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Multiplexed Cre-dependent selection yields systemic AAVs for targeting distinct brain cell types

Ravindra Kumar, Sripriya and Miles, Timothy F. and Chen, Xinhong and Brown, David and Dobreva, Tatyana and Huang, Qin and Ding, Xiaozhe and Luo, Yicheng and Einarsson, Petur H. and Greenbaum, Alon and Jang, Min J. and Deverman, Benjamin E. and Gradinaru, Viviana (2020) Multiplexed Cre-dependent selection yields systemic AAVs for targeting distinct brain cell types. Nature Methods, 17 (5). pp. 541-550. ISSN 1548-7091. PMCID PMC7219404. https://resolver.caltech.edu/CaltechAUTHORS:20200121-141523675

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[img] Video (MPEG) (Supplementary Video 1. Brain-Wide transduction of endothelial cells upon systemic delivery of the AAV-PHP.V1 capsid) - Supplemental Material
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[img] MS Excel (Supplementary Dataset 1. 7-mer-i spike-in library recovery in brain tissue across Cre transgenic lines) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 1: Extended Schematic for Multiplexed-CREATE and Analysis of Round-1 Selection) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 2: Analysis of 7-mer-i rAAV Libraries From Round-2 Selections) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 3: Analysis of Round-2 7-mer-i Tissue Libraries From Synthetic Pool And PCR Pool Methods) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 4: AAV-PHP.V1 Efficiently Targets the Brain Vasculature) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 5: AAV-PHP.V2 Variant Exhibits Biased Transduction Towards Brain Vascular Cells) - Supplemental Material
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[img] Image (JPEG) (Supplementary Figure 6: Further Validation of Synthetic Pool and PCR Pool Variants Demonstrates Higher Confidence in Synthetic Pool NGS Data) - Supplemental Material
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Abstract

