IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v12y2021i1d10.1038_s41467-021-25190-6.html
   My bibliography  Save this article

CRISPR-Cas9 globin editing can induce megabase-scale copy-neutral losses of heterozygosity in hematopoietic cells

Author

Listed:
  • J. Boutin

    (Bordeaux University
    Inflammatory disorders and Cancers
    University Hospital Bordeaux, Biochemistry Laboratory
    Laboratory of Excellence, Gr-Ex)

  • J. Rosier

    (Bordeaux University
    Inflammatory disorders and Cancers
    Laboratory of Excellence, Gr-Ex)

  • D. Cappellen

    (Bordeaux University
    Inflammatory disorders and Cancers
    Laboratory of Excellence, Gr-Ex
    University Hospital Bordeaux, Tumor Biology and Tumor Bank Laboratory)

  • F. Prat

    (Bordeaux University
    Inflammatory disorders and Cancers
    Laboratory of Excellence, Gr-Ex)

  • J. Toutain

    (Bordeaux University, MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale)

  • P. Pennamen

    (Bordeaux University, MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale)

  • J. Bouron

    (Bordeaux University, MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale)

  • C. Rooryck

    (Bordeaux University
    Bordeaux University, MRGM INSERM U1211, CHU de Bordeaux, Service de Génétique Médicale)

  • J. P. Merlio

    (Bordeaux University
    University Hospital Bordeaux, Tumor Biology and Tumor Bank Laboratory
    INSERM U1053, Bordeaux Research in Translational Oncology)

  • I. Lamrissi-Garcia

    (Bordeaux University
    Inflammatory disorders and Cancers
    Laboratory of Excellence, Gr-Ex)

  • G. Cullot

    (Bordeaux University
    Inflammatory disorders and Cancers
    Laboratory of Excellence, Gr-Ex)

  • S. Amintas

    (Bordeaux University
    Inflammatory disorders and Cancers
    Laboratory of Excellence, Gr-Ex
    University Hospital Bordeaux, Tumor Biology and Tumor Bank Laboratory)

  • V. Guyonnet-Duperat

    (Bordeaux University)

  • C. Ged

    (Bordeaux University
    Inflammatory disorders and Cancers
    University Hospital Bordeaux, Biochemistry Laboratory
    Laboratory of Excellence, Gr-Ex)

  • J. M. Blouin

    (Bordeaux University
    Inflammatory disorders and Cancers
    University Hospital Bordeaux, Biochemistry Laboratory
    Laboratory of Excellence, Gr-Ex)

  • E. Richard

    (Bordeaux University
    Inflammatory disorders and Cancers
    University Hospital Bordeaux, Biochemistry Laboratory
    Laboratory of Excellence, Gr-Ex)

  • S. Dabernat

    (Bordeaux University
    Inflammatory disorders and Cancers
    University Hospital Bordeaux, Biochemistry Laboratory
    Laboratory of Excellence, Gr-Ex)

  • F. Moreau-Gaudry

    (Bordeaux University
    Inflammatory disorders and Cancers
    University Hospital Bordeaux, Biochemistry Laboratory
    Laboratory of Excellence, Gr-Ex)

  • A. Bedel

    (Bordeaux University
    Inflammatory disorders and Cancers
    University Hospital Bordeaux, Biochemistry Laboratory
    Laboratory of Excellence, Gr-Ex)

Abstract

CRISPR-Cas9 is a promising technology for gene therapy. However, the ON-target genotoxicity of CRISPR-Cas9 nuclease due to DNA double-strand breaks has received little attention and is probably underestimated. Here we report that genome editing targeting globin genes induces megabase-scale losses of heterozygosity (LOH) from the globin CRISPR-Cas9 cut-site to the telomere (5.2 Mb). In established lines, CRISPR-Cas9 nuclease induces frequent terminal chromosome 11p truncations and rare copy-neutral LOH. In primary hematopoietic progenitor/stem cells, we detect 1.1% of clones (7/648) with acquired megabase LOH induced by CRISPR-Cas9. In-depth analysis by SNP-array reveals the presence of copy-neutral LOH. This leads to 11p15.5 partial uniparental disomy, comprising two Chr11p15.5 imprinting centers (H19/IGF2:IG-DMR/IC1 and KCNQ1OT1:TSS-DMR/IC2) and impacting H19 and IGF2 expression. While this genotoxicity is a safety concern for CRISPR clinical trials, it is also an opportunity to model copy-neutral-LOH for genetic diseases and cancers.

Suggested Citation

  • J. Boutin & J. Rosier & D. Cappellen & F. Prat & J. Toutain & P. Pennamen & J. Bouron & C. Rooryck & J. P. Merlio & I. Lamrissi-Garcia & G. Cullot & S. Amintas & V. Guyonnet-Duperat & C. Ged & J. M. B, 2021. "CRISPR-Cas9 globin editing can induce megabase-scale copy-neutral losses of heterozygosity in hematopoietic cells," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25190-6
    DOI: 10.1038/s41467-021-25190-6
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-021-25190-6
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-021-25190-6?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. M. Kyle Cromer & Valentin V. Barsan & Erich Jaeger & Mengchi Wang & Jessica P. Hampton & Feng Chen & Drew Kennedy & Jenny Xiao & Irina Khrebtukova & Ana Granat & Tiffany Truong & Matthew H. Porteus, 2022. "Ultra-deep sequencing validates safety of CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cells," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    2. Jianli Tao & Daniel E. Bauer & Roberto Chiarle, 2023. "Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA editing," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    3. Panagiotis Antoniou & Giulia Hardouin & Pierre Martinucci & Giacomo Frati & Tristan Felix & Anne Chalumeau & Letizia Fontana & Jeanne Martin & Cecile Masson & Megane Brusson & Giulia Maule & Marion Ro, 2022. "Base-editing-mediated dissection of a γ-globin cis-regulatory element for the therapeutic reactivation of fetal hemoglobin expression," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
    4. G. Cullot & J. Boutin & S. Fayet & F. Prat & J. Rosier & D. Cappellen & I. Lamrissi & P. Pennamen & J. Bouron & S. Amintas & C. Thibault & I. Moranvillier & E. Laharanne & J. P. Merlio & V. Guyonnet-D, 2023. "Cell cycle arrest and p53 prevent ON-target megabase-scale rearrangements induced by CRISPR-Cas9," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25190-6. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.