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Furlanis E, Dai M, Leyva Garcia B, Tran T, Vergara J, Pereira A, Gorissen BL, Wills S, Vlachos A, Hairston A, Dwivedi D, Du S, McMahon J, Huang S, Morabito A, Vazquez A, Kim S, Lee AT, Chang EF, Razzaq T, Qazi A, Vargish G, Yuan X, Caccavano A, Hunt S, Chittajallu R, McLean N, Hewitt L, Paranzino E, Rice H, Cummins AC, Plotnikova A, Mohanty A, Tangen AC, Shin JH, Azadi R, Eldridge MAG, Alvarez VA, Averbeck BB, Alyahyay M, Vallejo TR, Soheib M, Vattino LG, MacGregor CP, Chatain CP, Banks E, Olah VJ, Naskar S, Hill S, Liebergall S, Badiani R, Hyde L, Hanley E, Xu Q, Allaway KC, Goldberg EM, Rowan MJM, Nowakowski TJ, Lee S, Favuzzi E, Kaeser PS, Sjulson L, Batista-Brito R, Takesian AE, Ibrahim LA, Iqbal A, Pelkey KA, McBain CJ, Dimidschstein J, Fishell G, Wang Y. An enhancer-AAV toolbox to target and manipulate distinct interneuron subtypes. Neuron 2025; 113:1525-1547.e15. [PMID: 40403705 DOI: 10.1016/j.neuron.2025.05.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 03/18/2025] [Accepted: 05/01/2025] [Indexed: 05/24/2025]
Abstract
In recent years, we and others have identified a number of enhancers that, when incorporated into rAAV vectors, can restrict the transgene expression to particular neuronal populations. Yet, viral tools to access and manipulate specific neuronal subtypes are still limited. Here, we performed systematic analysis of single-cell genomic data to identify enhancer candidates for each of the telencephalic interneuron subtypes. We established a set of enhancer-AAV tools that are highly specific for distinct cortical interneuron populations and striatal cholinergic interneurons. These enhancers, when used in the context of different effectors, can target (fluorescent proteins), observe activity (GCaMP), and manipulate (opto-genetics) specific neuronal subtypes. We also validated our enhancer-AAV tools across species. Thus, we provide the field with a powerful set of tools to study neural circuits and functions and to develop precise and targeted therapy.
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Affiliation(s)
- Elisabetta Furlanis
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Min Dai
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Brenda Leyva Garcia
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thien Tran
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Josselyn Vergara
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ana Pereira
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bram L Gorissen
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sara Wills
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anna Vlachos
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Ariel Hairston
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
| | - Deepanjali Dwivedi
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah Du
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Justin McMahon
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shuhan Huang
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
| | - Annunziato Morabito
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
| | - Arenski Vazquez
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Soyoun Kim
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Anthony T Lee
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Edward F Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Geoffrey Vargish
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Xiaoqing Yuan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Adam Caccavano
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Steven Hunt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Ramesh Chittajallu
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Nadiya McLean
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Lauren Hewitt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Emily Paranzino
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Haley Rice
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Alex C Cummins
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892-4415, USA
| | - Anya Plotnikova
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892-4415, USA
| | - Arya Mohanty
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892-4415, USA
| | - Anne Claire Tangen
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892-4415, USA
| | - Jung Hoon Shin
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892-4415, USA
| | - Reza Azadi
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892-4415, USA
| | - Mark A G Eldridge
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892-4415, USA
| | - Veronica A Alvarez
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892-4415, USA
| | - Bruno B Averbeck
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892-4415, USA
| | - Mansour Alyahyay
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Tania Reyes Vallejo
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Mohammed Soheib
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Lucas G Vattino
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA, USA; Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
| | - Cathryn P MacGregor
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA, USA; Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
| | - Carolina Piletti Chatain
- Department of Neuroscience, Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Wu Tsai Institute, Yale University, New Haven, CT 06510, USA
| | - Emmie Banks
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Viktor Janos Olah
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Shovan Naskar
- Unit of Functional Neural Circuit, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sophie Hill
- Department of Neuroscience, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sophie Liebergall
- Department of Neuroscience, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Rohan Badiani
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lili Hyde
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ella Hanley
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Qing Xu
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia; Genomics & Systems Biology, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Kathryn C Allaway
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ethan M Goldberg
- Department of Neuroscience, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Matthew J M Rowan
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Tomasz J Nowakowski
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Soohyun Lee
- Unit of Functional Neural Circuit, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emilia Favuzzi
- Department of Neuroscience, Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT 06510, USA; Wu Tsai Institute, Yale University, New Haven, CT 06510, USA
| | - Pascal S Kaeser
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA
| | - Lucas Sjulson
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA; Dominick P. Purpura Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Renata Batista-Brito
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA; Dominick P. Purpura Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Anne E Takesian
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA, USA; Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, Boston, MA, USA
| | - Leena A Ibrahim
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | | | - Kenneth A Pelkey
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Chris J McBain
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Jordane Dimidschstein
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Gord Fishell
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Yating Wang
- Harvard Medical School, Blavatnik Institute, Department of Neurobiology, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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