1
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Choi DE, Shin JW, Zeng S, Hong EP, Jang JH, Loupe JM, Wheeler VC, Stutzman HE, Kleinstiver B, Lee JM. Base editing strategies to convert CAG to CAA diminish the disease-causing mutation in Huntington's disease. eLife 2024; 12:RP89782. [PMID: 38869243 PMCID: PMC11175616 DOI: 10.7554/elife.89782] [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] [Indexed: 06/14/2024] Open
Abstract
An expanded CAG repeat in the huntingtin gene (HTT) causes Huntington's disease (HD). Since the length of uninterrupted CAG repeat, not polyglutamine, determines the age-at-onset in HD, base editing strategies to convert CAG to CAA are anticipated to delay onset by shortening the uninterrupted CAG repeat. Here, we developed base editing strategies to convert CAG in the repeat to CAA and determined their molecular outcomes and effects on relevant disease phenotypes. Base editing strategies employing combinations of cytosine base editors and guide RNAs (gRNAs) efficiently converted CAG to CAA at various sites in the CAG repeat without generating significant indels, off-target edits, or transcriptome alterations, demonstrating their feasibility and specificity. Candidate BE strategies converted CAG to CAA on both expanded and non-expanded CAG repeats without altering HTT mRNA and protein levels. In addition, somatic CAG repeat expansion, which is the major disease driver in HD, was significantly decreased in the liver by a candidate BE strategy treatment in HD knock-in mice carrying canonical CAG repeats. Notably, CAG repeat expansion was abolished entirely in HD knock-in mice carrying CAA-interrupted repeats, supporting the therapeutic potential of CAG-to-CAA conversion strategies in HD and potentially other repeat expansion disorders.
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Affiliation(s)
- Doo Eun Choi
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Jun Wan Shin
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Sophia Zeng
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
| | - Eun Pyo Hong
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
- Medical and Population Genetics Program, The Broad Institute of MIT and HarvardCambridgeUnited States
| | - Jae-Hyun Jang
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Jacob M Loupe
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Vanessa C Wheeler
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
| | - Hannah E Stutzman
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Pathology, Massachusetts General HospitalBostonUnited States
| | - Ben Kleinstiver
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Pathology, Massachusetts General HospitalBostonUnited States
- Department of Pathology, Harvard Medical SchoolBostonUnited States
| | - Jong-Min Lee
- Center for Genomic Medicine, Massachusetts General HospitalBostonUnited States
- Department of Neurology, Harvard Medical SchoolBostonUnited States
- Medical and Population Genetics Program, The Broad Institute of MIT and HarvardCambridgeUnited States
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2
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Fitzgerald MQ, Chu T, Puppo F, Blanch R, Chillón M, Subramaniam S, Muotri AR. Generation of 'semi-guided' cortical organoids with complex neural oscillations. Nat Protoc 2024:10.1038/s41596-024-00994-0. [PMID: 38702386 DOI: 10.1038/s41596-024-00994-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 02/22/2024] [Indexed: 05/06/2024]
Abstract
Temporal development of neural electrophysiology follows genetic programming, similar to cellular maturation and organization during development. The emergent properties of this electrophysiological development, namely neural oscillations, can be used to characterize brain development. Recently, we utilized the innate programming encoded in the human genome to generate functionally mature cortical organoids. In brief, stem cells are suspended in culture via continuous shaking and naturally aggregate into embryoid bodies before being exposed to media formulations for neural induction, differentiation and maturation. The specific culture format, media composition and duration of exposure to these media distinguish organoid protocols and determine whether a protocol is guided or unguided toward specific neural fate. The 'semi-guided' protocol presented here has shorter induction and differentiation steps with less-specific patterning molecules than most guided protocols but maintains the use of neurotrophic factors such as brain-derived growth factor and neurotrophin-3, unlike unguided approaches. This approach yields the cell type diversity of unguided approaches while maintaining reproducibility for disease modeling. Importantly, we characterized the electrophysiology of these organoids and found that they recapitulate the maturation of neural oscillations observed in the developing human brain, a feature not shown with other approaches. This protocol represents the potential first steps toward bridging molecular and cellular biology to human cognition, and it has already been used to discover underlying features of human brain development, evolution and neurological conditions. Experienced cell culture technicians can expect the protocol to take 1 month, with extended maturation, electrophysiology recording, and adeno-associated virus transduction procedure options.
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Affiliation(s)
- Michael Q Fitzgerald
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
| | - Tiffany Chu
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Francesca Puppo
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
| | - Rebeca Blanch
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA
- Institut de Recerca Vall d'Hebron and Institut de Neurociències, Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Miguel Chillón
- Institut de Recerca Vall d'Hebron and Institut de Neurociències, Biochemistry and Molecular Biology Department, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Shankar Subramaniam
- Department of Bioengineering, University of California San Diego, San Diego, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Alysson R Muotri
- Department of Pediatrics, University of California San Diego, San Diego, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, San Diego, CA, USA.
- Center for Academic Research and Training in Anthropogeny and Archealization, University of California San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Education and Integrated Space Stem Cell Orbital Research Center, Sanford Stem Cell Institute, University of California San Diego, La Jolla, CA, USA.
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3
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Suárez-Herrera N, Riswick IB, Vázquez-Domínguez I, Duijkers L, Karjosukarso DW, Piccolo D, Bauwens M, De Baere E, Cheetham ME, Garanto A, Collin RWJ. Proof-of-concept for multiple AON delivery by a single U7snRNA vector to restore splicing defects in ABCA4. Mol Ther 2024; 32:837-851. [PMID: 38243599 PMCID: PMC10928313 DOI: 10.1016/j.ymthe.2024.01.019] [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: 09/13/2023] [Revised: 12/13/2023] [Accepted: 01/12/2024] [Indexed: 01/21/2024] Open
Abstract
The high allelic heterogeneity in Stargardt disease (STGD1) complicates the design of intervention strategies. A significant proportion of pathogenic intronic ABCA4 variants alters the pre-mRNA splicing process. Antisense oligonucleotides (AONs) are an attractive yet mutation-specific therapeutic strategy to restore these splicing defects. In this study, we experimentally assessed the potential of a splicing modulation therapy to target multiple intronic ABCA4 variants. AONs were inserted into U7snRNA gene cassettes and tested in midigene-based splice assays. Five potent antisense sequences were selected to generate a multiple U7snRNA cassette construct, and this combination vector showed substantial rescue of all of the splicing defects. Therefore, the combination cassette was used for viral synthesis and assessment in patient-derived photoreceptor precursor cells (PPCs). Simultaneous delivery of several modified U7snRNAs through a single AAV, however, did not show substantial splicing correction, probably due to suboptimal transduction efficiency in PPCs and/or a heterogeneous viral population containing incomplete AAV genomes. Overall, these data demonstrate the potential of the U7snRNA system to rescue multiple splicing defects, but also suggest that AAV-associated challenges are still a limiting step, underscoring the need for further optimization before implementing this strategy as a potential treatment for STGD1.
