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Article ; Online: Overview on Research and Clinical Applications of Optogenetics.

Towne, Chris / Thompson, Kimberly R

Current protocols in pharmacology

2016 Volume 75, Page(s) 11.19.1–11.19.21

Abstract: Optogenetics is a method that uses light to control cells in living tissue, typically neurons, that have been modified to express light-sensitive ion channels and pumps. The approach facilitates neuromodulation in brain preparations and freely moving ... ...

Abstract	Optogenetics is a method that uses light to control cells in living tissue, typically neurons, that have been modified to express light-sensitive ion channels and pumps. The approach facilitates neuromodulation in brain preparations and freely moving animals with unmatched spatial and temporal resolution. This optogenetics overview describes the vast array of light-sensitive proteins available and the methods used to deliver them to tissue and modulate them with light. How these methods have so far enhanced our knowledge of fundamental neuroscience and psychiatric disease will be discussed as well as how they may contribute to drug discovery in the future. Finally, the potential rewards and risks of therapeutic gene transfer of optogenetic proteins in humans will be considered. © 2016 by John Wiley & Sons, Inc.
MeSH term(s)	Animals ; Brain/physiology ; Brain Diseases/therapy ; Drug Discovery/methods ; Genetic Therapy/methods ; Humans ; Ion Channels/metabolism ; Ion Channels/physiology ; Light ; Nervous System Physiological Phenomena ; Neural Pathways ; Neurons/metabolism ; Neurons/physiology ; Neurotransmitter Agents/metabolism ; Opsins/genetics ; Opsins/metabolism ; Optogenetics/instrumentation ; Optogenetics/methods
Chemical Substances	Ion Channels ; Neurotransmitter Agents ; Opsins
Language	English
Publishing date	2016-12-13
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1934-8290
ISSN (online)	1934-8290
DOI	10.1002/cpph.13
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Article ; Online: eNpHR: a Natronomonas halorhodopsin enhanced for optogenetic applications.

Gradinaru, Viviana / Thompson, Kimberly R / Deisseroth, Karl

Brain cell biology

2008 Volume 36, Issue 1-4, Page(s) 129–139

Abstract: Temporally precise inhibition of distinct cell types in the intact nervous system has been enabled by the microbial halorhodopsin NpHR, a fast light-activated electrogenic Cl(-) pump. While neurons can be optically hyperpolarized and inhibited from ... ...

Abstract	Temporally precise inhibition of distinct cell types in the intact nervous system has been enabled by the microbial halorhodopsin NpHR, a fast light-activated electrogenic Cl(-) pump. While neurons can be optically hyperpolarized and inhibited from firing action potentials at moderate NpHR expression levels, we have encountered challenges with pushing expression to extremely high levels, including apparent intracellular accumulations. We therefore sought to molecularly engineer NpHR to achieve strong expression without these cellular side effects. We found that high expression correlated with endoplasmic reticulum (ER) accumulation, and that under these conditions NpHR colocalized with ER proteins containing the KDEL ER retention sequence. We screened a number of different putative modulators of membrane trafficking and identified a combination of two motifs, an N-terminal signal peptide and a C-terminal ER export sequence, that markedly promoted membrane localization and ER export defined by confocal microscopy and whole-cell patch clamp. The modified NpHR displayed increased peak photocurrent in the absence of aggregations or toxicity, and potent optical inhibition was observed not only in vitro but also in vivo with thalamic single-unit recording. The new enhanced NpHR (eNpHR) allows safe, high-level expression in mammalian neurons, without toxicity and with augmented inhibitory function, in vitro and in vivo.
MeSH term(s)	Action Potentials/physiology ; Animals ; Animals, Newborn ; Cells, Cultured ; Electrophysiology/methods ; Endoplasmic Reticulum/metabolism ; Halorhodopsins/genetics ; Halorhodopsins/metabolism ; Halorhodopsins/physiology ; Hippocampus/cytology ; Mice ; Mice, Inbred C57BL ; Microscopy, Confocal/instrumentation ; Microscopy, Confocal/methods ; Neurons/cytology ; Neurons/metabolism ; Neurons/physiology ; Patch-Clamp Techniques/methods ; Rats ; Rats, Sprague-Dawley
Chemical Substances	Halorhodopsins
Language	English
Publishing date	2008-08-02
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2215081-X
ISSN	1559-7113 ; 1559-7105
ISSN (online)	1559-7113
ISSN	1559-7105
DOI	10.1007/s11068-008-9027-6
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Article ; Online: Orderly recruitment of motor units under optical control in vivo.

