1
|
Saito S, Adachi N. Characterization and regulation of cell cycle-independent noncanonical gene targeting. Nat Commun 2024; 15:5044. [PMID: 38890315 PMCID: PMC11189520 DOI: 10.1038/s41467-024-49385-9] [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: 11/22/2023] [Accepted: 06/04/2024] [Indexed: 06/20/2024] Open
Abstract
Homology-dependent targeted DNA integration, generally referred to as gene targeting, provides a powerful tool for precise genome modification; however, its fundamental mechanisms remain poorly understood in human cells. Here we reveal a noncanonical gene targeting mechanism that does not rely on the homologous recombination (HR) protein Rad51. This mechanism is suppressed by Rad52 inhibition, suggesting the involvement of single-strand annealing (SSA). The SSA-mediated gene targeting becomes prominent when DSB repair by HR or end-joining pathways is defective and does not require isogenic DNA, permitting 5% sequence divergence. Intriguingly, loss of Msh2, loss of BLM, and induction of a target-site DNA break all significantly and synergistically enhance SSA-mediated targeted integration. Most notably, SSA-mediated integration is cell cycle-independent, occurring in the G1 phase as well. Our findings provide unequivocal evidence for Rad51-independent targeted integration and unveil multiple mechanisms to regulate SSA-mediated targeted as well as random integration.
Collapse
Affiliation(s)
- Shinta Saito
- Department of Life and Environmental System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama, 236-0027, Japan
| | - Noritaka Adachi
- Department of Life and Environmental System Science, Graduate School of Nanobioscience, Yokohama City University, Yokohama, 236-0027, Japan.
| |
Collapse
|
2
|
Luna SE, Camarena J, Hampton JP, Majeti KR, Charlesworth CT, Soupene E, Selvaraj S, Jia K, Sheehan VA, Cromer MK, Porteus MH. Enhancement of erythropoietic output by Cas9-mediated insertion of a natural variant in haematopoietic stem and progenitor cells. Nat Biomed Eng 2024:10.1038/s41551-024-01222-6. [PMID: 38886504 DOI: 10.1038/s41551-024-01222-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 05/02/2024] [Indexed: 06/20/2024]
Abstract
Some gene polymorphisms can lead to monogenic diseases, whereas other polymorphisms may confer beneficial traits. A well-characterized example is congenital erythrocytosis-the non-pathogenic hyper-production of red blood cells-that is caused by a truncated erythropoietin receptor. Here we show that Cas9-mediated genome editing in CD34+ human haematopoietic stem and progenitor cells (HSPCs) can recreate the truncated form of the erythropoietin receptor, leading to substantial increases in erythropoietic output. We also show that combining the expression of the cDNA of a truncated erythropoietin receptor with a previously reported genome-editing strategy to fully replace the HBA1 gene with an HBB transgene in HSPCs (to restore normal haemoglobin production in cells with a β-thalassaemia phenotype) gives the edited HSPCs and the healthy red blood cell phenotype a proliferative advantage. Combining knowledge of human genetics with precise genome editing to insert natural human variants into therapeutic cells may facilitate safer and more effective genome-editing therapies for patients with genetic diseases.
Collapse
Affiliation(s)
- Sofia E Luna
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Jessica P Hampton
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Kiran R Majeti
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Carsten T Charlesworth
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Eric Soupene
- Department of Pediatrics, University of California, San Francisco, Oakland, CA, USA
| | - Sridhar Selvaraj
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Kun Jia
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Vivien A Sheehan
- Aflac Cancer and Blood Disorders Center, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - M Kyle Cromer
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
- Eli and Edythe Broad Center for Regeneration Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
| |
Collapse
|
3
|
Drouyer M, Chu TH, Labit E, Haase F, Navarro RG, Nazareth D, Rosin N, Merjane J, Scott S, Cabanes-Creus M, Westhaus A, Zhu E, Midha R, Alexander IE, Biernaskie J, Ginn SL, Lisowski L. Novel AAV variants with improved tropism for human Schwann cells. Mol Ther Methods Clin Dev 2024; 32:101234. [PMID: 38558569 PMCID: PMC10978538 DOI: 10.1016/j.omtm.2024.101234] [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: 07/11/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Gene therapies and associated technologies are transforming biomedical research and enabling novel therapeutic options for patients living with debilitating and incurable genetic disorders. The vector system based on recombinant adeno-associated viral vectors (AAVs) has shown great promise in recent clinical trials for genetic diseases of multiple organs, such as the liver and the nervous system. Despite recent successes toward the development of novel bioengineered AAV variants for improved transduction of primary human tissues and cells, vectors that can efficiently transduce human Schwann cells (hSCs) have yet to be identified. Here, we report the application of the functional transduction-RNA selection method in primary hSCs for the development of AAV variants for specific and efficient transgene delivery to hSCs. The two identified capsid variants, Pep2hSC1 and Pep2hSC2, show conserved potency for delivery across various in vitro, in vivo, and ex vivo models of hSCs. These novel AAV capsids will serve as valuable research tools, forming the basis for therapeutic solutions for both SC-related disorders or peripheral nervous system injury.
Collapse
Affiliation(s)
- Matthieu Drouyer
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Tak-Ho Chu
- Department of Clinical Neurosciences and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Elodie Labit
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Florencia Haase
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Renina Gale Navarro
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Deborah Nazareth
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Nicole Rosin
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Jessica Merjane
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Suzanne Scott
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Marti Cabanes-Creus
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Adrian Westhaus
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Erhua Zhu
- Gene Therapy Research Unit, Children’s Medical Research Institute and Sydney Children’s Hospitals Network, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Rajiv Midha
- Department of Clinical Neurosciences and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ian E. Alexander
- Gene Therapy Research Unit, Children’s Medical Research Institute and Sydney Children’s Hospitals Network, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
- Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Jeff Biernaskie
- Department of Clinical Neurosciences and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Samantha L. Ginn
- Gene Therapy Research Unit, Children’s Medical Research Institute and Sydney Children’s Hospitals Network, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
- Australian Genome Therapeutics Centre, Children’s Medical Research Institute and Sydney Children’s Hospitals Network, Westmead, NSW, Australia
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine - National Research Institute, Warsaw, Poland
| |
Collapse
|
4
|
Wong JPH, Blazev R, Ng YK, Goodman CA, Montgomery MK, Watt KI, Carl CS, Watt MJ, Voldstedlund CT, Richter EA, Crouch PJ, Steyn FJ, Ngo ST, Parker BL. Characterization of the skeletal muscle arginine methylome in health and disease reveals remodeling in amyotrophic lateral sclerosis. FASEB J 2024; 38:e23647. [PMID: 38787599 DOI: 10.1096/fj.202400045r] [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: 01/08/2024] [Revised: 04/04/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024]
Abstract
Arginine methylation is a protein posttranslational modification important for the development of skeletal muscle mass and function. Despite this, our understanding of the regulation of arginine methylation under settings of health and disease remains largely undefined. Here, we investigated the regulation of arginine methylation in skeletal muscles in response to exercise and hypertrophic growth, and in diseases involving metabolic dysfunction and atrophy. We report a limited regulation of arginine methylation under physiological settings that promote muscle health, such as during growth and acute exercise, nor in disease models of insulin resistance. In contrast, we saw a significant remodeling of asymmetric dimethylation in models of atrophy characterized by the loss of innervation, including in muscle biopsies from patients with myotrophic lateral sclerosis (ALS). Mass spectrometry-based quantification of the proteome and asymmetric arginine dimethylome of skeletal muscle from individuals with ALS revealed the largest compendium of protein changes with the identification of 793 regulated proteins, and novel site-specific changes in asymmetric dimethyl arginine (aDMA) of key sarcomeric and cytoskeletal proteins. Finally, we show that in vivo overexpression of PRMT1 and aDMA resulted in increased fatigue resistance and functional recovery in mice. Our study provides evidence for asymmetric dimethylation as a regulator of muscle pathophysiology and presents a valuable proteomics resource and rationale for numerous methylated and nonmethylated proteins, including PRMT1, to be pursued for therapeutic development in ALS.
Collapse
Affiliation(s)
- Julian P H Wong
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ronnie Blazev
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yaan-Kit Ng
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Craig A Goodman
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Magdalene K Montgomery
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kevin I Watt
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, The Royal Children's Hospital, Melbourne, Victoria, Australia
- The Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Christian S Carl
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Matthew J Watt
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Christian T Voldstedlund
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Erik A Richter
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Peter J Crouch
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Frederik J Steyn
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Shyuan T Ngo
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Benjamin L Parker
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
5
|
Chu SN, Soupene E, Wienert B, Yin H, Sharma D, McCreary T, Jia K, Homma S, Hampton JP, Gardner JM, Conklin BR, MacKenzie TC, Porteus MH, Cromer MK. Dual α-globin and truncated EPO receptor knockin restores hemoglobin production in α-thalassemia-derived red blood cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.01.555926. [PMID: 38766216 PMCID: PMC11100611 DOI: 10.1101/2023.09.01.555926] [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
Alpha-thalassemia is an autosomal recessive disease with increasing worldwide prevalence. The molecular basis is due to mutation or deletion of one or more duplicated α-globin genes, and disease severity is directly related to the number of allelic copies compromised. The most severe form, α-thalassemia major (αTM), results from loss of all four copies of α-globin and has historically resulted in fatality in utero. However, in utero transfusions now enable survival to birth. Postnatally, patients face challenges similar to β-thalassemia, including severe anemia and erythrotoxicity due to imbalance of β-globin and α-globin chains. While curative, hematopoietic stem cell transplantation (HSCT) is limited by donor availability and potential transplant-related complications. Despite progress in genome editing treatments for β-thalassemia, there is no analogous curative option for patients suffering from α-thalassemia. To address this, we designed a novel Cas9/AAV6-mediated genome editing strategy that integrates a functional α-globin gene into the β-globin locus in αTM patient-derived hematopoietic stem and progenitor cells (HSPCs). Incorporation of a truncated erythropoietin receptor transgene into the α-globin integration cassette dramatically increased erythropoietic output from edited HSPCs and led to the most robust production of α-globin, and consequently normal hemoglobin. By directing edited HSPCs toward increased production of clinically relevant RBCs instead of other divergent cell types, this approach has the potential to mitigate the limitations of traditional HSCT for the hemoglobinopathies, including low genome editing and low engraftment rates. These findings support development of a definitive ex vivo autologous genome editing strategy that may be curative for α-thalassemia.
Collapse
Affiliation(s)
- Simon N. Chu
- Department of Surgery, University of California, San Francisco, San Francisco, CA
- Eli & Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, CA
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Eric Soupene
- Department of Pediatrics, University of California, San Francisco, Oakland, CA
| | | | - Han Yin
- Department of Surgery, University of California, San Francisco, San Francisco, CA
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Devesh Sharma
- Department of Surgery, University of California, San Francisco, San Francisco, CA
- Eli & Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, CA
| | - Travis McCreary
- Department of Surgery, University of California, San Francisco, San Francisco, CA
- Eli & Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, CA
| | - Kun Jia
- Department of Surgery, University of California, San Francisco, San Francisco, CA
- Eli & Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, CA
| | - Shota Homma
- Department of Genetics, Stanford University, Stanford, CA
| | | | - James M. Gardner
- Department of Surgery, University of California, San Francisco, San Francisco, CA
- Diabetes Center, University of California, San Francisco, San Francisco, CA
| | - Bruce R. Conklin
- Gladstone Institutes, San Francisco, CA
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Tippi C. MacKenzie
- Department of Surgery, University of California, San Francisco, San Francisco, CA
- Eli & Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, CA
| | | | - M. Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA
- Eli & Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, CA
- Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco,San Francisco, CA
| |
Collapse
|
6
|
Singh S, Pugliano CM, Honaker Y, Laird A, DeGottardi MQ, Lopez E, Lachkar S, Stoffers C, Sommer K, Khan IF, Rawlings DJ. Efficient and sustained FOXP3 locus editing in hematopoietic stem cells as a therapeutic approach for IPEX syndrome. Mol Ther Methods Clin Dev 2024; 32:101183. [PMID: 38282895 PMCID: PMC10818254 DOI: 10.1016/j.omtm.2023.101183] [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: 06/14/2022] [Accepted: 12/20/2023] [Indexed: 01/30/2024]
Abstract
Immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome is a monogenic disorder caused by mutations in the FOXP3 gene, required for generation of regulatory T (Treg) cells. Loss of Treg cells leads to immune dysregulation characterized by multi-organ autoimmunity and early mortality. Hematopoietic stem cell (HSC) transplantation can be curative, but success is limited by autoimmune complications, donor availability and/or graft-vs.-host disease. Correction of FOXP3 in autologous HSC utilizing a homology-directed repair (HDR)-based platform may provide a safer alternative therapy. Here, we demonstrate efficient editing of FOXP3 utilizing co-delivery of Cas9 ribonucleoprotein complexes and adeno-associated viral vectors to achieve HDR rates of >40% in vitro using mobilized CD34+ cells from multiple donors. Using this approach to deliver either a GFP or a FOXP3 cDNA donor cassette, we demonstrate sustained bone marrow engraftment of approximately 10% of HDR-edited cells in immune-deficient recipient mice at 16 weeks post-transplant. Further, we show targeted integration of FOXP3 cDNA in CD34+ cells from an IPEX patient and expression of the introduced FOXP3 transcript in gene-edited primary T cells from both healthy individuals and IPEX patients. Our combined findings suggest that refinement of this approach is likely to provide future clinical benefit in IPEX.
