1
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Yang T, Wang W, Xie L, Chen S, Ye X, Shen S, Chen H, Qi L, Cui Z, Xiong W, Guo Y, Chen J. Investigating retinal explant models cultured in static and perfused systems to test the performance of exosomes secreted from retinal organoids. J Neurosci Methods 2024; 408:110181. [PMID: 38823594 DOI: 10.1016/j.jneumeth.2024.110181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/05/2024] [Accepted: 05/22/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Ex vivo cultures of retinal explants are appropriate models for translational research. However, one of the difficult problems of retinal explants ex vivo culture is that their nutrient supply needs cannot be constantly met. NEW METHOD This study evaluated the effect of perfused culture on the survival of retinal explants, addressing the challenge of insufficient nutrition in static culture. Furthermore, exosomes secreted from retinal organoids (RO-Exos) were stained with PKH26 to track their uptake in retinal explants to mimic the efficacy of exosomal drugs in vivo. RESULTS We found that the retinal explants cultured with perfusion exhibited significantly higher viability, increased NeuN+ cells, and reduced apoptosis compared to the static culture group at Days Ex Vivo (DEV) 4, 7, and 14. The perfusion-cultured retinal explants exhibited reduced mRNA markers for gliosis and microglial activation, along with lower expression of GFAP and Iba1, as revealed by immunostaining. Additionally, RNA-sequencing analysis showed that perfusion culture mainly upregulated genes associated with visual perception and photoreceptor cell maintenance while downregulating the immune system process and immune response. RO-Exos promoted the uptake of PKH26-labelled exosomes and the growth of retinal explants in perfusion culture. COMPARISON WITH EXISTING METHODS Our perfusion culture system can provide a continuous supply of culture medium to achieve steady-state equilibrium in retinal explant culture. Compared to traditional static culture, it better preserves the vitality, provides better neuroprotection, and reduces glial activation. CONCLUSIONS This study provides a promising ex vivo model for further studies on degenerative retinal diseases and drug screening.
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Affiliation(s)
- Tingting Yang
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China; Department of Ophthalmology, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Wenxuan Wang
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Linyao Xie
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Sihui Chen
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Xiuhong Ye
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Shuhao Shen
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Hang Chen
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Ling Qi
- Central Laboratory, Affiliated Qingyuan Hospital, Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Zekai Cui
- Aier Eye Institute, Changsha, Hunan, China
| | - Wei Xiong
- Key Laboratory for Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China
| | - Yonglong Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.
| | - Jiansu Chen
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China; Institute of Ophthalmology, Medical College, Jinan University, Guangzhou, China; Key Laboratory for Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China; Aier Eye Institute, Changsha, Hunan, China.
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2
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Guo J, Lin LF, Oraskovich SV, Rivera de Jesús JA, Listgarten J, Schaffer DV. Computationally guided AAV engineering for enhanced gene delivery. Trends Biochem Sci 2024; 49:457-469. [PMID: 38531696 DOI: 10.1016/j.tibs.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/28/2024]
Abstract
Gene delivery vehicles based on adeno-associated viruses (AAVs) are enabling increasing success in human clinical trials, and they offer the promise of treating a broad spectrum of both genetic and non-genetic disorders. However, delivery efficiency and targeting must be improved to enable safe and effective therapies. In recent years, considerable effort has been invested in creating AAV variants with improved delivery, and computational approaches have been increasingly harnessed for AAV engineering. In this review, we discuss how computationally designed AAV libraries are enabling directed evolution. Specifically, we highlight approaches that harness sequences outputted by next-generation sequencing (NGS) coupled with machine learning (ML) to generate new functional AAV capsids and related regulatory elements, pushing the frontier of what vector engineering and gene therapy may achieve.
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Affiliation(s)
- Jingxuan Guo
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Li F Lin
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Sydney V Oraskovich
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA; Graduate Program in Bioengineering, University of California, San Francisco and University of California, Berkeley, CA 94720, USA
| | - Julio A Rivera de Jesús
- Department of Bioengineering, University of California, Berkeley, CA 94720, USA; Graduate Program in Bioengineering, University of California, San Francisco and University of California, Berkeley, CA 94720, USA; Department of Neurological Surgery, University of California, San Francisco, CA 94143, USA
| | - Jennifer Listgarten
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA 94720, USA
| | - David V Schaffer
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
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3
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Hu SW, Lv J, Wang Z, Tang H, Wang H, Wang F, Wang D, Zhang J, Zhang L, Cao Q, Chen Y, Gao Z, Han Y, Wang W, Li GL, Shu Y, Li H. Engineering of the AAV-Compatible Hair Cell-Specific Small-Size Myo15 Promoter for Gene Therapy in the Inner Ear. RESEARCH (WASHINGTON, D.C.) 2024; 7:0341. [PMID: 38665848 PMCID: PMC11045262 DOI: 10.34133/research.0341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/21/2024] [Indexed: 04/28/2024]
Abstract
Adeno-associated virus (AAV)-mediated gene therapy is widely applied to treat numerous hereditary diseases in animal models and humans. The specific expression of AAV-delivered transgenes driven by cell type-specific promoters should further increase the safety of gene therapy. However, current methods for screening cell type-specific promoters are labor-intensive and time-consuming. Herein, we designed a "multiple vectors in one AAV" strategy for promoter construction in vivo. Through this strategy, we truncated a native promoter for Myo15 expression in hair cells (HCs) in the inner ear, from 1,611 bp down to 1,157 bp, and further down to 956 bp. Under the control of these 2 promoters, green fluorescent protein packaged in AAV-PHP.eB was exclusively expressed in the HCs. The transcription initiation ability of the 2 promoters was further verified by intein-mediated otoferlin recombination in a dual-AAV therapeutic system. Driven by these 2 promoters, human otoferlin was selectively expressed in HCs, resulting in the restoration of hearing in treated Otof -/- mice for at least 52 weeks. In summary, we developed an efficient screening strategy for cell type-specific promoter engineering and created 2 truncated Myo15 promoters that not only restored hereditary deafness in animal models but also show great potential for treating human patients in future.
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Affiliation(s)
- Shao Wei Hu
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Jun Lv
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Zijing Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Honghai Tang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Hui Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Fang Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Daqi Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Juan Zhang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Longlong Zhang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Qi Cao
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Yuxin Chen
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Ziwen Gao
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Yu Han
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Wuqing Wang
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Geng-lin Li
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Yilai Shu
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
| | - Huawei Li
- ENT Institute and Department of Otorhinolaryngology, Eye & ENT Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science,
Fudan University, Shanghai, 200031, China
- Institute of Biomedical Science,
Fudan University, Shanghai, 200032, China
- NHC Key Laboratory of Hearing Medicine (Fudan University), Shanghai, 200032, China
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4
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Schmidheini L, Mathis N, Marquart KF, Rothgangl T, Kissling L, Böck D, Chanez C, Wang JP, Jinek M, Schwank G. Continuous directed evolution of a compact CjCas9 variant with broad PAM compatibility. Nat Chem Biol 2024; 20:333-343. [PMID: 37735239 DOI: 10.1038/s41589-023-01427-x] [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] [Received: 12/08/2022] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
CRISPR-Cas9 genome engineering is a powerful technology for correcting genetic diseases. However, the targeting range of Cas9 proteins is limited by their requirement for a protospacer adjacent motif (PAM), and in vivo delivery is challenging due to their large size. Here, we use phage-assisted continuous directed evolution to broaden the PAM compatibility of Campylobacter jejuni Cas9 (CjCas9), the smallest Cas9 ortholog characterized to date. The identified variant, termed evoCjCas9, primarily recognizes N4AH and N5HA PAM sequences, which occur tenfold more frequently in the genome than the canonical N3VRYAC PAM site. Moreover, evoCjCas9 exhibits higher nuclease activity than wild-type CjCas9 on canonical PAMs, with editing rates comparable to commonly used PAM-relaxed SpCas9 variants. Combined with deaminases or reverse transcriptases, evoCjCas9 enables robust base and prime editing, with the small size of evoCjCas9 base editors allowing for tissue-specific installation of A-to-G or C-to-T transition mutations from single adeno-associated virus vector systems.
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Affiliation(s)
- Lukas Schmidheini
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Nicolas Mathis
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Kim Fabiano Marquart
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Tanja Rothgangl
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Lucas Kissling
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Desirée Böck
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Christelle Chanez
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | | | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Gerald Schwank
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.
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5
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Spirig SE, Renner M. Toward Retinal Organoids in High-Throughput. Cold Spring Harb Perspect Med 2024; 14:a041275. [PMID: 37217280 PMCID: PMC10910359 DOI: 10.1101/cshperspect.a041275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Human retinal organoids recapitulate the cellular diversity, arrangement, gene expression, and functional aspects of the human retina. Protocols to generate human retinal organoids from pluripotent stem cells are typically labor intensive, include many manual handling steps, and the organoids need to be maintained for several months until they mature. To generate large numbers of human retinal organoids for therapy development and screening purposes, scaling up retinal organoid production, maintenance, and analysis is of utmost importance. In this review, we discuss strategies to increase the number of high-quality retinal organoids while reducing manual handling steps. We further review different approaches to analyze thousands of retinal organoids with currently available technologies and point to challenges that still await to be overcome both in culture and analysis of retinal organoids.
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Affiliation(s)
- Stefan Erich Spirig
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Magdalena Renner
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
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6
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Mougkogiannis P, Adamatzky A. On interaction of proteinoids with simulated neural networks. Biosystems 2024; 237:105175. [PMID: 38460836 DOI: 10.1016/j.biosystems.2024.105175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024]
Abstract
Proteinoid-neuron networks combine biological neurons with spiking proteinoid microspheres, which are generated by thermal condensation of amino acids. Complex and dynamic spiking patterns in response to varied stimuli make these networks suitable for unconventional computing. This research examines the interaction of proteinoid-neuron networks with function-generator-artificial neural networks (ANN) that may create distinct electrical waveforms. Function-generator- artificial neural network (ANN) stimulates and modulates proteinoid-neuron network spiking activity and synchronisation to encode and decode information. We employ function-generator-ANN to study proteinoid-neuron network nonlinear dynamics and chaos and optimise their performance and energy efficiency. Function-generator-ANN improves proteinoid-neuron networks' computational capacities and robustness and creates unique hybrid systems with electrical devices. We address the benefits as well as the drawbacks of employing proteinoid-neuron networks for unconventional computing with function-generator-ANN.
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7
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Company C, Schmitt MJ, Dramaretska Y, Serresi M, Kertalli S, Jiang B, Yin JA, Aguzzi A, Barozzi I, Gargiulo G. Logical design of synthetic cis-regulatory DNA for genetic tracing of cell identities and state changes. Nat Commun 2024; 15:897. [PMID: 38316783 PMCID: PMC10844330 DOI: 10.1038/s41467-024-45069-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Descriptive data are rapidly expanding in biomedical research. Instead, functional validation methods with sufficient complexity remain underdeveloped. Transcriptional reporters allow experimental characterization and manipulation of developmental and disease cell states, but their design lacks flexibility. Here, we report logical design of synthetic cis-regulatory DNA (LSD), a computational framework leveraging phenotypic biomarkers and trans-regulatory networks as input to design reporters marking the activity of selected cellular states and pathways. LSD uses bulk or single-cell biomarkers and a reference genome or custom cis-regulatory DNA datasets with user-defined boundary regions. By benchmarking validated reporters, we integrate LSD with a computational ranking of phenotypic specificity of putative cis-regulatory DNA. Experimentally, LSD-designed reporters targeting a wide range of cell states are functional without minimal promoters. Applied to broadly expressed genes from human and mouse tissues, LSD generates functional housekeeper-like sLCRs compatible with size constraints of AAV vectors for gene therapy applications. A mesenchymal glioblastoma reporter designed by LSD outperforms previously validated ones and canonical cell surface markers. In genome-scale CRISPRa screens, LSD facilitates the discovery of known and novel bona fide cell-state drivers. Thus, LSD captures core principles of cis-regulation and is broadly applicable to studying complex cell states and mechanisms of transcriptional regulation.
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Affiliation(s)
- Carlos Company
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Matthias Jürgen Schmitt
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Yuliia Dramaretska
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Michela Serresi
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Sonia Kertalli
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Ben Jiang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany
| | - Jiang-An Yin
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Iros Barozzi
- Center for Cancer Research, Medical University of Vienna, Borschkegasse 8a, 1090, Vienna, Austria
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Gaetano Gargiulo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, 13092, Berlin, Germany.
