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

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Pages (from-to)71-84
Number of pages14
JournalMolecular Therapy - Methods and Clinical Development
Volume12
DOIs
StatePublished - Mar 15 2019

Fingerprint

DNA Shuffling
Dependovirus
Capsid
Codon
Tropism
Gene Library
Genetic Therapy
Technology
Amino Acids

Keywords

  • AAV
  • capsid
  • codon optimization
  • directed evolution
  • DNA shuffling
  • library

ASJC Scopus subject areas

  • Molecular Medicine
  • Molecular Biology
  • Genetics

Cite this

Codon-Optimization of Wild-Type Adeno-Associated Virus Capsid Sequences Enhances DNA Family Shuffling while Conserving Functionality. / Cabanes-Creus, Marti; Ginn, Samantha L.; Amaya, Anais K.; Liao, Sophia H.Y.; Westhaus, Adrian; Hallwirth, Claus V.; Wilmott, Patrick; Ward, Jason; Dilworth, Kimberley L.; Santilli, Giorgia; Rybicki, Arkadiusz; Nakai, Hiroyuki; Thrasher, Adrian J.; Filip, Adrian C.; Alexander, Ian E.; Lisowski, Leszek.

In: Molecular Therapy - Methods and Clinical Development, Vol. 12, 15.03.2019, p. 71-84.

Research output: Contribution to journalArticle

Cabanes-Creus, M, Ginn, SL, Amaya, AK, Liao, SHY, Westhaus, A, Hallwirth, CV, Wilmott, P, Ward, J, Dilworth, KL, Santilli, G, Rybicki, A, Nakai, H, Thrasher, AJ, Filip, AC, Alexander, IE & Lisowski, L 2019, 'Codon-Optimization of Wild-Type Adeno-Associated Virus Capsid Sequences Enhances DNA Family Shuffling while Conserving Functionality' Molecular Therapy - Methods and Clinical Development, vol. 12, pp. 71-84. https://doi.org/10.1016/j.omtm.2018.10.016
Cabanes-Creus, Marti ; Ginn, Samantha L. ; Amaya, Anais K. ; Liao, Sophia H.Y. ; Westhaus, Adrian ; Hallwirth, Claus V. ; Wilmott, Patrick ; Ward, Jason ; Dilworth, Kimberley L. ; Santilli, Giorgia ; Rybicki, Arkadiusz ; Nakai, Hiroyuki ; Thrasher, Adrian J. ; Filip, Adrian C. ; Alexander, Ian E. ; Lisowski, Leszek. / Codon-Optimization of Wild-Type Adeno-Associated Virus Capsid Sequences Enhances DNA Family Shuffling while Conserving Functionality. In: Molecular Therapy - Methods and Clinical Development. 2019 ; Vol. 12. pp. 71-84.
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