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J. Mol. Sci.","IJMS"],"abstract":"<jats:p>The adeno-associated virus (AAV) has become the vector of choice for gene therapy and experimental gene delivery, owing to its non-pathogenic nature and ability to achieve persistent gene expression across diverse tissues. AAV has emerged as a key platform in cellular reprogramming and regenerative medicine, with applications spanning transcription factor delivery for in vivo lineage conversion and tissue repair across the CNS, heart, and musculoskeletal systems. However, significant limitations remain, particularly in the context of induced pluripotent stem cell (iPSC) engineering. We assess barriers to efficient iPSC transduction including receptor-dependent entry deficits and activation of p53-dependent DNA damage responses. Although AAV is widely described as non-integrating, evidence indicates that integration events occur in rapidly proliferating and actively reprogramming cells. Critically, we synthesize evidence that cell-type-specific promoters lose fidelity when paired with neurogenic transgene payloads, a cross-tissue problem not addressed in existing AAV reviews, and that published in vivo reprogramming efficiencies may be substantially confounded by promoter leakage in the absence of formal lineage tracing. These aspects, underrepresented in recent platform-level reviews, are specifically emphasized here as a resource for researchers designing rigorous AAV-based reprogramming and gene therapy strategies.<\/jats:p>","DOI":"10.3390\/ijms27156846","type":"journal-article","created":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T16:15:00Z","timestamp":1785428100000},"page":"6846","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["AAV Vectors in Regenerative Medicine and Cellular Reprogramming: Potential, Pitfalls, and Specificity Constraints"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-1674-4300","authenticated-orcid":false,"given":"Mariam","family":"Abdelnaby","sequence":"first","affiliation":[{"name":"Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Institutskiy Per., 141701 Dolgoprudny, Russia"},{"name":"Research Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov Street, 117997 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5317-4552","authenticated-orcid":false,"given":"Adelya","family":"Galiakberova","sequence":"additional","affiliation":[{"name":"Research Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov Street, 117997 Moscow, Russia"},{"name":"Research Institute of Molecular and Cellular Medicine, RUDN University, 117198 Moscow, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5640-7139","authenticated-orcid":false,"given":"Erdem","family":"Dashinimaev","sequence":"additional","affiliation":[{"name":"Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), Institutskiy Per., 141701 Dolgoprudny, Russia"},{"name":"Research Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov Street, 117997 Moscow, Russia"},{"name":"Research Institute of Molecular and Cellular Medicine, RUDN University, 117198 Moscow, Russia"},{"name":"Medical Institute, Banzarov Buryat State University, 670000 Ulan-Ude, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,30]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1038\/ng1094-148","article-title":"Long-Term Gene Expression and Phenotypic Correction Using Adeno-Associated Virus Vectors in the Mammalian Brain","volume":"8","author":"Kaplitt","year":"1994","journal-title":"Nat. Genet."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"754","DOI":"10.1126\/science.149.3685.754","article-title":"Adenovirus-Associated Defective Virus Particles","volume":"149","author":"Atchison","year":"1965","journal-title":"Science"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1128\/jvi.45.2.555-564.1983","article-title":"Nucleotide Sequence and Organization of the Adeno-Associated Virus 2 Genome","volume":"45","author":"Srivastava","year":"1983","journal-title":"J. Virol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1038\/s41573-019-0012-9","article-title":"Adeno-Associated Virus Vector as a Platform for Gene Therapy Delivery","volume":"18","author":"Wang","year":"2019","journal-title":"Nat. Rev. Drug Discov."