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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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2
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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: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [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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3
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Frasch MG, Yoon BJ, Helbing DL, Snir G, Antonelli MC, Bauer R. Autism Spectrum Disorder: A Neuro-Immunometabolic Hypothesis of the Developmental Origins. BIOLOGY 2023; 12:914. [PMID: 37508346 PMCID: PMC10375982 DOI: 10.3390/biology12070914] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/15/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023]
Abstract
Fetal neuroinflammation and prenatal stress (PS) may contribute to lifelong neurological disabilities. Astrocytes and microglia, among the brain's non-neuronal "glia" cell populations, play a pivotal role in neurodevelopment and predisposition to and initiation of disease throughout lifespan. One of the most common neurodevelopmental disorders manifesting between 1-4 years of age is the autism spectrum disorder (ASD). A pathological glial-neuronal interplay is thought to increase the risk for clinical manifestation of ASD in at-risk children, but the mechanisms remain poorly understood, and integrative, multi-scale models are needed. We propose a model that integrates the data across the scales of physiological organization, from genome to phenotype, and provides a foundation to explain the disparate findings on the genomic level. We hypothesize that via gene-environment interactions, fetal neuroinflammation and PS may reprogram glial immunometabolic phenotypes that impact neurodevelopment and neurobehavior. Drawing on genomic data from the recently published series of ovine and rodent glial transcriptome analyses with fetuses exposed to neuroinflammation or PS, we conducted an analysis on the Simons Foundation Autism Research Initiative (SFARI) Gene database. We confirmed 21 gene hits. Using unsupervised statistical network analysis, we then identified six clusters of probable protein-protein interactions mapping onto the immunometabolic and stress response networks and epigenetic memory. These findings support our hypothesis. We discuss the implications for ASD etiology, early detection, and novel therapeutic approaches. We conclude with delineation of the next steps to verify our model on the individual gene level in an assumption-free manner. The proposed model is of interest for the multidisciplinary community of stakeholders engaged in ASD research, the development of novel pharmacological and non-pharmacological treatments, early prevention, and detection as well as for policy makers.
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Affiliation(s)
- Martin G Frasch
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA
- Center on Human Development and Disability, University of Washington, Seattle, WA 98195, USA
| | - Byung-Jun Yoon
- Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Dario Lucas Helbing
- Institute for Molecular Cell Biology, Jena University Hospital, Friedrich Schiller University, 07747 Jena, Germany
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745 Jena, Germany
- Department of Psychiatry and Psychotherapy, Jena University Hospital, Friedrich Schiller University Jena, 07747 Jena, Germany
- Center for Intervention and Research on Adaptive and Maladaptive Brain Circuits Underlying Mental Health (C-I-R-C), Jena-Magdeburg-Halle, 07743 Jena, Germany
| | - Gal Snir
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA 98195, USA
| | - Marta C Antonelli
- Instituto de Biología Celular y Neurociencia "Prof. Eduardo De Robertis", Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires 1121, Argentina
- Institute for Advanced Study, Technical University of Munich, Lichtenbergstrasse 2 a, 85748 Garching, Germany
| | - Reinhard Bauer
- Institute for Molecular Cell Biology, Jena University Hospital, Friedrich Schiller University, 07747 Jena, Germany
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4
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Merlin S, Vidyasagar T. Optogenetics in primate cortical networks. Front Neuroanat 2023; 17:1193949. [PMID: 37284061 PMCID: PMC10239886 DOI: 10.3389/fnana.2023.1193949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
The implementation of optogenetics in studies on non-human primates has generally proven quite difficult, but recent successes have paved the way for its rapid increase. Limitations in the genetic tractability in primates, have been somewhat overcome by implementing tailored vectors and promoters to maximize expression and specificity in primates. More recently, implantable devices, including microLED arrays, have made it possible to deliver light deeper into brain tissue, allowing targeting of deeper structures. However, the greatest limitation in applying optogenetics to the primate brain is the complex connections that exist within many neural circuits. In the past, relatively cruder methods such as cooling or pharmacological blockade have been used to examine neural circuit functions, though their limitations were well recognized. In some ways, similar shortcomings remain for optogenetics, with the ability to target a single component of complex neural circuits being the greatest challenge in applying optogenetics to systems neuroscience in primate brains. Despite this, some recent approaches combining Cre-expressing and Cre-dependent vectors have overcome some of these limitations. Here we suggest that optogenetics provides its greatest advantage to systems neuroscientists when applied as a specific tool to complement the techniques of the past, rather than necessarily replacing them.
