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Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex

Mich, John K. and Graybuck, Lucas T. and Hess, Erik E. and Mahoney, Joseph T. and Kojimo, Yoshiko and Ding, Yi and Somasundaram, Saroja and Miller, Jeremy A. and Kalmbach, Brian E. and Radaelli, Cristina and Gore, Bryan B. and Weed, Natalie and Omstead, Victoria and Bishaw, Yemeserach and Shapovalova, Nadiya V. and Martinez, Refugio A. and Fong, Olivia and Yao, Shenqin and Mortrud, Marty and Chong, Peter and Loftus, Luke and Bertagnolli, Darren and Goldy, Jeff and Casper, Tamara and Dee, Nick and Opitz-Araya, Ximena and Cetin, Ali and Smith, Kimberly A. and Gwinn, Ryder P. and Cobbs, Charles and Ko, Andrew L. and Ojemann, Jeffrey G. and Keene, C. Dirk and Silbergeld, Daniel L. and Sunkin, Susan M. and Gradinaru, Viviana and Horwitz, Gregory D. and Zeng, Hongkui and Tasic, Bosiljka and Lein, Ed S. and Ting, Jonathan T. and Levi, Boaz P. (2021) Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex. Cell Reports, 34 (13). Art. No. 108754. ISSN 2211-1247. doi:10.1016/j.celrep.2021.108754. https://resolver.caltech.edu/CaltechAUTHORS:20200421-093728277

