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Changing trends in the development of AAV-based gene therapies: a meta-analysis of past and present therapies

Abstract

Gene therapy has seen a transformation from a proof-of-concept approach to a clinical reality over the past several decades, with adeno-associated virus (AAV)-mediated gene therapy emerging as the leading platform for in vivo gene transfer. A systematic review of AAV-based gene therapies in clinical development was conducted herein to determine why only a handful of AAV-based gene therapy products have achieved market approval. The indication to be treated, route of administration and vector design were investigated as critical factors and assessed for their impact on clinical safety and efficacy. A shift in recent years towards high-dose systemic administration for the treatment of metabolic, neurological and haematological diseases was identified, with intravenous administration demonstrating the highest efficacy and safety risks in clinical trials. Recent years have seen a decline in favour of traditional AAV serotypes and promoters, accompanied by an increase in favour and higher clinical success rate for novel capsids and tissue-specific promoters. Furthermore, a meta-analysis was performed to identify factors that may inhibit the translation of therapeutic efficacy from preclinical large animal studies to first-in-human clinical trials and a detrimental effect on clinical efficacy was associated with alterations to administration routes.

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Fig. 1: PRISMA 2020 flow diagram displaying the identification and screening process of study selection and the quantity and types of records included in the analysis.
Fig. 2: AAV-based gene therapy by therapeutic area (n = 217).
Fig. 3: Efficacy and safety of AAV-based gene therapy by therapeutic area.
Fig. 4: AAV-based gene therapy by route of administration.
Fig. 5: Efficacy and safety of AAV-based gene therapy by route of administration.
Fig. 6: AAV-based gene therapy by vector design.
Fig. 7: Efficacy and safety of AAV-based gene therapy by AAV serotypes.
Fig. 8: Efficacy and safety of AAV-based gene therapy by AAV promoters.
Fig. 9: The effect of changing route of administration from preclinical studies to clinical trials.
Fig. 10: The effect of fold change in dose from preclinical studies to clinical trials.

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Data availability

Data generated and analysed within this study can be found within the supplementary files associated with the submission.

References

  1. Kay MA. State-of-the-art gene-based therapies: the road ahead. Nat Rev Genet. 2011;12:316–28.

    Article  CAS  PubMed  Google Scholar 

  2. dos Santos Coura R, Nardi NB. A role for adeno-associated viral vectors in gene therapy. Genet Mol Biol. 2008;31:1–11.

    Article  Google Scholar 

  3. Dunbar CE, High KA, Joung JK, Kohn DB, Ozawa K, Sadelain M. Gene therapy comes of age. Science. 2018;359:eaan4672.

  4. Kotterman MA, Chalberg TW, Schaffer DV. Viral vectors for gene therapy: translational and clinical outlook. Annu Rev Biomed Eng. 2015;17:63–89. 101146/annurev-bioeng-071813-104938.

  5. Mendell JR, Al-Zaidy SA, Rodino-Klapac LR, Goodspeed K, Gray SJ, Kay CN, et al. Current clinical applications of in vivo gene therapy with AAVs. Mol Ther. 2021;29:464–88.

    Article  CAS  PubMed  Google Scholar 

  6. Bulcha JT, Wang Y, Ma H, Tai PWL, Gao G. Viral vector platforms within the gene therapy landscape. Signal Transduct Target Ther. 2021;6:1–24.

    Google Scholar 

  7. Naso MF, Tomkowicz B, Perry WL III, Strohl WR. Adeno-associated virus (AAV) as a vector for gene therapy. Biodrugs. 2017;31:317.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Shirley JL, Jong YP, de, Terhorst C, Herzog RW. Immune responses to viral gene therapy vectors. Mol Ther. 2020;28:709–22.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Kumar SR, Markusic DM, Biswas M, High KA, Herzog RW. Clinical development of gene therapy: results and lessons from recent successes. Mol Ther Methods Clin Dev. 2016;3:16034.

    Article  PubMed  PubMed Central  Google Scholar 

  10. Rose JA, Hoggan MD, Shatkin AJ. Nucleic acid from an adeno-associated virus: chemical and physical studies. Proc Natl Acad Sci USA 1966;56:86–92.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Daya S, Berns KI. Gene therapy using adeno-associated virus vectors. Clin Microbiol Rev. 2008;21:583.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Ogden PJ, Kelsic ED, Sinai S, Church GM. Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design. Science. 2019;366:1139–43.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Maurer AC, Cepeda Diaz AK, Vandenberghe LH. Residues on adeno-associated virus capsid lumen dictate interactions and compatibility with the assembly-activating protein. J Virol. 2019;93:2013–31.