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"3822","DOI":"10.1128\/jvi.63.9.3822-3828.1989","article-title":"Helper-Free Stocks of Recombinant Adeno-Associated Viruses: Normal Integration Does Not Require Viral Gene Expression","volume":"63","author":"Samulski","year":"1989","journal-title":"J. Virol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2211","DOI":"10.1073\/pnas.87.6.2211","article-title":"Site-Specific Integration by Adeno-Associated Virus","volume":"87","author":"Kotin","year":"1990","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1016\/j.tim.2021.09.005","article-title":"Adeno-Associated Virus (AAV) Cell Entry: Structural Insights","volume":"30","author":"Meyer","year":"2022","journal-title":"Trends Microbiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1007\/s40259-017-0234-5","article-title":"Adeno-Associated Virus (AAV) as a Vector for Gene Therapy","volume":"31","author":"Naso","year":"2017","journal-title":"BioDrugs"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1038\/s41392-024-01780-w","article-title":"Adeno-Associated Virus as a Delivery Vector for Gene Therapy of Human Diseases","volume":"9","author":"Wang","year":"2024","journal-title":"Signal Transduct. Target. Ther."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1038\/s41551-026-01643-5","article-title":"Engineering Challenges and Translational Opportunities in Emerging Gene Delivery Platforms","volume":"10","author":"Ma","year":"2026","journal-title":"Nat. Biomed. Eng."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1248","DOI":"10.1038\/sj.gt.3301514","article-title":"Self-Complementary Recombinant Adeno-Associated Virus (scAAV) Vectors Promote Efficient Transduction Independently of DNA Synthesis","volume":"8","author":"McCarty","year":"2001","journal-title":"Gene Ther."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1713","DOI":"10.1056\/NEJMoa1706198","article-title":"Single-Dose Gene-Replacement Therapy for Spinal Muscular Atrophy","volume":"377","author":"Mendell","year":"2017","journal-title":"N. Engl. J. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"2357","DOI":"10.1056\/NEJMoa1108046","article-title":"Adenovirus-Associated Virus Vector\u2013Mediated Gene Transfer in Hemophilia B","volume":"365","author":"Nathwani","year":"2011","journal-title":"N. Engl. J. Med."},{"key":"ref_14","first-page":"1183","article-title":"Adeno-Associated Virus Structural Biology as a Tool in Vector Development","volume":"7","author":"Drouin","year":"2014","journal-title":"Future Virol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.1089\/hum.2008.123","article-title":"Adeno-Associated Virus (AAV) Serotype 9 Provides Global Cardiac Gene Transfer Superior to AAV1, AAV6, AAV7, and AAV8 in the Mouse and Rat","volume":"19","author":"Bish","year":"2008","journal-title":"Hum. Gene Ther."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1186\/1743-422X-10-74","article-title":"A Survey of Ex Vivo\/in Vitro Transduction Efficiency of Mammalian Primary Cells and Cell Lines with Nine Natural Adeno-Associated Virus (AAV1-9) and One Engineered Adeno-Associated Virus Serotype","volume":"10","author":"Ellis","year":"2013","journal-title":"Virol. J."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1089\/hum.2019.264","article-title":"High-Throughput In Vitro, Ex Vivo, and In Vivo Screen of Adeno-Associated Virus Vectors Based on Physical and Functional Transduction","volume":"31","author":"Westhaus","year":"2020","journal-title":"Hum. Gene Ther."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"2000025","DOI":"10.1002\/biot.202000025","article-title":"Production, Processing, and Characterization of Synthetic AAV Gene Therapy Vectors","volume":"16","author":"Grimm","year":"2021","journal-title":"Biotechnol. J."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1343","DOI":"10.1089\/hum.2010.003","article-title":"Adeno-Associated Virus Serotype 6 Capsid Tyrosine-to-Phenylalanine Mutations Improve Gene Transfer to Skeletal Muscle","volume":"21","author":"Qiao","year":"2010","journal-title":"Hum. Gene Ther."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3279","DOI":"10.1038\/s41467-020-17047-1","article-title":"Structural Characterization of a Novel Human Adeno-Associated Virus Capsid with Neurotropic Properties","volume":"11","author":"Hsu","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.neuron.2012.05.019","article-title":"Restoration of Hearing in the VGLUT3 Knockout Mouse Using Virally Mediated Gene Therapy","volume":"75","author":"Akil","year":"2012","journal-title":"Neuron"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1438","DOI":"10.1128\/JVI.72.2.1438-1445.1998","article-title":"Membrane-associated heparan sulfate proteoglycan is a receptor for adeno-associated virus type 2 virions","volume":"72","author":"Summerford","year":"1998","journal-title":"J. Virol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.omtm.2020.05.028","article-title":"Cerebral organoids: A human model for AAV capsid selection and therapeutic transgene efficacy in the brain","volume":"18","author":"Depla","year":"2020","journal-title":"Mol. Ther. Methods Clin. Dev."