Structure-guided AAV capsid evolution strategies for enhanced CNS gene delivery

Trevor J. Gonzalez, Aaron Mitchell-Dick, Leo O. Blondel, Marco M. Fanous, Joshua A. Hull, Daniel K. Oh, Sven Moller-Tank, Ruth M. Castellanos Rivera, Jorge A. Piedrahita, Aravind Asokan

Published: 2023-09-20 DOI: 10.1038/s41596-023-00875-y

AAV capsid evolution

CNS gene delivery

structure-guided design

library cycling

humoral immunity evasion

AI 解读

Extraction of nuclei from archived postmortem tissues for single-nucleus sequencing applications

High-quality and robust protein quantification in large clinical/pharmaceutical cohorts with IonStar proteomics investigation

Longitudinal interrogation of sympathetic neural circuits and hemodynamics in preclinical models

Experimental modulation of physiological force application on leg joint neurons in intactDrosophila melanogaster

Combining surface-accessible Ag and Au colloidal nanomaterials with SERS for in situ analysis of molecule–metal interactions in complex solution environments

Generation of mouse–human chimeric embryos

Labeling and tracking of immune cells in ex vivo human skin

Large-scale preparation of fluorescence multiplex host cell reactivation (FM-HCR) reporters

Mutate-and-chemical-shift-fingerprint (MCSF) to characterize excited states in RNA using NMR spectroscopy

Comprehensive multi-attribute method workflow for biotherapeutic characterization and current good manufacturing practices testing