Collapse
Affiliation(s)
- Swati Singh
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Cole M. Pugliano
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Yuchi Honaker
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Aidan Laird
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - M. Quinn DeGottardi
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Ezra Lopez
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Stefan Lachkar
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Claire Stoffers
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Karen Sommer
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Iram F. Khan
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - David J. Rawlings
- Center for Immunity and Immunotherapies and the Program for Cell and Gene Therapy, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98101, USA
- Department of Immunology, University of Washington, Seattle, WA 98101, USA
| |
Collapse
|
7
|
Drouyer M, Merjane J, Nazareth D, Knight M, Scott S, Liao SHY, Ginn SL, Zhu E, Alexander IE, Lisowski L. Development of CNS tropic AAV1-like variants with reduced liver-targeting following systemic administration in mice. Mol Ther 2024; 32:818-836. [PMID: 38297833 PMCID: PMC10928139 DOI: 10.1016/j.ymthe.2024.01.024] [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: 07/19/2023] [Revised: 11/27/2023] [Accepted: 01/18/2024] [Indexed: 02/02/2024] Open
Abstract
Directed evolution of natural AAV9 using peptide display libraries have been widely used in the search for an optimal recombinant AAV (rAAV) for transgene delivery across the blood-brain barrier (BBB) to the CNS following intravenous ( IV) injection. In this study, we used a different approach by creating a shuffled rAAV capsid library based on parental AAV serotypes 1 through 12. Following selection in mice, 3 novel variants closely related to AAV1, AAV-BBB6, AAV-BBB28, and AAV-BBB31, emerged as top candidates. In direct comparisons with AAV9, our novel variants demonstrated an over 270-fold improvement in CNS transduction and exhibited a clear bias toward neuronal cells. Intriguingly, our AAV-BBB variants relied on the LY6A cellular receptor for CNS entry, similar to AAV9 peptide variants AAV-PHP.eB and AAV.CAP-B10, despite the different bioengineering methods used and parental backgrounds. The variants also showed reduced transduction of both mouse liver and human primary hepatocytes in vivo. To increase clinical translatability, we enhanced the immune escape properties of our new variants by introducing additional modifications based on rational design. Overall, our study highlights the potential of AAV1-like vectors for efficient CNS transduction with reduced liver tropism, offering promising prospects for CNS gene therapies.
Collapse
Affiliation(s)
- Matthieu Drouyer
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Jessica Merjane
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Deborah Nazareth
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Maddison Knight
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Suzanne Scott
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Sophia H Y Liao
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Samantha L Ginn
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Erhua Zhu
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia; Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW, Australia; Australian Genome Therapeutics Centre, Children's Medical Research Institute and Sydney Children's Hospitals Network, Westmead, NSW, Australia; Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine - National Research Institute, Warsaw, Poland.
| |
Collapse
|
8
|
Yu DL, van Lieshout LP, Stevens BAY, Near KJ(J, Stodola JK, Stinson KJ, Slavic D, Wootton SK. AAV Vectors Pseudotyped with Capsids from Porcine and Bovine Species Mediate In Vitro and In Vivo Gene Delivery. Viruses 2023; 16:57. [PMID: 38257756 PMCID: PMC10820940 DOI: 10.3390/v16010057] [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: 11/05/2023] [Revised: 12/19/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Adeno-associated virus (AAV) vectors are among the most widely used delivery vehicles for in vivo gene therapy as they mediate robust and sustained transgene expression with limited toxicity. However, a significant impediment to the broad clinical success of AAV-based therapies is the widespread presence of pre-existing humoral immunity to AAVs in the human population. This immunity arises from the circulation of non-pathogenic endemic human AAV serotypes. One possible solution is to use non-human AAV capsids to pseudotype transgene-containing AAV vector genomes of interest. Due to the low probability of human exposure to animal AAVs, pre-existing immunity to animal-derived AAV capsids should be low. Here, we characterize two novel AAV capsid sequences: one derived from porcine colon tissue and the other from a caprine adenovirus stock. Both AAV capsids proved to be effective transducers of HeLa and HEK293T cells in vitro. In vivo, both capsids were able to transduce the murine nose, lung, and liver after either intranasal or intraperitoneal administration. In addition, we demonstrate that the porcine AAV capsid likely arose from multiple recombination events involving human- and animal-derived AAV sequences. We hypothesize that recurrent recombination events with similar and distantly related AAV sequences represent an effective mechanism for enhancing the fitness of wildtype AAV populations.
Collapse
Affiliation(s)
- Darrick L. Yu
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | | | | | | | - Jenny K. Stodola
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Kevin J. Stinson
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Durda Slavic
- Animal Health Laboratory, Laboratory Services Division, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sarah K. Wootton
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
9
|
Del Rivero Morfin PJ, Chavez DS, Jayaraman S, Yang L, Kochiss AL, Colecraft HM, Liu XS, Marx SO, Rajadhyaksha AM, Ben-Johny M. A Genetically Encoded Actuator Selectively Boosts L-type Calcium Channels in Diverse Physiological Settings. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.558856. [PMID: 37790372 PMCID: PMC10542531 DOI: 10.1101/2023.09.22.558856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
L-type Ca 2+ channels (Ca V 1.2/1.3) convey influx of calcium ions (Ca 2+ ) that orchestrate a bevy of biological responses including muscle contraction and gene transcription. Deficits in Ca V 1 function play a vital role in cardiac and neurodevelopmental disorders. Yet conventional pharmacological approaches to upregulate Ca V 1 are limited, as excessive Ca 2+ influx leads to cytotoxicity. Here, we develop a genetically encoded enhancer of Ca V 1.2/1.3 channels (GeeC) to manipulate Ca 2+ entry in distinct physiological settings. Specifically, we functionalized a nanobody that targets the Ca V macromolecular complex by attaching a minimal effector domain from a Ca V enhancer-leucine rich repeat containing protein 10 (Lrrc10). In cardiomyocytes, GeeC evoked a 3-fold increase in L-type current amplitude. In neurons, GeeC augmented excitation-transcription (E-T) coupling. In all, GeeC represents a powerful strategy to boost Ca V 1.2/1.3 function in distinct physiological settings and, in so doing, lays the groundwork to illuminate new insights on neuronal and cardiac physiology and disease.
Collapse
|
10
|
Moço PD, Farnós O, Sharon D, Kamen AA. Targeted Delivery of Chimeric Antigen Receptor into T Cells via CRISPR-Mediated Homology-Directed Repair with a Dual-AAV6 Transduction System. Curr Issues Mol Biol 2023; 45:7705-7720. [PMID: 37886930 PMCID: PMC10605174 DOI: 10.3390/cimb45100486] [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: 08/26/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
CAR-T cell therapy involves genetically engineering T cells to recognize and attack tumour cells by adding a chimeric antigen receptor (CAR) to their surface. In this study, we have used dual transduction with AAV serotype 6 (AAV6) to integrate an anti-CD19 CAR into human T cells at a known genomic location. The first viral vector expresses the Cas9 endonuclease and a guide RNA (gRNA) targeting the T cell receptor alpha constant locus, while the second vector carries the DNA template for homology-mediated CAR insertion. We evaluated three gRNA candidates and determined their efficiency in generating indels. The AAV6 successfully delivered the CRISPR/Cas9 machinery in vitro, and molecular analysis of the dual transduction showed the integration of the CAR transgene into the desired location. In contrast to the random integration methods typically used to generate CAR-T cells, targeted integration into a known genomic locus can potentially lower the risk of insertional mutagenesis and provide more stable levels of CAR expression. Critically, this method also results in the knockout of the endogenous T cell receptor, allowing target cells to be derived from allogeneic donors. This raises the exciting possibility of "off-the-shelf" universal immunotherapies that would greatly simplify the production and administration of CAR-T cells.
Collapse
Affiliation(s)
| | | | | | - Amine A. Kamen
- Department of Bioengineering, McGill University, Montreal, QC H3A 0E9, Canada; (P.D.M.)
| |
Collapse
|
11
|
Ohba K, Sehara Y, Enoki T, Mineno J, Ozawa K, Mizukami H. Adeno-associated virus vector system controlling capsid expression improves viral quantity and quality. iScience 2023; 26:106487. [PMID: 37096037 PMCID: PMC10122016 DOI: 10.1016/j.isci.2023.106487] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 01/13/2023] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
Adeno-associated virus (AAV) vectors are promising tools for gene therapy. The current AAV vector system produces an abundance of empty capsids that are eliminated before clinical use, leading to increased costs for gene therapy. In the present study, we established an AAV production system that regulates the timing of capsid expression using a tetracycline-dependent promoter. Tetracycline-regulating capsid expression increased viral yield and reduced empty capsids in various serotypes without altering AAV vector infectivity in vitro and in vivo. The replicase expression pattern change observed in the developed AAV vector system improved viral quantity and quality, whereas timing control of capsid expression reduced empty capsids. These findings provide a new perspective on the development of AAV vector production systems in gene therapy.
Collapse
Affiliation(s)
- Kenji Ohba
- Division of Genetic Therapeutics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
- Corresponding author
| | - Yoshihide Sehara
- Division of Genetic Therapeutics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Tatsuji Enoki
- CDM Center, TAKARA Bio Inc., Kusatsu, Shiga 525-0058, Japan
| | - Junichi Mineno
- CDM Center, TAKARA Bio Inc., Kusatsu, Shiga 525-0058, Japan
| | - Keiya Ozawa
- Division of Genetic Therapeutics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
- Department of Immuno-Gene & Cell Therapy (Takara Bio), Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Hiroaki Mizukami
- Division of Genetic Therapeutics, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| |
Collapse
|
12
|
Cabanes-Creus M, Navarro RG, Liao SH, Scott S, Carlessi R, Roca-Pinilla R, Knight M, Baltazar G, Zhu E, Jones M, Denisenko E, Forrest AR, Alexander IE, Tirnitz-Parker JE, Lisowski L. Characterization of the humanized FRG mouse model and development of an AAV-LK03 variant with improved liver lobular biodistribution. Mol Ther Methods Clin Dev 2023; 28:220-237. [PMID: 36700121 PMCID: PMC9860073 DOI: 10.1016/j.omtm.2022.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 12/31/2022] [Indexed: 01/03/2023]
Abstract
Recent clinical successes have intensified interest in using adeno-associated virus (AAV) vectors for therapeutic gene delivery. The liver is a key clinical target, given its critical physiological functions and involvement in a wide range of genetic diseases. In the present study, we first investigated the validity of a liver xenograft mouse model repopulated with primary hepatocytes using single-nucleus RNA sequencing (sn-RNA-seq) by studying the transcriptomic profile of human hepatocytes pre- and post-engraftment. Complementary immunofluorescence analyses performed in highly engrafted animals confirmed that the human hepatocytes organize and present appropriate patterns of zone-dependent enzyme expression in this model. Next, we tested a set of rationally designed HSPG de-targeted AAV-LK03 variants for relative transduction performance in human hepatocytes. We used immunofluorescence, next-generation sequencing, and single-nucleus transcriptomics data from highly engrafted FRG mice to demonstrate that the optimally HSPG de-targeted AAV-LK03 displayed a significantly improved lobular transduction profile in this model.
Collapse
Affiliation(s)
- Marti Cabanes-Creus
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Renina Gale Navarro
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Sophia H.Y. Liao
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Suzanne Scott
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Rodrigo Carlessi
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Ramon Roca-Pinilla
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Maddison Knight
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Grober Baltazar
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Erhua Zhu
- Gene Therapy Research Unit, Children’s Medical Research Institute and The Children’s Hospital at Westmead, Faculty of Medicine and Health, The University of Sydney, and Sydney Children’s Hospitals Network, Westmead, NSW 2145, Australia
| | - Matthew Jones
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Elena Denisenko
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Alistair R.R. Forrest
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Ian E. Alexander
- Gene Therapy Research Unit, Children’s Medical Research Institute and The Children’s Hospital at Westmead, Faculty of Medicine and Health, The University of Sydney, and Sydney Children’s Hospitals Network, Westmead, NSW 2145, Australia,Discipline of Child and Adolescent Health, The University of Sydney, Sydney Medical School, Faculty of Medicine and Health, Westmead, NSW 2145, Australia
| | - Janina E.E. Tirnitz-Parker
- Curtin Medical School, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia,UWA Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia,Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, 04-141 Warsaw, Poland,Corresponding author: Dr. Leszek Lisowski, Translational Vectorology Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia.
| |
Collapse
|
13
|
Shahbazi R, Lipson P, Gottimukkala KSV, Lane DD, Adair JE. CRISPR Gene Editing of Hematopoietic Stem and Progenitor Cells. Methods Mol Biol 2023; 2567:39-62. [PMID: 36255694 DOI: 10.1007/978-1-0716-2679-5_4] [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: 06/16/2023]
Abstract
Genetic editing of hematopoietic stem and progenitor cells can be employed to understand gene-function relationships underlying hematopoietic cell biology, leading to new therapeutic approaches to treat disease. The ability to collect, purify, and manipulate primary cells outside the body permits testing of many different gene editing approaches. RNA-guided nucleases, such as CRISPR, have revolutionized gene editing based simply on Watson-Crick base-pairing, employed to direct activity to specific genomic loci. Given the ease and affordability of synthetic, custom RNA guides, testing of precision edits or large random pools in high-throughput screening studies is now widely available. With the ever-growing number of CRISPR nucleases being discovered or engineered, researchers now have a plethora of options for directed genomic change, including single base edits, nicks or double-stranded DNA cuts with blunt or staggered ends, as well as the ability to target CRISPR to other cellular oligonucleotides such as RNA or mitochondrial DNA. Except for single base editing strategies, precise rewriting of larger segments of the genetic code requires delivery of an additional component, templated DNA oligonucleotide(s) encoding the desired changes flanked by homologous sequences that permit recombination at or near the site of CRISPR activity. Altogether, the ever-growing CRISPR gene editing toolkit is an invaluable resource. This chapter outlines available technologies and the strategies for applying CRISPR-based editing in hematopoietic stem and progenitor cells.