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Affiliation(s)
- Nuria Suárez-Herrera
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands
| | - Iris B Riswick
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands
| | - Irene Vázquez-Domínguez
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands
| | - Lonneke Duijkers
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands
| | - Dyah W Karjosukarso
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands
| | | | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | | | - Alejandro Garanto
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands; Radboud University Medical Center, Amalia Children's Hospital, Department of Pediatrics, Nijmegen 6252GA, the Netherlands
| | - Rob W J Collin
- Radboud University Medical Center, Department of Human Genetics, 6525GA Nijmegen, the Netherlands.
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4
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Gurtsieva D, Minskaia E, Zhuravleva S, Subcheva E, Sakhibgaraeva E, Brovin A, Tumaev A, Karabelsky A. Engineered AAV2.7m8 Serotype Shows Significantly Higher Transduction Efficiency of ARPE-19 and HEK293 Cell Lines Compared to AAV5, AAV8 and AAV9 Serotypes. Pharmaceutics 2024; 16:138. [PMID: 38276507 PMCID: PMC10818700 DOI: 10.3390/pharmaceutics16010138] [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: 12/13/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
The level of transduction efficiency of the target retinal cells affects the choice of AAV serotype and the outcome of gene replacement therapy for inherited retinal diseases. This study focused on the tropism and transduction efficiency of AAV2.7m8-, AAV5-, AAV8-, and AAV9-GFP in ARPE-19 and HEK293 cells. Fluorescence intensity was assessed bi-hourly by means of IncuCyte S3 live imaging microscopy. Within 12 h, AAV2.7m8 demonstrated the highest transduction efficiency at four viral concentrations of 1-, 3-, 6-, and 8 × 104 VG/cell in a dose-dependent manner, followed by AAV5 in ARPE-19 and AAV9 in HEK293 cells. The transduction efficiency of AAV2.7m8 at a dose of 6 × 104 VG/cell was 21, 202, and 323 times higher in ARPE-19 cells and 324, 100, and 52 times higher in HEK293 cells compared to AAV5, AAV8, and AAV9, respectively. This trend remained for 4 days at all viral concentrations, as additionally shown by flow cytometry. At a dose of 6 × 104 VG/cell, AAV2.7m8 (97% GFP-positive cells, GFP +) was nearly two and 10 times as efficient as AAV5 (52% GFP+) and AAV9 or AAV8 (both 9%), respectively, in ARPE-19 cells. In HEK293 cells, 95% of AAV2.7m8-, 26% of AAV9-, 17% of AAV8-, and 12% of AAV5-transduced cells were GFP-positive.
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5
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Westhaus A, Eamegdool SS, Fernando M, Fuller-Carter P, Brunet AA, Miller AL, Rashwan R, Knight M, Daniszewski M, Lidgerwood GE, Pébay A, Hewitt A, Santilli G, Thrasher AJ, Carvalho LS, Gonzalez-Cordero A, Jamieson RV, Lisowski L. AAV capsid bioengineering in primary human retina models. Sci Rep 2023; 13:21946. [PMID: 38081924 PMCID: PMC10713676 DOI: 10.1038/s41598-023-49112-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
Adeno-associated viral (AAV) vector-mediated retinal gene therapy is an active field of both pre-clinical as well as clinical research. As with other gene therapy clinical targets, novel bioengineered AAV variants developed by directed evolution or rational design to possess unique desirable properties, are entering retinal gene therapy translational programs. However, it is becoming increasingly evident that predictive preclinical models are required to develop and functionally validate these novel AAVs prior to clinical studies. To investigate if, and to what extent, primary retinal explant culture could be used for AAV capsid development, this study performed a large high-throughput screen of 51 existing AAV capsids in primary human retina explants and other models of the human retina. Furthermore, we applied transgene expression-based directed evolution to develop novel capsids for more efficient transduction of primary human retina cells and compared the top variants to the strongest existing benchmarks identified in the screening described above. A direct side-by-side comparison of the newly developed capsids in four different in vitro and ex vivo model systems of the human retina allowed us to identify novel AAV variants capable of high transgene expression in primary human retina cells.
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Affiliation(s)
- Adrian Westhaus
- Translational Vectorology Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
- Infection, Immunity and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, UK
- Genethon, Evry, France
| | - Steven S Eamegdool
- Eye Genetics Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute and Sydney Children's Hospitals Network, The University of Sydney, Westmead, Australia
| | - Milan Fernando
- Stem Cell and Organoid Facility, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | | | - Alicia A Brunet
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Australia
| | - Annie L Miller
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Australia
| | | | - Maddison Knight
- Translational Vectorology Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Maciej Daniszewski
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Grace E Lidgerwood
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, Australia
| | - Alex Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Australia
| | - Giorgia Santilli
- Infection, Immunity and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Adrian J Thrasher
- Infection, Immunity and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Livia S Carvalho
- Lions Eye Institute, Nedlands, Australia
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Australia
| | - Anai Gonzalez-Cordero
- Stem Cell and Organoid Facility, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
- Stem Cell Medicine Group, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Robyn V Jamieson
- Eye Genetics Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute and Sydney Children's Hospitals Network, The University of Sydney, Westmead, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia.
- Australian Genome Therapeutics Centre, Children's Medical Research Institute and Sydney Children's Hospitals Network, Westmead, NSW, 2145, Australia.
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine - National Research Institute, Warsaw, Poland.
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6
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Schwartz MK, Likhite S, Vetter TA, Baird MC, McGovern V, Sierra Delgado A, Mendel T, Burghes A, Meyer KC. In-depth comparison of Anc80L65 and AAV9 retinal targeting and characterization of cross-reactivity to multiple AAV serotypes in humans. Mol Ther Methods Clin Dev 2023; 30:16-29. [PMID: 37746244 PMCID: PMC10512013 DOI: 10.1016/j.omtm.2023.05.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 05/12/2023] [Indexed: 09/26/2023]
Abstract
Anc80L65 is a synthetic, ancestral adeno-associated virus that has high tropism toward retinal photoreceptors after subretinal injection in mice and non-human primates. We characterized, for the first time, the post-intravitreal cell-specific transduction profile of Anc80L65 compared with AAV9. Here we use Anc80L65 and AAV9 to intravitreally deliver a copy of the gene encoding GFP into WT C57Bl/6J mice. GFP expression was driven by one of two clinically relevant promoters, chicken β actin (CB) or truncated MECP2 (P546). After qualitative assessment of relative GFP expression, we found Anc80L65 and AAV9 to have similar transduction profiles. Through the development of a novel method for quantifying GFP-positive retinal cells, we found Anc80L65 to have higher tropism in Müller glia and AAV9 to have higher tropism in horizontal cells. In addition, we found P546 to promote GFP expression at a more moderate level compared with the high levels seen under the CB promoter. Finally, for the first time, we characterized Anc80L65 cross-reactivity in human sera; 83% of patients with AAV2 pre-existing antibodies were found to be seropositive for Anc80L65. This study demonstrates the expanded therapeutic applications of Anc80L65 to treat retinal disease and provides the first insights to Anc80L65 pre-existing immunity in humans.
