IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v13y2022i1d10.1038_s41467-022-30465-7.html
   My bibliography  Save this article

Engineered Cas12i2 is a versatile high-efficiency platform for therapeutic genome editing

Author

Listed:
  • Colin McGaw

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Anthony J. Garrity

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Gabrielle Z. Munoz

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Jeffrey R. Haswell

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Sejuti Sengupta

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Elise Keston-Smith

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Pratyusha Hunnewell

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Alexa Ornstein

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Mishti Bose

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Quinton Wessells

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Noah Jakimo

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Paul Yan

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Huaibin Zhang

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Lauren E. Alfonse

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Roy Ziblat

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Jason M. Carte

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Wei-Cheng Lu

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Derek Cerchione

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Brendan Hilbert

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Shanmugapriya Sothiselvam

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Winston X. Yan

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • David R. Cheng

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • David A. Scott

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Tia DiTommaso

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

  • Shaorong Chong

    (Arbor Biotechnologies, 20 Acorn Park Drive, Tower 500)

Abstract

The CRISPR-Cas type V-I is a family of Cas12i-containing programmable nuclease systems guided by a short crRNA without requirement for a tracrRNA. Here we present an engineered Type V-I CRISPR system (Cas12i), ABR-001, which utilizes a tracr-less guide RNA. The compact Cas12i effector is capable of self-processing pre-crRNA and cleaving dsDNA targets, which facilitates versatile delivery options and multiplexing, respectively. We apply an unbiased mutational scanning approach to enhance initially low editing activity of Cas12i2. The engineered variant, ABR-001, exhibits broad genome editing capability in human cell lines, primary T cells, and CD34+ hematopoietic stem and progenitor cells, with both robust efficiency and high specificity. In addition, ABR-001 achieves a high level of genome editing when delivered via AAV vector to HEK293T cells. This work establishes ABR-001 as a versatile, specific, and high-performance platform for ex vivo and in vivo gene therapy.

Suggested Citation

  • Colin McGaw & Anthony J. Garrity & Gabrielle Z. Munoz & Jeffrey R. Haswell & Sejuti Sengupta & Elise Keston-Smith & Pratyusha Hunnewell & Alexa Ornstein & Mishti Bose & Quinton Wessells & Noah Jakimo , 2022. "Engineered Cas12i2 is a versatile high-efficiency platform for therapeutic genome editing," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30465-7
    DOI: 10.1038/s41467-022-30465-7
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-022-30465-7
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-022-30465-7?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
    ---><---

