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Wang Y, Jiang H, Li M, Xu Z, Xu H, Chen Y, Chen K, Zheng W, Lin W, Liu Z, Lin Z, Zhang M. Delivery of CRISPR/Cas9 system by AAV as vectors for gene therapy. Gene 2024; 927:148733. [PMID: 38945310 DOI: 10.1016/j.gene.2024.148733] [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: 10/24/2023] [Revised: 06/14/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
The adeno-associated virus (AAV) is a defective single-stranded DNA virus with the simplest structure reported to date. It constitutes a capsid protein and single-stranded DNA. With its high transduction efficiency, low immunogenicity, and tissue specificity, it is the most widely used and promising gene therapy vector. The clustered regularly interspaced short palindromic sequence (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing system is an emerging technology that utilizes cas9 nuclease to specifically recognize and cleave target genes under the guidance of small guide RNA and realizes gene editing through homologous directional repair and non-homologous recombination repair. In recent years, an increasing number of animal experiments and clinical studies have revealed the great potential of AAV as a vector to deliver the CRISPR/cas9 system for treating genetic diseases and viral infections. However, the immunogenicity, toxicity, low transmission efficiency in brain and ear tissues, packaging size limitations of AAV, and immunogenicity and off-target effects of Cas9 protein pose several clinical challenges. This research reviews the role, challenges, and countermeasures of the AAV-CRISPR/cas9 system in gene therapy.
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Affiliation(s)
- Yanan Wang
- Department of Neonatology, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Anesthesiology, 1st Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Haibin Jiang
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Mopu Li
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zidi Xu
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Hang Xu
- The First School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yuetong Chen
- The First School of Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Kepei Chen
- Department of Neonatology, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Key Laboratory of Perinatal Medicine of Wenzhou, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Key Laboratory of Structural Malformations in Children of Zhejiang Province, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Zhejiang Provincial Clinical Research Center for Pediatric Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Weihong Zheng
- Department of Neonatology, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Key Laboratory of Perinatal Medicine of Wenzhou, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Key Laboratory of Structural Malformations in Children of Zhejiang Province, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Zhejiang Provincial Clinical Research Center for Pediatric Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wei Lin
- Department of Neonatology, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Key Laboratory of Perinatal Medicine of Wenzhou, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Key Laboratory of Structural Malformations in Children of Zhejiang Province, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Zhejiang Provincial Clinical Research Center for Pediatric Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhiming Liu
- Department of Spinal Surgery, The Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Zhenlang Lin
- Department of Neonatology, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Key Laboratory of Perinatal Medicine of Wenzhou, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Key Laboratory of Structural Malformations in Children of Zhejiang Province, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Zhejiang Provincial Clinical Research Center for Pediatric Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Min Zhang
- Department of Neonatology, The Second School of Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Key Laboratory of Perinatal Medicine of Wenzhou, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Key Laboratory of Structural Malformations in Children of Zhejiang Province, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China; Zhejiang Provincial Clinical Research Center for Pediatric Disease, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
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2
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Puzzo F, Crossley MP, Goswami A, Zhang F, Pekrun K, Garzon JL, Cimprich KA, Kay MA. AAV-mediated genome editing is influenced by the formation of R-loops. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.07.592855. [PMID: 38766176 PMCID: PMC11100726 DOI: 10.1101/2024.05.07.592855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Recombinant adeno-associated viral vectors (rAAV) hold an intrinsic ability to stimulate homologous recombination (AAV-HR) and are the most used in clinical settings for in vivo gene therapy. However, rAAVs also integrate throughout the genome. Here, we describe DNA-RNA immunoprecipitation sequencing (DRIP-seq) in murine HEPA1-6 hepatoma cells and whole murine liver to establish the similarities and differences in genomic R-loop formation in a transformed cell line and intact tissue. We show enhanced AAV-HR in mice upon genetic and pharmacological upregulation of R-loops. Selecting the highly expressed Albumin gene as a model locus for genome editing in both in vitro and in vivo experiments showed that the R-loop prone, 3' end of Albumin was efficiently edited by AAV-HR, whereas the upstream R-loop-deficient region did not result in detectable vector integration. In addition, we found a positive correlation between previously reported off-target rAAV integration sites and R-loop enriched genomic regions. Thus, we conclude that high levels of R-loops, present in highly transcribed genes, promote rAAV vector genome integration. These findings may shed light on potential mechanisms for improving the safety and efficacy of genome editing by modulating R-loops and may enhance our ability to predict regions most susceptible to off-target insertional mutagenesis by rAAV vectors.
