1
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McNamara HM, Jia BZ, Guyer A, Parot VJ, Dobbs C, Schier AF, Cohen AE, Lord ND. Optogenetic control of Nodal signaling patterns. bioRxiv 2024:2024.04.11.588875. [PMID: 38645239 PMCID: PMC11030342 DOI: 10.1101/2024.04.11.588875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
A crucial step in early embryogenesis is the establishment of spatial patterns of signaling activity. Tools to perturb morphogen signals with high resolution in space and time can help reveal how embryonic cells decode these signals to make appropriate fate decisions. Here, we present new optogenetic reagents and an experimental pipeline for creaHng designer Nodal signaling patterns in live zebrafish embryos. Nodal receptors were fused to the light-sensitive heterodimerizing pair Cry2/CIB1N, and the Type II receptor was sequestered to the cytosol. The improved optoNodal2 reagents eliminate dark activity and improve response kinetics, without sacrificing dynamic range. We adapted an ultra-widefield microscopy platform for parallel light patterning in up to 36 embryos and demonstrated precise spatial control over Nodal signaling activity and downstream gene expression. Patterned Nodal activation drove precisely controlled internalization of endodermal precursors. Further, we used patterned illumination to generate synthetic signaling patterns in Nodal signaling mutants, rescuing several characteristic developmental defects. This study establishes an experimental toolkit for systematic exploration of Nodal signaling patterns in live embryos.
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Affiliation(s)
| | - Bill Z. Jia
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Alison Guyer
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vicente J. Parot
- Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Caleb Dobbs
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Adam E. Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Nathan D. Lord
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, USA
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2
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Combs DJ, Moult EM, England SK, Cohen AE. Mapping uterine calcium dynamics during the ovulatory cycle in live mice. bioRxiv 2024:2024.02.02.578395. [PMID: 38370720 PMCID: PMC10871303 DOI: 10.1101/2024.02.02.578395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Uterine contraction patterns vary during the ovulatory cycle and throughout pregnancy but prior measurements have produced limited and conflicting information on these patterns. We combined a virally delivered genetically encoded calcium reporter (GCaMP8m) and ultra-widefield imaging in live nonpregnant mice to characterize uterine calcium dynamics at organ scale throughout the estrous cycle. Prior to ovulation (proestrus and estrus) uterine excitations primarily initiated in a region near the oviduct, but after ovulation (metestrus and diestrus), excitations initiated at loci homogeneously distributed throughout the organ. The frequency of excitation events was lowest in proestrus and estrus, higher in metestrus and highest in diestrus. These results establish a platform for mapping uterine activity, and show that the question of whether there is an anatomically localized trigger for uterine excitations depends on the estrous cycle phase.
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Affiliation(s)
- David J. Combs
- Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital, Harvard Medical School
- Department of Chemistry and Chemical Biology, Harvard University
| | - Eric M. Moult
- Department of Chemistry and Chemical Biology, Harvard University
| | - Sarah K. England
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine
| | - Adam E. Cohen
- Department of Chemistry and Chemical Biology, Harvard University
- Department of Physics, Harvard University
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3
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Brooks FP, Davis HC, Park P, Qi Y, Cohen AE. Photophysics-informed two-photon voltage imaging using FRET-opsin voltage indicators. bioRxiv 2024:2024.04.01.587540. [PMID: 38617370 PMCID: PMC11014499 DOI: 10.1101/2024.04.01.587540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Microbial rhodopsin-derived genetically encoded voltage indicators (GEVIs) are powerful tools for mapping bioelectrical dynamics in cell culture and in live animals. Förster resonance energy transfer (FRET)-opsin GEVIs use voltage-dependent changes in opsin absorption to modulate the fluorescence of an attached fluorophore, achieving high brightness, speed, and voltage sensitivity. However, the voltage sensitivity of most FRET-opsin GEVIs has been reported to decrease or vanish under two-photon (2P) excitation. Here we investigated the photophysics of the FRET-opsin GEVIs Voltron1 and 2. We found that the voltage sensitivity came from a photocycle intermediate, not from the opsin ground state. The voltage sensitivities of both GEVIs were nonlinear functions of illumination intensity; for Voltron1, the sensitivity reversed sign under low-intensity illumination. Using photocycle-optimized 2P illumination protocols, we demonstrate 2P voltage imaging with Voltron2 in barrel cortex of a live mouse. These results open the door to high-speed 2P voltage imaging of FRET-opsin GEVIs in vivo.
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Affiliation(s)
| | | | - Pojeong Park
- Department of Chemistry and Chemical Biology, Harvard University
| | - Yitong Qi
- Department of Chemistry and Chemical Biology, Harvard University
| | - Adam E. Cohen
- Department of Chemistry and Chemical Biology, Harvard University
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4
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Liu PW, Zhang H, Werley CA, Pichler M, Ryan SJ, Lewarch CL, Jacques J, Grooms J, Ferrante J, Li G, Zhang D, Bremmer N, Barnett A, Chantre R, Elder AE, Cohen AE, Williams LA, Dempsey GT, McManus OB. A phenotypic screening platform for chronic pain therapeutics using all-optical electrophysiology. Pain 2024; 165:922-940. [PMID: 37963235 PMCID: PMC10950549 DOI: 10.1097/j.pain.0000000000003090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/16/2022] [Accepted: 08/30/2023] [Indexed: 11/16/2023]
Abstract
ABSTRACT Chronic pain associated with osteoarthritis (OA) remains an intractable problem with few effective treatment options. New approaches are needed to model the disease biology and to drive discovery of therapeutics. We present an in vitro model of OA pain, where dorsal root ganglion (DRG) sensory neurons were sensitized by a defined mixture of disease-relevant inflammatory mediators, here called Sensitizing PAin Reagent Composition or SPARC. Osteoarthritis-SPARC components showed synergistic or additive effects when applied in combination and induced pain phenotypes in vivo. To measure the effect of OA-SPARC on neural firing in a scalable format, we used a custom system for high throughput all-optical electrophysiology. This system enabled light-based membrane voltage recordings from hundreds of neurons in parallel with single cell and single action potential resolution and a throughput of up to 500,000 neurons per day. A computational framework was developed to construct a multiparameter OA-SPARC neuronal phenotype and to quantitatively assess phenotype reversal by candidate pharmacology. We screened ∼3000 approved drugs and mechanistically focused compounds, yielding data from over 1.2 million individual neurons with detailed assessment of functional OA-SPARC phenotype rescue and orthogonal "off-target" effects. Analysis of confirmed hits revealed diverse potential analgesic mechanisms including ion channel modulators and other mechanisms including MEK inhibitors and tyrosine kinase modulators. Our results suggest that the Raf-MEK-ERK axis in DRG neurons may integrate the inputs from multiple upstream inflammatory mediators found in osteoarthritis patient joints, and MAPK pathway activation in DRG neurons may contribute to chronic pain in patients with osteoarthritis.
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Affiliation(s)
- Pin W. Liu
- Quiver Bioscience, Cambridge, MA, United States
| | | | | | | | | | | | | | | | | | - Guangde Li
- Quiver Bioscience, Cambridge, MA, United States
| | - Dawei Zhang
- Quiver Bioscience, Cambridge, MA, United States
| | | | | | | | | | - Adam E. Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, United States
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5
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Henry WS, Müller S, Yang JS, Innes-Gold S, Das S, Reinhardt F, Sigmund K, Phadnis VV, Wan Z, Eaton E, Sampaio JL, Bell GW, Viravalli A, Hammond PT, Kamm RD, Cohen AE, Boehnke N, Hsu VW, Levental KR, Rodriguez R, Weinberg RA. Ether lipids influence cancer cell fate by modulating iron uptake. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585922. [PMID: 38562716 PMCID: PMC10983928 DOI: 10.1101/2024.03.20.585922] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Cancer cell fate has been widely ascribed to mutational changes within protein-coding genes associated with tumor suppressors and oncogenes. In contrast, the mechanisms through which the biophysical properties of membrane lipids influence cancer cell survival, dedifferentiation and metastasis have received little scrutiny. Here, we report that cancer cells endowed with a high metastatic ability and cancer stem cell-like traits employ ether lipids to maintain low membrane tension and high membrane fluidity. Using genetic approaches and lipid reconstitution assays, we show that these ether lipid-regulated biophysical properties permit non-clathrin-mediated iron endocytosis via CD44, leading directly to significant increases in intracellular redox-active iron and enhanced ferroptosis susceptibility. Using a combination of in vitro three-dimensional microvascular network systems and in vivo animal models, we show that loss of ether lipids also strongly attenuates extravasation, metastatic burden and cancer stemness. These findings illuminate a mechanism whereby ether lipids in carcinoma cells serve as key regulators of malignant progression while conferring a unique vulnerability that can be exploited for therapeutic intervention.
