@article{601e50caa08a4b9aacb1a5a0c51aa542,
title = "Codon-Optimization of Wild-Type Adeno-Associated Virus Capsid Sequences Enhances DNA Family Shuffling while Conserving Functionality",
abstract = "Adeno-associated virus (AAV) vectors have become one of the most widely used gene transfer tools in human gene therapy. Considerable effort is currently being focused on AAV capsid engineering strategies with the aim of developing novel variants with enhanced tropism for specific human cell types, decreased human seroreactivity, and increased manufacturability. Selection strategies based on directed evolution rely on the generation of highly variable AAV capsid libraries using methods such as DNA-family shuffling, a technique reliant on stretches of high DNA sequence identity between input parental capsid sequences. This identity dependence for reassembly of shuffled capsids is inherently limiting and results in decreased shuffling efficiency as the phylogenetic distance between parental AAV capsids increases. To overcome this limitation, we have developed a novel codon-optimization algorithm that exploits evolutionarily defined codon usage at each amino acid residue in the parental sequences. This method increases average sequence identity between capsids, while enhancing the probability of retaining capsid functionality, and facilitates incorporation of phylogenetically distant serotypes into the DNA-shuffled libraries. This technology will help accelerate the discovery of an increasingly powerful repertoire of AAV capsid variants for cell-type and disease-specific applications.",
keywords = "AAV, DNA shuffling, capsid, codon optimization, directed evolution, library",
author = "Marti Cabanes-Creus and Ginn, {Samantha L.} and Amaya, {Anais K.} and Liao, {Sophia H.Y.} and Adrian Westhaus and Hallwirth, {Claus V.} and Patrick Wilmott and Jason Ward and Dilworth, {Kimberley L.} and Giorgia Santilli and Arkadiusz Rybicki and Hiroyuki Nakai and Thrasher, {Adrian J.} and Filip, {Adrian C.} and Alexander, {Ian E.} and Leszek Lisowski",
note = "Funding Information: We thank CMRI Vector and Genome Engineering Facility for help in vector preparation. This work was supported by a Project grant to L.L. from Australian National Health and Medical Research Council (NHMRC) ( APP1108311 ) and a Discovery grant to I.E.A. from the Australian Research Council (ARC) ( DP150101253 ). A.J.T. is a Wellcome Trust Principal Research Fellow. All research at Great Ormond Street Hospital NHS Foundation Trust and UCL Great Ormond Street Institute of Child Health is made possible by the NIHR Great Ormond Street Hospital Biomedical Research Centre . The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, or the Department of Health. H.N. was supported by a grant ( R01 NS088399 ) from the National Institutes of Health ( NIH ). Funding Information: We thank CMRI Vector and Genome Engineering Facility for help in vector preparation. This work was supported by a Project grant to L.L. from Australian National Health and Medical Research Council (NHMRC) (APP1108311) and a Discovery grant to I.E.A. from the Australian Research Council (ARC) (DP150101253). A.J.T. is a Wellcome Trust Principal Research Fellow. All research at Great Ormond Street Hospital NHS Foundation Trust and UCL Great Ormond Street Institute of Child Health is made possible by the NIHR Great Ormond Street Hospital Biomedical Research Centre. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, or the Department of Health. H.N. was supported by a grant (R01 NS088399) from the National Institutes of Health (NIH). Publisher Copyright: {\textcopyright} 2018 The Authors",
year = "2019",
month = mar,
day = "15",
doi = "10.1016/j.omtm.2018.10.016",
language = "English (US)",
volume = "12",
pages = "71--84",
journal = "Molecular Therapy - Methods and Clinical Development",
issn = "2329-0501",
publisher = "Nature Publishing Group",
}