Codon-Optimization of Wild-Type Adeno-Associated Virus Capsid Sequences Enhances DNA Family Shuffling while Conserving Functionality

Marti Cabanes-Creus; Samantha L. Ginn; Anais K. Amaya; Sophia H.Y. Liao; Adrian Westhaus; Claus V. Hallwirth; Patrick Wilmott; Jason Ward; Kimberley L. Dilworth; Giorgia Santilli; Arkadiusz Rybicki; Hiroyuki Nakai; Adrian J. Thrasher; Adrian C. Filip; Ian E. Alexander; Leszek Lisowski

Molecular Therapy: Methods & Clinical Development (Mar 2019)

Codon-Optimization of Wild-Type Adeno-Associated Virus Capsid Sequences Enhances DNA Family Shuffling while Conserving Functionality

Marti Cabanes-Creus,
Samantha L. Ginn,
Anais K. Amaya,
Sophia H.Y. Liao,
Adrian Westhaus,
Claus V. Hallwirth,
Patrick Wilmott,
Jason Ward,
Kimberley L. Dilworth,
Giorgia Santilli,
Arkadiusz Rybicki,
Hiroyuki Nakai,
Adrian J. Thrasher,
Adrian C. Filip,
Ian E. Alexander,
Leszek Lisowski

Affiliations

Marti Cabanes-Creus: Translational Vectorology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; Great Ormond Street Institute of Child Health, University College London, London, UK
Samantha L. Ginn: Gene Therapy Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children’s Hospitals Network, Sydney, NSW 2006, Australia
Anais K. Amaya: Gene Therapy Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children’s Hospitals Network, Sydney, NSW 2006, Australia
Sophia H.Y. Liao: Translational Vectorology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; Gene Therapy Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children’s Hospitals Network, Sydney, NSW 2006, Australia
Adrian Westhaus: Translational Vectorology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
Claus V. Hallwirth: Gene Therapy Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children’s Hospitals Network, Sydney, NSW 2006, Australia
Patrick Wilmott: Translational Vectorology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
Jason Ward: Translational Vectorology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
Kimberley L. Dilworth: Vector and Genome Engineering Facility, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
Giorgia Santilli: Great Ormond Street Institute of Child Health, University College London, London, UK
Arkadiusz Rybicki: Vector and Genome Engineering Facility, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
Hiroyuki Nakai: Oregon Health & Science University, Portland, OR 97239, USA
Adrian J. Thrasher: Great Ormond Street Institute of Child Health, University College London, London, UK
Adrian C. Filip: Translational Vectorology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia
Ian E. Alexander: Gene Therapy Research Unit, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children’s Hospitals Network, Sydney, NSW 2006, Australia; Discipline of Child and Adolescent Health, Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2145, Australia
Leszek Lisowski: Translational Vectorology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; Vector and Genome Engineering Facility, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; Military Institute of Hygiene and Epidemiology, The Biological Threats Identification and Countermeasure Centre, 24-100 Puławy, Poland; Corresponding author: Leszek Lisowski, Translational Vectorology Group, Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, 214 Hawkesbury Road, Westmead, NSW 2145, Australia.

Journal volume & issue: Vol. 12
pp. 71 – 84

Abstract

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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, library, directed evolution, codon optimization, DNA shuffling, capsid

Published in Molecular Therapy: Methods & Clinical Development

ISSN: 2329-0501 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Biology (General): Genetics; Science: Biology (General): Cytology
Website: http://www.cell.com/molecular-therapy-family/methods/latest-content

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