Collapse
Affiliation(s)
| | | | | | | | - Jennifer E Adair
- Fred Hutchinson Cancer Center, Seattle, WA, USA.
- University of Washington, Seattle, WA, USA.
| |
Collapse
|
14
|
Blazev R, Carl CS, Ng YK, Molendijk J, Voldstedlund CT, Zhao Y, Xiao D, Kueh AJ, Miotto PM, Haynes VR, Hardee JP, Chung JD, McNamara JW, Qian H, Gregorevic P, Oakhill JS, Herold MJ, Jensen TE, Lisowski L, Lynch GS, Dodd GT, Watt MJ, Yang P, Kiens B, Richter EA, Parker BL. Phosphoproteomics of three exercise modalities identifies canonical signaling and C18ORF25 as an AMPK substrate regulating skeletal muscle function. Cell Metab 2022; 34:1561-1577.e9. [PMID: 35882232 DOI: 10.1016/j.cmet.2022.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/31/2022] [Accepted: 07/08/2022] [Indexed: 11/03/2022]
Abstract
Exercise induces signaling networks to improve muscle function and confer health benefits. To identify divergent and common signaling networks during and after different exercise modalities, we performed a phosphoproteomic analysis of human skeletal muscle from a cross-over intervention of endurance, sprint, and resistance exercise. This identified 5,486 phosphosites regulated during or after at least one type of exercise modality and only 420 core phosphosites common to all exercise. One of these core phosphosites was S67 on the uncharacterized protein C18ORF25, which we validated as an AMPK substrate. Mice lacking C18ORF25 have reduced skeletal muscle fiber size, exercise capacity, and muscle contractile function, and this was associated with reduced phosphorylation of contractile and Ca2+ handling proteins. Expression of C18ORF25 S66/67D phospho-mimetic reversed the decreased muscle force production. This work defines the divergent and canonical exercise phosphoproteome across different modalities and identifies C18ORF25 as a regulator of exercise signaling and muscle function.
Collapse
Affiliation(s)
- Ronnie Blazev
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Christian S Carl
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Yaan-Kit Ng
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Jeffrey Molendijk
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Christian T Voldstedlund
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Yuanyuan Zhao
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Di Xiao
- Children's Medical Research Institute, The University of Sydney, Camperdown, NSW, Australia; School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia
| | - Andrew J Kueh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Paula M Miotto
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Vanessa R Haynes
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Justin P Hardee
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Jin D Chung
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - James W McNamara
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia; Murdoch Children's Research Institute and Melbourne Centre for Cardiovascular Genomics and Regenerative Medicine, The Royal Children's Hospital, Parkville, VIC, Australia
| | - Hongwei Qian
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Paul Gregorevic
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | | | - Marco J Herold
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Thomas E Jensen
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Leszek Lisowski
- Children's Medical Research Institute, The University of Sydney, Camperdown, NSW, Australia; Military Institute of Medicine, Warsaw, Poland
| | - Gordon S Lynch
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia
| | - Garron T Dodd
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Matthew J Watt
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Pengyi Yang
- Children's Medical Research Institute, The University of Sydney, Camperdown, NSW, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Bente Kiens
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark.
| | - Erik A Richter
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark.
| | - Benjamin L Parker
- Department of Anatomy & Physiology, The University of Melbourne, Parkville, VIC, Australia; Centre for Muscle Research, The University of Melbourne, Parkville, VIC, Australia.
| |
Collapse
|
15
|
Kennedy A, Waters E, Rowshanravan B, Hinze C, Williams C, Janman D, Fox TA, Booth C, Pesenacker AM, Halliday N, Soskic B, Kaur S, Qureshi OS, Morris EC, Ikemizu S, Paluch C, Huo J, Davis SJ, Boucrot E, Walker LSK, Sansom DM. Differences in CD80 and CD86 transendocytosis reveal CD86 as a key target for CTLA-4 immune regulation. Nat Immunol 2022; 23:1365-1378. [PMID: 35999394 PMCID: PMC9477731 DOI: 10.1038/s41590-022-01289-w] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/15/2022] [Indexed: 01/07/2023]
Abstract
CD28 and CTLA-4 (CD152) play essential roles in regulating T cell immunity, balancing the activation and inhibition of T cell responses, respectively. Although both receptors share the same ligands, CD80 and CD86, the specific requirement for two distinct ligands remains obscure. In the present study, we demonstrate that, although CTLA-4 targets both CD80 and CD86 for destruction via transendocytosis, this process results in separate fates for CTLA-4 itself. In the presence of CD80, CTLA-4 remained ligand bound, and was ubiquitylated and trafficked via late endosomes and lysosomes. In contrast, in the presence of CD86, CTLA-4 detached in a pH-dependent manner and recycled back to the cell surface to permit further transendocytosis. Furthermore, we identified clinically relevant mutations that cause autoimmune disease, which selectively disrupted CD86 transendocytosis, by affecting either CTLA-4 recycling or CD86 binding. These observations provide a rationale for two distinct ligands and show that defects in CTLA-4-mediated transendocytosis of CD86 are associated with autoimmunity.
Collapse
Affiliation(s)
- Alan Kennedy
- UCL Institute of Immunity and Transplantation, London, UK
| | - Erin Waters
- UCL Institute of Immunity and Transplantation, London, UK
| | | | - Claudia Hinze
- UCL Institute of Immunity and Transplantation, London, UK
| | | | - Daniel Janman
- UCL Institute of Immunity and Transplantation, London, UK
| | - Thomas A Fox
- UCL Institute of Immunity and Transplantation, London, UK
| | - Claire Booth
- Molecular and Cellular Immunology Section, UCL Great Ormond Street Institute of Child Health, London, UK
| | | | - Neil Halliday
- UCL Institute of Immunity and Transplantation, London, UK
| | - Blagoje Soskic
- UCL Institute of Immunity and Transplantation, London, UK
| | - Satdip Kaur
- School of Immunity and Infection, Institute of Biomedical Research, University of Birmingham Medical School, Birmingham, UK
| | | | - Emma C Morris
- UCL Institute of Immunity and Transplantation, London, UK
| | - Shinji Ikemizu
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Christopher Paluch
- Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jiandong Huo
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
- Division of Structural Biology, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, Oxford, UK
- Protein Production UK, The Rosalind Franklin Institute-Diamond Light Source, The Research Complex at Harwell, Didcot, UK
| | - Simon J Davis
- Medical Research Council Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Emmanuel Boucrot
- Institute of Structural and Molecular Biology, University College London, London, UK
| | | | - David M Sansom
- UCL Institute of Immunity and Transplantation, London, UK.
| |
Collapse
|
16
|
Jiang Z, Fu M, Zhu D, Wang X, Li N, Ren L, He J, Yang G. Genetically modified immunomodulatory cell-based biomaterials in tissue regeneration and engineering. Cytokine Growth Factor Rev 2022; 66:53-73. [PMID: 35690567 DOI: 10.1016/j.cytogfr.2022.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 05/24/2022] [Indexed: 11/25/2022]
Abstract
To date, the wide application of cell-based biomaterials in tissue engineering and regeneration is remarkably hampered by immune rejection. Reducing the immunogenicity of cell-based biomaterials has become the latest direction in biomaterial research. Recently, genetically modified cell-based biomaterials with immunomodulatory genes have become a feasible solution to the immunogenicity problem. In this review, recent advances and future challenges of genetically modified immunomodulatory cell-based biomaterials are elaborated, including fabrication approaches, mechanisms of common immunomodulatory genes, application and, more importantly, current preclinical and clinical advances. The fabrication approaches can be categorized into commonly used (e.g., virus transfection) and newly developed approaches. The immunomodulatory mechanisms of representative genes involve complicated cell signaling pathways and metabolic activities. Wide application in curing multiple end-term diseases and replacing lifelong immunosuppressive therapy in multiple cell and organ transplantation models is demonstrated. Most significantly, practices of genetically modified organ transplantation have been conducted on brain-dead human decedent and even on living patients after a series of experiments on nonhuman primates. Nevertheless, uncertain biosecurity, nonspecific effects and overlooked personalization of current genetically modified immunomodulatory cell-based biomaterials are shortcomings that remain to be overcome.
Collapse
Affiliation(s)
- Zhiwei Jiang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Mengdie Fu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Danji Zhu
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Xueting Wang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Na Li
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Lingfei Ren
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Jin He
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China
| | - Guoli Yang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center of Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou 310000, China.
| |
Collapse
|
17
|
Cabanes-Creus M, Navarro RG, Zhu E, Baltazar G, Liao SHY, Drouyer M, Amaya AK, Scott S, Nguyen LH, Westhaus A, Hebben M, Wilson LOW, Thrasher AJ, Alexander IE, Lisowski L. Novel human liver-tropic AAV variants define transferable domains that markedly enhance the human tropism of AAV7 and AAV8. Mol Ther Methods Clin Dev 2022; 24:88-101. [PMID: 34977275 PMCID: PMC8693155 DOI: 10.1016/j.omtm.2021.11.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/07/2021] [Indexed: 12/19/2022]
Abstract
Recent clinical successes have intensified interest in using adeno-associated virus (AAV) vectors for therapeutic gene delivery. The liver is a key clinical target, given its critical physiological functions and involvement in a wide range of genetic diseases. Here, we report the bioengineering of a set of next-generation AAV vectors, named AAV-SYDs (where “SYD” stands for Sydney, Australia), with increased human hepato-tropism in a liver xenograft mouse model repopulated with primary human hepatocytes. We followed a two-step process that staggered directed evolution and domain-swapping approaches. Using DNA-family shuffling, we first mapped key AAV capsid regions responsible for efficient human hepatocyte transduction in vivo. Focusing on these regions, we next applied domain-swapping strategies to identify and study key capsid residues that enhance primary human hepatocyte uptake and transgene expression. Our findings underscore the potential of AAV-SYDs as liver gene therapy vectors and provide insights into the mechanism responsible for their enhanced transduction profile.
Collapse
Affiliation(s)
- Marti Cabanes-Creus
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Renina Gale Navarro
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Erhua Zhu
- Gene Therapy Research Unit, Children's Medical Research Institute & The Children's Hospital at Westmead, The University of Sydney, Westmead, NSW 2145, Australia
| | - Grober Baltazar
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Sophia H Y Liao
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Matthieu Drouyer
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Anais K Amaya
- Gene Therapy Research Unit, Children's Medical Research Institute & The Children's Hospital at Westmead, The University of Sydney, Westmead, NSW 2145, Australia
| | - Suzanne Scott
- Gene Therapy Research Unit, Children's Medical Research Institute & The Children's Hospital at Westmead, The University of Sydney, Westmead, NSW 2145, Australia.,Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - Loan Hanh Nguyen
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Adrian Westhaus
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia.,Great Ormond Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Matthias Hebben
- LogicBio Therapeutics, 65 Hayden avenue, Lexington, 02421 MA, USA
| | - Laurence O W Wilson
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - Adrian J Thrasher
- Great Ormond Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute & The Children's Hospital at Westmead, The University of Sydney, Westmead, NSW 2145, Australia.,Discipline of Child and Adolescent Health, The University of Sydney, Sydney Medical School, Faculty of Medicine and Health, Westmead, NSW 2145, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia.,Vector and Genome Engineering Facility, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia.,Military Institute of Medicine, Laboratory of Molecular Oncology and Innovative Therapies, 04-141 Warsaw, Poland
| |
Collapse
|
18
|
Bijlani S, Pang KM, Sivanandam V, Singh A, Chatterjee S. The Role of Recombinant AAV in Precise Genome Editing. Front Genome Ed 2022; 3:799722. [PMID: 35098210 PMCID: PMC8793687 DOI: 10.3389/fgeed.2021.799722] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/14/2021] [Indexed: 12/14/2022] Open
Abstract
The replication-defective, non-pathogenic, nearly ubiquitous single-stranded adeno-associated viruses (AAVs) have gained importance since their discovery about 50 years ago. Their unique life cycle and virus-cell interactions have led to the development of recombinant AAVs as ideal genetic medicine tools that have evolved into effective commercialized gene therapies. A distinctive property of AAVs is their ability to edit the genome precisely. In contrast to all current genome editing platforms, AAV exclusively utilizes the high-fidelity homologous recombination (HR) pathway and does not require exogenous nucleases for prior cleavage of genomic DNA. Together, this leads to a highly precise editing outcome that preserves genomic integrity without incorporation of indel mutations or viral sequences at the target site while also obviating the possibility of off-target genotoxicity. The stem cell-derived AAV (AAVHSCs) were found to mediate precise and efficient HR with high on-target accuracy and at high efficiencies. AAVHSC editing occurs efficiently in post-mitotic cells and tissues in vivo. Additionally, AAV also has the advantage of an intrinsic delivery mechanism. Thus, this distinctive genome editing platform holds tremendous promise for the correction of disease-associated mutations without adding to the mutational burden. This review will focus on the unique properties of direct AAV-mediated genome editing and their potential mechanisms of action.
