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

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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.

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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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  1. These authors contributed equally: Hsiangyu Hu, Nirmalya Saha.

Authors and Affiliations

  1. Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA

    Hsiangyu Hu, Nirmalya Saha, Yuting Yang, Ejaz Ahmad, Lauren Lachowski, Uttar Shrestha, Vidhya Premkumar, Lili Chen, Blaine Teahan, Sierrah Grigsby, Zaneta Nikolovska-Coleska & Andrew G. Muntean

  2. Department of Microbiology and Immunology, Indiana University School of Medicine, 950 West Walnut Street, R2-302, Indianapolis, IN, 46202-5181, USA

    James Ropa

  3. Institute of Pharmaceutical Biology / Diagnostic Center of Acute Leukemia, University of Frankfurt, Frankfurt/Main, Germany

    Rolf Marschalek

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Contributions

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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