Abstract

CRISPR/Cas9 provides a highly efficient and flexible genome editing technology with numerous potential applications ranging from gene therapy to population control. Some proposed applications involve the integration of CRISPR/Cas9 endonucleases into an organism's genome, which raises questions about potentially harmful effects to the transgenic individuals. One example for which this is particularly relevant are CRISPR-based gene drives conceived for the genetic alteration of entire populations. The performance of such drives can strongly depend on fitness costs experienced by drive carriers, yet relatively little is known about the magnitude and causes of these costs. Here, we assess the fitness effects of genomic CRISPR/Cas9 expression in Drosophila melanogaster cage populations by tracking allele frequencies of four different transgenic constructs that allow us to disentangle 'direct' fitness costs due to the integration, expression, and target-site activity of Cas9, from fitness costs due to potential off-target cleavage. Using a maximum likelihood framework, we find that a model with no direct fitness costs but moderate costs due to off-target effects fits our cage data best. Consistent with this, we do not observe fitness costs for a construct with Cas9HF1, a high-fidelity version of Cas9. We further demonstrate that using Cas9HF1 instead of standard Cas9 in a homing drive achieves similar drive conversion efficiency. These results suggest that gene drives should be designed with high-fidelity endonucleases and may have implications for other applications that involve genomic integration of CRISPR endonucleases.

Data availability

All data generated or analyzed during this study are included in the manuscript and supporting files.

Article and author information

Author details

  1. Anna M Langmüller

    Department of Computational Biology, Cornell University, Ithaca, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6102-8862
  2. Jackson Champer

    Center for Bioinformatics, Peking University, Beijing, China
    For correspondence
    jchamper@pku.edu.cn
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3814-3774
  3. Sandra Lapinska

    Department of Computational Biology, Cornell University, Ithaca, United States
    Competing interests
    No competing interests declared.
  4. Lin Xie

    Department of Computational Biology, Cornell University, Ithaca, United States
    Competing interests
    No competing interests declared.
  5. Matthew Metzloff

    Department of Computational Biology, Cornell University, Ithaca, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6108-5031
  6. Samuel E Champer

    Department of Computational Biology, Cornell University, Ithaca, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4559-7627
  7. Jingxian Liu

    Department of Biological Statistics, Cornell University, Ithaca, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2172-3297
  8. Yineng Xu

    Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4473-4052
  9. Jie Du

    Center for Bioinformatics, Peking University, Beijing, China
    Competing interests
    No competing interests declared.
  10. Andrew G Clark

    Department of Computational Biology, Cornell University, Ithaca, United States
    Competing interests
    No competing interests declared.
  11. Philipp W Messer

    Department of Computational Biology, Cornell University, Ithaca, United States
    For correspondence
    messer@cornell.edu
    Competing interests
    Philipp W Messer, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8453-9377

Funding

National Institutes of Health (R21AI130635)

  • Jackson Champer
  • Andrew G Clark
  • Philipp W Messer

National Institutes of Health (F32AI138476)

  • Jackson Champer

National Institutes of Health (R01GM127418)

  • Philipp W Messer

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 flies with an active homing gene drive system were kept at the Sarkaria Arthropod Research Laboratory at Cornell University under Arthropod Containment Level 2 protocols in accordance with USDA APHIS standards. All safety standards were approved by the Cornell University Institutional Biosafety Committee.

Copyright

© 2022, Langmüller 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. Anna M Langmüller
  2. Jackson Champer
  3. Sandra Lapinska
  4. Lin Xie
  5. Matthew Metzloff
  6. Samuel E Champer
  7. Jingxian Liu
  8. Yineng Xu
  9. Jie Du
  10. Andrew G Clark
  11. Philipp W Messer
(2022)
Fitness effects of CRISPR endonucleases in Drosophila melanogaster populations
eLife 11:e71809.
https://doi.org/10.7554/eLife.71809

Share this article

https://doi.org/10.7554/eLife.71809

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