1
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Zanganeh S, Zahedi AM, Sattarzadeh Bardsiri M, Bazi A, Bastanifard M, Shool S, Kouhbananinejad SM, Farsinejad A, Afgar A, Shahabi A, Mirzaei-Parsa MJ. Recent advances and applications of the CRISPR-Cas system in the gene therapy of blood disorders. Gene 2024; 931:148865. [PMID: 39168259 DOI: 10.1016/j.gene.2024.148865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 08/11/2024] [Accepted: 08/14/2024] [Indexed: 08/23/2024]
Affiliation(s)
- Saeed Zanganeh
- Stem Cells and Regenerative Medicine Innovation Center, Kerman University of Medical Sciences, Kerman, Iran; Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran.
| | - Amir Mohammad Zahedi
- Stem Cells and Regenerative Medicine Innovation Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Mahla Sattarzadeh Bardsiri
- Stem Cells and Regenerative Medicine Innovation Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Bazi
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mahdieh Bastanifard
- Stem Cells and Regenerative Medicine Innovation Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Sanaz Shool
- Stem Cells and Regenerative Medicine Innovation Center, Kerman University of Medical Sciences, Kerman, Iran
| | | | - Alireza Farsinejad
- Stem Cells and Regenerative Medicine Innovation Center, Kerman University of Medical Sciences, Kerman, Iran; Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Ali Afgar
- Research Center for Hydatid Disease in Iran, Kerman University of Medical Sciences, Kerman, Iran
| | - Arman Shahabi
- Stem Cells and Regenerative Medicine Innovation Center, Kerman University of Medical Sciences, Kerman, Iran
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2
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Zhang L, Li K, Liu Z, An L, Wei H, Pang S, Cao Z, Huang X, Jin X, Ma X. Restoring T and B cell generation in X-linked severe combined immunodeficiency mice through hematopoietic stem cells adenine base editing. Mol Ther 2024; 32:1658-1671. [PMID: 38532630 PMCID: PMC11184316 DOI: 10.1016/j.ymthe.2024.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 01/15/2024] [Accepted: 03/22/2024] [Indexed: 03/28/2024] Open
Abstract
Base editing of hematopoietic stem/progenitor cells (HSPCs) is an attractive strategy for treating immunohematologic diseases. However, the feasibility of using adenine-base-edited HSPCs for treating X-linked severe combined immunodeficiency (SCID-X1), the influence of dose-response relationships on immune cell generation, and the potential risks have not been demonstrated in vivo. Here, a humanized SCID-X1 mouse model was established, and 86.67% ± 2.52% (n = 3) of mouse hematopoietic stem cell (HSC) pathogenic mutations were corrected, with no single-guide-RNA (sgRNA)-dependent off-target effects detected. Analysis of peripheral blood over 16 weeks post-transplantation in mice with different immunodeficiency backgrounds revealed efficient immune cell generation following transplantation of different amounts of modified HSCs. Therefore, a large-scale infusion of gene-corrected HSCs within a safe range can achieve rapid, stable, and durable immune cell regeneration. Tissue-section staining further demonstrated the restoration of immune organ tissue structures, with no tumor formation in multiple organs. Collectively, these data suggest that base-edited HSCs are a potential therapeutic approach for SCID-X1 and that a threshold infusion dose of gene-corrected cells is required for immune cell regeneration. This study lays a theoretical foundation for the clinical application of base-edited HSCs in treating SCID-X1.
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Affiliation(s)
- Lu Zhang
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China
| | - Kai Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai 200433, China
| | - Zhiwei Liu
- Cambridge-Suda Genomic Resource Center, Suzhou Medical College of Soochow University, Suzhou 215123, China
| | - Lisha An
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China
| | - Haikun Wei
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China
| | - Shanshan Pang
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China
| | - Zongfu Cao
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaohua Jin
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China.
| | - Xu Ma
- National Research Institute for Family Planning, Beijing 100081, China; National Human Genetic Resources Center, Beijing 102206, China.
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3
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Mudde ACA, Kuo CY, Kohn DB, Booth C. What a Clinician Needs to Know About Genome Editing: Status and Opportunities for Inborn Errors of Immunity. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2024; 12:1139-1149. [PMID: 38246560 DOI: 10.1016/j.jaip.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/08/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024]
Abstract
During the past 20 years, gene editing has emerged as a novel form of gene therapy. Since the publication of the first potentially therapeutic gene editing platform for genetic disorders, increasingly sophisticated editing technologies have been developed. As with viral vector-mediated gene addition, inborn errors of immunity are excellent candidate diseases for a corrective autologous hematopoietic stem cell gene editing strategy. Research on gene editing for inborn errors of immunity is still entirely preclinical, with no trials yet underway. However, with editing techniques maturing, scientists are investigating this novel form of gene therapy in context of an increasing number of inborn errors of immunity. Here, we present an overview of these studies and the recent progress moving these technologies closer to clinical benefit.