    References listed on IDEAS

    as
    1. Liyang Zhang & John A. Zuris & Ramya Viswanathan & Jasmine N. Edelstein & Rolf Turk & Bernice Thommandru & H. Tomas Rube & Steve E. Glenn & Michael A. Collingwood & Nicole M. Bode & Sarah F. Beaudoin , 2021. "AsCas12a ultra nuclease facilitates the rapid generation of therapeutic cell medicines," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    2. Matthew C. Canver & Elenoe C. Smith & Falak Sher & Luca Pinello & Neville E. Sanjana & Ophir Shalem & Diane D. Chen & Patrick G. Schupp & Divya S. Vinjamur & Sara P. Garcia & Sidinh Luc & Ryo Kurita &, 2015. "BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis," Nature, Nature, vol. 527(7577), pages 192-197, November.
    3. Jonathan Strecker & Sara Jones & Balwina Koopal & Jonathan Schmid-Burgk & Bernd Zetsche & Linyi Gao & Kira S. Makarova & Eugene V. Koonin & Feng Zhang, 2019. "Engineering of CRISPR-Cas12b for human genome editing," Nature Communications, Nature, vol. 10(1), pages 1-8, December.
    4. Bo Zhang & Diyin Luo & Yu Li & Vanja Perčulija & Jing Chen & Jinying Lin & Yangmiao Ye & Songying Ouyang, 2021. "Mechanistic insights into the R-loop formation and cleavage in CRISPR-Cas12i1," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    5. F. Ann Ran & Le Cong & Winston X. Yan & David A. Scott & Jonathan S. Gootenberg & Andrea J. Kriz & Bernd Zetsche & Ophir Shalem & Xuebing Wu & Kira S. Makarova & Eugene V. Koonin & Phillip A. Sharp & , 2015. "In vivo genome editing using Staphylococcus aureus Cas9," Nature, Nature, vol. 520(7546), pages 186-191, April.
    6. Xue Huang & Wei Sun & Zhi Cheng & Minxuan Chen & Xueyan Li & Jiuyu Wang & Gang Sheng & Weimin Gong & Yanli Wang, 2020. "Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    7. Janice S. Chen & Yavuz S. Dagdas & Benjamin P. Kleinstiver & Moira M. Welch & Alexander A. Sousa & Lucas B. Harrington & Samuel H. Sternberg & J. Keith Joung & Ahmet Yildiz & Jennifer A. Doudna, 2017. "Enhanced proofreading governs CRISPR–Cas9 targeting accuracy," Nature, Nature, vol. 550(7676), pages 407-410, October.
    8. Liyang Zhang & John A. Zuris & Ramya Viswanathan & Jasmine N. Edelstein & Rolf Turk & Bernice Thommandru & H. Tomas Rube & Steve E. Glenn & Michael A. Collingwood & Nicole M. Bode & Sarah F. Beaudoin , 2021. "Author Correction: AsCas12a ultra nuclease facilitates the rapid generation of therapeutic cell medicines," Nature Communications, Nature, vol. 12(1), pages 1-1, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. 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.
    2. Daphne Collias & Elena Vialetto & Jiaqi Yu & Khoa Co & Éva d. H. Almási & Ann-Sophie Rüttiger & Tatjana Achmedov & Till Strowig & Chase L. Beisel, 2023. "Systematically attenuating DNA targeting enables CRISPR-driven editing in bacteria," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    3. Hang Su & Yuanchun Wang & Jin Xu & Ahmad A. Omar & Jude W. Grosser & Milica Calovic & Liyang Zhang & Yu Feng & Christopher A. Vakulskas & Nian Wang, 2023. "Generation of the transgene-free canker-resistant Citrus sinensis using Cas12a/crRNA ribonucleoprotein in the T0 generation," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    4. Guanhua Xun & Zhixin Zhu & Nilmani Singh & Jingxia Lu & Piyush K. Jain & Huimin Zhao, 2024. "Harnessing noncanonical crRNA for highly efficient genome editing," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    5. Dawn G. L. Thean & Hoi Yee Chu & John H. C. Fong & Becky K. C. Chan & Peng Zhou & Cynthia C. S. Kwok & Yee Man Chan & Silvia Y. L. Mak & Gigi C. G. Choi & Joshua W. K. Ho & Zongli Zheng & Alan S. L. W, 2022. "Machine learning-coupled combinatorial mutagenesis enables resource-efficient engineering of CRISPR-Cas9 genome editor activities," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    6. Yanbo Wang & W. Taylor Cottle & Haobo Wang & Momcilo Gavrilov & Roger S. Zou & Minh-Tam Pham & Srinivasan Yegnasubramanian & Scott Bailey & Taekjip Ha, 2022. "Achieving single nucleotide sensitivity in direct hybridization genome imaging," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    7. 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.
