1
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Sahel JA, Banin E, Bennett J, Duncan JL, Roska B. Retinal Disorders. Cold Spring Harb Perspect Med 2024:a041728. [PMID: 38565268 DOI: 10.1101/cshperspect.a041728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Retinal disorders caused by genetic or environmental factors cause severe visual impairment and often result in blindness. The past ten years have seen rapid progress in our understanding of the biological basis of these conditions, as well as significant advances towards gene and cell-based therapies. Regulatory challenges remain, but there is reason to hope that creative approaches will lead to safe and effective breakthrough treatments for these conditions in the near future.
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Affiliation(s)
- José-Alain Sahel
- The UPMC Vision Institute, University of Pittsburgh, Pittsburgh, Pennsylvania 15219, USA
| | - Eyal Banin
- Division of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Jean Bennett
- Center for Advanced Retinal and Ocular Therapeutics, 309C Stellar-Chance Labs, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Jacque L Duncan
- Department of Ophthalmology, University of California, San Francisco, California 94143, USA
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland
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2
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [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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3
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Busskamp V, Roska B, Sahel JA. Optogenetic Vision Restoration. Cold Spring Harb Perspect Med 2023:a041660. [PMID: 37734866 DOI: 10.1101/cshperspect.a041660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Optogenetics has emerged over the past 20 years as a powerful tool to investigate the various circuits underlying numerous functions, especially in neuroscience. The ability to control by light the activity of neurons has enabled the development of therapeutic strategies aimed at restoring some level of vision in blinding retinal conditions. Promising preclinical and initial clinical data support such expectations. Numerous challenges remain to be tackled (e.g., confirmation of safety, cell and circuit specificity, patterns, intensity and mode of stimulation, rehabilitation programs) on the path toward useful vision restoration.
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Affiliation(s)
- Volker Busskamp
- Degenerative Retinal Diseases, University Hospital Bonn, 53127 Bonn, Germany
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4001 Basel, Switzerland
| | - Jose-Alain Sahel
- Department of Ophthalmology, UPMC Vision Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
- Institut Hospitalo-Universitaire FOReSIGHT, Sorbonne Universite, Inserm, Quinze-Vingts Hopital de la Vision, 75012 Paris, France
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4
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Cadoni S, Demené C, Alcala I, Provansal M, Nguyen D, Nelidova D, Labernède G, Lubetzki J, Goulet R, Burban E, Dégardin J, Simonutti M, Gauvain G, Arcizet F, Marre O, Dalkara D, Roska B, Sahel JA, Tanter M, Picaud S. Ectopic expression of a mechanosensitive channel confers spatiotemporal resolution to ultrasound stimulations of neurons for visual restoration. Nat Nanotechnol 2023; 18:667-676. [PMID: 37012508 DOI: 10.1038/s41565-023-01359-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Remote and precisely controlled activation of the brain is a fundamental challenge in the development of brain-machine interfaces for neurological treatments. Low-frequency ultrasound stimulation can be used to modulate neuronal activity deep in the brain, especially after expressing ultrasound-sensitive proteins. But so far, no study has described an ultrasound-mediated activation strategy whose spatiotemporal resolution and acoustic intensity are compatible with the mandatory needs of brain-machine interfaces, particularly for visual restoration. Here we combined the expression of large-conductance mechanosensitive ion channels with uncustomary high-frequency ultrasonic stimulation to activate retinal or cortical neurons over millisecond durations at a spatiotemporal resolution and acoustic energy deposit compatible with vision restoration. The in vivo sonogenetic activation of the visual cortex generated a behaviour associated with light perception. Our findings demonstrate that sonogenetics can deliver millisecond pattern presentations via an approach less invasive than current brain-machine interfaces for visual restoration.
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Affiliation(s)
- Sara Cadoni
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Charlie Demené
- Physics for Medicine Paris, INSERM, CNRS, École Supérieure de Physique et de Chimie Industrielles (ESPCI Paris), Paris Sciences et Lettres (PSL) Research University, Paris, France
| | - Ignacio Alcala
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Diep Nguyen
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Dasha Nelidova
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | | | - Jules Lubetzki
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Ruben Goulet
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Emma Burban
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Julie Dégardin
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Manuel Simonutti
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Gregory Gauvain
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Fabrice Arcizet
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Olivier Marre
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Deniz Dalkara
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - José Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Ophthalmology and Vitreo-Retinal Diseases, Fondation Ophtalmologique Rothschild, Paris, France
- Centre Hospitalier National d'Ophtalmologie des XV-XX, Paris, France
| | - Mickael Tanter
- Physics for Medicine Paris, INSERM, CNRS, École Supérieure de Physique et de Chimie Industrielles (ESPCI Paris), Paris Sciences et Lettres (PSL) Research University, Paris, France
| | - Serge Picaud
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.
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5
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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: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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Bucci A, Diggelmann R, Znidaric M, De Gennaro M, Cowan C, Roska B, Hierlemann A, Franke F. Propagation speeds of action potentials in the human retina compensate for traveling distances. J Vis 2022. [DOI: 10.1167/jov.22.14.3588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Annalisa Bucci
- ETH Zürich
- Institute of Molecular and Clinical Ophthalmology Basel
| | | | - Matej Znidaric
- ETH Zürich
- Institute of Molecular and Clinical Ophthalmology Basel
| | | | - Cameron Cowan
- Institute of Molecular and Clinical Ophthalmology Basel
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel
| | | | - Felix Franke
- Institute of Molecular and Clinical Ophthalmology Basel
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Brunner C, Grillet M, Urban A, Roska B, Montaldo G, Macé E. Whole-brain functional ultrasound imaging in awake head-fixed mice. Nat Protoc 2021; 16:3547-3571. [PMID: 34089019 DOI: 10.1038/s41596-021-00548-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/30/2021] [Indexed: 12/13/2022]
Abstract
Most brain functions engage a network of distributed regions. Full investigation of these functions thus requires assessment of whole brains; however, whole-brain functional imaging of behaving animals remains challenging. This protocol describes how to follow brain-wide activity in awake head-fixed mice using functional ultrasound imaging, a method that tracks cerebral blood volume dynamics. We describe how to set up a functional ultrasound imaging system with a provided acquisition software (miniScan), establish a chronic cranial window (timing surgery: ~3-4 h) and image brain-wide activity associated with a stimulus at high resolution (100 × 110 × 300 µm and 10 Hz per brain slice, which takes ~45 min per imaging session). We include codes that enable data to be registered to a reference atlas, production of 3D activity maps, extraction of the activity traces of ~250 brain regions and, finally, combination of data from multiple sessions (timing analysis averages ~2 h). This protocol enables neuroscientists to observe global brain processes in mice.
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Affiliation(s)
- Clément Brunner
- Neuro-Electronics Research Flanders, Leuven, Belgium
- VIB, Leuven, Belgium
- Imec, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Micheline Grillet
- Neuro-Electronics Research Flanders, Leuven, Belgium
- VIB, Leuven, Belgium
- Imec, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Alan Urban
- Neuro-Electronics Research Flanders, Leuven, Belgium
- VIB, Leuven, Belgium
- Imec, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- University of Basel, Basel, Switzerland
- NCCR Molecular Systems Engineering, Basel, Switzerland
| | - Gabriel Montaldo
- Neuro-Electronics Research Flanders, Leuven, Belgium.
- VIB, Leuven, Belgium.
- Imec, Leuven, Belgium.
- Department of Neurosciences, KU Leuven, Leuven, Belgium.
| | - Emilie Macé
- Brain-Wide Circuits for Behavior Lab, Max Planck Institute of Neurobiology, Martinsried, Germany.
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9
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Cowan CS, Renner M, De Gennaro M, Gross-Scherf B, Goldblum D, Hou Y, Munz M, Rodrigues TM, Krol J, Szikra T, Cuttat R, Waldt A, Papasaikas P, Diggelmann R, Patino-Alvarez CP, Galliker P, Spirig SE, Pavlinic D, Gerber-Hollbach N, Schuierer S, Srdanovic A, Balogh M, Panero R, Kusnyerik A, Szabo A, Stadler MB, Orgül S, Picelli S, Hasler PW, Hierlemann A, Scholl HPN, Roma G, Nigsch F, Roska B. Cell Types of the Human Retina and Its Organoids at Single-Cell Resolution. Cell 2021; 182:1623-1640.e34. [PMID: 32946783 PMCID: PMC7505495 DOI: 10.1016/j.cell.2020.08.013] [Citation(s) in RCA: 287] [Impact Index Per Article: 95.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 06/14/2020] [Accepted: 08/06/2020] [Indexed: 01/05/2023]
Abstract
Human organoids recapitulating the cell-type diversity and function of their target organ are valuable for basic and translational research. We developed light-sensitive human retinal organoids with multiple nuclear and synaptic layers and functional synapses. We sequenced the RNA of 285,441 single cells from these organoids at seven developmental time points and from the periphery, fovea, pigment epithelium and choroid of light-responsive adult human retinas, and performed histochemistry. Cell types in organoids matured in vitro to a stable "developed" state at a rate similar to human retina development in vivo. Transcriptomes of organoid cell types converged toward the transcriptomes of adult peripheral retinal cell types. Expression of disease-associated genes was cell-type-specific in adult retina, and cell-type specificity was retained in organoids. We implicate unexpected cell types in diseases such as macular degeneration. This resource identifies cellular targets for studying disease mechanisms in organoids and for targeted repair in human retinas.