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8
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He X, Fu Y, Ma L, Yao Y, Ge S, Yang Z, Fan X. AAV for Gene Therapy in Ocular Diseases: Progress and Prospects. RESEARCH (WASHINGTON, D.C.) 2023; 6:0291. [PMID: 38188726 PMCID: PMC10768554 DOI: 10.34133/research.0291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024]
Abstract
Owing to the promising therapeutic effect and one-time treatment advantage, gene therapy may completely change the management of eye diseases, especially retinal diseases. Adeno-associated virus (AAV) is considered one of the most promising viral gene delivery tools because it can infect various types of tissues and is considered as a relatively safe gene delivery vector. The eye is one of the most popular organs for gene therapy, since its limited volume is suitable for small doses of AAV stably transduction. Recently, an increasing number of clinical trials of AAV-mediated gene therapy are underway. This review summarizes the biological functions of AAV and its application in the treatment of various ocular diseases, as well as the characteristics of different AAV delivery routes in clinical applications. Here, the latest research progresses in AAV-mediated gene editing and silencing strategies to modify that the genetic ocular diseases are systematically outlined, especially by base editing and prime editing. We discuss the progress of AAV in ocular optogenetic therapy. We also summarize the application of AAV-mediated gene therapy in animal models and the difficulties in its clinical transformation.
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Affiliation(s)
- Xiaoyu He
- Department of Ophthalmology, Ninth People’s Hospital,
Shanghai JiaoTong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Yidian Fu
- Department of Ophthalmology, Ninth People’s Hospital,
Shanghai JiaoTong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Liang Ma
- Department of Ophthalmology, Ninth People’s Hospital,
Shanghai JiaoTong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Yizheng Yao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University; Clinical Research Center of Neurological Disease,
The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People’s Hospital,
Shanghai JiaoTong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Zhi Yang
- Department of Ophthalmology, Ninth People’s Hospital,
Shanghai JiaoTong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People’s Hospital,
Shanghai JiaoTong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
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9
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Khabou H, Orendorff E, Trapani F, Rucli M, Desrosiers M, Yger P, Dalkara D, Marre O. Optogenetic targeting of AII amacrine cells restores retinal computations performed by the inner retina. Mol Ther Methods Clin Dev 2023; 31:101107. [PMID: 37868206 PMCID: PMC10589896 DOI: 10.1016/j.omtm.2023.09.003] [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: 07/28/2023] [Accepted: 09/08/2023] [Indexed: 10/24/2023]
Abstract
Most inherited retinal dystrophies display progressive photoreceptor cell degeneration leading to severe visual impairment. Optogenetic reactivation of inner retinal neurons is a promising avenue to restore vision in retinas having lost their photoreceptors. Expression of optogenetic proteins in surviving ganglion cells, the retinal output, allows them to take on the lost photoreceptive function. Nonetheless, this creates an exclusively ON retina by expression of depolarizing optogenetic proteins in all classes of ganglion cells, whereas a normal retina extracts several features from the visual scene, with different ganglion cells detecting light increase (ON) and light decrease (OFF). Refinement of this therapeutic strategy should thus aim at restoring these computations. Here we used a vector that targets gene expression to a specific interneuron of the retina called the AII amacrine cell. AII amacrine cells simultaneously activate the ON pathway and inhibit the OFF pathway. We show that the optogenetic stimulation of AII amacrine cells allows restoration of both ON and OFF responses in the retina, but also mediates other types of retinal processing such as sustained and transient responses. Targeting amacrine cells with optogenetics is thus a promising avenue to restore better retinal function and visual perception in patients suffering from retinal degeneration.
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Affiliation(s)
- Hanen Khabou
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
| | - Elaine Orendorff
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
| | - Francesco Trapani
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
| | - Marco Rucli
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
| | - Melissa Desrosiers
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
| | - Pierre Yger
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
| | - Deniz Dalkara
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
| | - Olivier Marre
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, 75012 Paris, France
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10
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Westhaus A, Eamegdool SS, Fernando M, Fuller-Carter P, Brunet AA, Miller AL, Rashwan R, Knight M, Daniszewski M, Lidgerwood GE, Pébay A, Hewitt A, Santilli G, Thrasher AJ, Carvalho LS, Gonzalez-Cordero A, Jamieson RV, Lisowski L. AAV capsid bioengineering in primary human retina models. Sci Rep 2023; 13:21946. [PMID: 38081924 PMCID: PMC10713676 DOI: 10.1038/s41598-023-49112-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
Adeno-associated viral (AAV) vector-mediated retinal gene therapy is an active field of both pre-clinical as well as clinical research. As with other gene therapy clinical targets, novel bioengineered AAV variants developed by directed evolution or rational design to possess unique desirable properties, are entering retinal gene therapy translational programs. However, it is becoming increasingly evident that predictive preclinical models are required to develop and functionally validate these novel AAVs prior to clinical studies. To investigate if, and to what extent, primary retinal explant culture could be used for AAV capsid development, this study performed a large high-throughput screen of 51 existing AAV capsids in primary human retina explants and other models of the human retina. Furthermore, we applied transgene expression-based directed evolution to develop novel capsids for more efficient transduction of primary human retina cells and compared the top variants to the strongest existing benchmarks identified in the screening described above. A direct side-by-side comparison of the newly developed capsids in four different in vitro and ex vivo model systems of the human retina allowed us to identify novel AAV variants capable of high transgene expression in primary human retina cells.
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Affiliation(s)
- Adrian Westhaus
- Translational Vectorology Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
- Infection, Immunity and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, UK
- Genethon, Evry, France
| | - Steven S Eamegdool
- Eye Genetics Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute and Sydney Children's Hospitals Network, The University of Sydney, Westmead, Australia
| | - Milan Fernando
- Stem Cell and Organoid Facility, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | | | - Alicia A Brunet
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Australia
| | - Annie L Miller
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Australia
| | | | - Maddison Knight
- Translational Vectorology Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Maciej Daniszewski
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Grace E Lidgerwood
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Melbourne, VIC, Australia
| | - Alex Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
- Centre for Eye Research Australia, University of Melbourne, Melbourne, Australia
| | - Giorgia Santilli
- Infection, Immunity and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Adrian J Thrasher
- Infection, Immunity and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Livia S Carvalho
- Lions Eye Institute, Nedlands, Australia
- Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Australia
| | - Anai Gonzalez-Cordero
- Stem Cell and Organoid Facility, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
- Stem Cell Medicine Group, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia
| | - Robyn V Jamieson
- Eye Genetics Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute and Sydney Children's Hospitals Network, The University of Sydney, Westmead, Australia
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Faculty of Medicine and Health, Children's Medical Research Institute, The University of Sydney, Westmead, Australia.
- Australian Genome Therapeutics Centre, Children's Medical Research Institute and Sydney Children's Hospitals Network, Westmead, NSW, 2145, Australia.
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine - National Research Institute, Warsaw, Poland.
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11
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Zhang Q, Liu X, Gong L, He M. Combinatorial genetic strategies for dissecting cell lineages, cell types, and gene function in the mouse brain. Dev Growth Differ 2023; 65:546-553. [PMID: 37963088 DOI: 10.1111/dgd.12902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/26/2023] [Accepted: 11/06/2023] [Indexed: 11/16/2023]
Abstract
Research in neuroscience has greatly benefited from the development of genetic approaches that enable lineage tracing, cell type targeting, and conditional gene regulation. Recent advances in combinatorial strategies, which integrate multiple cellular features, have significantly enhanced the spatiotemporal precision and flexibility of these manipulations. In this minireview, we introduce the concept and design of these strategies and provide a few examples of their application in genetic fate mapping, cell type targeting, and reversible conditional gene regulation. These advancements have facilitated in-depth investigation into the developmental principles underlying the assembly of brain circuits, granting experimental access to highly specific cell lineages and subtypes, as well as offering valuable new tools for modeling and studying neurological diseases. Additionally, we discuss future directions aimed at expanding and improving the existing genetic toolkit for a better understanding of the development, structure, and function of healthy and diseased brains.
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Affiliation(s)
- Qi Zhang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xue Liu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ling Gong
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Miao He
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Department of Neurobiology, Institutes of Brain Science, Zhongshan Hospital, Fudan University, Shanghai, China
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12
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Wahle P, Brancati G, Harmel C, He Z, Gut G, Del Castillo JS, Xavier da Silveira Dos Santos A, Yu Q, Noser P, Fleck JS, Gjeta B, Pavlinić D, Picelli S, Hess M, Schmidt GW, Lummen TTA, Hou Y, Galliker P, Goldblum D, Balogh M, Cowan CS, Scholl HPN, Roska B, Renner M, Pelkmans L, Treutlein B, Camp JG. Multimodal spatiotemporal phenotyping of human retinal organoid development. Nat Biotechnol 2023; 41:1765-1775. [PMID: 37156914 PMCID: PMC10713453 DOI: 10.1038/s41587-023-01747-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/13/2023] [Indexed: 05/10/2023]
Abstract
Organoids generated from human pluripotent stem cells provide experimental systems to study development and disease, but quantitative measurements across different spatial scales and molecular modalities are lacking. In this study, we generated multiplexed protein maps over a retinal organoid time course and primary adult human retinal tissue. We developed a toolkit to visualize progenitor and neuron location, the spatial arrangements of extracellular and subcellular components and global patterning in each organoid and primary tissue. In addition, we generated a single-cell transcriptome and chromatin accessibility timecourse dataset and inferred a gene regulatory network underlying organoid development. We integrated genomic data with spatially segmented nuclei into a multimodal atlas to explore organoid patterning and retinal ganglion cell (RGC) spatial neighborhoods, highlighting pathways involved in RGC cell death and showing that mosaic genetic perturbations in retinal organoids provide insight into cell fate regulation.
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Affiliation(s)
- Philipp Wahle
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Giovanna Brancati
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Christoph Harmel
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Zhisong He
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Gabriele Gut
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | | | - Aline Xavier da Silveira Dos Santos
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Qianhui Yu
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Pascal Noser
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Jonas Simon Fleck
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Bruno Gjeta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Dinko Pavlinić
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Simone Picelli
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Max Hess
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Gregor W Schmidt
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Tom T A Lummen
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Yanyan Hou
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Patricia Galliker
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - David Goldblum
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Marton Balogh
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Cameron S Cowan
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Magdalena Renner
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland.
| | - Barbara Treutlein
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
| | - J Gray Camp
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.
- Department of Ophthalmology, University of Basel, Basel, Switzerland.
- Institute of Human Biology (IHB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland.
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13
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Kruczek K, Swaroop A. Patient stem cell-derived in vitro disease models for developing novel therapies of retinal ciliopathies. Curr Top Dev Biol 2023; 155:127-163. [PMID: 38043950 DOI: 10.1016/bs.ctdb.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Primary cilia are specialized organelles on the surface of almost all cells in vertebrate tissues and are primarily involved in the detection of extracellular stimuli. In retinal photoreceptors, cilia are uniquely modified to form outer segments containing components required for the detection of light in stacks of membrane discs. Not surprisingly, vision impairment is a frequent phenotype associated with ciliopathies, a heterogeneous class of conditions caused by mutations in proteins required for formation, maintenance and/or function of primary cilia. Traditionally, immortalized cell lines and model organisms have been used to provide insights into the biology of ciliopathies. The advent of methods for reprogramming human somatic cells into pluripotent stem cells has enabled the generation of in vitro disease models directly from patients suffering from ciliopathies. Such models help us in investigating pathological mechanisms specific to human physiology and in developing novel therapeutic approaches. In this article, we review current protocols to differentiate human pluripotent stem cells into retinal cell types, and discuss how these cellular and/or organoid models can be utilized to interrogate pathobiology of ciliopathies affecting the retina and for testing prospective treatments.
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Affiliation(s)
- Kamil Kruczek
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, United States.
| | - Anand Swaroop
- Neurobiology, Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, United States.
