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Epigenetic therapies targeting histone lysine methylation: complex mechanisms and clinical challenges
Sarah Gold, Ali Shilatifard
Sarah Gold, Ali Shilatifard
Published October 15, 2024
Citation Information: J Clin Invest. 2024;134(20):e183391. https://doi.org/10.1172/JCI183391.
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Review

Epigenetic therapies targeting histone lysine methylation: complex mechanisms and clinical challenges

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Abstract

As epigenetic therapies continue to gain ground as potential treatment strategies for cancer and other diseases, compounds that target histone lysine methylation and the enzyme complexes represent a major frontier for therapeutic development. Clinically viable therapies targeting the activities of histone lysine methyltransferases (HKMT) and demethylases (HKDMs) have only recently begun to emerge following FDA approval of the EZH2 inhibitor tazemetostat in 2020 and remain limited to compounds targeting the well-studied SET domain–containing HKMTs and their opposing HKDMs. These include the H3K27 methyltransferases EZH2/EZH1, the singular H3K79 methyltransferase DOT1L, and the H3K4 methyltransferase MLL1/COMPASS as well as H3K9 and H3K36 methyltransferases. They additionally include the H3K4/9-preferential demethylase LSD1 and the H3K4-, H3K27-, and H3K36-preferential KDM5, KDM6, and KDM2 demethylase subfamilies, respectively. This Review discusses the results of recent clinical and preclinical studies relevant to all of these existing and potential therapies. It provides an update on advancements in therapeutic development, as well as more basic molecular understanding, within the past 5 years approximately. It also offers a perspective on histone lysine methylation that departs from the long-predominant “histone code” metaphor, emphasizing complex-disrupting inhibitors and proximity-based approaches rather than catalytic domain inhibitors in the outlook for future therapeutic development.

Authors

Sarah Gold, Ali Shilatifard

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Figure 3

Noncatalytic inhibitors evict MLL1 and its oncofusion partners from chromatin by disrupting the menin-MLL1 interface.

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Noncatalytic inhibitors evict MLL1 and its oncofusion partners from chro...
(A) The COMPASS methyltransferase MLL1 (left) epigenetically modifies histone 3 lysine 4 with dimethylation and trimethylation (H3K4me2/3) via the catalytic activity of its SET domain. MLL1/COMPASS contains MLL1N and MLL1C subunits, products of MLL1 cleavage by taspase1. Menin tethers the MLL1/COMPASS complex to chromatin via its interaction with LEDGF. It was recently reported that menin also binds chromatin via recognition of histone 3 lysine 79 dimethylation (H3K79me2), a modification that is exclusively deposited by the methyltransferase DOT1L, which is a frequent oncofusion partner of MLL1 in leukemias driven by 11q23 translocations. The SET domain–containing C-terminal region of MLL1 is lost in MLL1 oncofusion proteins. (B) Disruption-based inhibitors target an N-terminal domain of MLL1 that binds menin. Inhibitors that disrupt the menin-MLL1 interface can evict both MLL1/COMPASS and MLL1 oncofusion proteins from chromatin. (C) MLL1 oncofusion proteins, which lack the taspase1 cleavage site present in normal MLL1, form more stable chromatin-associated complexes than normal MLL1/COMPASS (left). Stabilizing MLL1/COMPASS (e.g., by targeting taspase1 activity) is a potential strategy for rebalancing chromatin occupancy in favor of normal MLL1/COMPASS (right).

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ISSN: 0021-9738 (print), 1558-8238 (online)

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