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Affiliation(s)
- Cameron S Cowan
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Magdalena Renner
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Martina De Gennaro
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Brigitte Gross-Scherf
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - David Goldblum
- Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Yanyan Hou
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Martin Munz
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Tiago M Rodrigues
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Jacek Krol
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Tamas Szikra
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Rachel Cuttat
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Annick Waldt
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Panagiotis Papasaikas
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Roland Diggelmann
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering of ETH Zurich, 4058 Basel, Switzerland
| | - Claudia P Patino-Alvarez
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Patricia Galliker
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Stefan E Spirig
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Dinko Pavlinic
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | | | - Sven Schuierer
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Aldin Srdanovic
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Marton Balogh
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Riccardo Panero
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Akos Kusnyerik
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, Semmelweis University, 1085 Budapest, Hungary
| | - Arnold Szabo
- Department of Anatomy, Histology and Embryology, Semmelweis University, 1085 Budapest, Hungary
| | - Michael B Stadler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Selim Orgül
- Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Simone Picelli
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Pascal W Hasler
- Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Andreas Hierlemann
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering of ETH Zurich, 4058 Basel, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland; Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Guglielmo Roma
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Florian Nigsch
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland.
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10
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Sahel JA, Bennett J, Roska B. Depicting brighter possibilities for treating blindness. Sci Transl Med 2020; 11:11/494/eaax2324. [PMID: 31142676 DOI: 10.1126/scitranslmed.aax2324] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 05/09/2019] [Indexed: 12/25/2022]
Abstract
Advances in preclinical research are now being translated into innovative clinical solutions for blindness.
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Affiliation(s)
- José-Alain Sahel
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA. .,Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France.,CHNO des Quinze-Vingts, INSERM-DGOS CIC 1423, 28 rue de Charenton, F-75012 Paris, France.,Fondation Ophtalmologique Rothschild, 29 rue Manin, F-75019 Paris, France
| | - Jean Bennett
- Center for Advanced Retinal and Ocular Therapeutics, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland. .,University of Basel, Basel, Switzerland.,Friedrich Miescher Institute, Basel, Switzerland
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11
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Nelidova D, Morikawa RK, Cowan CS, Raics Z, Goldblum D, Scholl HPN, Szikra T, Szabo A, Hillier D, Roska B. Restoring light sensitivity using tunable near-infrared sensors. Science 2020; 368:1108-1113. [DOI: 10.1126/science.aaz5887] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 04/09/2020] [Indexed: 12/29/2022]
Abstract
Enabling near-infrared light sensitivity in a blind human retina may supplement or restore visual function in patients with regional retinal degeneration. We induced near-infrared light sensitivity using gold nanorods bound to temperature-sensitive engineered transient receptor potential (TRP) channels. We expressed mammalian or snake TRP channels in light-insensitive retinal cones in a mouse model of retinal degeneration. Near-infrared stimulation increased activity in cones, ganglion cell layer neurons, and cortical neurons, and enabled mice to perform a learned light-driven behavior. We tuned responses to different wavelengths, by using nanorods of different lengths, and to different radiant powers, by using engineered channels with different temperature thresholds. We targeted TRP channels to human retinas, which allowed the postmortem activation of different cell types by near-infrared light.
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Affiliation(s)
- Dasha Nelidova
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Rei K. Morikawa
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Cameron S. Cowan
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Zoltan Raics
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - David Goldblum
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Hendrik P. N. Scholl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Tamas Szikra
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Arnold Szabo
- Department of Anatomy, Semmelweis University, Budapest, Hungary
| | - Daniel Hillier
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Deutsches Primatzentrum, Leibniz Institute for Primate Research, Göttingen, Germany
- Research Centre for Natural Sciences, Budapest, Hungary
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
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12
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Traber GL, Della Volpe-Waizel M, Maloca P, Schmidt-Erfurth U, Rubin G, Roska B, Cordeiro MF, Otto T, Weleber R, Lesmes LA, Arleo A, Scholl HPN. New Technologies for Outcome Measures in Glaucoma: Review by the European Vision Institute Special Interest Focus Group. Ophthalmic Res 2020; 63:88-96. [PMID: 31935739 DOI: 10.1159/000504892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/19/2019] [Indexed: 11/19/2022]
Abstract
Glaucoma is the leading cause of irreversible blindness worldwide, with an increasing prevalence. The complexity of the disease has been a major challenge in moving the field forward with regard to both pathophysiological insight and treatment. In this context, discussing possible outcome measures in glaucoma trials is of utmost importance and clinical relevance. A recent meeting of the European Vision Institute (EVI) special interest focus group was held on "New Technologies for Outcome Measures in Retina and Glaucoma," addressing both functional and structural outcomes, as well as translational hot topics in glaucoma and retina research. In conjunction with the published literature, this review summarizes the meeting focusing on glaucoma.
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Affiliation(s)
- Ghislaine L Traber
- Department of Ophthalmology, University Hospital Basel, University of Basel, Basel, Switzerland.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
| | - Maria Della Volpe-Waizel
- Department of Ophthalmology, University Hospital Basel, University of Basel, Basel, Switzerland.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
| | - Peter Maloca
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
| | | | - Gary Rubin
- Institute of Ophthalmology, UCL University College London, London, United Kingdom
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
| | - M Francesca Cordeiro
- Institute of Ophthalmology, UCL University College London, London, United Kingdom.,Western Eye Hospital, Imperial College Healthcare NHS Trust, London, United Kingdom.,Imperial College Ophthalmic Research Group (ICORG), Imperial College London, London, United Kingdom
| | - Tilman Otto
- Heidelberg Engineering GmbH, Heidelberg, Germany
| | - Richard Weleber
- Casey Eye Institute, Departments of Ophthalmology and Molecular and Medical Genetics, University of Oregon Health & Science University, Portland, Oregon, USA
| | | | - Angelo Arleo
- Institut de la Vision, CNRS, INSERM, Sorbonne Université, Paris, France
| | - Hendrik P N Scholl
- Department of Ophthalmology, University Hospital Basel, University of Basel, Basel, Switzerland, .,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland,
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13
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Voigt FF, Kirschenbaum D, Platonova E, Pagès S, Campbell RAA, Kastli R, Schaettin M, Egolf L, van der Bourg A, Bethge P, Haenraets K, Frézel N, Topilko T, Perin P, Hillier D, Hildebrand S, Schueth A, Roebroeck A, Roska B, Stoeckli ET, Pizzala R, Renier N, Zeilhofer HU, Karayannis T, Ziegler U, Batti L, Holtmaat A, Lüscher C, Aguzzi A, Helmchen F. The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue. Nat Methods 2019; 16:1105-1108. [PMID: 31527839 PMCID: PMC6824906 DOI: 10.1038/s41592-019-0554-0] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 07/31/2019] [Accepted: 08/06/2019] [Indexed: 11/09/2022]
Abstract
Light-sheet microscopy is an ideal technique for imaging large cleared samples; however, the community is still lacking instruments capable of producing volumetric images of centimeter-sized cleared samples with near-isotropic resolution within minutes. Here, we introduce the mesoscale selective plane-illumination microscopy initiative, an open-hardware project for building and operating a light-sheet microscope that addresses these challenges and is compatible with any type of cleared or expanded sample ( www.mesospim.org ).
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Affiliation(s)
- Fabian F Voigt
- Brain Research Institute, University of Zurich, Zurich, Switzerland.
- Neuroscience Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland.
| | | | - Evgenia Platonova
- Center for Microscopy and Image Analysis, University of Zurich, Zurich, Switzerland
| | - Stéphane Pagès
- Wyss Center for Bio- and Neuroengineering, Geneva, Switzerland
- Department of Basic Neurosciences, Geneva Neuroscience Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Rahel Kastli
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
| | - Martina Schaettin
- Neuroscience Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Ladan Egolf
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
| | - Alexander van der Bourg
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
| | - Philipp Bethge
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
| | - Karen Haenraets
- Neuroscience Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Noémie Frézel
- Neuroscience Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | | | - Paola Perin
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Daniel Hillier
- Hungarian Academy of Sciences Research Centre for Natural Sciences, Budapest, Hungary
- Faculty of Information Technology and Bionics, Pazmany Peter Catholic University, Budapest, Hungary
| | - Sven Hildebrand
- Faculty of Psychology & Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Anna Schueth
- Faculty of Psychology & Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Alard Roebroeck
- Faculty of Psychology & Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Botond Roska
- Friedrich Miescher Institute Basel, Basel, Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Esther T Stoeckli
- Neuroscience Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Roberto Pizzala
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Nicolas Renier
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Hanns Ulrich Zeilhofer
- Neuroscience Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Theofanis Karayannis
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
| | - Urs Ziegler
- Center for Microscopy and Image Analysis, University of Zurich, Zurich, Switzerland
| | - Laura Batti
- Wyss Center for Bio- and Neuroengineering, Geneva, Switzerland
| | - Anthony Holtmaat
- Department of Basic Neurosciences, Geneva Neuroscience Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Christian Lüscher
- Department of Basic Neurosciences, Geneva Neuroscience Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Clinic of Neurology, Department of Clinical Neurosciences, Geneva University Hospital, Geneva, Switzerland
| | | | - Fritjof Helmchen
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, ETH Zurich, Zurich, Switzerland
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14
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Schubert R, Herzog S, Trenholm S, Roska B, Müller DJ. Magnetically guided virus stamping for the targeted infection of single cells or groups of cells. Nat Protoc 2019; 14:3205-3219. [DOI: 10.1038/s41596-019-0221-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 07/02/2019] [Indexed: 01/10/2023]
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15
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Jüttner J, Szabo A, Gross-Scherf B, Morikawa RK, Rompani SB, Hantz P, Szikra T, Esposti F, Cowan CS, Bharioke A, Patino-Alvarez CP, Keles Ö, Kusnyerik A, Azoulay T, Hartl D, Krebs AR, Schübeler D, Hajdu RI, Lukats A, Nemeth J, Nagy ZZ, Wu KC, Wu RH, Xiang L, Fang XL, Jin ZB, Goldblum D, Hasler PW, Scholl HPN, Krol J, Roska B. Targeting neuronal and glial cell types with synthetic promoter AAVs in mice, non-human primates and humans. Nat Neurosci 2019; 22:1345-1356. [PMID: 31285614 DOI: 10.1038/s41593-019-0431-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 05/17/2019] [Indexed: 01/20/2023]
Abstract
Targeting genes to specific neuronal or glial cell types is valuable for both understanding and repairing brain circuits. Adeno-associated viruses (AAVs) are frequently used for gene delivery, but targeting expression to specific cell types is an unsolved problem. We created a library of 230 AAVs, each with a different synthetic promoter designed using four independent strategies. We show that a number of these AAVs specifically target expression to neuronal and glial cell types in the mouse and non-human primate retina in vivo and in the human retina in vitro. We demonstrate applications for recording and stimulation, as well as the intersectional and combinatorial labeling of cell types. These resources and approaches allow economic, fast and efficient cell-type targeting in a variety of species, both for fundamental science and for gene therapy.
