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Yang L, Liu F, Hahm H, Okuda T, Li X, Zhang Y, Kalyanaraman V, Heitmeier MR, Samineni VK. Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590975. [PMID: 38712231 PMCID: PMC11071495 DOI: 10.1101/2024.04.24.590975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Single-cell multiomic techniques have sparked immense interest in developing a comprehensive multi-modal map of diverse neuronal cell types and their brain wide projections. However, investigating the spatial organization, transcriptional and epigenetic landscapes of brain wide projection neurons is hampered by the lack of efficient and easily adoptable tools. Here we introduce Projection-TAGs, a retrograde AAV platform that allows multiplex tagging of projection neurons using RNA barcodes. By using Projection-TAGs, we performed multiplex projection tracing of the mouse cortex and high-throughput single-cell profiling of the transcriptional and epigenetic landscapes of the cortical projection neurons. Projection-TAGs can be leveraged to obtain a snapshot of activity-dependent recruitment of distinct projection neurons and their molecular features in the context of a specific stimulus. Given its flexibility, usability, and compatibility, we envision that Projection-TAGs can be readily applied to build a comprehensive multi-modal map of brain neuronal cell types and their projections.
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Affiliation(s)
- Lite Yang
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
- Neuroscience Graduate Program, Division of Biology & Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, United States
| | - Fang Liu
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Hannah Hahm
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Takao Okuda
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Xiaoyue Li
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Yufen Zhang
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Vani Kalyanaraman
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Monique R. Heitmeier
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
| | - Vijay K. Samineni
- Department of Anesthesiology, Washington University Pain Center, Washington University School of Medicine, St. Louis, MO, United States
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2
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Coughlin GM, Borsos M, Appling N, Barcelona BH, Mayfield AMH, Mackey ED, Eser RA, Chen X, Kumar SR, Gradinaru V. Spatial genomics of AAVs reveals mechanism of transcriptional crosstalk that enables targeted delivery of large genetic cargo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.23.573214. [PMID: 38187707 PMCID: PMC10769433 DOI: 10.1101/2023.12.23.573214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Integrating cell type-specific regulatory elements (e.g. enhancers) with recombinant adeno-associated viruses (AAVs) can provide broad and efficient genetic access to specific cell types. However, the packaging capacity of AAVs restricts the size of both the enhancers and the cargo that can be delivered. Transcriptional crosstalk offers a novel paradigm for cell type-specific expression of large cargo, by separating distally-acting regulatory elements into a second AAV genome. Here, we identify and profile transcriptional crosstalk in AAV genomes carrying 11 different enhancers active in mouse brain. To understand transcriptional crosstalk, we develop spatial genomics methods to identify and localize AAV genomes and their concatemeric forms in cultured cells and in tissue. Using these methods, we construct detailed views of the dynamics of AAV transduction and demonstrate that transcriptional crosstalk is dependent upon concatemer formation. Finally, we leverage transcriptional crosstalk to drive expression of a large Cas9 cargo in a cell type-specific manner with systemically-administered engineered AAVs and demonstrate AAV-delivered, minimally-invasive, cell type-specific gene editing in wildtype animals that recapitulates known disease phenotypes.
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Affiliation(s)
- Gerard M. Coughlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Máté Borsos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Nathan Appling
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Bre’Anna H. Barcelona
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Acacia M. H. Mayfield
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Elisha D. Mackey
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Rana A. Eser
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Xinhong Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Sripriya Ravindra Kumar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
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3
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Savell KE, Madangopal R, Saravanan P, Palaganas RG, Woods KD, Thompson DJ, Drake OR, Brenner MB, Weber SJ, Van Leer E, Choi JH, Martin TL, Martin JC, Steinberg MK, Austin JW, Charendoff CI, Hope BT. MultipleXed Population Selection and Enrichment single nucleus RNA sequencing (XPoSE-seq) enables sample identity retention during transcriptional profiling of rare populations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559834. [PMID: 38196637 PMCID: PMC10775316 DOI: 10.1101/2023.09.27.559834] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Single nucleus RNA-sequencing is critical in deciphering tissue heterogeneity and identifying rare populations. However, current high throughput techniques are not optimized for rare target populations and require tradeoffs in design due to feasibility. We provide a novel snRNA pipeline, MulipleXed Population Selection and Enrichment snRNA-sequencing (XPoSE-seq), to enable targeted snRNA-seq experiments and in-depth transcriptomic characterization of rare target populations while retaining individual sample identity.