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References

Mendell, J. R. et al. Current clinical applications of in vivo gene therapy with AAVs. Mol. Ther. 29, 464–488 (2021).
Kuzmin, D. A. et al. The clinical landscape for AAV gene therapies. Nat. Rev. Drug Discov. 20, 173–174 (2021).
Mingozzi, F. & High, K. A. Therapeutic in vivo gene transfer for genetic disease using AAV: progress and challenges. Nat. Rev. Genet 12, 341–355 (2011).
Hudry, E. & Vandenberghe, L. H. Therapeutic AAV gene transfer to the nervous system: a clinical reality. Neuron 101, 839–862 (2019).
Deverman, B. E. et al. Gene therapy for neurological disorders: progress and prospects. Nat. Rev. Drug Discov. 17, 641–659 (2018).
Rafii, M. S. et al. Adeno-associated viral vector (serotype 2)-nerve growth factor for patients with Alzheimer disease: a randomized clinical trial. JAMA Neurol. 75, 834–841 (2018).
Li, C. & Samulski, R. J. Engineering adeno-associated virus vectors for gene therapy. Nat. Rev. Genet 21, 255–272 (2020).
Barnes, C., Scheideler, O. & Schaffer, D. Engineering the AAV capsid to evade immune responses. Curr. Opin. Biotechnol. 60, 99–103 (2019).
Kotterman, M. A. & Schaffer, D. V. Engineering adeno-associated viruses for clinical gene therapy. Nat. Rev. Genet. 15, 445–451 (2014).
Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358–378 (2019).
Zolotukhin, S. & Vandenberghe, L. H. AAV capsid design: a Goldilocks challenge. Trends Mol. Med 28, 183–193 (2022).
Gonzalez, T. J. et al. Cross-species evolution of a highly potent AAV variant for therapeutic gene transfer and genome editing. Nat. Commun. 13, 5947 (2022).
Havlik, L. P. et al. Coevolution of adeno-associated virus capsid antigenicity and tropism through a structure-guided approach. J. Virol. 94, e00976-20 (2020).
Tse, L. V. et al. Structure-guided evolution of antigenically distinct adeno-associated virus variants for immune evasion. Proc. Natl Acad. Sci. USA 114, E4812–E4821 (2017).
Havlik, L. P. et al. Receptor switching in newly evolved adeno-associated viruses. J. Virol. 95, e0058721 (2021).
Albright, B. H. et al. Mapping the structural determinants required for AAVrh.10 transport across the blood-brain barrier. Mol. Ther. 26, 510–523 (2018).
Murlidharan, G. et al. Unique glycan signatures regulate adeno-associated virus tropism in the developing brain. J. Virol. 89, 3976–3987 (2015).
Shen, S. et al. Multiple roles for sialylated glycans in determining the cardiopulmonary tropism of adeno-associated virus 4. J. Virol. 87, 13206–13213 (2013).
Davidsson, M. et al. A systematic capsid evolution approach performed in vivo for the design of AAV vectors with tailored properties and tropism. Proc. Natl Acad. Sci. USA 116, 27053–27062 (2019).
Deverman, B. E. et al. Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain. Nat. Biotechnol. 34, 204–209 (2016).
Hordeaux, J. et al. The neurotropic properties of AAV-PHP.B are limited to C57BL/6J mice. Mol. Ther. 26, 664–668 (2018).
Shen, S. et al. Glycan binding avidity determines the systemic fate of adeno-associated virus type 9. J. Virol. 86, 10408–10417 (2012).
Shen, S. et al. Engraftment of a galactose receptor footprint onto adeno-associated viral capsids improves transduction efficiency. J. Biol. Chem. 288, 28814–28823 (2013).
Asokan, A. et al. Reengineering a receptor footprint of adeno-associated virus enables selective and systemic gene transfer to muscle. Nat. Biotechnol. 28, 79–82 (2010).
Madigan, V. J. & Asokan, A. Engineering AAV receptor footprints for gene therapy. Curr. Opin. Virol. 18, 89–96 (2016).
Tarantal, A. F. et al. Systemic and persistent muscle gene expression in rhesus monkeys with a liver de-targeted adeno-associated virus vector. Hum. Gene Ther. 28, 385–391 (2017).
Li, C. et al. Development of patient-specific AAV vectors after neutralizing antibody selection for enhanced muscle gene transfer. Mol. Ther. 24, 53–65 (2016).
Ogden, P. J. et al. Comprehensive AAV capsid fitness landscape reveals a viral gene and enables machine-guided design. Science 366, 1139–1143 (2019).
Bryant, D. H. et al. Deep diversification of an AAV capsid protein by machine learning. Nat. Biotechnol. 39, 691–696 (2021).
Tervo, D. G. et al. A designer AAV variant permits efficient retrograde access to projection neurons. Neuron 92, 372–382 (2016).
Jose, A. et al. High-resolution structural characterization of a new adeno-associated virus serotype 5 antibody epitope toward engineering antibody-resistant recombinant gene delivery vectors. J. Virol. 93, e01394-18 (2019).