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14
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Kerschensteiner D. Losing, preserving, and restoring vision from neurodegeneration in the eye. Curr Biol 2023; 33:R1019-R1036. [PMID: 37816323 PMCID: PMC10575673 DOI: 10.1016/j.cub.2023.08.044] [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: 10/12/2023]
Abstract
The retina is a part of the brain that sits at the back of the eye, looking out onto the world. The first neurons of the retina are the rod and cone photoreceptors, which convert changes in photon flux into electrical signals that are the basis of vision. Rods and cones are frequent targets of heritable neurodegenerative diseases that cause visual impairment, including blindness, in millions of people worldwide. This review summarizes the diverse genetic causes of inherited retinal degenerations (IRDs) and their convergence onto common pathogenic mechanisms of vision loss. Currently, there are few effective treatments for IRDs, but recent advances in disparate areas of biology and technology (e.g., genome editing, viral engineering, 3D organoids, optogenetics, semiconductor arrays) discussed here enable promising efforts to preserve and restore vision in IRD patients with implications for neurodegeneration in less approachable brain areas.
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Affiliation(s)
- Daniel Kerschensteiner
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO 63110, USA.
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15
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Perez-Sanchez J, Middleton SJ, Pattison LA, Hilton H, Awadelkareem MA, Zuberi SR, Renke MB, Hu H, Yang X, Clark AJ, Smith ESJ, Bennett DL. A humanized chemogenetic system inhibits murine pain-related behavior and hyperactivity in human sensory neurons. Sci Transl Med 2023; 15:eadh3839. [PMID: 37792955 PMCID: PMC7615191 DOI: 10.1126/scitranslmed.adh3839] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023]
Abstract
Hyperexcitability in sensory neurons is known to underlie many of the maladaptive changes associated with persistent pain. Chemogenetics has shown promise as a means to suppress such excitability, yet chemogenetic approaches suitable for human applications are needed. PSAM4-GlyR is a modular system based on the human α7 nicotinic acetylcholine and glycine receptors, which responds to inert chemical ligands and the clinically approved drug varenicline. Here, we demonstrated the efficacy of this channel in silencing both mouse and human sensory neurons by the activation of large shunting conductances after agonist administration. Virally mediated expression of PSAM4-GlyR in mouse sensory neurons produced behavioral hyposensitivity upon agonist administration, which was recovered upon agonist washout. Stable expression of the channel led to similar reversible suppression of pain-related behavior even after 10 months of viral delivery. Mechanical and spontaneous pain readouts were also ameliorated by PSAM4-GlyR activation in acute and joint pain inflammation mouse models. Furthermore, suppression of mechanical hypersensitivity generated by a spared nerve injury model of neuropathic pain was also observed upon activation of the channel. Effective silencing of behavioral hypersensitivity was reproduced in a human model of hyperexcitability and clinical pain: PSAM4-GlyR activation decreased the excitability of human-induced pluripotent stem cell-derived sensory neurons and spontaneous activity due to a gain-of-function NaV1.7 mutation causing inherited erythromelalgia. Our results demonstrate the contribution of sensory neuron hyperexcitability to neuropathic pain and the translational potential of an effective, stable, and reversible humanized chemogenetic system for the treatment of pain.
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Affiliation(s)
- Jimena Perez-Sanchez
- Nuffield Department of Clinical Neurosciences, University of Oxford; Oxford OX3 9DU, UK
| | - Steven J. Middleton
- Nuffield Department of Clinical Neurosciences, University of Oxford; Oxford OX3 9DU, UK
| | - Luke A. Pattison
- Department of Pharmacology, University of Cambridge; Cambridge CB2 1PD, UK
| | - Helen Hilton
- Department of Pharmacology, University of Cambridge; Cambridge CB2 1PD, UK
| | | | - Sana R. Zuberi
- Nuffield Department of Clinical Neurosciences, University of Oxford; Oxford OX3 9DU, UK
| | - Maria B. Renke
- Nuffield Department of Clinical Neurosciences, University of Oxford; Oxford OX3 9DU, UK
| | - Huimin Hu
- Nuffield Department of Clinical Neurosciences, University of Oxford; Oxford OX3 9DU, UK
| | - Xun Yang
- Nuffield Department of Clinical Neurosciences, University of Oxford; Oxford OX3 9DU, UK
| | - Alex J. Clark
- Blizard Institute, Barts and the London School of Medicine and Dentistry; London E1 2AT, UK
| | | | - David L. Bennett
- Nuffield Department of Clinical Neurosciences, University of Oxford; Oxford OX3 9DU, UK
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16
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Mich JK, Sunil S, Johansen N, Martinez RA, Leytze M, Gore BB, Mahoney JT, Ben-Simon Y, Bishaw Y, Brouner K, Campos J, Canfield R, Casper T, Dee N, Egdorf T, Gary A, Gibson S, Goldy J, Groce EL, Hirschstein D, Loftus L, Lusk N, Malone J, Martin NX, Monet D, Omstead V, Opitz-Araya X, Oster A, Pom CA, Potekhina L, Reding M, Rimorin C, Ruiz A, Sedeño-Cortés AE, Shapovalova NV, Taormina M, Taskin N, Tieu M, Valera Cuevas NJ, Weed N, Way S, Yao Z, McMillen DA, Kunst M, McGraw M, Thyagarajan B, Waters J, Bakken TE, Yao S, Smith KA, Svoboda K, Podgorski K, Kojima Y, Horwitz GD, Zeng H, Daigle TL, Lein ES, Tasic B, Ting JT, Levi BP. Enhancer-AAVs allow genetic access to oligodendrocytes and diverse populations of astrocytes across species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558718. [PMID: 37790503 PMCID: PMC10542530 DOI: 10.1101/2023.09.20.558718] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Proper brain function requires the assembly and function of diverse populations of neurons and glia. Single cell gene expression studies have mostly focused on characterization of neuronal cell diversity; however, recent studies have revealed substantial diversity of glial cells, particularly astrocytes. To better understand glial cell types and their roles in neurobiology, we built a new suite of adeno-associated viral (AAV)-based genetic tools to enable genetic access to astrocytes and oligodendrocytes. These oligodendrocyte and astrocyte enhancer-AAVs are highly specific (usually > 95% cell type specificity) with variable expression levels, and our astrocyte enhancer-AAVs show multiple distinct expression patterns reflecting the spatial distribution of astrocyte cell types. To provide the best glial-specific functional tools, several enhancer-AAVs were: optimized for higher expression levels, shown to be functional and specific in rat and macaque, shown to maintain specific activity in epilepsy where traditional promoters changed activity, and used to drive functional transgenes in astrocytes including Cre recombinase and acetylcholine-responsive sensor iAChSnFR. The astrocyte-specific iAChSnFR revealed a clear reward-dependent acetylcholine response in astrocytes of the nucleus accumbens during reinforcement learning. Together, this collection of glial enhancer-AAVs will enable characterization of astrocyte and oligodendrocyte populations and their roles across species, disease states, and behavioral epochs.
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17
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O'Toole SM, Oyibo HK, Keller GB. Molecularly targetable cell types in mouse visual cortex have distinguishable prediction error responses. Neuron 2023; 111:2918-2928.e8. [PMID: 37708892 DOI: 10.1016/j.neuron.2023.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 04/19/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Predictive processing postulates the existence of prediction error neurons in cortex. Neurons with both negative and positive prediction error response properties have been identified in layer 2/3 of visual cortex, but whether they correspond to transcriptionally defined subpopulations is unclear. Here we used the activity-dependent, photoconvertible marker CaMPARI2 to tag neurons in layer 2/3 of mouse visual cortex during stimuli and behaviors designed to evoke prediction errors. We performed single-cell RNA-sequencing on these populations and found that previously annotated Adamts2 and Rrad layer 2/3 transcriptional cell types were enriched when photolabeling during stimuli that drive negative or positive prediction error responses, respectively. Finally, we validated these results functionally by designing artificial promoters for use in AAV vectors to express genetically encoded calcium indicators. Thus, transcriptionally distinct cell types in layer 2/3 that can be targeted using AAV vectors exhibit distinguishable negative and positive prediction error responses.
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Affiliation(s)
- Sean M O'Toole
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Hassana K Oyibo
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg B Keller
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Science, University of Basel, Basel, Switzerland.
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18
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Cheng YM, Ma C, Jin K, Jin ZB. Retinal organoid and gene editing for basic and translational research. Vision Res 2023; 210:108273. [PMID: 37307693 DOI: 10.1016/j.visres.2023.108273] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/14/2023]
Abstract
The rapid evolution of two technologies has greatly transformed the basic, translational, and clinical research in the mammalian retina. One is the retinal organoid (RO) technology. Various induction methods have been created or adapted to generate species-specific, disease-specific, and experimental-targeted retinal organoids (ROs). The process of generating ROs can highly mimic the in vivo retinal development, and consequently, the ROs resemble the retina in many aspects including the molecular and cellular profiles. The other technology is the gene editing, represented by the classical CRISPR-Cas9 editing and its derivatives such as prime editing, homology independent targeted integration (HITI), base editing and others. The combination of ROs and gene editing has opened up countless possibilities in the study of retinal development, pathogenesis, and therapeutics. We review recent advances in the ROs, gene editing methodologies, delivery vectors, and related topics that are particularly relevant to retinal studies.
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Affiliation(s)
- You-Min Cheng
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing 100730 China
| | - Chao Ma
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing 100730 China
| | - Kangxin Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing 100730 China.
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing 100730 China.
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19
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Brown EE, Scandura MJ, Pierce EA. Expression of NMNAT1 in the photoreceptors is sufficient to prevent NMNAT1-associated retinal degeneration. Mol Ther Methods Clin Dev 2023; 29:319-328. [PMID: 37214313 PMCID: PMC10193288 DOI: 10.1016/j.omtm.2023.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 04/12/2023] [Indexed: 05/24/2023]
Abstract
Nicotinamide nucleotide adenylyltransferase 1 (NMNAT1) is a ubiquitously expressed enzyme involved in nuclear NAD+ production throughout the body. However, mutations in the NMNAT1 gene lead to retina-specific disease with few reports of systemic effects. We have previously demonstrated that AAV-mediated gene therapy using self-complementary AAV (scAAV) to ubiquitously express NMNAT1 throughout the retina prevents retinal degeneration in a mouse model of NMNAT1-associated disease. We aimed to develop a better understanding of the cell types in the retina that contribute to disease pathogenesis in NMNAT1-associated disease, and to identify the cell types that require NMNAT1 expression for therapeutic benefit. To achieve this goal, we treated Nmnat1V9M/V9M mice with scAAV using cell type-specific promoters to restrict NMNAT1 expression to distinct retinal cell types. We hypothesized that photoreceptors are uniquely vulnerable to NAD+ depletion due to mutations in NMNAT1. Consistent with this hypothesis, we identified that treatments that drove NMNAT1 expression in the photoreceptors led to preservation of retinal morphology. These findings suggest that gene therapies for NMNAT1-associated disease should aim to express NMNAT1 in the photoreceptor cells.
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Affiliation(s)
- Emily E. Brown
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Harvard Medical School, Boston, MA 02114, USA
| | - Michael J. Scandura
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Harvard Medical School, Boston, MA 02114, USA
| | - Eric A. Pierce
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Harvard Medical School, Boston, MA 02114, USA
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20
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Kropp M, Mohit M, Leroy-Ciocanea CI, Schwerm L, Harmening N, Bascuas T, De Clerck E, Kreis AJ, Pajic B, Johnen S, Thumann G. Mammalian Animal and Human Retinal Organ Culture as Pre-Clinical Model to Evaluate Oxidative Stress and Antioxidant Intraocular Therapeutics. Antioxidants (Basel) 2023; 12:1211. [PMID: 37371942 DOI: 10.3390/antiox12061211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Oxidative stress (OS) is involved in the pathogenesis of retinal neurodegenerative diseases such as age-related macular degeneration (AMD) and diabetic retinopathy (DR) and an important target of therapeutic treatments. New therapeutics are tested in vivo despite limits in terms of transferability and ethical concerns. Retina cultures using human tissue can deliver critical information and significantly reduce the number of animal experiments along with increased transferability. We cultured up to 32 retina samples derived from one eye, analyzed the model's quality, induced OS, and tested the efficiency of antioxidative therapeutics. Bovine, porcine, rat, and human retinae were cultured in different experimental settings for 3-14 d. OS was induced by a high amount of glucose or hydrogen peroxide (H2O2) and treated with scutellarin, pigment epithelium-derived factor (PEDF), and/or granulocyte macrophage colony-stimulating factor (GM-CSF). The tissue morphology, cell viability, inflammation, and glutathione level were determined. The retina samples showed only moderate necrosis (23.83 ± 5.05 increased to 27.00 ± 1.66 AU PI-staining over 14 d) after 14 days in culture. OS was successfully induced (reduced ATP content of 288.3 ± 59.9 vs. 435.7 ± 166.8 nM ATP in the controls) and the antioxidants reduced OS-induced apoptosis (from 124.20 ± 51.09 to 60.80 ± 319.66 cells/image after the scutellarin treatment). Enhanced mammalian animal and human retina cultures enable reliable, highly transferable research on OS-triggered age-related diseases and pre-clinical testing during drug development.
