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Barcoded Rational AAV Vector Evolution Enables Systematic In Vivo Mapping of Peptide Binding Motifs

490 Pages Posted: 10 Sep 2018 Sneak Peek Status: Review Complete

See all articles by Marcus Davidsson

Marcus Davidsson

Lund University - Molecular Neuromodulation

Gang Wang

Lund University - Molecular Neuromodulation

Patrick Aldrin-Kirk

Lund University - Molecular Neuromodulation

Tiago Cardoso

Lund University - Department of Developmental and Regerative Neurobiology

Sara Nolbrant

Lund University - Department of Developmental and Regerative Neurobiology

Morgan Hartnor

Lund University - Molecular Neuromodulation

Malin Parmar

Lund University - Department of Developmental and Regerative Neurobiology

Tomas Björklund

Lund University - Molecular Neuromodulation

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Abstract

Adeno-associated virus (AAV) capsid modification enables the generation of recombinant vectors with tailored properties and tropism. Such modifications can provide unique functions for pre-clinical and clinical vectors such as evading immune response, providing selective infectivity or unique transport capabilities in the host. Most development approaches to date depend on random screening, enrichment and serendipity. Here, we have developed a novel method for rational capsid evolution named BRAVE. We show that this approach enables the selection of novel capsid structures using only a single in vivo screening round in contrast to previous approaches requiring multiple generations of enrichment. With the BRAVE approach, each virus particle displays a peptide of known origin on the AAV capsid surface which is linked to a unique molecular barcode in the packaged genome. The barcodes and the de novo capsid structures are linked prior to in vivo screening using deep sequencing. Sequencing of RNA-expressed barcodes from the in vivo screen allows mapping, with high resolution, the putative binding sequences of large proteins libraries. Using the BRAVE approach, we here present 25 synthetic capsid variants with novel properties such as retrograde axonal transport in both rodent and human dopaminergic neurons. Through hidden Markov model-based clustering, we were able to identify novel consensus motifs for retrograde transport in neurons. We also identify neuronal binding domains of the protein Tau implicated in cell-to-cell spread of pathology in Alzheimer’s disease.

Suggested Citation

Davidsson, Marcus and Wang, Gang and Aldrin-Kirk, Patrick and Cardoso, Tiago and Nolbrant, Sara and Hartnor, Morgan and Parmar, Malin and Björklund, Tomas, Barcoded Rational AAV Vector Evolution Enables Systematic In Vivo Mapping of Peptide Binding Motifs (September 6, 2018). Available at SSRN: https://ssrn.com/abstract=3245528 or http://dx.doi.org/10.2139/ssrn.3245528
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Marcus Davidsson

Lund University - Molecular Neuromodulation

Box 117
Lund, S221 00
Sweden

Gang Wang

Lund University - Molecular Neuromodulation

Box 117
Lund, S221 00
Sweden

Patrick Aldrin-Kirk

Lund University - Molecular Neuromodulation

Box 117
Lund, S221 00
Sweden

Tiago Cardoso

Lund University - Department of Developmental and Regerative Neurobiology

Box 117
Lund, S221 00
Sweden

Sara Nolbrant

Lund University - Department of Developmental and Regerative Neurobiology

Box 117
Lund, S221 00
Sweden

Morgan Hartnor

Lund University - Molecular Neuromodulation

Box 117
Lund, S221 00
Sweden

Malin Parmar (Contact Author)

Lund University - Department of Developmental and Regerative Neurobiology

Box 117
Lund, S221 00
Sweden

Tomas Björklund

Lund University - Molecular Neuromodulation ( email )

Box 117
Lund, S221 00
Sweden

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