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Affiliation(s)
- Maura K. Schwartz
- The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH, USA
- Biomedical Sciences Graduate Program, the Ohio State University, Columbus, OH, USA
| | - Shibi Likhite
- The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH, USA
| | - Tatyana A. Vetter
- The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH, USA
- Department of Pediatrics, the Ohio State University, Columbus, OH, USA
| | - Megan C. Baird
- The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH, USA
- Biomedical Sciences Graduate Program, the Ohio State University, Columbus, OH, USA
| | - Vicki McGovern
- Department of Neurology, the Ohio State University, Columbus, OH, USA
| | | | - Tom Mendel
- Department of Ophthalmology, the Ohio State University, Columbus, OH, USA
| | - Arthur Burghes
- Department of Neurology, the Ohio State University, Columbus, OH, USA
| | - Kathrin C. Meyer
- The Center for Gene Therapy, Nationwide Children’s Hospital, Columbus, OH, USA
- Biomedical Sciences Graduate Program, the Ohio State University, Columbus, OH, USA
- Department of Pediatrics, the Ohio State University, Columbus, OH, USA
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7
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Belova L, Demchenko A, Kochergin-Nikitsky K, Kondrateva E, Slesarenko Y, Salikhova D, Lavrov A, Efremova A, Bukharova T, Goldshtein D, Smirnikhina S. Recombinant Adeno-associated Viral Vectors Serotypes 6 and 9 are Able to Transduce Human Tracheal Epithelial Cells but Not Human Induced Pluripotent Stem Cells. Mol Biotechnol 2023; 65:1539-1546. [PMID: 36707468 DOI: 10.1007/s12033-023-00668-4] [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] [Received: 09/19/2022] [Accepted: 01/14/2023] [Indexed: 01/28/2023]
Abstract
Recombinant adeno-associated viruses (rAAVs) may be useful for the development of gene therapy for hereditary diseases. Patient-specific human induced pluripotent stem cells (hiPSCs) can be differentiated into a variety of cells which are difficult or impossible to obtain by biopsy. To date, few research on the efficiency of rAAV transduction of hiPSCs has been published, but the obtained data are very contradictory and do not answer the actual question: how effective are rAAVs for the delivery of transgenes into hiPSCs. In this work, we used rAAV serotypes 5, 6, and 9 carrying the GFP transgene. The transduction efficiency of rAAV2/9-GFP and rAAV2/6-GFP for the immortalized tracheal epithelial cell line derived from a patient with cystic fibrosis (CFTE29o-) was relatively high. At the same time, the efficiency of transduction of iPSCs from a healthy donor and a cystic fibrosis (CF) donor was extremely low. Thus, our results show that the efficiency of hiPSC transduction by rAAV serotypes 5, 6, and 9 is not suitable for the delivery of transgenes.
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Affiliation(s)
- L Belova
- Research Centre for Medical Genetics, Moskvorechye 1, Moscow, 115478, Russia.
| | - A Demchenko
- Research Centre for Medical Genetics, Moskvorechye 1, Moscow, 115478, Russia
| | | | - E Kondrateva
- Research Centre for Medical Genetics, Moskvorechye 1, Moscow, 115478, Russia
| | - Ya Slesarenko
- Research Centre for Medical Genetics, Moskvorechye 1, Moscow, 115478, Russia
| | - D Salikhova
- Research Centre for Medical Genetics, Moskvorechye 1, Moscow, 115478, Russia
| | - A Lavrov
- Research Centre for Medical Genetics, Moskvorechye 1, Moscow, 115478, Russia
| | - A Efremova
- Research Centre for Medical Genetics, Moskvorechye 1, Moscow, 115478, Russia
| | - T Bukharova
- Research Centre for Medical Genetics, Moskvorechye 1, Moscow, 115478, Russia
| | - D Goldshtein
- Research Centre for Medical Genetics, Moskvorechye 1, Moscow, 115478, Russia
| | - S Smirnikhina
- Research Centre for Medical Genetics, Moskvorechye 1, Moscow, 115478, Russia
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8
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Weinmann J, Söllner J, Abele S, Zimmermann G, Zuckschwerdt K, Mayer C, Danner-Liskus J, Peltzer A, Schuler M, Lamla T, Strobel B. Identification of Broadly Applicable Adeno-Associated Virus Vectors by Systematic Comparison of Commonly Used Capsid Variants In Vitro. Hum Gene Ther 2022; 33:1197-1212. [PMID: 36097758 PMCID: PMC9700356 DOI: 10.1089/hum.2022.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Adeno-associated viruses (AAVs) represent highly attractive gene therapy vectors and potent research tools for the modulation of gene expression in animal models or difficult-to-transfect cell cultures. Engineered variants, comprising chimeric, mutated, or peptide-inserted capsids, have strongly broadened the utility of AAVs by altering cellular tropism, enabling immune evasion, or increasing transduction efficiency. In this work, the performance of 50 of the most used, predominantly published, AAVs was compared on several primary cells, cell lines, and induced pluripotent stem cell-derived models from different organs, including the adipose tissue, liver, lung, brain, and eyes. To identify the most efficient capsids for each cell type, self-complementary AAVs were standardized by digital polymerase chain reaction, arrayed on 96-well plates, and screened using high-content imaging. To enable best use of the data, all results are also provided in a web app. The utility of one selected AAV variant is further exemplified in a liver fibrosis assay based on primary hepatic stellate cells, where it successfully reversed a small interfering RNA (siRNA)-induced phenotype. Most importantly, our comparative analysis revealed that a subselection of only five AAV variants (AAV2.NN, AAV9-SLRSPPS, AAV6.2, AAV6TM, and AAV1P5) enabled efficient transduction of all tested cell types and markedly outperformed other well-established capsids, such as AAV2-7m8. These findings suggest that a core panel comprising these five capsid variants is a universally applicable and sufficient tool to identify potent AAVs for gene expression modulation in cellular systems.
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Affiliation(s)
- Jonas Weinmann
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Julia Söllner
- Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Sarah Abele
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Gudrun Zimmermann
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Kai Zuckschwerdt
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Christine Mayer
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Jenny Danner-Liskus
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Alexander Peltzer
- Translational Medicine & Clinical Pharmacology, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Michael Schuler
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Thorsten Lamla
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Benjamin Strobel
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany,Correspondence: Dr. Benjamin Strobel, Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, 88400 Biberach an der Riss, Germany.