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1038\/s41586-019-1191-6","article-title":"MicroRNA Therapy Stimulates Uncontrolled Cardiac Repair after Myocardial Infarction in Pigs","volume":"569","author":"Gabisonia","year":"2019","journal-title":"Nature"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1002\/jgm.1602","article-title":"Long-term Functional Adeno-associated Virus-microdystrophin Expression in the Dystrophic CXMDj Dog","volume":"13","author":"Koo","year":"2011","journal-title":"J. Gene Med."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1089\/hum.2022.037","article-title":"Cell-Selective Adeno-Associated Virus-Mediated SCN1A Gene Regulation Therapy Rescues Mortality and Seizure Phenotypes in a Dravet Syndrome Mouse Model and Is Well Tolerated in Nonhuman Primates","volume":"33","author":"Tanenhaus","year":"2022","journal-title":"Hum. Gene Ther."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1172","DOI":"10.1038\/nn.4593","article-title":"Engineered AAVs for Efficient Noninvasive Gene Delivery to the Central and Peripheral Nervous Systems","volume":"20","author":"Chan","year":"2017","journal-title":"Nat. Neurosci."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"4919","DOI":"10.1016\/j.cell.2021.08.028","article-title":"Directed Evolution of a Family of AAV Capsid Variants Enabling Potent Muscle-Directed Gene Delivery across Species","volume":"184","author":"Tabebordbar","year":"2021","journal-title":"Cell"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Garita-Hernandez, M., Routet, F., Guibbal, L., Khabou, H., Toualbi, L., Riancho, L., Reichman, S., Duebel, J., Sahel, J.-A., and Goureau, O. (2020). AAV-Mediated Gene Delivery to 3D Retinal Organoids Derived from Human Induced Pluripotent Stem Cells. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21030994"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1016\/j.omtm.2023.08.010","article-title":"Development of New Adeno-Associated Virus Capsid Variants for Targeted Gene Delivery to Human Cardiomyocytes","volume":"30","author":"Kok","year":"2023","journal-title":"Mol. Ther. Methods Clin. Dev."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1038\/s41434-021-00244-y","article-title":"Enhanced CNS Transduction from AAV.PHP.eB Infusion into the Cisterna Magna of Older Adult Rats Compared to AAV9","volume":"29","author":"Chatterjee","year":"2022","journal-title":"Gene Ther."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/s13395-024-00341-7","article-title":"Comparative in Vivo Characterization of Newly Discovered Myotropic Adeno-Associated Vectors","volume":"14","author":"Ji","year":"2024","journal-title":"Skelet. Muscle"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"7038","DOI":"10.1073\/pnas.1303829110","article-title":"Generation of Induced Neurons via Direct Conversion in Vivo","volume":"110","author":"Torper","year":"2013","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nbt.1515","article-title":"Intravascular AAV9 Preferentially Targets Neonatal Neurons and Adult Astrocytes","volume":"27","author":"Foust","year":"2009","journal-title":"Nat. Biotechnol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"7598","DOI":"10.1016\/j.biomaterials.2014.05.032","article-title":"Naturally Enveloped AAV Vectors for Shielding Neutralizing Antibodies and Robust Gene Delivery in Vivo","volume":"35","author":"Fitzpatrick","year":"2014","journal-title":"Biomaterials"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1186\/s12951-025-03261-w","article-title":"Biomimetic Gene Delivery System Coupled with Extracellular Vesicle\u2013Encapsulated AAV for Improving Diabetic Wound through Promoting Vascularization and Remodeling of Inflammatory Microenvironment","volume":"23","author":"He","year":"2025","journal-title":"J. Nanobiotechnol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1016\/j.cell.2006.07.024","article-title":"Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors","volume":"126","author":"Takahashi","year":"2006","journal-title":"Cell"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1242\/dev.10.4.622","article-title":"The Developmental