Single-cell chromatin accessibility profiling of glioblastoma identifies an Invasive cancer stem cell population associated with lower survival

Abstract

Chromatin accessibility discriminates stem from mature cell populations, enabling the identification of primitive stem-like cells in primary tumors, such as Glioblastoma (GBM) where self-renewing cells driving cancer progression and recurrence are prime targets for therapeutic intervention. We show, using single-cell chromatin accessibility, that primary human GBMs harbor a heterogeneous self-renewing population whose diversity is captured in patient-derived glioblastoma stem cells (GSCs). In depth characterization of chromatin accessibility in GSCs identifies three GSC states: Reactive, Constructive, and Invasive, each governed by uniquely essential transcription factors and present within GBMs in varying proportions. Orthotopic xenografts reveal that GSC states associate with survival, and identify an invasive GSC signature predictive of low patient survival, in line with the higher invasive properties of Invasive state GSCs compared to Reactive and Constructive GSCs as shown by in vitro and in vivo assays. Our chromatin-driven characterization of GSC states improves prognostic precision and identifies dependencies to guide combination therapies.

Data availability

The GSCs are available upon reasonable request from PBD and SW. The GSC ATAC-seq and DNA methylation data have been deposited at GEO (GSE109399). The scATAC-seq data has been deposited at GEO (GSE139136). RNA-seq data are available at EGA (EGAS00001003070).

The following data sets were generated

Article and author information

Author details

  1. Paul Guilhamon

    Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8276-5987
  2. Charles Chesnelong

    Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  3. Michelle M Kushida

    Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  4. Ana Nikolic

    Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
    Competing interests
    The authors declare that no competing interests exist.
  5. Divya Singhal

    Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
    Competing interests
    The authors declare that no competing interests exist.
  6. Graham MacLeod

    Leslie Dan Faculty of Pharmacy, Pharmaceutical Sciences, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6401-9307
  7. Seyed Ali Madani Tonekaboni

    Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  8. Florence MG Cavalli

    Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  9. Christopher Arlidge

    Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  10. Nishani Rajakulendran

    Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  11. Naghmeh Rastegar

    Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  12. Xiaoguang Hao

    Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2695-0111
  13. Rozina Hassam

    Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
    Competing interests
    The authors declare that no competing interests exist.
  14. Laura J Smith

    Medical Biophysics, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  15. Heather Whetstone

    Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  16. Fiona J Coutinho

    Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  17. Bettina Nadorp

    Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  18. Katrina I Ellestad

    Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
    Competing interests
    The authors declare that no competing interests exist.
  19. Artee H Luchman

    Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
    Competing interests
    The authors declare that no competing interests exist.
  20. Jennifer Ai-wen Chan

    Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
    Competing interests
    The authors declare that no competing interests exist.
  21. Molly S Shoichet

    Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1830-3475
  22. Michael D Taylor

    Developmental and Stem Cell Biology Program, Hospital for Sick Children, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  23. Benjamin Haibe-Kains

    Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  24. Sam Weiss

    Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
    Competing interests
    The authors declare that no competing interests exist.
  25. Stephane Angers

    Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7241-9044
  26. Marco Gallo

    Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Canada
    Competing interests
    The authors declare that no competing interests exist.
  27. Peter B Dirks

    Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Canada
    For correspondence
    peter.dirks@sickkids.ca
    Competing interests
    The authors declare that no competing interests exist.
  28. Mathieu Lupien

    Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
    For correspondence
    mlupien@uhnres.utoronto.ca
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0929-9478

Funding

CIHR (TGH-158221)

  • Stephane Angers
  • Peter B Dirks
  • Mathieu Lupien

SU2C canada (SU2C-AACR-DT-19-15)

  • Michael D Taylor
  • Sam Weiss
  • Peter B Dirks
  • Mathieu Lupien

CIHR (MFE 338954)

  • Paul Guilhamon

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

Ethics

Animal experimentation: All animal procedures were performed according to and approved by the Animal Care Committee of the Hospital for Sick Children or the University of Calgary. All attempts are made to minimize the handling time during surgery and treatment so as not to unduly stress the animals. Animals are observed daily after surgery to ensure there are no unexpected complications

Human subjects: All tissue samples were obtained following informed consent from patients, and all experimental procedures were performed in accordance with the Research Ethics Board at The Hospital for Sick Children (Toronto, Canada), the University of Calgary Ethics Review Board, and the Health Research Ethics Board of Alberta - Cancer Committee (HREBA). Approval to pathological data was obtained from the respective institutional review boards.

Reviewing Editor

  1. Lynne-Marie Postovit, University of Alberta, Canada

Publication history

  1. Received: October 17, 2020
  2. Accepted: January 8, 2021
  3. Accepted Manuscript published: January 11, 2021 (version 1)
  4. Version of Record published: January 29, 2021 (version 2)

Copyright

© 2021, Guilhamon 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.

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  1. Paul Guilhamon
  2. Charles Chesnelong
  3. Michelle M Kushida
  4. Ana Nikolic
  5. Divya Singhal
  6. Graham MacLeod
  7. Seyed Ali Madani Tonekaboni
  8. Florence MG Cavalli
  9. Christopher Arlidge
  10. Nishani Rajakulendran
  11. Naghmeh Rastegar
  12. Xiaoguang Hao
  13. Rozina Hassam
  14. Laura J Smith
  15. Heather Whetstone
  16. Fiona J Coutinho
  17. Bettina Nadorp
  18. Katrina I Ellestad
  19. Artee H Luchman
  20. Jennifer Ai-wen Chan
  21. Molly S Shoichet
  22. Michael D Taylor
  23. Benjamin Haibe-Kains
  24. Sam Weiss
  25. Stephane Angers
  26. Marco Gallo
  27. Peter B Dirks
  28. Mathieu Lupien
(2021)
Single-cell chromatin accessibility profiling of glioblastoma identifies an Invasive cancer stem cell population associated with lower survival
eLife 10:e64090.
https://doi.org/10.7554/eLife.64090

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