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Affiliation(s)
- Francesco Puzzo
- Department of Genetics, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
| | | | - Aranyak Goswami
- Department of Genetics, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
| | - Feijie Zhang
- Department of Genetics, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
| | - Katja Pekrun
- Department of Genetics, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
| | - Jada L Garzon
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA
| | - Mark A Kay
- Department of Genetics, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
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3
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Lisjak M, Iaconcig A, Guarnaccia C, Vicidomini A, Moretti L, Collaud F, Ronzitti G, Zentilin L, Muro AF. Lethality rescue and long-term amelioration of a citrullinemia type I mouse model by neonatal gene-targeting combined to SaCRISPR-Cas9. Mol Ther Methods Clin Dev 2023; 31:101103. [PMID: 37744006 PMCID: PMC10514469 DOI: 10.1016/j.omtm.2023.08.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023]
Abstract
Citrullinemia type I is a rare autosomal-recessive disorder caused by deficiency of argininosuccinate synthetase (ASS1). The clinical presentation includes the acute neonatal form, characterized by ammonia and citrulline accumulation in blood, which may lead to encephalopathy, coma, and death, and the milder late-onset form. Current treatments are unsatisfactory, and the only curative treatment is liver transplantation. We permanently modified the hepatocyte genome in lethal citrullinemia mice (Ass1fold/fold) by inserting the ASS1 cDNA into the albumin locus through the delivery of two AAV8 vectors carrying the donor DNA and the CRISPR-Cas9 platform. The neonatal treatment completely rescued mortality ensuring survival up to 5 months of age, with plasma citrulline levels significantly decreased, while plasma ammonia levels remained unchanged. In contrast, neonatal treatment with a liver-directed non-integrative AAV8-AAT-hASS1 vector failed to improve disease parameters. To model late-onset citrullinemia, we dosed postnatal day (P) 30 juvenile animals using the integrative approach, resulting in lifespan improvement and a minor reduction in disease markers. Conversely, treatment with the non-integrative vector completely rescued mortality, reducing plasma ammonia and citrulline to wild-type values. In summary, the integrative approach in neonates is effective, although further improvements are required to fully correct the phenotype. Non-integrative gene therapy application to juvenile mice ensures a stable and very efficient therapeutic effect.