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Affiliation(s)
- Anne C A Mudde
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Caroline Y Kuo
- Department of Pediatrics, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, Calif
| | - Donald B Kohn
- Department of Pediatrics, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, Calif; Department of Microbiology, Immunology & Molecular Genetics, UCLA David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, Calif
| | - Claire Booth
- UCL Great Ormond Street Institute of Child Health, London, United Kingdom; Department of Paediatric Immunology and Gene Therapy, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom.
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4
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Pavel-Dinu M, Gardner CL, Nakauchi Y, Kawai T, Delmonte OM, Palterer B, Bosticardo M, Pala F, Viel S, Malech HL, Ghanim HY, Bode NM, Kurgan GL, Detweiler AM, Vakulskas CA, Neff NF, Sheikali A, Menezes ST, Chrobok J, Hernández González EM, Majeti R, Notarangelo LD, Porteus MH. Genetically corrected RAG2-SCID human hematopoietic stem cells restore V(D)J-recombinase and rescue lymphoid deficiency. Blood Adv 2024; 8:1820-1833. [PMID: 38096800 PMCID: PMC11006817 DOI: 10.1182/bloodadvances.2023011766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 10/23/2023] [Indexed: 04/10/2024] Open
Abstract
ABSTRACT Recombination-activating genes (RAG1 and RAG2) are critical for lymphoid cell development and function by initiating the variable (V), diversity (D), and joining (J) (V(D)J)-recombination process to generate polyclonal lymphocytes with broad antigen specificity. The clinical manifestations of defective RAG1/2 genes range from immune dysregulation to severe combined immunodeficiencies (SCIDs), causing life-threatening infections and death early in life without hematopoietic cell transplantation (HCT). Despite improvements, haploidentical HCT without myeloablative conditioning carries a high risk of graft failure and incomplete immune reconstitution. The RAG complex is only expressed during the G0-G1 phase of the cell cycle in the early stages of T- and B-cell development, underscoring that a direct gene correction might capture the precise temporal expression of the endogenous gene. Here, we report a feasibility study using the CRISPR/Cas9-based "universal gene-correction" approach for the RAG2 locus in human hematopoietic stem/progenitor cells (HSPCs) from healthy donors and RAG2-SCID patient. V(D)J-recombinase activity was restored after gene correction of RAG2-SCID-derived HSPCs, resulting in the development of T-cell receptor (TCR) αβ and γδ CD3+ cells and single-positive CD4+ and CD8+ lymphocytes. TCR repertoire analysis indicated a normal distribution of CDR3 length and preserved usage of the distal TRAV genes. We confirmed the in vivo rescue of B-cell development with normal immunoglobulin M surface expression and a significant decrease in CD56bright natural killer cells. Together, we provide specificity, toxicity, and efficacy data supporting the development of a gene-correction therapy to benefit RAG2-deficient patients.
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Affiliation(s)
- Mara Pavel-Dinu
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Cameron L. Gardner
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Yusuke Nakauchi
- Division of Hematology, Department of Medicine, Cancer Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA
| | - Tomoki Kawai
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Ottavia M. Delmonte
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Boaz Palterer
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Marita Bosticardo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Francesca Pala
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Sebastien Viel
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
- Service d’immunologie biologique, Hospices Civils de Lyon, Centre International de Recherche en Infectivologie, Centre International de Recheerche in Infectivalogie, INSERM U1111, Université Claude Bernard Lyon 1, Centre National de la Recherge Scientifique, UMR5308, École Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Harry L. Malech
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Hana Y. Ghanim
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | | | | | | | | | | | - Adam Sheikali
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Sherah T. Menezes
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Jade Chrobok
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Elaine M. Hernández González
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Ravindra Majeti
- Division of Hematology, Department of Medicine, Cancer Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA
| | - Luigi D. Notarangelo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Matthew H. Porteus
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
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5
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Rai R, Steinberg Z, Romito M, Zinghirino F, Hu YT, White N, Naseem A, Thrasher AJ, Turchiano G, Cavazza A. CRISPR/Cas9-Based Disease Modeling and Functional Correction of Interleukin 7 Receptor Alpha Severe Combined Immunodeficiency in T-Lymphocytes and Hematopoietic Stem Cells. Hum Gene Ther 2024; 35:269-283. [PMID: 38251667 DOI: 10.1089/hum.2023.100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024] Open
Abstract
Interleukin 7 Receptor alpha Severe Combined Immunodeficiency (IL7R-SCID) is a life-threatening disorder caused by homozygous mutations in the IL7RA gene. Defective IL7R expression in humans hampers T cell precursors' proliferation and differentiation during lymphopoiesis resulting in the absence of T cells in newborns, who succumb to severe infections and death early after birth. Previous attempts to tackle IL7R-SCID by viral gene therapy have shown that unregulated IL7R expression predisposes to leukemia, suggesting the application of targeted gene editing to insert a correct copy of the IL7RA gene in its genomic locus and mediate its physiological expression as a more feasible therapeutic approach. To this aim, we have first developed a CRISPR/Cas9-based IL7R-SCID disease modeling system that recapitulates the disease phenotype in primary human T cells and hematopoietic stem and progenitor cells (HSPCs). Then, we have designed a knockin strategy that targets IL7RA exon 1 and introduces through homology-directed repair a corrective, promoterless IL7RA cDNA followed by a reporter cassette through AAV6 transduction. Targeted integration of the corrective cassette in primary T cells restored IL7R expression and rescued functional downstream IL7R signaling. When applied to HSPCs further induced to differentiate into T cells in an Artificial Thymic Organoid system, our gene editing strategy overcame the T cell developmental block observed in IL7R-SCID patients, while promoting full maturation of T cells with physiological and developmentally regulated IL7R expression. Finally, genotoxicity assessment of the CRISPR/Cas9 platform in HSPCs using biased and unbiased technologies confirmed the safety of the strategy, paving the way for a new, efficient, and safe therapeutic option for IL7R-SCID patients.