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Affiliation(s)
- Whitney S Henry
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Sebastian Müller
- Institut Curie, CNRS, INSERM, PSL Research University, Equipe Labellisée Ligue Contre le Cancer, Paris 75005, France
| | - Jia-Shu Yang
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, and Dept. of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Sarah Innes-Gold
- Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sunny Das
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Ferenc Reinhardt
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Kim Sigmund
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Vaishnavi V Phadnis
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Dept. of Biology, MIT, Cambridge, MA 02139, USA
| | - Zhengpeng Wan
- Dept. of Biological Engineering, MIT, Cambridge, MA 02139, USA
| | - Elinor Eaton
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Julio L Sampaio
- Institut Curie, INSERM, Mines ParisTech, Paris 75005, France
| | - George W Bell
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Amartya Viravalli
- Dept. of Chemical Engineering and Materials Science, University of Minnesota Minneapolis, MN 55455, USA
| | - Paula T Hammond
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
- Dept. of Chemical Engineering, MIT, Cambridge, MA 02139, USA
- Senior author
| | - Roger D Kamm
- Dept. of Biological Engineering, MIT, Cambridge, MA 02139, USA
- Dept. of Physics, Harvard University, Cambridge, MA 02138, USA
- Senior author
| | - Adam E Cohen
- Dept. of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Dept. of Physics, Harvard University, Cambridge, MA 02138, USA
- Senior author
| | - Natalie Boehnke
- Dept. of Chemical Engineering and Materials Science, University of Minnesota Minneapolis, MN 55455, USA
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
- Senior author
| | - Victor W Hsu
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, and Dept. of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Senior author
| | - Kandice R Levental
- Dept. of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA
- Senior author
| | - Raphaël Rodriguez
- Institut Curie, CNRS, INSERM, PSL Research University, Equipe Labellisée Ligue Contre le Cancer, Paris 75005, France
- Senior author
| | - Robert A Weinberg
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Dept. of Biology, MIT, Cambridge, MA 02139, USA
- Ludwig Center for Molecular Oncology, Cambridge, MA 02139, USA
- Senior author
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6
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Scheibner C, Ori H, Cohen AE, Vitelli V. Spiking at the edge: Excitability at interfaces in reaction-diffusion systems. Proc Natl Acad Sci U S A 2024; 121:e2307996120. [PMID: 38215183 PMCID: PMC10801884 DOI: 10.1073/pnas.2307996120] [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: 05/12/2023] [Accepted: 10/25/2023] [Indexed: 01/14/2024] Open
Abstract
Excitable media, ranging from bioelectric tissues and chemical oscillators to forest fires and competing populations, are nonlinear, spatially extended systems capable of spiking. Most investigations of excitable media consider situations where the amplifying and suppressing forces necessary for spiking coexist at every point in space. In this case, spikes arise due to local bistabilities, which require a fine-tuned ratio between local amplification and suppression strengths. But, in nature and engineered systems, these forces can be segregated in space, forming structures like interfaces and boundaries. Here, we show how boundaries can generate and protect spiking when the reacting components can spread out: Even arbitrarily weak diffusion can cause spiking at the edge between two non-excitable media. This edge spiking arises due to a global bistability, which can occur even if amplification and suppression strengths do not allow spiking when mixed. We analytically derive a spiking phase diagram that depends on two parameters: i) the ratio between the system size and the characteristic diffusive length-scale and ii) the ratio between the amplification and suppression strengths. Our analysis explains recent experimental observations of action potentials at the interface between two non-excitable bioelectric tissues. Beyond electrophysiology, we highlight how edge spiking emerges in predator-prey dynamics and in oscillating chemical reactions. Our findings provide a theoretical blueprint for a class of interfacial excitations in reaction-diffusion systems, with potential implications for spatially controlled chemical reactions, nonlinear waveguides and neuromorphic computation, as well as spiking instabilities, such as cardiac arrhythmias, that naturally occur in heterogeneous biological media.
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Affiliation(s)
- Colin Scheibner
- Department of Physics and The James Franck Institute, The University of Chicago, Chicago, IL60637
- Kadanoff Center for Theoretical Physics, The University of Chicago, Chicago, IL60637
| | - Hillel Ori
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
| | - Adam E. Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
- Department of Physics, Harvard University, Cambridge, MA02138
| | - Vincenzo Vitelli
- Department of Physics and The James Franck Institute, The University of Chicago, Chicago, IL60637
- Kadanoff Center for Theoretical Physics, The University of Chicago, Chicago, IL60637
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL60637
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7
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Kim D, Park P, Li X, Wong Campos JD, Tian H, Moult EM, Grimm JB, Lavis L, Cohen AE. Mapping memories: pulse-chase labeling reveals AMPA receptor dynamics during memory formation. bioRxiv 2023:2023.05.26.541296. [PMID: 37292614 PMCID: PMC10246012 DOI: 10.1101/2023.05.26.541296] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A tool to map changes in synaptic strength during a defined time window could provide powerful insights into the mechanisms governing learning and memory. We developed a technique, Extracellular Protein Surface Labeling in Neurons (EPSILON), to map α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) insertion in vivo by pulse-chase labeling of surface AMPARs with membrane-impermeable dyes. This approach allows for single-synapse resolution maps of plasticity in genetically targeted neurons during memory formation. We investigated the relationship between synapse-level and cell-level memory encodings by mapping synaptic plasticity and cFos expression in hippocampal CA1 pyramidal cells upon contextual fear conditioning (CFC). We observed a strong correlation between synaptic plasticity and cFos expression, suggesting a synaptic mechanism for the association of cFos expression with memory engrams. The EPSILON technique is a useful tool for mapping synaptic plasticity and may be extended to investigate trafficking of other transmembrane proteins.
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Affiliation(s)
- Doyeon Kim
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Pojeong Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Xiuyuan Li
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - J David Wong Campos
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - He Tian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Eric M Moult
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Luke Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
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8
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Hayward RF, Brooks FP, Yang S, Gao S, Cohen AE. Diminishing neuronal acidification by channelrhodopsins with low proton conduction. eLife 2023; 12:RP86833. [PMID: 37801078 PMCID: PMC10558203 DOI: 10.7554/elife.86833] [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] [Indexed: 10/07/2023] Open
Abstract
Many channelrhodopsins are permeable to protons. We found that in neurons, activation of a high-current channelrhodopsin, CheRiff, led to significant acidification, with faster acidification in the dendrites than in the soma. Experiments with patterned optogenetic stimulation in monolayers of HEK cells established that the acidification was due to proton transport through the opsin, rather than through other voltage-dependent channels. We identified and characterized two opsins which showed large photocurrents, but small proton permeability, PsCatCh2.0 and ChR2-3M. PsCatCh2.0 showed excellent response kinetics and was also spectrally compatible with simultaneous voltage imaging with QuasAr6a. Stimulation-evoked acidification is a possible source of disruptions to cell health in scientific and prospective therapeutic applications of optogenetics. Channelrhodopsins with low proton permeability are a promising strategy for avoiding these problems.
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Affiliation(s)
- Rebecca Frank Hayward
- School of Engineering and Applied Sciences, Harvard UniversityCambridgeUnited States
| | - F Phil Brooks
- Department of Chemistry, Harvard UniversityCambridgeUnited States
| | - Shang Yang
- Department of Neurophysiology, University of WurzburgWurzburgGermany
| | - Shiqiang Gao
- Department of Neurophysiology, University of WurzburgWurzburgGermany
| | - Adam E Cohen
- Department of Chemistry, Harvard UniversityCambridgeUnited States
- Department of Physics, Harvard UniversityCambridgeUnited States
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9
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Jia BZ, Qi Y, Wong-Campos JD, Megason SG, Cohen AE. A bioelectrical phase transition patterns the first vertebrate heartbeats. Nature 2023; 622:149-155. [PMID: 37758945 DOI: 10.1038/s41586-023-06561-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 08/22/2023] [Indexed: 09/29/2023]
Abstract
A regular heartbeat is essential to vertebrate life. In the mature heart, this function is driven by an anatomically localized pacemaker. By contrast, pacemaking capability is broadly distributed in the early embryonic heart1-3, raising the question of how tissue-scale activity is first established and then maintained during embryonic development. The initial transition of the heart from silent to beating has never been characterized at the timescale of individual electrical events, and the structure in space and time of the early heartbeats remains poorly understood. Using all-optical electrophysiology, we captured the very first heartbeat of a zebrafish and analysed the development of cardiac excitability and conduction around this singular event. The first few beats appeared suddenly, had irregular interbeat intervals, propagated coherently across the primordial heart and emanated from loci that varied between animals and over time. The bioelectrical dynamics were well described by a noisy saddle-node on invariant circle bifurcation with action potential upstroke driven by CaV1.2. Our work shows how gradual and largely asynchronous development of single-cell bioelectrical properties produces a stereotyped and robust tissue-scale transition from quiescence to coordinated beating.
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Affiliation(s)
- Bill Z Jia
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Systems, Synthetic and Quantitative Biology PhD Program, Harvard University, Cambridge, MA, USA
| | - Yitong Qi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - J David Wong-Campos
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Sean G Megason
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Department of Physics, Harvard University, Cambridge, MA, USA.
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10
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Eom M, Han S, Park P, Kim G, Cho ES, Sim J, Lee KH, Kim S, Tian H, Böhm UL, Lowet E, Tseng HA, Choi J, Lucia SE, Ryu SH, Rózsa M, Chang S, Kim P, Han X, Piatkevich KD, Choi M, Kim CH, Cohen AE, Chang JB, Yoon YG. Statistically unbiased prediction enables accurate denoising of voltage imaging data. Nat Methods 2023; 20:1581-1592. [PMID: 37723246 PMCID: PMC10555843 DOI: 10.1038/s41592-023-02005-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 11/16/2022] [Accepted: 08/10/2023] [Indexed: 09/20/2023]
Abstract
Here we report SUPPORT (statistically unbiased prediction utilizing spatiotemporal information in imaging data), a self-supervised learning method for removing Poisson-Gaussian noise in voltage imaging data. SUPPORT is based on the insight that a pixel value in voltage imaging data is highly dependent on its spatiotemporal neighboring pixels, even when its temporally adjacent frames alone do not provide useful information for statistical prediction. Such dependency is captured and used by a convolutional neural network with a spatiotemporal blind spot to accurately denoise voltage imaging data in which the existence of the action potential in a time frame cannot be inferred by the information in other frames. Through simulations and experiments, we show that SUPPORT enables precise denoising of voltage imaging data and other types of microscopy image while preserving the underlying dynamics within the scene.
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Affiliation(s)
- Minho Eom
- School of Electrical Engineering, KAIST, Daejeon, Republic of Korea
| | - Seungjae Han
- School of Electrical Engineering, KAIST, Daejeon, Republic of Korea
| | - Pojeong Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Gyuri Kim
- School of Electrical Engineering, KAIST, Daejeon, Republic of Korea
| | - Eun-Seo Cho
- School of Electrical Engineering, KAIST, Daejeon, Republic of Korea
| | - Jueun Sim
- Department of Materials Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Kang-Han Lee
- Department of Biology, Chungnam National University, Daejeon, Republic of Korea
| | - Seonghoon Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - He Tian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Urs L Böhm
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité University of Medicine Berlin, Berlin, Germany
| | - Eric Lowet
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Hua-An Tseng
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Jieun Choi
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
- KAIST Institute for Health Science and Technology, Daejeon, Republic of Korea
| | - Stephani Edwina Lucia
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
- KAIST Institute for Health Science and Technology, Daejeon, Republic of Korea
| | - Seung Hyun Ryu
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul, Republic of Korea
| | - Márton Rózsa
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Sunghoe Chang
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Pilhan Kim
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, Republic of Korea
- KAIST Institute for Health Science and Technology, Daejeon, Republic of Korea
- Graduate School of Nanoscience and Technology, KAIST, Daejeon, Republic of Korea
| | - Xue Han
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Kiryl D Piatkevich
- Research Center for Industries of the Future and School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Myunghwan Choi
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, Republic of Korea
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Jae-Byum Chang
- Department of Materials Science and Engineering, KAIST, Daejeon, Republic of Korea
| | - Young-Gyu Yoon
- School of Electrical Engineering, KAIST, Daejeon, Republic of Korea.