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Affiliation(s)
- Martina Kropp
- Experimental Ophthalmology, University of Geneva,1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Mohit Mohit
- Experimental Ophthalmology, University of Geneva,1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | | | - Laura Schwerm
- Department of Ophthalmology, University Hospital Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen, 52074 Aachen, Germany
| | - Nina Harmening
- Experimental Ophthalmology, University of Geneva,1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Thais Bascuas
- Experimental Ophthalmology, University of Geneva,1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Eline De Clerck
- Experimental Ophthalmology, University of Geneva,1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Andreas J Kreis
- Experimental Ophthalmology, University of Geneva,1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
| | - Bojan Pajic
- Experimental Ophthalmology, University of Geneva,1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
- Eye Clinic ORASIS, Swiss Eye Research Foundation, 5734 Reinach, Switzerland
- Department of Physics, Faculty of Sciences, University of Novi Sad, 21000 Novi Sad, Serbia
- Faculty of Medicine of the Military Medical Academy, University of Defense, 11000 Belgrade, Serbia
| | - Sandra Johnen
- Department of Ophthalmology, University Hospital Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen, 52074 Aachen, Germany
| | - Gabriele Thumann
- Experimental Ophthalmology, University of Geneva,1205 Geneva, Switzerland
- Department of Ophthalmology, University Hospitals of Geneva, 1205 Geneva, Switzerland
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21
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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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22
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Hammadi S, Tzoumas N, Ferrara M, Meschede IP, Lo K, Harris C, Lako M, Steel DH. Bruch's Membrane: A Key Consideration with Complement-Based Therapies for Age-Related Macular Degeneration. J Clin Med 2023; 12:2870. [PMID: 37109207 PMCID: PMC10145879 DOI: 10.3390/jcm12082870] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
The complement system is crucial for immune surveillance, providing the body's first line of defence against pathogens. However, an imbalance in its regulators can lead to inappropriate overactivation, resulting in diseases such as age-related macular degeneration (AMD), a leading cause of irreversible blindness globally affecting around 200 million people. Complement activation in AMD is believed to begin in the choriocapillaris, but it also plays a critical role in the subretinal and retinal pigment epithelium (RPE) spaces. Bruch's membrane (BrM) acts as a barrier between the retina/RPE and choroid, hindering complement protein diffusion. This impediment increases with age and AMD, leading to compartmentalisation of complement activation. In this review, we comprehensively examine the structure and function of BrM, including its age-related changes visible through in vivo imaging, and the consequences of complement dysfunction on AMD pathogenesis. We also explore the potential and limitations of various delivery routes (systemic, intravitreal, subretinal, and suprachoroidal) for safe and effective delivery of conventional and gene therapy-based complement inhibitors to treat AMD. Further research is needed to understand the diffusion of complement proteins across BrM and optimise therapeutic delivery to the retina.
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Affiliation(s)
- Sarah Hammadi
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Nikolaos Tzoumas
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Sunderland Eye Infirmary, Queen Alexandra Rd., Sunderland SR2 9H, UK
| | | | - Ingrid Porpino Meschede
- Gyroscope Therapeutics Limited, a Novartis Company, Rolling Stock Yard, 6th Floor, 188 York Way, London N7 9AS, UK
| | - Katharina Lo
- Gyroscope Therapeutics Limited, a Novartis Company, Rolling Stock Yard, 6th Floor, 188 York Way, London N7 9AS, UK
| | - Claire Harris
- Gyroscope Therapeutics Limited, a Novartis Company, Rolling Stock Yard, 6th Floor, 188 York Way, London N7 9AS, UK
- Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Majlinda Lako
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - David H. Steel
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Sunderland Eye Infirmary, Queen Alexandra Rd., Sunderland SR2 9H, UK
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23
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Munz M, Bharioke A, Kosche G, Moreno-Juan V, Brignall A, Rodrigues TM, Graff-Meyer A, Ulmer T, Haeuselmann S, Pavlinic D, Ledergerber N, Gross-Scherf B, Rózsa B, Krol J, Picelli S, Cowan CS, Roska B. Pyramidal neurons form active, transient, multilayered circuits perturbed by autism-associated mutations at the inception of neocortex. Cell 2023; 186:1930-1949.e31. [PMID: 37071993 PMCID: PMC10156177 DOI: 10.1016/j.cell.2023.03.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 02/01/2023] [Accepted: 03/22/2023] [Indexed: 04/20/2023]
Abstract
Cortical circuits are composed predominantly of pyramidal-to-pyramidal neuron connections, yet their assembly during embryonic development is not well understood. We show that mouse embryonic Rbp4-Cre cortical neurons, transcriptomically closest to layer 5 pyramidal neurons, display two phases of circuit assembly in vivo. At E14.5, they form a multi-layered circuit motif, composed of only embryonic near-projecting-type neurons. By E17.5, this transitions to a second motif involving all three embryonic types, analogous to the three adult layer 5 types. In vivo patch clamp recordings and two-photon calcium imaging of embryonic Rbp4-Cre neurons reveal active somas and neurites, tetrodotoxin-sensitive voltage-gated conductances, and functional glutamatergic synapses, from E14.5 onwards. Embryonic Rbp4-Cre neurons strongly express autism-associated genes and perturbing these genes interferes with the switch between the two motifs. Hence, pyramidal neurons form active, transient, multi-layered pyramidal-to-pyramidal circuits at the inception of neocortex, and studying these circuits could yield insights into the etiology of autism.
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Affiliation(s)
- Martin Munz
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Arjun Bharioke
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kosche
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Verónica Moreno-Juan
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Alexandra Brignall
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Tiago M Rodrigues
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Alexandra Graff-Meyer
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Talia Ulmer
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Stephanie Haeuselmann
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Dinko Pavlinic
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Nicole Ledergerber
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Brigitte Gross-Scherf
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Balázs Rózsa
- Two-Photon Imaging Center, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
| | - Jacek Krol
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Simone Picelli
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Cameron S Cowan
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland.
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24
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Zin EA, Ozturk BE, Dalkara D, Byrne LC. Developing New Vectors for Retinal Gene Therapy. Cold Spring Harb Perspect Med 2023; 13:a041291. [PMID: 36987583 PMCID: PMC10691475 DOI: 10.1101/cshperspect.a041291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Since their discovery over 55 years ago, adeno-associated virus (AAV) vectors have become powerful tools for experimental and therapeutic in vivo gene delivery, particularly in the retina. Increasing knowledge of AAV structure and biology has propelled forward the development of engineered AAV vectors with improved abilities for gene delivery. However, major obstacles to safe and efficient therapeutic gene delivery remain, including tropism, inefficient and untargeted gene delivery, and limited carrying capacity. Additional improvements to AAV vectors will be required to achieve therapeutic benefit while avoiding safety issues. In this review, we provide an overview of recent methods for engineering-enhanced AAV capsids, as well as remaining challenges that must be overcome to achieve optimized therapeutic gene delivery in the eye.
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Affiliation(s)
- Emilia A Zin
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France
| | - Bilge E Ozturk
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Deniz Dalkara
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France
| | - Leah C Byrne
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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25
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Hu X, Zhang B, Li X, Li M, Wang Y, Dan H, Zhou J, Wei Y, Ge K, Li P, Song Z. The application and progression of CRISPR/Cas9 technology in ophthalmological diseases. Eye (Lond) 2023; 37:607-617. [PMID: 35915232 PMCID: PMC9998618 DOI: 10.1038/s41433-022-02169-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/07/2022] [Accepted: 06/30/2022] [Indexed: 11/08/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas) system is an adaptive immune defence system that has gradually evolved in bacteria and archaea to combat invading viruses and exogenous DNA. Advances in technology have enabled researchers to enhance their understanding of the immune process in vivo and its potential for use in genome editing. Thus far, applications of CRISPR/Cas9 genome editing technology in ophthalmology have included gene therapy for corneal dystrophy, glaucoma, congenital cataract, Leber's congenital amaurosis, retinitis pigmentosa, Usher syndrome, fundus neovascular disease, proliferative vitreoretinopathy, retinoblastoma and other eye diseases. Additionally, the combination of CRISPR/Cas9 genome editing technology with adeno-associated virus vector and inducible pluripotent stem cells provides further therapeutic avenues for the treatment of eye diseases. Nonetheless, many challenges remain in the development of clinically feasible retinal genome editing therapy. This review discusses the development, as well as mechanism of CRISPR/Cas9 and its applications and challenges in gene therapy for eye diseases.
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Affiliation(s)
- Xumeng Hu
- Henan Eye Hospital, Henan Eye Institution, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Beibei Zhang
- Henan Eye Hospital, Henan Eye Institution, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Xiaoli Li
- Henan Eye Hospital, Henan Eye Institution, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Miao Li
- Henan Eye Hospital, Henan Eye Institution, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Yange Wang
- Henan Eye Hospital, Henan Eye Institution, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Handong Dan
- Henan Eye Hospital, Henan Eye Institution, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Jiamu Zhou
- Henan Eye Hospital, Henan Eye Institution, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Yuanmeng Wei
- Henan Eye Hospital, Henan Eye Institution, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Keke Ge
- Henan Eye Hospital, Henan Eye Institution, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Pan Li
- Henan Eye Hospital, Henan Eye Institution, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China
| | - Zongming Song
- Henan Eye Hospital, Henan Eye Institution, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, Henan, China.
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26
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Day-Cooney J, Dalangin R, Zhong H, Mao T. Genetically encoded fluorescent sensors for imaging neuronal dynamics in vivo. J Neurochem 2023; 164:284-308. [PMID: 35285522 DOI: 10.1111/jnc.15608] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 11/29/2022]
Abstract
The brain relies on many forms of dynamic activities in individual neurons, from synaptic transmission to electrical activity and intracellular signaling events. Monitoring these neuronal activities with high spatiotemporal resolution in the context of animal behavior is a necessary step to achieve a mechanistic understanding of brain function. With the rapid development and dissemination of highly optimized genetically encoded fluorescent sensors, a growing number of brain activities can now be visualized in vivo. To date, cellular calcium imaging, which has been largely used as a proxy for electrical activity, has become a mainstay in systems neuroscience. While challenges remain, voltage imaging of neural populations is now possible. In addition, it is becoming increasingly practical to image over half a dozen neurotransmitters, as well as certain intracellular signaling and metabolic activities. These new capabilities enable neuroscientists to test previously unattainable hypotheses and questions. This review summarizes recent progress in the development and delivery of genetically encoded fluorescent sensors, and highlights example applications in the context of in vivo imaging.
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Affiliation(s)
- Julian Day-Cooney
- Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Rochelin Dalangin
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA
| | - Haining Zhong
- Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Tianyi Mao
- Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA
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27
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Nieuwenhuis B, Laperrousaz E, Tribble JR, Verhaagen J, Fawcett JW, Martin KR, Williams PA, Osborne A. Improving adeno-associated viral (AAV) vector-mediated transgene expression in retinal ganglion cells: comparison of five promoters. Gene Ther 2023:10.1038/s41434-022-00380-z. [PMID: 36635457 DOI: 10.1038/s41434-022-00380-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 12/02/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023]
Abstract
Recombinant adeno-associated viral vectors (AAVs) are an effective system for gene transfer. AAV serotype 2 (AAV2) is commonly used to deliver transgenes to retinal ganglion cells (RGCs) via intravitreal injection. The AAV serotype however is not the only factor contributing to the effectiveness of gene therapies. Promoters influence the strength and cell-selectivity of transgene expression. This study compares five promoters designed to maximise AAV2 cargo space for gene delivery: chicken β-actin (CBA), cytomegalovirus (CMV), short CMV early enhancer/chicken β-actin/short β-globulin intron (sCAG), mouse phosphoglycerate kinase (PGK), and human synapsin (SYN). The promoters driving enhanced green fluorescent protein (eGFP) were examined in adult C57BL/6J mice eyes and tissues of the visual system. eGFP expression was strongest in the retina, optic nerves and brain when driven by the sCAG and SYN promoters. CBA, CMV, and PGK had moderate expression by comparison. The SYN promoter had almost exclusive transgene expression in RGCs. The PGK promoter had predominant expression in both RGCs and AII amacrine cells. The ubiquitous CBA, CMV, and sCAG promoters expressed eGFP in a variety of cell types across multiple retinal layers including Müller glia and astrocytes. We also found that these promoters could transduce human retina ex vivo, although expression was predominantly in glial cells due to low RGC viability. Taken together, this promoter comparison study contributes to optimising AAV-mediated transduction in the retina, and could be valuable for research in ocular disorders, particularly those with large or complex genetic cargos.