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Affiliation(s)
- Katherine E Savell
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Rajtarun Madangopal
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Padmashri Saravanan
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Ryan G Palaganas
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Kareem D Woods
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Drake J Thompson
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Olivia R Drake
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Megan B Brenner
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Sophia J Weber
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Elise Van Leer
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Jae H Choi
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | - Toni L Martin
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
| | | | | | | | | | - Bruce T Hope
- Intramural Research Program, National Institute on Drug Abuse, Baltimore, MD 21224
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4
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Gosai SJ, Castro RI, Fuentes N, Butts JC, Kales S, Noche RR, Mouri K, Sabeti PC, Reilly SK, Tewhey R. Machine-guided design of synthetic cell type-specific cis-regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552077. [PMID: 37609287 PMCID: PMC10441439 DOI: 10.1101/2023.08.08.552077] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Cis-regulatory elements (CREs) control gene expression, orchestrating tissue identity, developmental timing, and stimulus responses, which collectively define the thousands of unique cell types in the body. While there is great potential for strategically incorporating CREs in therapeutic or biotechnology applications that require tissue specificity, there is no guarantee that an optimal CRE for an intended purpose has arisen naturally through evolution. Here, we present a platform to engineer and validate synthetic CREs capable of driving gene expression with programmed cell type specificity. We leverage innovations in deep neural network modeling of CRE activity across three cell types, efficient in silico optimization, and massively parallel reporter assays (MPRAs) to design and empirically test thousands of CREs. Through in vitro and in vivo validation, we show that synthetic sequences outperform natural sequences from the human genome in driving cell type-specific expression. Synthetic sequences leverage unique sequence syntax to promote activity in the on-target cell type and simultaneously reduce activity in off-target cells. Together, we provide a generalizable framework to prospectively engineer CREs and demonstrate the required literacy to write regulatory code that is fit-for-purpose in vivo across vertebrates.
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Affiliation(s)
- SJ Gosai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston MA
- Department Of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - RI Castro
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - N Fuentes
- The Jackson Laboratory, Bar Harbor, ME, USA
- Harvard College, Harvard University, Cambridge, MA, USA
| | - JC Butts
- The Jackson Laboratory, Bar Harbor, ME, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
| | - S Kales
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - RR Noche
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA
- Yale Zebrafish Research Core, Yale School of Medicine, New Haven, CT, USA
| | - K Mouri
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - PC Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department Of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - SK Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Wu Tsai Institute, Yale University, New Haven, CT, USA
| | - R Tewhey
- The Jackson Laboratory, Bar Harbor, ME, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
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5
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Grogans SE, Bliss-Moreau E, Buss KA, Clark LA, Fox AS, Keltner D, Cowen AS, Kim JJ, Kragel PA, MacLeod C, Mobbs D, Naragon-Gainey K, Fullana MA, Shackman AJ. The nature and neurobiology of fear and anxiety: State of the science and opportunities for accelerating discovery. Neurosci Biobehav Rev 2023; 151:105237. [PMID: 37209932 PMCID: PMC10330657 DOI: 10.1016/j.neubiorev.2023.105237] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/11/2023] [Accepted: 05/13/2023] [Indexed: 05/22/2023]
Abstract
Fear and anxiety play a central role in mammalian life, and there is considerable interest in clarifying their nature, identifying their biological underpinnings, and determining their consequences for health and disease. Here we provide a roundtable discussion on the nature and biological bases of fear- and anxiety-related states, traits, and disorders. The discussants include scientists familiar with a wide variety of populations and a broad spectrum of techniques. The goal of the roundtable was to take stock of the state of the science and provide a roadmap to the next generation of fear and anxiety research. Much of the discussion centered on the key challenges facing the field, the most fruitful avenues for future research, and emerging opportunities for accelerating discovery, with implications for scientists, funders, and other stakeholders. Understanding fear and anxiety is a matter of practical importance. Anxiety disorders are a leading burden on public health and existing treatments are far from curative, underscoring the urgency of developing a deeper understanding of the factors governing threat-related emotions.
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Affiliation(s)
- Shannon E Grogans
- Department of Psychology, University of Maryland, College Park, MD 20742, USA
| | - Eliza Bliss-Moreau
- Department of Psychology, University of California, Davis, CA 95616, USA; California National Primate Research Center, University of California, Davis, CA 95616, USA
| | - Kristin A Buss
- Department of Psychology, The Pennsylvania State University, University Park, PA 16802 USA
| | - Lee Anna Clark
- Department of Psychology, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Andrew S Fox
- Department of Psychology, University of California, Davis, CA 95616, USA; California National Primate Research Center, University of California, Davis, CA 95616, USA
| | - Dacher Keltner
- Department of Psychology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | - Jeansok J Kim
- Department of Psychology, University of Washington, Seattle, WA 98195, USA
| | - Philip A Kragel
- Department of Psychology, Emory University, Atlanta, GA 30322, USA
| | - Colin MacLeod
- Centre for the Advancement of Research on Emotion, School of Psychological Science, The University of Western Australia, Perth, WA 6009, Australia
| | - Dean Mobbs
- Department of Humanities and Social Sciences, California Institute of Technology, Pasadena, California 91125, USA; Computation and Neural Systems Program, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kristin Naragon-Gainey
- School of Psychological Science, University of Western Australia, Perth, WA 6009, Australia
| | - Miquel A Fullana
- Adult Psychiatry and Psychology Department, Institute of Neurosciences, Hospital Clinic, Barcelona, Spain; Imaging of Mood, and Anxiety-Related Disorders Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer, CIBERSAM, University of Barcelona, Barcelona, Spain
| | - Alexander J Shackman
- Department of Psychology, University of Maryland, College Park, MD 20742, USA; Neuroscience and Cognitive Science Program, University of Maryland, College Park, MD 20742, USA; Maryland Neuroimaging Center, University of Maryland, College Park, MD 20742, USA.