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Affiliation(s)
- Michela Lisjak
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Alessandra Iaconcig
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Corrado Guarnaccia
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Antonio Vicidomini
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Laura Moretti
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Fanny Collaud
- Généthon, 91000 Évry, France
- Université Paris-Saclay, Université d’Évry, Inserm, Généthon, Integrare Research Unit UMR_S951, 91000 Évry, France
| | - Giuseppe Ronzitti
- Généthon, 91000 Évry, France
- Université Paris-Saclay, Université d’Évry, Inserm, Généthon, Integrare Research Unit UMR_S951, 91000 Évry, France
| | - Lorena Zentilin
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
| | - Andrés F. Muro
- International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy
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4
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Thomas SP, Domm JM, van Vloten JP, Xu L, Vadivel A, Yates JGE, Pei Y, Ingrao J, van Lieshout LP, Jackson SR, Minott JA, Achuthan A, Mehrani Y, McAusland TM, Zhang W, Karimi K, Vaughan AE, de Jong J, Kang MH, Thebaud B, Wootton SK. A promoterless AAV6.2FF-based lung gene editing platform for the correction of surfactant protein B deficiency. Mol Ther 2023; 31:3457-3477. [PMID: 37805711 PMCID: PMC10727957 DOI: 10.1016/j.ymthe.2023.10.002] [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: 02/17/2023] [Revised: 09/07/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023] Open
Abstract
Surfactant protein B (SP-B) deficiency is a rare genetic disease that causes fatal respiratory failure within the first year of life. Currently, the only corrective treatment is lung transplantation. Here, we co-transduced the murine lung with adeno-associated virus 6.2FF (AAV6.2FF) vectors encoding a SaCas9-guide RNA nuclease or donor template to mediate insertion of promoterless reporter genes or the (murine) Sftpb gene in frame with the endogenous surfactant protein C (SP-C) gene, without disrupting SP-C expression. Intranasal administration of 3 × 1011 vg donor template and 1 × 1011 vg nuclease consistently edited approximately 6% of lung epithelial cells. Frequency of gene insertion increased in a dose-dependent manner, reaching 20%-25% editing efficiency with the highest donor template and nuclease doses tested. We next evaluated whether this promoterless gene editing platform could extend survival in the conditional SP-B knockout mouse model. Administration of 1 × 1012 vg SP-B-donor template and 5 × 1011 vg nuclease significantly extended median survival (p = 0.0034) from 5 days in the untreated off doxycycline group to 16 days in the donor AAV and nuclease group, with one gene-edited mouse living 243 days off doxycycline. This AAV6.2FF-based gene editing platform has the potential to correct SP-B deficiency, as well as other disorders of alveolar type II cells.
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Affiliation(s)
- Sylvia P Thomas
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Jakob M Domm
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Jacob P van Vloten
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Liqun Xu
- Regenerative Medicine Program, The Ottawa Hospital Research Institute (OHRI), Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada; Neonatology, Department of Pediatrics, Children's Hospital of Eastern Ontario (CHEO), and CHEO Research Institute, Ottawa, ON K1Y 4E9, Canada
| | - Arul Vadivel
- Regenerative Medicine Program, The Ottawa Hospital Research Institute (OHRI), Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada; Neonatology, Department of Pediatrics, Children's Hospital of Eastern Ontario (CHEO), and CHEO Research Institute, Ottawa, ON K1Y 4E9, Canada
| | - Jacob G E Yates
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Yanlong Pei
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Joelle Ingrao
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | | | - Sergio R Jackson
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Jessica A Minott
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Adithya Achuthan
- Regenerative Medicine Program, The Ottawa Hospital Research Institute (OHRI), Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada; Neonatology, Department of Pediatrics, Children's Hospital of Eastern Ontario (CHEO), and CHEO Research Institute, Ottawa, ON K1Y 4E9, Canada
| | - Yeganeh Mehrani
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Thomas M McAusland
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Khalil Karimi
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Andrew E Vaughan
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Jondavid de Jong
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Martin H Kang
- Department of Pediatrics, Darby Children's Research Institute, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Bernard Thebaud
- Regenerative Medicine Program, The Ottawa Hospital Research Institute (OHRI), Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada; Neonatology, Department of Pediatrics, Children's Hospital of Eastern Ontario (CHEO), and CHEO Research Institute, Ottawa, ON K1Y 4E9, Canada
| | - Sarah K Wootton
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada.
