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CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations

Author

Listed:
  • Grégoire Cullot

    (Univ. Bordeaux
    INSERM U1035, Biotherapy of genetic diseases, inflammatory disorders and cancers)

  • Julian Boutin

    (Univ. Bordeaux
    INSERM U1035, Biotherapy of genetic diseases, inflammatory disorders and cancers
    CHU Bordeaux)

  • Jérôme Toutain

    (CHU Bordeaux)

  • Florence Prat

    (Univ. Bordeaux
    INSERM U1035, Biotherapy of genetic diseases, inflammatory disorders and cancers)

  • Perrine Pennamen

    (CHU Bordeaux)

  • Caroline Rooryck

    (CHU Bordeaux)

  • Martin Teichmann

    (Univ. Bordeaux
    UMR 5320, INSERM U1212, ARNA Laboratory)

  • Emilie Rousseau

    (Univ. Bordeaux
    UMR 5320, INSERM U1212, ARNA Laboratory)

  • Isabelle Lamrissi-Garcia

    (Univ. Bordeaux
    INSERM U1035, Biotherapy of genetic diseases, inflammatory disorders and cancers)

  • Véronique Guyonnet-Duperat

    (INSERM U1035, Biotherapy of genetic diseases, inflammatory disorders and cancers
    Vectorology Platform)

  • Alice Bibeyran

    (INSERM U1035, Biotherapy of genetic diseases, inflammatory disorders and cancers
    Vectorology Platform)

  • Magalie Lalanne

    (Univ. Bordeaux
    INSERM U1035, Biotherapy of genetic diseases, inflammatory disorders and cancers)

  • Valérie Prouzet-Mauléon

    (Univ. Bordeaux
    INSERM U1218, ACTION)

  • Béatrice Turcq

    (Univ. Bordeaux
    INSERM U1218, ACTION)

  • Cécile Ged

    (Univ. Bordeaux
    INSERM U1035, Biotherapy of genetic diseases, inflammatory disorders and cancers
    CHU Bordeaux
    Laboratory of excellence, GR-Ex, Imagine institute)

  • Jean-Marc Blouin

    (Univ. Bordeaux
    INSERM U1035, Biotherapy of genetic diseases, inflammatory disorders and cancers
    CHU Bordeaux
    Laboratory of excellence, GR-Ex, Imagine institute)

  • Emmanuel Richard

    (Univ. Bordeaux
    INSERM U1035, Biotherapy of genetic diseases, inflammatory disorders and cancers
    CHU Bordeaux
    Laboratory of excellence, GR-Ex, Imagine institute)

  • Sandrine Dabernat

    (Univ. Bordeaux
    INSERM U1035, Biotherapy of genetic diseases, inflammatory disorders and cancers
    CHU Bordeaux)

  • François Moreau-Gaudry

    (Univ. Bordeaux
    INSERM U1035, Biotherapy of genetic diseases, inflammatory disorders and cancers
    CHU Bordeaux
    Vectorology Platform)

  • Aurélie Bedel

    (Univ. Bordeaux
    INSERM U1035, Biotherapy of genetic diseases, inflammatory disorders and cancers
    CHU Bordeaux
    Laboratory of excellence, GR-Ex, Imagine institute)

Abstract

CRISPR-Cas9 is a promising technology for genome editing. Here we use Cas9 nuclease-induced double-strand break DNA (DSB) at the UROS locus to model and correct congenital erythropoietic porphyria. We demonstrate that homology-directed repair is rare compared with NHEJ pathway leading to on-target indels and causing unwanted dysfunctional protein. Moreover, we describe unexpected chromosomal truncations resulting from only one Cas9 nuclease-induced DSB in cell lines and primary cells by a p53-dependent mechanism. Altogether, these side effects may limit the promising perspectives of the CRISPR-Cas9 nuclease system for disease modeling and gene therapy. We show that the single nickase approach could be safer since it prevents on- and off-target indels and chromosomal truncations. These results demonstrate that the single nickase and not the nuclease approach is preferable, not only for modeling disease but also and more importantly for the safe management of future CRISPR-Cas9-mediated gene therapies.

Suggested Citation

  • Grégoire Cullot & Julian Boutin & Jérôme Toutain & Florence Prat & Perrine Pennamen & Caroline Rooryck & Martin Teichmann & Emilie Rousseau & Isabelle Lamrissi-Garcia & Véronique Guyonnet-Duperat & Al, 2019. "CRISPR-Cas9 genome editing induces megabase-scale chromosomal truncations," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-09006-2
    DOI: 10.1038/s41467-019-09006-2
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    Cited by:

    1. Jianhang Yin & Kailun Fang & Yanxia Gao & Liqiong Ou & Shaopeng Yuan & Changchang Xin & Weiwei Wu & Wei-wei Wu & Jiaxu Hong & Hui Yang & Jiazhi Hu, 2022. "Safeguarding genome integrity during gene-editing therapy in a mouse model of age-related macular degeneration," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    2. Behrouz Eslami-Mossallam & Misha Klein & Constantijn V. D. Smagt & Koen V. D. Sanden & Stephen K. Jones & John A. Hawkins & Ilya J. Finkelstein & Martin Depken, 2022. "A kinetic model predicts SpCas9 activity, improves off-target classification, and reveals the physical basis of targeting fidelity," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    3. Arianna Moiani & Gil Letort & Sabrina Lizot & Anne Chalumeau & Chloe Foray & Tristan Felix & Diane Clerre & Sonal Temburni-Blake & Patrick Hong & Sophie Leduc & Noemie Pinard & Alan Marechal & Eduardo, 2024. "Non-viral DNA delivery and TALEN editing correct the sickle cell mutation in hematopoietic stem cells," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    4. Changchang Xin & Jianhang Yin & Shaopeng Yuan & Liqiong Ou & Mengzhu Liu & Weiwei Zhang & Jiazhi Hu, 2022. "Comprehensive assessment of miniature CRISPR-Cas12f nucleases for gene disruption," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    5. Jianhang Yin & Rusen Lu & Changchang Xin & Yuhong Wang & Xinyu Ling & Dong Li & Weiwei Zhang & Mengzhu Liu & Wutao Xie & Lingyun Kong & Wen Si & Ping Wei & Bingbing Xiao & Hsiang-Ying Lee & Tao Liu & , 2022. "Cas9 exo-endonuclease eliminates chromosomal translocations during genome editing," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    6. Sundaram Acharya & Asgar Hussain Ansari & Prosad Kumar Das & Seiichi Hirano & Meghali Aich & Riya Rauthan & Sudipta Mahato & Savitri Maddileti & Sajal Sarkar & Manoj Kumar & Rhythm Phutela & Sneha Gul, 2024. "PAM-flexible Engineered FnCas9 variants for robust and ultra-precise genome editing and diagnostics," Nature Communications, Nature, vol. 15(1), pages 1-23, December.
    7. 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.
    8. 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.
    9. Lukas Möller & Eric J. Aird & Markus S. Schröder & Lena Kobel & Lucas Kissling & Lilly van de Venn & Jacob E. Corn, 2022. "Recursive Editing improves homology-directed repair through retargeting of undesired outcomes," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    10. Burcu Bestas & Sandra Wimberger & Dmitrii Degtev & Alexandra Madsen & Antje K. Rottner & Fredrik Karlsson & Sergey Naumenko & Megan Callahan & Julia Liz Touza & Margherita Francescatto & Carl Ivar Möl, 2023. "A Type II-B Cas9 nuclease with minimized off-targets and reduced chromosomal translocations in vivo," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    11. Hsiu-Hui Tsai & Hsiao-Jung Kao & Ming-Wei Kuo & Chin-Hsien Lin & Chun-Min Chang & Yi-Yin Chen & Hsiao-Huei Chen & Pui-Yan Kwok & Alice L. Yu & John Yu, 2023. "Whole genomic analysis reveals atypical non-homologous off-target large structural variants induced by CRISPR-Cas9-mediated genome editing," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    12. Yong Tao & Veronica Lamas & Wan Du & Wenliang Zhu & Yiran Li & Madelynn N. Whittaker & John A. Zuris & David B. Thompson & Arun Prabhu Rameshbabu & Yilai Shu & Xue Gao & Johnny H. Hu & Charles Pei & W, 2023. "Treatment of monogenic and digenic dominant genetic hearing loss by CRISPR-Cas9 ribonucleoprotein delivery in vivo," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    13. Sanju Sinha & Karina Barbosa & Kuoyuan Cheng & Mark D. M. Leiserson & Prashant Jain & Anagha Deshpande & David M. Wilson & Bríd M. Ryan & Ji Luo & Ze’ev A. Ronai & Joo Sang Lee & Aniruddha J. Deshpand, 2021. "A systematic genome-wide mapping of oncogenic mutation selection during CRISPR-Cas9 genome editing," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    14. Michael Kosicki & Felicity Allen & Frances Steward & Kärt Tomberg & Yangyang Pan & Allan Bradley, 2022. "Cas9-induced large deletions and small indels are controlled in a convergent fashion," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    15. Jianli Tao & Qi Wang & Carlos Mendez-Dorantes & Kathleen H. Burns & Roberto Chiarle, 2022. "Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    16. Maarten H. Geurts & Shashank Gandhi & Matteo G. Boretto & Ninouk Akkerman & Lucca L. M. Derks & Gijs Son & Martina Celotti & Sarina Harshuk-Shabso & Flavia Peci & Harry Begthel & Delilah Hendriks & Pa, 2023. "One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    17. András Tálas & Dorottya A. Simon & Péter I. Kulcsár & Éva Varga & Sarah L. Krausz & Ervin Welker, 2021. "BEAR reveals that increased fidelity variants can successfully reduce the mismatch tolerance of adenine but not cytosine base editors," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    18. 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.

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