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Affiliation(s)
- Rajeev Rai
- Infection, Immunity, and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Zohar Steinberg
- Infection, Immunity, and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Marianna Romito
- Infection, Immunity, and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Federica Zinghirino
- Infection, Immunity, and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Yi-Ting Hu
- Infection, Immunity, and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Nathan White
- Infection, Immunity, and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Asma Naseem
- Infection, Immunity, and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Adrian J Thrasher
- Infection, Immunity, and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Center, London, United Kingdom
| | - Giandomenico Turchiano
- Infection, Immunity, and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Alessia Cavazza
- Infection, Immunity, and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- NIHR Great Ormond Street Hospital Biomedical Research Center, London, United Kingdom
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia School of Medicine, Modena, Italy
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6
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Castiello MC, Brandas C, Ferrari S, Porcellini S, Sacchetti N, Canarutto D, Draghici E, Merelli I, Barcella M, Pelosi G, Vavassori V, Varesi A, Jacob A, Scala S, Basso Ricci L, Paulis M, Strina D, Di Verniere M, Sergi Sergi L, Serafini M, Holland SM, Bergerson JRE, De Ravin SS, Malech HL, Pala F, Bosticardo M, Brombin C, Cugnata F, Calzoni E, Crooks GM, Notarangelo LD, Genovese P, Naldini L, Villa A. Exonic knockout and knockin gene editing in hematopoietic stem and progenitor cells rescues RAG1 immunodeficiency. Sci Transl Med 2024; 16:eadh8162. [PMID: 38324638 PMCID: PMC11149094 DOI: 10.1126/scitranslmed.adh8162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 01/17/2024] [Indexed: 02/09/2024]
Abstract
Recombination activating genes (RAGs) are tightly regulated during lymphoid differentiation, and their mutations cause a spectrum of severe immunological disorders. Hematopoietic stem and progenitor cell (HSPC) transplantation is the treatment of choice but is limited by donor availability and toxicity. To overcome these issues, we developed gene editing strategies targeting a corrective sequence into the human RAG1 gene by homology-directed repair (HDR) and validated them by tailored two-dimensional, three-dimensional, and in vivo xenotransplant platforms to assess rescue of expression and function. Whereas integration into intron 1 of RAG1 achieved suboptimal correction, in-frame insertion into exon 2 drove physiologic human RAG1 expression and activity, allowing disruption of the dominant-negative effects of unrepaired hypomorphic alleles. Enhanced HDR-mediated gene editing enabled the correction of human RAG1 in HSPCs from patients with hypomorphic RAG1 mutations to overcome T and B cell differentiation blocks. Gene correction efficiency exceeded the minimal proportion of functional HSPCs required to rescue immunodeficiency in Rag1-/- mice, supporting the clinical translation of HSPC gene editing for the treatment of RAG1 deficiency.
