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Enhancer viruses for combinatorial cell-subclass-specific labeling

Graybuck, Lucas T. and Daigle, Tanya L. and Sedeño-Cortés, Adriana E. and Walker, Miranda and Kalmbach, Brian and Lenz, Garreck H. and Morin, Elyse and Nguyen, Thuc Nghi and Garren, Emma and Bendrick, Jacqueline L. and Kim, Tae Kyung and Zhou, Thomas and Mortrud, Marty and Yao, Shenqin and Sieverts, La'Akea and Larsen, Rachael and Gore, Bryan B. and Szelenyi, Eric R. and Trader, Cameron and Balaram, Pooja and van Velthoven, Cindy T. J. and Chiang, Megan and Mich, John K. and Dee, Nick and Goldy, Jeff and Cetin, Ali H. and Smith, Kimberly and Way, Sharon W. and Esposito, Luke and Yao, Zizhen and Gradinaru, Viviana and Sunkin, Susan M. and Lein, Ed and Levi, Boaz P. and Ting, Jonathan T. and Zeng, Hongkui and Tasic, Bosiljka (2021) Enhancer viruses for combinatorial cell-subclass-specific labeling. Neuron, 109 (9). pp. 1449-1464. ISSN 0896-6273. PMCID PMC8610077. doi:10.1016/j.neuron.2021.03.011.

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Rapid cell type identification by new genomic single-cell analysis methods has not been met with efficient experimental access to these cell types. To facilitate access to specific neural populations in mouse cortex, we collected chromatin accessibility data from individual cells and identified enhancers specific for cell subclasses and types. When cloned into recombinant adeno-associated viruses (AAVs) and delivered to the brain, these enhancers drive transgene expression in specific cortical cell subclasses. We extensively characterized several enhancer AAVs to show that they label different projection neuron subclasses as well as a homologous neuron subclass in human cortical slices. We also show how coupling enhancer viruses expressing recombinases to a newly generated transgenic mouse, Ai213, enables strong labeling of three different neuronal classes/subclasses in the brain of a single transgenic animal. This approach combines unprecedented flexibility with specificity for investigation of cell types in the mouse brain and beyond.