Llewellyn, Michael E / Thompson, Kimberly R / Deisseroth, Karl / Delp, Scott L

Nature medicine

2010 Volume 16, Issue 10, Page(s) 1161–1165

Abstract: A drawback of electrical stimulation for muscle control is that large, fatigable motor units are preferentially recruited before smaller motor units by the lowest-intensity electrical cuff stimulation. This phenomenon limits therapeutic applications ... ...

Abstract	A drawback of electrical stimulation for muscle control is that large, fatigable motor units are preferentially recruited before smaller motor units by the lowest-intensity electrical cuff stimulation. This phenomenon limits therapeutic applications because it is precisely the opposite of the normal physiological (orderly) recruitment pattern; therefore, a mechanism to achieve orderly recruitment has been a long-sought goal in physiology, medicine and engineering. Here we demonstrate a technology for reliable orderly recruitment in vivo. We find that under optical control with microbial opsins, recruitment of motor units proceeds in the physiological recruitment sequence, as indicated by multiple independent measures of motor unit recruitment including conduction latency, contraction and relaxation times, stimulation threshold and fatigue. As a result, we observed enhanced performance and reduced fatigue in vivo. These findings point to an unanticipated new modality of neural control with broad implications for nervous system and neuromuscular physiology, disease research and therapeutic innovation.
MeSH term(s)	Animals ; Channelrhodopsins ; Electric Stimulation ; Electromyography/methods ; Mice ; Mice, Inbred C57BL ; Motor Neurons/physiology ; Muscle Contraction ; Peripheral Nerves/physiology ; Reaction Time ; Recruitment, Neurophysiological/physiology
Chemical Substances	Channelrhodopsins
Language	English
Publishing date	2010-09-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1220066-9
ISSN	1546-170X ; 1078-8956
ISSN (online)	1546-170X
ISSN	1078-8956
DOI	10.1038/nm.2228
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Article: Importin-mediated nuclear transport in neurons.

Otis, Klara Olofsdotter / Thompson, Kimberly R / Martin, Kelsey C

Current opinion in neurobiology

2006 Volume 16, Issue 3, Page(s) 329–335

Abstract: The polarized morphology of neurons poses a particular challenge to intracellular signal transduction. Local signals generated at distal sites must be retrogradely transported to the nucleus to produce persistent changes in neuronal function. Such ... ...

Abstract	The polarized morphology of neurons poses a particular challenge to intracellular signal transduction. Local signals generated at distal sites must be retrogradely transported to the nucleus to produce persistent changes in neuronal function. Such communication of signals between distal neuronal compartments and the nucleus occurs during axon guidance, synapse formation, synaptic plasticity and following neuronal injury. Recent studies have begun to delineate a role for the active nuclear import pathway in transporting signals from axons and dendrites to the nucleus. In this pathway, soluble cargo proteins are recognized by nuclear transport carriers, called importins, which mediate their translocation from the cytoplasm into the nucleus. In neurons, importins might serve an additional function by carrying signals from distal sites to the soma.
MeSH term(s)	Active Transport, Cell Nucleus/physiology ; Animals ; Axons/metabolism ; Axons/ultrastructure ; Cell Nucleus/metabolism ; Central Nervous System/cytology ; Central Nervous System/metabolism ; Dendrites/metabolism ; Dendrites/ultrastructure ; Humans ; Karyopherins/metabolism ; Neurons/cytology ; Neurons/metabolism ; Protein Transport/physiology ; Signal Transduction/physiology
Chemical Substances	Karyopherins
Language	English
Publishing date	2006-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	1078046-4
ISSN	1873-6882 ; 0959-4388
ISSN (online)	1873-6882
ISSN	0959-4388
DOI	10.1016/j.conb.2006.05.001
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Article: A Guide to Single-Cell Transcriptomics in Adult Rodent Brain: The Medium Spiny Neuron Transcriptome Revisited.