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9
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Keng CT, Guo K, Liu YC, Shen KY, Lim DS, Lovatt M, Ang HP, Mehta JS, Chew WL. Multiplex viral tropism assay in complex cell populations with single-cell resolution. Gene Ther 2022; 29:555-565. [PMID: 35999303 PMCID: PMC9482877 DOI: 10.1038/s41434-022-00360-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/23/2022] [Accepted: 07/12/2022] [Indexed: 11/09/2022]
Abstract
Gene therapy constitutes one of the most promising mode of disease treatments. Two key properties for therapeutic delivery vectors are its transduction efficiency (how well the vector delivers therapeutic cargo to desired target cells) and specificity (how well it avoids off-target delivery into unintended cells within the body). Here we developed an integrated bioinformatics and experimental pipeline that enables multiplex measurement of transduction efficiency and specificity, particularly by measuring how libraries of delivery vectors transduce libraries of diverse cell types. We demonstrated that pairing high-throughput measurement of AAV identity with high-resolution single-cell RNA transcriptomic sequencing maps how natural and engineered AAV variants transduce individual cells within human cerebral and ocular organoids. We further demonstrate that efficient AAV transduction observed in organoids is recapitulated in vivo in non-human primates. This library-on-library technology will be important for determining the safety and efficacy of therapeutic delivery vectors.
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Affiliation(s)
- Choong Tat Keng
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Ke Guo
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Yu-Chi Liu
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore, Singapore.,Cornea and Refractive Surgery Group, Singapore Eye Research Institute, Singapore, Singapore.,Cornea and External Eye Diseases, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology Academic Clinical Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Kimberle Yanyin Shen
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Daryl Shern Lim
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Matthew Lovatt
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore, Singapore
| | - Heng Pei Ang
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore, Singapore
| | - Jodhbir S Mehta
- Tissue Engineering and Cell Therapy Group, Singapore Eye Research Institute, Singapore, Singapore.,Cornea and Refractive Surgery Group, Singapore Eye Research Institute, Singapore, Singapore.,Cornea and External Eye Diseases, Singapore National Eye Centre, Singapore, Singapore.,Ophthalmology Academic Clinical Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Wei Leong Chew
- Genome Institute of Singapore, Agency for Science, Technology and Research, 60 Biopolis Street, Singapore, 138672, Singapore. .,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore.
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10
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Ross AG, Chaqour B, McDougald DS, Dine KE, Duong TT, Shindler RE, Yue J, Liu T, Shindler KS. Selective Upregulation of SIRT1 Expression in Retinal Ganglion Cells by AAV-Mediated Gene Delivery Increases Neuronal Cell Survival and Alleviates Axon Demyelination Associated with Optic Neuritis. Biomolecules 2022; 12:830. [PMID: 35740955 PMCID: PMC9221096 DOI: 10.3390/biom12060830] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/07/2022] [Accepted: 06/11/2022] [Indexed: 11/16/2022] Open
Abstract
Optic neuritis (ON), the most common ocular manifestation of multiple sclerosis, is an autoimmune inflammatory demyelinating disease also characterized by degeneration of retinal ganglion cells (RGCs) and their axons, which commonly leads to visual impairment despite attempted treatments. Although ON disease etiology is not known, changes in the redox system and exacerbated optic nerve inflammation play a major role in the pathogenesis of the disease. Silent information regulator 1 (sirtuin-1/SIRT1) is a ubiquitously expressed NAD+-dependent deacetylase, which functions to reduce/prevent both oxidative stress and inflammation in various tissues. Non-specific upregulation of SIRT1 by pharmacologic and genetic approaches attenuates RGC loss in experimental ON. Herein, we hypothesized that targeted expression of SIRT1 selectively in RGCs using an adeno-associated virus (AAV) vector as a delivery vehicle is an effective approach to reducing neurodegeneration and preserving vision in ON. We tested this hypothesis through intravitreal injection of AAV7m8.SNCG.SIRT1, an AAV2-derived vector optimized for highly efficient SIRT1 transgene transfer and protein expression into RGCs in mice with experimental autoimmune encephalomyelitis (EAE), a model of multiple sclerosis that recapitulates optic neuritis RGC loss and axon demyelination. Our data show that EAE mice injected with a control vehicle exhibit progressive alteration of visual function reflected by decreasing optokinetic response (OKR) scores, whereas comparatively, AAV7m8.SNCG.SIRT1-injected EAE mice maintain higher OKR scores, suggesting that SIRT1 reduces the visual deficit imparted by EAE. Consistent with this, RGC survival determined by immunolabeling is increased and axon demyelination is decreased in the AAV7m8.SNCG.SIRT1 RGC-injected group of EAE mice compared to the mouse EAE counterpart injected with a vehicle or with control vector AAV7m8.SNCG.eGFP. However, immune cell infiltration of the optic nerve is not significantly different among all EAE groups of mice injected with either vehicle or AAV7m8.SNCG.SIRT1. We conclude that despite minimally affecting the inflammatory response in the optic nerve, AAV7m8-mediated SIRT1 transfer into RGCs has a neuroprotective potential against RGC loss, axon demyelination and vison deficits associated with EAE. Together, these data suggest that SIRT1 exerts direct effects on RGC survival and function.
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Affiliation(s)
- Ahmara G. Ross
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.G.R.); (B.C.); (D.S.M.); (K.E.D.); (T.T.D.); (R.E.S.); (J.Y.); (T.L.)
- F. M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Brahim Chaqour
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.G.R.); (B.C.); (D.S.M.); (K.E.D.); (T.T.D.); (R.E.S.); (J.Y.); (T.L.)
- F. M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Devin S. McDougald
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.G.R.); (B.C.); (D.S.M.); (K.E.D.); (T.T.D.); (R.E.S.); (J.Y.); (T.L.)
- F. M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kimberly E. Dine
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.G.R.); (B.C.); (D.S.M.); (K.E.D.); (T.T.D.); (R.E.S.); (J.Y.); (T.L.)
- F. M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Thu T. Duong
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.G.R.); (B.C.); (D.S.M.); (K.E.D.); (T.T.D.); (R.E.S.); (J.Y.); (T.L.)
- F. M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ryan E. Shindler
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.G.R.); (B.C.); (D.S.M.); (K.E.D.); (T.T.D.); (R.E.S.); (J.Y.); (T.L.)
- F. M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jipeng Yue
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.G.R.); (B.C.); (D.S.M.); (K.E.D.); (T.T.D.); (R.E.S.); (J.Y.); (T.L.)
- F. M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Tehui Liu
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.G.R.); (B.C.); (D.S.M.); (K.E.D.); (T.T.D.); (R.E.S.); (J.Y.); (T.L.)
