibitors provide clinical benefit, but resistance frequently develops, highlighting the need for alternative therapeutic targets. Here, we identify the PRC2 accessory protein AEBP2 as a specific genetic dependency in EZH2-mutant DLBCL. While AEBP2 acts through PRC2, its essential role is surprisingly independent of canonical H3K27me3-mediated gene silencing. Instead, AEBP2 functions within a PRC2.2 complex lacking JARID2, using its zinc-finger domains to sample intergenic chromatin to sustain H3K27me2. Notably, loss of AEBP2 or NSD2 caused contrasting changes in intergenic H3K27me2 levels, driving sensitivity or resistance to PRC2 inhibitors, respectively. Our findings identify AEBP2-PRC2.2-maintained intergenic H3K27me2 as a therapeutic vulnerability in EZH2-mutant DLBCL and highlight dysregulated H3K27me2 as an underappreciated form of PRC2 dysfunction in cancer, with important therapeutic implications.

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Angelov, D., Nolan, J., Holland, G., Nimmo, D., Davies, M., Monger, C., Dillon, E., Mucha, M., Wang, C., Gannon, D., Lagan, E., Malcolm, A., Yang, L., Chen, A., Vandenberghe, E., Flaus, A., Chen, D., Brien, G., Conway, E., Bracken, A. P.. 2025-10-15. AEBP2-Directed H3K27me2 Defines a Specific Vulnerability in EZH2-mutant Lymphoma. https://doi.org/10.1101/2025.10.14.682307

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