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Affiliation(s)
- Maria Carmina Castiello
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Rozzano (MI) 20089, Italy
| | - Chiara Brandas
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Translational and Molecular Medicine (DIMET), University of Milano-Bicocca, Monza 20900, Italy
| | - Samuele Ferrari
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Simona Porcellini
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Nicolò Sacchetti
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Daniele Canarutto
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Vita-Salute San Raffaele University, Milan 20132, Italy
- Pediatric Immunohematology Unit and BMT Program, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Elena Draghici
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Ivan Merelli
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- National Research Council (CNR), Institute for Biomedical Technologies, Segrate (MI) 20054, Italy
| | - Matteo Barcella
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- National Research Council (CNR), Institute for Biomedical Technologies, Segrate (MI) 20054, Italy
| | - Gabriele Pelosi
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Valentina Vavassori
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Angelica Varesi
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Aurelien Jacob
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Serena Scala
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Luca Basso Ricci
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Marianna Paulis
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Rozzano (MI) 20089, Italy
- Humanitas Clinical and Research Center IRCCS, Rozzano (MI) 20089, Italy
| | - Dario Strina
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Rozzano (MI) 20089, Italy
- Humanitas Clinical and Research Center IRCCS, Rozzano (MI) 20089, Italy
| | - Martina Di Verniere
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Rozzano (MI) 20089, Italy
| | - Lucia Sergi Sergi
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Marta Serafini
- Translational and Molecular Medicine (DIMET), University of Milano-Bicocca, Monza 20900, Italy
- Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza (MI) 20900, Italy
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Suk See De Ravin
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Harry L Malech
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Chiara Brombin
- University Center for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Federica Cugnata
- University Center for Statistics in the Biomedical Sciences, Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Enrica Calzoni
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Gay M Crooks
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Pietro Genovese
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA 02115, USA
| | - Luigi Naldini
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Anna Villa
- San Raffaele-Telethon Institute for Gene Therapy (SR-Tiget), IRCSS San Raffaele Scientific Institute, Milan 20132, Italy
- Milan Unit, Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Rozzano (MI) 20089, Italy
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7
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Hammad R, Alzubi J, Rhiel M, Chmielewski KO, Mosti L, Rositzka J, Heugel M, Lawrenz J, Pennucci V, Gläser B, Fischer J, Schambach A, Moritz T, Lachmann N, Cornu TI, Mussolino C, Schäfer R, Cathomen T. CRISPR-Cas12a for Highly Efficient and Marker-Free Targeted Integration in Human Pluripotent Stem Cells. Int J Mol Sci 2024; 25:985. [PMID: 38256061 PMCID: PMC10816062 DOI: 10.3390/ijms25020985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/04/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The CRISPR-Cas12a platform has attracted interest in the genome editing community because the prototypical Acidaminococcus Cas12a generates a staggered DNA double-strand break upon binding to an AT-rich protospacer-adjacent motif (PAM, 5'-TTTV). The broad application of the platform in primary human cells was enabled by the development of an engineered version of the natural Cas12a protein, called Cas12a Ultra. In this study, we confirmed that CRISPR-Cas12a Ultra ribonucleoprotein complexes enabled allelic gene disruption frequencies of over 90% at multiple target sites in human T cells, hematopoietic stem and progenitor cells (HSPCs), and induced pluripotent stem cells (iPSCs). In addition, we demonstrated, for the first time, the efficient knock-in potential of the platform in human iPSCs and achieved targeted integration of a GFP marker gene into the AAVS1 safe harbor site and a CSF2RA super-exon into CSF2RA in up to 90% of alleles without selection. Clonal analysis revealed bi-allelic integration in >50% of the screened iPSC clones without compromising their pluripotency and genomic integrity. Thus, in combination with the adeno-associated virus vector system, CRISPR-Cas12a Ultra provides a highly efficient genome editing platform for performing targeted knock-ins in human iPSCs.
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Affiliation(s)
- Ruba Hammad
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Freiburg iPS Core Facility, Medical Center—University of Freiburg, 79106 Freiburg, Germany
- PhD Program, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Jamal Alzubi
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Manuel Rhiel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Kay O. Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- PhD Program, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Laura Mosti
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Julia Rositzka
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Marcel Heugel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Jan Lawrenz
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Valentina Pennucci
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
| | - Birgitta Gläser
- Institute of Human Genetics, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (B.G.); (J.F.)
| | - Judith Fischer
- Institute of Human Genetics, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (B.G.); (J.F.)
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Axel Schambach
- Institute for Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (A.S.); (T.M.)
- REBIRTH Center for Regenerative and Translational Medicine, Hannover Medical School, 30625 Hannover, Germany;
| | - Thomas Moritz
- Institute for Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; (A.S.); (T.M.)
- REBIRTH Center for Regenerative and Translational Medicine, Hannover Medical School, 30625 Hannover, Germany;
| | - Nico Lachmann
- REBIRTH Center for Regenerative and Translational Medicine, Hannover Medical School, 30625 Hannover, Germany;
- Department of Pediatric Pulmonology, Allergology and Neonatology, Hannover Medical School, 30625 Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease, German Center for Lung Research, Hannover Medical School, 30625 Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
- Fraunhofer Institute for Toxicology and Experimental Medicine (ITEM), 30625 Hannover, Germany
| | - Tatjana I. Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Richard Schäfer
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Freiburg iPS Core Facility, Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, 79106 Freiburg, Germany; (R.H.); (J.A.); (M.R.); (K.O.C.); (L.M.); (J.R.); (M.H.); (V.P.); (T.I.C.); (C.M.); (R.S.)