- F. M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Kenneth S. Shindler
- Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA; (A.G.R.); (B.C.); (D.S.M.); (K.E.D.); (T.T.D.); (R.E.S.); (J.Y.); (T.L.)
- F. M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, PA 19104, USA
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11
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Flitsch LJ, Börner K, Stüllein C, Ziegler S, Sonntag-Buck V, Wiedtke E, Semkova V, Au Yeung SWC, Schlee J, Hajo M, Mathews M, Ludwig BS, Kossatz S, Kessler H, Grimm D, Brüstle O. Identification of adeno-associated virus variants for gene transfer into human neural cell types by parallel capsid screening. Sci Rep 2022; 12:8356. [PMID: 35589936 PMCID: PMC9120183 DOI: 10.1038/s41598-022-12404-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/09/2022] [Indexed: 12/11/2022] Open
Abstract
Human brain cells generated by in vitro cell programming provide exciting prospects for disease modeling, drug discovery and cell therapy. These applications frequently require efficient and clinically compliant tools for genetic modification of the cells. Recombinant adeno-associated viruses (AAVs) fulfill these prerequisites for a number of reasons, including the availability of a myriad of AAV capsid variants with distinct cell type specificity (also called tropism). Here, we harnessed a customizable parallel screening approach to assess a panel of natural or synthetic AAV capsid variants for their efficacy in lineage-related human neural cell types. We identified common lead candidates suited for the transduction of directly converted, early-stage induced neural stem cells (iNSCs), induced pluripotent stem cell (iPSC)-derived later-stage, radial glia-like neural progenitors, as well as differentiated astrocytic and mixed neuroglial cultures. We then selected a subset of these candidates for functional validation in iNSCs and iPSC-derived astrocytes, using shRNA-induced downregulation of the citrate transporter SLC25A1 and overexpression of the transcription factor NGN2 for proofs-of-concept. Our study provides a comparative overview of the susceptibility of different human cell programming-derived brain cell types to AAV transduction and a critical discussion of the assets and limitations of this specific AAV capsid screening approach.
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Affiliation(s)
- Lea Jessica Flitsch
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Venusberg-Campus 1, Building 76, 53127, Bonn, Germany
| | - Kathleen Börner
- Center for Infectious Diseases, Virology, Medical Faculty, Heidelberg University, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany.,BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.,German Center for Infection Research (DZIF), partner site Heidelberg, 69120, Heidelberg, Germany.,AskBio GmbH, Am Taubenfeld 21, 69123, Heidelberg, Germany
| | - Christian Stüllein
- CLADIAC GmbH, Kurfürsten-Anlage 52-58, 69115, Heidelberg, Germany.,Stüllein Software Engineering (SSE), Friedrich-Hartung-Str. 16, 64560, Riedstadt, Germany
| | - Simon Ziegler
- CLADIAC GmbH, Kurfürsten-Anlage 52-58, 69115, Heidelberg, Germany.,KINSYS GmbH, Holtzstr. 2, 76135, Karlsruhe, Germany
| | - Vera Sonntag-Buck
- Center for Infectious Diseases, Virology, Medical Faculty, Heidelberg University, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany.,BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany.,German Center for Infection Research (DZIF), partner site Heidelberg, 69120, Heidelberg, Germany
| | - Ellen Wiedtke
- Center for Infectious Diseases, Virology, Medical Faculty, Heidelberg University, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany.,BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
| | - Vesselina Semkova
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Venusberg-Campus 1, Building 76, 53127, Bonn, Germany.,LIFE and BRAIN GmbH, Venusberg-Campus 1, Building 76, 53127, Bonn, Germany
| | - Si Wah Christina Au Yeung
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Venusberg-Campus 1, Building 76, 53127, Bonn, Germany
| | - Julia Schlee
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Venusberg-Campus 1, Building 76, 53127, Bonn, Germany
| | - Mohamad Hajo
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Venusberg-Campus 1, Building 76, 53127, Bonn, Germany.,Federal Institute for Drugs and Medical Devices (BfArM), Kurt-Georg-Kiesinger-Allee 3, 53175, Bonn, Germany
| | - Mona Mathews
- LIFE and BRAIN GmbH, Venusberg-Campus 1, Building 76, 53127, Bonn, Germany
| | - Beatrice Stefanie Ludwig
- Department of Nuclear Medicine, School of Medicine, Technical University Munich (TUM), University Hospital Klinikum Rechts der Isar and Central Institute for Translational Cancer Research (Transla TUM, Einsteinstr. 25, 81675, Munich, Germany
| | - Susanne Kossatz
- Department of Nuclear Medicine, School of Medicine, Technical University Munich (TUM), University Hospital Klinikum Rechts der Isar and Central Institute for Translational Cancer Research (Transla TUM, Einsteinstr. 25, 81675, Munich, Germany
| | - Horst Kessler
- Institute for Advanced Study, Department Chemie, Technical University Munich (TUM), Lichtenbergstr. 4, 85747, Garching, Germany
| | - Dirk Grimm
- Center for Infectious Diseases, Virology, Medical Faculty, Heidelberg University, Im Neuenheimer Feld 344, 69120, Heidelberg, Germany. .,BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany. .,German Center for Infection Research (DZIF), partner site Heidelberg, 69120, Heidelberg, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Heidelberg, 69120, Heidelberg, Germany.
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn, Venusberg-Campus 1, Building 76, 53127, Bonn, Germany. .,LIFE and BRAIN GmbH, Venusberg-Campus 1, Building 76, 53127, Bonn, Germany.
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12
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Fischer S, Strobel B, Weinmann J, Gillardon F. Two engineered AAV capsid variants for efficient transduction of human cortical neurons directly converted from iPSC. J Neurosci Methods 2021; 368:109457. [PMID: 34953937 DOI: 10.1016/j.jneumeth.2021.109457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/09/2021] [Accepted: 12/19/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Recombinant adeno-associated virus (AAV) is the most widely used vector for gene therapy in clinical trials. To increase transduction efficiency and specificity, novel engineered AAV variants with modified capsid sequences are evaluated in human cell cultures and non-human primates. METHODS We tested two novel AAV capsid variants, AAV2-NNPTPSR and AAV9-NVVRSSS, in human cortical neurons, which were directly converted from human induced pluripotent stem cells and cocultured with rat primary astrocytes. RESULTS AAV2-NNPTPSR variant efficiently transduced both induced human cortical glutamatergic neurons and induced human cortical GABAergic interneurons. By contrast, AAV9-NVVRSSS variant transduced both induced human cortical neurons and cocultured rat primary astrocytes. High viral titers (1E+5 viral genomes per cell) caused a significant decrease in viability of induced human cortical neurons. Low viral titers (1E+4 viral genomes per cell) led to a significant increase in the neuronal activity marker c-Fos in transduced human neurons following treatment with a potassium channel blocker. CONCLUSIONS We identified two engineered AAV capsid variants that efficiently transduce induced human cortical neurons. The threefold higher percentage of c-Fos positive, transduced human neurons may indicate functional alterations induced by viral transduction and/or transgene expression.