Ho, Hanson / Both, Matt De / Siniard, Ashley / Sharma, Sasha / Notwell, James H / Wallace, Michelle / Leone, Dino P / Nguyen, Amy / Zhao, Eric / Lee, Hannah / Zwilling, Daniel / Thompson, Kimberly R / Braithwaite, Steven P / Huentelman, Matthew / Portmann, Thomas

Frontiers in cellular neuroscience

2018 Volume 12, Page(s) 159

Abstract: Recent advances in single-cell technologies are paving the way to a comprehensive understanding of the cellular complexity in the brain. Protocols for single-cell transcriptomics combine a variety of sophisticated methods for the purpose of isolating the ...

Abstract	Recent advances in single-cell technologies are paving the way to a comprehensive understanding of the cellular complexity in the brain. Protocols for single-cell transcriptomics combine a variety of sophisticated methods for the purpose of isolating the heavily interconnected and heterogeneous neuronal cell types in a relatively intact and healthy state. The emphasis of single-cell transcriptome studies has thus far been on comparing library generation and sequencing techniques that enable measurement of the minute amounts of starting material from a single cell. However, in order for data to be comparable, standardized cell isolation techniques are essential. Here, we analyzed and simplified methods for the different steps critically involved in single-cell isolation from brain. These include enzymatic digestion, tissue trituration, improved methods for efficient fluorescence-activated cell sorting in samples containing high degree of debris from the neuropil, and finally, highly region-specific cellular labeling compatible with use of stereotaxic coordinates. The methods are exemplified using medium spiny neurons (MSN) from dorsomedial striatum, a cell type that is clinically relevant for disorders of the basal ganglia, including psychiatric and neurodegenerative diseases. We present single-cell RNA sequencing (scRNA-Seq) data from D1 and D2 dopamine receptor expressing MSN subtypes. We illustrate the need for single-cell resolution by comparing to available population-based gene expression data of striatal MSN subtypes. Our findings contribute toward standardizing important steps of single-cell isolation from adult brain tissue to increase comparability of data. Furthermore, our data redefine the transcriptome of MSNs at unprecedented resolution by confirming established marker genes, resolving inconsistencies from previous gene expression studies, and identifying novel subtype-specific marker genes in this important cell type.
Language	English
Publishing date	2018-06-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2452963-1
ISSN	1662-5102
ISSN	1662-5102
DOI	10.3389/fncel.2018.00159
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Article: Optical Deconstruction of Parkinsonian Neural Circuitry

Gradinaru, Viviana / Mogri, Murtaza / Thompson, Kimberly R / Henderson, Jaimie M / Deisseroth, Karl

Science. 2009 Apr. 17, v. 324, no. 5925

2009

Abstract: Deep brain stimulation (DBS) is a therapeutic option for intractable neurological and psychiatric disorders, including Parkinson's disease and major depression. Because of the heterogeneity of brain tissues where electrodes are placed, it has been ... ...

Abstract	Deep brain stimulation (DBS) is a therapeutic option for intractable neurological and psychiatric disorders, including Parkinson's disease and major depression. Because of the heterogeneity of brain tissues where electrodes are placed, it has been challenging to elucidate the relevant target cell types or underlying mechanisms of DBS. We used optogenetics and solid-state optics to systematically drive or inhibit an array of distinct circuit elements in freely moving parkinsonian rodents and found that therapeutic effects within the subthalamic nucleus can be accounted for by direct selective stimulation of afferent axons projecting to this region. In addition to providing insight into DBS mechanisms, these results demonstrate an optical approach for dissection of disease circuitry and define the technological toolbox needed for systematic deconstruction of disease circuits by selectively controlling individual components.
Keywords	Parkinson disease ; axons ; behavior disorders ; brain ; electrodes ; optics ; optogenetics ; rodents ; therapeutics ; tissues
Language	English
Dates of publication	2009-0417
Size	p. 354-359.
Publishing place	American Association for the Advancement of Science
Document type	Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.1167093
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Article ; Online: Optical deconstruction of parkinsonian neural circuitry.

