1
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Rao S, Yao Y, Soares de Brito J, Yao Q, Shen AH, Watkinson RE, Kennedy AL, Coyne S, Ren C, Zeng J, Serbin AV, Studer S, Ballotti K, Harris CE, Luk K, Stevens CS, Armant M, Pinello L, Wolfe SA, Chiarle R, Shimamura A, Lee B, Newburger PE, Bauer DE. Dissecting ELANE neutropenia pathogenicity by human HSC gene editing. Cell Stem Cell 2021; 28:833-845.e5. [PMID: 33513358 PMCID: PMC8106646 DOI: 10.1016/j.stem.2020.12.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/15/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023]
Abstract
Severe congenital neutropenia (SCN) is a life-threatening disorder most often caused by dominant mutations of ELANE that interfere with neutrophil maturation. We conducted a pooled CRISPR screen in human hematopoietic stem and progenitor cells (HSPCs) that correlated ELANE mutations with neutrophil maturation potential. Highly efficient gene editing of early exons elicited nonsense-mediated decay (NMD), overcame neutrophil maturation arrest in HSPCs from ELANE-mutant SCN patients, and produced normal hematopoietic engraftment function. Conversely, terminal exon frameshift alleles that mimic SCN-associated mutations escaped NMD, recapitulated neutrophil maturation arrest, and established an animal model of ELANE-mutant SCN. Surprisingly, only -1 frame insertions or deletions (indels) impeded neutrophil maturation, whereas -2 frame late exon indels repressed translation and supported neutrophil maturation. Gene editing of primary HSPCs allowed faithful identification of variant pathogenicity to clarify molecular mechanisms of disease and encourage a universal therapeutic approach to ELANE-mutant neutropenia, returning normal neutrophil production and preserving HSPC function.
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Affiliation(s)
- Shuquan Rao
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Yao Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Josias Soares de Brito
- Departments of Pediatrics and of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Qiuming Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Boston, MA 02129, USA
| | - Anne H Shen
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Ruth E Watkinson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alyssa L Kennedy
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Steven Coyne
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Chunyan Ren
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Victoria Serbin
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard College, Cambridge, MA 02138, USA
| | - Sabine Studer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Kaitlyn Ballotti
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Chad E Harris
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Christian S Stevens
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Myriam Armant
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Luca Pinello
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Boston, MA 02129, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Akiko Shimamura
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter E Newburger
- Departments of Pediatrics and of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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2
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Demirci S, Zeng J, Wu Y, Uchida N, Shen AH, Pellin D, Gamer J, Yapundich M, Drysdale C, Bonanno J, Bonifacino AC, Krouse AE, Linde NS, Engels T, Donahue RE, Haro-Mora JJ, Leonard A, Nassehi T, Luk K, Porter SN, Lazzarotto CR, Tsai SQ, Weiss MJ, Pruett-Miller SM, Wolfe SA, Bauer DE, Tisdale JF. BCL11A enhancer-edited hematopoietic stem cells persist in rhesus monkeys without toxicity. J Clin Invest 2020; 130:6677-6687. [PMID: 32897878 PMCID: PMC7685754 DOI: 10.1172/jci140189] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 09/02/2020] [Indexed: 12/11/2022] Open
Abstract
Gene editing of the erythroid-specific BCL11A enhancer in hematopoietic stem and progenitor cells (HSPCs) from patients with sickle cell disease (SCD) induces fetal hemoglobin (HbF) without detectable toxicity, as assessed by mouse xenotransplant. Here, we evaluated autologous engraftment and HbF induction potential of erythroid-specific BCL11A enhancer-edited HSPCs in 4 nonhuman primates. We used a single guide RNA (sgRNA) with identical human and rhesus target sequences to disrupt a GATA1 binding site at the BCL11A +58 erythroid enhancer. Cas9 protein and sgRNA ribonucleoprotein complex (RNP) was electroporated into rhesus HSPCs, followed by autologous infusion after myeloablation. We found that gene edits persisted in peripheral blood (PB) and bone marrow (BM) for up to 101 weeks similarly for BCL11A enhancer- or control locus-targeted (AAVS1-targeted) cells. Biallelic BCL11A enhancer editing resulted in robust γ-globin induction, with the highest levels observed during stress erythropoiesis. Indels were evenly distributed across PB and BM lineages. Off-target edits were not observed. Nonhomologous end-joining repair alleles were enriched in engrafting HSCs. In summary, we found that edited HSCs can persist for at least 101 weeks after transplant and biallelic-edited HSCs provide substantial HbF levels in PB red blood cells, together supporting further clinical translation of this approach.