Capacity of Nuclei Taken from Intestinal Epithelium Cells of Feeding Tadpoles","volume":"10","author":"Gurdon","year":"1962","journal-title":"Development"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1016\/j.stem.2007.05.014","article-title":"Directly Reprogrammed Fibroblasts Show Global Epigenetic Remodeling and Widespread Tissue Contribution","volume":"1","author":"Maherali","year":"2007","journal-title":"Cell Stem Cell"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1016\/j.cell.2007.11.019","article-title":"Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors","volume":"131","author":"Takahashi","year":"2007","journal-title":"Cell"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1038\/nature05944","article-title":"In Vitro Reprogramming of Fibroblasts into a Pluripotent ES-Cell-like State","volume":"448","author":"Wernig","year":"2007","journal-title":"Nature"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.1126\/science.1158799","article-title":"Induced Pluripotent Stem Cells Generated from Patients with ALS Can Be Differentiated into Motor Neurons","volume":"321","author":"Dimos","year":"2008","journal-title":"Science"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1920","DOI":"10.1126\/science.1152092","article-title":"Treatment of Sickle Cell Anemia Mouse Model with iPS Cells Generated from Autologous Skin","volume":"318","author":"Hanna","year":"2007","journal-title":"Science"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1038\/nature08592","article-title":"Direct Cell Reprogramming Is a Stochastic Process Amenable to Acceleration","volume":"462","author":"Hanna","year":"2009","journal-title":"Nature"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nbt1374","article-title":"Generation of Induced Pluripotent Stem Cells without Myc from Mouse and Human Fibroblasts","volume":"26","author":"Nakagawa","year":"2007","journal-title":"Nat. Biotechnol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/nature05934","article-title":"Generation of Germline-Competent Induced Pluripotent Stem Cells","volume":"448","author":"Okita","year":"2007","journal-title":"Nature"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1126\/science.1164270","article-title":"Generation of Mouse Induced Pluripotent Stem Cells Without Viral Vectors","volume":"322","author":"Okita","year":"2008","journal-title":"Science"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1126\/science.1172482","article-title":"Human Induced Pluripotent Stem Cells Free of Vector and Transgene Sequences","volume":"324","author":"Yu","year":"2009","journal-title":"Science"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/nmeth.1591","article-title":"A More Efficient Method to Generate Integration-Free Human iPS Cells","volume":"8","author":"Okita","year":"2011","journal-title":"Nat. Methods"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1016\/j.stem.2010.08.012","article-title":"Highly Efficient Reprogramming to Pluripotency and Directed Differentiation of Human Cells with Synthetic Modified mRNA","volume":"7","author":"Warren","year":"2010","journal-title":"Cell Stem Cell"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"4463","DOI":"10.1128\/JVI.06302-11","article-title":"Induced Pluripotent Stem Cell Clones Reprogrammed via Recombinant Adeno-Associated Virus-Mediated Transduction Contain Integrated Vector Sequences","volume":"86","author":"Weltner","year":"2012","journal-title":"J. Virol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"2651","DOI":"10.1038\/s41467-018-05059-x","article-title":"AAV Vector-Mediated in Vivo Reprogramming into Pluripotency","volume":"9","author":"Mosteiro","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"2304551","DOI":"10.1002\/advs.202304551","article-title":"AAV-mediated Gene Cocktails Enhance Supporting Cell Reprogramming and Hair Cell Regeneration","volume":"11","author":"Zhang","year":"2024","journal-title":"Adv. Sci."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1192","DOI":"10.1038\/mt.2010.55","article-title":"Engineering of Human Pluripotent Stem Cells by AAV-Mediated Gene Targeting","volume":"18","author":"Khan","year":"2010","journal-title":"Mol. Ther."