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6
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Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP, Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science 2023; 380:eabm7993. [PMID: 37104615 DOI: 10.1126/science.abm7993] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challenging because enhancer activity can be tissue-dependent and functionally conserved despite low sequence conservation. We developed the Tissue-Aware Conservation Inference Toolkit (TACIT) to associate candidate enhancers with species' phenotypes using predictions from machine learning models trained on specific tissues. Applying TACIT to associate motor cortex and parvalbumin-positive interneuron enhancers with neurological phenotypes revealed dozens of enhancer-phenotype associations, including brain size-associated enhancers that interact with genes implicated in microcephaly or macrocephaly. TACIT provides a foundation for identifying enhancers associated with the evolution of any convergently evolved phenotype in any large group of species with aligned genomes.
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Affiliation(s)
- Irene M Kaplow
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Alyssa J Lawler
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Daniel E Schäffer
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Chaitanya Srinivasan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Heather H Sestili
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Morgan E Wirthlin
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
| | - BaDoi N Phan
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kavya Prasad
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Ashley R Brown
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Xiaomeng Zhang
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Kathleen Foley
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Diane P Genereux
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Elinor K Karlsson
- Broad Institute, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kerstin Lindblad-Toh
- Broad Institute, Cambridge, MA, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Wynn K Meyer
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Andreas R Pfenning
- Department of Computational Biology, Carnegie Mellon University, Pittsburgh, PA, USA
- Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA
- Department of Biology, Carnegie Mellon University, Pittsburgh, PA, USA
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7
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Campos LJ, Arokiaraj CM, Chuapoco MR, Chen X, Goeden N, Gradinaru V, Fox AS. Advances in AAV technology for delivering genetically encoded cargo to the nonhuman primate nervous system. CURRENT RESEARCH IN NEUROBIOLOGY 2023; 4:100086. [PMID: 37397806 PMCID: PMC10313870 DOI: 10.1016/j.crneur.2023.100086] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/05/2023] [Accepted: 03/17/2023] [Indexed: 07/04/2023] Open
Abstract
Modern neuroscience approaches including optogenetics, calcium imaging, and other genetic manipulations have facilitated our ability to dissect specific circuits in rodent models to study their role in neurological disease. These approaches regularly use viral vectors to deliver genetic cargo (e.g., opsins) to specific tissues and genetically-engineered rodents to achieve cell-type specificity. However, the translatability of these rodent models, cross-species validation of identified targets, and translational efficacy of potential therapeutics in larger animal models like nonhuman primates remains difficult due to the lack of efficient primate viral vectors. A refined understanding of the nonhuman primate nervous system promises to deliver insights that can guide the development of treatments for neurological and neurodegenerative diseases. Here, we outline recent advances in the development of adeno-associated viral vectors for optimized use in nonhuman primates. These tools promise to help open new avenues for study in translational neuroscience and further our understanding of the primate brain.
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Affiliation(s)
- Lillian J. Campos
- Department of Psychology and the California National Primate Research Center, University of California, Davis, CA, 05616, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Cynthia M. Arokiaraj
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Miguel R. Chuapoco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Xinhong Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Nick Goeden
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Capsida Biotherapeutics, Thousand Oaks, CA, 91320, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Andrew S. Fox
- Department of Psychology and the California National Primate Research Center, University of California, Davis, CA, 05616, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
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8
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In silico prediction and in vivo testing of promoters targeting GABAergic inhibitory neurons. Mol Ther Methods Clin Dev 2023; 28:330-343. [PMID: 36874244 PMCID: PMC9974971 DOI: 10.1016/j.omtm.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/31/2023] [Indexed: 02/07/2023]
Abstract
Impairment of GABAergic inhibitory neuronal function is linked to epilepsy and other neurological and psychiatric disorders. Recombinant adeno-associated virus (rAAV)-based gene therapy targeting GABAergic neurons is a promising treatment for GABA-associated disorders. However, there is a need to develop rAAV-compatible gene-regulatory elements capable of selectively driving expression in GABAergic neurons throughout the brain. Here, we designed several novel GABAergic gene promoters. In silico analyses, including evolutionarily conserved DNA sequence alignments and transcription factor binding site searches among GABAergic neuronal genes, were carried out to reveal novel sequences for use as rAAV-compatible promoters. rAAVs (serotype 9) were injected into the CSF of neonatal mice and into the brain parenchyma of adult mice to assess promoter specificity. In mice injected neonatally, transgene expression was detected in multiple brain regions with very high neuronal specificity and moderate-to-high GABAergic neuronal selectivity. The GABA promoters differed greatly in their levels of expression and, in some brain regions, showed strikingly different patterns of GABAergic neuron transduction. This study is the first report of rAAV vectors that are functional in multiple brain regions using promoters designed by in silico analyses from multiple GABAergic genes. These novel GABA-targeting vectors may be useful tools to advance gene therapy for GABA-associated disorders.
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