Gradinaru, Viviana / Mogri, Murtaza / Thompson, Kimberly R / Henderson, Jaimie M / Deisseroth, Karl

Science (New York, N.Y.)

2009 Volume 324, Issue 5925, Page(s) 354–359

Abstract	Deep brain stimulation (DBS) is a therapeutic option for intractable neurological and psychiatric disorders, including Parkinson's disease and major depression. Because of the heterogeneity of brain tissues where electrodes are placed, it has been challenging to elucidate the relevant target cell types or underlying mechanisms of DBS. We used optogenetics and solid-state optics to systematically drive or inhibit an array of distinct circuit elements in freely moving parkinsonian rodents and found that therapeutic effects within the subthalamic nucleus can be accounted for by direct selective stimulation of afferent axons projecting to this region. In addition to providing insight into DBS mechanisms, these results demonstrate an optical approach for dissection of disease circuitry and define the technological toolbox needed for systematic deconstruction of disease circuits by selectively controlling individual components.
MeSH term(s)	Action Potentials ; Animals ; Astrocytes/metabolism ; Axons/physiology ; Deep Brain Stimulation ; Fiber Optic Technology ; Halorhodopsins/metabolism ; Light ; Motor Activity ; Motor Cortex/pathology ; Motor Cortex/physiopathology ; Neural Inhibition ; Neurons, Afferent/physiology ; Optics and Photonics ; Parkinsonian Disorders/pathology ; Parkinsonian Disorders/physiopathology ; Parkinsonian Disorders/therapy ; Rats ; Rhodopsin/metabolism ; Subthalamic Nucleus/pathology ; Subthalamic Nucleus/physiopathology
Chemical Substances	Halorhodopsins ; Rhodopsin (9009-81-8)
Language	English
Publishing date	2009-03-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.1167093
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Article ; Online: Temporally precise in vivo control of intracellular signalling.

Airan, Raag D / Thompson, Kimberly R / Fenno, Lief E / Bernstein, Hannah / Deisseroth, Karl

Nature

2009 Volume 458, Issue 7241, Page(s) 1025–1029

Abstract: In the study of complex mammalian behaviours, technological limitations have prevented spatiotemporally precise control over intracellular signalling processes. Here we report the development of a versatile family of genetically encoded optical tools (' ... ...

Abstract	In the study of complex mammalian behaviours, technological limitations have prevented spatiotemporally precise control over intracellular signalling processes. Here we report the development of a versatile family of genetically encoded optical tools ('optoXRs') that leverage common structure-function relationships among G-protein-coupled receptors (GPCRs) to recruit and control, with high spatiotemporal precision, receptor-initiated biochemical signalling pathways. In particular, we have developed and characterized two optoXRs that selectively recruit distinct, targeted signalling pathways in response to light. The two optoXRs exerted opposing effects on spike firing in nucleus accumbens in vivo, and precisely timed optoXR photostimulation in nucleus accumbens by itself sufficed to drive conditioned place preference in freely moving mice. The optoXR approach allows testing of hypotheses regarding the causal impact of biochemical signalling in behaving mammals, in a targetable and temporally precise manner.
MeSH term(s)	Animals ; Cattle ; Cell Line ; Cricetinae ; Cyclic AMP Response Element-Binding Protein/metabolism ; Genetic Engineering ; Humans ; Intracellular Space/metabolism ; Intracellular Space/radiation effects ; Mice ; Nucleus Accumbens/cytology ; Nucleus Accumbens/physiology ; Nucleus Accumbens/radiation effects ; Receptors, Adrenergic, alpha-1/genetics ; Receptors, Adrenergic, alpha-1/metabolism ; Receptors, Adrenergic, beta-2/genetics ; Receptors, Adrenergic, beta-2/metabolism ; Receptors, G-Protein-Coupled/genetics ; Receptors, G-Protein-Coupled/metabolism ; Recombinant Fusion Proteins/genetics ; Recombinant Fusion Proteins/metabolism ; Reward ; Rhodopsin/genetics ; Rhodopsin/metabolism ; Signal Transduction/radiation effects ; Structure-Activity Relationship ; Time Factors
Chemical Substances	ADRA1A protein, human ; Adra1a protein, mouse ; Cyclic AMP Response Element-Binding Protein ; Receptors, Adrenergic, alpha-1 ; Receptors, Adrenergic, beta-2 ; Receptors, G-Protein-Coupled ; Recombinant Fusion Proteins ; Rhodopsin (9009-81-8)
Language	English
Publishing date	2009-03-18
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/nature07926
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Article: Essential Control of the Function of the Striatopallidal Neuron by Pre-coupled Complexes of Adenosine A