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Affiliation(s)
- Josephine Jüttner
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Arnold Szabo
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Brigitte Gross-Scherf
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Rei K Morikawa
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Santiago B Rompani
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Monterotondo, Italy
| | - Peter Hantz
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Tamas Szikra
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Federico Esposti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Division of Neuroscience, San Raffaele Research Institute, Università Vita-Salute San Raffaele, Milan, Italy
| | - Cameron S Cowan
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Arjun Bharioke
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Claudia P Patino-Alvarez
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Özkan Keles
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Akos Kusnyerik
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | | | - Dominik Hartl
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Arnaud R Krebs
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Rozina I Hajdu
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Akos Lukats
- Department of Anatomy, Histology and Embryology, Semmelweis University, Budapest, Hungary
| | - Janos Nemeth
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Zoltan Z Nagy
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Kun-Chao Wu
- Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory of Ophthalmology, Optometry and Visual Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou, China
| | - Rong-Han Wu
- Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory of Ophthalmology, Optometry and Visual Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou, China
| | - Lue Xiang
- Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory of Ophthalmology, Optometry and Visual Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou, China
| | - Xiao-Long Fang
- Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory of Ophthalmology, Optometry and Visual Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou, China
| | - Zi-Bing Jin
- Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, State Key Laboratory of Ophthalmology, Optometry and Visual Science, National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou, China
| | - David Goldblum
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Pascal W Hasler
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Jacek Krol
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland.
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland.
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16
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Della Volpe-Waizel M, Traber GL, Maloca P, Zinkernagel M, Schmidt-Erfurth U, Rubin G, Roska B, Otto T, Weleber RG, Scholl HPN. New Technologies for Outcome Measures in Retinal Disease: Review from the European Vision Institute Special Interest Focus Group. Ophthalmic Res 2019; 63:77-87. [PMID: 31352462 DOI: 10.1159/000501887] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/03/2019] [Indexed: 01/03/2023]
Abstract
Novel diagnostic tools to measure retinal function and structure are rapidly being developed and introduced into clinical use. Opportunities exist to use these informative and robust measures as endpoints for clinical trials to determine efficacy and to monitor safety of therapeutic interventions. In order to inform researchers and clinician-scientists about these new diagnostic tools, a workshop was organized by the European Vision Institute. Invited speakers highlighted the recent advances in state-of-the-art technologies for outcome measures in the field of retina. This review highlights the workshop's presentations in the context of published literature.
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Affiliation(s)
- Maria Della Volpe-Waizel
- Department of Ophthalmology, University of Basel, Basel, Switzerland.,Institute of Molecular and Clinical Ophthalmology (IOB), Basel, Switzerland
| | - Ghislaine L Traber
- Department of Ophthalmology, University of Basel, Basel, Switzerland.,Institute of Molecular and Clinical Ophthalmology (IOB), Basel, Switzerland
| | - Peter Maloca
- Institute of Molecular and Clinical Ophthalmology (IOB), Basel, Switzerland
| | - Martin Zinkernagel
- Department of Ophthalmology and Department of Clinical Research, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | | | - Gary Rubin
- UCL University College London, Institute of Ophthalmology, London, United Kingdom
| | - Botond Roska
- Institute of Molecular and Clinical Ophthalmology (IOB), Basel, Switzerland
| | - Tilman Otto
- Heidelberg Engineering GmbH, Heidelberg, Germany
| | - Richard G Weleber
- Casey Eye Institute, Departments of Ophthalmology and Molecular and Medical Genetics, University of Oregon Health and Science University, Portland, Oregon, USA
| | - Hendrik P N Scholl
- Department of Ophthalmology, University of Basel, Basel, Switzerland, .,Institute of Molecular and Clinical Ophthalmology (IOB), Basel, Switzerland,
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17
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Abstract
Dysfunction of the key sense of vision, leading to visual handicap or blindness, has a crucial effect on day-to-day life. In this commentary, I will summarize the work in my laboratory that is focused on a basic understanding of visual processing and the use of this information to understand disease mechanism and to develop correcting therapies. We are beginning to understand how cell types of the visual system interact in local circuits and compute visual information. This has brought insight into mechanisms of cell-type-specific diseases and has allowed us to design new therapies for restoring vision in genetic forms of blindness.
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Affiliation(s)
- Botond Roska
- Institute of Molecular and Clinical Ophthalmology BaselBaselSwitzerland
- University of BaselBaselSwitzerland
- Friedrich Miescher InstituteBaselSwitzerland
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18
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Walters S, Schwarz C, Sharma R, Rossi EA, Fischer WS, DiLoreto DA, Strazzeri J, Nelidova D, Roska B, Hunter JJ, Williams DR, Merigan WH. Cellular-scale evaluation of induced photoreceptor degeneration in the living primate eye. Biomed Opt Express 2019; 10:66-82. [PMID: 30775083 PMCID: PMC6363191 DOI: 10.1364/boe.10.000066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 05/06/2023]
Abstract
Progress is needed in developing animal models of photoreceptor degeneration and evaluating such models with longitudinal, noninvasive techniques. We employ confocal scanning laser ophthalmoscopy, optical coherence tomography (OCT) and high-resolution retinal imaging to noninvasively observe the retina of non-human primates with induced photoreceptor degeneration. Photoreceptors were imaged at the single-cell scale in three modalities of adaptive optics scanning light ophthalmoscopy: traditional confocal reflectance, indicative of waveguiding; a non-confocal offset aperture technique visualizing scattered light; and two-photon excited fluorescence, the time-varying signal of which, at 730 nm excitation, is representative of visual cycle function. Assessment of photoreceptor structure and function using these imaging modalities revealed a reduction in retinoid production in cone photoreceptor outer segments while inner segments appeared to remain present. Histology of one retina confirmed loss of outer segments and the presence of intact inner segments. This unique combination of imaging modalities can provide essential, clinically-relevant information on both the structural integrity and function of photoreceptors to not only validate models of photoreceptor degeneration but potentially evaluate the efficacy of future cell and gene-based therapies for vision restoration.
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Affiliation(s)
- Sarah Walters
- The Institute of Optics, University of Rochester, Rochester, NY, USA
- Center for Visual Science, University of Rochester, Rochester, NY, USA
| | - Christina Schwarz
- Center for Visual Science, University of Rochester, Rochester, NY, USA
- Currently with the Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Robin Sharma
- The Institute of Optics, University of Rochester, Rochester, NY, USA
- Center for Visual Science, University of Rochester, Rochester, NY, USA
- Currently with Facebook Reality Labs, Redmond, WA, USA
| | - Ethan A. Rossi
- Center for Visual Science, University of Rochester, Rochester, NY, USA
- Currently with the Departments of Ophthalmology & Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Jennifer Strazzeri
- Center for Visual Science, University of Rochester, Rochester, NY, USA
- Flaum Eye Institute, University of Rochester, Rochester, NY, USA
| | - Dasha Nelidova
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Botond Roska
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jennifer J. Hunter
- The Institute of Optics, University of Rochester, Rochester, NY, USA
- Center for Visual Science, University of Rochester, Rochester, NY, USA
- Flaum Eye Institute, University of Rochester, Rochester, NY, USA
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, USA
| | - David R. Williams
- The Institute of Optics, University of Rochester, Rochester, NY, USA
- Center for Visual Science, University of Rochester, Rochester, NY, USA
- Flaum Eye Institute, University of Rochester, Rochester, NY, USA
| | - William H. Merigan
- Center for Visual Science, University of Rochester, Rochester, NY, USA
- Flaum Eye Institute, University of Rochester, Rochester, NY, USA
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19
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Drinnenberg A, Franke F, Morikawa RK, Jüttner J, Hillier D, Hantz P, Hierlemann A, Azeredo da Silveira R, Roska B. How Diverse Retinal Functions Arise from Feedback at the First Visual Synapse. Neuron 2018; 99:117-134.e11. [PMID: 29937281 PMCID: PMC6101199 DOI: 10.1016/j.neuron.2018.06.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/20/2018] [Accepted: 06/01/2018] [Indexed: 11/21/2022]
Abstract
Many brain regions contain local interneurons of distinct types. How does an interneuron type contribute to the input-output transformations of a given brain region? We addressed this question in the mouse retina by chemogenetically perturbing horizontal cells, an interneuron type providing feedback at the first visual synapse, while monitoring the light-driven spiking activity in thousands of ganglion cells, the retinal output neurons. We uncovered six reversible perturbation-induced effects in the response dynamics and response range of ganglion cells. The effects were enhancing or suppressive, occurred in different response epochs, and depended on the ganglion cell type. A computational model of the retinal circuitry reproduced all perturbation-induced effects and led us to assign specific functions to horizontal cells with respect to different ganglion cell types. Our combined experimental and theoretical work reveals how a single interneuron type can differentially shape the dynamical properties of distinct output channels of a brain region.