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Abstract

Viral genetic tools that target specific brain cell types could transform basic neuroscience and targeted gene therapy. Here, we use comparative open chromatin analysis to identify thousands of human-neocortical-subclass-specific putative enhancers from across the genome to control gene expression in adeno-associated virus (AAV) vectors. The cellular specificity of reporter expression from enhancer-AAVs is established by molecular profiling after systemic AAV delivery in mouse. Over 30% of enhancer-AAVs produce specific expression in the targeted subclass, including both excitatory and inhibitory subclasses. We present a collection of Parvalbumin (PVALB) enhancer-AAVs that show highly enriched expression not only in cortical PVALB cells but also in some subcortical PVALB populations. Five vectors maintain PVALB-enriched expression in primate neocortex. These results demonstrate how genome-wide open chromatin data mining and cross-species AAV validation can be used to create the next generation of non-species-restricted viral genetic tools.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1016/j.celrep.2021.108754DOIArticle
https://doi.org/10.1101/555318DOIDiscussion Paper
ORCID:
AuthorORCID
Kalmbach, Brian E.0000-0003-3136-8097
Gradinaru, Viviana0000-0001-5868-348X
Additional Information:© 2021 The Author(s). This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Received 14 April 2020, Revised 7 July 2020, Accepted 25 January 2021, Available online 30 March 2021. We thank Allison Beller, Nathan Hansen, Caryl Tongco, Jae-Guen Yoon, and Gina DeNoble for assistance with obtaining patient consent and human neurosurgical tissue research specimens. We thank Rebecca D. Hodge, Trygve E. Bakken, and Zizhen Yao for assistance with sc/snRNA-seq data. We thank Lisa McConnell for assisting with NHP virus injection surgery and NHP animal care. We thank Allen Institute Tissue Procurement and Facilities teams for institutional support during tissue collections. In addition, we wish to thank the Allen Institute for Brain Science founder, Paul G. Allen, for his vision, encouragement, and support. This work is supported by NIH BRAIN Initiative award 1RF1MH114126-01 from the National Institute of Mental Health to E.S.L., J.T.T., and B.P.L.; National Institute on Drug Abuse award 1R01DA036909-01 to B.T.; the Nancy and Buster Alvord Endowment to C.D.K.; and National Eye Institute award 1R01EY030441-01 to G.D.H. This project was also supported in part by NIH grant P51OD010425 from the Office of Research Infrastructure Programs (ORIP) and grant UL1TR000423 from the National Center for Advancing Translational Sciences (NCATS). Its contents are solely the responsibility of the authors and do not necessarily represent the official view of NIH, ORIP, NCATS, the Institute of Translational Health Sciences, or the University of Washington National Primate Research Center. Author contributions: J.T.T., N.S., E.E.H., T.C., N.D., and J.K.M. performed tissue processing and flow cytometry. E.E.H., B.P.L., and J.K.M. performed ATAC-seq with assistance from D.B. and K.A.S. J.K.M. analyzed ATAC-seq data using techniques developed by L.T.G., with assistance from S.S., J.A.M., L.T.G., J.G., and Y.D. B.P.L., J.T.T., and J.K.M. curated candidate enhancers for testing. E.E.H., J.K.M., J.T.T., R.A.M., and X.O.-A. performed AAV vector design and molecular biology. C.R. and B.E.K. performed electrophysiology. J.K.M. and J.T.T. tested AAV vectors with assistance from P.C. and X.O.-A. R.P.G., C.C., J.G.O., A.L.K., C.D.K., and D.L.S. procured human surgical tissue for research. J.T.T. and J.K.M. performed human ex vivo brain slice culture and viral labeling experiments with assistance from P.C. J.T.M., L.L., and Y.D. performed mFISH. scRNA-seq was conducted by J.K.M., D.B., and K.A.S. and analysis by O.F., J.G., and B.P.L. M.M., S.Y., A.C., E.E.H., and X.O.-A. performed viral packaging. J.T.T. carried out NHP ex vivo slice culture experiments with assistance from G.D.H., N.W., and X.O.-A. G.D.H. and Y.K. performed NHP in vivo virus injection surgery with assistance from J.T.T. J.K.M. and J.T.T. processed NHP brain tissue from in vivo virus testing with assistance from V.O. and Y.B. B.P.L., J.T.T., J.K.M., and E.L. conceived of the study design. J.K.M. wrote the manuscript and prepared figures with assistance from B.B.G., B.P.L., and J.T.T. L.T.G. and B.T. provided mouse ATAC-seq data. V.G. provided PHP.eB capsid plasmid DNA. S.M.S. provided program and budgetary management. H.Z. and E.S.L. provided program leadership. Declaration of interests: J.K.M., L.T.G., E.E.H., H.Z., B.T., E.L., J.T.T., and B.P.L. are inventors on several U.S. patent applications related to this work. The remaining authors declare no competing interests.
Funders:
Funding AgencyGrant Number
NIH1RF1MH114126-01
NIH1R01DA036909-01
Nancy and Buster Alvord EndowmentUNSPECIFIED
NIH1R01EY030441-01
NIHP51OD010425
NIHUL1TR000423
Subject Keywords:human; macaque; brain cell types; epigenetics; enhancers; AAVs; genetic tools; ex vivo brain slice; ATAC-seq; parvalbumin
Issue or Number:13
DOI:10.1016/j.celrep.2021.108754
Record Number:CaltechAUTHORS:20200421-093728277
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200421-093728277
Official Citation:John K. Mich, Lucas T. Graybuck, Erik E. Hess, Joseph T. Mahoney, Yoshiko Kojima, Yi Ding, Saroja Somasundaram, Jeremy A. Miller, Brian E. Kalmbach, Cristina Radaelli, Bryan B. Gore, Natalie Weed, Victoria Omstead, Yemeserach Bishaw, Nadiya V. Shapovalova, Refugio A. Martinez, Olivia Fong, Shenqin Yao, Marty Mortrud, Peter Chong, Luke Loftus, Darren Bertagnolli, Jeff Goldy, Tamara Casper, Nick Dee, Ximena Opitz-Araya, Ali Cetin, Kimberly A. Smith, Ryder P. Gwinn, Charles Cobbs, Andrew L. Ko, Jeffrey G. Ojemann, C. Dirk Keene, Daniel L. Silbergeld, Susan M. Sunkin, Viviana Gradinaru, Gregory D. Horwitz, Hongkui Zeng, Bosiljka Tasic, Ed S. Lein, Jonathan T. Ting, Boaz P. Levi, Functional enhancer elements drive subclass-selective expression from mouse to primate neocortex, Cell Reports, Volume 34, Issue 13, 2021, 108754, ISSN 2211-1247, https://doi.org/10.1016/j.celrep.2021.108754. (https://www.sciencedirect.com/science/article/pii/S221112472100067X)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:102694
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:21 Apr 2020 17:04
Last Modified:06 Apr 2021 20:14

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