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Affiliation(s)
- Sam Merlin
- Medical Science, School of Science, Western Sydney University, Campbelltown, NSW, Australia
| | - Trichur Vidyasagar
- Department of Optometry and Vision Sciences, School of Health Science, The University of Melbourne, Parkville, VIC, Australia
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
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Chan YC, Kienle E, Oti M, Di Liddo A, Mendez-Lago M, Aschauer DF, Peter M, Pagani M, Arnold C, Vonderheit A, Schön C, Kreuz S, Stark A, Rumpel S. An unbiased AAV-STARR-seq screen revealing the enhancer activity map of genomic regions in the mouse brain in vivo. Sci Rep 2023; 13:6745. [PMID: 37185990 PMCID: PMC10130037 DOI: 10.1038/s41598-023-33448-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
Enhancers are important cis-regulatory elements controlling cell-type specific expression patterns of genes. Furthermore, combinations of enhancers and minimal promoters are utilized to construct small, artificial promoters for gene delivery vectors. Large-scale functional screening methodology to construct genomic maps of enhancer activities has been successfully established in cultured cell lines, however, not yet applied to terminally differentiated cells and tissues in a living animal. Here, we transposed the Self-Transcribing Active Regulatory Region Sequencing (STARR-seq) technique to the mouse brain using adeno-associated-viruses (AAV) for the delivery of a highly complex screening library tiling entire genomic regions and covering in total 3 Mb of the mouse genome. We identified 483 sequences with enhancer activity, including sequences that were not predicted by DNA accessibility or histone marks. Characterizing the expression patterns of fluorescent reporters controlled by nine candidate sequences, we observed differential expression patterns also in sparse cell types. Together, our study provides an entry point for the unbiased study of enhancer activities in organisms during health and disease.
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Affiliation(s)
- Ya-Chien Chan
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Eike Kienle
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Martin Oti
- Institute of Molecular Biology GmbH (IMB), Mainz, Germany
- Global Computational Biology and Digital Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an Der Riß, Germany
| | | | | | - Dominik F Aschauer
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Manuel Peter
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Michaela Pagani
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Cosmas Arnold
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, Vienna, Austria
| | | | - Christian Schön
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an Der Riß, Germany
| | - Sebastian Kreuz
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an Der Riß, Germany
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Simon Rumpel
- Institute of Physiology, Focus Program Translational Neurosciences, University Medical Center, Johannes Gutenberg University Mainz, Mainz, Germany.
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6
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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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7
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Sharma R, Frasch MG, Zelgert C, Zimmermann P, Fabre B, Wilson R, Waldenberger M, MacDonald JW, Bammler TK, Lobmaier SM, Antonelli MC. Maternal-fetal stress and DNA methylation signatures in neonatal saliva: an epigenome-wide association study. Clin Epigenetics 2022; 14:87. [PMID: 35836289 PMCID: PMC9281078 DOI: 10.1186/s13148-022-01310-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 07/05/2022] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Maternal stress before, during and after pregnancy has profound effects on the development and lifelong function of the infant's neurocognitive development. We hypothesized that the programming of the central nervous system (CNS), hypothalamic-pituitary-adrenal (HPA) axis and autonomic nervous system (ANS) induced by prenatal stress (PS) is reflected in electrophysiological and epigenetic biomarkers. In this study, we aimed to find noninvasive epigenetic biomarkers of PS in the newborn salivary DNA. RESULTS A total of 728 pregnant women were screened for stress exposure using Cohen Perceived Stress Scale (PSS), 164 women were enrolled, and 114 dyads were analyzed. Prenatal Distress Questionnaire (PDQ) was also administered to assess specific pregnancy worries. Transabdominal fetal electrocardiograms (taECG) were recorded to derive coupling between maternal and fetal heart rates resulting in a 'Fetal Stress Index' (FSI). Upon delivery, we collected maternal hair strands for cortisol measurements and newborn's saliva for epigenetic analyses. DNA was extracted from saliva samples, and DNA methylation was measured using EPIC BeadChip array (850 k CpG sites). Linear regression was used to identify associations between PSS/PDQ/FSI/Cortisol and DNA methylation. We found epigenome-wide significant associations for 5 CpG with PDQ and cortisol at FDR < 5%. Three CpGs were annotated to genes (Illumina Gene annotation file): YAP1, TOMM20 and CSMD1, and two CpGs were located approximately lay at 50 kb from SSBP4 and SCAMP1. In addition, two differentiated methylation regions (DMR) related to maternal stress measures PDQ and cortisol were found: DAXX and ARL4D. CONCLUSIONS Genes annotated to these CpGs were found to be involved in secretion and transportation, nuclear signaling, Hippo signaling pathways, apoptosis, intracellular trafficking and neuronal signaling. Moreover, some CpGs are annotated to genes related to autism, post-traumatic stress disorder (PTSD) and schizophrenia. However, our results should be viewed as hypothesis generating until replicated in a larger sample. Early assessment of such noninvasive PS biomarkers will allow timelier detection of babies at risk and a more effective allocation of resources for early intervention programs to improve child development. A biomarker-guided early intervention strategy is the first step in the prevention of future health problems, reducing their personal and societal impact.
