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Comparative optimization of combinatorial CRISPR screens

Author

Listed:
  • Ruitong Li

    (Broad Institute of Harvard and MIT)

  • Olaf Klingbeil

    (Cold Spring Harbor Laboratory)

  • Davide Monducci

    (Broad Institute of Harvard and MIT)

  • Michael J. Young

    (Broad Institute of Harvard and MIT)

  • Diego J. Rodriguez

    (Broad Institute of Harvard and MIT)

  • Zaid Bayyat

    (Broad Institute of Harvard and MIT)

  • Joshua M. Dempster

    (Broad Institute of Harvard and MIT)

  • Devishi Kesar

    (Broad Institute of Harvard and MIT)

  • Xiaoping Yang

    (Broad Institute of Harvard and MIT)

  • Mahdi Zamanighomi

    (Broad Institute of Harvard and MIT)

  • Christopher R. Vakoc

    (Cold Spring Harbor Laboratory)

  • Takahiro Ito

    (Broad Institute of Harvard and MIT
    Harvard Medical School
    Dana-Farber Cancer Institute
    Scorpion Therapeutics)

  • William R. Sellers

    (Broad Institute of Harvard and MIT
    Harvard Medical School
    Dana-Farber Cancer Institute)

Abstract

Combinatorial CRISPR technologies have emerged as a transformative approach to systematically probe genetic interactions and dependencies of redundant gene pairs. However, the performance of different functional genomic tools for multiplexing sgRNAs vary widely. Here, we generate and benchmark ten distinct pooled combinatorial CRISPR libraries targeting paralog pairs to optimize digenic knockout screens. Libraries composed of dual Streptococcus pyogenes Cas9 (spCas9), orthogonal spCas9 and Staphylococcus aureus (saCas9), and enhanced Cas12a from Acidaminococcus were evaluated. We demonstrate a combination of alternative tracrRNA sequences from spCas9 consistently show superior effect size and positional balance between the sgRNAs as a robust combinatorial approach to profile genetic interactions of multiple genes.

Suggested Citation

  • Ruitong Li & Olaf Klingbeil & Davide Monducci & Michael J. Young & Diego J. Rodriguez & Zaid Bayyat & Joshua M. Dempster & Devishi Kesar & Xiaoping Yang & Mahdi Zamanighomi & Christopher R. Vakoc & Ta, 2022. "Comparative optimization of combinatorial CRISPR screens," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30196-9
    DOI: 10.1038/s41467-022-30196-9
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    as
    1. Nicola A. Thompson & Marco Ranzani & Louise Weyden & Vivek Iyer & Victoria Offord & Alastair Droop & Fiona Behan & Emanuel Gonçalves & Anneliese Speak & Francesco Iorio & James Hewinson & Victoria Har, 2021. "Combinatorial CRISPR screen identifies fitness effects of gene paralogues," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    2. Meghna Das Thakur & Fernando Salangsang & Allison S. Landman & William R. Sellers & Nancy K. Pryer & Mitchell P. Levesque & Reinhard Dummer & Martin McMahon & Darrin D. Stuart, 2013. "Modelling vemurafenib resistance in melanoma reveals a strategy to forestall drug resistance," Nature, Nature, vol. 494(7436), pages 251-255, February.
    3. Mahmoud Ghandi & Franklin W. Huang & Judit Jané-Valbuena & Gregory V. Kryukov & Christopher C. Lo & E. Robert McDonald & Jordi Barretina & Ellen T. Gelfand & Craig M. Bielski & Haoxin Li & Kevin Hu & , 2019. "Next-generation characterization of the Cancer Cell Line Encyclopedia," Nature, Nature, vol. 569(7757), pages 503-508, May.
    4. Joshua M. Dempster & Clare Pacini & Sasha Pantel & Fiona M. Behan & Thomas Green & John Krill-Burger & Charlotte M. Beaver & Scott T. Younger & Victor Zhivich & Hanna Najgebauer & Felicity Allen & Ema, 2019. "Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets," Nature Communications, Nature, vol. 10(1), pages 1-14, December.
    5. Fiona M. Behan & Francesco Iorio & Gabriele Picco & Emanuel Gonçalves & Charlotte M. Beaver & Giorgia Migliardi & Rita Santos & Yanhua Rao & Francesco Sassi & Marika Pinnelli & Rizwan Ansari & Sarah H, 2019. "Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens," Nature, Nature, vol. 568(7753), pages 511-516, April.
    6. Clare Pacini & Joshua M. Dempster & Isabella Boyle & Emanuel Gonçalves & Hanna Najgebauer & Emre Karakoc & Dieudonne Meer & Andrew Barthorpe & Howard Lightfoot & Patricia Jaaks & James M. McFarland & , 2021. "Integrated cross-study datasets of genetic dependencies in cancer," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    7. Edmond M. Chan & Tsukasa Shibue & James M. McFarland & Benjamin Gaeta & Mahmoud Ghandi & Nancy Dumont & Alfredo Gonzalez & Justine S. McPartlan & Tianxia Li & Yanxi Zhang & Jie Liu & Jean-Bernard Laza, 2019. "WRN helicase is a synthetic lethal target in microsatellite unstable cancers," Nature, Nature, vol. 568(7753), pages 551-556, April.
    8. James M. McFarland & Zandra V. Ho & Guillaume Kugener & Joshua M. Dempster & Phillip G. Montgomery & Jordan G. Bryan & John M. Krill-Burger & Thomas M. Green & Francisca Vazquez & Jesse S. Boehm & Tod, 2018. "Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration," Nature Communications, Nature, vol. 9(1), pages 1-13, December.
    9. Kendall R. Sanson & Ruth E. Hanna & Mudra Hegde & Katherine F. Donovan & Christine Strand & Meagan E. Sullender & Emma W. Vaimberg & Amy Goodale & David E. Root & Federica Piccioni & John G. Doench, 2018. "Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities," Nature Communications, Nature, vol. 9(1), pages 1-15, December.
    10. Rodrigo A. Gier & Krista A. Budinich & Niklaus H. Evitt & Zhendong Cao & Elizabeth S. Freilich & Qingzhou Chen & Jun Qi & Yemin Lan & Rahul M. Kohli & Junwei Shi, 2020. "High-performance CRISPR-Cas12a genome editing for combinatorial genetic screening," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    11. Yoav Benjamini, 2010. "Discovering the false discovery rate," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 72(4), pages 405-416, September.
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    1. Nazanin Esmaeili Anvar & Chenchu Lin & Xingdi Ma & Lori L. Wilson & Ryan Steger & Annabel K. Sangree & Medina Colic & Sidney H. Wang & John G. Doench & Traver Hart, 2024. "Efficient gene knockout and genetic interaction screening using the in4mer CRISPR/Cas12a multiplex knockout platform," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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