    Article  Google Scholar 

  14. Cao M, You H, Hermonat PL. The X gene of adeno-associated virus 2 (AAV2) is involved in viral DNA replication. PLoS One. 2014;9:e104596.

    Article  PubMed  PubMed Central  Google Scholar 

  15. Srivastava A. In vivo tissue-tropism of adeno-associated viral vectors. Curr Opin Virol. 2016;21:75.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Bennett A, Patel S, Mietzsch M, Jose A, Lins-Austin B, Yu JC, et al. Thermal stability as a determinant of AAV serotype identity. Mol Ther Methods Clin Dev. 2017;6:171–82.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Nault JC, Datta S, Imbeaud S, Franconi A, Mallet M, Couchy G, et al. Recurrent AAV2-related insertional mutagenesis in human hepatocellular carcinomas. Nat Genet. 2015;47:1187–93.

    Article  CAS  PubMed  Google Scholar 

  18. Bartlett JS, Wilcher R, Samulski RJ. Infectious entry pathway of adeno-associated virus and adeno-associated virus vectors. J Virol. 2000;74:2777.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Hamilton H, Gomos J, Berns KI, Falck-Pedersen E. Adeno-associated virus site-specific integration and AAVS1 disruption. J Virol. 2004;78:7874–82.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. McCarty DM, Young SM, Samulski RJ. Integration of adeno-associated virus (AAV) and recombinant AAV vectors. Annu Rev Genet. 2004;38:819–45.

    Article  CAS  PubMed  Google Scholar 

  21. Schnepp BC, Jensen RL, Chen C-L, Johnson PR, Clark KR. Characterization of adeno-associated virus genomes isolated from human tissues. J Virol. 2005;79:14793–803.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Yan Z, Zhang Y, Duan D, Engelhardt JF. Trans-splicing vectors expand the utility of adeno-associated virus for gene therapy. Proc Natl Acad Sci USA 2000;97:6716–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Earley LF, Conatser LM, Lue VM, Dobbins AL, Li C, Hirsch ML, et al. Adeno-associated virus serotype-specific inverted terminal repeat sequence role in vector transgene expression. Hum Gene Ther. 2020;31:151.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Ehrhardt A, Xu H, Kay MA. Episomal persistence of recombinant adenoviral vector genomes during the cell cycle in vivo. J Virol. 2003;77:7689.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Riyad JM, Weber T. Intracellular trafficking of adeno-associated virus (AAV) vectors: challenges and future directions. Gene Ther. 2021;28:683–96.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Balakrishnan B, Jayandharan G. Basic biology of adeno-associated virus (AAV) vectors used in gene therapy. Curr Gene Ther. 2014;14:86–100.

    Article  CAS  PubMed  Google Scholar 

  27. Weinmann J, Grimm D. Next-generation AAV vectors for clinical use: an ever-accelerating race. Virus Genes. 2017;53:707–13.

    Article  CAS  PubMed  Google Scholar 

  28. Bowles DE, McPhee SWJ, Li C, Gray SJ, Samulski JJ, Camp AS, et al. Phase 1 gene therapy for Duchenne muscular dystrophy using a translational optimized AAV vector. Mol Ther. 2012;20:443–55.

    Article  CAS  PubMed  Google Scholar 

  29. Domenger C, Grimm D. Next-generation AAV vectors—do not judge a virus (only) by its cover. Hum Mol Genet. 2019;28:R3–14.

    Article  CAS  PubMed  Google Scholar 

  30. Verdera HC, Kuranda K, Mingozzi F. AAV vector immunogenicity in humans: a long journey to successful gene transfer. Mol Ther. 2020;28:723.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Muhuri M, Maeda Y, Ma H, Ram S, Fitzgerald KA, Tai PWL, et al. Overcoming innate immune barriers that impede AAV gene therapy vectors. J Clin Invest. 2021;131:e143780.

  32. Mingozzi F, High KA. Immune responses to AAV vectors: overcoming barriers to successful gene therapy. Blood. 2013;122:23–36.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Lykken EA, Shyng C, Edwards RJ, Rozenberg A, Gray SJ. Recent progress and considerations for AAV gene therapies targeting the central nervous system. J Neurodev Disord. 2018;10:1–10.