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Affiliation(s)
- Antonia Drinnenberg
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, 4003 Basel, Switzerland
| | - Felix Franke
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering of ETH Zurich, 4058 Basel, Switzerland
| | - Rei K Morikawa
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Josephine Jüttner
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Daniel Hillier
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Peter Hantz
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Andreas Hierlemann
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering of ETH Zurich, 4058 Basel, Switzerland
| | - Rava Azeredo da Silveira
- Department of Physics, Ecole Normale Supérieure, 75005 Paris, France; Laboratoire de Physique Statistique, École Normale Supérieure, PSL Research University; Université Paris Diderot Sorbonne Paris-Cité; Sorbonne Universités UPMC Univ Paris 06; CNRS, 75005 Paris, France; Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA.
| | - Botond Roska
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland.
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20
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Scholl HPN, Strauss RW, Singh MS, Dalkara D, Roska B, Picaud S, Sahel JA. Emerging therapies for inherited retinal degeneration. Sci Transl Med 2017; 8:368rv6. [PMID: 27928030 DOI: 10.1126/scitranslmed.aaf2838] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 11/17/2016] [Indexed: 12/13/2022]
Abstract
Inherited retinal degenerative diseases, a genetically and phenotypically heterogeneous group of disorders, affect the function of photoreceptor cells and are among the leading causes of blindness. Recent advances in molecular genetics and cell biology are elucidating the pathophysiological mechanisms underlying these disorders and are helping to identify new therapeutic approaches, such as gene therapy, stem cell therapy, and optogenetics. Several of these approaches have entered the clinical phase of development. Artificial replacement of dying photoreceptor cells using retinal prostheses has received regulatory approval. Precise retinal imaging and testing of visual function are facilitating more efficient clinical trial design. In individual patients, disease stage will determine whether the therapeutic strategy should comprise photoreceptor cell rescue to delay or arrest vision loss or retinal replacement for vision restoration.
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Affiliation(s)
- Hendrik P N Scholl
- Department of Ophthalmology, University of Basel, 4056 Basel, Switzerland. .,Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Rupert W Strauss
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD 21287, USA.,Moorfields Eye Hospital, London EC1V 2PD, U.K.,UCL Institute of Ophthalmology, University College London, London EC1V 9EL, U.K.,Department of Ophthalmology, Medical University Graz, Graz, Austria.,Department of Ophthalmology, Johannes Kepler University Linz, 4021 Linz, Austria
| | - Mandeep S Singh
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Deniz Dalkara
- INSERM, UMR S 968, 75012 Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Institut de la Vision, Paris, France.,CNRS, UMR 7210, 75012 Paris, France
| | - Botond Roska
- Department of Ophthalmology, University of Basel, 4056 Basel, Switzerland.,Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Serge Picaud
- INSERM, UMR S 968, 75012 Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Institut de la Vision, Paris, France.,CNRS, UMR 7210, 75012 Paris, France
| | - José-Alain Sahel
- INSERM, UMR S 968, 75012 Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, Institut de la Vision, Paris, France.,CNRS, UMR 7210, 75012 Paris, France.,Fondation Ophtalmologique Adolphe de Rothschild, 75019 Paris, France.,Centre d'Investigation Clinique 1423, INSERM-Center Hospitalier National d'Ophtalmologie des Quinze-Vingts, 75012 Paris, France.,Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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21
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Schubert R, Trenholm S, Balint K, Kosche G, Cowan CS, Mohr MA, Munz M, Martinez-Martin D, Fläschner G, Newton R, Krol J, Scherf BG, Yonehara K, Wertz A, Ponti A, Ghanem A, Hillier D, Conzelmann KK, Müller DJ, Roska B. Virus stamping for targeted single-cell infection in vitro and in vivo. Nat Biotechnol 2017; 36:81-88. [DOI: 10.1038/nbt.4034] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/13/2017] [Indexed: 11/09/2022]
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22
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Hartl D, Krebs AR, Jüttner J, Roska B, Schübeler D. Cis-regulatory landscapes of four cell types of the retina. Nucleic Acids Res 2017; 45:11607-11621. [PMID: 29059322 PMCID: PMC5714137 DOI: 10.1093/nar/gkx923] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/28/2017] [Accepted: 10/02/2017] [Indexed: 12/18/2022] Open
Abstract
The retina is composed of ∼50 cell-types with specific functions for the process of vision. Identification of the cis-regulatory elements active in retinal cell-types is key to elucidate the networks controlling this diversity. Here, we combined transcriptome and epigenome profiling to map the regulatory landscape of four cell-types isolated from mouse retinas including rod and cone photoreceptors as well as rare inter-neuron populations such as horizontal and starburst amacrine cells. Integration of this information reveals sequence determinants and candidate transcription factors for controlling cellular specialization. Additionally, we refined parallel reporter assays to enable studying the transcriptional activity of large collection of sequences in individual cell-types isolated from a tissue. We provide proof of concept for this approach and its scalability by characterizing the transcriptional capacity of several hundred putative regulatory sequences within individual retinal cell-types. This generates a catalogue of cis-regulatory regions active in retinal cell types and we further demonstrate their utility as potential resource for cellular tagging and manipulation.
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Affiliation(s)
- Dominik Hartl
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
- University of Basel, Faculty of Sciences, Petersplatz 1, CH 4003 Basel, Switzerland
| | - Arnaud R. Krebs
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
| | - Josephine Jüttner
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
| | - Botond Roska
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
- University of Basel, Department of Ophthalmology, Mittlere Strasse 91, CH 4031 Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH 4058 Basel, Switzerland
- University of Basel, Faculty of Sciences, Petersplatz 1, CH 4003 Basel, Switzerland
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23
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Daum JM, Keles Ö, Holwerda SJ, Kohler H, Rijli FM, Stadler M, Roska B. The formation of the light-sensing compartment of cone photoreceptors coincides with a transcriptional switch. eLife 2017; 6:31437. [PMID: 29106373 PMCID: PMC5685475 DOI: 10.7554/elife.31437] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/03/2017] [Indexed: 11/16/2022] Open
Abstract
High-resolution daylight vision is mediated by cone photoreceptors. The molecular program responsible for the formation of their light sensor, the outer segment, is not well understood. We correlated daily changes in ultrastructure and gene expression in postmitotic mouse cones, between birth and eye opening, using serial block-face electron microscopy (EM) and RNA sequencing. Outer segments appeared rapidly at postnatal day six and their appearance coincided with a switch in gene expression. The switch affected over 14% of all expressed genes. Genes that switched off were rich in transcription factors and neurogenic genes. Those that switched on contained genes relevant for cone function. Chromatin rearrangements in enhancer regions occurred before the switch was completed, but not after. We provide a resource comprised of correlated EM, RNAseq, and ATACseq data, showing that the growth of a key compartment of a postmitotic cell involves an extensive switch in gene expression and chromatin accessibility.
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Affiliation(s)
- Janine M Daum
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Özkan Keles
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Sjoerd Jb Holwerda
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Hubertus Kohler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Filippo M Rijli
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Michael Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Swiss Insitute of Bioinformatics, Basel, Switzerland
| | - Botond Roska
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
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24
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25
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Walters S, Schwarz C, Sharma R, Fischer WS, DiLoreto D, Nelidova D, Drinnenberg A, Juettner J, Roska B, Williams DR, Hunter JJ, Merigan WH. In vivo imaging of photoreceptor structure and function in a non-human primate model of retinal degeneration. J Vis 2017. [DOI: 10.1167/17.7.53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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26
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Hillier D, Fiscella M, Drinnenberg A, Trenholm S, Rompani SB, Raics Z, Katona G, Juettner J, Hierlemann A, Rozsa B, Roska B. Causal evidence for retina-dependent and -independent visual motion computations in mouse cortex. Nat Neurosci 2017; 20:960-968. [PMID: 28530661 PMCID: PMC5490790 DOI: 10.1038/nn.4566] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 04/22/2017] [Indexed: 12/14/2022]
Abstract
How neuronal computations in the sensory periphery contribute to computations in the cortex is not well understood. We examined this question in the context of visual-motion processing in the retina and primary visual cortex (V1) of mice. We disrupted retinal direction selectivity, either exclusively along the horizontal axis using FRMD7 mutants or along all directions by ablating starburst amacrine cells, and monitored neuronal activity in layer 2/3 of V1 during stimulation with visual motion. In control mice, we found an over-representation of cortical cells preferring posterior visual motion, the dominant motion direction an animal experiences when it moves forward. In mice with disrupted retinal direction selectivity, the over-representation of posterior-motion-preferring cortical cells disappeared, and their responses at higher stimulus speeds were reduced. This work reveals the existence of two functionally distinct, sensory-periphery-dependent and -independent computations of visual motion in the cortex.
