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Therapeutic homology-independent targeted integration in retina and liver

Author

Listed:
  • Patrizia Tornabene

    (Telethon Institute of Genetics and Medicine (TIGEM)
    Federico II University)

  • Rita Ferla

    (Telethon Institute of Genetics and Medicine (TIGEM)
    Federico II University)

  • Manel Llado-Santaeularia

    (Telethon Institute of Genetics and Medicine (TIGEM))

  • Miriam Centrulo

    (Telethon Institute of Genetics and Medicine (TIGEM))

  • Margherita Dell’Anno

    (Telethon Institute of Genetics and Medicine (TIGEM)
    Federico II University)

  • Federica Esposito

    (Telethon Institute of Genetics and Medicine (TIGEM))

  • Elena Marrocco

    (Telethon Institute of Genetics and Medicine (TIGEM))

  • Emanuela Pone

    (Telethon Institute of Genetics and Medicine (TIGEM)
    Federico II University)

  • Renato Minopoli

    (Telethon Institute of Genetics and Medicine (TIGEM))

  • Carolina Iodice

    (Telethon Institute of Genetics and Medicine (TIGEM))

  • Edoardo Nusco

    (Telethon Institute of Genetics and Medicine (TIGEM))

  • Settimio Rossi

    (University of Campania L. Vanvitelli)

  • Hristiana Lyubenova

    (Telethon Institute of Genetics and Medicine (TIGEM))

  • Anna Manfredi

    (Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics
    Next Generation Diagnostic Srl)

  • Lucio Filippo

    (Next Generation Diagnostic Srl)

  • Antonella Iuliano

    (Telethon Institute of Genetics and Medicine (TIGEM))

  • Annalaura Torella

    (Telethon Institute of Genetics and Medicine (TIGEM)
    University of Campania L. Vanvitelli)

  • Giulio Piluso

    (University of Campania L. Vanvitelli)

  • Francesco Musacchia

    (Telethon Institute of Genetics and Medicine (TIGEM))

  • Enrico Maria Surace

    (Federico II University)

  • Davide Cacchiarelli

    (Telethon Institute of Genetics and Medicine (TIGEM), Armenise/Harvard Laboratory of Integrative Genomics
    Federico II University)

  • Vincenzo Nigro

    (Telethon Institute of Genetics and Medicine (TIGEM)
    University of Campania L. Vanvitelli)

  • Alberto Auricchio

    (Telethon Institute of Genetics and Medicine (TIGEM)
    Federico II University)

Abstract

Challenges to the widespread application of gene therapy with adeno-associated viral (AAV) vectors include dominant conditions due to gain-of-function mutations which require allele-specific knockout, as well as long-term transgene expression from proliferating tissues, which is hampered by AAV DNA episomal status. To overcome these challenges, we used CRISPR/Cas9-mediated homology-independent targeted integration (HITI) in retina and liver as paradigmatic target tissues. We show that AAV-HITI targets photoreceptors of both mouse and pig retina, and this results in significant improvements to retinal morphology and function in mice with autosomal dominant retinitis pigmentosa. In addition, we show that neonatal systemic AAV-HITI delivery achieves stable liver transgene expression and phenotypic improvement in a mouse model of a severe lysosomal storage disease. We also show that HITI applications predominantly result in on-target editing. These results lay the groundwork for the application of AAV-HITI for the treatment of diseases affecting various organs.

Suggested Citation

  • Patrizia Tornabene & Rita Ferla & Manel Llado-Santaeularia & Miriam Centrulo & Margherita Dell’Anno & Federica Esposito & Elena Marrocco & Emanuela Pone & Renato Minopoli & Carolina Iodice & Edoardo N, 2022. "Therapeutic homology-independent targeted integration in retina and liver," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-29550-8
    DOI: 10.1038/s41467-022-29550-8
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    References listed on IDEAS

    as
    1. Koji M. Nishiguchi & Kosuke Fujita & Fuyuki Miya & Shota Katayama & Toru Nakazawa, 2020. "Single AAV-mediated mutation replacement genome editing in limited number of photoreceptors restores vision in mice," Nature Communications, Nature, vol. 11(1), pages 1-9, December.
    2. Keiichiro Suzuki & Yuji Tsunekawa & Reyna Hernandez-Benitez & Jun Wu & Jie Zhu & Euiseok J. Kim & Fumiyuki Hatanaka & Mako Yamamoto & Toshikazu Araoka & Zhe Li & Masakazu Kurita & Tomoaki Hishida & Mo, 2016. "In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration," Nature, Nature, vol. 540(7631), pages 144-149, December.
    3. Daniel H. Lackner & Alexia Carré & Paloma M. Guzzardo & Carina Banning & Ramu Mangena & Tom Henley & Sarah Oberndorfer & Bianca V. Gapp & Sebastian M.B. Nijman & Thijn R. Brummelkamp & Tilmann Bürckst, 2015. "A generic strategy for CRISPR-Cas9-mediated gene tagging," Nature Communications, Nature, vol. 6(1), pages 1-7, December.
    4. A. Barzel & N. K. Paulk & Y. Shi & Y. Huang & K. Chu & F. Zhang & P. N. Valdmanis & L. P. Spector & M. H. Porteus & K. M. Gaensler & M. A. Kay, 2015. "Promoterless gene targeting without nucleases ameliorates haemophilia B in mice," Nature, Nature, vol. 517(7534), pages 360-364, January.
    5. Andrew V. Anzalone & Peyton B. Randolph & Jessie R. Davis & Alexander A. Sousa & Luke W. Koblan & Jonathan M. Levy & Peter J. Chen & Christopher Wilson & Gregory A. Newby & Aditya Raguram & David R. L, 2019. "Search-and-replace genome editing without double-strand breaks or donor DNA," Nature, Nature, vol. 576(7785), pages 149-157, December.
    6. Alexis C. Komor & Yongjoo B. Kim & Michael S. Packer & John A. Zuris & David R. Liu, 2016. "Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage," Nature, Nature, vol. 533(7603), pages 420-424, May.
    7. Hojun Li & Virginia Haurigot & Yannick Doyon & Tianjian Li & Sunnie Y. Wong & Anand S. Bhagwat & Nirav Malani & Xavier M. Anguela & Rajiv Sharma & Lacramiora Ivanciu & Samuel L. Murphy & Jonathan D. F, 2011. "In vivo genome editing restores haemostasis in a mouse model of haemophilia," Nature, Nature, vol. 475(7355), pages 217-221, July.
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