Collapse
|
19
|
Taha EA, Lee J, Hotta A. Delivery of CRISPR-Cas tools for in vivo genome editing therapy: Trends and challenges. J Control Release 2022; 342:345-361. [PMID: 35026352 DOI: 10.1016/j.jconrel.2022.01.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/12/2022]
Abstract
The discovery of clustered regularly interspaced short palindromic repeats (CRISPR) genome editing technology opened the door to provide a versatile approach for treating multiple diseases. Promising results have been shown in numerous pre-clinical studies and clinical trials. However, a safe and effective method to deliver genome-editing components is still a key challenge for in vivo genome editing therapy. Adeno-associated virus (AAV) is one of the most commonly used vector systems to date, but immunogenicity against capsid, liver toxicity at high dose, and potential genotoxicity caused by off-target mutagenesis and genomic integration remain unsolved. Recently developed transient delivery systems, such as virus-like particle (VLP) and lipid nanoparticle (LNP), may solve some of the issues. This review summarizes existing in vivo delivery systems and possible solutions to overcome their limitations. Also, we highlight the ongoing clinical trials for in vivo genome editing therapy and recently developed genome editing tools for their potential applications.
Collapse
Affiliation(s)
- Eman A Taha
- Center for iPS cell Research and Application, Kyoto University, Kyoto 606-8507, Japan; Department of Biochemistry, Ain Shams University Faculty of Science, Cairo 11566, Egypt
| | - Joseph Lee
- Center for iPS cell Research and Application, Kyoto University, Kyoto 606-8507, Japan
| | - Akitsu Hotta
- Center for iPS cell Research and Application, Kyoto University, Kyoto 606-8507, Japan; Takeda-CiRA Joint Program (T-CiRA), Fujisawa, Kanagawa 251-8555, Japan.
| |
Collapse
|
20
|
Molendijk J, Blazev R, Mills RJ, Ng YK, Watt KI, Chau D, Gregorevic P, Crouch PJ, Hilton JBW, Lisowski L, Zhang P, Reue K, Lusis AJ, Hudson JE, James DE, Seldin MM, Parker BL. Proteome-wide systems genetics identifies UFMylation as a regulator of skeletal muscle function. eLife 2022; 11:82951. [PMID: 36472367 PMCID: PMC9833826 DOI: 10.7554/elife.82951] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022] Open
Abstract
Improving muscle function has great potential to improve the quality of life. To identify novel regulators of skeletal muscle metabolism and function, we performed a proteomic analysis of gastrocnemius muscle from 73 genetically distinct inbred mouse strains, and integrated the data with previously acquired genomics and >300 molecular/phenotypic traits via quantitative trait loci mapping and correlation network analysis. These data identified thousands of associations between protein abundance and phenotypes and can be accessed online (https://muscle.coffeeprot.com/) to identify regulators of muscle function. We used this resource to prioritize targets for a functional genomic screen in human bioengineered skeletal muscle. This identified several negative regulators of muscle function including UFC1, an E2 ligase for protein UFMylation. We show UFMylation is up-regulated in a mouse model of amyotrophic lateral sclerosis, a disease that involves muscle atrophy. Furthermore, in vivo knockdown of UFMylation increased contraction force, implicating its role as a negative regulator of skeletal muscle function.
Collapse
Affiliation(s)
- Jeffrey Molendijk
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia,Centre for Muscle Research, University of MelbourneMelbourneAustralia
| | - Ronnie Blazev
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia,Centre for Muscle Research, University of MelbourneMelbourneAustralia
| | | | - Yaan-Kit Ng
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia,Centre for Muscle Research, University of MelbourneMelbourneAustralia
| | - Kevin I Watt
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia,Centre for Muscle Research, University of MelbourneMelbourneAustralia
| | - Daryn Chau
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, IrvineIrvineUnited States
| | - Paul Gregorevic
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia,Centre for Muscle Research, University of MelbourneMelbourneAustralia
| | - Peter J Crouch
- Department of Biochemistry and Pharmacology, University of MelbourneMelbourneAustralia
| | - James BW Hilton
- Department of Biochemistry and Pharmacology, University of MelbourneMelbourneAustralia
| | - Leszek Lisowski
- Children's Medical Research Institute, University of SydneySydneyAustralia,Military Institute of MedicineWarszawaPoland
| | - Peixiang Zhang
- Department of Human Genetics/Medicine, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Karen Reue
- Department of Human Genetics/Medicine, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Aldons J Lusis
- Department of Human Genetics/Medicine, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los AngelesLos AngelesUnited States
| | - James E Hudson
- QIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - David E James
- Charles Perkins Centre, School of Life and Environmental Science, School of Medical Science, University of SydneySydneyAustralia
| | - Marcus M Seldin
- Department of Biological Chemistry and Center for Epigenetics and Metabolism, University of California, IrvineIrvineUnited States
| | - Benjamin L Parker
- Department of Anatomy and Physiology, University of MelbourneMelbourneAustralia,Centre for Muscle Research, University of MelbourneMelbourneAustralia
| |
Collapse
|
21
|
Guo X, Starr C, Zhou J, Chen B. Protocol for evaluating the role of a gene in protecting mouse retinal ganglion cells. STAR Protoc 2021; 2:100932. [PMID: 34806045 PMCID: PMC8581646 DOI: 10.1016/j.xpro.2021.100932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The degeneration of retinal ganglion cells (RGCs) leads to irreversible vision loss in a variety of pathological states. Here, we describe a protocol to evaluate the role of a gene in protecting mouse RGCs when they sustain injuries from excitotoxicity or axonal damage. This protocol includes the procedures for gene transfer through AAV intravitreal injection, induction of RGC injuries by NMDA-induced excitotoxicity or optic nerve crush, and retina immunohistochemistry to assess RGC survival. For complete details on the use and execution of this protocol, please refer to Guo et al. (2021).
Collapse
Affiliation(s)
- Xinzheng Guo
- Departments of Ophthalmology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Christopher Starr
- Departments of Ophthalmology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jing Zhou
- Departments of Ophthalmology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bo Chen
- Departments of Ophthalmology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
22
|
Chatterjee S, Sivanandam V, Wong KKM. Adeno-Associated Virus and Hematopoietic Stem Cells: The Potential of Adeno-Associated Virus Hematopoietic Stem Cells in Genetic Medicines. Hum Gene Ther 2021; 31:542-552. [PMID: 32253938 DOI: 10.1089/hum.2020.049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Adeno-associated virus (AAV)-based vectors have transformed into powerful elements of genetic medicine with proven therapeutic efficacy and a good safety profile. Over the years, efforts to transduce hematopoietic stem cells (HSCs) with AAV2 vectors have, however, been challenging. While there was evidence that AAV2 delivered vector genomes to primitive, quiescent, multipotential, self-renewing, in vivo engrafting HSCs, transgene expression was elusive. In this study, we review the evolution of AAV transduction of HSC, starting with AAV2 vectors leading to the isolation of a family of naturally occurring AAVs from human CD34+ HSC, the AAVHSC. The stem cell-derived AAVHSCs have turned out to have remarkable potentials for genetic therapies well beyond the hematopoietic system. AAVHSCs have tropism for a wide variety of peripheral tissues, including the liver, muscle, and the retina. They cross the blood-brain barrier and transduce cells of the central nervous system. Preclinical gene therapy studies underway using AAVHSC vectors are discussed. We review the notable ability of AAVHSCs to mediate efficient, seamless homologous recombination in the absence of exogenous nuclease activity and discuss the therapeutic implications. We also discuss early results from an AAVHSC-based clinical gene therapy trial that is underway for the treatment of phenylketonuria. Thus, the stem cell-derived AAVHSC, offer a multifaceted platform for in vivo gene therapy and genome editing for the treatment of inherited diseases.
Collapse
Affiliation(s)
- Saswati Chatterjee
- Department of Surgery, Beckman Research Institute of City of Hope Medical Center, Duarte, California, USA
| | - Venkatesh Sivanandam
- Department of Surgery, Beckman Research Institute of City of Hope Medical Center, Duarte, California, USA
| | - Kamehameha Kai-Min Wong
- Department of Hematology and Stem Cell Transplantation, City of Hope Medical Center, Duarte, California, USA
| |
Collapse
|
23
|
Lattanzi A, Camarena J, Lahiri P, Segal H, Srifa W, Vakulskas CA, Frock RL, Kenrick J, Lee C, Talbott N, Skowronski J, Cromer MK, Charlesworth CT, Bak RO, Mantri S, Bao G, DiGiusto D, Tisdale J, Wright JF, Bhatia N, Roncarolo MG, Dever DP, Porteus MH. Development of β-globin gene correction in human hematopoietic stem cells as a potential durable treatment for sickle cell disease. Sci Transl Med 2021; 13:13/598/eabf2444. [PMID: 34135108 DOI: 10.1126/scitranslmed.abf2444] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 05/25/2021] [Indexed: 12/11/2022]
Abstract
Sickle cell disease (SCD) is the most common serious monogenic disease with 300,000 births annually worldwide. SCD is an autosomal recessive disease resulting from a single point mutation in codon six of the β-globin gene (HBB). Ex vivo β-globin gene correction in autologous patient-derived hematopoietic stem and progenitor cells (HSPCs) may potentially provide a curative treatment for SCD. We previously developed a CRISPR-Cas9 gene targeting strategy that uses high-fidelity Cas9 precomplexed with chemically modified guide RNAs to induce recombinant adeno-associated virus serotype 6 (rAAV6)-mediated HBB gene correction of the SCD-causing mutation in HSPCs. Here, we demonstrate the preclinical feasibility, efficacy, and toxicology of HBB gene correction in plerixafor-mobilized CD34+ cells from healthy and SCD patient donors (gcHBB-SCD). We achieved up to 60% HBB allelic correction in clinical-scale gcHBB-SCD manufacturing. After transplant into immunodeficient NSG mice, 20% gene correction was achieved with multilineage engraftment. The long-term safety, tumorigenicity, and toxicology study demonstrated no evidence of abnormal hematopoiesis, genotoxicity, or tumorigenicity from the engrafted gcHBB-SCD drug product. Together, these preclinical data support the safety, efficacy, and reproducibility of this gene correction strategy for initiation of a phase 1/2 clinical trial in patients with SCD.
Collapse
Affiliation(s)
- Annalisa Lattanzi
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.,Center for Definitive and Curative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Premanjali Lahiri
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Helen Segal
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Waracharee Srifa
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Richard L Frock
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Josefin Kenrick
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Ciaran Lee
- APC Microbiome Ireland, University College Cork, T12 YN60 Cork, Ireland
| | - Narae Talbott
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Jason Skowronski
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - M Kyle Cromer
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, DK-8000 Aarhus, Denmark.,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, DK-8000 Aarhus, Denmark
| | - Sruthi Mantri
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77006, USA
| | - David DiGiusto
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - John Tisdale
- Molecular and Clinical Hematology Branch, NHLBI, Bethesda, MD 20814, USA
| | - J Fraser Wright
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.,Center for Definitive and Curative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Neehar Bhatia
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA.,Deceased
| | - Maria Grazia Roncarolo
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.,Center for Definitive and Curative Medicine, Stanford University, Stanford, CA 94305, USA.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA. .,Center for Definitive and Curative Medicine, Stanford University, Stanford, CA 94305, USA.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
24
|
Cabanes-Creus M, Hallwirth CV, Westhaus A, Ng BH, Liao SHY, Zhu E, Navarro RG, Baltazar G, Drouyer M, Scott S, Logan GJ, Santilli G, Bennett A, Ginn SL, McCaughan G, Thrasher AJ, Agbandje-McKenna M, Alexander IE, Lisowski L. Restoring the natural tropism of AAV2 vectors for human liver. Sci Transl Med 2021; 12:12/560/eaba3312. [PMID: 32908003 DOI: 10.1126/scitranslmed.aba3312] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/25/2020] [Accepted: 08/20/2020] [Indexed: 12/27/2022]
Abstract
Recent clinical successes in gene therapy applications have intensified interest in using adeno-associated viruses (AAVs) as vectors for therapeutic gene delivery. Although prototypical AAV2 shows robust in vitro transduction of human hepatocyte-derived cell lines, it has not translated into an effective vector for liver-directed gene therapy in vivo. This is consistent with observations made in Fah-/-/Rag2-/-/Il2rg-/- (FRG) mice with humanized livers, showing that AAV2 functions poorly in this xenograft model. Here, we derived naturally hepatotropic AAV capsid sequences from primary human liver samples. We demonstrated that capsid mutations, likely acquired as an unintentional consequence of tissue culture propagation, attenuated the intrinsic human hepatic tropism of natural AAV2 and related human liver AAV isolates. These mutations resulted in amino acid changes that increased binding to heparan sulfate proteoglycan (HSPG), which has been regarded as the primary cellular receptor mediating AAV2 infection of human hepatocytes. Propagation of natural AAV variants in vitro showed tissue culture adaptation with resulting loss of tropism for human hepatocytes. In vivo readaptation of the prototypical AAV2 in FRG mice with a humanized liver resulted in restoration of the intrinsic hepatic tropism of AAV2 through decreased binding to HSPG. Our results challenge the notion that high affinity for HSPG is essential for AAV2 entry into human hepatocytes and suggest that natural AAV capsids of human liver origin are likely to be more effective for liver-targeted gene therapy applications than culture-adapted AAV2.