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Affiliation(s)
- Bart Nieuwenhuis
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK. .,Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK.
| | - Elise Laperrousaz
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - James R Tribble
- Department of Clinical Neuroscience, Division of Eye and Vision, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Joost Verhaagen
- Laboratory for Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences (KNAW), Amsterdam, The Netherlands.,Centre for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - James W Fawcett
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.,Centre of Reconstructive Neuroscience, Institute of Experimental Medicine, Prague, Czech Republic
| | - Keith R Martin
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.,Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, VIC, Australia.,Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, VIC, Australia
| | - Pete A Williams
- Department of Clinical Neuroscience, Division of Eye and Vision, St. Erik Eye Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Andrew Osborne
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK. .,Ikarovec Ltd, The Norwich Research Park Innovation Centre, Norwich, UK.
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28
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Bassetto M, Sen M, Poulhes F, Arango-Gonzalez B, Ueffing M, Zelphati O. Method for siRNA delivery in retina explants. Methods Cell Biol 2023; 176:199-216. [PMID: 37164538 DOI: 10.1016/bs.mcb.2022.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Several barriers prevent the delivery of nucleic acids to the retina and limit the application of established technologies, such as RNA interference (RNAi), in the study of retinae biology. Organotypic culture of retinal explants is a convenient method to decrease the complexity of the biological environment surrounding the retina while preserving most of its physiological features. Nevertheless, eliciting significant, non-toxic RNAi in retina explants is not straightforward. Retina explants are mainly constituted by neurons organized in discrete circuits embedded within a complex 3D extracellular matrix. About 70% of these neurons are post-mitotic ciliated cells that respond to light. Unfortunately, like the other cells of the retina, photoreceptors are refractory to transfection, and a toxic delivery of nucleic acid often results in permanent cell loss. RNAi has been applied to retina explants using electroporation, viral, and non-viral vectors but with reproducible, poor gene silencing efficiency. In addition, only a few superficial cells can be transduced/transfected in adult retina explants. Therefore, viruses are often injected into the eye of embryos prior to excision of the retina. However, embryonic explants are not the best model to study most retina diseases since even if they are viable for several weeks, the pathological phenotype often appears later in development. We describe a robust and straightforward method to elicit significant RNAi in adult retina explant using Reverse Magnetofection. This transfection method offers a simple tool for non-toxic gene knockdown of specific genes in adult retina explants by using cationic magnetic nanoparticles (MNPs) to complex and deliver short interfering-RNAs (siRNA) in retina cells under the action of a magnetic field.
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Affiliation(s)
- Marco Bassetto
- OZ Biosciences, Parc Scientifique de Luminy, CEDEX 9, Marseille, France; Gavin Herbert Eye Institute, Center for Translational Vision Research, Department of Physiology & Biophysics, University of California, Irvine, CA, United States
| | - Merve Sen
- Centre of Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Florent Poulhes
- OZ Biosciences, Parc Scientifique de Luminy, CEDEX 9, Marseille, France.
| | - Blanca Arango-Gonzalez
- Centre of Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Marius Ueffing
- Centre of Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Olivier Zelphati
- OZ Biosciences, Parc Scientifique de Luminy, CEDEX 9, Marseille, France
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29
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Seyednejad SA, Sartor GC. Noncoding RNA therapeutics for substance use disorder. ADVANCES IN DRUG AND ALCOHOL RESEARCH 2022; 2:10807. [PMID: 36601439 PMCID: PMC9808746 DOI: 10.3389/adar.2022.10807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although noncoding RNAs (ncRNAs) have been shown to regulate maladaptive neuroadaptations that drive compulsive drug use, ncRNA-targeting therapeutics for substance use disorder (SUD) have yet to be clinically tested. Recent advances in RNA-based drugs have improved many therapeutic issues related to immune response, specificity, and delivery, leading to multiple successful clinical trials for other diseases. As the need for safe and effective treatments for SUD continues to grow, novel nucleic acid-based therapeutics represent an appealing approach to target ncRNA mechanisms in SUD. Here, we review ncRNA processes implicated in SUD, discuss recent therapeutic approaches for targeting ncRNAs, and highlight potential opportunities and challenges of ncRNA-targeting therapeutics for SUD.
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Affiliation(s)
- Seyed Afshin Seyednejad
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
- Connecticut Institute for the Brain and Cognitive Sciences (CT IBACS), Storrs, CT, United States
| | - Gregory C. Sartor
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
- Connecticut Institute for the Brain and Cognitive Sciences (CT IBACS), Storrs, CT, United States
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30
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Rotov AY, Firsov ML. Optogenetic Prosthetization of Retinal Bipolar Cells. J EVOL BIOCHEM PHYS+ 2022. [DOI: 10.1134/s0022093022060011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Abstract
Although the experience of optogenetic retinal prosthetics
in animal models dates back to more than 16 years, the first results
obtained on humans have only been reported in the last year. Over this
period, the main challenges of prosthetics became clear and the
approaches to their solution were proposed. In this review, we aim
to present the achievements in the field of optogenetic prosthetization
of retinal bipolar cells with a focus mainly on relatively recent
publications. The review addresses the advantages and disadvantages
of bipolar cell prosthetics as compared to the alternative target,
retinal ganglion cells, and provides a comparative analysis of the
effectiveness of ionotropic light-sensitive proteins (channelrhodopsins)
or metabotropic receptors (rhodopsins) as prosthetic tools.
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31
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Tkatch T, Rysevaite-Kyguoliene K, Sabeckis I, Sabeckiene D, Pauza DH, Baranauskas G. An efficient rAAV vector for protein expression in cortical parvalbumin expressing interneurons. Sci Rep 2022; 12:17851. [PMID: 36284123 PMCID: PMC9596399 DOI: 10.1038/s41598-022-21867-0] [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: 12/29/2021] [Accepted: 10/04/2022] [Indexed: 01/20/2023] Open
Abstract
Recombinant adeno-associated viruses (rAAV) are extensively used in both research and clinical applications. Despite significant advances, there is a lack of short promoters able to drive the expression of virus delivered genes in specific classes of neurons. We designed an efficient rAAV vector suitable for the rAAV-mediated gene expression in cortical interneurons, mainly in the parvalbumin expressing cells. The vector includes a short parvalbumin promoter and a specialized poly(A) sequence. The degree of conservation of the parvalbumin gene adjoining non-coding regions was used in both the promoter design and the selection of the poly(A) sequence. The specificity was established by co-localizing the fluorescence of the virus delivered eGFP and the antibody for a neuronal marker. rAAV particles were injected in the visual cortex area V1/V2 of adult rats (2-4 months old). Neurons expressing the virus delivered eGFP were mainly positive for interneuronal markers: 66.5 ± 2.8% for parvalbumin, 14.6 ± 2.4% for somatostatin, 7.1 ± 1.2% for vasoactive intestinal peptide, 2.8 ± 0.6% for cholecystokinin. Meanwhile, only 2.1 ± 0.5% were positive for CaMKII, a marker for principal cells in the cortex. The efficiency of the construct was verified by optogenetic experiments: the expression of the virus delivered ChR2 channels was sufficient to evoke by blue light laser high frequency bursts of action potentials in putative fast spiking neurons. We conclude that our promoter allows highly specific expression of the rAAV delivered cDNAs in cortical interneurons with a strong preference for the parvalbumin positive cells.
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Affiliation(s)
- Tatiana Tkatch
- grid.45083.3a0000 0004 0432 6841Neurophysiology Laboratory, Neuroscience Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania ,grid.16753.360000 0001 2299 3507Present Address: Department of Physiology, Northwestern University, Chicago, IL USA
| | | | - Ignas Sabeckis
- grid.45083.3a0000 0004 0432 6841Anatomy Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Deimante Sabeckiene
- grid.45083.3a0000 0004 0432 6841Anatomy Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Dainius H. Pauza
- grid.45083.3a0000 0004 0432 6841Anatomy Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Gytis Baranauskas
- grid.45083.3a0000 0004 0432 6841Neurophysiology Laboratory, Neuroscience Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
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32
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Qian Y, Li J, Zhao S, Matthews EA, Adoff M, Zhong W, An X, Yeo M, Park C, Yang X, Wang BS, Southwell DG, Huang ZJ. Programmable RNA sensing for cell monitoring and manipulation. Nature 2022; 610:713-721. [PMID: 36198803 PMCID: PMC10348343 DOI: 10.1038/s41586-022-05280-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 08/26/2022] [Indexed: 12/22/2022]
Abstract
RNA is a central and universal mediator of genetic information underlying the diversity of cell types and cell states, which together shape tissue organization and organismal function across species and lifespans. Despite numerous advances in RNA sequencing technologies and the massive accumulation of transcriptome datasets across the life sciences1,2, the dearth of technologies that use RNAs to observe and manipulate cell types remains a bottleneck in biology and medicine. Here we describe CellREADR (Cell access through RNA sensing by Endogenous ADAR), a programmable RNA-sensing technology that leverages RNA editing mediated by ADAR to couple the detection of cell-defining RNAs with the translation of effector proteins. Viral delivery of CellREADR conferred specific cell-type access in mouse and rat brains and in ex vivo human brain tissues. Furthermore, CellREADR enabled the recording and control of specific types of neurons in behaving mice. CellREADR thus highlights the potential for RNA-based monitoring and editing of animal cells in ways that are specific, versatile, simple and generalizable across organ systems and species, with wide applications in biology, biotechnology and programmable RNA medicine.
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Affiliation(s)
- Yongjun Qian
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Jiayun Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Shengli Zhao
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Elizabeth A Matthews
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Michael Adoff
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Weixin Zhong
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Xu An
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Michele Yeo
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Christine Park
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Xiaolu Yang
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
| | - Bor-Shuen Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Derek G Southwell
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Z Josh Huang
- Department of Neurobiology, Duke University Medical Center, Durham, NC, USA.
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA.
- Department of Biomedical Engineering, Duke University Pratt School of Engineering, Durham, NC, USA.
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33
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Directed evolution of adeno-associated virus for efficient gene delivery to microglia. Nat Methods 2022; 19:976-985. [PMID: 35879607 DOI: 10.1038/s41592-022-01547-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 06/10/2022] [Indexed: 12/12/2022]
Abstract
As the resident immune cells in the central nervous system (CNS), microglia orchestrate immune responses and dynamically sculpt neural circuits in the CNS. Microglial dysfunction and mutations of microglia-specific genes have been implicated in many diseases of the CNS. Developing effective and safe vehicles for transgene delivery into microglia will facilitate the studies of microglia biology and microglia-associated disease mechanisms. Here, we report the discovery of adeno-associated virus (AAV) variants that mediate efficient in vitro and in vivo microglial transduction via directed evolution of the AAV capsid protein. These AAV-cMG and AAV-MG variants are capable of delivering various genetic payloads into microglia with high efficiency, and enable sufficient transgene expression to support fluorescent labeling, Ca2+ and neurotransmitter imaging and genome editing in microglia in vivo. Furthermore, single-cell RNA sequencing shows that the AAV-MG variants mediate in vivo transgene delivery without inducing microglia immune activation. These AAV variants should facilitate the use of various genetically encoded sensors and effectors in the study of microglia-related biology.