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Affiliation(s)
- Sandra Fischer
- CNS Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riss, Germany
| | - Benjamin Strobel
- CNS Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riss, Germany
| | - Jonas Weinmann
- CNS Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riss, Germany
| | - Frank Gillardon
- CNS Diseases Research, Boehringer Ingelheim Pharma GmbH & Co. KG, 88397 Biberach an der Riss, Germany.
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13
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Abulimiti A, Lai MSL, Chang RCC. Applications of adeno-associated virus vector-mediated gene delivery for neurodegenerative diseases and psychiatric diseases: Progress, advances, and challenges. Mech Ageing Dev 2021; 199:111549. [PMID: 34352323 DOI: 10.1016/j.mad.2021.111549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 07/31/2021] [Indexed: 12/19/2022]
Abstract
Neurodegeneration is the most common disease in the elderly population due to its slowly progressive nature of neuronal deterioration, eventually leading to executive dysfunction. The pathological markers of neurological disorders are relatively well-established, however, detailed molecular mechanisms of progression and therapeutic targets are needed to develop novel treatments in human patients. Treating known therapeutic targets of neurological diseases has been aided by recent advancements in adeno-associated virus (AAV) technology. AAVs are known for their low-immunogenicity, blood-brain barrier (BBB) penetrating ability, selective neuronal tropism, stable transgene expression, and pleiotropy. In addition, the usage of AAVs has enormous potential to be optimized. Therefore, AAV can be a powerful tool used to uncover the underlying pathophysiology of neurological disorders and to increase the success in human gene therapy. This review summarizes different optimization approaches of AAV vectors with their current applications in disease modeling, neural tracing and gene therapy, hence exploring progressive mechanisms of neurodegenerative diseases as well as effective therapy. Lastly, this review discusses the limitations and future perspectives of the AAV-mediated transgene delivery system.
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Affiliation(s)
- Amina Abulimiti
- Laboratory of Neurodegenerative Diseases, School of Biomedical Science, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Michael Siu-Lun Lai
- Laboratory of Neurodegenerative Diseases, School of Biomedical Science, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Raymond Chuen-Chung Chang
- Laboratory of Neurodegenerative Diseases, School of Biomedical Science, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region; State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region.
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14
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Cappella M, Elouej S, Biferi MG. The Potential of Induced Pluripotent Stem Cells to Test Gene Therapy Approaches for Neuromuscular and Motor Neuron Disorders. Front Cell Dev Biol 2021; 9:662837. [PMID: 33937264 PMCID: PMC8080375 DOI: 10.3389/fcell.2021.662837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022] Open
Abstract
The reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) represents a major advance for the development of human disease models. The emerging of this technique fostered the concept of "disease in a dish," which consists into the generation of patient-specific models in vitro. Currently, iPSCs are used to study pathological molecular mechanisms caused by genetic mutations and they are considered a reliable model for high-throughput drug screenings. Importantly, precision-medicine approaches to treat monogenic disorders exploit iPSCs potential for the selection and validation of lead candidates. For example, antisense oligonucleotides (ASOs) were tested with promising results in myoblasts or motor neurons differentiated from iPSCs of patients affected by either Duchenne muscular dystrophy or Amyotrophic lateral sclerosis. However, the use of iPSCs needs additional optimization to ensure translational success of the innovative strategies based on gene delivery through adeno associated viral vectors (AAV) for these diseases. Indeed, to establish an efficient transduction of iPSCs with AAV, several aspects should be optimized, including viral vector serotype, viral concentration and timing of transduction. This review will outline the use of iPSCs as a model for the development and testing of gene therapies for neuromuscular and motor neuron disorders. It will then discuss the advantages for the use of this versatile tool for gene therapy, along with the challenges associated with the viral vector transduction of iPSCs.
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Affiliation(s)
- Marisa Cappella
- Sorbonne University, INSERM, Institute of Myology, Center of Research in Myology, Paris, France
| | - Sahar Elouej
- Sorbonne University, INSERM, Institute of Myology, Center of Research in Myology, Paris, France
| | - Maria Grazia Biferi
- Sorbonne University, INSERM, Institute of Myology, Center of Research in Myology, Paris, France
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15
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Strategies for Optimizing the Production of Proteins and Peptides with Multiple Disulfide Bonds. Antibiotics (Basel) 2020; 9:antibiotics9090541. [PMID: 32858882 PMCID: PMC7558204 DOI: 10.3390/antibiotics9090541] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023] Open
Abstract
Bacteria can produce recombinant proteins quickly and cost effectively. However, their physiological properties limit their use for the production of proteins in their native form, especially polypeptides that are subjected to major post-translational modifications. Proteins that rely on disulfide bridges for their stability are difficult to produce in Escherichia coli. The bacterium offers the least costly, simplest, and fastest method for protein production. However, it is difficult to produce proteins with a very large size. Saccharomyces cerevisiae and Pichia pastoris are the most commonly used yeast species for protein production. At a low expense, yeasts can offer high protein yields, generate proteins with a molecular weight greater than 50 kDa, extract signal sequences, and glycosylate proteins. Both eukaryotic and prokaryotic species maintain reducing conditions in the cytoplasm. Hence, the formation of disulfide bonds is inhibited. These bonds are formed in eukaryotic cells during the export cycle, under the oxidizing conditions of the endoplasmic reticulum. Bacteria do not have an advanced subcellular space, but in the oxidizing periplasm, they exhibit both export systems and enzymatic activities directed at the formation and quality of disulfide bonds. Here, we discuss current techniques used to target eukaryotic and prokaryotic species for the generation of correctly folded proteins with disulfide bonds.
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16
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Buck TM, Wijnholds J. Recombinant Adeno-Associated Viral Vectors (rAAV)-Vector Elements in Ocular Gene Therapy Clinical Trials and Transgene Expression and Bioactivity Assays. Int J Mol Sci 2020; 21:E4197. [PMID: 32545533 PMCID: PMC7352801 DOI: 10.3390/ijms21124197] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 02/06/2023] Open
Abstract
Inherited retinal dystrophies and optic neuropathies cause chronic disabling loss of visual function. The development of recombinant adeno-associated viral vectors (rAAV) gene therapies in all disease fields have been promising, but the translation to the clinic has been slow. The safety and efficacy profiles of rAAV are linked to the dose of applied vectors. DNA changes in the rAAV gene cassette affect potency, the expression pattern (cell-specificity), and the production yield. Here, we present a library of rAAV vectors and elements that provide a workflow to design novel vectors. We first performed a meta-analysis on recombinant rAAV elements in clinical trials (2007-2020) for ocular gene therapies. We analyzed 33 unique rAAV gene cassettes used in 57 ocular clinical trials. The rAAV gene therapy vectors used six unique capsid variants, 16 different promoters, and six unique polyadenylation sequences. Further, we compiled a list of promoters, enhancers, and other sequences used in current rAAV gene cassettes in preclinical studies. Then, we give an update on pro-viral plasmid backbones used to produce the gene therapy vectors, inverted terminal repeats, production yield, and rAAV safety considerations. Finally, we assess rAAV transgene and bioactivity assays applied to cells or organoids in vitro, explants ex vivo, and clinical studies.