    Article  Google Scholar 

  34. Page MJ, McKenzie JE, Bossuyt PM, Boutron I, Hoffmann TC, Mulrow CD, et al. The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. BMJ. 2021;372:n71.

  35. Brown D. A review of the PubMed PICO tool: using evidence-based practice in health education. Health Promot Pract. 2020;21:496–8. https://doi.org/10.1177/1524839919893361.

  36. Alexander IE, Cunningham SC, Logan GJ, Christodoulou J. Potential of AAV vectors in the treatment of metabolic disease. Gene Ther. 2008;15:831–9.

    Article  CAS  PubMed  Google Scholar 

  37. Lee JH, Wang JH, Chen J, Li F, Edwards TL, Hewitt AW, et al. Gene therapy for visual loss: opportunities and concerns. Prog Retin Eye Res. 2019;68:31–53.

    Article  CAS  PubMed  Google Scholar 

  38. Blankinship MJ, Gregorevic P, Chamberlain JS. Gene therapy strategies for duchenne muscular dystrophy utilizing recombinant adeno-associated virus vectors. Mol Ther. 2006;13:241–9.

    Article  CAS  PubMed  Google Scholar 

  39. Phillips JL, Hegge J, Wolff JA, Samulski RJ, Asokan A. Systemic gene transfer to skeletal muscle using reengineered AAV vectors. Methods Mol Biol. 2011;709:141.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. High-dose AAV gene therapy deaths. Nat Biotechnol. 2020;38:910.

  41. Kishimoto TK, Samulski RJ. Addressing high dose AAV toxicity – ‘one and done’ or ‘slower and lower’? Expert Opin Biol Ther. 2022;1–5. https://doi.org/10.1080/14712598.2022.2060737.

  42. Mullard A. Gene therapy community grapples with toxicity issues, as pipeline matures. Nat Rev Drug Discov. 2021;20:804–5.

    Article  CAS  PubMed  Google Scholar 

  43. Duan D. Systemic delivery of adeno-associated viral vectors. Curr Opin Virol. 2016;21:16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Clément N, Grieger JC. Manufacturing of recombinant adeno-associated viral vectors for clinical trials. Mol Ther Methods Clin Dev. 2016;3:16002.

    Article  PubMed  PubMed Central  Google Scholar 

  45. Zhu J, Huang X, Yang Y. The TLR9-MyD88 pathway is critical for adaptive immune responses to adeno-associated virus gene therapy vectors in mice. J Clin Invest. 2009;119:2388–98.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Faust SM, Bell P, Cutler BJ, Ashley SN, Zhu Y, Rabinowitz JE, et al. CpG-depleted adeno-associated virus vectors evade immune detection. J Clin Invest. 2013;123:2994–3001.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Martino AT, Markusic DM. Immune response mechanisms against AAV vectors in animal models. Mol Ther Methods Clin Dev. 2020;17:198.

    Article  CAS  PubMed  Google Scholar 

  48. Rabinowitz J, Chan YK, Samulski RJ. Adeno-associated virus (AAV) versus immune response. Viruses. 2019;11:102.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Chan YK, Wang SK, Chu CJ, Copland DA, Letizia AJ, Verdera HC, et al. Engineering adeno-associated viral vectors to evade innate immune and inflammatory responses. Sci Transl Med. 2021;13:eabd3438.

  50. Haery L, Deverman BE, Matho KS, Cetin A, Woodard K, Cepko C, et al. Adeno-associated virus technologies and methods for targeted neuronal manipulation. Front Neuroanat. 2019;13:93.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Foust KD, Nurre E, Montgomery CL, Hernandez A, Chan CM, Kaspar BK. Intravascular AAV9 preferentially targets neonatal neurons and adult astrocytes. Nat Biotechnol. 2008;27:59–65.

    Article  PubMed  PubMed Central  Google Scholar 

  52. Sands MS. AAV-mediated liver-directed gene therapy. Methods Mol Biol. 2012;807:141–57.

    Article  Google Scholar 

  53. Saraiva J, Nobre RJ, Pereira de Almeida L. Gene therapy for the CNS using AAVs: the impact of systemic delivery by AAV9. J Control Release. 2016;241:94–109.