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Affiliation(s)
- Ritika Sharma
- Department of Obstetrics and Gynecology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Munich, Munich, Germany
| | - Martin G Frasch
- Department of Obstetrics and Gynecology and Center On Human Development and Disability (CHDD), University of Washington, Seattle, WA, USA
| | - Camila Zelgert
- Department of Obstetrics and Gynecology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Peter Zimmermann
- Department of Obstetrics and Gynecology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Bibiana Fabre
- Instituto de Fisiopatología y Bioquímica Clínica (INFIBIOC), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Munich, Munich, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Munich, Munich, Germany
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Silvia M Lobmaier
- Department of Obstetrics and Gynecology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Marta C Antonelli
- Department of Obstetrics and Gynecology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.
- Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis", Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina.
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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: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [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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9
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Warren TL, Lambert JT, Nord AS. AAV Deployment of Enhancer-Based Expression Constructs In Vivo in Mouse Brain. J Vis Exp 2022:10.3791/62650. [PMID: 35435902 PMCID: PMC10010840 DOI: 10.3791/62650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Enhancers are binding platforms for a diverse array of transcription factors that drive specific expression patterns of tissue- and cell-type-specific genes. Multiple means of assessing non-coding DNA and various chromatin states have proven useful in predicting the presence of enhancer sequences in the genome, but validating the activity of these sequences and finding the organs and developmental stages they are active in is a labor-intensive process. Recent advances in adeno-associated virus (AAV) vectors have enabled the widespread delivery of transgenes to mouse tissues, enabling in vivo enhancer testing without necessitating a transgenic animal. This protocol shows how a reporter construct that expresses EGFP under the control of a minimal promoter, which does not drive significant expression on its own, can be used to study the activity patterns of candidate enhancer sequences in the mouse brain. An AAV-packaged reporter construct is delivered to the mouse brain and incubated for 1-4 weeks, after which the animal is sacrificed, and brain sections are observed under a microscope. EGFP appears in cells in which the tested enhancer is sufficient to initiate gene expression, pinpointing the location and developmental stage in which the enhancer is active in the brain. Standard cloning methods, low-cost AAV packaging, and expanding AAV serotypes and methods for in vivo delivery and standard imaging readout make this an accessible approach for the study of how gene expression is regulated in the brain.
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Affiliation(s)
- Tracy L Warren
- Department of Psychiatry and Behavioral Sciences, University of California, Davis; Department of Neurobiology, Physiology and Behavior, University of California, Davis
| | - Jason T Lambert
- Department of Psychiatry and Behavioral Sciences, University of California, Davis; Department of Neurobiology, Physiology and Behavior, University of California, Davis;
| | - Alex S Nord
- Department of Psychiatry and Behavioral Sciences, University of California, Davis; Department of Neurobiology, Physiology and Behavior, University of California, Davis;
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10
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Dudok B, Klein PM, Soltesz I. Toward Understanding the Diverse Roles of Perisomatic Interneurons in Epilepsy. Epilepsy Curr 2021; 22:54-60. [PMID: 35233202 PMCID: PMC8832350 DOI: 10.1177/15357597211053687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Epileptic seizures are associated with excessive neuronal spiking. Perisomatic
γ-aminobutyric acid (GABA)ergic interneurons specifically innervate the subcellular
domains of postsynaptic excitatory cells that are critical for spike generation. With a
revolution in transcriptomics-based cell taxonomy driving the development of novel
transgenic mouse lines, selectively monitoring and modulating previously elusive
interneuron types is becoming increasingly feasible. Emerging evidence suggests that the
three types of hippocampal perisomatic interneurons, axo-axonic cells, along with
parvalbumin- and cholecystokinin-expressing basket cells, each follow unique activity
patterns in vivo, suggesting distinctive roles in regulating epileptic networks.