Frontiers in pharmacology

2018 Volume 9, Page(s) 243

Abstract: The central adenosine system and adenosine receptors play a fundamental role in the modulation of dopaminergic neurotransmission. This is mostly achieved by the strategic co-localization of different adenosine and dopamine receptor subtypes in the two ... ...

Abstract	The central adenosine system and adenosine receptors play a fundamental role in the modulation of dopaminergic neurotransmission. This is mostly achieved by the strategic co-localization of different adenosine and dopamine receptor subtypes in the two populations of striatal efferent neurons, striatonigral and striatopallidal, that give rise to the direct and indirect striatal efferent pathways, respectively. With optogenetic techniques it has been possible to dissect a differential role of the direct and indirect pathways in mediating "Go" responses upon exposure to reward-related stimuli and "NoGo" responses upon exposure to non-rewarded or aversive-related stimuli, respectively, which depends on their different connecting output structures and their differential expression of dopamine and adenosine receptor subtypes. The striatopallidal neuron selectively expresses dopamine D
Language	English
Publishing date	2018-04-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587355-6
ISSN	1663-9812
ISSN	1663-9812
DOI	10.3389/fphar.2018.00243
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Article ; Online: Wiring and Molecular Features of Prefrontal Ensembles Representing Distinct Experiences.

Ye, Li / Allen, William E / Thompson, Kimberly R / Tian, Qiyuan / Hsueh, Brian / Ramakrishnan, Charu / Wang, Ai-Chi / Jennings, Joshua H / Adhikari, Avishek / Halpern, Casey H / Witten, Ilana B / Barth, Alison L / Luo, Liqun / McNab, Jennifer A / Deisseroth, Karl

Cell

2016 Volume 165, Issue 7, Page(s) 1776–1788

Abstract: A major challenge in understanding the cellular diversity of the brain has been linking activity during behavior with standard cellular typology. For example, it has not been possible to determine whether principal neurons in prefrontal cortex active ... ...

Abstract	A major challenge in understanding the cellular diversity of the brain has been linking activity during behavior with standard cellular typology. For example, it has not been possible to determine whether principal neurons in prefrontal cortex active during distinct experiences represent separable cell types, and it is not known whether these differentially active cells exert distinct causal influences on behavior. Here, we develop quantitative hydrogel-based technologies to connect activity in cells reporting on behavioral experience with measures for both brain-wide wiring and molecular phenotype. We find that positive and negative-valence experiences in prefrontal cortex are represented by cell populations that differ in their causal impact on behavior, long-range wiring, and gene expression profiles, with the major discriminant being expression of the adaptation-linked gene NPAS4. These findings illuminate cellular logic of prefrontal cortex information processing and natural adaptive behavior and may point the way to cell-type-specific understanding and treatment of disease-associated states.
MeSH term(s)	Animals ; Appetitive Behavior ; Basic Helix-Loop-Helix Transcription Factors/genetics ; Behavior, Animal ; Brain Mapping/methods ; Cocaine/administration & dosage ; Electroshock ; Female ; Male ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; Prefrontal Cortex/cytology ; Prefrontal Cortex/metabolism
Chemical Substances	Basic Helix-Loop-Helix Transcription Factors ; Npas4 protein, mouse ; Cocaine (I5Y540LHVR)
Language	English
Publishing date	2016-05-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2016.05.010
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