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Affiliation(s)
- Daniel Hillier
- Neural Circuits Laboratory, Friedrich Miescher Institute, Basel, Switzerland
| | - Michele Fiscella
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Antonia Drinnenberg
- Neural Circuits Laboratory, Friedrich Miescher Institute, Basel, Switzerland
| | - Stuart Trenholm
- Neural Circuits Laboratory, Friedrich Miescher Institute, Basel, Switzerland
| | - Santiago B Rompani
- Neural Circuits Laboratory, Friedrich Miescher Institute, Basel, Switzerland
| | - Zoltan Raics
- Neural Circuits Laboratory, Friedrich Miescher Institute, Basel, Switzerland
| | - Gergely Katona
- Laboratory of 3D Functional Network and Dendritic Imaging, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary.,The Faculty of Information Technology, Pázmány Péter Catholic University, Budapest, Hungary
| | - Josephine Juettner
- Neural Circuits Laboratory, Friedrich Miescher Institute, Basel, Switzerland
| | - Andreas Hierlemann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Balazs Rozsa
- Laboratory of 3D Functional Network and Dendritic Imaging, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
| | - Botond Roska
- Neural Circuits Laboratory, Friedrich Miescher Institute, Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
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27
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Rompani SB, Müllner FE, Wanner A, Zhang C, Roth CN, Yonehara K, Roska B. Different Modes of Visual Integration in the Lateral Geniculate Nucleus Revealed by Single-Cell-Initiated Transsynaptic Tracing. Neuron 2017; 93:1519. [PMID: 28334614 PMCID: PMC6381445 DOI: 10.1016/j.neuron.2017.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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28
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Glangetas C, Massi L, Fois GR, Jalabert M, Girard D, Diana M, Yonehara K, Roska B, Xu C, Lüthi A, Caille S, Georges F. NMDA-receptor-dependent plasticity in the bed nucleus of the stria terminalis triggers long-term anxiolysis. Nat Commun 2017; 8:14456. [PMID: 28218243 PMCID: PMC5321732 DOI: 10.1038/ncomms14456] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 01/03/2017] [Indexed: 01/07/2023] Open
Abstract
Anxiety is controlled by multiple neuronal circuits that share robust and reciprocal connections with the bed nucleus of the stria terminalis (BNST), a key structure controlling negative emotional states. However, it remains unknown how the BNST integrates diverse inputs to modulate anxiety. In this study, we evaluated the contribution of infralimbic cortex (ILCx) and ventral subiculum/CA1 (vSUB/CA1) inputs in regulating BNST activity at the single-cell level. Using trans-synaptic tracing from single-electroporated neurons and in vivo recordings, we show that vSUB/CA1 stimulation promotes opposite forms of in vivo plasticity at the single-cell level in the anteromedial part of the BNST (amBNST). We find that an NMDA-receptor-dependent homosynaptic long-term potentiation is instrumental for anxiolysis. These findings suggest that the vSUB/CA1-driven LTP in the amBNST is involved in eliciting an appropriate response to anxiogenic context and dysfunction of this compensatory mechanism may underlie pathologic anxiety states.
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Affiliation(s)
- Christelle Glangetas
- Université de Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33076 Bordeaux, France.,Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33076 Bordeaux, France
| | - Léma Massi
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Giulia R Fois
- Centre National de la Recherche Scientifique, Neurodegeneratives Diseases Institute, UMR 5293, F-33076 Bordeaux, France
| | - Marion Jalabert
- Université de la Méditerranée UMR S901, F-13009 Aix-Marseille 2, France.,INMED, F-13009 Marseille, France
| | - Delphine Girard
- Université de Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33076 Bordeaux, France.,Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33076 Bordeaux, France.,Centre National de la Recherche Scientifique, Neurodegeneratives Diseases Institute, UMR 5293, F-33076 Bordeaux, France
| | - Marco Diana
- 'G. Minardi' Cognitive Neuroscience Laboratory, Department of Chemistry and Pharmacy, University of Sassari, 07100 Sassari, Italy
| | - Keisuke Yonehara
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Botond Roska
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Chun Xu
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Andreas Lüthi
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Stéphanie Caille
- Université de Bordeaux, Institut de Neurosciences Cognitives et Intégrative d'Aquitaine, BP31, F-33076 Bordeaux, France.,Centre National de la Recherche Scientifique, UMR 5287-Institut de Neurosciences Cognitives et Intégrative d'Aquitaine, F-33076 Bordeaux, France
| | - François Georges
- Université de Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33076 Bordeaux, France.,Centre National de la Recherche Scientifique, Interdisciplinary Institute for Neuroscience, UMR 5297, F-33076 Bordeaux, France.,Centre National de la Recherche Scientifique, Neurodegeneratives Diseases Institute, UMR 5293, F-33076 Bordeaux, France
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29
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Alsteens D, Newton R, Schubert R, Martinez-Martin D, Delguste M, Roska B, Müller DJ. Nanomechanical mapping of first binding steps of a virus to animal cells. Nat Nanotechnol 2017; 12:177-183. [PMID: 27798607 DOI: 10.1038/nnano.2016.228] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 09/18/2016] [Indexed: 05/23/2023]
Abstract
Viral infection is initiated when a virus binds to cell surface receptors. Because the cell membrane is dynamic and heterogeneous, imaging living cells and simultaneously quantifying the first viral binding events is difficult. Here, we show an atomic force and confocal microscopy set-up that allows the surface receptor landscape of cells to be imaged and the virus binding events within the first millisecond of contact with the cell to be mapped at high resolution (<50 nm). We present theoretical approaches to contour the free-energy landscape of early binding events between an engineered virus and cell surface receptors. We find that the first bond formed between the viral glycoprotein and its cognate cell surface receptor has relatively low lifetime and free energy, but this increases as additional bonds form rapidly (≤1 ms). The formation of additional bonds occurs with positive allosteric modulation and the three binding sites of the viral glycoprotein are quickly occupied. Our quantitative approach can be readily applied to study the binding of other viruses to animal cells.
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Affiliation(s)
- David Alsteens
- ETH Zürich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
- Université Catholique de Louvain, Institute of Life Sciences, 1348 Louvain-La-Neuve, Belgium
| | - Richard Newton
- ETH Zürich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
| | - Rajib Schubert
- ETH Zürich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
| | - David Martinez-Martin
- ETH Zürich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
| | - Martin Delguste
- Université Catholique de Louvain, Institute of Life Sciences, 1348 Louvain-La-Neuve, Belgium
| | - Botond Roska
- Friedrich Miescher Institute (FMI), 4058 Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4056 Basel, Switzerland
| | - Daniel J Müller
- ETH Zürich, Department of Biosystems Science and Engineering, 4058 Basel, Switzerland
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30
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Yonehara K, Roska B. "MAPseq"-uencing Long-Range Neuronal Projections. Neuron 2016; 91:945-947. [PMID: 27608754 DOI: 10.1016/j.neuron.2016.08.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kebschull et al. (2016a) describe "MAPseq," which tags individual neurons from a specific brain region with individual mRNA barcodes and sequences these barcodes in other brain regions. This allows the simultaneous mapping of long-range neuronal projections at single-cell resolution.
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Affiliation(s)
- Keisuke Yonehara
- Department of Biomedicine, Danish Research Institute of Translational Neuroscience-DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Botond Roska
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4003 Basel, Switzerland.
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31
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Affiliation(s)
- Jacek Krol
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland, and
| | - Botond Roska
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland, and.,University of Basel, Basel, Switzerland
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32
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Yue L, Weiland JD, Roska B, Humayun MS. Retinal stimulation strategies to restore vision: Fundamentals and systems. Prog Retin Eye Res 2016; 53:21-47. [DOI: 10.1016/j.preteyeres.2016.05.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 05/13/2016] [Accepted: 05/21/2016] [Indexed: 11/28/2022]
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33
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Yonehara K, Fiscella M, Drinnenberg A, Esposti F, Trenholm S, Krol J, Franke F, Scherf BG, Kusnyerik A, Müller J, Szabo A, Jüttner J, Cordoba F, Reddy AP, Németh J, Nagy ZZ, Munier F, Hierlemann A, Roska B. Congenital Nystagmus Gene FRMD7 Is Necessary for Establishing a Neuronal Circuit Asymmetry for Direction Selectivity. Neuron 2015; 89:177-93. [PMID: 26711119 PMCID: PMC4712192 DOI: 10.1016/j.neuron.2015.11.032] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/14/2015] [Accepted: 11/18/2015] [Indexed: 12/24/2022]
Abstract
Neuronal circuit asymmetries are important components of brain circuits, but the molecular pathways leading to their establishment remain unknown. Here we found that the mutation of FRMD7, a gene that is defective in human congenital nystagmus, leads to the selective loss of the horizontal optokinetic reflex in mice, as it does in humans. This is accompanied by the selective loss of horizontal direction selectivity in retinal ganglion cells and the transition from asymmetric to symmetric inhibitory input to horizontal direction-selective ganglion cells. In wild-type retinas, we found FRMD7 specifically expressed in starburst amacrine cells, the interneuron type that provides asymmetric inhibition to direction-selective retinal ganglion cells. This work identifies FRMD7 as a key regulator in establishing a neuronal circuit asymmetry, and it suggests the involvement of a specific inhibitory neuron type in the pathophysiology of a neurological disease. Video Abstract
FRMD7 is required for the horizontal optokinetic reflex in mice as in humans Horizontal direction selectivity is lost in the retina of FRMD7 mutant mice Asymmetry of inhibitory inputs to horizontal DS cells is lost in FRMD7 mutant mice FRMD7 is expressed in ChAT-expressing cells in the retina of mice and primates
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Affiliation(s)
- Keisuke Yonehara
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Michele Fiscella
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering of ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Antonia Drinnenberg
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Federico Esposti
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Stuart Trenholm
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Jacek Krol
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Felix Franke
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering of ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Brigitte Gross Scherf
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Akos Kusnyerik
- Department of Ophthalmology, Semmelweis University, Mária u. 39, 1085 Budapest, Hungary
| | - Jan Müller
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering of ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Arnold Szabo
- Department of Human Morphology and Developmental Biology, Faculty of Medicine, Semmelweis University, Tűzoltó u. 58, 1094 Budapest, Hungary
| | - Josephine Jüttner
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Francisco Cordoba
- Laboratory and Animal Services, Novartis Institute for Biomedical Research, Fabrikstrasse 28, 4056 Basel, Switzerland
| | - Ashrithpal Police Reddy
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - János Németh
- Department of Ophthalmology, Semmelweis University, Mária u. 39, 1085 Budapest, Hungary
| | - Zoltán Zsolt Nagy
- Department of Ophthalmology, Semmelweis University, Mária u. 39, 1085 Budapest, Hungary
| | - Francis Munier
- Jules-Gonin Eye Hospital, Avenue de France 15, 1000 Lausanne, Switzerland
| | - Andreas Hierlemann
- Bio Engineering Laboratory, Department of Biosystems Science and Engineering of ETH Zurich, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Botond Roska
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Department of Ophthalmology, University of Basel, Mittlere Strasse 91, 4031 Basel, Switzerland.