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5
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Padula A, Spinelli M, Nusco E, Bujanda Cundin X, Capolongo F, Campione S, Perna C, Bastille A, Ericson M, Wang CC, Zhang S, Amoresano A, Nacht M, Piccolo P. Genome editing without nucleases confers proliferative advantage to edited hepatocytes and corrects Wilson disease. JCI Insight 2023; 8:e171281. [PMID: 37707949 PMCID: PMC10721260 DOI: 10.1172/jci.insight.171281] [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: 06/27/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023] Open
Abstract
Application of classic liver-directed gene replacement strategies is limited in genetic diseases characterized by liver injury due to hepatocyte proliferation, resulting in decline of therapeutic transgene expression and potential genotoxic risk. Wilson disease (WD) is a life-threatening autosomal disorder of copper homeostasis caused by pathogenic variants in copper transporter ATP7B and characterized by toxic copper accumulation, resulting in severe liver and brain diseases. Genome editing holds promise for the treatment of WD; nevertheless, to rescue copper homeostasis, ATP7B function must be restored in at least 25% of the hepatocytes, which surpasses by far genome-editing correction rates. We applied a liver-directed, nuclease-free genome editing approach, based on adeno-associated viral vector-mediated (AAV-mediated) targeted integration of a promoterless mini-ATP7B cDNA into the albumin (Alb) locus. Administration of AAV-Alb-mini-ATP7B in 2 WD mouse models resulted in extensive liver repopulation by genome-edited hepatocytes holding a proliferative advantage over nonedited ones, and ameliorated liver injury and copper metabolism. Furthermore, combination of genome editing with a copper chelator, currently used for WD treatment, achieved greater disease improvement compared with chelation therapy alone. Nuclease-free genome editing provided therapeutic efficacy and may represent a safer and longer-lasting alternative to classic gene replacement strategies for WD.
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Affiliation(s)
- Agnese Padula
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Michele Spinelli
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Edoardo Nusco
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | | | | | | | - Claudia Perna
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Amy Bastille
- LogicBio Therapeutics, Lexington, Massachusetts, USA
| | - Megan Ericson
- LogicBio Therapeutics, Lexington, Massachusetts, USA
| | | | | | - Angela Amoresano
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Mariana Nacht
- LogicBio Therapeutics, Lexington, Massachusetts, USA
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6
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Sun Q, Qi YK, Qi KM, Yan ZL, Cheng H, Chen W, Zhu F, Sang W, Li DP, Cao J, Shi M, Li ZY, Xu KL. [Observation of liver indexes in patients with relapsed/refractory multiple myeloma treated with CAR-T-cells based on BCMA]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2023; 44:832-837. [PMID: 38049335 PMCID: PMC10694074 DOI: 10.3760/cma.j.issn.0253-2727.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Indexed: 12/06/2023]
Abstract
Objective: To observe the characteristics of the evolution of liver indexes in patients with relapsed/refractory multiple myeloma (RRMM) treated with CAR-T-cells based on BCMA. Methods: Retrospective analysis was performed of patients with RRMM who received an infusion of anti-BCMA CAR-T-cells and anti-BCMA combined with anti-CD19 CAR-T-cells at our center between June 1, 2019, and February 28, 2023. Clinical data were collected to observe the characteristics of changes in liver indexes such as alanine aminotransferase (ALT), aspartate aminotransferase (AST), total bilirubin (TBIL), and direct bilirubin (DBIL) in patients, and its relationship with cytokine-release syndrome (CRS) . Results: Ninety-two patients were included in the analysis, including 41 patients (44.6%) in the group receiving a single infusion of anti-BCMA CAR-T-cells, and 51 patients (55.4%) in the group receiving an infusion of anti-BCMA combined with anti-CD19 CAR-T-cells. After infusing CAR-T-cells, 31 patients (33.7%) experienced changes in liver indexes at or above grade 2, which included 20 patients (21.7%) with changes in one index, five patients (5.4%) with changes in two indexes, and six patients (6.5%) with changes in three or more indexes. The median time of peak values of ALT and AST were d17 and d14, respectively, and the median duration of exceeding grade 2 was 5.0 and 3.5 days, respectively. The median time of peak values of TBIL and DBIL was on d19 and d21, respectively, and the median duration of exceeding grade 2 was 4.0 days, respectively. The median time of onset of CRS was d8, and the peak time of fever was d9. The ALT, AST, and TBIL of patients with CRS were higher than those of patients without CRS (P=0.011, 0.002, and 0.015, respectively). CRS is an independent factor that affects ALT and TBIL levels (OR=19.668, 95% CI 18.959-20.173, P=0.001). The evolution of liver indexes can be reversed through anti-CRS and liver-protection treatments, and no patient died of liver injury. Conclusions: In BCMA-based CAR-T-cell therapy for RRMM, CRS is an important factor causing the evolution of liver indexes. The evolution of liver indexes after CAR-T-cell infusion is transient and reversible after treatment.