- KAIST Institute for Health Science and Technology, Daejeon, Republic of Korea.
- Department of Semiconductor System Engineering, KAIST, Daejeon, Republic of Korea.
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11
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Hayward RF, Brooks FP, Yang S, Gao S, Cohen AE. Diminishing neuronal acidification by channelrhodopsins with low proton conduction. bioRxiv 2023:2023.02.07.527404. [PMID: 36798192 PMCID: PMC9934520 DOI: 10.1101/2023.02.07.527404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Many channelrhodopsins are permeable to protons. We found that in neurons, activation of a high-current channelrhodopsin, CheRiff, led to significant acidification, with faster acidification in the dendrites than in the soma. Experiments with patterned optogenetic stimulation in monolayers of HEK cells established that the acidification was due to proton transport through the opsin, rather than through other voltage-dependent channels. We identified and characterized two opsins which showed large photocurrents, but small proton permeability, PsCatCh2.0 and ChR2-3M. PsCatCh2.0 showed excellent response kinetics and was also spectrally compatible with simultaneous voltage imaging with QuasAr6a. Stimulation-evoked acidification is a possible source of disruptions to cell health in scientific and prospective therapeutic applications of optogenetics. Channelrhodopsins with low proton permeability are a promising strategy for avoiding these problems. Statement of Significance Acidification is an undesirable artifact of optogenetic stimulation. Low proton-permeability opsins minimize this artifact while still allowing robust optogenetic control.
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Affiliation(s)
| | - F. Phil Brooks
- Department of Chemistry, Harvard University, Cambridge, MA 02138
| | - Shang Yang
- Department of Neurophysiology, University of Wurzburg, Germany
| | - Shiqiang Gao
- Department of Neurophysiology, University of Wurzburg, Germany
| | - Adam E Cohen
- Department of Chemistry, Harvard University, Cambridge, MA 02138
- Department of Physics, Harvard University, Cambridge, MA 02138
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12
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Tian H, Davis HC, Wong-Campos JD, Park P, Fan LZ, Gmeiner B, Begum S, Werley CA, Borja GB, Upadhyay H, Shah H, Jacques J, Qi Y, Parot V, Deisseroth K, Cohen AE. Video-based pooled screening yields improved far-red genetically encoded voltage indicators. Nat Methods 2023; 20:1082-1094. [PMID: 36624211 PMCID: PMC10329731 DOI: 10.1038/s41592-022-01743-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [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: 04/28/2022] [Accepted: 11/28/2022] [Indexed: 01/11/2023]
Abstract
Video-based screening of pooled libraries is a powerful approach for directed evolution of biosensors because it enables selection along multiple dimensions simultaneously from large libraries. Here we develop a screening platform, Photopick, which achieves precise phenotype-activated photoselection over a large field of view (2.3 × 2.3 mm, containing >103 cells, per shot). We used the Photopick platform to evolve archaerhodopsin-derived genetically encoded voltage indicators (GEVIs) with improved signal-to-noise ratio (QuasAr6a) and kinetics (QuasAr6b). These GEVIs gave improved signals in cultured neurons and in live mouse brains. By combining targeted in vivo optogenetic stimulation with high-precision voltage imaging, we characterized inhibitory synaptic coupling between individual cortical NDNF (neuron-derived neurotrophic factor) interneurons, and excitatory electrical synapses between individual hippocampal parvalbumin neurons. The QuasAr6 GEVIs are powerful tools for all-optical electrophysiology and the Photopick approach could be adapted to evolve a broad range of biosensors.
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Affiliation(s)
- He Tian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hunter C Davis
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - J David Wong-Campos
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Pojeong Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Linlin Z Fan
- Department of Bioengineering, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Benjamin Gmeiner
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Shahinoor Begum
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | | | | | | | | | - Yitong Qi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Vicente Parot
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Karl Deisseroth
- Department of Bioengineering, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MA, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Department of Physics, Harvard University, Cambridge, MA, USA.
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13
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Wong-Campos JD, Park P, Davis H, Qi Y, Tian H, Itkis DG, Kim D, Grimm JB, Plutkis SE, Lavis L, Cohen AE. Voltage dynamics of dendritic integration and back-propagation in vivo. bioRxiv 2023:2023.05.25.542363. [PMID: 37292691 PMCID: PMC10245993 DOI: 10.1101/2023.05.25.542363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Neurons integrate synaptic inputs within their dendrites and produce spiking outputs, which then propagate down the axon and back into the dendrites where they contribute to plasticity. Mapping the voltage dynamics in dendritic arbors of live animals is crucial for understanding neuronal computation and plasticity rules. Here we combine patterned channelrhodopsin activation with dual-plane structured illumination voltage imaging, for simultaneous perturbation and monitoring of dendritic and somatic voltage in Layer 2/3 pyramidal neurons in anesthetized and awake mice. We examined the integration of synaptic inputs and compared the dynamics of optogenetically evoked, spontaneous, and sensory-evoked back-propagating action potentials (bAPs). Our measurements revealed a broadly shared membrane voltage throughout the dendritic arbor, and few signatures of electrical compartmentalization among synaptic inputs. However, we observed spike rate acceleration-dependent propagation of bAPs into distal dendrites. We propose that this dendritic filtering of bAPs may play a critical role in activity-dependent plasticity.
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Affiliation(s)
- J David Wong-Campos
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Pojeong Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hunter Davis
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Yitong Qi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - He Tian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Daniel G Itkis
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Doyeon Kim
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Sarah E Plutkis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Luke Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
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14
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Lin D, Li X, Moult E, Park P, Tang B, Shen H, Grimm JB, Falco N, Jia BZ, Baker D, Lavis LD, Cohen AE. Time-tagged ticker tapes for intracellular recordings. Nat Biotechnol 2023; 41:631-639. [PMID: 36593408 PMCID: PMC10192119 DOI: 10.1038/s41587-022-01524-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [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: 10/13/2021] [Accepted: 09/22/2022] [Indexed: 01/03/2023]
Abstract
Recording transcriptional histories of a cell would enable deeper understanding of cellular developmental trajectories and responses to external perturbations. Here we describe an engineered protein fiber that incorporates diverse fluorescent marks during its growth to store a ticker tape-like history. An embedded HaloTag reporter incorporates user-supplied dyes, leading to colored stripes that map the growth of each individual fiber to wall clock time. A co-expressed eGFP tag driven by a promoter of interest records a history of transcriptional activation. High-resolution multi-spectral imaging on fixed samples reads the cellular histories, and interpolation of eGFP marks relative to HaloTag timestamps provides accurate absolute timing. We demonstrate recordings of doxycycline-induced transcription in HEK cells and cFos promoter activation in cultured neurons, with a single-cell absolute accuracy of 30-40 minutes over a 12-hour recording. The protein-based ticker tape design we present here could be generalized to achieve massively parallel single-cell recordings of diverse physiological modalities.
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Affiliation(s)
- Dingchang Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, USA.
| | - Xiuyuan Li
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Eric Moult
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Pojeong Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Benjamin Tang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hao Shen
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jonathan B Grimm
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Natalie Falco
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Bill Z Jia
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Luke D Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Department of Physics, Harvard University, Cambridge, MA, USA.
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15
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Tian H, Davis HC, Wong-Campos JD, Park P, Fan LZ, Gmeiner B, Begum S, Werley CA, Borja GB, Upadhyay H, Shah H, Jacques J, Qi Y, Parot V, Deisseroth K, Cohen AE. Author Correction: Video-based pooled screening yields improved far-red genetically encoded voltage indicators. Nat Methods 2023; 20:469. [PMID: 36765248 DOI: 10.1038/s41592-023-01805-2] [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: 02/12/2023]
Affiliation(s)
- He Tian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hunter C Davis
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - J David Wong-Campos
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Pojeong Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Linlin Z Fan
- Department of Bioengineering, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Benjamin Gmeiner
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Shahinoor Begum
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | | | | | | | | | - Yitong Qi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Vicente Parot
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Karl Deisseroth
- Department of Bioengineering, Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Chevy Chase, MA, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Department of Physics, Harvard University, Cambridge, MA, USA.
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16
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Frank Hayward R, Brooks Iii FP, Yang S, Gao S, Cohen AE. Diminishing neuronal acidification by channelrhodopsins with low proton conduction. Biophys J 2023; 122:540a. [PMID: 36784802 DOI: 10.1016/j.bpj.2022.11.2861] [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: 02/12/2023] Open
Affiliation(s)
- Rebecca Frank Hayward
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | | | - Shang Yang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Adam E Cohen
- Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
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17
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Fan LZ, Kim DK, Jennings JH, Tian H, Wang PY, Ramakrishnan C, Randles S, Sun Y, Thadhani E, Kim YS, Quirin S, Giocomo L, Cohen AE, Deisseroth K. All-optical physiology resolves a synaptic basis for behavioral timescale plasticity. Cell 2023; 186:543-559.e19. [PMID: 36669484 PMCID: PMC10327443 DOI: 10.1016/j.cell.2022.12.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [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: 02/06/2022] [Revised: 10/19/2022] [Accepted: 12/19/2022] [Indexed: 01/20/2023]
Abstract
Learning has been associated with modifications of synaptic and circuit properties, but the precise changes storing information in mammals have remained largely unclear. We combined genetically targeted voltage imaging with targeted optogenetic activation and silencing of pre- and post-synaptic neurons to study the mechanisms underlying hippocampal behavioral timescale plasticity. In mice navigating a virtual-reality environment, targeted optogenetic activation of individual CA1 cells at specific places induced stable representations of these places in the targeted cells. Optical elicitation, recording, and modulation of synaptic transmission in behaving mice revealed that activity in presynaptic CA2/3 cells was required for the induction of plasticity in CA1 and, furthermore, that during induction of these place fields in single CA1 cells, synaptic input from CA2/3 onto these same cells was potentiated. These results reveal synaptic implementation of hippocampal behavioral timescale plasticity and define a methodology to resolve synaptic plasticity during learning and memory in behaving mammals.
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Affiliation(s)
- Linlin Z Fan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Doo Kyung Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Joshua H Jennings
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - He Tian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Peter Y Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Sawyer Randles
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Yanjun Sun
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Elina Thadhani
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Sean Quirin
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Lisa Giocomo
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Department of Physics, Harvard University, Cambridge, MA, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford, CA, USA.