- Center for Chronic Immunodeficiency (CCI), Medical Center—University of Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
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8
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Cavazza A, Hendel A, Bak RO, Rio P, Güell M, Lainšček D, Arechavala-Gomeza V, Peng L, Hapil FZ, Harvey J, Ortega FG, Gonzalez-Martinez C, Lederer CW, Mikkelsen K, Gasiunas G, Kalter N, Gonçalves MA, Petersen J, Garanto A, Montoliu L, Maresca M, Seemann SE, Gorodkin J, Mazini L, Sanchez R, Rodriguez-Madoz JR, Maldonado-Pérez N, Laura T, Schmueck-Henneresse M, Maccalli C, Grünewald J, Carmona G, Kachamakova-Trojanowska N, Miccio A, Martin F, Turchiano G, Cathomen T, Luo Y, Tsai SQ, Benabdellah K. Progress and harmonization of gene editing to treat human diseases: Proceeding of COST Action CA21113 GenE-HumDi. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102066. [PMID: 38034032 PMCID: PMC10685310 DOI: 10.1016/j.omtn.2023.102066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
The European Cooperation in Science and Technology (COST) is an intergovernmental organization dedicated to funding and coordinating scientific and technological research in Europe, fostering collaboration among researchers and institutions across countries. Recently, COST Action funded the "Genome Editing to treat Human Diseases" (GenE-HumDi) network, uniting various stakeholders such as pharmaceutical companies, academic institutions, regulatory agencies, biotech firms, and patient advocacy groups. GenE-HumDi's primary objective is to expedite the application of genome editing for therapeutic purposes in treating human diseases. To achieve this goal, GenE-HumDi is organized in several working groups, each focusing on specific aspects. These groups aim to enhance genome editing technologies, assess delivery systems, address safety concerns, promote clinical translation, and develop regulatory guidelines. The network seeks to establish standard procedures and guidelines for these areas to standardize scientific practices and facilitate knowledge sharing. Furthermore, GenE-HumDi aims to communicate its findings to the public in accessible yet rigorous language, emphasizing genome editing's potential to revolutionize the treatment of many human diseases. The inaugural GenE-HumDi meeting, held in Granada, Spain, in March 2023, featured presentations from experts in the field, discussing recent breakthroughs in delivery methods, safety measures, clinical translation, and regulatory aspects related to gene editing.
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Affiliation(s)
- Alessia Cavazza
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Ayal Hendel
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Rasmus O. Bak
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Paula Rio
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), 28040 Madrid, Spain
- Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
| | - Marc Güell
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Integra Therapeutics S.L., Barcelona, Spain
| | - Duško Lainšček
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Virginia Arechavala-Gomeza
- Nucleic Acid Therapeutics for Rare Disorders (NAT-RD), Biobizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Ling Peng
- Aix Marseille University, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, UMR 7325, Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
| | - Fatma Zehra Hapil
- Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - Joshua Harvey
- Institute of Ophthalmology, University College London, London, UK
| | - Francisco G. Ortega
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Avenida de la Ilustración 114, 18016 Granada, Spain
- IBS Granada, Institute of Biomedical Research, Avenida de Madrid 15, 18012 Granada, Spain
| | - Coral Gonzalez-Martinez
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Avenida de la Ilustración 114, 18016 Granada, Spain
- IBS Granada, Institute of Biomedical Research, Avenida de Madrid 15, 18012 Granada, Spain
| | - Carsten W. Lederer
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kasper Mikkelsen
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | | | - Nechama Kalter
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Manuel A.F.V. Gonçalves
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Julie Petersen
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8200 Aarhus N, Denmark
| | - Alejandro Garanto
- Department of Pediatrics and Department of Human Genetics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Lluis Montoliu
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC) and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain
| | - Marcello Maresca
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
| | - Stefan E. Seemann
- Center for Non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jan Gorodkin
- Center for Non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Loubna Mazini
- Laboratory of Genetic Engineering, Technologic, Medical and Academic Park (TMAP), Marrakech, Morocco
| | - Rosario Sanchez
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
- Department of Medicinal & Organic Chemistry and Excellence Research Unit of "Chemistry Applied to Biomedicine and the Environment," Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Universidad de Granada, Granada, Spain
| | - Juan R. Rodriguez-Madoz
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Madrid, Spain
| | | | - Torella Laura
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA) Universidad de Navarra, 31008 Pamplona, Spain
| | - Michael Schmueck-Henneresse
- Berlin Institute for Health (BIH) at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Charitéplatz 1, 10117 Berlin, Germany
| | - Cristina Maccalli
- Laboratory of Immune Biological Therapy, Research Branch, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Julian Grünewald
- Department of Medicine, Cardiology, Angiology, Pneumology, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, TranslaTUM, MIBE, Munich, Germany
- Center for Organoid Systems, Munich, Germany
| | - Gloria Carmona
- Red Andaluza de diseño y traslación de Terapias Avanzadas-RAdytTA, Fundación Pública Andaluza Progreso y Salud-FPS, Sevilla, España