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Affiliation(s)
- Thilo M. Buck
- Department of Ophthalmology, Leiden University Medical Center (LUMC), 2333 ZC Leiden, The Netherlands;
| | - Jan Wijnholds
- Department of Ophthalmology, Leiden University Medical Center (LUMC), 2333 ZC Leiden, The Netherlands;
- Netherlands Institute of Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), 1105 BA Amsterdam, The Netherlands
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17
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Westhaus A, Cabanes-Creus M, Rybicki A, Baltazar G, Navarro RG, Zhu E, Drouyer M, Knight M, Albu RF, Ng BH, Kalajdzic P, Kwiatek M, Hsu K, Santilli G, Gold W, Kramer B, Gonzalez-Cordero A, Thrasher AJ, Alexander IE, Lisowski L. High-Throughput In Vitro, Ex Vivo, and In Vivo Screen of Adeno-Associated Virus Vectors Based on Physical and Functional Transduction. Hum Gene Ther 2020; 31:575-589. [PMID: 32000541 PMCID: PMC7232709 DOI: 10.1089/hum.2019.264] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [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 virus (AAV) vectors are quickly becoming the vectors of choice for therapeutic gene delivery. To date, hundreds of natural isolates and bioengineered variants have been reported. While factors such as high production titer and low immunoreactivity are important to consider, the ability to deliver the genetic payload (physical transduction) and to drive high transgene expression (functional transduction) remains the most important feature when selecting AAV variants for clinical applications. Reporter expression assays are the most commonly used methods for determining vector fitness. However, such approaches are time consuming and become impractical when evaluating a large number of variants. Limited access to primary human tissues or challenging model systems further complicates vector testing. To address this problem, convenient high-throughput methods based on next-generation sequencing (NGS) are being developed. To this end, we built an AAV Testing Kit that allows inherent flexibility in regard to number and type of AAV variants included, and is compatible with in vitro, ex vivo, and in vivo applications. The Testing Kit presented here consists of a mix of 30 known AAVs where each variant encodes a CMV-eGFP cassette and a unique barcode in the 3′-untranslated region of the eGFP gene, allowing NGS-barcode analysis at both the DNA and RNA/cDNA levels. To validate the AAV Testing Kit, individually packaged barcoded variants were mixed at an equal ratio and used to transduce cells/tissues of interest. DNA and RNA/cDNA were extracted and subsequently analyzed by NGS to determine the physical/functional transduction efficiencies. We were able to assess the transduction efficiencies of immortalized cells, primary cells, and induced pluripotent stem cells in vitro, as well as in vivo transduction in naïve mice and a xenograft liver model. Importantly, while our data validated previously reported transduction characteristics of individual capsids, we also identified novel previously unknown tropisms for some AAV variants.
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Affiliation(s)
- Adrian Westhaus
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia.,Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Marti Cabanes-Creus
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Arkadiusz Rybicki
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Grober Baltazar
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Renina Gale Navarro
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Erhua Zhu
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, The University of Sydney, Westmead, Australia
| | - Matthieu Drouyer
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Maddison Knight
- Vector and Genome Engineering Facility, Children's Medical Research Institute, , The University of Sydney, Westmead, Australia
| | - Razvan F Albu
- Vector and Genome Engineering Facility, Children's Medical Research Institute, , The University of Sydney, Westmead, Australia
| | - Boaz H Ng
- Vector and Genome Engineering Facility, Children's Medical Research Institute, , The University of Sydney, Westmead, Australia
| | - Predrag Kalajdzic
- Vector and Genome Engineering Facility, Children's Medical Research Institute, , The University of Sydney, Westmead, Australia
| | - Magdalena Kwiatek
- Military Institute of Hygiene and Epidemiology, The Biological Threats Identification and Countermeasure Centre, Puławy, Poland
| | - Kenneth Hsu
- Children's Cancer Research Unit, The Children's Hospital at Westmead, Westmead, Australia
| | - Giorgia Santilli
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Wendy Gold
- Molecular Neurobiology Research Lab, The Children's Hospital at Westmead, Westmead, Australia.,Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.,Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, Australia
| | - Belinda Kramer
- Children's Cancer Research Unit, The Children's Hospital at Westmead, Westmead, Australia
| | - Anai Gonzalez-Cordero
- Stem Cell & Organoid Facility and Stem Cell Medicine Group, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Adrian J Thrasher
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute and Sydney Children's Hospitals Network, The University of Sydney, Westmead, Australia.,Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, Australia.,Vector and Genome Engineering Facility, Children's Medical Research Institute, , The University of Sydney, Westmead, Australia.,Military Institute of Hygiene and Epidemiology, The Biological Threats Identification and Countermeasure Centre, Puławy, Poland
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18
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Garita-Hernandez M, Routet F, Guibbal L, Khabou H, Toualbi L, Riancho L, Reichman S, Duebel J, Sahel JA, Goureau O, Dalkara D. AAV-Mediated Gene Delivery to 3D Retinal Organoids Derived from Human Induced Pluripotent Stem Cells. Int J Mol Sci 2020; 21:ijms21030994. [PMID: 32028585 PMCID: PMC7036814 DOI: 10.3390/ijms21030994] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 01/01/2023] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) promise a great number of future applications to investigate retinal development, pathophysiology and cell therapies for retinal degenerative diseases. Specific approaches to genetically modulate hiPSC would be valuable for all of these applications. Vectors based on adeno-associated virus (AAV) have shown the ability for gene delivery to retinal organoids derived from hiPSCs. Thus far, little work has been carried out to investigate mechanisms of AAV-mediated gene delivery and the potential advantages of engineered AAVs to genetically modify retinal organoids. In this study, we compared the early transduction efficiency of several recombinant and engineered AAVs in hiPSC-derived RPE cells and retinal organoids in relation to the availability of their cell-surface receptors and as a function of time. The genetic variant AAV2-7m8 had a superior transduction efficiency when applied at day 44 of differentiation on retinal organoids and provided long-lasting expressions for at least 4 weeks after infection without compromising cell viability. All of the capsids we tested transduced the hiPSC-RPE cells, with the AAV2-7m8 variant being the most efficient. Transduction efficiency was correlated with the presence of primary cell-surface receptors on the hiPS-derived organoids. Our study explores some of the mechanisms of cell attachment of AAVs and reports long-term gene expression resulting from gene delivery in retinal organoids.