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Adamantidis A, Arber S, Bains JS, Bamberg E, Bonci A, Buzsáki G, Cardin JA, Costa RM, Dan Y, Goda Y, Graybiel AM, Häusser M, Hegemann P, Huguenard JR, Insel TR, Janak PH, Johnston D, Josselyn SA, Koch C, Kreitzer AC, Lüscher C, Malenka RC, Miesenböck G, Nagel G, Roska B, Schnitzer MJ, Shenoy KV, Soltesz I, Sternson SM, Tsien RW, Tsien RY, Turrigiano GG, Tye KM, Wilson RI. Optogenetics: 10 years after ChR2 in neurons--views from the community. Nat Neurosci 2015; 18:1202-12. [PMID: 26308981 DOI: 10.1038/nn.4106] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Antoine Adamantidis
- Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montréal, Canada, and the Department of Neurology, Inselspital University Hospital, University of Bern, Bern, Switzerland
| | - Silvia Arber
- Biozentrum, Department of Cell Biology, University of Basel, Basel, Switzerland, and the Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jaideep S Bains
- Department of Physiology and Pharmacology, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Antonello Bonci
- Intramural Research Program, Synaptic Plasticity Section, National Institute on Drug Abuse, Baltimore, Maryland, USA, the Solomon H. Snyder Neuroscience Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA, and in the Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - György Buzsáki
- The Neuroscience Institute, School of Medicine and Center for Neural Science, New York University, New York, New York, USA
| | - Jessica A Cardin
- Department of Neurobiology, Yale University School of Medicine, New Haven, Connecticut, USA, and at the Kavli Institute of Neuroscience, Yale University, New Haven, Connecticut, USA
| | - Rui M Costa
- Champalimaud Neuroscience Programme, Champalimaud Center for the Unknown, Lisbon, Portugal
| | - Yang Dan
- Division of Neurobiology, Department of Molecular and Cell Biology, Helen Wills Neuroscience Institute, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, USA
| | - Yukiko Goda
- RIKEN Brain Science Institute, Wako-shi, Saitama, Japan
| | - Ann M Graybiel
- McGovern Institute for Brain Research and Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Michael Häusser
- Wolfson Institute for Biomedical Research and Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - Peter Hegemann
- Institut für Biologie/Experimentelle Biophysik, Humboldt Universität zu Berlin, Berlin, Germany
| | - John R Huguenard
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Thomas R Insel
- National Institute of Mental Health, Bethesda, Maryland, USA
| | - Patricia H Janak
- Department of Psychological and Brain Sciences, Johns Hopkins University, Baltimore, Maryland, USA, and the Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland, USA
| | - Daniel Johnston
- Department of Neuroscience and Center for Learning and Memory, University of Texas at Austin, Austin, Texas, USA
| | - Sheena A Josselyn
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada, and the Departments of Psychology and Physiology and Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Christof Koch
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Anatol C Kreitzer
- The Gladstone Institutes, San Francisco, California, USA, and the Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, California, USA
| | - Christian Lüscher
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland, and the Service of Neurology, Department of Clinical Neurosciences, University Hospital of Geneva, Geneva, Switzerland
| | - Robert C Malenka
- Nancy Pritzker Laboratory, Department of Psychiatry and Behavioral Sciences, School of Medicine, Stanford University, Stanford, California, USA
| | - Gero Miesenböck
- Centre for Neural Circuits and Behaviour, University of Oxford, Tinsley Building, Mansfield Road, Oxford, UK
| | - Georg Nagel
- Institute for Molecular Plant Physiology and Biophysics, Biocenter, Julius-Maximilians-University of Würzburg, Würzburg, Germany
| | - Botond Roska
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Mark J Schnitzer
- James H. Clark Center for Biomedical Engineering and Sciences, Stanford University, Stanford, California, USA, the Howard Hughes Medical Institute, Stanford University, Stanford, California, USA, and the CNC Program, Stanford University, Stanford, California, USA
| | - Krishna V Shenoy
- Departments of Electrical Engineering, Bioengineering and Neurobiology, the Neurosciences and Bio-X Programs, the Stanford Neurosciences Institute and the Howard Hughes Medical Institute, Stanford University, Stanford, California, USA
| | - Ivan Soltesz
- Department of Neurosurgery, Stanford University, Stanford, California, USA
| | - Scott M Sternson
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Richard W Tsien
- Department of Neuroscience and Physiology, Neuroscience Institute, New York University Langone Medical Center, New York, New York, USA
| | - Roger Y Tsien
- Department of Pharmacology, Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA
| | - Gina G Turrigiano
- Department of Biology and Center for Behavioral Genomics, Brandeis University, Waltham, Massachusetts, USA
| | - Kay M Tye
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rachel I Wilson
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA
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Fiscella M, Franke F, Farrow K, Müller J, Roska B, da Silveira RA, Hierlemann A. Visual coding with a population of direction-selective neurons. J Neurophysiol 2015; 114:2485-99. [PMID: 26289471 DOI: 10.1152/jn.00919.2014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 08/13/2015] [Indexed: 11/22/2022] Open
Abstract
The brain decodes the visual scene from the action potentials of ∼20 retinal ganglion cell types. Among the retinal ganglion cells, direction-selective ganglion cells (DSGCs) encode motion direction. Several studies have focused on the encoding or decoding of motion direction by recording multiunit activity, mainly in the visual cortex. In this study, we simultaneously recorded from all four types of ON-OFF DSGCs of the rabbit retina using a microelectronics-based high-density microelectrode array (HDMEA) and decoded their concerted activity using probabilistic and linear decoders. Furthermore, we investigated how the modification of stimulus parameters (velocity, size, angle of moving object) and the use of different tuning curve fits influenced decoding precision. Finally, we simulated ON-OFF DSGC activity, based on real data, in order to understand how tuning curve widths and the angular distribution of the cells' preferred directions influence decoding performance. We found that probabilistic decoding strategies outperformed, on average, linear methods and that decoding precision was robust to changes in stimulus parameters such as velocity. The removal of noise correlations among cells, by random shuffling trials, caused a drop in decoding precision. Moreover, we found that tuning curves are broad in order to minimize large errors at the expense of a higher average error, and that the retinal direction-selective system would not substantially benefit, on average, from having more than four types of ON-OFF DSGCs or from a perfect alignment of the cells' preferred directions.
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Affiliation(s)
| | - Felix Franke
- Bio Engineering Laboratory, ETH Zurich, Basel, Switzerland
| | - Karl Farrow
- Neuro-Electronics Research Flanders IMEC, Leuven, Belgium
| | - Jan Müller
- Bio Engineering Laboratory, ETH Zurich, Basel, Switzerland
| | - Botond Roska
- Neural Circuits Laboratory, Friedrich Miescher Institute, Basel, Switzerland
| | - Rava Azeredo da Silveira
- Department of Physics, Ecole Normale Supérieure, Paris, France; and Laboratoire de Physique Statistique, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, Université Denis Diderot, Paris, France
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36
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Wertz A, Trenholm S, Yonehara K, Hillier D, Raics Z, Leinweber M, Szalay G, Ghanem A, Keller G, Rózsa B, Conzelmann KK, Roska B. PRESYNAPTIC NETWORKS. Single-cell-initiated monosynaptic tracing reveals layer-specific cortical network modules. Science 2015; 349:70-4. [PMID: 26138975 DOI: 10.1126/science.aab1687] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Individual cortical neurons can selectively respond to specific environmental features, such as visual motion or faces. How this relates to the selectivity of the presynaptic network across cortical layers remains unclear. We used single-cell-initiated, monosynaptically restricted retrograde transsynaptic tracing with rabies viruses expressing GCaMP6s to image, in vivo, the visual motion-evoked activity of individual layer 2/3 pyramidal neurons and their presynaptic networks across layers in mouse primary visual cortex. Neurons within each layer exhibited similar motion direction preferences, forming layer-specific functional modules. In one-third of the networks, the layer modules were locked to the direction preference of the postsynaptic neuron, whereas for other networks the direction preference varied by layer. Thus, there exist feature-locked and feature-variant cortical networks.
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Affiliation(s)
- Adrian Wertz
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Stuart Trenholm
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Keisuke Yonehara
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Daniel Hillier
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Zoltan Raics
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marcus Leinweber
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Gergely Szalay
- Two-Photon Imaging Center, Institute of Experimental Medicine, Hungarian Academy of Sciences, Budapest, Hungary
| | - Alexander Ghanem
- Max von Pettenkofer-Institute and Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Georg Keller
- 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
| | - Karl-Klaus Conzelmann
- Max von Pettenkofer-Institute and Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Botond Roska
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. Department of Ophthalmology, University of Basel, Basel, Switzerland.
