Abstract

Recurrent chromosomal translocations producing a chimaeric MLL oncogene give rise to a highly aggressive acute leukaemia associated with poor clinical outcome1. The preferential involvement of chromatin-associated factors as MLL fusion partners belies a dependency on transcription control2. Despite recent progress made in targeting chromatin regulators in cancer3, available therapies for this well-characterized disease remain inadequate, prompting the need to identify new targets for therapeutic intervention. Here, using unbiased CRISPR–Cas9 technology to perform a genome-scale loss-of-function screen in an MLL-AF4-positive acute leukaemia cell line, we identify ENL as an unrecognized gene that is specifically required for proliferation in vitro and in vivo. To explain the mechanistic role of ENL in leukaemia pathogenesis and dynamic transcription control, a chemical genetic strategy was developed to achieve targeted protein degradation. Acute loss of ENL suppressed the initiation and elongation of RNA polymerase II at active genes genome-wide, with pronounced effects at genes featuring a disproportionate ENL load. Notably, an intact YEATS chromatin-reader domain was essential for ENL-dependent leukaemic growth. Overall, these findings identify a dependency factor in acute leukaemia and suggest a mechanistic rationale for disrupting the YEATS domain in disease.

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Acknowledgements

The authors thank S. A. Armstrong, C. D. Allis, and X. Shi for transparent and supportive dialogue. We also thank J. A. Perry for editing the manuscript and N. S. Gray and C. J. Ott for suggestions. Quantitative proteomics studies were performed by R. Kunz. This research was supported by philanthropic gifts from K. Lubin and E. Woods, as well as NIH grants (R01-CA176745 and P01-CA109901 to J.E.B.). G.E.W. was supported by an EMBO long-term fellowship. D.L.B. is a Merck Fellow of the Damon Runyon Cancer Research Foundation (DRG-2196-14). N.E.S. is supported by a Pathway to Independence Award (R00-HG008171) from the NHGRI.

Author information

Author notes

    • Georg E. Winter
    •  & James E. Bradner

    Present addresses: Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria (G.E.W.); Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, USA (J.E.B.).

Affiliations

  1. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA

    • Michael A. Erb
    • , Thomas G. Scott
    • , Joshiawa Paulk
    • , Amanda Souza
    • , Justin M. Roberts
    • , Shiva Dastjerdi
    • , Dennis L. Buckley
    • , Behnam Nabet
    • , Rhamy Zeid
    • , Georg E. Winter
    •  & James E. Bradner
  2. Division of Hematology/Oncology, Boston Children’s Hospital, Boston, Massachusetts 02115, USA

    • Bin E. Li
    • , Huafeng Xie
    •  & Stuart H. Orkin
  3. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA

    • Bin E. Li
    • , Huafeng Xie
    •  & Stuart H. Orkin
  4. Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Bin E. Li
    • , Huafeng Xie
    •  & Stuart H. Orkin
  5. Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA

    • Hyuk-Soo Seo
    • , Nana K. Offei-Addo
    •  & Sirano Dhe-Paganon
  6. Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA

    • Neville E. Sanjana
    • , Ophir Shalem
    •  & Feng Zhang
  7. McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

    • Neville E. Sanjana
    • , Ophir Shalem
    •  & Feng Zhang
  8. Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts 02115, USA

    • Stuart H. Orkin
  9. Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA

    • James E. Bradner

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Contributions

M.A.E. performed experiments and analysed data. G.E.W. designed plasmids for the dTAG system with J.M.R. and performed CRISPR–Cas9 screens collaboratively with N.E.S., O.S. and F.Z. T.G.S. assisted cellular assays. B.E.L., H.X. and S.H.O. performed experiments on HSPCs. J.P., H.-S.S., N.K.O.-A. and S.D.-P. performed protein biochemistry. A.S. performed mouse experiments. S.D. and D.L.B. designed and synthesized dTAG molecules. B.N. assisted in sgRNA validation. R.Z. assisted in exon-scanning CRISPR–Cas9. M.A.E., G.E.W. and J.E.B. designed the experimental strategy and wrote the manuscript.

Competing interests

J.E.B. is now an employee, shareholder, and executive of Novartis Pharmaceuticals; G.E.W. is a consultant for C4 Therapeutics; and N.E.S., O.S. and F.Z. are inventors on a patent application related to the CRISPR screening technology.

Corresponding author

Correspondence to James E. Bradner.

Extended data

Supplementary information

PDF files

  1. 1.

    Supplementary Figure 1

    This file contains the uncropped versions of all gel images in the manuscript.

  2. 2.

    Supplementary Information

    This file contains Supplementary Methods, dTAG molecule characterizations and additional references.

Excel files

  1. 1.

    Supplementary Table 1

    This file contains the source data for the genome scale CRISPR/Cas9 screen.

About this article

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DOI

https://doi.org/10.1038/nature21688

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