TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells

  1. Debjani Pal
  2. Anja Pertot
  3. Nitin H Shirole
  4. Zhan Yao
  5. Naishitha Anaparthy
  6. Tyler Garvin
  7. Hilary Cox
  8. Kenneth Chang
  9. Fred Rollins
  10. Jude Kendall
  11. Leyla Edwards
  12. Vijay A. Singh
  13. Gary C. Stone
  14. Michael C. Schatz
  15. James Hicks
  16. Gregory Hannon
  17. Raffaella Sordella  Is a corresponding author
  1. Cold Spring Harbor Laboratory, United States
  2. Huntington Hospital, Northwell Health, United States
  3. Cold Spring Harbor Laboratory/ Johns Hopkins University, United States
  4. Cold Spring Harbor Laboratory/ University of Southern California, United States
  5. University of Cambridge, United Kingdom

Abstract

Many lines of evidence have indicated that both genetic and non-genetic determinants can contribute to intra-tumor heterogeneity and influence cancer outcomes. Among the best described sub-population of cancer cells generated by non-genetic mechanisms are cells characterized by a CD44+/CD24- cell surface marker profile. Here, we report that human CD44+/CD24- cancer cells are genetically highly unstable due to intrinsic defects in their DNA repair capabilities. In fact, in CD44+/CD24- cells constitutive activation of the TGF-beta axis was both necessary and sufficient to reduce the expression of genes that are critical in coordinating DNA damage repair mechanisms. Consequently, we observed that cancer cells that reside in a CD44+/CD24- state are characterized by increased accumulation of DNA copy number alterations, greater genetic diversity and improved adaptability to drug treatment. Together, these data suggest that the transition into a CD44+/CD24- cell state can promote intra-tumor genetic heterogeneity, spur tumor evolution and increase tumor fitness.

Data availability

The following previously published data sets were used

Article and author information

Author details

  1. Debjani Pal

    Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Anja Pertot

    Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Nitin H Shirole

    Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Zhan Yao

    Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Naishitha Anaparthy

    Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Tyler Garvin

    Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Hilary Cox

    Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Kenneth Chang

    Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Fred Rollins

    Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Jude Kendall

    Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Leyla Edwards

    Pathology, Huntington Hospital, Northwell Health, Huntington, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Vijay A. Singh

    Pathology, Huntington Hospital, Northwell Health, Huntington, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Gary C. Stone

    Pathology, Huntington Hospital, Northwell Health, Huntington, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Michael C. Schatz

    Quantitative Biology, Cold Spring Harbor Laboratory/ Johns Hopkins University, Cold Spring Harbor/ Baltimore, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. James Hicks

    Quantitative Biology, Cold Spring Harbor Laboratory/ University of Southern California, Cold Spring Harbor/ Los Angeles, United States
    Competing interests
    The authors declare that no competing interests exist.
  16. Gregory Hannon

    cruk cambridge insititue, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  17. Raffaella Sordella

    Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
    For correspondence
    sordella@cshl.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9745-1227

Funding

National Cancer Institute (NCI P01 CA129243-06)

  • Raffaella Sordella

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

Ethics

Human subjects: Informed consent was received from all patients who participated in the study 14-496 (PI V Singh) .

Reviewing Editor

  1. Rik Derynck, University of California, San Francisco, United States

Publication history

  1. Received: September 17, 2016
  2. Accepted: January 14, 2017
  3. Accepted Manuscript published: January 16, 2017 (version 1)
  4. Version of Record published: March 10, 2017 (version 2)

Copyright

© 2017, Pal 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

  • 3,591
    Page views
  • 736
    Downloads
  • 21
    Citations

Article citation count generated by polling the highest count across the following sources: Scopus, PubMed Central, Crossref.

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. Debjani Pal
  2. Anja Pertot
  3. Nitin H Shirole
  4. Zhan Yao
  5. Naishitha Anaparthy
  6. Tyler Garvin
  7. Hilary Cox
  8. Kenneth Chang
  9. Fred Rollins
  10. Jude Kendall
  11. Leyla Edwards
  12. Vijay A. Singh
  13. Gary C. Stone
  14. Michael C. Schatz
  15. James Hicks
  16. Gregory Hannon
  17. Raffaella Sordella
(2017)
TGF-β reduces DNA ds-break repair mechanisms to heighten genetic diversity and adaptability of CD44+/CD24- cancer cells
eLife 6:e21615.
https://doi.org/10.7554/eLife.21615
  1. Further reading

Further reading

    1. Cancer Biology
    2. Computational and Systems Biology
    Erika K Ramos, Chia-Feng Tsai ... Huiping Liu
    Research Article

    Tumor-initiating cells with reprogramming plasticity or stem-progenitor cell properties (stemness) are thought to be essential for cancer development and metastatic regeneration in many cancers; however, elucidation of the underlying molecular network and pathways remains demanding. Combining machine learning and experimental investigation, here we report CD81, a tetraspanin transmembrane protein known to be enriched in extracellular vesicles (EVs), as a newly identified driver of breast cancer stemness and metastasis. Using protein structure modeling and interface prediction-guided mutagenesis, we demonstrate that membrane CD81 interacts with CD44 through their extracellular regions in promoting tumor cell cluster formation and lung metastasis of triple negative breast cancer (TNBC) in human and mouse models. In-depth global and phosphoproteomic analyses of tumor cells deficient with CD81 or CD44 unveils endocytosis-related pathway alterations, leading to further identification of a quality-keeping role of CD44 and CD81 in EV secretion as well as in EV-associated stemness-promoting function. CD81 is co-expressed along with CD44 in human circulating tumor cells (CTCs) and enriched in clustered CTCs that promote cancer stemness and metastasis, supporting the clinical significance of CD81 in association with patient outcomes. Our study highlights machine learning as a powerful tool in facilitating the molecular understanding of new molecular targets in regulating stemness and metastasis of TNBC.

    1. Biochemistry and Chemical Biology
    2. Cancer Biology
    Adi Amar-Schwartz, Vered Ben Hur ... Rotem Karni
    Research Article

    The mTORC1 substrate, S6 Kinase 1 (S6K1), is involved in the regulation of cell growth, ribosome biogenesis, glucose homeostasis, and adipogenesis. Accumulating evidence has suggested a role for mTORC1 signaling in the DNA damage response. This is mostly based on the findings that mTORC1 inhibitors sensitized cells to DNA damage. However, a direct role of the mTORC1-S6K1 signaling pathway in DNA repair and the mechanism by which this signaling pathway regulates DNA repair is unknown. In this study, we discovered a novel role for S6K1 in regulating DNA repair through the coordinated regulation of the cell cycle, homologous recombination (HR) DNA repair (HRR) and mismatch DNA repair (MMR) mechanisms. Here, we show that S6K1 orchestrates DNA repair by phosphorylation of Cdk1 at serine 39, causing G2/M cell cycle arrest enabling homologous recombination and by phosphorylation of MSH6 at serine 309, enhancing MMR. Moreover, breast cancer cells harboring RPS6KB1 gene amplification show increased resistance to several DNA damaging agents and S6K1 expression is associated with poor survival of breast cancer patients treated with chemotherapy. Our findings reveal an unexpected function of S6K1 in the DNA repair pathway, serving as a tumorigenic barrier by safeguarding genomic stability.