Collapse
Affiliation(s)
- Marti Cabanes-Creus
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute and Children's Hospital at Westmead, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW 2145, Australia
| | - Adrian Westhaus
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia.,Great Ormond Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Boaz H Ng
- Vector and Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Sophia H Y Liao
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Erhua Zhu
- Gene Therapy Research Unit, Children's Medical Research Institute and Children's Hospital at Westmead, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW 2145, Australia
| | - Renina Gale Navarro
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Grober Baltazar
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Matthieu Drouyer
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Suzanne Scott
- Gene Therapy Research Unit, Children's Medical Research Institute and Children's Hospital at Westmead, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW 2145, Australia.,Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - Grant J Logan
- Gene Therapy Research Unit, Children's Medical Research Institute and Children's Hospital at Westmead, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW 2145, Australia
| | - Giorgia Santilli
- Great Ormond Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Antonette Bennett
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Samantha L Ginn
- Gene Therapy Research Unit, Children's Medical Research Institute and Children's Hospital at Westmead, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW 2145, Australia
| | - Geoff McCaughan
- Liver Injury and Cancer Program, Centenary Research Institute, A.W Morrow Gastroenterology and Liver Centre, Australian National Liver Transplant Unit, Royal Prince Alfred Hospital, The University of Sydney, Sydney, NSW 2006, Australia
| | - Adrian J Thrasher
- Great Ormond Institute of Child Health, University College London, WC1N 1EH London, UK
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute and Children's Hospital at Westmead, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW 2145, Australia.,Discipline of Child and Adolescent Health, The University of Sydney, Sydney Medical School, Faculty of Medicine and Health, Westmead, NSW 2145, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia. .,Vector and Genome Engineering Facility, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia.,Military Institute of Hygiene and Epidemiology, Biological Threats Identification and Countermeasure Centre, 24-100 Puławy, Poland
| |
Collapse
|
25
|
Ferrari S, Beretta S, Jacob A, Cittaro D, Albano L, Merelli I, Naldini L, Genovese P. BAR-Seq clonal tracking of gene-edited cells. Nat Protoc 2021; 16:2991-3025. [PMID: 34031609 DOI: 10.1038/s41596-021-00529-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/26/2021] [Indexed: 02/04/2023]
Abstract
Gene editing by engineered nucleases has revolutionized the field of gene therapy by enabling targeted and precise modification of the genome. However, the limited availability of methods for clonal tracking of edited cells has resulted in a paucity of information on the diversity, abundance and behavior of engineered clones. Here we detail the wet laboratory and bioinformatic BAR-Seq pipeline, a strategy for clonal tracking of cells harboring homology-directed targeted integration of a barcoding cassette. We present the BAR-Seq web application, an online, freely available and easy-to-use software that allows performing clonal tracking analyses on raw sequencing data without any computational resources or advanced bioinformatic skills. BAR-Seq can be applied to most editing strategies, and we describe its use to investigate the clonal dynamics of human edited hematopoietic stem/progenitor cells in xenotransplanted hosts. Notably, BAR-Seq may be applied in both basic and translational research contexts to investigate the biology of edited cells and stringently compare editing protocols at a clonal level. Our BAR-Seq pipeline allows library preparation and validation in a few days and clonal analyses of edited cell populations in 1 week.
Collapse
Affiliation(s)
- Samuele Ferrari
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy. .,Vita-Salute San Raffaele University, Milan, Italy.
| | - Stefano Beretta
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Aurelien Jacob
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy.,Milano-Bicocca University, Monza, Italy
| | - Davide Cittaro
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luisa Albano
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy.,National Research Council, Institute for Biomedical Technologies, Segrate, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy
| | - Pietro Genovese
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy.,Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Department of Pediatric Oncology, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
26
|
Tissue and cell-type-specific transduction using rAAV vectors in lung diseases. J Mol Med (Berl) 2021; 99:1057-1071. [PMID: 34021360 DOI: 10.1007/s00109-021-02086-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 04/20/2021] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
Gene therapy of genetically determined diseases, including some pathologies of the respiratory system, requires an efficient method for transgene delivery. Recombinant adeno-associated viral (rAAV) vectors are well studied and employed in gene therapy, as they are relatively simple and low immunogenic and able to efficiently transduce eukaryotic cells. To date, many natural and artificial (with modified capsids) AAV serotypes have been isolated, demonstrating preferential tropism toward different tissues and cells in accordance with the prevalent receptors on the cell surface. However, rAAV-mediated delivery is not strictly specific due to wide tropism of some viral serotypes. Thus, the development of the methods allowing modulating specificity of these vectors could be beneficial in some cases. This review describes various approaches for retargeting rAAV to respiratory cells, for example, using different types of capsid modifications and regulation of a transgene expression by tissue-specific promoters. Part of the review is devoted to the issues of transduction of stem and progenitor lung cells using AAV, which is a complicated task today.
Collapse
|
27
|
Cabanes-Creus M, Navarro RG, Liao SHY, Baltazar G, Drouyer M, Zhu E, Scott S, Luong C, Wilson LOW, Alexander IE, Lisowski L. Single amino acid insertion allows functional transduction of murine hepatocytes with human liver tropic AAV capsids. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 21:607-620. [PMID: 34095344 PMCID: PMC8142051 DOI: 10.1016/j.omtm.2021.04.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/21/2021] [Indexed: 12/19/2022]
Abstract
Recent successes in clinical gene therapy applications have intensified the interest in using adeno-associated viruses (AAVs) as vectors for gene delivery into human liver. An inherent intriguing characteristic of AAVs is that vector variants vary substantially in their ability to transduce hepatocytes from different species. This has historically limited the value of preclinical studies using rodent models for predicting the efficiency of AAV vectors in liver-targeted gene therapy clinical studies. In this work, we aimed to investigate the key determinants of the observed differential interspecies transduction abilities among AAV variants. We took advantage of domain swapping strategies between AAV-KP1, a newly identified variant with enhanced murine liver tropism, and AAV3b, which functions poorly in mice. The systematic in vivo comparison of AAV3b/AAV-KP1 chimeric variants allowed us to identify a threonine insertion at position 265 within variable region I (VR-I) as the key residue that confers murine hepatic transduction to human-derived clade B (AAV2-like) and clade C (AAV3b-like) variants. We propose to use this insertion to generate phylogenetically related AAV surrogates in support of toxicology and dosing studies in the murine liver model.
Collapse
Affiliation(s)
- Marti Cabanes-Creus
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Renina Gale Navarro
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Sophia H Y Liao
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Grober Baltazar
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Matthieu Drouyer
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Erhua Zhu
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, The University of Sydney, Westmead, NSW 2145, Australia
| | - Suzanne Scott
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, The University of Sydney, Westmead, NSW 2145, Australia.,Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, NSW 2113, Australia
| | - Clement Luong
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Laurence O W Wilson
- Australian e-Health Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, NSW 2113, Australia
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, The University of Sydney, Westmead, NSW 2145, Australia.,Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW 2145, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia.,Vector and Genome Engineering Facility, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia.,Military Institute of Medicine, Laboratory of Molecular Oncology and Innovative Therapies, 04-141 Warsaw, Poland
| |
Collapse
|
28
|
Cromer MK, Camarena J, Martin RM, Lesch BJ, Vakulskas CA, Bode NM, Kurgan G, Collingwood MA, Rettig GR, Behlke MA, Lemgart VT, Zhang Y, Goyal A, Zhao F, Ponce E, Srifa W, Bak RO, Uchida N, Majeti R, Sheehan VA, Tisdale JF, Dever DP, Porteus MH. Gene replacement of α-globin with β-globin restores hemoglobin balance in β-thalassemia-derived hematopoietic stem and progenitor cells. Nat Med 2021; 27:677-687. [PMID: 33737751 PMCID: PMC8265212 DOI: 10.1038/s41591-021-01284-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/09/2021] [Indexed: 12/12/2022]
Abstract
β-Thalassemia pathology is due not only to loss of β-globin (HBB), but also to erythrotoxic accumulation and aggregation of the β-globin-binding partner, α-globin (HBA1/2). Here we describe a Cas9/AAV6-mediated genome editing strategy that can replace the entire HBA1 gene with a full-length HBB transgene in β-thalassemia-derived hematopoietic stem and progenitor cells (HSPCs), which is sufficient to normalize β-globin:α-globin messenger RNA and protein ratios and restore functional adult hemoglobin tetramers in patient-derived red blood cells. Edited HSPCs were capable of long-term and bilineage hematopoietic reconstitution in mice, establishing proof of concept for replacement of HBA1 with HBB as a novel therapeutic strategy for curing β-thalassemia.
Collapse
Affiliation(s)
- M Kyle Cromer
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Renata M Martin
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Benjamin J Lesch
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | - Nicole M Bode
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Gavin Kurgan
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | | | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Viktor T Lemgart
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Yankai Zhang
- Division of Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Ankush Goyal
- Division of Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Feifei Zhao
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Ezequiel Ponce
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Waracharee Srifa
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark
| | - Naoya Uchida
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Vivien A Sheehan
- Division of Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - John F Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
| |
Collapse
|
29
|
Adeno-associated Virus (AAV) Capsid Chimeras with Enhanced Infectivity Reveal a Core Element in the AAV Genome Critical for both Cell Transduction and Capsid Assembly. J Virol 2021; 95:JVI.02023-20. [PMID: 33441336 PMCID: PMC8092683 DOI: 10.1128/jvi.02023-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Adeno-associated viruses (AAV) have attracted significant attention in the field of gene and cell therapy due to highly effective delivery of therapeutic genes into human cells. The ability to generate recombinant AAV vectors compromised of unique or substituted protein sequences has led to the development of capsid variants with improved therapeutic properties. Seeking novel AAV vectors capable of enhanced transduction for therapeutic applications, we have developed a series of unique capsid variants termed AAV X-Vivo (AAV-XV) derived from chimeras of AAV12 VP1/2 sequences and the VP3 sequence of AAV6. These AAV variants showed enhanced infection of human primary T cells, hematopoietic stem cells, and neuronal cell lines over wildtype parental viruses, and superiority over AAV6 for genomic integration of DNA sequences by AAV alone or in combination with CRISPR gene editing. AAV-XV variants demonstrate transduction efficiency equivalent to AAV6 at multiplicities of infection 2 logs lower, enabling T cell engineering at low AAV doses. The protein coding sequence of these novel AAV chimeras revealed disruptions within the assembly-activating protein (AAP) which likely accounted for observed lower virus yield. A series of genome alterations, reverting the AAP sequence back to wildtype AAV6, had a negative impact on the enhanced transduction seen with AAV-VX, indicating overlapping functions within this sequence for both viral assembly and effective T cell transduction. Our findings show these AAV-XV variants are highly efficient at cell transduction at low dose and demonstrates the importance of the AAP coding region in both viral particle assembly and cell infection.IMPORTANCE A major hurdle to the therapeutic potential of AAV in gene therapy lies in achieving clinically meaningful AAV doses, and secondarily, ability to manufacture commercially viable titers of AAV to support this. By virtue of neutralizing antibodies against AAV that impede patient repeat-dosing, the dose of AAV for in vivo gene delivery has been high, which has resulted in unfortunate recent safety concerns and deaths in patients given higher-dose AAV gene therapy. We have generated new AAV variants possessing unique combinations of capsid proteins for gene and cell therapy applications termed AAV-XV, which have high levels of cell transduction and gene delivery at lower MOI. Furthermore, we demonstrate a novel finding, and an important consideration for recombinant AAV design, that a region of the AAV genome encoding the capsid viral protein and AAP is critical for both virus yield and the enhancement of infection/transduction.
Collapse
|
30
|
He X, Kim JS, Diaz-Martinez LA, Han C, Lane WS, Budnik B, Waldman T. USP13 interacts with cohesin and regulates its ubiquitination in human cells. J Biol Chem 2021; 296:100194. [PMID: 33334891 PMCID: PMC7948425 DOI: 10.1074/jbc.ra120.015762] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 01/26/2023] Open
Abstract
Cohesin is a multiprotein ring complex that regulates 3D genome organization, sister chromatid cohesion, gene expression, and DNA repair. Cohesin is known to be ubiquitinated, although the mechanism, regulation, and effects of cohesin ubiquitination remain poorly defined. We previously used gene editing to introduce a dual epitope tag into the endogenous allele of each of 11 known components of cohesin in human HCT116 cells. Here we report that mass spectrometry analysis of dual-affinity purifications identified the USP13 deubiquitinase as a novel cohesin-interacting protein. Subsequent immunoprecipitation/Western blots confirmed the endogenous interaction in HCT116, 293T, HeLa, and RPE-hTERT cells; demonstrated that the interaction occurs specifically in the soluble nuclear fraction (not in the chromatin); requires the ubiquitin-binding domains (UBA1/2) of USP13; and occurs preferentially during DNA replication. Reciprocal dual-affinity purification of endogenous USP13 followed by mass spectrometry demonstrated that cohesin is its primary interactor in the nucleus. Ectopic expression and CRISPR knockout of USP13 showed that USP13 is paradoxically required for both deubiquitination and ubiquitination of cohesin subunits in human cells. USP13 was dispensable for sister chromatid cohesion in HCT116 and HeLa cells, whereas it was required for the dissociation of cohesin from chromatin as cells transit through mitosis. Together these results identify USP13 as a new cohesin-interacting protein that regulates the ubiquitination of cohesin and its cell cycle regulated interaction with chromatin.