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Affiliation(s)
- Q Sun
- Hematology Institute of Xuzhou Medical University, Hematology Department of The Affiliated Hospital of Xuzhou Medical University, Jiangsu Provincial Key Laboratory of Bone Marrow Stem Cells, Xuzhou 221002, China
| | - Y K Qi
- Hematology Institute of Xuzhou Medical University, Hematology Department of The Affiliated Hospital of Xuzhou Medical University, Jiangsu Provincial Key Laboratory of Bone Marrow Stem Cells, Xuzhou 221002, China
| | - K M Qi
- Hematology Institute of Xuzhou Medical University, Hematology Department of The Affiliated Hospital of Xuzhou Medical University, Jiangsu Provincial Key Laboratory of Bone Marrow Stem Cells, Xuzhou 221002, China
| | - Z L Yan
- Hematology Institute of Xuzhou Medical University, Hematology Department of The Affiliated Hospital of Xuzhou Medical University, Jiangsu Provincial Key Laboratory of Bone Marrow Stem Cells, Xuzhou 221002, China
| | - H Cheng
- Hematology Institute of Xuzhou Medical University, Hematology Department of The Affiliated Hospital of Xuzhou Medical University, Jiangsu Provincial Key Laboratory of Bone Marrow Stem Cells, Xuzhou 221002, China
| | - W Chen
- Hematology Institute of Xuzhou Medical University, Hematology Department of The Affiliated Hospital of Xuzhou Medical University, Jiangsu Provincial Key Laboratory of Bone Marrow Stem Cells, Xuzhou 221002, China
| | - F Zhu
- Hematology Institute of Xuzhou Medical University, Hematology Department of The Affiliated Hospital of Xuzhou Medical University, Jiangsu Provincial Key Laboratory of Bone Marrow Stem Cells, Xuzhou 221002, China
| | - W Sang
- Hematology Institute of Xuzhou Medical University, Hematology Department of The Affiliated Hospital of Xuzhou Medical University, Jiangsu Provincial Key Laboratory of Bone Marrow Stem Cells, Xuzhou 221002, China
| | - D P Li
- Hematology Institute of Xuzhou Medical University, Hematology Department of The Affiliated Hospital of Xuzhou Medical University, Jiangsu Provincial Key Laboratory of Bone Marrow Stem Cells, Xuzhou 221002, China
| | - J Cao
- Hematology Institute of Xuzhou Medical University, Hematology Department of The Affiliated Hospital of Xuzhou Medical University, Jiangsu Provincial Key Laboratory of Bone Marrow Stem Cells, Xuzhou 221002, China
| | - M Shi
- Hematology Institute of Xuzhou Medical University, Hematology Department of The Affiliated Hospital of Xuzhou Medical University, Jiangsu Provincial Key Laboratory of Bone Marrow Stem Cells, Xuzhou 221002, China
| | - Z Y Li
- Hematology Institute of Xuzhou Medical University, Hematology Department of The Affiliated Hospital of Xuzhou Medical University, Jiangsu Provincial Key Laboratory of Bone Marrow Stem Cells, Xuzhou 221002, China
| | - K L Xu
- Hematology Institute of Xuzhou Medical University, Hematology Department of The Affiliated Hospital of Xuzhou Medical University, Jiangsu Provincial Key Laboratory of Bone Marrow Stem Cells, Xuzhou 221002, China
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7
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De Giorgi M, Park SH, Castoreno A, Cao M, Hurley A, Saxena L, Chuecos MA, Walkey CJ, Doerfler AM, Furgurson MN, Ljungberg MC, Patel KR, Hyde S, Chickering T, Lefebvre S, Wassarman K, Miller P, Qin J, Schlegel MK, Zlatev I, Li RG, Kim J, Martin JF, Bissig KD, Jadhav V, Bao G, Lagor WR. In vivo expansion of gene-targeted hepatocytes through transient inhibition of an essential gene. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550728. [PMID: 37546995 PMCID: PMC10402145 DOI: 10.1101/2023.07.26.550728] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Homology Directed Repair (HDR)-based genome editing is an approach that could permanently correct a broad range of genetic diseases. However, its utility is limited by inefficient and imprecise DNA repair mechanisms in terminally differentiated tissues. Here, we tested "Repair Drive", a novel method for improving targeted gene insertion in the liver by selectively expanding correctly repaired hepatocytes in vivo. Our system consists of transient conditioning of the liver by knocking down an essential gene, and delivery of an untargetable version of the essential gene in cis with a therapeutic transgene. We show that Repair Drive dramatically increases the percentage of correctly targeted hepatocytes, up to 25%. This resulted in a five-fold increased expression of a therapeutic transgene. Repair Drive was well-tolerated and did not induce toxicity or tumorigenesis in long term follow up. This approach will broaden the range of liver diseases that can be treated with somatic genome editing.