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18
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Shi Z, Innes-Gold S, Cohen AE. Membrane tension propagation couples axon growth and collateral branching. Sci Adv 2022; 8:eabo1297. [PMID: 36044581 PMCID: PMC9432834 DOI: 10.1126/sciadv.abo1297] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 07/15/2022] [Indexed: 05/31/2023]
Abstract
Neuronal axons must navigate a mechanically heterogeneous environment to reach their targets, but the biophysical mechanisms coupling mechanosensation, growth, and branching are not fully understood. Here, we show that local changes in membrane tension propagate along axons at approximately 20 μm/s, more than 1000-fold faster than in most other nonmotile cells where this property has been measured. Local perturbations to tension decay along the axon with a length constant of approximately 41 μm. This rapid and long-range mechanical signaling mediates bidirectional competition between axonal branch initiation and growth cone extension. Our data suggest a mechanism by which mechanical cues at one part of a growing axon can affect growth dynamics remotely.
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Affiliation(s)
- Zheng Shi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sarah Innes-Gold
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Adam E. Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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19
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Armbruster M, Naskar S, Garcia JP, Sommer M, Kim E, Adam Y, Haydon PG, Boyden ES, Cohen AE, Dulla CG. Neuronal activity drives pathway-specific depolarization of peripheral astrocyte processes. Nat Neurosci 2022; 25:607-616. [PMID: 35484406 PMCID: PMC9988390 DOI: 10.1038/s41593-022-01049-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 03/14/2022] [Indexed: 12/16/2022]
Abstract
Astrocytes are glial cells that interact with neuronal synapses via their distal processes, where they remove glutamate and potassium (K+) from the extracellular space following neuronal activity. Astrocyte clearance of both glutamate and K+ is voltage dependent, but astrocyte membrane potential (Vm) is thought to be largely invariant. As a result, these voltage dependencies have not been considered relevant to astrocyte function. Using genetically encoded voltage indicators to enable the measurement of Vm at peripheral astrocyte processes (PAPs) in mice, we report large, rapid, focal and pathway-specific depolarizations in PAPs during neuronal activity. These activity-dependent astrocyte depolarizations are driven by action potential-mediated presynaptic K+ efflux and electrogenic glutamate transporters. We find that PAP depolarization inhibits astrocyte glutamate clearance during neuronal activity, enhancing neuronal activation by glutamate. This represents a novel class of subcellular astrocyte membrane dynamics and a new form of astrocyte-neuron interaction.
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Affiliation(s)
- Moritz Armbruster
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, USA.
| | - Saptarnab Naskar
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, USA
| | - Jacqueline P Garcia
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, USA.,Cell, Molecular, and Developmental Biology Program, Tufts Graduate School of Biomedical Sciences, Boston, MA, USA
| | - Mary Sommer
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, USA
| | - Elliot Kim
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, USA
| | - Yoav Adam
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Edmond and Lily Safra Center for Brain Sciences, the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Philip G Haydon
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, USA
| | - Edward S Boyden
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.,McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.,Koch Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Neurobiological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Department of Physics, Harvard University, Cambridge, MA, USA
| | - Chris G Dulla
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, USA.
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20
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Böhm UL, Kimura Y, Kawashima T, Ahrens MB, Higashijima SI, Engert F, Cohen AE. Voltage imaging identifies spinal circuits that modulate locomotor adaptation in zebrafish. Neuron 2022; 110:1211-1222.e4. [PMID: 35104451 PMCID: PMC8989672 DOI: 10.1016/j.neuron.2022.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 08/22/2021] [Revised: 11/17/2021] [Accepted: 01/04/2022] [Indexed: 12/20/2022]
Abstract
Motor systems must continuously adapt their output to maintain a desired trajectory. While the spinal circuits underlying rhythmic locomotion are well described, little is known about how the network modulates its output strength. A major challenge has been the difficulty of recording from spinal neurons during behavior. Here, we use voltage imaging to map the membrane potential of large populations of glutamatergic neurons throughout the spinal cord of the larval zebrafish during fictive swimming in a virtual environment. We characterized a previously undescribed subpopulation of tonic-spiking ventral V3 neurons whose spike rate correlated with swimming strength and bout length. Optogenetic activation of V3 neurons led to stronger swimming and longer bouts but did not affect tail beat frequency. Genetic ablation of V3 neurons led to reduced locomotor adaptation. The power of voltage imaging allowed us to identify V3 neurons as a critical driver of locomotor adaptation in zebrafish.
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Affiliation(s)
- Urs L Böhm
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yukiko Kimura
- National Institutes of Natural Sciences, Okazaki Institute for Integrative Bioscience, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan
| | - Takashi Kawashima
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Misha B Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Shin-Ichi Higashijima
- National Institutes of Natural Sciences, Okazaki Institute for Integrative Bioscience, National Institute for Physiological Sciences, Okazaki, Aichi 444-8787, Japan
| | - Florian Engert
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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21
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Landau AT, Park P, Wong-Campos JD, Tian H, Cohen AE, Sabatini BL. Dendritic branch structure compartmentalizes voltage-dependent calcium influx in cortical layer 2/3 pyramidal cells. eLife 2022; 11:76993. [PMID: 35319464 PMCID: PMC8979587 DOI: 10.7554/elife.76993] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 01/11/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Back-propagating action potentials (bAPs) regulate synaptic plasticity by evoking voltage-dependent calcium influx throughout dendrites. Attenuation of bAP amplitude in distal dendritic compartments alters plasticity in a location-specific manner by reducing bAP-dependent calcium influx. However, it is not known if neurons exhibit branch-specific variability in bAP-dependent calcium signals, independent of distance-dependent attenuation. Here, we reveal that bAPs fail to evoke calcium influx through voltage-gated calcium channels (VGCCs) in a specific population of dendritic branches in mouse cortical layer 2/3 pyramidal cells, despite evoking substantial VGCC-mediated calcium influx in sister branches. These branches contain VGCCs and successfully propagate bAPs in the absence of synaptic input; nevertheless, they fail to exhibit bAP-evoked calcium influx due to a branch-specific reduction in bAP amplitude. We demonstrate that these branches have more elaborate branch structure compared to sister branches, which causes a local reduction in electrotonic impedance and bAP amplitude. Finally, we show that bAPs still amplify synaptically-mediated calcium influx in these branches because of differences in the voltage-dependence and kinetics of VGCCs and NMDA-type glutamate receptors. Branch-specific compartmentalization of bAP-dependent calcium signals may provide a mechanism for neurons to diversify synaptic tuning across the dendritic tree.
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Affiliation(s)
- Andrew T Landau
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
| | - Pojeong Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - J David Wong-Campos
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - He Tian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, United States
| | - Bernardo L Sabatini
- Department of Neurobiology, Howard Hughes Medical Institute, Harvard Medical School, Boston, United States
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22
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Abstract
Is it possible to form an image using light produced by stimulated emission? Here we study light scatter off an assembly of excited chromophores. Due to the Optical Theorem, stimulated emission is necessarily accompanied by excited state Rayleigh scattering. Both processes can be used to form images, though they have different dependencies on scattering direction, wavelength and chromophore configuration. Our results suggest several new approaches to optical imaging using fluorophore excited states.
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Affiliation(s)
- J David Wong-Campos
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - J V Porto
- Joint Quantum Institute, NIST and the University of Maryland, College Park, Maryland 20742, United States
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Physics, Harvard University, Cambridge, Massachusetts 02138, United States
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23
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Bloxham W, Brinks D, Kheifets S, Cohen AE. Linearly polarized excitation enhances signals from fluorescent voltage indicators. Biophys J 2021; 120:5333-5342. [PMID: 34710379 DOI: 10.1016/j.bpj.2021.10.028] [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] [Received: 07/21/2021] [Revised: 10/10/2021] [Accepted: 10/20/2021] [Indexed: 10/20/2022] Open
Abstract
Voltage imaging in cells requires high-speed recording of small fluorescent signals, often leading to low signal/noise ratios. Because voltage indicators are membrane bound, their orientations are partially constrained by the plane of the membrane. We explored whether tuning the linear polarization of excitation light could enhance voltage indicator fluorescence. We tested a panel of dye- and protein-based voltage indicators in mammalian cells. The dye BeRST1 showed a 73% increase in brightness between the least and most favorable polarizations. The protein-based reporter ASAP1 showed a 22% increase in brightness, and QuasAr3 showed a 14% increase in brightness. In very thin neurites expressing QuasAr3, improvements were anomalously large, with a 170% increase in brightness between polarization parallel versus perpendicular to the dendrite. Signal/noise ratios of optically recorded action potentials were increased by up to 50% in neurites expressing QuasAr3. These results demonstrate that polarization control can be a facile means to enhance signals from fluorescent voltage indicators, particularly in thin neurites or in high-background environments.
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Affiliation(s)
- William Bloxham
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; Department of Physics, Harvard University, Cambridge, Massachusetts; Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Daan Brinks
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands; Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Simon Kheifets
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; Department of Physics, Harvard University, Cambridge, Massachusetts.
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24
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Al Tanoury Z, Zimmerman JF, Rao J, Sieiro D, McNamara HM, Cherrier T, Rodríguez-delaRosa A, Hick-Colin A, Bousson F, Fugier-Schmucker C, Marchiano F, Habermann B, Chal J, Nesmith AP, Gapon S, Wagner E, Gupta VA, Bassel-Duby R, Olson EN, Cohen AE, Parker KK, Pourquié O. Prednisolone rescues Duchenne muscular dystrophy phenotypes in human pluripotent stem cell-derived skeletal muscle in vitro. Proc Natl Acad Sci U S A 2021; 118:e2022960118. [PMID: 34260377 PMCID: PMC8285911 DOI: 10.1073/pnas.2022960118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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] [Indexed: 12/15/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a devastating genetic disease leading to degeneration of skeletal muscles and premature death. How dystrophin absence leads to muscle wasting remains unclear. Here, we describe an optimized protocol to differentiate human induced pluripotent stem cells (iPSC) to a late myogenic stage. This allows us to recapitulate classical DMD phenotypes (mislocalization of proteins of the dystrophin-associated glycoprotein complex, increased fusion, myofiber branching, force contraction defects, and calcium hyperactivation) in isogenic DMD-mutant iPSC lines in vitro. Treatment of the myogenic cultures with prednisolone (the standard of care for DMD) can dramatically rescue force contraction, fusion, and branching defects in DMD iPSC lines. This argues that prednisolone acts directly on myofibers, challenging the largely prevalent view that its beneficial effects are caused by antiinflammatory properties. Our work introduces a human in vitro model to study the onset of DMD pathology and test novel therapeutic approaches.