| | | | - Annarita Miccio
- Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, Université de Paris Cité, INSERM UMR 1163, 75015 Paris, France
| | - Francisco Martin
- Bioquímica y Biología Molecular III e Immunology Department, Facultad de Medicina, Universidad de Granada and Department of Genomic Medicine, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), PTS, Av. de la Ilustración 114, 18016 Granada, Spain
| | - Giandomenico Turchiano
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
- Medical Faculty, University of Freiburg, 79106 Freiburg, Germany
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8200 Aarhus N, Denmark
| | - Shengdar Q. Tsai
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Karim Benabdellah
- Department of Genomic Medicine, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), PTS, Av. de la Ilustración 114, 18016 Granada, Spain
| | - on behalf of the COST Action CA21113
- Infection, Immunity and Inflammation Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, WC1N 1EH London, UK
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), 28040 Madrid, Spain
- Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), 28040 Madrid, Spain
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Integra Therapeutics S.L., Barcelona, Spain
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- Nucleic Acid Therapeutics for Rare Disorders (NAT-RD), Biobizkaia Health Research Institute, Barakaldo, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Aix Marseille University, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, UMR 7325, Equipe Labellisée Ligue Contre le Cancer, 13288 Marseille, France
- Department of Medical Biology and Genetics, Faculty of Medicine, Akdeniz University, Antalya, Turkey
- Institute of Ophthalmology, University College London, London, UK
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Avenida de la Ilustración 114, 18016 Granada, Spain
- IBS Granada, Institute of Biomedical Research, Avenida de Madrid 15, 18012 Granada, Spain
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- CasZyme, 10224 Vilnius, Lithuania
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
- Department of Pediatrics and Department of Human Genetics, Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Molecular and Cellular Biology, National Centre for Biotechnology (CNB-CSIC) and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain
- Genome Engineering, Discovery Sciences, BioPharmaceuticals R&D Unit, AstraZeneca, Gothenburg, Sweden
- Center for Non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Genetic Engineering, Technologic, Medical and Academic Park (TMAP), Marrakech, Morocco
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
- Department of Medicinal & Organic Chemistry and Excellence Research Unit of "Chemistry Applied to Biomedicine and the Environment," Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Universidad de Granada, Granada, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Instituto de Investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Madrid, Spain
- DNA & RNA Medicine Division, Center for Applied Medical Research (CIMA) Universidad de Navarra, 31008 Pamplona, Spain
- Berlin Institute for Health (BIH) at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies (BCRT), Charitéplatz 1, 10117 Berlin, Germany
- Laboratory of Immune Biological Therapy, Research Branch, Sidra Medicine, PO Box 26999, Doha, Qatar
- Department of Medicine, Cardiology, Angiology, Pneumology, Klinikum rechts der Isar, Technical University of Munich, TUM School of Medicine and Health, TranslaTUM, MIBE, Munich, Germany
- Center for Organoid Systems, Munich, Germany
- Red Andaluza de diseño y traslación de Terapias Avanzadas-RAdytTA, Fundación Pública Andaluza Progreso y Salud-FPS, Sevilla, España
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
- Imagine Institute, Laboratory of Chromatin and Gene Regulation During Development, Université de Paris Cité, INSERM UMR 1163, 75015 Paris, France
- Bioquímica y Biología Molecular III e Immunology Department, Facultad de Medicina, Universidad de Granada and Department of Genomic Medicine, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), PTS, Av. de la Ilustración 114, 18016 Granada, Spain
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany
- Medical Faculty, University of Freiburg, 79106 Freiburg, Germany
- Steno Diabetes Center Aarhus, Aarhus University Hospital, 8200 Aarhus N, Denmark
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN, USA
- Department of Genomic Medicine, Pfizer-University of Granada-Andalusian Regional Government Centre for Genomics and Oncological Research (GENYO), PTS, Av. de la Ilustración 114, 18016 Granada, Spain
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9
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Allen D, Knop O, Itkowitz B, Kalter N, Rosenberg M, Iancu O, Beider K, Lee YN, Nagler A, Somech R, Hendel A. CRISPR-Cas9 engineering of the RAG2 locus via complete coding sequence replacement for therapeutic applications. Nat Commun 2023; 14:6771. [PMID: 37891182 PMCID: PMC10611791 DOI: 10.1038/s41467-023-42036-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
RAG2-SCID is a primary immunodeficiency caused by mutations in Recombination-activating gene 2 (RAG2), a gene intimately involved in the process of lymphocyte maturation and function. ex-vivo manipulation of a patient's own hematopoietic stem and progenitor cells (HSPCs) using CRISPR-Cas9/rAAV6 gene editing could provide a therapeutic alternative to the only current treatment, allogeneic hematopoietic stem cell transplantation (HSCT). Here we show an innovative RAG2 correction strategy that replaces the entire endogenous coding sequence (CDS) for the purpose of preserving the critical endogenous spatiotemporal gene regulation and locus architecture. Expression of the corrective transgene leads to successful development into CD3+TCRαβ+ and CD3+TCRγδ+ T cells and promotes the establishment of highly diverse TRB and TRG repertoires in an in-vitro T-cell differentiation platform. Thus, our proof-of-concept study holds promise for safer gene therapy techniques of tightly regulated genes.