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Affiliation(s)
- Marco De Giorgi
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - So Hyun Park
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Adam Castoreno
- Alnylam Pharmaceuticals Inc, 675 W Kendall St, Cambridge, MA 02142, USA
| | - Mingming Cao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Ayrea Hurley
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lavanya Saxena
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Marcel A. Chuecos
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
- Translational Biology and Molecular Medicine Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher J. Walkey
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alexandria M. Doerfler
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mia N. Furgurson
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - M. Cecilia Ljungberg
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Kalyani R. Patel
- Department of Pathology, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Sarah Hyde
- Alnylam Pharmaceuticals Inc, 675 W Kendall St, Cambridge, MA 02142, USA
| | - Tyler Chickering
- Alnylam Pharmaceuticals Inc, 675 W Kendall St, Cambridge, MA 02142, USA
| | | | - Kelly Wassarman
- Alnylam Pharmaceuticals Inc, 675 W Kendall St, Cambridge, MA 02142, USA
| | - Patrick Miller
- Alnylam Pharmaceuticals Inc, 675 W Kendall St, Cambridge, MA 02142, USA
| | - June Qin
- Alnylam Pharmaceuticals Inc, 675 W Kendall St, Cambridge, MA 02142, USA
| | - Mark K. Schlegel
- Alnylam Pharmaceuticals Inc, 675 W Kendall St, Cambridge, MA 02142, USA
| | - Ivan Zlatev
- Alnylam Pharmaceuticals Inc, 675 W Kendall St, Cambridge, MA 02142, USA
| | - Rich Gang Li
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Heart Institute, Houston, TX 77030, USA
| | - Jong Kim
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Heart Institute, Houston, TX 77030, USA
| | - James F. Martin
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Heart Institute, Houston, TX 77030, USA
| | - Karl-Dimiter Bissig
- Department of Pediatrics, Alice and Y. T. Chen Center for Genetics and Genomics, Division of Medical Genetics, Duke University, Durham, NC 27710, USA
| | - Vasant Jadhav
- Alnylam Pharmaceuticals Inc, 675 W Kendall St, Cambridge, MA 02142, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - William R. Lagor
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX 77030, USA
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8
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Huang J, Zhou Y, Li J, Lu A, Liang C. CRISPR/Cas systems: Delivery and application in gene therapy. Front Bioeng Biotechnol 2022; 10:942325. [PMID: 36483767 PMCID: PMC9723151 DOI: 10.3389/fbioe.2022.942325] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/04/2022] [Indexed: 10/17/2023] Open
Abstract
The CRISPR/Cas systems in prokaryotes such as bacteria and archaea are the adaptive immune system to prevent infection from viruses, phages, or other foreign substances. When viruses or phages first invade the bacteria, Cas proteins recognize and cut the DNA from viruses or phages into short fragments that will be integrated into the CRISPR array. Once bacteria are invaded again, the modified CRISPR and Cas proteins react quickly to cut DNA at the specified target location, protecting the host. Due to its high efficiency, versatility, and simplicity, the CRISPR/Cas system has become one of the most popular gene editing technologies. In this review, we briefly introduce the CRISPR/Cas systems, focus on several delivery methods including physical delivery, viral vector delivery, and non-viral vector delivery, and the applications of disease therapy. Finally, some problems in CRISPR/Cas9 technology have been proposed, such as the off-target effects, the efficiency of DNA repair mechanisms, and delivery of CRISPR/Cas system safely and efficiently to the target location.