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37
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Krol J, Krol I, Alvarez CPP, Fiscella M, Hierlemann A, Roska B, Filipowicz W. A network comprising short and long noncoding RNAs and RNA helicase controls mouse retina architecture. Nat Commun 2015; 6:7305. [PMID: 26041499 PMCID: PMC4468907 DOI: 10.1038/ncomms8305] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 04/27/2015] [Indexed: 12/25/2022] Open
Abstract
Brain regions, such as the cortex and retina, are composed of layers of uniform thickness. The molecular mechanism that controls this uniformity is not well understood. Here we show that during mouse postnatal development the timed expression of Rncr4, a retina-specific long noncoding RNA, regulates the similarly timed processing of pri-miR-183/96/182, which is repressed at an earlier developmental stage by RNA helicase Ddx3x. Shifting the timing of mature miR-183/96/182 accumulation or interfering with Ddx3x expression leads to the disorganization of retinal architecture, with the photoreceptor layer being most affected. We identify Crb1, a component of the adhesion belt between glial and photoreceptor cells, as a link between Rncr4-regulated miRNA metabolism and uniform retina layering. Our results suggest that the precise timing of glia–neuron interaction controlled by noncoding RNAs and Ddx3x is important for the even distribution of cells across layers. The mammalian retina is a modular brain region, in which cell layers are of uniform thickness but the molecular mechanism controlling this process is not well understood. Here the authors identify a regulatory network consisting of the long noncoding RNA Rncr4, RNA helicase Ddx3x and miR-183/96/182 that controls the even distribution of cells across layers.
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Affiliation(s)
- Jacek Krol
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Ilona Krol
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | | | | | | | - Botond Roska
- 1] Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland [2] Faculty of Medicine, University of Basel, 4056 Basel, Switzerland
| | - Witold Filipowicz
- 1] Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland [2] Biozentrum, University of Basel, 4056 Basel, Switzerland
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38
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Cronin T, Vandenberghe LH, Hantz P, Juttner J, Reimann A, Kacsó AE, Huckfeldt RM, Busskamp V, Kohler H, Lagali PS, Roska B, Bennett J. Efficient transduction and optogenetic stimulation of retinal bipolar cells by a synthetic adeno-associated virus capsid and promoter. EMBO Mol Med 2015; 6:1175-90. [PMID: 25092770 PMCID: PMC4197864 DOI: 10.15252/emmm.201404077] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In this report, we describe the development of a modified adeno-associated virus (AAV) capsid and promoter for transduction of retinal ON-bipolar cells. The bipolar cells, which are post-synaptic to the photoreceptors, are important retinal targets for both basic and preclinical research. In particular, a therapeutic strategy under investigation for advanced forms of blindness involves using optogenetic molecules to render ON-bipolar cells light-sensitive. Currently, delivery of adequate levels of gene expression is a limiting step for this approach. The synthetic AAV capsid and promoter described here achieves high level of optogenetic transgene expression in ON-bipolar cells. This evokes high-frequency (∼100 Hz) spiking responses in ganglion cells of previously blind, rd1, mice. Our vector is a promising vehicle for further development toward potential clinical use.
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Affiliation(s)
- Therese Cronin
- Center for Advanced Retinal and Ophthalmic Therapeutics, F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, USA Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Luk H Vandenberghe
- Center for Advanced Retinal and Ophthalmic Therapeutics, F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, USA Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Péter Hantz
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Josephine Juttner
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Andreas Reimann
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Rachel M Huckfeldt
- Center for Advanced Retinal and Ophthalmic Therapeutics, F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Volker Busskamp
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland Genetics Department, Harvard Medical School, Boston, MA, USA
| | - Hubertus Kohler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Pamela S Lagali
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Botond Roska
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jean Bennett
- Center for Advanced Retinal and Ophthalmic Therapeutics, F.M. Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, USA
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Szikra T, Trenholm S, Drinnenberg A, Jüttner J, Raics Z, Farrow K, Biel M, Awatramani G, Clark DA, Sahel JA, da Silveira RA, Roska B. Rods in daylight act as relay cells for cone-driven horizontal cell-mediated surround inhibition. Nat Neurosci 2014; 17:1728-35. [PMID: 25344628 DOI: 10.1038/nn.3852] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 09/29/2014] [Indexed: 12/18/2022]
Abstract
Vertebrate vision relies on two types of photoreceptors, rods and cones, which signal increments in light intensity with graded hyperpolarizations. Rods operate in the lower range of light intensities while cones operate at brighter intensities. The receptive fields of both photoreceptors exhibit antagonistic center-surround organization. Here we show that at bright light levels, mouse rods act as relay cells for cone-driven horizontal cell-mediated surround inhibition. In response to large, bright stimuli that activate their surrounds, rods depolarize. Rod depolarization increases with stimulus size, and its action spectrum matches that of cones. Rod responses at high light levels are abolished in mice with nonfunctional cones and when horizontal cells are reversibly inactivated. Rod depolarization is conveyed to the inner retina via postsynaptic circuit elements, namely the rod bipolar cells. Our results show that the retinal circuitry repurposes rods, when they are not directly sensing light, to relay cone-driven surround inhibition.
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Affiliation(s)
- Tamas Szikra
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Stuart Trenholm
- 1] Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. [2] Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Antonia Drinnenberg
- 1] Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. [2] University of Basel, Basel, Switzerland
| | - Josephine Jüttner
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Zoltan Raics
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Karl Farrow
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Martin Biel
- Department of Pharmacy-Center for Drug Research, Center for Integrated Protein Science Munich, Ludwig-Maximilians University, Munich, Germany
| | - Gautam Awatramani
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Damon A Clark
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - José-Alain Sahel
- 1] Université Pierre et Marie Curie-Sorbonne Universités, Institut de la Vision, Paris, France. [2] Institut national de la santé et de la recherche médicale, Institut de la Vision, Paris, France. [3] Centre national de la recherche scientifique, Institut de la Vision, Paris, France. [4] Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Département Hospitalo-Universitaire ViewMaintain, Paris, France. [5] Fondation Ophtalmologique Adolphe de Rothschild, Paris, France
| | - Rava Azeredo da Silveira
- 1] Department of Physics, École Normale Supérieure, Paris, France. [2] Laboratoire de Physique Statistique, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, Université Denis Diderot, Paris, France
| | - Botond Roska
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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40
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Yonehara K, Roska B. Neuroscience: retinal projectome reveals organizing principles of the visual system. Curr Biol 2014; 24:R833-R835. [PMID: 25247353 DOI: 10.1016/j.cub.2014.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A new study using zebrafish genetics and whole-brain imaging has identified more than 50 retinal ganglion cell morphologies and produced the first comprehensive map of connectivity between retina and its target visual centers.
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Affiliation(s)
- Keisuke Yonehara
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Botond Roska
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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41
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Zhang C, Rompani SB, Roska B, McCall MA. Adeno-associated virus-RNAi of GlyRα1 and characterization of its synapse-specific inhibition in OFF alpha transient retinal ganglion cells. J Neurophysiol 2014; 112:3125-37. [PMID: 25231618 DOI: 10.1152/jn.00505.2014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In the central nervous system, inhibition shapes neuronal excitation. In spinal cord glycinergic inhibition predominates, whereas GABAergic inhibition predominates in the brain. The retina uses GABA and glycine in approximately equal proportions. Glycinergic crossover inhibition, initiated in the On retinal pathway, controls glutamate release from presynaptic OFF cone bipolar cells (CBCs) and directly shapes temporal response properties of OFF retinal ganglion cells (RGCs). In the retina, four glycine receptor (GlyR) α-subunit isoforms are expressed in different sublaminae and their synaptic currents differ in decay kinetics. GlyRα1, expressed in both On and Off sublaminae of the inner plexiform layer, could be the glycinergic isoform that mediates On-to-Off crossover inhibition. However, subunit-selective glycine contributions remain unknown because we lack selective antagonists or cell class-specific subunit knockouts. To examine the role of GlyRα1 in direct inhibition in mature RGCs, we used retrogradely transported adeno-associated virus (AAV) that performed RNAi and eliminated almost all glycinergic spontaneous and visually evoked responses in PV5 (OFFα(Transient)) RGCs. Comparisons of responses in PV5 RGCs infected with AAV-scrambled-short hairpin RNA (shRNA) or AAV-Glra1-shRNA confirm a role for GlyRα1 in crossover inhibition in cone-driven circuits. Our results also define a role for direct GlyRα1 inhibition in setting the resting membrane potential of PV5 RGCs. The absence of GlyRα1 input unmasked a serial and a direct feedforward GABA(A)ergic modulation in PV5 RGCs, reflecting a complex interaction between glycinergic and GABA(A)ergic inhibition.
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Affiliation(s)
- C Zhang
- Department of Ophthalmology and Visual Science, University of Louisville, Louisville, Kentucky; Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, Kentucky; and
| | - S B Rompani
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - B Roska
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - M A McCall
- Department of Ophthalmology and Visual Science, University of Louisville, Louisville, Kentucky; Department of Anatomical Sciences and Neurobiology, University of Louisville, Louisville, Kentucky; and
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Abstract
In this issue of Neuron, Jepson et al. (2014) demonstrate that electric stimulation of primate ON parasol ganglion cells evokes spiking patterns similar to those elicited by visual motion. This work represents progress in the development of cell-type-specific retinal prosthetics for vision restoration.
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Affiliation(s)
- Stuart Trenholm
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Botond Roska
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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43
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Chuong AS, Miri ML, Busskamp V, Matthews GAC, Acker LC, Sørensen AT, Young A, Klapoetke NC, Henninger MA, Kodandaramaiah SB, Ogawa M, Ramanlal SB, Bandler RC, Allen BD, Forest CR, Chow BY, Han X, Lin Y, Tye KM, Roska B, Cardin JA, Boyden ES. Noninvasive optical inhibition with a red-shifted microbial rhodopsin. Nat Neurosci 2014; 17:1123-9. [PMID: 24997763 PMCID: PMC4184214 DOI: 10.1038/nn.3752] [Citation(s) in RCA: 346] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/01/2014] [Indexed: 12/11/2022]
Abstract
Optogenetic inhibition of the electrical activity of neurons enables the causal assessment of their contributions to brain functions. Red light penetrates deeper into tissue than other visible wavelengths. We present a red-shifted cruxhalorhodopsin, Jaws, derived from Haloarcula (Halobacterium) salinarum (strain Shark) and engineered to result in red light-induced photocurrents three times those of earlier silencers. Jaws exhibits robust inhibition of sensory-evoked neural activity in the cortex and results in strong light responses when used in retinas of retinitis pigmentosa model mice. We also demonstrate that Jaws can noninvasively mediate transcranial optical inhibition of neurons deep in the brains of awake mice. The noninvasive optogenetic inhibition opened up by Jaws enables a variety of important neuroscience experiments and offers a powerful general-use chloride pump for basic and applied neuroscience.
