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

Creators: Mich, John K.; Graybuck, Lucas T.; Hess, Erik E.; Mahoney, Joseph T.; Kojimo, Yoshiko; Ding, Yi; Somasundaram, Saroja; Miller, Jeremy A.; Kalmbach, Brian E.; Radaelli, Cristina; Gore, Bryan B.; Weed, Natalie; Omstead, Victoria; Bishaw, Yemeserach; Shapovalova, Nadiya V.; Martinez, Refugio A.; Fong, Olivia; Yao, Shenqin; Mortrud, Marty; Chong, Peter; Loftus, Luke; Bertagnolli, Darren; Goldy, Jeff; Casper, Tamara; Dee, Nick; Opitz-Araya, Ximena; Cetin, Ali; Smith, Kimberly A.; Gwinn, Ryder P.; Cobbs, Charles; Ko, Andrew L.; Ojemann, Jeffrey G.; Keene, C. Dirk; Silbergeld, Daniel L.; Sunkin, Susan M.; Gradinaru, Viviana; Horwitz, Gregory D.; Zeng, Hongkui; Tasic, Bosiljka; Lein, Ed S.; Ting, Jonathan T.; Levi, Boaz P.

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.

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.

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