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Affiliation(s)
- Jie Huang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yitong Zhou
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jie Li
- Department of Laboratory Medicine, Peking University Shenzhen Hospital, Shenzhen, China
| | - Aiping Lu
- Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, China
| | - Chao Liang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- Institute of Integrated Bioinfomedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
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9
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Venturoni LE, Chandler RJ, Liao J, Hoffmann V, Ramesh N, Gordo S, Chau N, Venditti CP. Growth advantage of corrected hepatocytes in a juvenile model of methylmalonic acidemia following liver directed adeno-associated viral mediated nuclease-free genome editing. Mol Genet Metab 2022; 137:1-8. [PMID: 35868241 PMCID: PMC9872049 DOI: 10.1016/j.ymgme.2022.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 01/26/2023]
Abstract
Methylmalonic acidemia (MMA) is a rare and severe inherited metabolic disease typically caused by mutations of the methylmalonyl-CoA mutase (MMUT) gene. Despite medical management, patients with MMA experience frequent episodes of metabolic instability, severe morbidity, and early mortality. In several preclinical studies, systemic gene therapy has demonstrated impressive improvement in biochemical and clinical phenotypes of MMA murine models. One approach uses a promoterless adeno-associated viral (AAV) vector that relies upon homologous recombination to achieve site-specific in vivo gene addition of MMUT into the last coding exon of albumin (Alb), generating a fused Alb-MMUT transcript after successful editing. We have previously demonstrated that nuclease-free AAV mediated Alb editing could effectively treat MMA mice in the neonatal period and noted that hepatocytes had a growth advantage after correction. Here, we use a transgenic knock-out mouse model of MMA that recapitulates severe clinical and biochemical symptoms to assess the benefits of Alb editing in juvenile animals. As was first noted in the neonatal gene therapy studies, we observe that gene edited hepatocytes in the MMA mice treated as juveniles exhibit a growth advantage, which allows them to repopulate the liver slowly but dramatically by 8-10 months post treatment, and subsequently manifest a biochemical and enzymatic response. In conclusion, our results suggest that the benefit of AAV mediated nuclease-free gene editing of the Alb locus to treat MMA could potentially be therapeutic for older patients.
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Affiliation(s)
- Leah E Venturoni
- National Human Genome Research Institute, NIH, Bethesda, MD, United States of America
| | - Randy J Chandler
- National Human Genome Research Institute, NIH, Bethesda, MD, United States of America
| | - Jing Liao
- LogicBio Therapeutics, Lexington, MA, United States of America
| | - Victoria Hoffmann
- Office of Research Services, NIH, Bethesda, MD, United States of America
| | - Nikhil Ramesh
- LogicBio Therapeutics, Lexington, MA, United States of America
| | - Susana Gordo
- LogicBio Therapeutics, Lexington, MA, United States of America
| | - Nelson Chau
- LogicBio Therapeutics, Lexington, MA, United States of America
| | - Charles P Venditti
- National Human Genome Research Institute, NIH, Bethesda, MD, United States of America.
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