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Affiliation(s)
- Daniel Allen
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Orli Knop
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Bryan Itkowitz
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Nechama Kalter
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Michael Rosenberg
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Ortal Iancu
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Katia Beider
- The Division of Hematology and Bone Marrow Transplantation, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, 5266202, Israel
| | - Yu Nee Lee
- Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, 5266202, Israel
| | - Arnon Nagler
- The Division of Hematology and Bone Marrow Transplantation, Chaim Sheba Medical Center, Tel-Hashomer, Ramat Gan, 5266202, Israel
- Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Raz Somech
- Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, 5266202, Israel
| | - Ayal Hendel
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
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10
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Hunt MS, Yang SJ, Mortensen E, Boukhris A, Buckner J, Cook PJ, Rawlings DJ. Dual-locus, dual-HDR editing permits efficient generation of antigen-specific regulatory T cells with robust suppressive activity. Mol Ther 2023; 31:2872-2886. [PMID: 37481700 PMCID: PMC10556186 DOI: 10.1016/j.ymthe.2023.07.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/23/2023] [Accepted: 07/19/2023] [Indexed: 07/24/2023] Open
Abstract
Adoptive regulatory T (Treg) cell therapy is predicted to modulate immune tolerance in autoimmune diseases, including type 1 diabetes (T1D). However, the requirement for antigen (ag) specificity to optimally orchestrate tissue-specific, Treg cell-mediated tolerance limits effective clinical application. To address this challenge, we present a single-step, combinatorial gene editing strategy utilizing dual-locus, dual-homology-directed repair (HDR) to generate and specifically expand ag-specific engineered Treg (EngTreg) cells derived from donor CD4+ T cells. Concurrent delivery of CRISPR nucleases and recombinant (r)AAV homology donor templates targeting FOXP3 and TRAC was used to achieve three parallel goals: enforced, stable expression of FOXP3; replacement of the endogenous T cell receptor (TCR) with an islet-specific TCR; and selective enrichment of dual-edited cells. Each HDR donor template contained an alternative component of a heterodimeric chemically inducible signaling complex (CISC), designed to activate interleukin-2 (IL-2) signaling in response to rapamycin, promoting expansion of only dual-edited EngTreg cells. Using this approach, we generated purified, islet-specific EngTreg cells that mediated robust direct and bystander suppression of effector T (Teff) cells recognizing the same or a different islet antigen peptide, respectively. This platform is broadly adaptable for use with alternative TCRs or other targeting moieties for application in tissue-specific autoimmune or inflammatory diseases.
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Affiliation(s)
- Martina S Hunt
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, 1900 Ninth Avenue, Seattle, WA 98101, USA
| | - Soo Jung Yang
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle WA 98101, USA
| | - Emma Mortensen
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle WA 98101, USA
| | - Ahmad Boukhris
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, 1900 Ninth Avenue, Seattle, WA 98101, USA
| | - Jane Buckner
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle WA 98101, USA
| | - Peter J Cook
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, 1900 Ninth Avenue, Seattle, WA 98101, USA.
| | - David J Rawlings
- Center for Immunity and Immunotherapies and Program for Cell and Gene Therapy, Seattle Children's Research Institute, 1900 Ninth Avenue, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA; Department of Immunology, University of Washington, Seattle, WA, USA.
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11
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Zhu WS, Wheeler BD, Ansel KM. RNA circuits and RNA-binding proteins in T cells. Trends Immunol 2023; 44:792-806. [PMID: 37599172 PMCID: PMC10890840 DOI: 10.1016/j.it.2023.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]
Abstract
RNA is integral to the regulatory circuits that control cell identity and behavior. Cis-regulatory elements in mRNAs interact with RNA-binding proteins (RBPs) that can alter RNA sequence, stability, and translation into protein. Similarly, long noncoding RNAs (lncRNAs) scaffold ribonucleoprotein complexes that mediate transcriptional and post-transcriptional regulation of gene expression. Indeed, cell programming is fundamental to multicellular life and, in this era of cellular therapies, it is of particular interest in T cells. Here, we review key concepts and recent advances in our understanding of the RNA circuits and RBPs that govern mammalian T cell differentiation and immune function.
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Affiliation(s)
- Wandi S Zhu
- Department of Microbiology & Immunology, Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Benjamin D Wheeler
- Department of Microbiology & Immunology, Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - K Mark Ansel
- Department of Microbiology & Immunology, Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA 94143, USA.
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12
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Braams M, Pike-Overzet K, Staal FJT. The recombinase activating genes: architects of immune diversity during lymphocyte development. Front Immunol 2023; 14:1210818. [PMID: 37497222 PMCID: PMC10367010 DOI: 10.3389/fimmu.2023.1210818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023] Open
Abstract
The mature lymphocyte population of a healthy individual has the remarkable ability to recognise an immense variety of antigens. Instead of encoding a unique gene for each potential antigen receptor, evolution has used gene rearrangements, also known as variable, diversity, and joining gene segment (V(D)J) recombination. This process is critical for lymphocyte development and relies on recombination-activating genes-1 (RAG1) and RAG2, here collectively referred to as RAG. RAG serves as powerful genome editing tools for lymphocytes and is strictly regulated to prevent dysregulation. However, in the case of dysregulation, RAG has been implicated in cases of cancer, autoimmunity and severe combined immunodeficiency (SCID). This review examines functional protein domains and motifs of RAG, describes advances in our understanding of the function and (dys)regulation of RAG, discuss new therapeutic options, such as gene therapy, for RAG deficiencies, and explore in vitro and in vivo methods for determining RAG activity and target specificity.