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Affiliation(s)
- Selami Demirci
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Yuxuan Wu
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, Massachusetts, USA
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Naoya Uchida
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Anne H. Shen
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Danilo Pellin
- Gene Therapy Program, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Jackson Gamer
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Morgan Yapundich
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Claire Drysdale
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Jasmine Bonanno
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Allen E. Krouse
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, Maryland, USA
| | - Nathaniel S. Linde
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, Maryland, USA
| | - Theresa Engels
- Translational Stem Cell Biology Branch, NHLBI, NIH, Bethesda, Maryland, USA
| | - Robert E. Donahue
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Juan J. Haro-Mora
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Alexis Leonard
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Tina Nassehi
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Shaina N. Porter
- Department of Cell and Molecular Biology, Center for Advanced Genome Engineering, and
| | - Cicera R. Lazzarotto
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Shengdar Q. Tsai
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Mitchell J. Weiss
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | | | - Scot A. Wolfe
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Daniel E. Bauer
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, and Department of Pediatrics, Harvard Stem Cell Institute, Broad Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - John F. Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart Lung and Blood Institute (NHLBI)/National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
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3
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Zeng J, Wu Y, Ren C, Bonanno J, Shen AH, Shea D, Gehrke JM, Clement K, Luk K, Yao Q, Kim R, Wolfe SA, Manis JP, Pinello L, Joung JK, Bauer DE. Therapeutic base editing of human hematopoietic stem cells. Nat Med 2020; 26:535-541. [PMID: 32284612 DOI: 10.1038/s41591-020-0790-y] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 02/04/2020] [Indexed: 02/06/2023]
Abstract
Base editing by nucleotide deaminases linked to programmable DNA-binding proteins represents a promising approach to permanently remedy blood disorders, although its application in engrafting hematopoietic stem cells (HSCs) remains unexplored. In this study, we purified A3A (N57Q)-BE3 base editor for ribonucleoprotein (RNP) electroporation of human-peripheral-blood-mobilized CD34+ hematopoietic stem and progenitor cells (HSPCs). We observed frequent on-target cytosine base edits at the BCL11A erythroid enhancer at +58 with few indels. Fetal hemoglobin (HbF) induction in erythroid progeny after base editing or nuclease editing was similar. A single therapeutic base edit of the BCL11A enhancer prevented sickling and ameliorated globin chain imbalance in erythroid progeny from sickle cell disease and β-thalassemia patient-derived HSPCs, respectively. Moreover, efficient multiplex editing could be achieved with combined disruption of the BCL11A erythroid enhancer and correction of the HBB -28A>G promoter mutation. Finally, base edits could be produced in multilineage-repopulating self-renewing human HSCs with high frequency as assayed in primary and secondary recipient animals resulting in potent HbF induction in vivo. Together, these results demonstrate the potential of RNP base editing of human HSPCs as a feasible alternative to nuclease editing for HSC-targeted therapeutic genome modification.
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Affiliation(s)
- Jing Zeng
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Yuxuan Wu
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Chunyan Ren
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Jasmine Bonanno
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Anne H Shen
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Devlin Shea
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Jason M Gehrke
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Kendell Clement
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - Qiuming Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Rachel Kim
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA.,Department of Chemistry, Wellesley College, Wellesley, MA, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - John P Manis
- Department of Laboratory Medicine, Boston Children's Hospital, Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - J Keith Joung
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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4
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Xu S, Luk K, Yao Q, Shen AH, Zeng J, Wu Y, Luo HY, Brendel C, Pinello L, Chui DHK, Wolfe SA, Bauer DE. Editing aberrant splice sites efficiently restores β-globin expression in β-thalassemia. Blood 2019; 133:2255-2262. [PMID: 30704988 PMCID: PMC6533605 DOI: 10.1182/blood-2019-01-895094] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 01/21/2019] [Indexed: 12/15/2022] Open
Abstract
The thalassemias are compelling targets for therapeutic genome editing in part because monoallelic correction of a subset of hematopoietic stem cells (HSCs) would be sufficient for enduring disease amelioration. A primary challenge is the development of efficient repair strategies that are effective in HSCs. Here, we demonstrate that allelic disruption of aberrant splice sites, one of the major classes of thalassemia mutations, is a robust approach to restore gene function. We target the IVS1-110G>A mutation using Cas9 ribonucleoprotein (RNP) and the IVS2-654C>T mutation by Cas12a/Cpf1 RNP in primary CD34+ hematopoietic stem and progenitor cells (HSPCs) from β-thalassemia patients. Each of these nuclease complexes achieves high efficiency and penetrance of therapeutic edits. Erythroid progeny of edited patient HSPCs show reversal of aberrant splicing and restoration of β-globin expression. This strategy could enable correction of a substantial fraction of transfusion-dependent β-thalassemia genotypes with currently available gene-editing technology.