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"8356","DOI":"10.1038\/s41598-022-12404-0","article-title":"Identification of Adeno-Associated Virus Variants for Gene Transfer into Human Neural Cell Types by Parallel Capsid Screening","volume":"12","author":"Flitsch","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1038\/nature08797","article-title":"Direct Conversion of Fibroblasts to Functional Neurons by Defined Factors","volume":"463","author":"Vierbuchen","year":"2010","journal-title":"Nature"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"2300040","DOI":"10.1002\/adtp.202300040","article-title":"Synergistic Enhancement of Adeno-Associated Virus-Mediated In Vivo Direct Neuronal Reprogramming by Spatially Aligned Fibrous Matrices in Spinal Cord Injury Models","volume":"6","author":"Kim","year":"2023","journal-title":"Adv. Ther."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Puglisi, M., Lao, C.L., Wani, G., Masserdotti, G., Bocchi, R., and G\u00f6tz, M. (2024). Comparing Viral Vectors and Fate Mapping Approaches for Astrocyte-to-Neuron Reprogramming in the Injured Mouse Cerebral Cortex. Cells, 13.","DOI":"10.3390\/cells13171408"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"104531","DOI":"10.1016\/j.ebiom.2023.104531","article-title":"New AAV Tools Fail to Detect Neurod1-Mediated Neuronal Conversion of M\u00fcller Glia and Astrocytes in Vivo","volume":"90","author":"Xie","year":"2023","journal-title":"eBioMedicine"},{"key":"ref_60","doi-asserted-by":"crossref","unstructured":"Cappella, M., Elouej, S., and Biferi, M.G. (2021). The Potential of Induced Pluripotent Stem Cells to Test Gene Therapy Approaches for Neuromuscular and Motor Neuron Disorders. Front. Cell Dev. Biol., 9.","DOI":"10.3389\/fcell.2021.662837"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"14067","DOI":"10.1038\/mtm.2014.67","article-title":"Effectiveness of Gene Delivery Systems for Pluripotent and Differentiated Cells","volume":"2","author":"Rapti","year":"2015","journal-title":"Mol. Ther. Methods Clin. Dev."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1161\/CIRCULATIONAHA.122.063759","article-title":"Extracellular Vesicle\u2013Encapsulated Adeno-Associated Viruses for Therapeutic Gene Delivery to the Heart","volume":"148","author":"Li","year":"2023","journal-title":"Circulation"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"101467","DOI":"10.1016\/j.omtm.2025.101467","article-title":"iPSC-Hepatocyte Organoids as a Novel Platform to Predict AAV Gene Therapy Efficacy","volume":"33","author":"Berreur","year":"2025","journal-title":"Mol. Ther. Methods Clin. Dev."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1038\/s41551-023-01058-6","article-title":"AAV-Mediated Delivery of a Sleeping Beauty Transposon and an mRNA-Encoded Transposase for the Engineering of Therapeutic Immune Cells","volume":"8","author":"Ye","year":"2024","journal-title":"Nat. Biomed. Eng."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1165\/rcmb.2022-0424MA","article-title":"Efficient Adeno-Associated Virus\u2013Mediated Transgenesis in Alveolar Stem Cells and Associated Niches","volume":"69","author":"Konkimalla","year":"2023","journal-title":"Am. J. Respir. Cell Mol. Biol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1038\/mt.2011.255","article-title":"Directed Evolution of Adeno-Associated Virus for Enhanced Gene Delivery and Gene Targeting in Human Pluripotent Stem Cells","volume":"20","author":"Asuri","year":"2012","journal-title":"Mol. Ther."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"3694","DOI":"10.1038\/s41467-025-58778-3","article-title":"AAV Vectors Trigger DNA Damage Response-Dependent pro-Inflammatory Signalling in Human iPSC-Derived CNS Models and Mouse Brain","volume":"16","author":"Meneghini","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1080\/14712598.2022.2060737","article-title":"Addressing High Dose AAV Toxicity\u2014\u2018One and Done\u2019 or \u2018Slower and Lower\u2019?","volume":"22","author":"Kishimoto","year":"2022","journal-title":"Expert Opin. Biol. Ther."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"3515","DOI":"10.1016\/j.ymthe.2022.09.015","article-title":"AAV Vectors: The Rubik\u2019s Cube of Human Gene Therapy","volume":"30","author":"Pupo","year":"2022","journal-title":"Mol. Ther."