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34
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Satou C, Neve RL, Oyibo HK, Zmarz P, Huang KH, Arn Bouldoires E, Mori T, Higashijima SI, Keller GB, Friedrich RW. A viral toolbox for conditional and transneuronal gene expression in zebrafish. eLife 2022; 11:77153. [PMID: 35866706 PMCID: PMC9307271 DOI: 10.7554/elife.77153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/06/2022] [Indexed: 12/13/2022] Open
Abstract
The zebrafish is an important model in systems neuroscience but viral tools to dissect the structure and function of neuronal circuitry are not established. We developed methods for efficient gene transfer and retrograde tracing in adult and larval zebrafish by herpes simplex viruses (HSV1). HSV1 was combined with the Gal4/UAS system to target cell types with high spatial, temporal, and molecular specificity. We also established methods for efficient transneuronal tracing by modified rabies viruses in zebrafish. We demonstrate that HSV1 and rabies viruses can be used to visualize and manipulate genetically or anatomically identified neurons within and across different brain areas of adult and larval zebrafish. An expandable library of viruses is provided to express fluorescent proteins, calcium indicators, optogenetic probes, toxins and other molecular tools. This toolbox creates new opportunities to interrogate neuronal circuits in zebrafish through combinations of genetic and viral approaches.
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Affiliation(s)
- Chie Satou
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Rachael L Neve
- Gene Delivery Technology Core, Massachusetts General Hospital, Cambridge, United States
| | - Hassana K Oyibo
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Pawel Zmarz
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Kuo-Hua Huang
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Takuma Mori
- Department of Molecular and Cellular Physiology, Institute of Medicine, Academic Assembly, Shinshu University, Nagano, Japan
| | - Shin-Ichi Higashijima
- National Institutes of Natural Sciences, Exploratory Research Center on Life and Living Systems, National Institute for Basic Biology, Okazaki, Japan.,Graduate University for Advanced Studies, Okazaki, Japan
| | - Georg B Keller
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, Switzerland
| | - Rainer W Friedrich
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, Switzerland
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35
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Emiliani V, Entcheva E, Hedrich R, Hegemann P, Konrad KR, Lüscher C, Mahn M, Pan ZH, Sims RR, Vierock J, Yizhar O. Optogenetics for light control of biological systems. NATURE REVIEWS. METHODS PRIMERS 2022; 2:55. [PMID: 37933248 PMCID: PMC10627578 DOI: 10.1038/s43586-022-00136-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/30/2022] [Indexed: 11/08/2023]
Abstract
Optogenetic techniques have been developed to allow control over the activity of selected cells within a highly heterogeneous tissue, using a combination of genetic engineering and light. Optogenetics employs natural and engineered photoreceptors, mostly of microbial origin, to be genetically introduced into the cells of interest. As a result, cells that are naturally light-insensitive can be made photosensitive and addressable by illumination and precisely controllable in time and space. The selectivity of expression and subcellular targeting in the host is enabled by applying control elements such as promoters, enhancers and specific targeting sequences to the employed photoreceptor-encoding DNA. This powerful approach allows precise characterization and manipulation of cellular functions and has motivated the development of advanced optical methods for patterned photostimulation. Optogenetics has revolutionized neuroscience during the past 15 years and is primed to have a similar impact in other fields, including cardiology, cell biology and plant sciences. In this Primer, we describe the principles of optogenetics, review the most commonly used optogenetic tools, illumination approaches and scientific applications and discuss the possibilities and limitations associated with optogenetic manipulations across a wide variety of optical techniques, cells, circuits and organisms.
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Affiliation(s)
- Valentina Emiliani
- Wavefront Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Emilia Entcheva
- Department of Biomedical Engineering, George Washington University, Washington, DC, USA
| | - Rainer Hedrich
- Julius-von-Sachs Institute for Biosciences, Molecular Plant Physiology and Biophysics, University of Wuerzburg, Wuerzburg, Germany
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universitaet zu Berlin, Berlin, Germany
| | - Kai R. Konrad
- Julius-von-Sachs Institute for Biosciences, Molecular Plant Physiology and Biophysics, University of Wuerzburg, Wuerzburg, Germany
| | - Christian Lüscher
- Department of Basic Neurosciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Clinic of Neurology, Department of Clinical Neurosciences, Geneva University Hospital, Geneva, Switzerland
| | - Mathias Mahn
- Department of Neurobiology, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Zhuo-Hua Pan
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, USA
| | - Ruth R. Sims
- Wavefront Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Johannes Vierock
- Institute for Biology, Experimental Biophysics, Humboldt-Universitaet zu Berlin, Berlin, Germany
- Neuroscience Research Center, Charité – Universitaetsmedizin Berlin, Berlin, Germany
| | - Ofer Yizhar
- Departments of Brain Sciences and Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
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36
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Lake EMR, Higley MJ. Building bridges: simultaneous multimodal neuroimaging approaches for exploring the organization of brain networks. NEUROPHOTONICS 2022; 9:032202. [PMID: 36159712 PMCID: PMC9506627 DOI: 10.1117/1.nph.9.3.032202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Brain organization is evident across spatiotemporal scales as well as from structural and functional data. Yet, translating from micro- to macroscale (vice versa) as well as between different measures is difficult. Reconciling disparate observations from different modes is challenging because each specializes within a restricted spatiotemporal milieu, usually has bounded organ coverage, and has access to different contrasts. True intersubject biological heterogeneity, variation in experiment implementation (e.g., use of anesthesia), and true moment-to-moment variations in brain activity (maybe attributable to different brain states) also contribute to variability between studies. Ultimately, for a deeper and more actionable understanding of brain organization, an ability to translate across scales, measures, and species is needed. Simultaneous multimodal methods can contribute to bettering this understanding. We consider four modes, three optically based: multiphoton imaging, single-photon (wide-field) imaging, and fiber photometry, as well as magnetic resonance imaging. We discuss each mode as well as their pairwise combinations with regard to the definition and study of brain networks.
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Affiliation(s)
- Evelyn M. R. Lake
- Yale School of Medicine, Department of Radiology and Biomedical Imaging, New Haven, Connecticut, United States
| | - Michael J. Higley
- Yale School of Medicine, Departments of Neuroscience and Psychiatry, New Haven, Connecticut, United States
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, Connecticut, United States
- Program in Cellular Neuroscience, Neurodegeneration, and Repair, New Haven, Connecticut, United States
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37
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Pouchelon G, Vergara J, McMahon J, Gorissen BL, Lin JD, Vormstein-Schneider D, Niehaus JL, Burbridge TJ, Wester JC, Sherer M, Fernandez-Otero M, Allaway KC, Pelkey K, Chittajallu R, McBain CJ, Fan M, Nasse JS, Wildenberg GA, Fishell G, Dimidschstein J. A versatile viral toolkit for functional discovery in the nervous system. CELL REPORTS METHODS 2022; 2:100225. [PMID: 35784651 PMCID: PMC9243523 DOI: 10.1016/j.crmeth.2022.100225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/21/2022] [Accepted: 05/04/2022] [Indexed: 12/24/2022]
Abstract
The ability to precisely control transgene expression is essential for basic research and clinical applications. Adeno-associated viruses (AAVs) are non-pathogenic and can be used to drive stable expression in virtually any tissue, cell type, or species, but their limited genomic payload results in a trade-off between the transgenes that can be incorporated and the complexity of the regulatory elements controlling their expression. Resolving these competing imperatives in complex experiments inevitably results in compromises. Here, we assemble an optimized viral toolkit (VTK) that addresses these limitations and allows for efficient combinatorial targeting of cell types. Moreover, their modular design explicitly enables further refinements. We achieve this in compact vectors by integrating structural improvements of AAV vectors with innovative molecular tools. We illustrate the potential of this approach through a systematic demonstration of their utility for targeting cell types and querying their biology using a wide array of genetically encoded tools.
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Affiliation(s)
- Gabrielle Pouchelon
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
- Harvard Medical School, Blavatnik Institute, Neurobiology, Boston, MA 02115, USA
| | - Josselyn Vergara
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Justin McMahon
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Bram L. Gorissen
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
- Harvard Medical School, Blavatnik Institute, Neurobiology, Boston, MA 02115, USA
| | - Jessica D. Lin
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | | | | | - Timothy J. Burbridge
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
- Harvard Medical School, Blavatnik Institute, Neurobiology, Boston, MA 02115, USA
| | - Jason C. Wester
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | - Mia Sherer
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
- Harvard Medical School, Blavatnik Institute, Neurobiology, Boston, MA 02115, USA
| | - Marian Fernandez-Otero
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
- Harvard Medical School, Blavatnik Institute, Neurobiology, Boston, MA 02115, USA
| | - Kathryn C. Allaway
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
- Harvard Medical School, Blavatnik Institute, Neurobiology, Boston, MA 02115, USA
| | - Kenneth Pelkey
- 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
| | - Chris J. McBain
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20892, USA
| | | | | | - Gregg A. Wildenberg
- Department of Neurobiology, University of Chicago, Chicago, IL 60637, USA
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Gordon Fishell
- Broad Institute, Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
- Harvard Medical School, Blavatnik Institute, Neurobiology, Boston, MA 02115, USA
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Gilhooley MJ, Lindner M, Palumaa T, Hughes S, Peirson SN, Hankins MW. A systematic comparison of optogenetic approaches to visual restoration. Mol Ther Methods Clin Dev 2022; 25:111-123. [PMID: 35402632 PMCID: PMC8956963 DOI: 10.1016/j.omtm.2022.03.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/04/2022] [Indexed: 02/06/2023]
Abstract
During inherited retinal degenerations (IRDs), vision is lost due to photoreceptor cell death; however, a range of optogenetic tools have been shown to restore light responses in animal models. Restored response characteristics vary between tools and the neuronal cell population to which they are delivered: the interplay between these is complex, but targeting upstream neurons (such as retinal bipolar cells) may provide functional benefit by retaining intraretinal signal processing. In this study, our aim was to compare two optogenetic tools: mammalian melanopsin (hOPN4) and microbial red-shifted channelrhodopsin (ReaChR) expressed within two subpopulations of surviving cells in a degenerate retina. Intravitreal adeno-associated viral vectors and mouse models utilising the Cre/lox system restricted expression to populations dominated by bipolar cells or retinal ganglion cells and was compared with non-targeted delivery using the chicken beta actin (CBA) promoter. In summary, we found bipolar-targeted optogenetic tools produced faster kinetics and flatter intensity-response relationships compared with non-targeted or retinal-ganglion-cell-targeted hOPN4. Hence, optogenetic tools of both mammalian and microbial origins show advantages when targeted to bipolar cells. This demonstrates the advantage of bipolar-cell-targeted optogenetics for vision restoration in IRDs. We therefore developed a bipolar-cell-specific gene delivery system employing a compressed promoter with the potential for clinical translation.
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Affiliation(s)
- Michael J. Gilhooley
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX1 3QU, UK
- Jules Thorne SCNi, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX1 3QU, UK
- The Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
- Moorfields Eye Hospital, 162, City Road, London EC1V 2PD, UK
| | - Moritz Lindner
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX1 3QU, UK
- Jules Thorne SCNi, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX1 3QU, UK
- Institute of Physiology and Pathophysiology, Department of Neurophysiology, Philipps University, Deutschhausstrasse 1-2, Marburg 35037, Germany
| | - Teele Palumaa
- Jules Thorne SCNi, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX1 3QU, UK
- East Tallinn Central Hospital Eye Clinic, Ravi 18, 10138 Tallinn, Estonia
| | - Steven Hughes
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX1 3QU, UK
- Jules Thorne SCNi, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX1 3QU, UK
| | - Stuart N. Peirson
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX1 3QU, UK
- Jules Thorne SCNi, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX1 3QU, UK
| | - Mark W. Hankins
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX1 3QU, UK
- Jules Thorne SCNi, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX1 3QU, UK
- Corresponding author Mark W. Hankins, Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford OX1 3QU, UK.
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39
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Lindner M, Gilhooley MJ, Hughes S, Hankins MW. Optogenetics for visual restoration: From proof of principle to translational challenges. Prog Retin Eye Res 2022; 91:101089. [PMID: 35691861 DOI: 10.1016/j.preteyeres.2022.101089] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 01/04/2023]
Abstract
Degenerative retinal disorders are a diverse family of diseases commonly leading to irreversible photoreceptor death, while leaving the inner retina relatively intact. Over recent years, innovative gene replacement therapies aiming to halt the progression of certain inherited retinal disorders have made their way into clinics. By rendering surviving retinal neurons light sensitive optogenetic gene therapy now offers a feasible treatment option that can restore lost vision, even in late disease stages and widely independent of the underlying cause of degeneration. Since proof-of-concept almost fifteen years ago, this field has rapidly evolved and a detailed first report on a treated patient has recently been published. In this article, we provide a review of optogenetic approaches for vision restoration. We discuss the currently available optogenetic tools and their relative advantages and disadvantages. Possible cellular targets will be discussed and we will address the question how retinal remodelling may affect the choice of the target and to what extent it may limit the outcomes of optogenetic vision restoration. Finally, we will analyse the evidence for and against optogenetic tool mediated toxicity and will discuss the challenges associated with clinical translation of this promising therapeutic concept.