Collapse
Affiliation(s)
- Xiaoyuan He
- Departments of Oncology, Biochemistry & Molecular Biology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia, USA
| | - Jung-Sik Kim
- Departments of Oncology, Biochemistry & Molecular Biology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia, USA
| | | | - Cecil Han
- Departments of Oncology, Biochemistry & Molecular Biology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia, USA
| | - William S Lane
- Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts, USA
| | - Bogdan Budnik
- Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts, USA
| | - Todd Waldman
- Departments of Oncology, Biochemistry & Molecular Biology, Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, District of Columbia, USA.
| |
Collapse
|
31
|
Chen S, Sun S, Moonen D, Lee C, Lee AYF, Schaffer DV, He L. CRISPR-READI: Efficient Generation of Knockin Mice by CRISPR RNP Electroporation and AAV Donor Infection. Cell Rep 2020; 27:3780-3789.e4. [PMID: 31242412 DOI: 10.1016/j.celrep.2019.05.103] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 04/01/2019] [Accepted: 05/29/2019] [Indexed: 01/08/2023] Open
Abstract
Genetically engineered mouse models harboring large sequence insertions or modifications are critical for a wide range of applications including endogenous gene tagging, conditional knockout, site-specific transgene insertion, and gene replacement; however, existing methods to generate such animals remain laborious and costly. To address this, we developed an approach called CRISPR-READI (CRISPR RNP electroporation and AAV donor infection), combining adeno-associated virus (AAV)-mediated HDR donor delivery with Cas9/sgRNA RNP electroporation to engineer large site-specific modifications in the mouse genome with high efficiency and throughput. We successfully targeted a 774 bp fluorescent reporter, a 2.1 kb CreERT2 driver, and a 3.3 kb expression cassette into endogenous loci in both embryos and live mice. CRISPR-READI is applicable to most widely used knockin schemes requiring donor lengths within the 4.9 kb AAV packaging capacity. Altogether, CRISPR-READI is an efficient, high-throughput, microinjection-free approach for sophisticated mouse genome engineering with potential applications in other mammalian species.
Collapse
Affiliation(s)
- Sean Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Sabrina Sun
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Dewi Moonen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Clancy Lee
- Department of Environmental Science and Policy Management, University of California, Berkeley, Berkeley, CA, USA
| | - Angus Yiu-Fai Lee
- Cancer Research Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - David V Schaffer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; The Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Lin He
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
| |
Collapse
|
32
|
Engineering monocyte/macrophage-specific glucocerebrosidase expression in human hematopoietic stem cells using genome editing. Nat Commun 2020; 11:3327. [PMID: 32620863 PMCID: PMC7335164 DOI: 10.1038/s41467-020-17148-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 06/10/2020] [Indexed: 02/06/2023] Open
Abstract
Gaucher disease is a lysosomal storage disorder caused by insufficient glucocerebrosidase activity. Its hallmark manifestations are attributed to infiltration and inflammation by macrophages. Current therapies for Gaucher disease include life-long intravenous administration of recombinant glucocerebrosidase and orally-available glucosylceramide synthase inhibitors. An alternative approach is to engineer the patient's own hematopoietic system to restore glucocerebrosidase expression, thereby replacing the affected cells, and constituting a potential one-time therapy for this disease. Here, we report an efficient CRISPR/Cas9-based approach that targets glucocerebrosidase expression cassettes with a monocyte/macrophage-specific element to the CCR5 safe-harbor locus in human hematopoietic stem and progenitor cells. The targeted cells generate glucocerebrosidase-expressing macrophages and maintain long-term repopulation and multi-lineage differentiation potential with serial transplantation. The combination of a safe-harbor and a lineage-specific promoter establishes a universal correction strategy and circumvents potential toxicity of ectopic glucocerebrosidase in the stem cells. Furthermore, it constitutes an adaptable platform for other lysosomal enzyme deficiencies.
Collapse
|
33
|
Larsson C, Cordeddu L, Siggens L, Pandzic T, Kundu S, He L, Ali MA, Pristovšek N, Hartman K, Ekwall K, Sjöblom T. Restoration of KMT2C/MLL3 in human colorectal cancer cells reinforces genome-wide H3K4me1 profiles and influences cell growth and gene expression. Clin Epigenetics 2020; 12:74. [PMID: 32471474 PMCID: PMC7257146 DOI: 10.1186/s13148-020-00863-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 05/14/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The histone 3 lysine 4 (H3K4) monomethylase KMT2C is mutated across several cancer types; however, the effects of mutations on epigenome organization, gene expression, and cell growth are not clear. A frequently recurring mutation in colorectal cancer (CRC) with microsatellite instability is a single nucleotide deletion within the exon 38 poly-A(9) repeat (c.8390delA) which results in frameshift preceding the functional carboxy-terminal SET domain. To study effects of KMT2C expression in CRC cells, we restored one allele to wild type KMT2C in the two CRC cell lines RKO and HCT116, which both are homozygous c.8390delA mutant. RESULTS Gene editing resulted in increased KMT2C expression, increased H3K4me1 levels, altered gene expression profiles, and subtle negative effects on cell growth, where higher dependence and stronger effects of KMT2C expression were observed in RKO compared to HCT116 cells. Surprisingly, we found that the two RKO and HCT116 CRC cell lines have distinct baseline H3K4me1 epigenomic profiles. In RKO cells, a flatter genome-wide H3K4me1 profile was associated with more increased H3K4me1 deposition at enhancers, reduced cell growth, and more differential gene expression relative to HCT116 cells when KMT2C was restored. Profiling of H3K4me1 did not indicate a highly specific regulation of gene expression as KMT2C-induced H3K4me1 deposition was found globally and not at a specific enhancer sub-set in the engineered cells. Although we observed variation in differentially regulated gene sets between cell lines and individual clones, differentially expressed genes in both cell lines included genes linked to known cancer signaling pathways, estrogen response, hypoxia response, and aspects of immune system regulation. CONCLUSIONS Here, KMT2C restoration reduced CRC cell growth and reinforced genome-wide H3K4me1 deposition at enhancers; however, the effects varied depending upon the H3K4me1 status of KMT2C deficient cells. Results indicate that KMT2C inactivation may promote colorectal cancer development through transcriptional dysregulation in several pathways with known cancer relevance.
Collapse
Affiliation(s)
- Chatarina Larsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden
| | - Lina Cordeddu
- Department of Biosciences and Nutrition, NEO, Karolinska Institute, SE-141 83, Huddinge, Sweden
| | - Lee Siggens
- Department of Biosciences and Nutrition, NEO, Karolinska Institute, SE-141 83, Huddinge, Sweden
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden
| | - Snehangshu Kundu
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden
| | - Liqun He
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden
| | - Muhammad Akhtar Ali
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden.,Present address: School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Nuša Pristovšek
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden.,Present address: The Novo Nordisk Foundation for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Karin Hartman
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden
| | - Karl Ekwall
- Department of Biosciences and Nutrition, NEO, Karolinska Institute, SE-141 83, Huddinge, Sweden
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden.
| |
Collapse
|
34
|
Snyder AG, Hubbard NW, Messmer MN, Kofman SB, Hagan CE, Orozco SL, Chiang K, Daniels BP, Baker D, Oberst A. Intratumoral activation of the necroptotic pathway components RIPK1 and RIPK3 potentiates antitumor immunity. Sci Immunol 2020; 4:4/36/eaaw2004. [PMID: 31227597 DOI: 10.1126/sciimmunol.aaw2004] [Citation(s) in RCA: 233] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 04/24/2019] [Indexed: 12/13/2022]
Abstract
Although the signaling events that induce different forms of programmed cell death are well defined, the subsequent immune responses to dying cells in the context of cancer remain relatively unexplored. Necroptosis occurs downstream of the receptor-interacting protein kinases RIPK1 and RIPK3, whose activation leads to lytic cell death accompanied by de novo production of proinflammatory mediators. Here, we show that ectopic introduction of necroptotic cells to the tumor microenvironment promotes BATF3+ cDC1- and CD8+ leukocyte-dependent antitumor immunity accompanied by increased tumor antigen loading by tumor-associated antigen-presenting cells. Furthermore, we report the development of constitutively active forms of the necroptosis-inducing enzyme RIPK3 and show that delivery of a gene encoding this enzyme to tumor cells using adeno-associated viruses induces tumor cell necroptosis, which synergizes with immune checkpoint blockade to promote durable tumor clearance. These findings support a role for RIPK1/RIPK3 activation as a beneficial proximal target in the initiation of tumor immunity. Considering that successful tumor immunotherapy regimens will require the rational application of multiple treatment modalities, we propose that maximizing the immunogenicity of dying cells within the tumor microenvironment through specific activation of the necroptotic pathway represents a beneficial treatment approach that may warrant further clinical development.
Collapse
Affiliation(s)
- Annelise G Snyder
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Nicholas W Hubbard
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Michelle N Messmer
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Sigal B Kofman
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Cassidy E Hagan
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Susana L Orozco
- Department of Immunology, University of Washington, Seattle, WA 98109, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98109, USA
| | - Kristy Chiang
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98109, USA
| | - Brian P Daniels
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA 98109, USA
| | - Andrew Oberst
- Department of Immunology, University of Washington, Seattle, WA 98109, USA.
| |
Collapse
|
35
|
Cabanes-Creus M, Westhaus A, Navarro RG, Baltazar G, Zhu E, Amaya AK, Liao SHY, Scott S, Sallard E, Dilworth KL, Rybicki A, Drouyer M, Hallwirth CV, Bennett A, Santilli G, Thrasher AJ, Agbandje-McKenna M, Alexander IE, Lisowski L. Attenuation of Heparan Sulfate Proteoglycan Binding Enhances In Vivo Transduction of Human Primary Hepatocytes with AAV2. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 17:1139-1154. [PMID: 32490035 PMCID: PMC7260615 DOI: 10.1016/j.omtm.2020.05.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/07/2020] [Indexed: 12/19/2022]
Abstract
Use of the prototypical adeno-associated virus type 2 (AAV2) capsid delivered unexpectedly modest efficacy in an early liver-targeted gene therapy trial for hemophilia B. This result is consistent with subsequent data generated in chimeric mouse-human livers showing that the AAV2 capsid transduces primary human hepatocytes in vivo with low efficiency. In contrast, novel variants generated by directed evolution in the same model, such as AAV-NP59, transduce primary human hepatocytes with high efficiency. While these empirical data have immense translational implications, the mechanisms underpinning this enhanced AAV capsid transduction performance in primary human hepatocytes are yet to be fully elucidated. Remarkably, AAV-NP59 differs from the prototypical AAV2 capsid by only 11 aa and can serve as a tool to study the correlation between capsid sequence/structure and vector function. Using two orthogonal vectorological approaches, we have determined that just 2 of the 11 changes present in AAV-NP59 (T503A and N596D) account for the enhanced transduction performance of this capsid variant in primary human hepatocytes in vivo, an effect that we have associated with attenuation of heparan sulfate proteoglycan (HSPG) binding affinity. In support of this hypothesis, we have identified, using directed evolution, two additional single amino acid substitution AAV2 variants, N496D and N582S, which are highly functional in vivo. Both substitution mutations reduce AAV2's affinity for HSPG. Finally, we have modulated the ability of AAV8, a highly murine-hepatotropic serotype, to interact with HSPG. The results support our hypothesis that enhanced HSPG binding can negatively affect the in vivo function of otherwise strongly hepatotropic variants and that modulation of the interaction with HSPG is critical to ensure maximum efficiency in vivo. The insights gained through this study can have powerful implications for studies into AAV biology and capsid development for preclinical and clinical applications targeting liver and other organs.
Collapse
Affiliation(s)
- Marti Cabanes-Creus
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Adrian Westhaus
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia.,Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Renina Gale Navarro
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Grober Baltazar
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Erhua Zhu
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia.,Gene Therapy Research Unit, Children's Medical Research Institute & The Children's Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia
| | - Anais K Amaya
- Gene Therapy Research Unit, Children's Medical Research Institute & The Children's Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia
| | - Sophia H Y Liao
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Suzanne Scott
- Gene Therapy Research Unit, Children's Medical Research Institute & The Children's Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia.,Commonwealth Scientific and Industrial Research Organisation (CSIRO), North Ryde, NSW 2113, Australia
| | - Erwan Sallard
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Kimberley L Dilworth
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Arkadiusz Rybicki
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Matthieu Drouyer
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute & The Children's Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia
| | - Antonette Bennett
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Giorgia Santilli
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Adrian J Thrasher
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, Center for Structural Biology, University of Florida, Gainesville, FL 32610, USA
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute & The Children's Hospital at Westmead, University of Sydney, Westmead, NSW 2145, Australia.,Discipline of Child and Adolescent Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia.,Vector and Genome Engineering Facility, Children's Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia.,Military Institute of Hygiene and Epidemiology, Biological Threats Identification and Countermeasure Center, 24-100 Puławy, Poland
| |
Collapse
|
36
|
Maurer AC, Weitzman MD. Adeno-Associated Virus Genome Interactions Important for Vector Production and Transduction. Hum Gene Ther 2020; 31:499-511. [PMID: 32303138 PMCID: PMC7232694 DOI: 10.1089/hum.2020.069] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022] Open
Abstract
Recombinant adeno-associated virus has emerged as one of the most promising gene therapy delivery vectors. Development of these vectors took advantage of key features of the wild-type adeno-associated virus (AAV), enabled by basic studies of the underlying biology and requirements for transcription, replication, and packaging of the viral genome. Each step in generating and utilizing viral vectors involves numerous molecular interactions that together determine the efficiency of vector production and gene delivery. Once delivered into the cell, interactions with host proteins will determine the fate of the viral genome, and these will impact the intended goal of gene delivery. Here, we provide an overview of known interactions of the AAV genome with viral and cellular proteins involved in its amplification, packaging, and expression. Further appreciation of how the AAV genome interacts with host factors will enhance how this simple virus can be harnessed for an array of vector purposes that benefit human health.