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Affiliation(s)
- Amy S Chuong
- 1] Media Lab, Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mitra L Miri
- 1] Department of Neurobiology, Yale School of Medicine, Yale University, New Haven, Connecticut, USA. [2]
| | - Volker Busskamp
- 1] Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA. [3]
| | - Gillian A C Matthews
- 1] Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2]
| | - Leah C Acker
- 1] Media Lab, Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [4]
| | - Andreas T Sørensen
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Andrew Young
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Nathan C Klapoetke
- 1] Media Lab, Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Mike A Henninger
- 1] Media Lab, Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Suhasa B Kodandaramaiah
- 1] Media Lab, Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [4] George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Masaaki Ogawa
- 1] Media Lab, Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Shreshtha B Ramanlal
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Rachel C Bandler
- Media Lab, Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Brian D Allen
- Media Lab, Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Craig R Forest
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Brian Y Chow
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xue Han
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Yingxi Lin
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Kay M Tye
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Botond Roska
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jessica A Cardin
- 1] Department of Neurobiology, Yale School of Medicine, Yale University, New Haven, Connecticut, USA. [2] Kavli Institute for Neuroscience, Yale University, New Haven, Connecticut, USA
| | - Edward S Boyden
- 1] Media Lab, Department of Media Arts and Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3] Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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44
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Busskamp V, Krol J, Nelidova D, Daum J, Szikra T, Tsuda B, Jüttner J, Farrow K, Scherf BG, Alvarez CPP, Genoud C, Sothilingam V, Tanimoto N, Stadler M, Seeliger M, Stoffel M, Filipowicz W, Roska B. miRNAs 182 and 183 are necessary to maintain adult cone photoreceptor outer segments and visual function. Neuron 2014; 83:586-600. [PMID: 25002228 DOI: 10.1016/j.neuron.2014.06.020] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2014] [Indexed: 12/31/2022]
Abstract
The outer segments of cones serve as light detectors for daylight color vision, and their dysfunction leads to human blindness conditions. We show that the cone-specific disruption of DGCR8 in adult mice led to the loss of miRNAs and the loss of outer segments, resulting in photoreceptors with significantly reduced light responses. However, the number of cones remained unchanged. The loss of the outer segments occurred gradually over 1 month, and during this time the genetic signature of cones decreased. Reexpression of the sensory-cell-specific miR-182 and miR-183 prevented outer segment loss. These miRNAs were also necessary and sufficient for the formation of inner segments, connecting cilia and short outer segments, as well as light responses in stem-cell-derived retinal cultures. Our results show that miR-182- and miR-183-regulated pathways are necessary for cone outer segment maintenance in vivo and functional outer segment formation in vitro.
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Affiliation(s)
- Volker Busskamp
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Jacek Krol
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Dasha Nelidova
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4058 Basel, Switzerland
| | - Janine Daum
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4058 Basel, Switzerland
| | - Tamas Szikra
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Ben Tsuda
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Josephine Jüttner
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Karl Farrow
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Brigitte Gross Scherf
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | | | - Christel Genoud
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Vithiyanjali Sothilingam
- Division of Ocular Neurodegeneration, Institute for Ophthalmic Research, Department of Ophthalmology, Eberhard-Karls University, 72076 Tübingen, Germany
| | - Naoyuki Tanimoto
- Division of Ocular Neurodegeneration, Institute for Ophthalmic Research, Department of Ophthalmology, Eberhard-Karls University, 72076 Tübingen, Germany
| | - Michael Stadler
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Mathias Seeliger
- Division of Ocular Neurodegeneration, Institute for Ophthalmic Research, Department of Ophthalmology, Eberhard-Karls University, 72076 Tübingen, Germany
| | - Markus Stoffel
- Institute for Molecular Health Sciences, ETH, 8093 Zürich
| | - Witold Filipowicz
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, 4058 Basel, Switzerland.
| | - Botond Roska
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland.
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45
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Abstract
Motion detection in fly vision has been investigated experimentally and theoretically for half of a century, yet mechanistic insights into the neuronal computation have only started to emerge. In a recent issue of Nature, two studies provide major insights into how motion direction is extracted from the image flow projected onto the retina.
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Affiliation(s)
- Keisuke Yonehara
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
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46
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Tang JCY, Szikra T, Kozorovitskiy Y, Teixiera M, Sabatini BL, Roska B, Cepko CL. A nanobody-based system using fluorescent proteins as scaffolds for cell-specific gene manipulation. Cell 2013; 154:928-39. [PMID: 23953120 PMCID: PMC4096992 DOI: 10.1016/j.cell.2013.07.021] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 05/31/2013] [Accepted: 07/15/2013] [Indexed: 01/22/2023]
Abstract
Fluorescent proteins are commonly used to label cells across organisms, but the unmodified forms cannot control biological activities. Using GFP-binding proteins derived from Camelid antibodies, we co-opted GFP as a scaffold for inducing formation of biologically active complexes, developing a library of hybrid transcription factors that control gene expression only in the presence of GFP or its derivatives. The modular design allows for variation in key properties such as DNA specificity, transcriptional potency, and drug dependency. Production of GFP controlled cell-specific gene expression and facilitated functional perturbations in the mouse retina and brain. Further, retrofitting existing transgenic GFP mouse and zebrafish lines for GFP-dependent transcription enabled applications such as optogenetic probing of neural circuits. This work establishes GFP as a multifunctional scaffold and opens the door to selective manipulation of diverse GFP-labeled cells across transgenic lines. This approach may also be extended to exploit other intracellular products as cell-specific scaffolds in multicellular organisms.
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Affiliation(s)
- Jonathan C Y Tang
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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47
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Abstract
Retinitis pigmentosa (RP) is a hereditary retinal disease leading to blindness, which affects two million people worldwide. Restoring vision in these blind patients was proposed by gene delivery of microbial light-activated ionic channels or pumps "optogenetic proteins" to transform surviving cells into artificial photoreceptors. This therapeutic strategy was validated in blind animal models of RP by recording at the level of the retina and cortex and by behavioural tests. The translational potentials of these optogenetic approaches have been evaluated using in vitro studies on post-mortem human retinal tissues. Here, we review these recent results and discuss the potential clinical applications of the optogenetic therapy for RP patients.
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Affiliation(s)
- Botond Roska
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66F, 4058 Basel, Switzerland
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48
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Yonehara K, Farrow K, Ghanem A, Hillier D, Balint K, Teixeira M, Jüttner J, Noda M, Neve RL, Conzelmann KK, Roska B. The first stage of cardinal direction selectivity is localized to the dendrites of retinal ganglion cells. Neuron 2013; 79:1078-85. [PMID: 23973208 DOI: 10.1016/j.neuron.2013.08.005] [Citation(s) in RCA: 125] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2013] [Indexed: 11/28/2022]
Abstract
Inferring the direction of image motion is a fundamental component of visual computation and essential for visually guided behavior. In the retina, the direction of image motion is computed in four cardinal directions, but it is not known at which circuit location along the flow of visual information the cardinal direction selectivity first appears. We recorded the concerted activity of the neuronal circuit elements of single direction-selective (DS) retinal ganglion cells at subcellular resolution by combining GCaMP3-functionalized transsynaptic viral tracing and two-photon imaging. While the visually evoked activity of the dendritic segments of the DS cells were direction selective, direction-selective activity was absent in the axon terminals of bipolar cells. Furthermore, the glutamate input to DS cells, recorded using a genetically encoded glutamate sensor, also lacked direction selectivity. Therefore, the first stage in which extraction of a cardinal motion direction occurs is the dendrites of DS cells.
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Affiliation(s)
- Keisuke Yonehara
- Neural Circuit Laboratories, Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
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49
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Abstract
Optogenetic approaches promise to revolutionize neuroscience by using light to manipulate neural activity in genetically or functionally defined neurons with millisecond precision. Harnessing the full potential of optogenetic tools, however, requires light to be targeted to the right neurons at the right time. Here we discuss some barriers and potential solutions to this problem. We review methods for targeting the expression of light-activatable molecules to specific cell types, under genetic, viral or activity-dependent control. Next we explore new ways to target light to individual neurons to allow their precise activation and inactivation. These techniques provide a precision in the temporal and spatial activation of neurons that was not achievable in previous experiments. In combination with simultaneous recording and imaging techniques, these strategies will allow us to mimic the natural activity patterns of neurons in vivo, enabling previously impossible 'dream experiments'.
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Affiliation(s)
- Adam M Packer
- Wolfson Institute for Biomedical Research and Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
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50
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Abstract
Sight-restoring therapy for the visually impaired and blind is a major unmet medical need. Ocular gene therapy is a rational choice for restoring vision or preventing the loss of vision because most blinding diseases originate in cellular components of the eye, a compartment that is optimally suited for the delivery of genes, and many of these diseases have a genetic origin or genetic component. In recent years we have witnessed major advances in the field of ocular gene therapy, and proof-of-concept studies are under way to evaluate the safety and efficacy of human gene therapies. Here we discuss the concepts and recent advances in gene therapy in the retina. Our review discusses traditional approaches such as gene replacement and neuroprotection and also new avenues such as optogenetic therapies. We conjecture that advances in gene therapy in the retina will pave the way for gene therapies in other parts of the brain.
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Affiliation(s)
- José-Alain Sahel
- INSERM UMR_S 968, UPMC, University of Paris 06, Institut de la Vision, Paris, France.
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