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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Jang MJ, Coughlin GM, Jackson CR, Chen X, Chuapoco MR, Vendemiatti JL, Wang AZ, Gradinaru V. Spatial transcriptomics for profiling the tropism of viral vectors in tissues. Nat Biotechnol 2023; 41:1272-1286. [PMID: 36702899 PMCID: PMC10443732 DOI: 10.1038/s41587-022-01648-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/15/2022] [Indexed: 01/27/2023]
Abstract
A barrier to advancing engineered adeno-associated viral vectors (AAVs) for precision access to cell subtypes is a lack of high-throughput, high-resolution assays to characterize in vivo transduction profiles. In this study, we developed an ultrasensitive, sequential fluorescence in situ hybridization (USeqFISH) method for spatial transcriptomic profiling of endogenous and viral RNA with a short barcode in intact tissue volumes by integrating hydrogel-based tissue clearing, enhanced signal amplification and multiplexing using sequential labeling. Using USeqFISH, we investigated the transduction and cell subtype tropisms across mouse brain regions of six systemic AAVs, including AAV-PHP.AX, a new variant that transduces robustly and efficiently across neurons and astrocytes. Here we reveal distinct cell subtype biases of each AAV variant, including a bias of AAV-PHP.N toward excitatory neurons. USeqFISH also enables profiling of pooled regulatory cargos, as we show for a 13-variant pool of microRNA target sites in AAV genomes. Lastly, we demonstrate potential applications of USeqFISH for in situ AAV profiling and multimodal single-cell analysis in non-human primates.
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Affiliation(s)
- Min J Jang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Gerard M Coughlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Cameron R Jackson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Xinhong Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Miguel R Chuapoco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Julia L Vendemiatti
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alexander Z Wang
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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Challis RC, Ravindra Kumar S, Chen X, Goertsen D, Coughlin GM, Hori AM, Chuapoco MR, Otis TS, Miles TF, Gradinaru V. Adeno-Associated Virus Toolkit to Target Diverse Brain Cells. Annu Rev Neurosci 2022; 45:447-469. [PMID: 35440143 DOI: 10.1146/annurev-neuro-111020-100834] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Recombinant adeno-associated viruses (AAVs) are commonly used gene delivery vehicles for neuroscience research. They have two engineerable features: the capsid (outer protein shell) and cargo (encapsulated genome). These features can be modified to enhance cell type or tissue tropism and control transgene expression, respectively. Several engineered AAV capsids with unique tropisms have been identified, including variants with enhanced central nervous system transduction, cell type specificity, and retrograde transport in neurons. Pairing these AAVs with modern gene regulatory elements and state-of-the-art reporter, sensor, and effector cargo enables highly specific transgene expression for anatomical and functional analyses of brain cells and circuits. Here, we discuss recent advances that provide a comprehensive (capsid and cargo) AAV toolkit for genetic access to molecularly defined brain cell types. Expected final online publication date for the Annual Review of Neuroscience, Volume 45 is July 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Rosemary C Challis
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Sripriya Ravindra Kumar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Xinhong Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - David Goertsen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Gerard M Coughlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Acacia M Hori
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Miguel R Chuapoco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Thomas S Otis
- Sainsbury Wellcome Centre, University College London, London, United Kingdom
| | - Timothy F Miles
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA;
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Brown AR, Coughlin GM, Teskey GC. Seizures Alter Cortical Representations for Complex Movements. Neuroscience 2020; 449:134-146. [DOI: 10.1016/j.neuroscience.2020.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/11/2020] [Accepted: 09/01/2020] [Indexed: 01/31/2023]
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Robinson JE, Coughlin GM, Hori AM, Cho JR, Mackey ED, Turan Z, Patriarchi T, Tian L, Gradinaru V. Optical dopamine monitoring with dLight1 reveals mesolimbic phenotypes in a mouse model of neurofibromatosis type 1. eLife 2019; 8:e48983. [PMID: 31545171 PMCID: PMC6819083 DOI: 10.7554/elife.48983] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 09/21/2019] [Indexed: 12/12/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is an autosomal dominant disorder whose neurodevelopmental symptoms include impaired executive function, attention, and spatial learning and could be due to perturbed mesolimbic dopaminergic circuitry. However, these circuits have never been directly assayed in vivo. We employed the genetically encoded optical dopamine sensor dLight1 to monitor dopaminergic neurotransmission in the ventral striatum of NF1 mice during motivated behavior. Additionally, we developed novel systemic AAV vectors to facilitate morphological reconstruction of dopaminergic populations in cleared tissue. We found that NF1 mice exhibit reduced spontaneous dopaminergic neurotransmission that was associated with excitation/inhibition imbalance in the ventral tegmental area and abnormal neuronal morphology. NF1 mice also had more robust dopaminergic and behavioral responses to salient visual stimuli, which were independent of learning, and rescued by optogenetic inhibition of non-dopaminergic neurons in the VTA. Overall, these studies provide a first in vivo characterization of dopaminergic circuit function in the context of NF1 and reveal novel pathophysiological mechanisms.
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Affiliation(s)
- J Elliott Robinson
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
| | - Gerard M Coughlin
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
| | - Acacia M Hori
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
| | - Jounhong Ryan Cho
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
| | - Elisha D Mackey
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
| | - Zeynep Turan
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
| | - Tommaso Patriarchi
- Department of Biochemistry and Molecular MedicineUniversity of California, DavisDavisUnited States
| | - Lin Tian
- Department of Biochemistry and Molecular MedicineUniversity of California, DavisDavisUnited States
| | - Viviana Gradinaru
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
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Coughlin GM, Kurrasch DM. Protocadherins and hypothalamic development: do they play an unappreciated role? J Neuroendocrinol 2015; 27:544-55. [PMID: 25845440 DOI: 10.1111/jne.12280] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Revised: 03/26/2015] [Accepted: 03/27/2015] [Indexed: 12/17/2022]
Abstract
Normal brain development requires coordinated cell movements at precise times. It has long been established that cell-cell adhesion proteins of the cadherin superfamily are involved in the adhesion and sorting of cells during tissue morphogenesis. In the present review, we focus on protocadherins, which form the largest subfamily of the cadherin superfamily and mediate homophilic cell-cell adhesion in the developing brain. These molecules are highly expressed during neural development and the exact roles that they play are still emerging. Although, historically, protocadherins were considered to provide mechanical and chemical connections between adjacent cells, recent research suggests that they may also serve as molecular identity markers of neurones to help guide cell recognition and sorting, cell migration, outgrowth of neuronal processes, and synapse formation. This phenomenon of single cell diversity stems, in part, from the vast variation in protein structure, genomic organisation and molecular function of the protocadherins. Although expression profiles and genetic manipulations have provided evidence for the role of protocadherins in the developing brain, we have only begun to construct a complete understanding of protocadherin function. We examine our current understanding of how protocadherins influence brain development and discuss the possible roles for this large superfamily within the hypothalamus. We conclude that further research into these underappreciated but vitally important genes will shed insight into hypothalamic development and perhaps the underlying aetiology of neuroendocrine disorders.
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Affiliation(s)
- G M Coughlin
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - D M Kurrasch
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
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