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Affiliation(s)
- Merijn Braams
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
| | - Karin Pike-Overzet
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
- Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Leiden University Medical Centre, Leiden, Netherlands
- Department of Paediatrics, Leiden University Medical Centre, Leiden, Netherlands
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13
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Mikkelsen NS, Bak RO. Enrichment strategies to enhance genome editing. J Biomed Sci 2023; 30:51. [PMID: 37393268 PMCID: PMC10315055 DOI: 10.1186/s12929-023-00943-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/26/2023] [Indexed: 07/03/2023] Open
Abstract
Genome editing technologies hold great promise for numerous applications including the understanding of cellular and disease mechanisms and the development of gene and cellular therapies. Achieving high editing frequencies is critical to these research areas and to achieve the overall goal of being able to manipulate any target with any desired genetic outcome. However, gene editing technologies sometimes suffer from low editing efficiencies due to several challenges. This is often the case for emerging gene editing technologies, which require assistance for translation into broader applications. Enrichment strategies can support this goal by selecting gene edited cells from non-edited cells. In this review, we elucidate the different enrichment strategies, their many applications in non-clinical and clinical settings, and the remaining need for novel strategies to further improve genome research and gene and cellular therapy studies.
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Affiliation(s)
- Nanna S Mikkelsen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Høegh-Guldbergsgade 10, Bldg. 1115, 8000, Aarhus C., Denmark.
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14
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Allen D, Kalter N, Rosenberg M, Hendel A. Homology-Directed-Repair-Based Genome Editing in HSPCs for the Treatment of Inborn Errors of Immunity and Blood Disorders. Pharmaceutics 2023; 15:pharmaceutics15051329. [PMID: 37242571 DOI: 10.3390/pharmaceutics15051329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/13/2023] [Accepted: 04/19/2023] [Indexed: 05/28/2023] Open
Abstract
Genome engineering via targeted nucleases, specifically CRISPR-Cas9, has revolutionized the field of gene therapy research, providing a potential treatment for diseases of the blood and immune system. While numerous genome editing techniques have been used, CRISPR-Cas9 homology-directed repair (HDR)-mediated editing represents a promising method for the site-specific insertion of large transgenes for gene knock-in or gene correction. Alternative methods, such as lentiviral/gammaretroviral gene addition, gene knock-out via non-homologous end joining (NHEJ)-mediated editing, and base or prime editing, have shown great promise for clinical applications, yet all possess significant drawbacks when applied in the treatment of patients suffering from inborn errors of immunity or blood system disorders. This review aims to highlight the transformational benefits of HDR-mediated gene therapy and possible solutions for the existing problems holding the methodology back. Together, we aim to help bring HDR-based gene therapy in CD34+ hematopoietic stem progenitor cells (HSPCs) from the lab bench to the bedside.
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Affiliation(s)
- Daniel Allen
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Nechama Kalter
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Michael Rosenberg
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Ayal Hendel
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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15
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Pavel-Dinu M, Borna S, Bacchetta R. Rare immune diseases paving the road for genome editing-based precision medicine. Front Genome Ed 2023; 5:1114996. [PMID: 36846437 PMCID: PMC9945114 DOI: 10.3389/fgeed.2023.1114996] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 01/26/2023] [Indexed: 02/11/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) genome editing platform heralds a new era of gene therapy. Innovative treatments for life-threatening monogenic diseases of the blood and immune system are transitioning from semi-random gene addition to precise modification of defective genes. As these therapies enter first-in-human clinical trials, their long-term safety and efficacy will inform the future generation of genome editing-based medicine. Here we discuss the significance of Inborn Errors of Immunity as disease prototypes for establishing and advancing precision medicine. We will review the feasibility of clustered regularly interspaced short palindromic repeats-based genome editing platforms to modify the DNA sequence of primary cells and describe two emerging genome editing approaches to treat RAG2 deficiency, a primary immunodeficiency, and FOXP3 deficiency, a primary immune regulatory disorder.
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Affiliation(s)
- Mara Pavel-Dinu
- Division of Hematology-Oncology-Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford Medical School, Palo Alto, CA, United States
| | - Simon Borna
- Division of Hematology-Oncology-Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford Medical School, Palo Alto, CA, United States
| | - Rosa Bacchetta
- Division of Hematology-Oncology-Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford Medical School, Palo Alto, CA, United States,Center for Definitive and Curative Medicine, Stanford University School of Medicine, Palo Alto, CA, United States,*Correspondence: Rosa Bacchetta,
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