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Affiliation(s)
- Ziad Al Tanoury
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67411 Illkirch Graffenstaden, France
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Harvard Stem Cell Institute, Harvard University, Boston, MA 02138
| | - John F Zimmerman
- Harvard Stem Cell Institute, Harvard University, Boston, MA 02138
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, Harvard John A. Paulson School of Engineering and Applied Sciences, Boston, MA 02134
| | - Jyoti Rao
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Harvard Stem Cell Institute, Harvard University, Boston, MA 02138
| | - Daniel Sieiro
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Harvard Stem Cell Institute, Harvard University, Boston, MA 02138
| | - Harold M McNamara
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Department of Physics, Harvard University, Cambridge, MA 02138
| | - Thomas Cherrier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67411 Illkirch Graffenstaden, France
| | - Alejandra Rodríguez-delaRosa
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Harvard Stem Cell Institute, Harvard University, Boston, MA 02138
| | | | - Fanny Bousson
- Anagenesis Biotechnologies, 67400 Illkirch Graffenstaden, France
| | | | - Fabio Marchiano
- Aix-Marseille University, CNRS, Institut de Biologie du Développement de Marseille UMR 7288, The Turing Center for Living Systems, 13009 Marseille, France
| | - Bianca Habermann
- Aix-Marseille University, CNRS, Institut de Biologie du Développement de Marseille UMR 7288, The Turing Center for Living Systems, 13009 Marseille, France
| | - Jérome Chal
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67411 Illkirch Graffenstaden, France
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Harvard Stem Cell Institute, Harvard University, Boston, MA 02138
| | - Alexander P Nesmith
- Harvard Stem Cell Institute, Harvard University, Boston, MA 02138
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, Harvard John A. Paulson School of Engineering and Applied Sciences, Boston, MA 02134
| | - Svetlana Gapon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Erica Wagner
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
| | - Vandana A Gupta
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Eric N Olson
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Senator Paul D. Wellstone Muscular Dystrophy Cooperative Research Center, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
- Department of Physics, Harvard University, Cambridge, MA 02138
| | - Kevin Kit Parker
- Harvard Stem Cell Institute, Harvard University, Boston, MA 02138
- Disease Biophysics Group, Wyss Institute for Biologically Inspired Engineering, Harvard John A. Paulson School of Engineering and Applied Sciences, Boston, MA 02134
| | - Olivier Pourquié
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67411 Illkirch Graffenstaden, France;
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Harvard Stem Cell Institute, Harvard University, Boston, MA 02138
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25
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Chien MP, Brinks D, Testa-Silva G, Tian H, Phil Brooks F, Adam Y, Bloxham B, Gmeiner B, Kheifets S, Cohen AE. Photoactivated voltage imaging in tissue with an archaerhodopsin-derived reporter. Sci Adv 2021; 7:7/19/eabe3216. [PMID: 33952514 PMCID: PMC8099184 DOI: 10.1126/sciadv.abe3216] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 03/15/2021] [Indexed: 05/19/2023]
Abstract
Photoactivated genetically encoded voltage indicators (GEVIs) have the potential to enable optically sectioned voltage imaging at the intersection of a photoactivation beam and an imaging beam. We developed a pooled high-throughput screen to identify archaerhodopsin mutants with enhanced photoactivation. After screening ~105 cells, we identified a novel GEVI, NovArch, whose one-photon near-infrared fluorescence is reversibly enhanced by weak one-photon blue or two-photon near-infrared excitation. Because the photoactivation leads to fluorescent signals catalytically rather than stoichiometrically, high fluorescence signals, optical sectioning, and high time resolution are achieved simultaneously at modest blue or two-photon laser power. We demonstrate applications of the combined molecular and optical tools to optical mapping of membrane voltage in distal dendrites in acute mouse brain slices and in spontaneously active neurons in vivo.
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Affiliation(s)
- Miao-Ping Chien
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Daan Brinks
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Imaging Physics, Delft University of Technology, Delft, Netherlands
| | - Guilherme Testa-Silva
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Cambridge, MA 02138, USA
| | - He Tian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - F Phil Brooks
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yoav Adam
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Blox Bloxham
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Benjamin Gmeiner
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Simon Kheifets
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
- Howard Hughes Medical Institute, Cambridge, MA 02138, USA
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26
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Xie ME, Adam Y, Fan LZ, Böhm UL, Kinsella I, Zhou D, Rozsa M, Singh A, Svoboda K, Paninski L, Cohen AE. High-fidelity estimates of spikes and subthreshold waveforms from 1-photon voltage imaging in vivo. Cell Rep 2021; 35:108954. [PMID: 33826882 PMCID: PMC8095336 DOI: 10.1016/j.celrep.2021.108954] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [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: 12/22/2020] [Revised: 02/24/2021] [Accepted: 03/15/2021] [Indexed: 11/24/2022] Open
Abstract
The ability to probe the membrane potential of multiple genetically defined neurons simultaneously would have a profound impact on neuroscience research. Genetically encoded voltage indicators are a promising tool for this purpose, and recent developments have achieved a high signal-to-noise ratio in vivo with 1-photon fluorescence imaging. However, these recordings exhibit several sources of noise and signal extraction remains a challenge. We present an improved signal extraction pipeline, spike-guided penalized matrix decomposition-nonnegative matrix factorization (SGPMD-NMF), which resolves supra- and subthreshold voltages in vivo. The method incorporates biophysical and optical constraints. We validate the pipeline with simultaneous patch-clamp and optical recordings from mouse layer 1 in vivo and with simulated and composite datasets with realistic noise. We demonstrate applications to mouse hippocampus expressing paQuasAr3-s or SomArchon1, mouse cortex expressing SomArchon1 or Voltron, and zebrafish spines expressing zArchon1.
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Affiliation(s)
- Michael E Xie
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yoav Adam
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Linlin Z Fan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Urs L Böhm
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ian Kinsella
- Department of Statistics, Columbia University, New York, NY 10027, USA
| | - Ding Zhou
- Department of Statistics, Columbia University, New York, NY 10027, USA
| | - Marton Rozsa
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Amrita Singh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Liam Paninski
- Department of Statistics, Columbia University, New York, NY 10027, USA.
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
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27
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Werley CA, Boccardo S, Rigamonti A, Hansson EM, Cohen AE. Multiplexed Optical Sensors in Arrayed Islands of Cells for multimodal recordings of cellular physiology. Nat Commun 2020; 11:3881. [PMID: 32753572 PMCID: PMC7403318 DOI: 10.1038/s41467-020-17607-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 09/15/2019] [Accepted: 07/07/2020] [Indexed: 11/29/2022] Open
Abstract
Cells typically respond to chemical or physical perturbations via complex signaling cascades which can simultaneously affect multiple physiological parameters, such as membrane voltage, calcium, pH, and redox potential. Protein-based fluorescent sensors can report many of these parameters, but spectral overlap prevents more than ~4 modalities from being recorded in parallel. Here we introduce the technique, MOSAIC, Multiplexed Optical Sensors in Arrayed Islands of Cells, where patterning of fluorescent sensor-encoding lentiviral vectors with a microarray printer enables parallel recording of multiple modalities. We demonstrate simultaneous recordings from 20 sensors in parallel in human embryonic kidney (HEK293) cells and in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), and we describe responses to metabolic and pharmacological perturbations. Together, these results show that MOSAIC can provide rich multi-modal data on complex physiological responses in multiple cell types.
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Affiliation(s)
- Christopher A Werley
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Q-State Biosciences, Cambridge, MA, 02139, USA
| | - Stefano Boccardo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Nobel Biocare AG, Kloten, Switzerland
| | - Alessandra Rigamonti
- Integrated Cardio Metabolic Centre, Department of Medicine Huddinge, Karolinska Institute, Huddinge, Sweden
| | - Emil M Hansson
- Integrated Cardio Metabolic Centre, Department of Medicine Huddinge, Karolinska Institute, Huddinge, Sweden
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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28
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McNamara HM, Salegame R, Al Tanoury Z, Xu H, Begum S, Ortiz G, Pourquie O, Cohen AE. Bioelectrical domain walls in homogeneous tissues. Nat Phys 2020; 16:357-364. [PMID: 33790984 PMCID: PMC8008956 DOI: 10.1038/s41567-019-0765-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Electrical signaling in biology is typically associated with action potentials, transient spikes in membrane voltage that return to baseline. Hodgkin-Huxley and related conductance-based models of electrophysiology belong to a more general class of reaction-diffusion equations which could, in principle, support spontaneous emergence of patterns of membrane voltage which are stable in time but structured in space. Here we show theoretically and experimentally that homogeneous or nearly homogeneous tissues can undergo spontaneous spatial symmetry breaking through a purely electrophysiological mechanism, leading to formation of domains with different resting potentials separated by stable bioelectrical domain walls. Transitions from one resting potential to another can occur through long-range migration of these domain walls. We map bioelectrical domain wall motion using all-optical electrophysiology in an engineered cell line and in human induced pluripotent stem cell (iPSC)-derived myoblasts. Bioelectrical domain wall migration may occur during embryonic development and during physiological signaling processes in polarized tissues. These results demonstrate that nominally homogeneous tissues can undergo spontaneous bioelectrical symmetry breaking.