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Affiliation(s)
- Barna Dudok
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Peter M. Klein
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Ivan Soltesz
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
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11
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Duba-Kiss R, Niibori Y, Hampson DR. GABAergic Gene Regulatory Elements Used in Adeno-Associated Viral Vectors. Front Neurol 2021; 12:745159. [PMID: 34671313 PMCID: PMC8521139 DOI: 10.3389/fneur.2021.745159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Several neurological and psychiatric disorders have been associated with impairments in GABAergic inhibitory neurons in the brain. Thus, in the current era of accelerated development of molecular medicine and biologically-based drugs, there is a need to identify gene regulatory sequences that can be utilized for selectively manipulating the expression of nucleic acids and proteins in GABAergic neurons. This is particularly important for the use of viral vectors in gene therapy. In this Mini Review, we discuss the use of various gene regulatory elements for targeting GABAergic neurons, with an emphasis on adeno-associated viral vectors, the most widely used class of viral vectors for treating brain diseases.
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Affiliation(s)
- Robert Duba-Kiss
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Yosuke Niibori
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - David R Hampson
- Department of Pharmacology and Toxicology, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.,Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
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12
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Lambert JT, Su-Feher L, Cichewicz K, Warren TL, Zdilar I, Wang Y, Lim KJ, Haigh JL, Morse SJ, Canales CP, Stradleigh TW, Castillo Palacios E, Haghani V, Moss SD, Parolini H, Quintero D, Shrestha D, Vogt D, Byrne LC, Nord AS. Parallel functional testing identifies enhancers active in early postnatal mouse brain. eLife 2021; 10:69479. [PMID: 34605404 PMCID: PMC8577842 DOI: 10.7554/elife.69479] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/02/2021] [Indexed: 01/07/2023] Open
Abstract
Enhancers are cis-regulatory elements that play critical regulatory roles in modulating developmental transcription programs and driving cell-type-specific and context-dependent gene expression in the brain. The development of massively parallel reporter assays (MPRAs) has enabled high-throughput functional screening of candidate DNA sequences for enhancer activity. Tissue-specific screening of in vivo enhancer function at scale has the potential to greatly expand our understanding of the role of non-coding sequences in development, evolution, and disease. Here, we adapted a self-transcribing regulatory element MPRA strategy for delivery to early postnatal mouse brain via recombinant adeno-associated virus (rAAV). We identified and validated putative enhancers capable of driving reporter gene expression in mouse forebrain, including regulatory elements within an intronic CACNA1C linkage disequilibrium block associated with risk in neuropsychiatric disorder genetic studies. Paired screening and single enhancer in vivo functional testing, as we show here, represents a powerful approach towards characterizing regulatory activity of enhancers and understanding how enhancer sequences organize gene expression in the brain.
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Affiliation(s)
- Jason T Lambert
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Linda Su-Feher
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Karol Cichewicz
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Tracy L Warren
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Iva Zdilar
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Yurong Wang
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Kenneth J Lim
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Jessica L Haigh
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Sarah J Morse
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Cesar P Canales
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Tyler W Stradleigh
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Erika Castillo Palacios
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Viktoria Haghani
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Spencer D Moss
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Hannah Parolini
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Diana Quintero
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Diwash Shrestha
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
| | - Daniel Vogt
- Department of Pediatrics and Human Development, Grand Rapids Research Center, Michigan State UniversityGrand RapidsUnited States
| | - Leah C Byrne
- Helen Wills Neuroscience Institute, University of California, BerkeleyBerkeleyUnited States,Departments of Ophthalmology and Neurobiology, University of PittsburghPittsburghUnited States
| | - Alex S Nord
- Department of Psychiatry and Behavioral Sciences, University of California, DavisDavisUnited States,Department of Neurobiology, Physiology and Behavior, University of California, DavisDavisUnited States
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