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Affiliation(s)
- Moritz Lindner
- The Nuffield Laboratory of Ophthalmology, Jules Thorn SCNi, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX1 3QU, United Kingdom; Institute of Physiology and Pathophysiology, Department of Neurophysiology, Philipps University, 35037, Marburg, Germany
| | - Michael J Gilhooley
- The Nuffield Laboratory of Ophthalmology, Jules Thorn SCNi, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX1 3QU, United Kingdom; The Institute of Ophthalmology, University College London, EC1V 9EL, United Kingdom; Moorfields Eye Hospital, London, EC1V 2PD, United Kingdom
| | - Steven Hughes
- The Nuffield Laboratory of Ophthalmology, Jules Thorn SCNi, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Mark W Hankins
- The Nuffield Laboratory of Ophthalmology, Jules Thorn SCNi, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX1 3QU, United Kingdom.
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40
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Bharioke A, Munz M, Brignall A, Kosche G, Eizinger MF, Ledergerber N, Hillier D, Gross-Scherf B, Conzelmann KK, Macé E, Roska B. General anesthesia globally synchronizes activity selectively in layer 5 cortical pyramidal neurons. Neuron 2022; 110:2024-2040.e10. [PMID: 35452606 PMCID: PMC9235854 DOI: 10.1016/j.neuron.2022.03.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 10/30/2021] [Accepted: 03/28/2022] [Indexed: 12/27/2022]
Abstract
General anesthetics induce loss of consciousness, a global change in behavior. However, a corresponding global change in activity in the context of defined cortical cell types has not been identified. Here, we show that spontaneous activity of mouse layer 5 pyramidal neurons, but of no other cortical cell type, becomes consistently synchronized in vivo by different general anesthetics. This heightened neuronal synchrony is aperiodic, present across large distances, and absent in cortical neurons presynaptic to layer 5 pyramidal neurons. During the transition to and from anesthesia, changes in synchrony in layer 5 coincide with the loss and recovery of consciousness. Activity within both apical and basal dendrites is synchronous, but only basal dendrites’ activity is temporally locked to somatic activity. Given that layer 5 is a major cortical output, our results suggest that brain-wide synchrony in layer 5 pyramidal neurons may contribute to the loss of consciousness during general anesthesia. Activity of layer 5 PNs synchronizes globally in different anesthetics Other mouse cortical cell types show no consistent increase in synchrony Changes in layer 5 synchrony coincide with the loss and recovery of consciousness Basal, but not apical, layer 5 dendrites are in synchrony with somas
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Affiliation(s)
- Arjun Bharioke
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Martin Munz
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Alexandra Brignall
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Georg Kosche
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Max Ferdinand Eizinger
- Max von Pettenkofer-Institute, Virology, Medical Faculty and Gene Center, Ludwig Maximilians University, Munich, Germany
| | - Nicole Ledergerber
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Daniel Hillier
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Institute of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Brigitte Gross-Scherf
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Karl-Klaus Conzelmann
- Max von Pettenkofer-Institute, Virology, Medical Faculty and Gene Center, Ludwig Maximilians University, Munich, Germany
| | - Emilie Macé
- Brain-Wide Circuits for Behavior Research Group, Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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Lin CH, Sun Y, Chan CSY, Wu MR, Gu L, Davis AE, Gu B, Zhang W, Tanasa B, Zhong LR, Emerson MM, Chen L, Ding JB, Wang S. Identification of cis-regulatory modules for adeno-associated virus-based cell-type-specific targeting in the retina and brain. J Biol Chem 2022; 298:101674. [PMID: 35148987 PMCID: PMC8980332 DOI: 10.1016/j.jbc.2022.101674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/25/2022] Open
Abstract
Adeno-associated viruses (AAVs) targeting specific cell types are powerful tools for studying distinct cell types in the central nervous system (CNS). Cis-regulatory modules (CRMs), e.g., enhancers, are highly cell-type-specific and can be integrated into AAVs to render cell type specificity. Chromatin accessibility has been commonly used to nominate CRMs, which have then been incorporated into AAVs and tested for cell type specificity in the CNS. However, chromatin accessibility data alone cannot accurately annotate active CRMs, as many chromatin-accessible CRMs are not active and fail to drive gene expression in vivo. Using available large-scale datasets on chromatin accessibility, such as those published by the ENCODE project, here we explored strategies to increase efficiency in identifying active CRMs for AAV-based cell-type-specific labeling and manipulation. We found that prescreening of chromatin-accessible putative CRMs based on the density of cell-type-specific transcription factor binding sites (TFBSs) can significantly increase efficiency in identifying active CRMs. In addition, generation of synthetic CRMs by stitching chromatin-accessible regions flanking cell-type-specific genes can render cell type specificity in many cases. Using these straightforward strategies, we generated AAVs that can target the extensively studied interneuron and glial cell types in the retina and brain. Both strategies utilize available genomic datasets and can be employed to generate AAVs targeting specific cell types in CNS without conducting comprehensive screening and sequencing experiments, making a step forward in cell-type-specific research.
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Affiliation(s)
- Cheng-Hui Lin
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, California, USA
| | - Yue Sun
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, California, USA; Department of Neurosurgery, Stanford University, Stanford, California, USA
| | - Candace S Y Chan
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, California, USA
| | - Man-Ru Wu
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, California, USA
| | - Lei Gu
- Epigenetics Laboratory, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Alexander E Davis
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, California, USA
| | - Baokun Gu
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, California, USA
| | - Wenlin Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Bogdan Tanasa
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, California, USA
| | - Lei R Zhong
- Department of Neurosurgery, Stanford University, Stanford, California, USA
| | - Mark M Emerson
- Department of Biology, The City College of New York, New York, New York, USA
| | - Lu Chen
- Department of Neurosurgery, Stanford University, Stanford, California, USA
| | - Jun B Ding
- Department of Neurosurgery, Stanford University, Stanford, California, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, California, USA
| | - Sui Wang
- Department of Ophthalmology, Mary M. and Sash A. Spencer Center for Vision Research, Byers Eye Institute, Stanford University, Stanford, California, USA.
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42
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Amamoto R, Wallick GK, Cepko CL. Retinoic acid signaling mediates peripheral cone photoreceptor survival in a mouse model of retina degeneration. eLife 2022; 11:76389. [PMID: 35315776 PMCID: PMC8940176 DOI: 10.7554/elife.76389] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/25/2022] [Indexed: 12/16/2022] Open
Abstract
Retinitis Pigmentosa (RP) is a progressive, debilitating visual disorder caused by mutations in a diverse set of genes. In both humans with RP and mouse models of RP, rod photoreceptor dysfunction leads to loss of night vision, and is followed by secondary cone photoreceptor dysfunction and degeneration, leading to loss of daylight color vision. A strategy to prevent secondary cone death could provide a general RP therapy to preserve daylight color vision regardless of the underlying mutation. In mouse models of RP, cones in the peripheral retina survive long-term, despite complete rod loss. The mechanism for such peripheral cone survival had not been explored. Here, we found that active retinoic acid (RA) signaling in peripheral Muller glia is necessary for the abnormally long survival of these peripheral cones. RA depletion by conditional knockout of RA synthesis enzymes, or overexpression of an RA degradation enzyme, abrogated the extended survival of peripheral cones. Conversely, constitutive activation of RA signaling in the central retina promoted long-term cone survival. These results indicate that RA signaling mediates the prolonged peripheral cone survival in the rd1 mouse model of retinal degeneration, and provide a basis for a generic strategy for cone survival in the many diseases that lead to loss of cone-mediated vision.
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Affiliation(s)
- Ryoji Amamoto
- Department of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, United States
| | - Grace K Wallick
- Department of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, United States
| | - Constance L Cepko
- Department of Genetics and Ophthalmology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, United States
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43
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Heffernan KS, Rahman K, Smith Y, Galvan A. Characterization of the GfaABC1D Promoter to Selectively Target Astrocytes in the Rhesus Macaque Brain. J Neurosci Methods 2022; 372:109530. [PMID: 35202614 PMCID: PMC8940704 DOI: 10.1016/j.jneumeth.2022.109530] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/04/2022] [Accepted: 02/14/2022] [Indexed: 10/19/2022]
Abstract
BACKGROUND The study of astrocytic functions in non-human primates (NHPs) has been hampered by the lack of genetic tools to selectively target astrocytes. Viral vectors with selective and efficient transduction of astrocytes could be a potent tool to express marker proteins, modulators, or sensors in NHP astrocytes, but the availability of thoroughly characterized astrocytic selective promoter sequences to use in these species remains extremely limited. NEW METHOD We describe the specificity and efficiency of an astrocyte-specific promoter, GfaABC1D in the brain of the rhesus macaque, with emphasis in basal ganglia regions. AAV5-pZac2.1-GfaABC1D-tdTomato was locally injected into the globus pallidus external segment (GPe) and putamen. The extent, efficiency, and specificity of transduction was analyzed with immunohistochemistry at the light and electron microscope levels. RESULTS The GfaABC1D promoter directed the expression of tdTomato in an astrocyte-specific manner in directly or indirectly targeted regions (including both segments of the globus pallidus, putamen, subthalamic nucleus and cortex). COMPARISON WITH EXISTING METHODS Due to its small size, the GfaABC1D promoter is advantageous over other previously used glial fibrillary acidic protein-based promoter sequences, facilitating its use to drive expression of various transgenes in adeno-associated viruses (AAV) or other viral vectors. CONCLUSION GfaABC1D is an efficient promoter that selectively targets astrocytes in the monkey basal ganglia and expands the viral vector toolbox to study astrocytic functions in non-human primates.
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Affiliation(s)
- Kate S Heffernan
- Division of Neuropharmacology and Neurological Disorders, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Kazi Rahman
- Division of Neuropharmacology and Neurological Disorders, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Yoland Smith
- Division of Neuropharmacology and Neurological Disorders, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA; Udall Center of Excellence for Parkinson's Disease Research, Emory University, Atlanta, GA, USA; Department of Neurology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Adriana Galvan
- Division of Neuropharmacology and Neurological Disorders, Yerkes National Primate Research Center, Emory University, Atlanta, GA, USA; Udall Center of Excellence for Parkinson's Disease Research, Emory University, Atlanta, GA, USA; Department of Neurology, School of Medicine, Emory University, Atlanta, GA, USA.
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44
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Norton TT, Savier EL, Sedigh-Sarvestani M. DeBruyn and Casagrande manuscripts on tree shrew retinal ganglion cells as a basis for cross-species retina research. Vis Neurosci 2022; 39:E001. [PMID: 35094741 PMCID: PMC8807137 DOI: 10.1017/s0952523821000171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 12/30/2022]
Abstract
The purpose of this brief communication is to make publicly available three unpublished manuscripts on the organization of retinal ganglion cells in the tree shrew. The manuscripts were authored in 1986 by Dr. Edward DeBruyn, a PhD student in the laboratory of the late Dr. Vivien Casagrande at Vanderbilt University. As diurnal animals closely related to primates, tree shrews are ideally suited for comparative analyses of visual structures including the retina. We hope that providing this basic information in a citable form inspires other groups to pursue further characterization of the tree shrew retina using modern techniques.