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"2118","DOI":"10.1038\/s41467-025-57382-9","article-title":"Impact of Liver Fibrosis on AAV-Mediated Gene Transfer to Mouse Hepatocytes","volume":"16","author":"Ferriero","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"bio058678","DOI":"10.1242\/bio.058678","article-title":"Specificity and Off-Target Effects of AAV8-TBG Viral Vectors for the Manipulation of Hepatocellular Gene Expression in Mice","volume":"10","author":"Kiourtis","year":"2021","journal-title":"Biol. Open"},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"McGinnis, J., Ortiz-Guzman, J., Guevara, M.C., Mallannagari, S., Belfort, B.D.W., Bao, S., Srivastava, S., Morkas, M., Ji, E., and Addison, A. (2024). Common AAV Gene Therapy Vectors Show Indiscriminate Transduction of Living Human Brain Cell Types. bioRxiv.","DOI":"10.1101\/2024.11.14.623624"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1016\/j.ymthe.2005.11.015","article-title":"Wolfe Transduction Characteristics of Adeno-Associated Virus Vectors Expressing Cap Serotypes 7, 8, 9, and Rh10 in the Mouse Brain","volume":"13","author":"Cearley","year":"2006","journal-title":"Mol. Ther."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/gt.2010.105","article-title":"Robust Cardiomyocyte-Specific Gene Expression Following Systemic Injection of AAV: In Vivo Gene Delivery Follows a Poisson Distribution","volume":"18","author":"Prasad","year":"2011","journal-title":"Gene Ther."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"1389","DOI":"10.1016\/j.stemcr.2024.08.002","article-title":"Development of Adeno-Associated Viral Vectors Targeting Cardiac Fibroblasts for Efficient in Vivo Cardiac Reprogramming","volume":"19","author":"Nakano","year":"2024","journal-title":"Stem Cell Rep."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"2096","DOI":"10.1038\/mt.2009.181","article-title":"Inner Limiting Membrane Barriers to AAV-Mediated Retinal Transduction from the Vitreous","volume":"17","author":"Dalkara","year":"2009","journal-title":"Mol. Ther."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1038\/mt.2012.280","article-title":"A Comprehensive Review of Retinal Gene Therapy","volume":"21","author":"Boye","year":"2013","journal-title":"Mol. Ther."},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Verberne, A.J.M., Sabetghadam, A., and Korim, W.S. (2014). Neural Pathways That Control the Glucose Counterregulatory Response. Front. Neurosci., 8.","DOI":"10.3389\/fnins.2014.00038"},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Van Wyk, M., Hulliger, E.C., Girod, L., Ebneter, A., and Kleinlogel, S. (2017). Present Molecular Limitations of ON-Bipolar Cell Targeted Gene Therapy. Front. Neurosci., 11.","DOI":"10.3389\/fnins.2017.00161"},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Le, N., Appel, H., Pannullo, N., Hoang, T., and Blackshaw, S. (2022). Ectopic Insert-Dependent Neuronal Expression of GFAP Promoter-Driven AAV Constructs in Adult Mouse Retina. Front. Cell Dev. Biol., 10.","DOI":"10.3389\/fcell.2022.914386"},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"31583","DOI":"10.1038\/s41598-024-79124-5","article-title":"Regionally Distinct GFAP Promoter Expression Plays a Role in Off-Target Neuron Expression Following AAV5 Transduction","volume":"14","author":"Enbar","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.omtn.2017.03.009","article-title":"A MicroRNA124 Target Sequence Restores Astrocyte Specificity of gfaABC1D-Driven Transgene Expression in AAV-Mediated Gene Transfer","volume":"8","author":"Taschenberger","year":"2017","journal-title":"Mol. Ther. Nucleic Acids"},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Hirsch, M.L., Fagan, B.M., Dumitru, R., Bower, J.J., Yadav, S., Porteus, M.H., Pevny, L.H., and Samulski, R.J. (2011). Viral Single-Strand DNA Induces P53-Dependent Apoptosis in Human Embryonic Stem Cells. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0027520"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"gkaf013","DOI":"10.1093\/nar\/gkaf013","article-title":"AAV Vector Transduction Restriction and Attenuated Toxicity in hESCs via a Rationally Designed Inverted Terminal Repeat","volume":"53","author":"Song","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"2242","DOI":"10.1016\/j.stemcr.2021.08.008","article-title":"Human Stem Cell-Based Retina on Chip as New Translational Model for Validation of AAV Retinal Gene Therapy Vectors","volume":"16","author":"Achberger","year":"2021","journal-title":"Stem Cell Rep."