Meyer, N. L. & Chapman, M. S. Adeno-associated virus (AAV) cell entry: structural insights. Trends Microbiol 30, 432–451 (2022).
Emmanuel, S. N. et al. Parvovirus capsid-antibody complex structures reveal conservation of antigenic epitopes across the family. Viral Immunol. 34, 3–17 (2021).
Tseng, Y. S. et al. Adeno-associated virus serotype 1 (AAV1)- and AAV5-antibody complex structures reveal evolutionary commonalities in parvovirus antigenic reactivity. J. Virol. 89, 1794–1808 (2015).
Mietzsch, M. et al. Structural study of Aavrh.10 receptor and antibody interactions. J. Virol. 95, e0124921 (2021).
Emmanuel, S. N. et al. Structurally mapping antigenic epitopes of adeno-associated virus 9: development of antibody escape variants. J. Virol. 96, e0125121 (2022).
Hemmi, S. & Spindler, K. R. Murine adenoviruses: tools for studying adenovirus pathogenesis in a natural host. FEBS Lett. 593, 3649–3659 (2019).
Gralinski, L. E. et al. Mouse adenovirus type 1-induced breakdown of the blood-brain barrier. J. Virol. 83, 9398–9410 (2009).
Guida, J. D. et al. Mouse adenovirus type 1 causes a fatal hemorrhagic encephalomyelitis in adult C57BL/6 but not BALB/c mice. J. Virol. 69, 7674–7681 (1995).
Weinberg, J. B. et al. Acute respiratory infection with mouse adenovirus type 1. Virology 340, 245–254 (2005).
Kajon, A. E., Brown, C. C. & Spindler, K. R. Distribution of mouse adenovirus type 1 in intraperitoneally and intranasally infected adult outbred mice. J. Virol. 72, 1219–1223 (1998).
Klempa, B. et al. A novel cardiotropic murine adenovirus representing a distinct species of mastadenoviruses. J. Virol. 83, 5749–5759 (2009).
Ashley, S. L. et al. Matrix metalloproteinase activity in infections by an encephalitic virus, mouse adenovirus type 1. J. Virol. 91, e01412–e01416 (2017).
Stier, M. T. & Spindler, K. R. Polymorphisms in Ly6 genes in Msq1 encoding susceptibility to mouse adenovirus type 1. Mamm. Genome 23, 250–258 (2012).
Maheshri, N. et al. Directed evolution of adeno-associated virus yields enhanced gene delivery vectors. Nat. Biotechnol. 24, 198–204 (2006).
Grimm, D. et al. In vitro and in vivo gene therapy vector evolution via multispecies interbreeding and retargeting of adeno-associated viruses. J. Virol. 82, 5887–5911 (2008).
Gray, S. J. et al. Directed evolution of a novel adeno-associated virus (AAV) vector that crosses the seizure-compromised blood-brain barrier (BBB). Mol. Ther. 18, 570–578 (2010).
Weinmann, J. et al. Identification of a myotropic AAV by massively parallel in vivo evaluation of barcoded capsid variants. Nat. Commun. 11, 5432 (2020).
Tabebordbar, M. et al. Directed evolution of a family of AAV capsid variants enabling potent muscle-directed gene delivery across species. Cell 184, 4919–4938.e22 (2021).
El Andari, J. et al. Semirational bioengineering of AAV vectors with increased potency and specificity for systemic gene therapy of muscle disorders. Sci. Adv. 8, eabn4704 (2022).
Nonnenmacher, M. et al. Rapid evolution of blood-brain-barrier-penetrating AAV capsids by RNA-driven biopanning. Mol. Ther. Methods Clin. Dev. 20, 366–378 (2021).
Rapti, K. et al. Neutralizing antibodies against AAV serotypes 1, 2, 6, and 9 in sera of commonly used animal models. Mol. Ther. 20, 73–83 (2012).
Smola, M. J. et al. Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis. Nat. Protoc. 10, 1643–1669 (2015).
Percie du Sert, N. et al. The ARRIVE guidelines 2.0: updated guidelines for reporting animal research. Br. J. Pharm. 177, 3617–3624 (2020).
Montiel-Garcia, D. et al. VIPERdb v3.0: a structure-based data analytics platform for viral capsids. Nucleic Acids Res. 49, D809–D816 (2021).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Varadi, M. et al. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 50, D439–D444 (2022).
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Emsley, P. et al. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
Grieger, J. C., Choi, V. W. & Samulski, R. J. Production and characterization of adeno-associated viral vectors. Nat. Protoc. 1, 1412–1428 (2006).
Schmit, P. F. et al. Cross-packaging and capsid mosaic formation in multiplexed AAV libraries. Mol. Ther. Methods Clin. Dev. 17, 107–121 (2020).
Xiao, X., Li, J. & Samulski, R. J. Production of high-titer recombinant adeno-associated virus vectors in the absence of helper adenovirus. J. Virol. 72, 2224–2232 (1998).
Mietzsch, M., Penzes, J. J. & Agbandje-McKenna, M. Twenty-five years of structural parvovirology. Viruses 11, 362 (2019).
Tseng, Y. S. & Agbandje-McKenna, M. Mapping the AAV capsid host antibody response toward the development of second generation gene delivery vectors. Front. Immunol. 5, 9 (2014).
