Welcome to the new version of CaltechAUTHORS. Login is currently restricted to library staff. If you notice any issues, please email coda@library.caltech.edu
Published May 5, 2021 | Accepted Version + Supplemental Material + Submitted
Journal Article Open

Enhancer viruses for combinatorial cell-subclass-specific labeling


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.

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.

Attached Files

Accepted Version - nihms-1689242.pdf

Submitted - 525014v3.full.pdf

Supplemental Material - 1-s2.0-S0896627321001598-mmc1.pdf

Supplemental Material - 1-s2.0-S0896627321001598-mmc2.xlsx

Supplemental Material - 1-s2.0-S0896627321001598-mmc3.xlsx

Supplemental Material - 1-s2.0-S0896627321001598-mmc4.xlsx

Supplemental Material - 1-s2.0-S0896627321001598-mmc5.xlsx

Supplemental Material - 1-s2.0-S0896627321001598-mmc6.xlsx

Supplemental Material - 1-s2.0-S0896627321001598-mmc7.xlsx

Supplemental Material - 1-s2.0-S0896627321001598-mmc8.xlsx

Supplemental Material - 1-s2.0-S0896627321001598-mmc9.xlsx


Files (26.1 MB)
Name Size Download all
11.6 MB Preview Download
27.6 kB Download
20.8 kB Download
19.6 kB Download
24.4 kB Download
8.7 MB Preview Download
374.1 kB Download
4.4 MB Preview Download
616.8 kB Download
255.3 kB Download
22.6 kB Download

Additional details

August 22, 2023
December 22, 2023