    Article  CAS  PubMed  Google Scholar 

  54. Meng Y, Sun D, Qin Y, Dong X, Luo G, Liu Y. Cell-penetrating peptides enhance the transduction of adeno-associated virus serotype 9 in the central nervous system. Mol Ther Methods Clin Dev. 2021;21:28–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Boutin S, Monteilhet V, Veron P, Leborgne C, Benveniste O, Montus MF, et al. 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. Hum Gene Ther. 2010;21:704–12. https://home.liebertpub.com/hum.

  56. Kruzik A, Fetahagic D, Hartlieb B, Dorn S, Koppensteiner H, Horling FM, et al. Prevalence of anti-adeno-associated virus immune responses in international cohorts of healthy donors. Mol Ther Methods Clin Dev. 2019;14:126–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Manno CS, Arruda VR, Pierce GF, Glader B, Ragni M, Rasko J, et al. Successful transduction of liver in hemophilia by AAV-Factor IX and limitations imposed by the host immune response. Nat Med. 2006;12:342–7.

    Article  CAS  PubMed  Google Scholar 

  58. Jiang H, Couto LB, Patarroyo-White S, Liu T, Nagy D, Vargas JA, et al. Effects of transient immunosuppression on adenoassociated, virus-mediated, liver-directed gene transfer in rhesus macaques and implications for human gene therapy. Blood. 2006;108:3321–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. George LA, Sullivan SK, Giermasz A, Rasko JEJ, Samelson-Jones BJ, Ducore J, et al. Hemophilia B gene therapy with a high-specific-activity factor IX variant. N Engl J Med. 2017;377:2215–27.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Nathwani AC, Reiss UM, Tuddenham EGD, Rosales C, Chowdary P, McIntosh J, et al. Long-term safety and efficacy of factor IX gene therapy in hemophilia B. N Engl J Med. 2014;371:1994–2004.

    Article  PubMed  PubMed Central  Google Scholar 

  61. Georgiadis A, Duran Y, Ribeiro J, Abelleira-Hervas L, Robbie SJ, Sünkel-Laing B, et al. Development of an optimized AAV2/5 gene therapy vector for Leber congenital amaurosis owing to defects in RPE65. Gene Ther. 2016;23:857–62.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Beltran WA, Cideciyan AV, Boye SE, Ye GJ, Iwabe S, Dufour VL, et al. Optimization of retinal gene therapy for X-linked retinitis pigmentosa due to RPGR mutations. Mol Ther. 2017;25:1866–80.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Stein S, Ott MG, Schultze-Strasser S, Jauch A, Burwinkel B, Kinner A, et al. Genomic instability and myelodysplasia with monosomy 7 consequent to EVI1 activation after gene therapy for chronic granulomatous disease. Nat Med. 2010;16:198–204.

    Article  CAS  PubMed  Google Scholar 

  64. Prösen S, Stein J, Staak K, Liebenthal C, Volk HD, Krüger DH. Inactivation of the very strong HCMV immediate early promoter by DNA CpG methylation in vitro. Biol Chem Hoppe Seyler. 1996;377:195–201.

    Article  Google Scholar 

  65. Brooks AR, Harkins RN, Wang P, Qian HS, Liu P, Rubanyi GM. Transcriptional silencing is associated with extensive methylation of the CMV promoter following adenoviral gene delivery to muscle. J Gene Med. 2004;6:395–404.

    Article  CAS  PubMed  Google Scholar 

  66. Chandler RJ, La Fave MC, Varshney GK, Trivedi NS, Carrillo-Carrasco N, Senac JS, et al. Vector design influences hepatic genotoxicity after adeno-associated virus gene therapy. J Clin Invest. 2015;125:870–80.

    Article  PubMed  PubMed Central  Google Scholar 

  67. Kornegay JN, Li J, Bogan JR, Bogan DJ, Chen C, Zheng H, et al. Widespread muscle expression of an AAV9 human mini-dystrophin vector after intravenous injection in neonatal dystrophin-deficient dogs. Mol Ther. 2010;18:1501.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Lange AM, Altynova ES, Nguyen GN, Sabatino DE. Overexpression of factor VIII after AAV delivery is transiently associated with cellular stress in hemophilia A mice. Mol Ther Methods Clin Dev. 2016;3:16064.