Recombinant adeno-associated viruses (rAAVs) are efficient gene delivery vectors via intravenous delivery; however, natural serotypes display a finite set of tropisms. To expand their utility, we evolved AAV capsids to efficiently transduce specific cell types in adult mouse brains. Building upon our Cre-recombination-based AAV targeted evolution (CREATE) platform, we developed Multiplexed-CREATE (M-CREATE) to identify variants of interest in a given selection landscape through multiple positive and negative selection criteria. M-CREATE incorporates next-generation sequencing, synthetic library generation and a dedicated analysis pipeline. We have identified capsid variants that can transduce the central nervous system broadly, exhibit bias toward vascular cells and astrocytes, target neurons with greater specificity or cross the blood–brain barrier across diverse murine strains. Collectively, the M-CREATE methodology accelerates the discovery of capsids for use in neuroscience and gene-therapy applications.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1038/s41592-020-0799-7DOIArticle
https://rdcu.be/b3FGoPublisherFree ReadCube access
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7219404PubMed CentralArticle
https://github.com/GradinaruLab/mCREATERelated ItemCode
https://github.com/GradinaruLab/HCRprobeRelated ItemCode
ORCID:
AuthorORCID
Ravindra Kumar, Sripriya0000-0001-6033-7631
Miles, Timothy F.0000-0001-6591-3271
Chen, Xinhong0000-0003-0408-0813
Brown, David0000-0002-9757-1744
Dobreva, Tatyana0000-0002-2625-8873
Ding, Xiaozhe0000-0002-0267-0791
Luo, Yicheng0000-0003-3704-2389
Greenbaum, Alon0000-0002-2897-876X
Jang, Min J.0000-0002-1536-7177
Deverman, Benjamin E.0000-0002-6223-9303
Gradinaru, Viviana0000-0001-5868-348X
Additional Information:© 2020 Springer Nature Limited. Received 08 April 2019; Accepted 10 March 2020; Published 20 April 2020. We thank the following alumni and current members of the Gradinaru group for their assistance in this study: K. Y. Chan and R. Challis for performing mouse injections, R. Hurt for performing preliminary characterization of vectors, Y. Lei for assistance with cloning, K. Beadle for vector production, E. Sullivan for tissue sectioning, E. Mackey for tissue sectioning and mouse colony management, N. Flytzanis and N. Goeden for their contributions towards histology, imaging, data analysis and manuscript preparation, P. Anguiano for administrative assistance, and the entire Gradinaru group for discussions. We thank L. V. Sibener at Stanford University for sharing the Matlab scripts used in amino acid clustering analysis. We thank the Biological Imaging Facility at Caltech (supported by Caltech Beckman Institute and the Arnold and Mabel Beckman Foundation). We also thank the Millard and Muriel Jacobs Genetics and Genomics Laboratory at Caltech; and Integrative Genomics Core at City of Hope for providing sequencing service. This work was primarily supported by grants from the National Institutes of Health (NIH) to V.G.: NIH Director’s New Innovator DP2NS087949 and PECASE, NIH BRAIN R01MH117069, NIH Pioneer DP1OD025535 and SPARC 1OT2OD024899. Additional funding includes the Vallee Foundation (V.G.), the Moore Foundation (V.G.), the CZI Neurodegeneration Challenge Network (V.G.), and the NSF NeuroNex Technology Hub grant 1707316 (V.G.), the Heritage Medical Research Institute (V.G.) and the Beckman Institute for CLARITY, Optogenetics and Vector Engineering Research (CLOVER) for technology development and dissemination (V.G.). Data availability: The NGS datasets using the synthetic pool and PCR pool selection methods that are reported in this article are available under the SRA accession code PRJNA610987. The following vector plasmids are deposited on Addgene for distribution (http://www.addgene.org) AAV-PHP.V1: 127847, AAV-PHP.V2: 127848, AAV-PHP.B4: 127849, and AAV-PHP.N: 127851, and viruses may be available for commonly packaged genomes. Other plasmids or viruses not available at Addgene may be requested from Caltech, CLOVER Center (http://clover.caltech.edu/). GenBank: AAV-PHP.V1: MT162422, AAV-PHP.V2: MT162423, AAV-PHP.N: MT162424, AAV- PHP.C1: MT162425, AAV-PHP.C2: MT162426, AAV-PHP.C3: MT162427, AAV-PHP.B4: MT162428, AAV-PHP.B5: MT162429, AAV-PHP.B6: MT162430, AAV-PHP.B7: MT162431 and AAV-PHP.B8: MT162432. Code availability: The codes used for M-CREATE data analysis were written in python or MATLAB and are made available on GitHub: https://github.com/GradinaruLab/mCREATE. The custom MATLAB scripts to generate HCR probes is accessible through GitHub on a different repository: https://github.com/GradinaruLab/HCRprobe. Author Contributions: S.R.K., B.E.D., T.F.M. and V.G. designed the experiments. S.R.K., B.E.D., X.C., T.F.M., Y.L., A.G., Q.H. and M.J.J. performed experiments. X.C. assisted with virus production and characterization of AAV-PHP variants in mice. Q.H. assisted with method optimization, cloning, virus production and tissue harvest. Y.L. assisted with method optimization and processed tissues for deep sequencing for 3-mer-s library. T.F.M. performed the clustering analysis, contributed to experiments related to NGS data validation, variant assessment across mice strains and amino acid bias heat map analysis. A.G. processed and imaged cleared brain hemisphere, and compiled the Supplementary Video 1 with input from S.R.K., and V.G. D.B., T.D. and P.H.E. built the software to process the NGS raw data for analysis with input from B.E.D., T.F.M., V.G. and S.R.K. M.J.J. performed the HCR experiments. X.D. produced structural models for AAV9 and contributed to the data analysis pipeline. S.R.K. prepared the figures with input from all authors. S.R.K., T.F.M., B.E.D. and V.G. wrote the manuscript with input from all authors. V.G. supervised all aspects of the work. Competing interests: The California Institute of Technology has filed and licensed a patent application for the work described in this manuscript with S.R.K., B.E.D., and V.G. listed as inventors (Caltech disclosure reference no. CIT 8198).
Group:Heritage Medical Research Institute, Tianqiao and Chrissy Chen Institute for Neuroscience
Funders:
Funding AgencyGrant Number
Caltech Beckman InstituteUNSPECIFIED
Arnold and Mabel Beckman FoundationUNSPECIFIED
NIHDP2NS087949
NIHR01MH117069
NIHDP1OD025535
NIHSPARC 1OT2OD024899
Vallee FoundationUNSPECIFIED
Gordon and Betty Moore FoundationUNSPECIFIED
Chan Zuckerberg InitiativeUNSPECIFIED
NSFDBI-1707316
Heritage Medical Research InstituteUNSPECIFIED
Subject Keywords:Blood–brain barrier; Molecular engineering; Mouse
Issue or Number:5
PubMed Central ID:PMC7219404
Record Number:CaltechAUTHORS:20200121-141523675
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200121-141523675
Official Citation:Ravindra Kumar, S., Miles, T.F., Chen, X. et al. Multiplexed Cre-dependent selection yields systemic AAVs for targeting distinct brain cell types. Nat Methods 17, 541–550 (2020). https://doi.org/10.1038/s41592-020-0799-7
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:100820
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:20 Apr 2020 15:38
Last Modified:30 Aug 2021 22:22

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