},{"key":"ref_86","doi-asserted-by":"crossref","unstructured":"Dudek, A.M., and Porteus, M.H. (2021). Answered and Unanswered Questions in Early-Stage Viral Vector Transduction Biology and Innate Primary Cell Toxicity for Ex-Vivo Gene Editing. Front. Immunol., 12.","DOI":"10.3389\/fimmu.2021.660302"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"2606983","DOI":"10.1080\/15592294.2025.2606983","article-title":"Silencing of Optogenetic and Chemogenetic Transgenes in Human iPSCs Involves Promoter Methylation and Methylation-Independent Mechanisms","volume":"21","author":"Wang","year":"2026","journal-title":"Epigenetics"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1093\/nar\/gkv019","article-title":"A Minimal Ubiquitous Chromatin Opening Element (UCOE) Effectively Prevents Silencing of Juxtaposed Heterologous Promoters by Epigenetic Remodeling in Multipotent and Pluripotent Stem Cells","volume":"43","author":"Ackermann","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"2101","DOI":"10.1089\/hum.1996.7.17-2101","article-title":"Quantitative Analysis of the Packaging Capacity of Recombinant Adeno-Associated Virus","volume":"7","author":"Dong","year":"1996","journal-title":"Hum. Gene Ther."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1038\/343180a0","article-title":"Very Mild Muscular Dystrophy Associated with the Deletion of 46% of Dystrophin","volume":"343","author":"England","year":"1990","journal-title":"Nature"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"2224","DOI":"10.1182\/blood-2012-10-460733","article-title":"Engineered AAV Vector Minimizes in Vivo Targeting of Transduced Hepatocytes by Capsid-Specific CD8+ T Cells","volume":"121","author":"Martino","year":"2013","journal-title":"Blood"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1038\/nm0302-253","article-title":"Modular Flexibility of Dystrophin: Implications for Gene Therapy of Duchenne Muscular Dystrophy","volume":"8","author":"Harper","year":"2002","journal-title":"Nat. Med."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"13714","DOI":"10.1073\/pnas.240335297","article-title":"Adeno-Associated Virus Vector Carrying Human Minidystrophin Genes Effectively Ameliorates Muscular Dystrophy in Mdx Mouse Model","volume":"97","author":"Wang","year":"2000","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1089\/hum.2009.182","article-title":"Prevalence of Serum IgG and Neutralizing Factors Against Adeno-Associated Virus (AAV) Types 1, 2, 5, 6, 8, and 9 in the Healthy Population: Implications for Gene Therapy Using AAV Vectors","volume":"21","author":"Boutin","year":"2010","journal-title":"Hum. Gene Ther."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1038\/nm1358","article-title":"Successful Transduction of Liver in Hemophilia by AAV-Factor IX and Limitations Imposed by the Host Immune Response","volume":"12","author":"Manno","year":"2006","journal-title":"Nat. Med."},{"key":"ref_96","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1038\/nm1549","article-title":"CD8+ T-Cell Responses to Adeno-Associated Virus Capsid in Humans","volume":"13","author":"Mingozzi","year":"2007","journal-title":"Nat. Med."},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"2727","DOI":"10.1128\/JVI.01990-07","article-title":"Complement Is an Essential Component of the Immune Response to Adeno-Associated Virus Vectors","volume":"82","author":"Zaiss","year":"2008","journal-title":"J. Virol."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"2388","DOI":"10.1172\/JCI37607","article-title":"The TLR9-MyD88 Pathway Is Critical for Adaptive Immune Responses to Adeno-Associated Virus Gene Therapy Vectors in Mice","volume":"119","author":"Zhu","year":"2009","journal-title":"J. Clin. Investig."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1016\/j.jpeds.2020.05.044","article-title":"Subacute Liver Failure Following Gene Replacement Therapy for Spinal Muscular Atrophy Type 1","volume":"225","author":"Feldman","year":"2020","journal-title":"J. Pediatr."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1182\/blood-2013-01-306647","article-title":"Immune Responses to AAV Vectors: Overcoming Barriers to Successful Gene Therapy","volume":"122","author":"Mingozzi","year":"2013","journal-title":"Blood"},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1016\/S1474-4422(23)00313-7","article-title":"Safety and Efficacy of Gene Replacement Therapy for X-Linked Myotubular Myopathy (ASPIRO): A Multinational, Open-Label, Dose-Escalation Trial","volume":"22","author":"Shieh","year":"2023","journal-title":"Lancet Neurol."},{"key":"ref_102","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1089\/hum.2018.015","article-title":"Severe Toxicity in Nonhuman Primates and Piglets Following High-Dose Intravenous Administration of an Adeno-Associated Virus Vector Expressing Human SMN","volume":"29","author":"Hinderer","year":"2018","journal-title":"Hum. Gene Ther."