Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia

  1. Sumiko Takao
  2. Lauren Forbes
  3. Masahiro Uni
  4. Shuyuan Cheng
  5. Jose Mario Bello Pineda
  6. Yusuke Tarumoto
  7. Paolo Cifani
  8. Gerard Minuesa
  9. Celine Chen
  10. Michael G Kharas
  11. Robert K Bradley
  12. Christopher R Vakoc
  13. Richard P Koche
  14. Alex Kentsis  Is a corresponding author
  1. Memorial Sloan Kettering Cancer Center, United States
  2. Fred Hutchinson Cancer Research Center, United States
  3. Kyoto University, Japan
  4. Cold Spring Harbor Laboratory, United States

Abstract

Dysregulated gene expression contributes to most prevalent features in human cancers. Here, we show that most subtypes of acute myeloid leukemia (AML) depend on the aberrant assembly of MYB transcriptional co-activator complex. By rapid and selective peptidomimetic interference with the binding of CBP/P300 to MYB, but not CREB or MLL1, we find that the leukemic functions of MYB are mediated by CBP/P300 co-activation of a distinct set of transcription factor complexes. These MYB complexes assemble aberrantly with LYL1, E2A, C/EBP family members, LMO2 and SATB1. They are organized convergently in genetically diverse subtypes of AML, and are at least in part associated with inappropriate transcription factor co-expression. Peptidomimetic remodeling of oncogenic MYB complexes is accompanied by specific proteolysis and dynamic redistribution of CBP/P300 with alternative transcription factors such as RUNX1 to induce myeloid differentiation and apoptosis. Thus, aberrant assembly and sequestration of MYB:CBP/P300 complexes provide a unifying mechanism of oncogenic gene expression in AML. This work establishes a compelling strategy for their pharmacologic reprogramming and therapeutic targeting for diverse leukemias and possibly other human cancers caused by dysregulated gene control.

Data availability

All supplemental data are available openly via Zenodo (https://doi.org/10.5281/zenodo. 4321824). Mass spectrometry proteomics data are available via PRIDE (PXD019708). Gene expression and chromatin dynamics data are available via Gene Expression Omnibus (GSE163470).

The following data sets were generated

Article and author information

Author details

  1. Sumiko Takao

    SKI, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  2. Lauren Forbes

    SKI, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  3. Masahiro Uni

    SKI, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  4. Shuyuan Cheng

    SKI, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  5. Jose Mario Bello Pineda

    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1417-9200
  6. Yusuke Tarumoto

    Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6652-9618
  7. Paolo Cifani

    SKI, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  8. Gerard Minuesa

    SKI, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  9. Celine Chen

    SKI, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  10. Michael G Kharas

    Molecular Pharmacology and Chemistry, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
  11. Robert K Bradley

    Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8046-1063
  12. Christopher R Vakoc

    Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
    Competing interests
    No competing interests declared.
  13. Richard P Koche

    Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6820-5083
  14. Alex Kentsis

    Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, United States
    For correspondence
    kentsisresearchgroup@gmail.com
    Competing interests
    Alex Kentsis, AK is a consultant for Novartis and Rgenta. A patent application related to this work has been submitted to the U.S. Patent and Trademark Office entitled 'Agents and methods for treating CREB binding protein-dependent cancers' (application PCT/US2017/059579)..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8063-9191

Funding

National Institutes of Health (R01 CA204396)

  • Alex Kentsis

National Institutes of Health (P30 CA008748)

  • Alex Kentsis

National Institutes of Health (T32 GM073546)

  • Lauren Forbes

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2021, Takao et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 5,873
    views
  • 657
    downloads
  • 46
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Sumiko Takao
  2. Lauren Forbes
  3. Masahiro Uni
  4. Shuyuan Cheng
  5. Jose Mario Bello Pineda
  6. Yusuke Tarumoto
  7. Paolo Cifani
  8. Gerard Minuesa
  9. Celine Chen
  10. Michael G Kharas
  11. Robert K Bradley
  12. Christopher R Vakoc
  13. Richard P Koche
  14. Alex Kentsis
(2021)
Convergent organization of aberrant MYB complex controls oncogenic gene expression in acute myeloid leukemia
eLife 10:e65905.
https://doi.org/10.7554/eLife.65905