Collapse
Affiliation(s)
- Anna C. Maurer
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Matthew D. Weitzman
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| |
Collapse
|
37
|
Zhou Y, Deng J, Chu X, Zhao Y, Guo Y. Role of Post-Transcriptional Control of Calpain by miR-124-3p in the Development of Alzheimer's Disease. J Alzheimers Dis 2020; 67:571-581. [PMID: 30584150 DOI: 10.3233/jad-181053] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease prevalent in aged people, clinically characterized by progressive memory loss, behavioral and learning dysfunction, and cognitive deficits. The pathogenesis of AD is hallmarked by formation of amyloid-β peptide aggregates (Aβ) and intraneuronal neurofibrillary tangles (NFTs), which are induced by hyperphosphorylation of amyloid-β protein precursor and tau protein, respectively. The hyperphosphorylation is controlled by cyclin-dependent kinase-5 (CDK5), the aberrant activation of which is mediated by calpain (CAPN)-induced cleavage of p35 into p25. However, the regulation of CAPN in AD remains largely unknown. Here, we studied the post-transcriptional control of CAPN1 by microRNAs (miRNAs) in the setting of AD. We found that miR-124-3p, previously reported as a miRNA that was downregulated in AD, was a CAPN1-targeting miRNA that functionally inhibited the protein translation of CAPN1 in a human neural cell line, HCN-2. In vitro, transfection with miR-124-3p reduced the levels of CAPN1 protein, the cleavage of p35 into p25, and cell apoptosis dose-dependently in HCN-2 cells. Moreover, a significant inverse correlation was detected between the levels of miR-124-3p and CAPN1 in AD specimens. Furthermore, intracranial injection of adeno-associated virus expressing miR-124-3p into APP/PS1-AD mice significantly reduced Aβ deposition and significantly improved the AD-mouse behavior in the social recognition test and plus-maze discriminative avoidance task. Together, our data suggest that post-transcriptional control of calpain by miR-124-3p plays an essential role in the development of AD.
Collapse
Affiliation(s)
- Yajun Zhou
- Department of Neurology, Shanghai Jiao Tong University affiliated Sixth People's Hospital, Shanghai, China
| | - Jiangshan Deng
- Department of Neurology, Shanghai Jiao Tong University affiliated Sixth People's Hospital, Shanghai, China
| | - Xiuli Chu
- Department of Neurology, Shanghai Jiao Tong University affiliated Sixth People's Hospital, Shanghai, China
| | - Yuwu Zhao
- Department of Neurology, Shanghai Jiao Tong University affiliated Sixth People's Hospital, Shanghai, China
| | - Yong Guo
- Department of Critical Care Medicine, Shanghai Jiao Tong University affiliated Sixth People's Hospital, Shanghai, China
| |
Collapse
|
38
|
RAD52: Viral Friend or Foe? Cancers (Basel) 2020; 12:cancers12020399. [PMID: 32046320 PMCID: PMC7072633 DOI: 10.3390/cancers12020399] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/06/2020] [Accepted: 02/06/2020] [Indexed: 02/06/2023] Open
Abstract
Mammalian Radiation Sensitive 52 (RAD52) is a gene whose scientific reputation has recently seen a strong resurgence. In the past decade, RAD52, which was thought to be dispensable for most DNA repair and recombination reactions in mammals, has been shown to be important for a bevy of DNA metabolic pathways. One of these processes is termed break-induced replication (BIR), a mechanism that can be used to re-start broken replication forks and to elongate the ends of chromosomes in telomerase-negative cells. Viruses have historically evolved a myriad of mechanisms in which they either conscript cellular factors or, more frequently, inactivate them as a means to enable their own replication and survival. Recent data suggests that Adeno-Associated Virus (AAV) may replicate its DNA in a BIR-like fashion and/or utilize RAD52 to facilitate viral transduction and, as such, likely conscripts/requires the host RAD52 protein to promote its perpetuation.
Collapse
|
39
|
Zhao X, Jin Y, Li H, Jia Y, Wang Y. Sevoflurane impairs learning and memory of the developing brain through post-transcriptional inhibition of CCNA2 via microRNA-19-3p. Aging (Albany NY) 2019; 10:3794-3805. [PMID: 30540563 PMCID: PMC6326694 DOI: 10.18632/aging.101673] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/15/2018] [Indexed: 12/04/2022]
Abstract
The molecular mechanisms underlying sevoflurane (SEVO)-induced impairment of learning and memory remain unclear. Specifically, a role of microRNAs (miRNAs) in the control of the neuron proliferation in the developing brain exposed to SEVO has not been reported previously. Here, we studied the effects of SEVO exposure on the neural cell proliferation, and on the learning and memory of neonatal rats. We found that SEVO exposure significantly decreased neuron cell proliferation, reduced BDNF levels in brain, and impaired learning and memory of neonatal rats in Morris water maze test and Plus-Maze discriminative avoidance task (PM-DAT), likely through downregulation of CCNA2 protein. Next, we used bioinformatic tools to predict CCNA2-binding microRNAs (miRNAs), and found that miR-19-3p was upregulated in neurons exposed to SEVO. Moreover, miR-19-3p functionally inhibited the protein translation of CCNA2 in a human neural cell line, HCN-2. Furthermore, intracranial injection of adeno-associated virus carrying antisense of miR-19-3p under a CMV promoter into the neonatal rats significantly alleviated SEVO exposure-induced impairment of neuron cell proliferation, as well as the learning and memory of the rats. Together, our data suggest that SEVO-induced upregulation of miR-19-3p post-transcriptionally inhibits CCNA2, which contributes to the SEVO-associated impairment of learning and memory of the neonatal rats.
Collapse
Affiliation(s)
- Xin Zhao
- Department of Anesthesiology, the Second Hospital of Shandong University, Jinan 250033, China
| | - Yanwu Jin
- Department of Anesthesiology, the Second Hospital of Shandong University, Jinan 250033, China
| | - Haibo Li
- Operating Room, Jinan Central Hospital, Affiliated to Shandong University, Jinan 250013, China
| | - Yuxiu Jia
- Department of Research, the Second Hospital of Shandong University, Jinan 250033, China
| | - Yuelan Wang
- Department of Anesthesiology, Qianfoshan Hospital of Shandong Province, Affiliated to Shandong University, Jinan 250014, China
| |
Collapse
|
40
|
Anderson W, Thorpe J, Long SA, Rawlings DJ. Efficient CRISPR/Cas9 Disruption of Autoimmune-Associated Genes Reveals Key Signaling Programs in Primary Human T Cells. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 203:3166-3178. [PMID: 31722988 PMCID: PMC6904544 DOI: 10.4049/jimmunol.1900848] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/10/2019] [Indexed: 12/18/2022]
Abstract
Risk of autoimmunity is associated with multiple genetic variants. Genome-wide association studies have linked single-nucleotide polymorphisms in the phosphatases PTPN22 (rs2476601) and PTPN2 (rs1893217) to increased risk for multiple autoimmune diseases. Previous mouse studies of loss of function or risk variants in these genes revealed hyperactive T cell responses, whereas studies of human lymphocytes revealed contrasting phenotypes. To better understand this dichotomy, we established a robust gene editing platform to rapidly address the consequences of loss of function of candidate genes in primary human CD4+ T cells. Using CRISPR/Cas9, we obtained efficient gene disruption (>80%) of target genes encoding proteins involved in Ag and cytokine receptor signaling pathways including PTPN22 and PTPN2 Loss-of-function data in all genes studied correlated with previous data from mouse models. Further analyses of PTPN2 gene-disrupted T cells demonstrated dynamic effects, by which hyperactive IL-2R signaling promoted compensatory transcriptional events, eventually resulting in T cells that were hyporesponsive to IL-2. These results imply that altered phosphatase activity promotes evolving phenotypes based on Ag experience and/or other programming signals. This approach enables the discovery of molecular mechanisms modulating risk of autoimmunity that have been difficult to parse in traditional mouse models or cross-sectional human studies.
Collapse
Affiliation(s)
- Warren Anderson
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101
- Department of Pathology, University of Washington, Seattle, WA 98195
| | - Jerill Thorpe
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - S Alice Long
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - David J Rawlings
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101;
- Department of Pediatrics, University of Washington, Seattle, WA 98109; and
- Department of Immunology, University of Washington, Seattle, WA 98109
| |
Collapse
|
41
|
Chatterjee S. Efficient Nuclease-free HR by Clade F AAV Requires High MOIs with High Quality Vectors. Mol Ther 2019; 27:2058-2061. [PMID: 31735603 DOI: 10.1016/j.ymthe.2019.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Saswati Chatterjee
- Department of Surgery, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
| |
Collapse
|
42
|
Ruis B, Molan A, Takasugi T, Hendrickson EA. Absence of XRCC4 and its paralogs in human cells reveal differences in outcomes for DNA repair and V(D)J recombination. DNA Repair (Amst) 2019; 85:102738. [PMID: 31731258 DOI: 10.1016/j.dnarep.2019.102738] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 02/06/2023]
Abstract
The repair of DNA double-stranded breaks (DSBs) is an essential function performed by the Classical Non-Homologous End-Joining (C-NHEJ) pathway in higher eukaryotes. C-NHEJ, in fact, does double duty as it is also required for the repair of the intermediates formed during lymphoid B- and T-cell recombination. Consequently, the failure to properly repair DSBs leads to both genomic instability and immunodeficiency. A critical DSB protein required for C-NHEJ is the DNA Ligase IV (LIGIV) accessory factor, X-Ray Cross Complementing 4 (XRCC4). XRCC4 is believed to stabilize LIGIV, participate in LIGIV activation, and to help tether the broken DSB ends together. XRCC4's role in these processes has been muddied by the identification of two additional XRCC4 paralogs, XRCC4-Like Factor (XLF), and Paralog of XRCC4 and XLF (PAXX). The roles that these paralogs play in C-NHEJ is partially understood, but, in turn, has itself been obscured by species-specific differences observed in the absence of one or the other paralogs. In order to investigate the role(s) that XRCC4 may play, with or without XLF and/or PAXX, in lymphoid variable(diversity)joining [V(D)J] recombination as well as in DNA DSB repair in human somatic cells, we utilized gene targeting to inactivate the XRCC4 gene in both parental and XLF- HCT116 cells and then inactivated PAXX in those same cell lines. The loss of XRCC4 expression by itself led, as anticipated, to increased sensitivity to DNA damaging agents as well as an increased dependence on microhomology-mediated DNA repair whether in the context of DSB repair or during V(D)J recombination. The additional loss of XLF in these cell lines sensitized the cells even more whereas the presence or absence of PAXX was scarcely negligible. These studies demonstrate that, of the three LIG4 accessory factor paralogs, the absence of XRCC4 influences DNA repair and recombination the most in human cells.
Collapse
Affiliation(s)
- Brian Ruis
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States
| | - Amy Molan
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States
| | - Taylor Takasugi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, MN, 55455, United States.
| |
Collapse
|
43
|
Pattabhi S, Lotti SN, Berger MP, Singh S, Lux CT, Jacoby K, Lee C, Negre O, Scharenberg AM, Rawlings DJ. In Vivo Outcome of Homology-Directed Repair at the HBB Gene in HSC Using Alternative Donor Template Delivery Methods. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 17:277-288. [PMID: 31279229 PMCID: PMC6611979 DOI: 10.1016/j.omtn.2019.05.025] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 12/22/2022]
Abstract
Gene editing following designer nuclease cleavage in the presence of a DNA donor template can revert mutations in disease-causing genes. For optimal benefit, reversion of the point mutation in HBB leading to sickle cell disease (SCD) would permit precise homology-directed repair (HDR) while concurrently limiting on-target non-homologous end joining (NHEJ)-based HBB disruption. In this study, we directly compared the relative efficiency of co-delivery of a novel CRISPR/Cas9 ribonucleoprotein targeting HBB in association with recombinant adeno-associated virus 6 (rAAV6) versus single-stranded oligodeoxynucleotides (ssODNs) to introduce the sickle mutation (GTC or GTG; encoding E6V) or a silent change (GAA; encoding E6optE) in human CD34+ mobilized peripheral blood stem cells (mPBSCs) derived from healthy donors. In vitro, rAAV6 outperformed ssODN donor template delivery and mediated greater HDR correction, leading to both higher HDR rates and a higher HDR:NHEJ ratio. In contrast, at 12-14 weeks post-transplant into recipient, immunodeficient, NOD, B6, SCID Il2rγ-/- Kit(W41/W41) (NBSGW) mice, a ∼6-fold higher proportion of ssODN-modified cells persisted in vivo compared to recipients of rAAV6-modified mPBSCs. Together, our findings highlight that methodology for donor template delivery markedly impacts long-term persistence of HBB gene-modified mPBSCs, and they suggest that the ssODN platform is likely to be most amenable to direct clinical translation.