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Affiliation(s)
- Thomas T. Norton
- Department of Optometry and Vision Science, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Elise L. Savier
- Department of Biology, University of Virginia, Charlottesville, Virginia, USA
| | - Madineh Sedigh-Sarvestani
- Functional Architecture and Development of Cerebral Cortex, Max Planck Florida Institute for Neuroscience, Jupiter, Florida, USA
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45
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Jeschke M, Ohl FW, Wang X. Effects of Cortical Cooling on Sound Processing in Auditory Cortex and Thalamus of Awake Marmosets. Front Neural Circuits 2022; 15:786740. [PMID: 35069125 PMCID: PMC8766342 DOI: 10.3389/fncir.2021.786740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/10/2021] [Indexed: 12/15/2022] Open
Abstract
The auditory thalamus is the central nexus of bottom-up connections from the inferior colliculus and top-down connections from auditory cortical areas. While considerable efforts have been made to investigate feedforward processing of sounds in the auditory thalamus (medial geniculate body, MGB) of non-human primates, little is known about the role of corticofugal feedback in the MGB of awake non-human primates. Therefore, we developed a small, repositionable cooling probe to manipulate corticofugal feedback and studied neural responses in both auditory cortex and thalamus to sounds under conditions of normal and reduced cortical temperature. Cooling-induced increases in the width of extracellularly recorded spikes in auditory cortex were observed over the distance of several hundred micrometers away from the cooling probe. Cortical neurons displayed reduction in both spontaneous and stimulus driven firing rates with decreased cortical temperatures. In thalamus, cortical cooling led to increased spontaneous firing and either increased or decreased stimulus driven activity. Furthermore, response tuning to modulation frequencies of temporally modulated sounds and spatial tuning to sound source location could be altered (increased or decreased) by cortical cooling. Specifically, best modulation frequencies of individual MGB neurons could shift either toward higher or lower frequencies based on the vector strength or the firing rate. The tuning of MGB neurons for spatial location could both sharpen or widen. Elevation preference could shift toward higher or lower elevations and azimuth tuning could move toward ipsilateral or contralateral locations. Such bidirectional changes were observed in many parameters which suggests that the auditory thalamus acts as a filter that could be adjusted according to behaviorally driven signals from auditory cortex. Future work will have to delineate the circuit elements responsible for the observed effects.
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Affiliation(s)
- Marcus Jeschke
- Laboratory of Auditory Neurophysiology, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Department Systems Physiology of Learning, Leibniz Institute for Neurobiology, Magdeburg, Germany,Auditory Neuroscience and Optogenetics Group, Cognitive Hearing in Primates Laboratory, German Primate Center-Leibniz Institute for Primate Research, Göttingen, Germany,*Correspondence: Marcus Jeschke
| | - Frank W. Ohl
- Department Systems Physiology of Learning, Leibniz Institute for Neurobiology, Magdeburg, Germany,Institute of Biology, Otto-von-Guericke-University Magdeburg, Magdeburg, Germany,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Xiaoqin Wang
- Laboratory of Auditory Neurophysiology, Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States,Xiaoqin Wang
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46
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Graßhoff H, Müller-Fielitz H, Dogbevia GK, Körbelin J, Bannach J, Vahldieck CM, Kusche-Vihrog K, Jöhren O, Müller OJ, Nogueiras R, Prevot V, Schwaninger M. Short regulatory DNA sequences to target brain endothelial cells for gene therapy. J Cereb Blood Flow Metab 2022; 42:104-120. [PMID: 34427142 PMCID: PMC8721777 DOI: 10.1177/0271678x211039617] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Gene vectors targeting CNS endothelial cells allow to manipulate the blood-brain barrier and to correct genetic defects in the CNS. Because vectors based on the adeno-associated virus (AAV) have a limited capacity, it is essential that the DNA sequence controlling gene expression is short. In addition, it must be specific for endothelial cells to avoid off-target effects. To develop improved regulatory sequences with selectivity for brain endothelial cells, we tested the transcriptional activity of truncated promoters of eleven (brain) endothelial-specific genes in combination with short regulatory elements, i.e., the woodchuck post-transcriptional regulatory element (W), the CMV enhancer element (C), and a fragment of the first intron of the Tie2 gene (S), by transfecting brain endothelial cells of three species. Four combinations of regulatory elements and short promoters (Cdh5, Ocln, Slc2a1, and Slco1c1) progressed through this in-vitro pipeline displaying suitable activity. When tested in mice, the regulatory sequences C-Ocln-W and C-Slc2a1-S-W enabled a stronger and more specific gene expression in brain endothelial cells than the frequently used CAG promoter. In summary, the new regulatory elements efficiently control gene expression in brain endothelial cells and may help to specifically target the blood-brain barrier with gene therapy vectors.
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Affiliation(s)
- Hanna Graßhoff
- Institute for Experimental and Clinical Pharmacology and Toxicology, Center of Brain, Behavior and Metabolism, University of Lübeck, Lübeck, Germany
| | - Helge Müller-Fielitz
- Institute for Experimental and Clinical Pharmacology and Toxicology, Center of Brain, Behavior and Metabolism, University of Lübeck, Lübeck, Germany
| | - Godwin K Dogbevia
- Institute for Experimental and Clinical Pharmacology and Toxicology, Center of Brain, Behavior and Metabolism, University of Lübeck, Lübeck, Germany
| | - Jakob Körbelin
- Institute for Experimental and Clinical Pharmacology and Toxicology, Center of Brain, Behavior and Metabolism, University of Lübeck, Lübeck, Germany.,Department of Oncology, Hematology and Bone Marrow Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jacqueline Bannach
- Institute for Experimental and Clinical Pharmacology and Toxicology, Center of Brain, Behavior and Metabolism, University of Lübeck, Lübeck, Germany
| | | | | | - Olaf Jöhren
- Institute for Experimental and Clinical Pharmacology and Toxicology, Center of Brain, Behavior and Metabolism, University of Lübeck, Lübeck, Germany
| | - Oliver J Müller
- Department of Internal Medicine III (Cardiology, Angiology and Internal Intensive Care Medicine), University Hospital Schleswig-Holstein, University of Kiel, Kiel, Germany.,DZHK (German Research Centre for Cardiovascular Research), Partner Site Hamburg/Lübeck/Kiel, Lübeck, Germany
| | - Ruben Nogueiras
- Department of Physiology, CIMUS, University of Santiago de Compostela-Instituto de Investigación Sanitaria, Santiago de Compostela, Spain
| | - Vincent Prevot
- Inserm, CHU Lille, Laboratory of Development and Plasticity of the Neuroendocrine Brain, Lille Neuroscience & Cognition, UMR-S 1172, DISTALZ, European Genomic Institute for Diabetes, University of Lille, Lille, France
| | - Markus Schwaninger
- Institute for Experimental and Clinical Pharmacology and Toxicology, Center of Brain, Behavior and Metabolism, University of Lübeck, Lübeck, Germany.,DZHK (German Research Centre for Cardiovascular Research), Partner Site Hamburg/Lübeck/Kiel, Lübeck, Germany
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47
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Emerging strategies for the genetic dissection of gene functions, cell types, and neural circuits in the mammalian brain. Mol Psychiatry 2022; 27:422-435. [PMID: 34561609 DOI: 10.1038/s41380-021-01292-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 08/17/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023]
Abstract
The mammalian brain is composed of a large number of highly diverse cell types with different molecular, anatomical, and functional features. Distinct cellular identities are generated during development under the regulation of intricate genetic programs and manifested through unique combinations of gene expression. Recent advancements in our understanding of the molecular and cellular mechanisms underlying the assembly, function, and pathology of the brain circuitry depend on the invention and application of genetic strategies that engage intrinsic gene regulatory mechanisms. Here we review the strategies for gene regulation on DNA, RNA, and protein levels and their applications in cell type targeting and neural circuit dissection. We highlight newly emerged strategies and emphasize the importance of combinatorial approaches. We also discuss the potential caveats and pitfalls in current methods and suggest future prospects to improve their comprehensiveness and versatility.
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48
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Maes ME, Wögenstein GM, Colombo G, Casado-Polanco R, Siegert S. Optimizing AAV2/6 microglial targeting identified enhanced efficiency in the photoreceptor degenerative environment. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 23:210-224. [PMID: 34703843 PMCID: PMC8516996 DOI: 10.1016/j.omtm.2021.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/07/2021] [Indexed: 12/13/2022]
Abstract
Adeno-associated viruses (AAVs) are widely used to deliver genetic material in vivo to distinct cell types such as neurons or glial cells, allowing for targeted manipulation. Transduction of microglia is mostly excluded from this strategy, likely due to the cells’ heterogeneous state upon environmental changes, which makes AAV design challenging. Here, we established the retina as a model system for microglial AAV validation and optimization. First, we show that AAV2/6 transduced microglia in both synaptic layers, where layer preference corresponds to the intravitreal or subretinal delivery method. Surprisingly, we observed significantly enhanced microglial transduction during photoreceptor degeneration. Thus, we modified the AAV6 capsid to reduce heparin binding by introducing four point mutations (K531E, R576Q, K493S, and K459S), resulting in increased microglial transduction in the outer plexiform layer. Finally, to improve microglial-specific transduction, we validated a Cre-dependent transgene delivery cassette for use in combination with the Cx3cr1CreERT2 mouse line. Together, our results provide a foundation for future studies optimizing AAV-mediated microglia transduction and highlight that environmental conditions influence microglial transduction efficiency.
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Affiliation(s)
- Margaret E Maes
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | | | - Gloria Colombo
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
| | | | - Sandra Siegert
- Institute of Science and Technology (IST) Austria, 3400 Klosterneuburg, Austria
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49
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Nano PR, Nguyen CV, Mil J, Bhaduri A. Cortical Cartography: Mapping Arealization Using Single-Cell Omics Technology. Front Neural Circuits 2021; 15:788560. [PMID: 34955761 PMCID: PMC8707733 DOI: 10.3389/fncir.2021.788560] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/05/2021] [Indexed: 11/30/2022] Open
Abstract
The cerebral cortex derives its cognitive power from a modular network of specialized areas processing a multitude of information. The assembly and organization of these regions is vital for human behavior and perception, as evidenced by the prevalence of area-specific phenotypes that manifest in neurodevelopmental and psychiatric disorders. Generations of scientists have examined the architecture of the human cortex, but efforts to capture the gene networks which drive arealization have been hampered by the lack of tractable models of human neurodevelopment. Advancements in "omics" technologies, imaging, and computational power have enabled exciting breakthroughs into the molecular and structural characteristics of cortical areas, including transcriptomic, epigenomic, metabolomic, and proteomic profiles of mammalian models. Here we review the single-omics atlases that have shaped our current understanding of cortical areas, and their potential to fuel a new era of multi-omic single-cell endeavors to interrogate both the developing and adult human cortex.
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Affiliation(s)
| | | | | | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
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50
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Botto C, Dalkara D, El-Amraoui A. Progress in Gene Editing Tools and Their Potential for Correcting Mutations Underlying Hearing and Vision Loss. Front Genome Ed 2021; 3:737632. [PMID: 34778871 PMCID: PMC8581640 DOI: 10.3389/fgeed.2021.737632] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/14/2021] [Indexed: 12/12/2022] Open
Abstract
Blindness and deafness are the most frequent sensory disorders in humans. Whatever their cause - genetic, environmental, or due to toxic agents, or aging - the deterioration of these senses is often linked to irreversible damage to the light-sensing photoreceptor cells (blindness) and/or the mechanosensitive hair cells (deafness). Efforts are increasingly focused on preventing disease progression by correcting or replacing the blindness and deafness-causal pathogenic alleles. In recent years, gene replacement therapies for rare monogenic disorders of the retina have given positive results, leading to the marketing of the first gene therapy product for a form of childhood hereditary blindness. Promising results, with a partial restoration of auditory function, have also been reported in preclinical models of human deafness. Silencing approaches, including antisense oligonucleotides, adeno-associated virus (AAV)-mediated microRNA delivery, and genome-editing approaches have also been applied to various genetic forms of blindness and deafness The discovery of new DNA- and RNA-based CRISPR/Cas nucleases, and the new generations of base, prime, and RNA editors offers new possibilities for directly repairing point mutations and therapeutically restoring gene function. Thanks to easy access and immune-privilege status of self-contained compartments, the eye and the ear continue to be at the forefront of developing therapies for genetic diseases. Here, we review the ongoing applications and achievements of this new class of emerging therapeutics in the sensory organs of vision and hearing, highlighting the challenges ahead and the solutions to be overcome for their successful therapeutic application in vivo.
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Affiliation(s)
- Catherine Botto
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Deniz Dalkara
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Aziz El-Amraoui
- Unit Progressive Sensory Disorders, Pathophysiology and Therapy, Institut Pasteur, Institut de l'Audition, Université de Paris, INSERM-UMRS1120, Paris, France
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