Share this article

https://doi.org/10.7554/eLife.65905

Further reading

    1. Cancer Biology
    2. Immunology and Inflammation
    Sofia V Krasik, Ekaterina A Bryushkova ... Ekaterina O Serebrovskaya
    Research Article

    The current understanding of humoral immune response in cancer patients suggests that tumors may be infiltrated with diffuse B cells of extra-tumoral origin or may develop organized lymphoid structures, where somatic hypermutation and antigen-driven selection occur locally. These processes are believed to be significantly influenced by the tumor microenvironment through secretory factors and biased cell-cell interactions. To explore the manifestation of this influence, we used deep unbiased immunoglobulin profiling and systematically characterized the relationships between B cells in circulation, draining lymph nodes (draining LNs), and tumors in 14 patients with three human cancers. We demonstrated that draining LNs are differentially involved in the interaction with the tumor site, and that significant heterogeneity exists even between different parts of a single lymph node (LN). Next, we confirmed and elaborated upon previous observations regarding intratumoral immunoglobulin heterogeneity. We identified B cell receptor (BCR) clonotypes that were expanded in tumors relative to draining LNs and blood and observed that these tumor-expanded clonotypes were less hypermutated than non-expanded (ubiquitous) clonotypes. Furthermore, we observed a shift in the properties of complementarity-determining region 3 of the BCR heavy chain (CDR-H3) towards less mature and less specific BCR repertoire in tumor-infiltrating B-cells compared to circulating B-cells, which may indicate less stringent control for antibody-producing B cell development in tumor microenvironment (TME). In addition, we found repertoire-level evidence that B-cells may be selected according to their CDR-H3 physicochemical properties before they activate somatic hypermutation (SHM). Altogether, our work outlines a broad picture of the differences in the tumor BCR repertoire relative to non-tumor tissues and points to the unexpected features of the SHM process.

    1. Cancer Biology
    2. Computational and Systems Biology
    Rosalyn W Sayaman, Masaru Miyano ... Mark A LaBarge
    Research Article Updated

    Effects from aging in single cells are heterogenous, whereas at the organ- and tissue-levels aging phenotypes tend to appear as stereotypical changes. The mammary epithelium is a bilayer of two major phenotypically and functionally distinct cell lineages: luminal epithelial and myoepithelial cells. Mammary luminal epithelia exhibit substantial stereotypical changes with age that merit attention because these cells are the putative cells-of-origin for breast cancers. We hypothesize that effects from aging that impinge upon maintenance of lineage fidelity increase susceptibility to cancer initiation. We generated and analyzed transcriptomes from primary luminal epithelial and myoepithelial cells from younger <30 (y)ears old and older >55 y women. In addition to age-dependent directional changes in gene expression, we observed increased transcriptional variance with age that contributed to genome-wide loss of lineage fidelity. Age-dependent variant responses were common to both lineages, whereas directional changes were almost exclusively detected in luminal epithelia and involved altered regulation of chromatin and genome organizers such as SATB1. Epithelial expression variance of gap junction protein GJB6 increased with age, and modulation of GJB6 expression in heterochronous co-cultures revealed that it provided a communication conduit from myoepithelial cells that drove directional change in luminal cells. Age-dependent luminal transcriptomes comprised a prominent signal that could be detected in bulk tissue during aging and transition into cancers. A machine learning classifier based on luminal-specific aging distinguished normal from cancer tissue and was highly predictive of breast cancer subtype. We speculate that luminal epithelia are the ultimate site of integration of the variant responses to aging in their surrounding tissue, and that their emergent phenotype both endows cells with the ability to become cancer-cells-of-origin and represents a biosensor that presages cancer susceptibility.