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Affiliation(s)
- Shuqian Xu
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Broad Institute, Cambridge, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Department of Haematology, Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
| | - Qiuming Yao
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Broad Institute, Cambridge, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Molecular Pathology Unit
- Center for Cancer Research, and
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA
- Department of Pathology, Harvard Medical School, Boston, MA
| | - Anne H Shen
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Broad Institute, Cambridge, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Broad Institute, Cambridge, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Yuxuan Wu
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Broad Institute, Cambridge, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Shanghai Key Laboratory of Regulatory Biology
- Institute of Biomedical Sciences, and
- School of Life Sciences, East China Normal University, Shanghai, China
| | - Hong-Yuan Luo
- Department of Medicine and
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, MA
- Hemoglobin Diagnostic Reference Laboratory, Boston Medical Center, Boston, MA
| | - Christian Brendel
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA; and
| | - Luca Pinello
- Broad Institute, Cambridge, MA
- Molecular Pathology Unit
- Center for Cancer Research, and
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA
- Department of Pathology, Harvard Medical School, Boston, MA
| | - David H K Chui
- Department of Medicine and
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, MA
- Hemoglobin Diagnostic Reference Laboratory, Boston Medical Center, Boston, MA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, MA
| | - Daniel E Bauer
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Cambridge, MA
- Broad Institute, Cambridge, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
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5
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Wu Y, Zeng J, Roscoe BP, Liu P, Yao Q, Lazzarotto CR, Clement MK, Cole MA, Luk K, Baricordi C, Shen AH, Ren C, Esrick EB, Manis JP, Dorfman DM, Williams DA, Biffi A, Brugnara C, Biasco L, Brendel C, Pinello L, Tsai SQ, Wolfe SA, Bauer DE. Highly efficient therapeutic gene editing of human hematopoietic stem cells. Nat Med 2019; 25:776-783. [PMID: 30911135 PMCID: PMC6512986 DOI: 10.1038/s41591-019-0401-y] [Citation(s) in RCA: 289] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/14/2019] [Indexed: 02/08/2023]
Abstract
Re-expression of the paralogous γ-globin genes (HBG1/2) could be a universal strategy to ameliorate the severe β-globin disorders sickle cell disease (SCD) and β-thalassemia by induction of fetal hemoglobin (HbF, α2γ2)1. Previously, we and others have shown that core sequences at the BCL11A erythroid enhancer are required for repression of HbF in adult-stage erythroid cells but are dispensable in non-erythroid cells2-6. CRISPR-Cas9-mediated gene modification has demonstrated variable efficiency, specificity, and persistence in hematopoietic stem cells (HSCs). Here, we demonstrate that Cas9:sgRNA ribonucleoprotein (RNP)-mediated cleavage within a GATA1 binding site at the +58 BCL11A erythroid enhancer results in highly penetrant disruption of this motif, reduction of BCL11A expression, and induction of fetal γ-globin. We optimize conditions for selection-free on-target editing in patient-derived HSCs as a nearly complete reaction lacking detectable genotoxicity or deleterious impact on stem cell function. HSCs preferentially undergo non-homologous compared with microhomology-mediated end joining repair. Erythroid progeny of edited engrafting SCD HSCs express therapeutic levels of HbF and resist sickling, while those from patients with β-thalassemia show restored globin chain balance. Non-homologous end joining repair-based BCL11A enhancer editing approaching complete allelic disruption in HSCs is a practicable therapeutic strategy to produce durable HbF induction.
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Affiliation(s)
- Yuxuan Wu
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jing Zeng
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Benjamin P. Roscoe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Pengpeng Liu
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Qiuming Yao
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Boston, Massachusetts 02129, USA
| | - Cicera R. Lazzarotto
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
| | - M. Kendell Clement
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Boston, Massachusetts 02129, USA
| | - Mitchel A. Cole
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kevin Luk
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Cristina Baricordi
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Gene Therapy Program, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center
| | - Anne H. Shen
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Chunyan Ren
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Erica B. Esrick
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - John P. Manis
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David M. Dorfman
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David A. Williams
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alessandra Biffi
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Gene Therapy Program, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center
| | - Carlo Brugnara
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Luca Biasco
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Gene Therapy Program, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center
- University College of London, Great Ormond Street Institute of Child Health, Faculty of Population Health Sciences, London, UK
| | - Christian Brendel
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Gene Therapy Program, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center
| | - Luca Pinello
- Molecular Pathology Unit, Center for Cancer Research, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Boston, Massachusetts 02129, USA
| | - Shengdar Q. Tsai
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, USA
| | - Scot A. Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Daniel E. Bauer
- Division of Hematology/Oncology, Boston Children’s Hospital, Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Broad Institute, Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
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