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Affiliation(s)
- Harold M. McNamara
- Department of Physics, Harvard University
- Harvard-MIT Division of Health Sciences and Technology
| | - Rajath Salegame
- Department of Chemistry and Chemical Biology, Harvard University
| | - Ziad Al Tanoury
- Department of Genetics, Harvard Medical School
- Department of Pathology, Brigham and Women’s Hospital
| | - Haitan Xu
- Department of Chemistry and Chemical Biology, Harvard University
- Current address: State Key Laboratory for Mesoscopic Physics and Frontiers Science Center for Nano-optoelectronics, School of Physics, Peking University
| | - Shahinoor Begum
- Department of Chemistry and Chemical Biology, Harvard University
| | - Gloria Ortiz
- Department of Chemistry, University of California Berkeley
| | - Olivier Pourquie
- Department of Genetics, Harvard Medical School
- Department of Pathology, Brigham and Women’s Hospital
| | - Adam E. Cohen
- Department of Physics, Harvard University
- Department of Chemistry and Chemical Biology, Harvard University
- Howard Hughes Medical Institute
- Correspondence:
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29
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Fan LZ, Kheifets S, Böhm UL, Wu H, Piatkevich KD, Xie ME, Parot V, Ha Y, Evans KE, Boyden ES, Takesian AE, Cohen AE. All-Optical Electrophysiology Reveals the Role of Lateral Inhibition in Sensory Processing in Cortical Layer 1. Cell 2020; 180:521-535.e18. [PMID: 31978320 PMCID: PMC7259440 DOI: 10.1016/j.cell.2020.01.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [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: 05/23/2019] [Revised: 11/06/2019] [Accepted: 01/03/2020] [Indexed: 11/22/2022]
Abstract
Cortical layer 1 (L1) interneurons have been proposed as a hub for attentional modulation of underlying cortex, but the transformations that this circuit implements are not known. We combined genetically targeted voltage imaging with optogenetic activation and silencing to study the mechanisms underlying sensory processing in mouse barrel cortex L1. Whisker stimuli evoked precisely timed single spikes in L1 interneurons, followed by strong lateral inhibition. A mild aversive stimulus activated cholinergic inputs and evoked a bimodal distribution of spiking responses in L1. A simple conductance-based model that only contained lateral inhibition within L1 recapitulated the sensory responses and the winner-takes-all cholinergic responses, and the model correctly predicted that the network would function as a spatial and temporal high-pass filter for excitatory inputs. Our results demonstrate that all-optical electrophysiology can reveal basic principles of neural circuit function in vivo and suggest an intuitive picture for how L1 transforms sensory and modulatory inputs. VIDEO ABSTRACT.
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Affiliation(s)
- Linlin Z Fan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Simon Kheifets
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Urs L Böhm
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hao Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Kiryl D Piatkevich
- Media Lab and McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Michael E Xie
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Vicente Parot
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Yooree Ha
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - Edward S Boyden
- Media Lab and McGovern Institute for Brain Research, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Anne E Takesian
- Harvard Medical School, Boston, MA, USA; Massachusetts Eye and Ear Infirmary, Boston, MA, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Department of Physics, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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30
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McNamara HM, Salegame R, Al Tanoury Z, Xu H, Ortiz G, Pourquie O, Cohen AE. Bioelectrical Signaling and Pattern Formation via Domain Wall Migration. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.3299] [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: 10/25/2022] Open
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31
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Affiliation(s)
- Adam E. Cohen
- Departments of Chemistry and Chemical Biology and PhysicsHarvard University Cambridge MA USA
- Howard Hughes Medical Institute Chevy Chase MD USA
| | - Zheng Shi
- Departments of Chemistry and Chemical Biology and PhysicsHarvard University Cambridge MA USA
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32
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Abstract
The fluid-mosaic model posits a liquid-like plasma membrane, which can flow in response to tension gradients. It is widely assumed that membrane flow transmits local changes in membrane tension across the cell in milliseconds, mediating long-range signaling. Here, we show that propagation of membrane tension occurs quickly in cell-attached blebs but is largely suppressed in intact cells. The failure of tension to propagate in cells is explained by a fluid dynamical model that incorporates the flow resistance from cytoskeleton-bound transmembrane proteins. Perturbations to tension propagate diffusively, with a diffusion coefficient Dσ ∼0.024 μm2/s in HeLa cells. In primary endothelial cells, local increases in membrane tension lead only to local activation of mechanosensitive ion channels and to local vesicle fusion. Thus, membrane tension is not a mediator of long-range intracellular signaling, but local variations in tension mediate distinct processes in sub-cellular domains.
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Affiliation(s)
- Zheng Shi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute
| | - Zachary T Graber
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute.
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33
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McNamara HM, Dodson S, Huang YL, Miller EW, Sandstede B, Cohen AE. Geometry-Dependent Arrhythmias in Electrically Excitable Tissues. Cell Syst 2018; 7:359-370.e6. [PMID: 30292705 PMCID: PMC6204347 DOI: 10.1016/j.cels.2018.08.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 04/26/2018] [Revised: 07/14/2018] [Accepted: 08/28/2018] [Indexed: 12/12/2022]
Abstract
Little is known about how individual cells sense the macroscopic geometry of their tissue environment. Here, we explore whether long-range electrical signaling can convey information on tissue geometry to individual cells. First, we studied an engineered electrically excitable cell line. Cells grown in patterned islands of different shapes showed remarkably diverse firing patterns under otherwise identical conditions, including regular spiking, period-doubling alternans, and arrhythmic firing. A Hodgkin-Huxley numerical model quantitatively reproduced these effects, showing how the macroscopic geometry affected the single-cell electrophysiology via the influence of gap junction-mediated electrical coupling. Qualitatively similar geometry-dependent dynamics were observed in human induced pluripotent stem cell (iPSC)-derived cardiomyocytes. The cardiac results urge caution in translating observations of arrhythmia in vitro to predictions in vivo, where the tissue geometry is very different. We study how to extrapolate electrophysiological measurements between tissues with different geometries and different gap junction couplings.
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Affiliation(s)
- Harold M McNamara
- Department of Physics, Harvard University, Cambridge, MA 02138, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA 02138, USA
| | - Stephanie Dodson
- Department of Applied Mathematics, Brown University, Providence, RI 02912, USA
| | - Yi-Lin Huang
- Departments of Chemistry, Molecular and Cell Biology, and Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Evan W Miller
- Departments of Chemistry, Molecular and Cell Biology, and Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Björn Sandstede
- Department of Applied Mathematics, Brown University, Providence, RI 02912, USA
| | - Adam E Cohen
- Department of Physics, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Cambridge, MA 02138, USA.
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34
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Fan LZ, Nehme R, Adam Y, Jung ES, Wu H, Eggan K, Arnold DB, Cohen AE. All-optical synaptic electrophysiology probes mechanism of ketamine-induced disinhibition. Nat Methods 2018; 15:823-831. [PMID: 30275587 PMCID: PMC6204345 DOI: 10.1038/s41592-018-0142-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [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: 12/20/2017] [Accepted: 07/15/2018] [Indexed: 02/02/2023]
Abstract
Optical assays of synaptic strength would greatly facilitate studies of neuronal transmission and its dysregulation in disease. Here we introduce a genetic toolbox for all-optical interrogation of synaptic electrophysiology (‘synOptopatch’) via mutually exclusive expression of a channelrhodopsin actuator and an archaerhodopsin-derived voltage indicator. Optically induced activity in the channelrhodopsin-expressing neurons generated excitatory and inhibitory post-synaptic potentials which were optically resolved in the reporter-expressing neurons. We further developed a yellow spine-targeted Ca2+ indicator to localize optogenetically triggered synaptic inputs. We demonstrated synOptopatch recordings in cultured rodent neurons and in acute rodent brain slice. In synOptopatch measurements of primary rodent cultures, acute ketamine administration suppressed disynaptic inhibitory feedbacks, mimicking the effect of this drug on network function in both rodents and humans. We localized this action of ketamine to excitatory synapses onto interneurons. These results establish an in vitro all-optical model of disynaptic disinhibition, a synaptic defect hypothesized in schizophrenia-associated psychosis.
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Affiliation(s)
- Linlin Z Fan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Ralda Nehme
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yoav Adam
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Eun Sun Jung
- Department of Biology, Section of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Hao Wu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stanley Center for Psychiatric Research, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Don B Arnold
- Department of Biology, Section of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA. .,Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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35
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36
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Kiskinis E, Kralj JM, Zou P, Weinstein EN, Zhang H, Tsioras K, Wiskow O, Ortega JA, Eggan K, Cohen AE. All-Optical Electrophysiology for High-Throughput Functional Characterization of a Human iPSC-Derived Motor Neuron Model of ALS. Stem Cell Reports 2018; 10:1991-2004. [PMID: 29779896 PMCID: PMC5993648 DOI: 10.1016/j.stemcr.2018.04.020] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [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: 10/17/2017] [Revised: 04/20/2018] [Accepted: 04/22/2018] [Indexed: 11/26/2022] Open
Abstract
Human induced pluripotent stem cell (iPSC)-derived neurons are an attractive substrate for modeling disease, yet the heterogeneity of these cultures presents a challenge for functional characterization by manual patch-clamp electrophysiology. Here, we describe an optimized all-optical electrophysiology, “Optopatch,” pipeline for high-throughput functional characterization of human iPSC-derived neuronal cultures. We demonstrate the method in a human iPSC-derived motor neuron (iPSC-MN) model of amyotrophic lateral sclerosis (ALS). In a comparison of iPSC-MNs with an ALS-causing mutation (SOD1 A4V) with their genome-corrected controls, the mutants showed elevated spike rates under weak or no stimulus and greater likelihood of entering depolarization block under strong optogenetic stimulus. We compared these results with numerical simulations of simple conductance-based neuronal models and with literature results in this and other iPSC-based models of ALS. Our data and simulations suggest that deficits in slowly activating potassium channels may underlie the changes in electrophysiology in the SOD1 A4V mutation. All-optical electrophysiology enables high-throughput assays in hiPSC-derived neurons Neurons derived from ALS patients fire differently from genome-corrected controls A deficit in the Kv7 potassium current can explain the difference in firing
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Affiliation(s)
- Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Joel M Kralj
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Peng Zou
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Eli N Weinstein
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Hongkang Zhang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Konstantinos Tsioras
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ole Wiskow
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - J Alberto Ortega
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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Werley CA, Chien MP, Cohen AE. Ultrawidefield microscope for high-speed fluorescence imaging and targeted optogenetic stimulation. Biomed Opt Express 2017; 8:5794-5813. [PMID: 29296505 PMCID: PMC5745120 DOI: 10.1364/boe.8.005794] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/16/2017] [Accepted: 10/31/2017] [Indexed: 05/08/2023]
Abstract
The rapid increase in the number and quality of fluorescent reporters and optogenetic actuators has yielded a powerful set of tools for recording and controlling cellular state and function. To achieve the full benefit of these tools requires improved optical systems with high light collection efficiency, high spatial and temporal resolution, and patterned optical stimulation, in a wide field of view (FOV). Here we describe our 'Firefly' microscope, which achieves these goals in a Ø6 mm FOV. The Firefly optical system is optimized for simultaneous photostimulation and fluorescence imaging in cultured cells. All but one of the optical elements are commercially available, yet the microscope achieves 10-fold higher light collection efficiency at its design magnification than the comparable commercially available microscope using the same objective. The Firefly microscope enables all-optical electrophysiology ('Optopatch') in cultured neurons with a throughput and information content unmatched by other neuronal phenotyping systems. This capability opens possibilities in disease modeling and phenotypic drug screening. We also demonstrate applications of the system to voltage and calcium recordings in human induced pluripotent stem cell derived cardiomyocytes.