},{"key":"ref_103","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1089\/hum.2019.006","article-title":"Gene Delivery for Limb-Girdle Muscular Dystrophy Type 2D by Isolated Limb Infusion","volume":"30","author":"Mendell","year":"2019","journal-title":"Hum. Gene Ther."},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"870","DOI":"10.1172\/JCI79213","article-title":"Vector Design Influences Hepatic Genotoxicity after Adeno-Associated Virus Gene Therapy","volume":"125","author":"Chandler","year":"2015","journal-title":"J. Clin. Investig."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1126\/science.1142658","article-title":"AAV Vector Integration Sites in Mouse Hepatocellular Carcinoma","volume":"317","author":"Donsante","year":"2007","journal-title":"Science"},{"key":"ref_106","doi-asserted-by":"crossref","first-page":"3311","DOI":"10.1182\/blood-2010-08-302729","article-title":"Assessing the Potential for AAV Vector Genotoxicity in a Murine Model","volume":"117","author":"Li","year":"2011","journal-title":"Blood"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"4439","DOI":"10.1038\/s41467-019-12449-2","article-title":"High Levels of AAV Vector Integration into CRISPR-Induced DNA Breaks","volume":"10","author":"Hanlon","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1038\/s41591-019-0344-3","article-title":"Long-Term Evaluation of AAV-CRISPR Genome Editing for Duchenne Muscular Dystrophy","volume":"25","author":"Nelson","year":"2019","journal-title":"Nat. Med."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1002\/jgm.516","article-title":"Transcriptional Silencing Is Associated with Extensive Methylation of the CMV Promoter Following Adenoviral Gene Delivery to Muscle","volume":"6","author":"Brooks","year":"2004","journal-title":"J. Gene Med."},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.gene.2008.09.033","article-title":"Epigenetic Regulation of Cytomegalovirus Major Immediate-Early Promoter Activity in Transgenic Mice","volume":"428","author":"Mehta","year":"2009","journal-title":"Gene"},{"key":"ref_111","doi-asserted-by":"crossref","first-page":"6969","DOI":"10.1128\/JVI.75.15.6969-6976.2001","article-title":"Extrachromosomal Recombinant Adeno-Associated Virus Vector Genomes Are Primarily Responsible for Stable Liver Transduction In Vivo","volume":"75","author":"Nakai","year":"2001","journal-title":"J. Virol."},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"3495","DOI":"10.1128\/JVI.77.6.3495-3504.2003","article-title":"Genetic Fate of Recombinant Adeno-Associated Virus Vector Genomes in Muscle","volume":"77","author":"Schnepp","year":"2003","journal-title":"J. Virol."},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/j.cels.2022.05.001","article-title":"Diploid Hepatocytes Drive Physiological Liver Renewal in Adult Humans","volume":"13","author":"Heinke","year":"2022","journal-title":"Cell Syst."},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1038\/mt.2008.103","article-title":"Recombinant Adeno-Associated Virus Transduction and Integration","volume":"16","author":"Schultz","year":"2008","journal-title":"Mol. Ther."},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1038\/mt.2013.244","article-title":"Plasmapheresis Eliminates the Negative Impact of AAV Antibodies on Microdystrophin Gene Expression Following Vascular Delivery","volume":"22","author":"Chicoine","year":"2014","journal-title":"Mol. Ther."},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1038\/s41591-020-0911-7","article-title":"IgG-Cleaving Endopeptidase Enables in Vivo Gene Therapy in the Presence of Anti-AAV Neutralizing Antibodies","volume":"26","author":"Leborgne","year":"2020","journal-title":"Nat. Med."},{"key":"ref_117","doi-asserted-by":"crossref","first-page":"101496","DOI":"10.1016\/j.omtm.2025.101496","article-title":"The Manufacture of AAV for Gene Therapy Applications Using a Closed, Semi-Automated Hollow-Fiber Bioreactor","volume":"33","author":"Soula","year":"2025","journal-title":"Mol. Ther. Methods Clin. Dev."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/15\/6846\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T16:15:36Z","timestamp":1785428136000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/27\/15\/6846"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,30]]},"references-count":117,"journal-issue":{"issue":"15","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["ijms27156846"],"URL":"https:\/\/doi.org\/10.3390\/ijms27156846","relation":{},"ISSN":["1422-0067"],"issn-type":[{"value":"1422-0067","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,30]]}}}