Item Type:Article
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URLURL TypeDescription CentralArticle Paper
Graybuck, Lucas T.0000-0002-8814-6818
Daigle, Tanya L.0000-0001-9700-8452
Sedeño-Cortés, Adriana E.0000-0001-7959-8970
Walker, Miranda0000-0002-3767-1591
Kalmbach, Brian0000-0003-3136-8097
Lenz, Garreck H.0000-0002-3233-0763
Morin, Elyse0000-0002-7310-1561
Nguyen, Thuc Nghi0000-0002-6466-5883
Bendrick, Jacqueline L.0000-0002-2694-9914
Kim, Tae Kyung0000-0001-9646-5969
Mortrud, Marty0000-0002-4570-9887
Yao, Shenqin0000-0003-2992-4752
Sieverts, La'Akea0000-0002-1385-086X
Larsen, Rachael0000-0003-0178-003X
Gore, Bryan B.0000-0003-1721-4235
Szelenyi, Eric R.0000-0003-2636-0912
Trader, Cameron0000-0001-8214-1541
van Velthoven, Cindy T. J.0000-0001-5120-4546
Chiang, Megan0000-0002-7306-3016
Mich, John K.0000-0002-1626-1139
Dee, Nick0000-0002-2831-9254
Goldy, Jeff0000-0001-5140-6922
Cetin, Ali H.0000-0003-1510-0517
Smith, Kimberly0000-0002-3142-1970
Way, Sharon W.0000-0002-9598-2240
Esposito, Luke0000-0002-3565-9126
Yao, Zizhen0000-0002-9361-5607
Gradinaru, Viviana0000-0001-5868-348X
Sunkin, Susan M.0000-0001-9893-3834
Lein, Ed0000-0001-9012-6552
Levi, Boaz P.0000-0002-8346-872X
Ting, Jonathan T.0000-0001-8266-0392
Zeng, Hongkui0000-0002-0326-5878
Tasic, Bosiljka0000-0002-6861-4506
Alternate Title:Enhancer viruses and a transgenic platform for combinatorial cell subclass-specific labeling
Additional Information:© 2021 Elsevier Inc. Received 17 April 2020, Revised 14 December 2020, Accepted 8 March 2021, Available online 30 March 2021. We could not have performed this study without the support of the following Allen Institute teams and departments: Lab Animal Services, Transgenic Colony Management, Tissue Processing, FACS Core, Molecular Biology, Molecular Genetics, and Human Cell Types. We thank Aaron Oster for Addgene reagent submission; Dr. Andrew Ko and Dr. C. Dirk Keene and associated teams at Harborview Medical Center (UW Medicine) for providing the human surgical tissue specimen in this study; Andrew Hill and Darren Cusanovich for assistance with data from Cusanovich et al. (2018), and Advanced Cell Diagnostics for early access to RNAscope HiPlex. The project described was supported by award number R01DA036909 from the National Institute on Drug Abuse to B.T. and H.Z.; by National Institutes of Health (NIH) BRAIN Initiative award RF1MH121274 to B.T., T.L.D., and H.Z.; and by National Institute of Mental Health grant RF1MH114126 to B.P.L., J.T.T., E.L., and B.T. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of the NIH, the National Institute on Drug Abuse, or the National Institute of Mental Health. We thank the Allen Institute founder, Paul G. Allen, for his vision, encouragement, and support. Author contributions: B.T., L.T.G., and T.L.D. designed the study. A.E.S.-C., T.N.N., and L.T.G. performed scATAC-seq. L.T.G., A.E.S.-C., J.G., and Z.Y. performed scRNA-seq and scATAC-seq analyses. J.T.T., B.P.L., V.G., and J.K.M. provided viral constructs and protocols. L.T.G., G.H.L., and M.W. generated viral constructs. T.L.D., L.A.S., G.H.L., and M.W. designed and generated Ai213. B.K. and J.T.T. performed electrophysiology experiments and analysis. S.Y., M.M., T.Z., and A.H.C. packaged viruses. T.N.N., T.K.K., M.M., M.W., L.A.S., B.B.G., and E.R.S. performed injections. M.W., J.L.B., C.T., E.M., L.A.S., and T.L.D. performed histology and analysis. T.N.N., E.G., J.L.B., E.M., and P.B. performed mFISH and analysis. N.D. managed tissue processing for RNA-seq. K.S. managed RNA-seq experiments. R.L. and L.E. managed the transgenic colony. S.M.S. provided project management. C.T.J.v.V. and M.C. managed deposition of single-cell omics data. S.W.W. provided editorial assistance. H.Z. and E.L. lead the Cell Types Program at the Allen Institute. L.T.G., T.L.D., and B.T. wrote the manuscript with input from all co-authors. Declaration of interests: L.T.G., T.L.D., J.T.T., J.K.M., B.P.L., E.L., B.K., H.Z., and B.T. are inventors on several U.S. provisional patent applications related to this work. All authors declare no other competing interests.
Funding AgencyGrant Number
Subject Keywords:AAV; enhancer; transgenic mouse; cell types; recombinase; ATAC-seq; cortex
Issue or Number:9
PubMed Central ID:PMC8610077
Record Number:CaltechAUTHORS:20200421-092814882
Persistent URL:
Official Citation:Lucas T. Graybuck, Tanya L. Daigle, Adriana E. Sedeño-Cortés, Miranda Walker, Brian Kalmbach, Garreck H. Lenz, Elyse Morin, Thuc Nghi Nguyen, Emma Garren, Jacqueline L. Bendrick, Tae Kyung Kim, Thomas Zhou, Marty Mortrud, Shenqin Yao, La’ Akea Siverts, Rachael Larsen, Bryan B. Gore, Eric R. Szelenyi, Cameron Trader, Pooja Balaram, Cindy T.J. van Velthoven, Megan Chiang, John K. Mich, Nick Dee, Jeff Goldy, Ali H. Cetin, Kimberly Smith, Sharon W. Way, Luke Esposito, Zizhen Yao, Viviana Gradinaru, Susan M. Sunkin, Ed Lein, Boaz P. Levi, Jonathan T. Ting, Hongkui Zeng, Bosiljka Tasic, Enhancer viruses for combinatorial cell-subclass-specific labeling, Neuron, Volume 109, Issue 9, 2021, Pages 1449-1464.e13, ISSN 0896-6273,
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:102693
Deposited By: Tony Diaz
Deposited On:21 Apr 2020 16:39
Last Modified:11 May 2022 21:17

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