Challis, R. C. et al. Systemic AAV vectors for widespread and targeted gene delivery in rodents. Nat. Protoc. 14, 379–414 (2019).
Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).
Goertsen, D. et al. AAV capsid variants with brain-wide transgene expression and decreased liver targeting after intravenous delivery in mouse and marmoset. Nat. Neurosci. 25, 106–115 (2022).
Nonnenmacher, M. et al. High capsid-genome correlation facilitates creation of AAV libraries for directed evolution. Mol. Ther. 23, 675–682 (2015).
Govindasamy, L. et al. Structurally mapping the diverse phenotype of adeno-associated virus serotype 4. J. Virol. 80, 11556–11570 (2006).
Mietzsch, M. et al. Characterization of AAV-specific affinity ligands: consequences for vector purification and development strategies. Mol. Ther. Methods Clin. Dev. 19, 362–373 (2020).
Huang, L. Y. et al. Characterization of the adeno-associated virus 1 and 6 sialic acid binding site. J. Virol. 90, 5219–5230 (2016).
Meyer, N. L. et al. Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR. Elife 8, e44707 (2019).
Earley, L. F. et al. Adeno-associated virus (AAV) assembly-activating protein is not an essential requirement for capsid assembly of AAV serotypes 4, 5, and 11. J. Virol. 91, e01980-16 (2017).
Bleker, S., Sonntag, F. & Kleinschmidt, J. A. Mutational analysis of narrow pores at the fivefold symmetry axes of adeno-associated virus type 2 capsids reveals a dual role in genome packaging and activation of phospholipase A2 activity. J. Virol. 79, 2528–2540 (2005).
Bleker, S., Pawlita, M. & Kleinschmidt, J. A. Impact of capsid conformation and Rep-capsid interactions on adeno-associated virus type 2 genome packaging. J. Virol. 80, 810–820 (2006).
Grieger, J. C. et al. Surface-exposed adeno-associated virus Vp1-NLS capsid fusion protein rescues infectivity of noninfectious wild-type Vp2/Vp3 and Vp3-only capsids but not that of fivefold pore mutant virions. J. Virol. 81, 7833–7843 (2007).
Kronenberg, S. et al. A conformational change in the adeno-associated virus type 2 capsid leads to the exposure of hidden VP1 N termini. J. Virol. 79, 5296–5303 (2005).
Kotchey, N. M. et al. A potential role of distinctively delayed blood clearance of recombinant adeno-associated virus serotype 9 in robust cardiac transduction. Mol. Ther. 19, 1079–1089 (2011).
Judd, J. et al. Random insertion of mCherry into VP3 domain of adeno-associated virus yields fluorescent capsids with no loss of infectivity. Mol. Ther. Nucleic Acids 1, e54 (2012).
Jackson, C. B. et al. AAV vectors engineered to target insulin receptor greatly enhance intramuscular gene delivery. Mol. Ther. Methods Clin. Dev. 19, 496–506 (2020).
DiMattia, M. A. et al. Structural insight into the unique properties of adeno-associated virus serotype 9. J. Virol. 86, 6947–6958 (2012).
Mietzsch, M. et al. Characterization of the serpentine adeno-associated virus (SAAV) capsid structure: receptor interactions and antigenicity. J. Virol. 96, e0033522 (2022).
Li, W. et al. Generation of novel AAV variants by directed evolution for improved CFTR delivery to human ciliated airway epithelium. Mol. Ther. 17, 2067–2077 (2009).
Gurda, B. L. et al. Capsid antibodies to different adeno-associated virus serotypes bind common regions. J. Virol. 87, 9111–9124 (2013).
Pulicherla, N. et al. Engineering liver-detargeted AAV9 vectors for cardiac and musculoskeletal gene transfer. Mol. Ther. 19, 1070–1078 (2011).
Afione, S. et al. Identification and mutagenesis of the adeno-associated virus 5 sialic acid binding region. J. Virol. 89, 1660–1672 (2015).
Lerch, T. F., Xie, Q. & Chapman, M. S. The structure of adeno-associated virus serotype 3B (AAV-3B): insights into receptor binding and immune evasion. Virology 403, 26–36 (2010).
Naumer, M. et al. Development and validation of novel AAV2 random libraries displaying peptides of diverse lengths and at diverse capsid positions. Hum. Gene Ther. 23, 492–507 (2012).
Michelfelder, S. et al. Peptide ligands incorporated into the threefold spike capsid domain to re-direct gene transduction of AAV8 and AAV9 in vivo. PLoS ONE 6, e23101 (2011).
DiPrimio, N. et al. Surface loop dynamics in adeno-associated virus capsid assembly. J. Virol. 82, 5178–5189 (2008).
Horowitz, E. D., Finn, M. G. & Asokan, A. Tyrosine cross-linking reveals interfacial dynamics in adeno-associated viral capsids during infection. ACS Chem. Biol. 7, 1059–1066 (2012).

Structure-guided AAV capsid evolution strategies for enhanced CNS gene delivery

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