Collapse
Affiliation(s)
- Sowmya Pattabhi
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Samantha N Lotti
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Mason P Berger
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Swati Singh
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Christopher T Lux
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | - Kyle Jacoby
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA
| | | | | | - Andrew M Scharenberg
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Casebia Therapeutics, Cambridge, MA, USA; Department of Pediatrics, University of Washington, School of Medicine, Seattle, WA, USA; Department of Immunology, University of Washington, School of Medicine, Seattle, WA, USA
| | - David J Rawlings
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington, School of Medicine, Seattle, WA, USA; Department of Immunology, University of Washington, School of Medicine, Seattle, WA, USA.
| |
Collapse
|
44
|
Gomez-Ospina N, Scharenberg SG, Mostrel N, Bak RO, Mantri S, Quadros RM, Gurumurthy CB, Lee C, Bao G, Suarez CJ, Khan S, Sawamoto K, Tomatsu S, Raj N, Attardi LD, Aurelian L, Porteus MH. Human genome-edited hematopoietic stem cells phenotypically correct Mucopolysaccharidosis type I. Nat Commun 2019; 10:4045. [PMID: 31492863 PMCID: PMC6731271 DOI: 10.1038/s41467-019-11962-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/09/2019] [Indexed: 12/26/2022] Open
Abstract
Lysosomal enzyme deficiencies comprise a large group of genetic disorders that generally lack effective treatments. A potential treatment approach is to engineer the patient’s own hematopoietic system to express high levels of the deficient enzyme, thereby correcting the biochemical defect and halting disease progression. Here, we present an efficient ex vivo genome editing approach using CRISPR-Cas9 that targets the lysosomal enzyme iduronidase to the CCR5 safe harbor locus in human CD34+ hematopoietic stem and progenitor cells. The modified cells secrete supra-endogenous enzyme levels, maintain long-term repopulation and multi-lineage differentiation potential, and can improve biochemical and phenotypic abnormalities in an immunocompromised mouse model of Mucopolysaccharidosis type I. These studies provide support for the development of genome-edited CD34+ hematopoietic stem and progenitor cells as a potential treatment for Mucopolysaccharidosis type I. The safe harbor approach constitutes a flexible platform for the expression of lysosomal enzymes making it applicable to other lysosomal storage disorders. Mucopolysaccharidosis type I (MPSI) is a lysosomal storage disease caused by insufficient iduronidase (IDUA) activity. Here, the authors use an ex vivo genome editing approach to overexpress IDUA in human hematopoietic stem and progenitor cells and show it can phenotypically correct MSPI in mouse model.
Collapse
Affiliation(s)
- Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| | | | - Nathalie Mostrel
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C., Denmark.,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, DK-8000, Aarhus C., Denmark
| | - Sruthi Mantri
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ciaran Lee
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Carlos J Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shaukat Khan
- Nemours/ Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA
| | - Kazuki Sawamoto
- Nemours/ Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA
| | - Shunji Tomatsu
- Nemours/ Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA
| | - Nitin Raj
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Laura D Attardi
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Laure Aurelian
- Stanford University School of Medicine, Stanford, CA, 94305, USA.,University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
45
|
CRISPR-Cas9 fusion to dominant-negative 53BP1 enhances HDR and inhibits NHEJ specifically at Cas9 target sites. Nat Commun 2019; 10:2866. [PMID: 31253785 PMCID: PMC6598984 DOI: 10.1038/s41467-019-10735-7] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/29/2019] [Indexed: 12/22/2022] Open
Abstract
Precise genome editing/correction of DNA double-strand breaks (DSBs) induced by CRISPR-Cas9 by homology-dependent repair (HDR) is limited by the competing error-prone non-homologous end-joining (NHEJ) DNA repair pathway. Here, we define a safer and efficient system that promotes HDR-based precise genome editing, while reducing NHEJ locally, only at CRISPR-Cas9-induced DSBs. We fused a dominant-negative mutant of 53BP1, DN1S, to Cas9 nucleases, and the resulting Cas9-DN1S fusion proteins significantly block NHEJ events specifically at Cas9 cut sites and improve HDR frequency; HDR frequency reached 86% in K562 cells. Cas9-DN1S protein maintains this effect in different human cell types, including leukocyte adhesion deficiency (LAD) patient-derived immortalized B lymphocytes, where nearly 70% of alleles were repaired by HDR and 7% by NHEJ. Our CRISPR-Cas9-DN1S system is clinically relevant to improve the efficiencies of precise gene correction/insertion, significantly reducing error-prone NHEJ events at the nuclease cleavage site, while avoiding the unwanted effects of global NHEJ inhibition. Global inhibition of NHEJ factors has been one strategy to improve CRISPR-Cas9 mediated HDR. Here the authors fuse a dominant-negative mutant of 53BP1 to Cas9 to enhance HDR frequency, reduce NHEJ specifically at the Cas9 cut sites, and reduce the toxicity associated with global NHEJ inhibition.
Collapse
|
46
|
Marro SG, Chanda S, Yang N, Janas JA, Valperga G, Trotter J, Zhou B, Merrill S, Yousif I, Shelby H, Vogel H, Kalani MYS, Südhof TC, Wernig M. Neuroligin-4 Regulates Excitatory Synaptic Transmission in Human Neurons. Neuron 2019; 103:617-626.e6. [PMID: 31257103 DOI: 10.1016/j.neuron.2019.05.043] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 04/17/2019] [Accepted: 05/28/2019] [Indexed: 12/26/2022]
Abstract
The autism-associated synaptic-adhesion gene Neuroligin-4 (NLGN4) is poorly conserved evolutionarily, limiting conclusions from Nlgn4 mouse models for human cells. Here, we show that the cellular and subcellular expression of human and murine Neuroligin-4 differ, with human Neuroligin-4 primarily expressed in cerebral cortex and localized to excitatory synapses. Overexpression of NLGN4 in human embryonic stem cell-derived neurons resulted in an increase in excitatory synapse numbers but a remarkable decrease in synaptic strength. Human neurons carrying the syndromic autism mutation NLGN4-R704C also formed more excitatory synapses but with increased functional synaptic transmission due to a postsynaptic mechanism, while genetic loss of NLGN4 did not significantly affect synapses in the human neurons analyzed. Thus, the NLGN4-R704C mutation represents a change-of-function mutation. Our work reveals contrasting roles of NLGN4 in human and mouse neurons, suggesting that human evolution has impacted even fundamental cell biological processes generally assumed to be highly conserved.
Collapse
Affiliation(s)
- Samuele G Marro
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Soham Chanda
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nan Yang
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Justyna A Janas
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Giulio Valperga
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Justin Trotter
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bo Zhou
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sean Merrill
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Issa Yousif
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hannah Shelby
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hannes Vogel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - M Yashar S Kalani
- Departments of Neurosurgery and Neuroscience, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Marius Wernig
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
47
|
Kim JS, He X, Liu J, Duan Z, Kim T, Gerard J, Kim B, Pillai MM, Lane WS, Noble WS, Budnik B, Waldman T. Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing factors and RNA-binding proteins required for mitotic progression. J Biol Chem 2019; 294:8760-8772. [PMID: 31010829 PMCID: PMC6552432 DOI: 10.1074/jbc.ra119.007832] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/18/2019] [Indexed: 12/23/2022] Open
Abstract
The cohesin complex regulates sister chromatid cohesion, chromosome organization, gene expression, and DNA repair. Cohesin is a ring complex composed of four core subunits and seven regulatory subunits. In an effort to comprehensively identify additional cohesin-interacting proteins, we used gene editing to introduce a dual epitope tag into the endogenous allele of each of 11 known components of cohesin in cultured human cells, and we performed MS analyses on dual-affinity purifications. In addition to reciprocally identifying all known components of cohesin, we found that cohesin interacts with a panoply of splicing factors and RNA-binding proteins (RBPs). These included diverse components of the U4/U6.U5 tri-small nuclear ribonucleoprotein complex and several splicing factors that are commonly mutated in cancer. The interaction between cohesin and splicing factors/RBPs was RNA- and DNA-independent, occurred in chromatin, was enhanced during mitosis, and required RAD21. Furthermore, cohesin-interacting splicing factors and RBPs followed the cohesin cycle and prophase pathway of cell cycle-regulated interactions with chromatin. Depletion of cohesin-interacting splicing factors and RBPs resulted in aberrant mitotic progression. These results provide a comprehensive view of the endogenous human cohesin interactome and identify splicing factors and RBPs as functionally significant cohesin-interacting proteins.
Collapse
Affiliation(s)
- Jung-Sik Kim
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Xiaoyuan He
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Jie Liu
- the Department of Genome Sciences
| | - Zhijun Duan
- Institute for Stem Cell and Regenerative Medicine, and
- Division of Hematology, University of Washington, Seattle, Washington 98195
| | - Taeyeon Kim
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Julia Gerard
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Brian Kim
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057
| | - Manoj M Pillai
- the Section of Hematology, Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, and
| | - William S Lane
- the Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts 02138
| | | | - Bogdan Budnik
- the Mass Spectrometry and Proteomics Resource Laboratory, Harvard University, Cambridge, Massachusetts 02138
| | - Todd Waldman
- From the Departments of Oncology and Biochemistry & Molecular Biology, Georgetown University School of Medicine, Washington, D. C. 20057,
| |
Collapse
|
48
|
CRISPR/Cas9 applications in gene therapy for primary immunodeficiency diseases. Emerg Top Life Sci 2019; 3:277-287. [PMID: 33523134 DOI: 10.1042/etls20180157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 02/07/2023]
Abstract
Primary immunodeficiency diseases (PIDs) encompass a range of diseases due to mutations in genes that are critical for immunity. Haploinsufficiency and gain-of-function mutations are more complex than simple loss-of-function mutations; in addition to increased susceptibility to infections, immune dysregulations like autoimmunity and hyperinflammation are common presentations. Hematopoietic stem cell (HSC) gene therapy, using integrating vectors, provides potential cure of disease, but genome-wide transgene insertions and the lack of physiological endogenous gene regulation may yet present problems, and not applicable in PIDs where immune regulation is paramount. Targeted genome editing addresses these concerns; we discuss some approaches of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas system applicable for gene therapy in PIDs. Preclinical repair of gene mutations and insertion of complementary DNA restore endogenous gene regulation and they have shown very promising data for clinical application. However, ongoing studies to characterize off-target genotoxicity, careful donor designs to ensure physiological expression, and maneuvers to optimize engraftment potential are critical to ensure successful application of this next-gen targeted HSC gene therapy.
Collapse
|
49
|
Fu J, Bai P, Chen Y, Yu T, Li F. Inhibition of miR-495 Improves Both Vascular Remodeling and Angiogenesis in Pulmonary Hypertension. J Vasc Res 2019; 56:97-106. [PMID: 31030195 DOI: 10.1159/000500024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 03/29/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND AND AIMS Pulmonary hypertension (PH) is a chronic progressing vascular disease characterized by pulmonary arteriole remodeling and loss of pulmonary microvasculature. The aim of this study was to investigate a potential role for the miR-495 in PH pathogenesis and to explore its therapeutic potential in PH. METHODS Male C57BL/6J mice were injected with SU5416 weekly during 3 weeks of exposure to 10% oxygen to cause PH. We first tested the effects of adeno-associated virus 9 (AAV9) delivery which was specifically designed to block miR-495 in the lungs of the PH model. Then, the biological function of miR-495 was analyzed in cultured pulmonary arterial endothelial cells (PAECs) under hypoxic condition. RESULTS The inhibition of miR-495 improves hemodynamics and vascular remodeling in PH. At the same time, these effects were associated with increases in angiogenic transcription factor VEZF1 and marked upregulation of other angiogenic genes such as Angpt-1 and IGF1. In vitro, cultured mouse PAECs were transfected with miR-495 inhibitor or miR-495 mimics. Both the flow cytometry results and CCK8 assay showed that miR-495 inhibitor increased the percentage of cells in the G2/M+S phase, and the wound healing assays indicated that the migration capacity of PAECs transfected with miR-495 inhibitor was increased compared to the inhibitor-NC cells. CONCLUSIONS Our results indicate that AAV9-TuD-miR-495 delivery improves hemodynamic and pulmonary vascular structural changes in PH mice.
Collapse
Affiliation(s)
- Jie Fu
- Department of Cardiology, Shanghai Children's Medical Center Affiliated with Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Peiyuan Bai
- Department of Cardiology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yiwei Chen
- Department of Cardiology, Shanghai Children's Medical Center Affiliated with Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Tingting Yu
- Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Fen Li
- Department of Cardiology, Shanghai Children's Medical Center Affiliated with Shanghai Jiaotong University School of Medicine, Shanghai, China, .,Shanghai Pediatric Congenital Heart Disease Institute, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China,
| |
Collapse
|
50
|
Harvey A, Mielke N, Grimstead JW, Jones RE, Nguyen T, Mueller M, Baird DM, Hendrickson EA. PARP1 is required for preserving telomeric integrity but is dispensable for A-NHEJ. Oncotarget 2018; 9:34821-34837. [PMID: 30410680 PMCID: PMC6205175 DOI: 10.18632/oncotarget.26201] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Accepted: 09/15/2018] [Indexed: 01/07/2023] Open
Abstract
Poly-ADP ribose polymerase 1 (PARP1) is clinically important because of its synthetic lethality with breast cancer allele 1 and 2 mutations, which are causative for inherited breast and ovarian cancers. Biochemically, PARP1 is a single-stranded DNA break repair protein that is needed for preserving genomic integrity. In addition, PARP1 has been implicated in a veritable plethora of additional cellular pathways and thus its precise contribution(s) to human biology has remained obscure. To help address this deficiency, we utilized gene editing to construct genetically-null PARP1 human cancer cells. We found a minor role for PARP1 in an alternative form of DNA double-strand break (DSB) repair, but only when these cells were deficient for the classical form of DSB repair. Despite being proficient for DSB repair, however, cell cycle progression defects and elevated endogenous DNA damage signaling were observed. These deficiencies were instead linked to telomere defects, where PARP1 -/- cells had short telomeres that co-localized with markers of endogenous DNA damage and were compromised in their ability to escape a telomere-driven crisis. Our data suggest that while PARP1 does not participate significantly in DNA DSB repair itself, it does prevent the incidence of telomeric DSBs, which, in turn, can drive genomic instability.
Collapse
Affiliation(s)
- Adam Harvey
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Nicholas Mielke
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Julia W. Grimstead
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Rhiannon E. Jones
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Thanh Nguyen
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Matthew Mueller
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| | - Duncan M. Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Eric A. Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
| |
Collapse
|