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Affiliation(s)
- Christopher A. Werley
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA 02138, USA
| | - Miao-Ping Chien
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA 02138, USA
| | - Adam E. Cohen
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, 17 Oxford St, Cambridge, MA 02138, USA
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Zhang H, Cohen AE. Optogenetic Approaches to Drug Discovery in Neuroscience and Beyond. Trends Biotechnol 2017; 35:625-639. [PMID: 28552428 DOI: 10.1016/j.tibtech.2017.04.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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: 03/03/2017] [Revised: 04/08/2017] [Accepted: 04/10/2017] [Indexed: 12/11/2022]
Abstract
Recent advances in optogenetics have opened new routes to drug discovery, particularly in neuroscience. Physiological cellular assays probe functional phenotypes that connect genomic data to patient health. Optogenetic tools, in particular tools for all-optical electrophysiology, now provide a means to probe cellular disease models with unprecedented throughput and information content. These techniques promise to identify functional phenotypes associated with disease states and to identify compounds that improve cellular function regardless of whether the compound acts directly on a target or through a bypass mechanism. This review discusses opportunities and unresolved challenges in applying optogenetic techniques throughout the discovery pipeline - from target identification and validation, to target-based and phenotypic screens, to clinical trials.
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Affiliation(s)
- Hongkang Zhang
- Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Howard Hughes Medical Institute, Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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Abstract
Membrane voltages are ubiquitous throughout cell biology. Voltage is most commonly associated with excitable cells such as neurons and cardiomyocytes, although many other cell types and organelles also support electrical signaling. Voltage imaging in vivo would offer unique capabilities in reporting the spatial pattern and temporal dynamics of electrical signaling at the cellular and circuit levels. Voltage is not directly visible, and so a longstanding challenge has been to develop genetically encoded fluorescent voltage indicator proteins. Recent advances have led to a profusion of new voltage indicators, based on different scaffolds and with different tradeoffs between voltage sensitivity, speed, brightness, and spectrum. In this review, we describe recent advances in design and applications of genetically-encoded voltage indicators (GEVIs). We also highlight the protein engineering strategies employed to improve the dynamic range and kinetics of GEVIs and opportunities for future advances.
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Affiliation(s)
- Yongxian Xu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Peng Zou
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China.
| | - Adam E Cohen
- Departments of Chemistry and Chemical Biology and of Physics, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute.
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Affiliation(s)
- Adam E Cohen
- Departments of Chemistry and Chemical Biology and Physics, Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts.
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Brinks D, Adam Y, Kheifets S, Cohen AE. Painting with Rainbows: Patterning Light in Space, Time, and Wavelength for Multiphoton Optogenetic Sensing and Control. Acc Chem Res 2016; 49:2518-2526. [PMID: 27786461 DOI: 10.1021/acs.accounts.6b00415] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Photons are a fascinating reagent, flowing and reacting quite differently compared to more massive and less ephemeral particles of matter. The optogenetic palette comprises an ever growing set of light-responsive proteins, which open the possibility of using light to perturb and to measure biological processes with great precision in space and time. Yet there are limits on what light can achieve. Diffraction limits the smallest features, and scattering in tissue limits the largest. Photobleaching, diffusion of photogenerated products, and optical crosstalk between overlapping absorption spectra further muddy the optogenetic picture, particularly when one wants to use multiple optogenetic tools simultaneously. But these obstacles are surmountable. Most light-responsive proteins and small molecules undergo more than one light-driven transition, often with different action spectra and kinetics. By overlapping multiple laser beams, carefully patterned in space, time, and wavelength, one can steer molecules into fluorescent or nonfluorescent, active or inactive conformations. By doing so, one can often circumvent the limitations of simple one-photon excitation and achieve new imaging and stimulation capabilities. These include subdiffraction spatial resolution, optical sectioning, robustness to light scattering, and multiplexing of more channels than can be achieved with simple one-photon excitation. The microbial rhodopsins are a particularly rich substrate for this type of multiphoton optical control. The natural diversity of these proteins presents a huge range of starting materials. The spectroscopy and photocycles of microbial rhodopsins are relatively well understood, providing states with absorption maxima across the visible spectrum, which can be accessed on experimentally convenient time scales. A long history of mutational studies in microbial rhodopsins allows semirational protein engineering. Mutants of Archaerhodopsin 3 (Arch) come in all the colors of the rainbow. In a solution of purified Arch-eGFP, a focused green laser excites eGFP fluorescence throughout the laser path, while a focused red laser excites fluorescence of Arch only near the focus, indicative of multiphoton fluorescence. This nonlinearity occurs at a laser intensity ∼1010-fold lower than in conventional two-photon microscopy! The mutant Arch(D95H) shows photoswitchable optical bistability. In a lawn of E. coli expressing this mutant, illumination with patterned blue light converts the molecule into a state that is fluorescent. Illumination with red light excites this fluorescence, and gradually resets the molecules back to the non-fluorescent state. This review describes the new types of molecular logic that can be implemented with multi-photon control of microbial rhodopsins, from whole-brain activity mapping to measurements of absolute membrane voltage. Part of our goal in this Account is to describe recent work in nonlinear optogenetics, but we also present a variety of interesting things one could do if only the right optogenetic molecules were available. This latter component is intended to inspire future spectroscopic, protein discovery, and protein engineering work.
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Affiliation(s)
- Daan Brinks
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Yoav Adam
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Simon Kheifets
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Adam E. Cohen
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department
of Physics, Harvard University, Cambridge, Massachusetts 02138, United States
- Howard
Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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Dempsey GT, Chaudhary KW, Atwater N, Nguyen C, Brown BS, McNeish JD, Cohen AE, Kralj JM. Cardiotoxicity screening with simultaneous optogenetic pacing, voltage imaging and calcium imaging. J Pharmacol Toxicol Methods 2016; 81:240-50. [DOI: 10.1016/j.vascn.2016.05.003] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 05/02/2016] [Accepted: 05/09/2016] [Indexed: 12/23/2022]
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Brinks D, Klein AJ, Cohen AE. Two-Photon Lifetime Imaging of Voltage Indicating Proteins as a Probe of Absolute Membrane Voltage. Biophys J 2016; 109:914-21. [PMID: 26331249 DOI: 10.1016/j.bpj.2015.07.038] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 06/15/2015] [Accepted: 07/28/2015] [Indexed: 01/03/2023] Open
Abstract
Genetically encoded voltage indicators (GEVIs) can report cellular electrophysiology with high resolution in space and time. Two-photon (2P) fluorescence has been explored as a means to image voltage in tissue. Here, we used the 2P electronic excited-state lifetime to probe absolute membrane voltage in a manner that is insensitive to the protein expression level, illumination intensity, or photon detection efficiency. First, we tested several GEVIs for 2P brightness, response speed, and voltage sensitivity. ASAP1 and a previously described citrine-Arch electrochromic Förster resonance energy transfer sensor (dubbed CAESR) showed the best characteristics. We then characterized the voltage-dependent lifetime of ASAP1, CAESR, and ArcLight under voltage-clamp conditions. ASAP1 and CAESR showed voltage-dependent lifetimes, whereas ArcLight did not. These results establish 2P fluorescence lifetime imaging as a viable means of measuring absolute membrane voltage. We discuss the prospects and improvements necessary for applications in tissue.
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Affiliation(s)
- Daan Brinks
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Aaron J Klein
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; Department of Physics, Harvard University, Cambridge, Massachusetts; Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts.
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Zhang H, Reichert E, Cohen AE. Optical electrophysiology for probing function and pharmacology of voltage-gated ion channels. eLife 2016; 5. [PMID: 27215841 PMCID: PMC4907688 DOI: 10.7554/elife.15202] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [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: 02/12/2016] [Accepted: 05/12/2016] [Indexed: 12/15/2022] Open
Abstract
Voltage-gated ion channels mediate electrical dynamics in excitable tissues and are an important class of drug targets. Channels can gate in sub-millisecond timescales, show complex manifolds of conformational states, and often show state-dependent pharmacology. Mechanistic studies of ion channels typically involve sophisticated voltage-clamp protocols applied through manual or automated electrophysiology. Here, we develop all-optical electrophysiology techniques to study activity-dependent modulation of ion channels, in a format compatible with high-throughput screening. Using optical electrophysiology, we recapitulate many voltage-clamp protocols and apply to Nav1.7, a channel implicated in pain. Optical measurements reveal that a sustained depolarization strongly potentiates the inhibitory effect of PF-04856264, a Nav1.7-specific blocker. In a pilot screen, we stratify a library of 320 FDA-approved compounds by binding mechanism and kinetics, and find close concordance with patch clamp measurements. Optical electrophysiology provides a favorable tradeoff between throughput and information content for studies of NaV channels, and possibly other voltage-gated channels. DOI:http://dx.doi.org/10.7554/eLife.15202.001 Ion channels are specialized proteins that span the cell membrane. When activated, these channels allow ions to pass through them, which can produce electrical spikes that carry information in nerve cells and regulate the beating of the heart. Researchers interested in understanding how ion channels behave often use a technique called patch clamp electrophysiology to measure the electrical current across the cell membrane. The technique can be used to probe if a specific drug can block an ion channel, but it is not well suited to screening lots of potential drugs because it is slow and expensive. A group of ion channels known as voltage-gated sodium channels play an important role in generating the electrical spikes in nerve cells. One subtype called NaV1.7 is involved in sensing pain and drugs that block NaV1.7 might be useable as painkillers, but only if they are specific to this channel. This is because there are many similar sodium channels that are important in other processes in the body. Zhang et al. have now developed a new light-based technique to measure how ion channels behave. The technique uses light to activate the channel and a fluorescent protein to report on the membrane’s voltage. Zhang et al. used the new technique to probe how sodium channels, in particular NaV1.7, interact with drugs. Mammalian cells grown in the lab were engineered to produce NaV1.7, a light-activated ion channel (called CheRiff), and a fluorescent reporter protein. A flash of blue light delivered to the cells activated CheRiff, which in turn activated NaV1.7. At the same time, the fluorescence of the reporter protein was used as a read-out of NaV1.7’s activity. Zhang et al. showed that they could reproduce many conventional electrophysiology measurements using their new light-based approach. Optical measurements were then used to screen 320 drugs to see whether they could block NaV1.7. The results of the screen corresponded closely with measurements made using conventional electrophysiology. These results demonstrate that the new optical technique is both fast and precise enough to be used in drug discovery. Further studies could now ask if this optical technique can also be used to study other ion channels, such as potassium channels and calcium channels. DOI:http://dx.doi.org/10.7554/eLife.15202.002
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Affiliation(s)
- Hongkang Zhang
- Departments of Chemistry and Chemical Biology and Physics, Harvard University, Cambridge, United States.,Howard Hughes Medical Institute, Harvard University, Cambridge, United States
| | - Elaine Reichert
- Departments of Chemistry and Chemical Biology and Physics, Harvard University, Cambridge, United States
| | - Adam E Cohen
- Departments of Chemistry and Chemical Biology and Physics, Harvard University, Cambridge, United States.,Howard Hughes Medical Institute, Harvard University, Cambridge, United States
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Abdelfattah AS, Farhi SL, Zhao Y, Brinks D, Zou P, Ruangkittisakul A, Platisa J, Pieribone VA, Ballanyi K, Cohen AE, Campbell RE. A Bright and Fast Red Fluorescent Protein Voltage Indicator That Reports Neuronal Activity in Organotypic Brain Slices. J Neurosci 2016; 36:2458-72. [PMID: 26911693 PMCID: PMC4764664 DOI: 10.1523/jneurosci.3484-15.2016] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [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: 09/15/2015] [Revised: 12/16/2015] [Accepted: 01/15/2016] [Indexed: 01/09/2023] Open
Abstract
Optical imaging of voltage indicators based on green fluorescent proteins (FPs) or archaerhodopsin has emerged as a powerful approach for detecting the activity of many individual neurons with high spatial and temporal resolution. Relative to green FP-based voltage indicators, a bright red-shifted FP-based voltage indicator has the intrinsic advantages of lower phototoxicity, lower autofluorescent background, and compatibility with blue-light-excitable channelrhodopsins. Here, we report a bright red fluorescent voltage indicator (fluorescent indicator for voltage imaging red; FlicR1) with properties that are comparable to the best available green indicators. To develop FlicR1, we used directed protein evolution and rational engineering to screen libraries of thousands of variants. FlicR1 faithfully reports single action potentials (∼3% ΔF/F) and tracks electrically driven voltage oscillations at 100 Hz in dissociated Sprague Dawley rat hippocampal neurons in single trial recordings. Furthermore, FlicR1 can be easily imaged with wide-field fluorescence microscopy. We demonstrate that FlicR1 can be used in conjunction with a blue-shifted channelrhodopsin for all-optical electrophysiology, although blue light photoactivation of the FlicR1 chromophore presents a challenge for applications that require spatially overlapping yellow and blue excitation.