    Article  PubMed  PubMed Central  Google Scholar 

  69. Watakabe A, Ohtsuka M, Kinoshita M, Takaji M, Isa K, Mizukami H, et al. Comparative analyses of adeno-associated viral vector serotypes 1, 2, 5, 8 and 9 in marmoset, mouse and macaque cerebral cortex. Neurosci Res. 2015;93:144–57.

    Article  PubMed  Google Scholar 

  70. Klein RL, Dayton RD, Leidenheimer NJ, Jansen K, Golde TE, Zweig RM. Efficient neuronal gene transfer with AAV8 leads to neurotoxic levels of tau or green fluorescent proteins. Mol Ther. 2006;13:517–27.

    Article  CAS  PubMed  Google Scholar 

  71. Follenzi A, Battaglia M, Lombardo A, Annoni A, Roncarolo MG, Naldini L. Targeting lentiviral vector expression to hepatocytes limits transgene-specific immune response and establishes long-term expression of human antihemophilic factor IX in mice. Blood. 2004;103:3700–9.

    Article  CAS  PubMed  Google Scholar 

  72. Gernoux G, Guilbaud M, Dubreil L, Larcher T, Babarit C, Ledevin M, et al. Early interaction of adeno-associated virus serotype 8 vector with the host immune system following intramuscular delivery results in weak but detectable lymphocyte and dendritic cell transduction. Hum Gene Ther. 2015;26:1–13. https://home.liebertpub.com/hum.

  73. Xiong W, Wu DM, Xue Y, Wang SK, Chung MJ, Ji X, et al. AAV cis-regulatory sequences are correlated with ocular toxicity. Proc Natl Acad Sci USA 2019;116:5785–94.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Kim S, Peng Z, Kaneda Y. Current status of gene therapy in Asia. Mol Ther. 2008;16:237–43.

    Article  CAS  PubMed  Google Scholar 

  75. Deng H-X, Wang Y, Ding Q, Li D, Wei Y. Gene therapy research in Asia. Gene Ther. 2017;24:572–7.

    Article  CAS  PubMed  Google Scholar 

  76. Au HKE, Isalan M, Mielcarek M. Gene therapy advances: a meta-analysis of AAV usage in clinical settings. Front Med. 2022;8:2746.

    Article  Google Scholar 

  77. Mingozzi F, Büning H. Adeno-associated viral vectors at the frontier between tolerance and immunity. Front Immunol. 2015;6:120.

  78. CBER. Guidance for industry. Preclinical assessment of investigational cellular and gene therapy products. 2009.

  79. European Medicines Agency. Guideline on the quality, non-clinical and clinical aspects of gene therapy medicinal products. 2014.

  80. Assaf BT, Whiteley LO. Considerations for preclinical safety assessment of adeno-associated virus gene therapy products. Toxicol Pathol. 2018;46:1020–7. https://doi.org/10.1177/0192623318803867.

  81. Brown HC, Zakas PM, George SN, Parker ET, Spencer HT, Doering CB. Target-cell-directed bioengineering approaches for gene therapy of hemophilia A. Mol Ther Methods Clin Dev. 2018;9:57–69.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. McCarty DM. Self-complementary AAV vectors; advances and applications. Mol Ther. 2008;16:1648–56.

    Article  CAS  PubMed  Google Scholar 

  83. Wu T, Töpfer K, Lin S-W, Li H, Bian A, Zhou XY, et al. Self-complementary AAVs induce more potent transgene product-specific immune responses compared to a single-stranded genome. Mol Ther. 2012;20:572.

    Article  CAS  PubMed  Google Scholar 

  84. El Andari J, Grimm D, El Andari J, Grimm D, Grimm Bioquant D. Production, processing, and characterization of synthetic AAV gene therapy vectors. Biotechnol J. 2021;16:2000025.

    Article  CAS  Google Scholar 

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Acknowledgements

I thank Clinton Greggor for his encouragement and support throughout the writing of this article.

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TB was responsible for conducting all data collection/extraction and analysis, interpretation of results and writing. SN acted as project supervisor and provided the initial concept and framework in addition to thorough feedback/assistance in data collection, analysis and writing of the report.

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Correspondence to Tamara Burdett.

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Burdett, T., Nuseibeh, S. Changing trends in the development of AAV-based gene therapies: a meta-analysis of past and present therapies. Gene Ther 30, 323–335 (2023). https://doi.org/10.1038/s41434-022-00363-0

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