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Affiliation(s)
- Marcela Garita-Hernandez
- Sorbonne Université,, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France; (M.G.-H.); (F.R.); (L.G.); (H.K.); (L.T.); (L.R.); (S.R.); (J.D.); (J.-A.S.); (O.G.)
- Institut de Neurosciences de Montpellier, Université de Montpellier, INSERM, 34090 Montpellier, France
| | - Fiona Routet
- Sorbonne Université,, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France; (M.G.-H.); (F.R.); (L.G.); (H.K.); (L.T.); (L.R.); (S.R.); (J.D.); (J.-A.S.); (O.G.)
| | - Laure Guibbal
- Sorbonne Université,, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France; (M.G.-H.); (F.R.); (L.G.); (H.K.); (L.T.); (L.R.); (S.R.); (J.D.); (J.-A.S.); (O.G.)
| | - Hanen Khabou
- Sorbonne Université,, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France; (M.G.-H.); (F.R.); (L.G.); (H.K.); (L.T.); (L.R.); (S.R.); (J.D.); (J.-A.S.); (O.G.)
| | - Lyes Toualbi
- Sorbonne Université,, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France; (M.G.-H.); (F.R.); (L.G.); (H.K.); (L.T.); (L.R.); (S.R.); (J.D.); (J.-A.S.); (O.G.)
| | - Luisa Riancho
- Sorbonne Université,, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France; (M.G.-H.); (F.R.); (L.G.); (H.K.); (L.T.); (L.R.); (S.R.); (J.D.); (J.-A.S.); (O.G.)
| | - Sacha Reichman
- Sorbonne Université,, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France; (M.G.-H.); (F.R.); (L.G.); (H.K.); (L.T.); (L.R.); (S.R.); (J.D.); (J.-A.S.); (O.G.)
| | - Jens Duebel
- Sorbonne Université,, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France; (M.G.-H.); (F.R.); (L.G.); (H.K.); (L.T.); (L.R.); (S.R.); (J.D.); (J.-A.S.); (O.G.)
- Department of Ophthalmology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jose-Alain Sahel
- Sorbonne Université,, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France; (M.G.-H.); (F.R.); (L.G.); (H.K.); (L.T.); (L.R.); (S.R.); (J.D.); (J.-A.S.); (O.G.)
- CHNO des Quinze−Vingts, DHU Sight Restore, INSERM-DGOS CIC 1423, 75012 Paris, France
- Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, PA 15106, USA
| | - Olivier Goureau
- Sorbonne Université,, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France; (M.G.-H.); (F.R.); (L.G.); (H.K.); (L.T.); (L.R.); (S.R.); (J.D.); (J.-A.S.); (O.G.)
| | - Deniz Dalkara
- Sorbonne Université,, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France; (M.G.-H.); (F.R.); (L.G.); (H.K.); (L.T.); (L.R.); (S.R.); (J.D.); (J.-A.S.); (O.G.)
- Correspondence:
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19
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Green MV, Pengo T, Raybuck JD, Naqvi T, McMullan HM, Hawkinson JE, Marron Fernandez de Velasco E, Muntean BS, Martemyanov KA, Satterfield R, Young SM, Thayer SA. Automated Live-Cell Imaging of Synapses in Rat and Human Neuronal Cultures. Front Cell Neurosci 2019; 13:467. [PMID: 31680875 PMCID: PMC6811609 DOI: 10.3389/fncel.2019.00467] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/01/2019] [Indexed: 01/10/2023] Open
Abstract
Synapse loss and dendritic damage correlate with cognitive decline in many neurodegenerative diseases, underlie neurodevelopmental disorders, and are associated with environmental and drug-induced CNS toxicities. However, screening assays designed to measure loss of synaptic connections between live cells are lacking. Here, we describe the design and validation of automated synaptic imaging assay (ASIA), an efficient approach to label, image, and analyze synapses between live neurons. Using viral transduction to express fluorescent proteins that label synapses and an automated computer-controlled microscope, we developed a method to identify agents that regulate synapse number. ASIA is compatible with both confocal and wide-field microscopy; wide-field image acquisition is faster but requires a deconvolution step in the analysis. Both types of images feed into batch processing analysis software that can be run on ImageJ, CellProfiler, and MetaMorph platforms. Primary analysis endpoints are the number of structural synapses and cell viability. Thus, overt cell death is differentiated from subtle changes in synapse density, an important distinction when studying neurodegenerative processes. In rat hippocampal cultures treated for 24 h with 100 μM 2-bromopalmitic acid (2-BP), a compound that prevents clustering of postsynaptic density 95 (PSD95), ASIA reliably detected loss of postsynaptic density 95-enhanced green fluorescent protein (PSD95-eGFP)-labeled synapses in the absence of cell death. In contrast, treatment with 100 μM glutamate produced synapse loss and significant cell death, determined from morphological changes in a binary image created from co-expressed mCherry. Treatment with 3 mM lithium for 24 h significantly increased the number of fluorescent puncta, showing that ASIA also detects synaptogenesis. Proof of concept studies show that cell-specific promoters enable the selective study of inhibitory or principal neurons and that alternative reporter constructs enable quantification of GABAergic or glutamatergic synapses. ASIA can also be used to study synapse loss between human induced pluripotent stem cell (iPSC)-derived cortical neurons. Significant synapse loss in the absence of cell death was detected in the iPSC-derived neuronal cultures treated with either 100 μM 2-BP or 100 μM glutamate for 24 h, while 300 μM glutamate produced synapse loss and cell death. ASIA shows promise for identifying agents that evoke synaptic toxicities and screening for compounds that prevent or reverse synapse loss.
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Affiliation(s)
- Matthew V. Green
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Thomas Pengo
- Informatics Institute, University of Minnesota, Minneapolis, MN, United States
| | - Jonathan D. Raybuck
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Tahmina Naqvi
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, United States
| | - Hannah M. McMullan
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Jon E. Hawkinson
- Institute for Therapeutics Discovery and Development, University of Minnesota, Minneapolis, MN, United States
| | | | - Brian S. Muntean
- Department of Neuroscience, Scripps Research Institute, Jupiter, FL, United States
| | | | - Rachel Satterfield
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, United States
| | - Samuel M. Young
- Department of Anatomy and Cell Biology, Iowa Neuroscience Institute, University of Iowa, Iowa City, IA, United States
- Department of Otolaryngology, University of Iowa, Iowa City, IA, United States
| | - Stanley A. Thayer
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN, United States
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