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Base editing of haematopoietic stem cells rescues sickle cell disease in mice

Author

Listed:
  • Gregory A. Newby

    (Broad Institute of Harvard and MIT
    Harvard University
    Harvard University)

  • Jonathan S. Yen

    (St. Jude Children’s Research Hospital)

  • Kaitly J. Woodard

    (St. Jude Children’s Research Hospital)

  • Thiyagaraj Mayuranathan

    (St. Jude Children’s Research Hospital)

  • Cicera R. Lazzarotto

    (St. Jude Children’s Research Hospital)

  • Yichao Li

    (St. Jude Children’s Research Hospital)

  • Heather Sheppard-Tillman

    (St. Jude Children’s Research Hospital)

  • Shaina N. Porter

    (St. Jude Children’s Research Hospital)

  • Yu Yao

    (St. Jude Children’s Research Hospital)

  • Kalin Mayberry

    (St. Jude Children’s Research Hospital)

  • Kelcee A. Everette

    (Broad Institute of Harvard and MIT
    Harvard University
    Harvard University)

  • Yoonjeong Jang

    (St. Jude Children’s Research Hospital)

  • Christopher J. Podracky

    (Broad Institute of Harvard and MIT
    Harvard University
    Harvard University)

  • Elizabeth Thaman

    (Cincinnati Children’s Hospital Medical Center)

  • Christophe Lechauve

    (St. Jude Children’s Research Hospital)

  • Akshay Sharma

    (St Jude Children’s Research Hospital)

  • Jordana M. Henderson

    (TriLink BioTechnologies)

  • Michelle F. Richter

    (Broad Institute of Harvard and MIT
    Harvard University
    Harvard University)

  • Kevin T. Zhao

    (Broad Institute of Harvard and MIT
    Harvard University
    Harvard University)

  • Shannon M. Miller

    (Broad Institute of Harvard and MIT
    Harvard University
    Harvard University)

  • Tina Wang

    (Broad Institute of Harvard and MIT
    Harvard University
    Harvard University)

  • Luke W. Koblan

    (Broad Institute of Harvard and MIT
    Harvard University
    Harvard University)

  • Anton P. McCaffrey

    (TriLink BioTechnologies)

  • John F. Tisdale

    (Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute and National Institute of Diabetes and Digestive and Kidney Diseases)

  • Theodosia A. Kalfa

    (Cincinnati Children’s Hospital Medical Center
    University of Cincinnati College of Medicine)

  • Shondra M. Pruett-Miller

    (St. Jude Children’s Research Hospital)

  • Shengdar Q. Tsai

    (St. Jude Children’s Research Hospital)

  • Mitchell J. Weiss

    (St. Jude Children’s Research Hospital)

  • David R. Liu

    (Broad Institute of Harvard and MIT
    Harvard University
    Harvard University)

Abstract

Sickle cell disease (SCD) is caused by a mutation in the β-globin gene HBB1. We used a custom adenine base editor (ABE8e-NRCH)2,3 to convert the SCD allele (HBBS) into Makassar β-globin (HBBG), a non-pathogenic variant4,5. Ex vivo delivery of mRNA encoding the base editor with a targeting guide RNA into haematopoietic stem and progenitor cells (HSPCs) from patients with SCD resulted in 80% conversion of HBBS to HBBG. Sixteen weeks after transplantation of edited human HSPCs into immunodeficient mice, the frequency of HBBG was 68% and hypoxia-induced sickling of bone marrow reticulocytes had decreased fivefold, indicating durable gene editing. To assess the physiological effects of HBBS base editing, we delivered ABE8e-NRCH and guide RNA into HSPCs from a humanized SCD mouse6 and then transplanted these cells into irradiated mice. After sixteen weeks, Makassar β-globin represented 79% of β-globin protein in blood, and hypoxia-induced sickling was reduced threefold. Mice that received base-edited HSPCs showed near-normal haematological parameters and reduced splenic pathology compared to mice that received unedited cells. Secondary transplantation of edited bone marrow confirmed that the gene editing was durable in long-term haematopoietic stem cells and showed that HBBS-to-HBBG editing of 20% or more is sufficient for phenotypic rescue. Base editing of human HSPCs avoided the p53 activation and larger deletions that have been observed following Cas9 nuclease treatment. These findings point towards a one-time autologous treatment for SCD that eliminates pathogenic HBBS, generates benign HBBG, and minimizes the undesired consequences of double-strand DNA breaks.

