2. Academic Validation
  3. Context-defined cancer co-dependency mapping identifies a functional interplay between PRC2 and MLL-MEN1 complex in lymphoma

Context-defined cancer co-dependency mapping identifies a functional interplay between PRC2 and MLL-MEN1 complex in lymphoma

  • Nat Commun. 2023 Jul 17;14(1):4259. doi: 10.1038/s41467-023-39990-5.
Xiao Chen # 1 2,  Yinglu Li # 1,  Fang Zhu 1 3,  Xinjing Xu 1,  Brian Estrella 4,  Manuel A Pazos 2nd 4,  John T McGuire 1,  Dimitris Karagiannis 1,  Varun Sahu 1,  Mustafo Mustafokulov 1,  Claudio Scuoppo 5 6,  Francisco J Sánchez-Rivera 7 8,  Yadira M Soto-Feliciano 7 8,  Laura Pasqualucci 5 6 9,  Alberto Ciccia 1 5 9,  Jennifer E Amengual 4 9,  Chao Lu 10 11
Affiliations

Affiliations

  • 1 Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.
  • 2 Marine College, Shandong University, 264209, Weihai, China.
  • 3 Union Hospital Cancer Center, Tongji Medical College, Huazhong University of Science and Technology, 430022, Wuhan, China.
  • 4 Division of Hematology and Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA.
  • 5 Institute for Cancer Genetics, Columbia University Irving Medical Center, New York, NY, 10032, USA.
  • 6 Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA.
  • 7 David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
  • 8 Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
  • 9 Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA.
  • 10 Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA. cl3684@cumc.columbia.edu.
  • 11 Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, 10032, USA. cl3684@cumc.columbia.edu.
  • # Contributed equally.
PMID: 37460547 DOI: 10.1038/s41467-023-39990-5
Abstract

Interplay between chromatin-associated complexes and modifications critically contribute to the partitioning of epigenome into stable and functionally distinct domains. Yet there is a lack of systematic identification of chromatin crosstalk mechanisms, limiting our understanding of the dynamic transition between chromatin states during development and disease. Here we perform co-dependency mapping of genes using CRISPR-Cas9-mediated fitness screens in pan-cancer cell lines to quantify gene-gene functional relationships. We identify 145 co-dependency modules and further define the molecular context underlying the essentiality of these modules by incorporating mutational, epigenome, gene expression and drug sensitivity profiles of cell lines. These analyses assign new protein complex composition and function, and predict new functional interactions, including an unexpected co-dependency between two transcriptionally counteracting chromatin complexes - polycomb repressive complex 2 (PRC2) and MLL-MEN1 complex. We show that PRC2-mediated H3K27 tri-methylation regulates the genome-wide distribution of MLL1 and MEN1. In lymphoma cells with EZH2 gain-of-function mutations, the re-localization of MLL-MEN1 complex drives oncogenic gene expression and results in a hypersensitivity to pharmacologic inhibition of MEN1. Together, our findings provide a resource for discovery of trans-regulatory interactions as mechanisms of chromatin regulation and potential targets of synthetic lethality.

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