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Affiliation(s)
- Ahmed S Abdelfattah
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Samouil L Farhi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Yongxin Zhao
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Daan Brinks
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Peng Zou
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | | | - Jelena Platisa
- The John B. Pierce Laboratory, Inc., New Haven, Connecticut 06519, Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Vincent A Pieribone
- The John B. Pierce Laboratory, Inc., New Haven, Connecticut 06519, Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06520, Neurobiology, Yale University School of Medicine, New Haven, Connecticut 06510
| | - Klaus Ballanyi
- Department of Physiology, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, Department of Physics, Harvard University, Cambridge, Massachusetts 02138, and Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts 02138
| | - Robert E Campbell
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada,
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Lee H, Brinks D, Cohen AE. Two-photon imaging of a magneto-fluorescent indicator for 3D optical magnetometry. Opt Express 2015; 23:28022-28030. [PMID: 26480460 DOI: 10.1364/oe.23.028022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We developed an optical method to visualize the three-dimensional distribution of magnetic field strength around magnetic microstructures. We show that the two-photon-excited fluorescence of a chained donor-bridge-acceptor compound, phenanthrene-(CH2)12-O-(CH2)2-N,N-dimethylaniline, is sensitive to ambient magnetic field strength. A test structure is immersed in a solution of the magneto-fluorescent indicator and a custom two-photon microscope maps the fluorescence of this compound. The decay kinetics of the electronic excited state provide a measure of magnetic field that is insensitive to photobleaching, indicator concentration, or local variations in optical excitation or collection efficiency.
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Henderson MJ, Baldwin HA, Werley CA, Boccardo S, Whitaker LR, Yan X, Holt GT, Schreiter ER, Looger LL, Cohen AE, Kim DS, Harvey BK. A Low Affinity GCaMP3 Variant (GCaMPer) for Imaging the Endoplasmic Reticulum Calcium Store. PLoS One 2015; 10:e0139273. [PMID: 26451944 PMCID: PMC4599735 DOI: 10.1371/journal.pone.0139273] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [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: 05/12/2015] [Accepted: 09/09/2015] [Indexed: 12/22/2022] Open
Abstract
Endoplasmic reticulum calcium homeostasis is critical for cellular functions and is disrupted in diverse pathologies including neurodegeneration and cardiovascular disease. Owing to the high concentration of calcium within the ER, studying this subcellular compartment requires tools that are optimized for these conditions. To develop a single-fluorophore genetically encoded calcium indicator for this organelle, we targeted a low affinity variant of GCaMP3 to the ER lumen (GCaMPer (10.19)). A set of viral vectors was constructed to express GCaMPer in human neuroblastoma cells, rat primary cortical neurons, and human induced pluripotent stem cell-derived cardiomyocytes. We observed dynamic changes in GCaMPer (10.19) fluorescence in response to pharmacologic manipulations of the ER calcium store. Additionally, periodic calcium efflux from the ER was observed during spontaneous beating of cardiomyocytes. GCaMPer (10.19) has utility in imaging ER calcium in living cells and providing insight into luminal calcium dynamics under physiologic and pathologic states.
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Affiliation(s)
- Mark J. Henderson
- National Institute on Drug Abuse, National Institutes of Health, 251 Bayview Blvd, Baltimore, Maryland, 21224, United States of America
- * E-mail: (MJH); (BKH)
| | - Heather A. Baldwin
- National Institute on Drug Abuse, National Institutes of Health, 251 Bayview Blvd, Baltimore, Maryland, 21224, United States of America
| | - Christopher A. Werley
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02138, United States of America
| | - Stefano Boccardo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02138, United States of America
| | - Leslie R. Whitaker
- National Institute on Drug Abuse, National Institutes of Health, 251 Bayview Blvd, Baltimore, Maryland, 21224, United States of America
| | - Xiaokang Yan
- National Institute on Drug Abuse, National Institutes of Health, 251 Bayview Blvd, Baltimore, Maryland, 21224, United States of America
| | - Graham T. Holt
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, United States of America
| | - Eric R. Schreiter
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, United States of America
| | - Loren L. Looger
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, United States of America
| | - Adam E. Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, 02138, United States of America
- Department of Physics, Harvard University, Cambridge, Massachusetts, 02138, United States of America
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, 02138, United States of America
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, 02138, United States of America
| | - Douglas S. Kim
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, United States of America
| | - Brandon K. Harvey
- National Institute on Drug Abuse, National Institutes of Health, 251 Bayview Blvd, Baltimore, Maryland, 21224, United States of America
- * E-mail: (MJH); (BKH)
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Labay BJ, Hendrickson DA, Cohen AE, Bonner TH, King RS, Kleinsasser LJ, Linam GW, Winemiller KO. Can Species Distribution Models Aid Bioassessment when Reference Sites are Lacking? Tests Based on Freshwater Fishes. Environ Manage 2015; 56:835-846. [PMID: 26092052 DOI: 10.1007/s00267-015-0567-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 06/15/2015] [Indexed: 06/04/2023]
Abstract
Recent literature reviews of bioassessment methods raise questions about use of least-impacted reference sites to characterize natural conditions that no longer exist within contemporary landscapes. We explore an alternate approach for bioassessment that uses species site occupancy data from museum archives as input for species distribution models (SDMs) stacked to predict species assemblages of freshwater fishes in Texas. When data for estimating reference conditions are lacking, deviation between richness of contemporary versus modeled species assemblages could provide a means to infer relative biological integrity at appropriate spatial scales. We constructed SDMs for 100 freshwater fish species to compare predicted species assemblages to data on contemporary assemblages acquired by four independent surveys that sampled 269 sites. We then compared site-specific observed/predicted ratios of the number of species at sites to scores from a multimetric index of biotic integrity (IBI). Predicted numbers of species were moderately to strongly correlated with the numbers observed by the four surveys. We found significant, though weak, relationships between observed/predicted ratios and IBI scores. SDM-based assessments identified patterns of local assemblage change that were congruent with IBI inferences; however, modeling artifacts that likely contributed to over-prediction of species presence may restrict the stand-alone use of SDM-derived patterns for bioassessment and therefore warrant examination. Our results suggest that when extensive standardized survey data that include reference sites are lacking, as is commonly the case, SDMs derived from generally much more readily available species site occupancy data could be used to provide a complementary tool for bioassessment.
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Affiliation(s)
- Ben J Labay
- Department of Integrative Biology, Biodiversity Collections, University of Texas, Austin, TX, USA,
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Shon MJ, Cohen AE. Nano-mechanical measurements of protein-DNA interactions with a silicon nitride pulley. Nucleic Acids Res 2015; 44:e7. [PMID: 26338777 PMCID: PMC4705685 DOI: 10.1093/nar/gkv866] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 04/17/2014] [Accepted: 08/15/2015] [Indexed: 01/13/2023] Open
Abstract
Proteins adhere to DNA at locations and with strengths that depend on the protein conformation, the underlying DNA sequence and the ionic content of the solution. A facile technique to probe the positions and strengths of protein-DNA binding would aid in understanding these important interactions. Here, we describe a 'DNA pulley' for position-resolved nano-mechanical measurements of protein-DNA interactions. A molecule of λ DNA is tethered by one end to a glass surface, and by the other end to a magnetic bead. The DNA is stretched horizontally by a magnet, and a nanoscale knife made of silicon nitride is manipulated to contact, bend and scan along the DNA. The mechanical profile of the DNA at the contact with the knife is probed via nanometer-precision optical tracking of the magnetic bead. This system enables detection of protein bumps on the DNA and localization of their binding sites. We study theoretically the technical requirements to detect mechanical heterogeneities in the DNA itself.
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Affiliation(s)
- Min Ju Shon
- Department of Chemistry and Chemical Biology and Department of Physics, Harvard University and Howard Hughes Medical Institute, Cambridge, MA 02138, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology and Department of Physics, Harvard University and Howard Hughes Medical Institute, Cambridge, MA 02138, USA
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