    8. Greta Bigelyte & Joshua K. Young & Tautvydas Karvelis & Karolina Budre & Rimante Zedaveinyte & Vesna Djukanovic & Elizabeth Ginkel & Sushmitha Paulraj & Stephen Gasior & Spencer Jones & Lanie Feigenbu, 2021. "Miniature type V-F CRISPR-Cas nucleases enable targeted DNA modification in cells," Nature Communications, Nature, vol. 12(1), pages 1-8, December.
    9. Shunsuke Kawasaki & Hiroki Ono & Moe Hirosawa & Takeru Kuwabara & Shunsuke Sumi & Suji Lee & Knut Woltjen & Hirohide Saito, 2023. "Programmable mammalian translational modulators by CRISPR-associated proteins," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    10. Raed Ibraheim & Phillip W. L. Tai & Aamir Mir & Nida Javeed & Jiaming Wang & Tomás C. Rodríguez & Suk Namkung & Samantha Nelson & Eraj Shafiq Khokhar & Esther Mintzer & Stacy Maitland & Zexiang Chen &, 2021. "Self-inactivating, all-in-one AAV vectors for precision Cas9 genome editing via homology-directed repair in vivo," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    11. Xiangjun He & Zhenjie Zhang & Junyi Xue & Yaofeng Wang & Siqi Zhang & Junkang Wei & Chenzi Zhang & Jue Wang & Brian Anugerah Urip & Chun Christopher Ngan & Junjiang Sun & Yuefeng Li & Zhiqian Lu & Hui, 2022. "Low-dose AAV-CRISPR-mediated liver-specific knock-in restored hemostasis in neonatal hemophilia B mice with subtle antibody response," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    12. Zhaohui Zhong & Guanqing Liu & Zhongjie Tang & Shuyue Xiang & Liang Yang & Lan Huang & Yao He & Tingting Fan & Shishi Liu & Xuelian Zheng & Tao Zhang & Yiping Qi & Jian Huang & Yong Zhang, 2023. "Efficient plant genome engineering using a probiotic sourced CRISPR-Cas9 system," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    13. Qiao Liu & Di He & Lei Xie, 2019. "Prediction of off-target specificity and cell-specific fitness of CRISPR-Cas System using attention boosted deep learning and network-based gene feature," PLOS Computational Biology, Public Library of Science, vol. 15(10), pages 1-22, October.
    14. Xiangfeng Kong & Hainan Zhang & Guoling Li & Zikang Wang & Xuqiang Kong & Lecong Wang & Mingxing Xue & Weihong Zhang & Yao Wang & Jiajia Lin & Jingxing Zhou & Xiaowen Shen & Yinghui Wei & Na Zhong & W, 2023. "Engineered CRISPR-OsCas12f1 and RhCas12f1 with robust activities and expanded target range for genome editing," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    15. Péter István Kulcsár & András Tálas & Zoltán Ligeti & Sarah Laura Krausz & Ervin Welker, 2022. "SuperFi-Cas9 exhibits remarkable fidelity but severely reduced activity yet works effectively with ABE8e," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    16. Nathan Bamidele & Han Zhang & Xiaolong Dong & Haoyang Cheng & Nicholas Gaston & Hailey Feinzig & Hanbing Cao & Karen Kelly & Jonathan K. Watts & Jun Xie & Guangping Gao & Erik J. Sontheimer, 2024. "Domain-inlaid Nme2Cas9 adenine base editors with improved activity and targeting scope," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    17. Inês A. M. Barbosa & Rajaraman Gopalakrishnan & Samuele Mercan & Thanos P. Mourikis & Typhaine Martin & Simon Wengert & Caibin Sheng & Fei Ji & Rui Lopes & Judith Knehr & Marc Altorfer & Alicia Lindem, 2023. "Cancer lineage-specific regulation of YAP responsive elements revealed through large-scale functional epigenomic screens," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    18. Patrick C Fiaux & Hsiuyi V Chen & Poshen B Chen & Aaron R Chen & Graham McVicker, 2020. "Discovering functional sequences with RELICS, an analysis method for CRISPR screens," PLOS Computational Biology, Public Library of Science, vol. 16(9), pages 1-23, September.
    19. Ang Li & Hitoshi Mitsunobu & Shin Yoshioka & Takahisa Suzuki & Akihiko Kondo & Keiji Nishida, 2022. "Cytosine base editing systems with minimized off-target effect and molecular size," Nature Communications, Nature, vol. 13(1), pages 1-8, December.
    20. Hongzhi Zeng & Qichen Yuan & Fei Peng & Dacheng Ma & Ananya Lingineni & Kelly Chee & Peretz Gilberd & Emmanuel C. Osikpa & Zheng Sun & Xue Gao, 2023. "A split and inducible adenine base editor for precise in vivo base editing," Nature Communications, Nature, vol. 14(1), pages 1-14, 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:13:y:2022:i:1:d:10.1038_s41467-022-30465-7. 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.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with 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.