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MOLECULAR TARGETS FOR THERAPY

The ENL YEATS epigenetic reader domain critically links MLL-ENL to leukemic stem cell frequency in t(11;19) Leukemia

Abstract

MLL (KMT2a) translocations are found in ~10% of acute leukemia patients, giving rise to oncogenic MLL-fusion proteins. A common MLL translocation partner is ENL and associated with a poor prognosis in t(11;19) patients. ENL contains a highly conserved N-terminal YEATS domain that binds acetylated histones and interacts with the PAF1c, an epigenetic regulator protein complex essential for MLL-fusion leukemogenesis. Recently, wild-type ENL, and specifically the YEATS domain, was shown to be essential for leukemic cell growth. However, the inclusion and importance of the YEATS domain in MLL-ENL-mediated leukemogenesis remains unexplored. We found the YEATS domain is retained in 84.1% of MLL-ENL patients and crucial for MLL-ENL-mediated leukemogenesis in mouse models. Mechanistically, deletion of the YEATS domain impaired MLL-ENL fusion protein binding and decreased expression of pro-leukemic genes like Eya1 and Meis1. Point mutations that disrupt YEATS domain binding to acetylated histones decreased stem cell frequency and increased MLL-ENL-mediated leukemia latency. Therapeutically, YEATS containing MLL-ENL leukemic cells display increased sensitivity to the YEATS inhibitor SGC-iMLLT compared to control AML cells. Our results demonstrate that the YEATS domain is important for MLL-ENL fusion protein-mediated leukemogenesis and exposes an “Achilles heel” that may be therapeutically targeted for treating t(11;19) patients.

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Fig. 1: ENL breakpoint locations in t(11;19) patients.
Fig. 2: The ENL YEATS domain and downstream sequence is required for MLL-ENL-mediated leukemogenesis.
Fig. 3: YEATS domain mutations impact H3Kac binding.
Fig. 4: Disruption of the YEATS domain epigenetic reader function impacts MLL-ENL leukemic stem cell frequency.
Fig. 5: Transcriptomic changes associated with MLL-ENLΔYEATS cells.
Fig. 6: YEATS domain of ENL is required for epigenetic regulation of Eya1.
Fig. 7: MLL-ENL cells display increased sensitivity to SGC-iMLLT.
Fig. 8: The YEATS domain impacts MLL-ENL fusion protein localization.

Data availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request and in the Gene Expression Omnibus (GEO) repository: GSE211523.

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Acknowledgements

We thank Drs. Tomek Cierpicki, Jolanta Grembecka, Yali Dou and Mark Chiang for helpful discussion and Dr. Lili Zhao for statistical help. We thank Dr. Michael Cleary for MLL-ENL expression plasmids and Dr. Akihiko Yokoyama for HB1119 cells. This work was supported by NIH grants: MCubed (ZNC, AGM), Michigan Drug Discovery (ZNC), R01-HL-136420 (AGM), B+ Foundation (AGM) and P30CA046592 (University of Michigan Flow Cytometry Core).

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HH, NS, ZNC and AGM designed the experiments. All authors participated in conducting experiments and collecting or analyzing the data. YY conducted cloning, expression and purification of recombinant proteins; EA conducted FP and BLI binding assays; US performed synthesis of the fluorescent-labeled inhibitor. RM provided chromosomal breakpoint data and analysis. HH, ZNC and AGM wrote the manuscript. The project was overseen by AGM.

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Correspondence to Andrew G. Muntean.

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Hu, H., Saha, N., Yang, Y. et al. The ENL YEATS epigenetic reader domain critically links MLL-ENL to leukemic stem cell frequency in t(11;19) Leukemia. Leukemia 37, 190–201 (2023). https://doi.org/10.1038/s41375-022-01765-0

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