Suggested Citation

  • Gregory A. Newby & Jonathan S. Yen & Kaitly J. Woodard & Thiyagaraj Mayuranathan & Cicera R. Lazzarotto & Yichao Li & Heather Sheppard-Tillman & Shaina N. Porter & Yu Yao & Kalin Mayberry & Kelcee A. , 2021. "Base editing of haematopoietic stem cells rescues sickle cell disease in mice," Nature, Nature, vol. 595(7866), pages 295-302, July.
  • Handle: RePEc:nat:nature:v:595:y:2021:i:7866:d:10.1038_s41586-021-03609-w
    DOI: 10.1038/s41586-021-03609-w
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    Citations

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    Cited by:

    1. Elliot H. Choi & Susie Suh & Andrzej T. Foik & Henri Leinonen & Gregory A. Newby & Xin D. Gao & Samagya Banskota & Thanh Hoang & Samuel W. Du & Zhiqian Dong & Aditya Raguram & Sajeev Kohli & Seth Blac, 2022. "In vivo base editing rescues cone photoreceptors in a mouse model of early-onset inherited retinal degeneration," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    2. 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.
    3. 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.
    4. Zhenxing Yu & Zhike Lu & Jingjing Li & Yingying Wang & Panfeng Wu & Yini Li & Yangfan Zhou & Bailun Li & Heng Zhang & Yingzheng Liu & Lijia Ma, 2022. "PEAC-seq adopts Prime Editor to detect CRISPR off-target and DNA translocation," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    5. Emily Zhang & Monica E. Neugebauer & Nicholas A. Krasnow & David R. Liu, 2024. "Phage-assisted evolution of highly active cytosine base editors with enhanced selectivity and minimal sequence context preference," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    6. Mohsin Badat & Ayesha Ejaz & Peng Hua & Siobhan Rice & Weijiao Zhang & Lance D. Hentges & Christopher A. Fisher & Nicholas Denny & Ron Schwessinger & Nirmani Yasara & Noemi B. A. Roy & Fadi Issa & And, 2023. "Direct correction of haemoglobin E β-thalassaemia using base editors," Nature Communications, Nature, vol. 14(1), pages 1-7, December.
    7. Panagiotis Antoniou & Giulia Hardouin & Pierre Martinucci & Giacomo Frati & Tristan Felix & Anne Chalumeau & Letizia Fontana & Jeanne Martin & Cecile Masson & Megane Brusson & Giulia Maule & Marion Ro, 2022. "Base-editing-mediated dissection of a γ-globin cis-regulatory element for the therapeutic reactivation of fetal hemoglobin expression," Nature Communications, Nature, vol. 13(1), pages 1-22, December.
    8. Jiaoyang Liao & Shuanghong Chen & Shenlin Hsiao & Yanhong Jiang & Yang Yang & Yuanjin Zhang & Xin Wang & Yongrong Lai & Daniel E. Bauer & Yuxuan Wu, 2023. "Therapeutic adenine base editing of human hematopoietic stem cells," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    9. Sebastian M. Siegner & Laura Ugalde & Alexandra Clemens & Laura Garcia-Garcia & Juan A. Bueren & Paula Rio & Mehmet E. Karasu & Jacob E. Corn, 2022. "Adenine base editing efficiently restores the function of Fanconi anemia hematopoietic stem and progenitor cells," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    10. Ju-Chan Park & Yun-Jeong Kim & Gue-Ho Hwang & Chan Young Kang & Sangsu Bae & Hyuk-Jin Cha, 2024. "Enhancing genome editing in hPSCs through dual inhibition of DNA damage response and repair pathways," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    11. Wei Qin & Fang Liang & Sheng-Jia Lin & Cassidy Petree & Kevin Huang & Yu Zhang & Lin Li & Pratishtha Varshney & Philippe Mourrain & Yanmei Liu & Gaurav K. Varshney, 2024. "ABE-ultramax for high-efficiency biallelic adenine base editing in zebrafish," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    12. 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.

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