1
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O'Toole SM, Keller GB. Sample collection protocol for single-cell RNA sequencing of functionally identified neuronal populations in vivo. STAR Protoc 2024; 5:103135. [PMID: 38875113 DOI: 10.1016/j.xpro.2024.103135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/28/2024] [Accepted: 05/29/2024] [Indexed: 06/16/2024] Open
Abstract
Here, we present a sample collection protocol for single-cell RNA sequencing of functionally identified neuronal populations in vivo with a virally delivered activity-dependent labeling tool (CaMPARI2). We describe steps for photoconversion in mice during the onset of computationally relevant events in a virtual reality environment, followed by removal and dissociation of the photo-labeled tissue, and separation of differentially labeled groups with fluorescence-activated cell sorting (FACS). We then detail procedures for characterizing and examining functionally relevant groups using standard bioinformatic techniques. For complete details on the use and execution of this protocol, please refer to O'Toole et al.1.
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Affiliation(s)
- Sean M O'Toole
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Georg B Keller
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
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2
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Murata K, Itakura T, Touhara K. Neural basis for pheromone signal transduction in mice. Front Neural Circuits 2024; 18:1409994. [PMID: 38742089 PMCID: PMC11089125 DOI: 10.3389/fncir.2024.1409994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
Pheromones are specialized chemical messengers used for inter-individual communication within the same species, playing crucial roles in modulating behaviors and physiological states. The detection mechanisms of these signals at the peripheral organ and their transduction to the brain have been unclear. However, recent identification of pheromone molecules, their corresponding receptors, and advancements in neuroscientific technology have started to elucidate these processes. In mammals, the detection and interpretation of pheromone signals are primarily attributed to the vomeronasal system, which is a specialized olfactory apparatus predominantly dedicated to decoding socio-chemical cues. In this mini-review, we aim to delineate the vomeronasal signal transduction pathway initiated by specific vomeronasal receptor-ligand interactions in mice. First, we catalog the previously identified pheromone ligands and their corresponding receptor pairs, providing a foundational understanding of the specificity inherent in pheromonal communication. Subsequently, we examine the neural circuits involved in processing each pheromone signal. We focus on the anatomical pathways, the sexually dimorphic and physiological state-dependent aspects of signal transduction, and the neural coding strategies underlying behavioral responses to pheromonal cues. These insights provide further critical questions regarding the development of innate circuit formation and plasticity within these circuits.
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Affiliation(s)
- Ken Murata
- Laboratory of Biological Chemistry, Graduate School of Agricultural and Life Sciences, Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan
| | - Takumi Itakura
- Laboratory of Biological Chemistry, Graduate School of Agricultural and Life Sciences, Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan
- Division of Biology and Biological Engineering, TianQiao and Chrissy Chen Institute for Neuroscience, California Institute of Technology, Pasadena, CA, United States
| | - Kazushige Touhara
- Laboratory of Biological Chemistry, Graduate School of Agricultural and Life Sciences, Department of Applied Biological Chemistry, The University of Tokyo, Tokyo, Japan
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3
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Yagishita H, Go Y, Okamoto K, Arimura N, Ikegaya Y, Sasaki T. A method to analyze gene expression profiles from hippocampal neurons electrophysiologically recorded in vivo. Front Neurosci 2024; 18:1360432. [PMID: 38694898 PMCID: PMC11061373 DOI: 10.3389/fnins.2024.1360432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 03/26/2024] [Indexed: 05/04/2024] Open
Abstract
Hippocampal pyramidal neurons exhibit diverse spike patterns and gene expression profiles. However, their relationships with single neurons are not fully understood. In this study, we designed an electrophysiology-based experimental procedure to identify gene expression profiles using RNA sequencing of single hippocampal pyramidal neurons whose spike patterns were recorded in living mice. This technique involves a sequence of experiments consisting of in vivo juxtacellular recording and labeling, brain slicing, cell collection, and transcriptome analysis. We demonstrated that the expression levels of a subset of genes in individual hippocampal pyramidal neurons were significantly correlated with their spike burstiness, submillisecond-level spike rise times or spike rates, directly measured by in vivo electrophysiological recordings. Because this methodological approach can be applied across a wide range of brain regions, it is expected to contribute to studies on various neuronal heterogeneities to understand how physiological spike patterns are associated with gene expression profiles.
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Affiliation(s)
- Haruya Yagishita
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasuhiro Go
- Graduate School of Information Science, University of Hyogo, Hyogo, Japan
- Department of System Neuroscience, Division of Behavioral Development, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Kazuki Okamoto
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- Department of Neuroanatomy, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Department of Cell Biology and Neuroscience, Graduate School of Medicine, Juntendo University, Bunkyo, Tokyo, Japan
| | - Nariko Arimura
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Yuji Ikegaya
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- Center for Information and Neural Networks, National Institute of Information and Communications Technology, Osaka, Japan
- Institute for AI and Beyond, The University of Tokyo, Tokyo, Japan
| | - Takuya Sasaki
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
- Laboratory of Chemical Pharmacology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
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4
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Shi J, Nutkovich B, Kushinsky D, Rao BY, Herrlinger SA, Mihaila TS, Malina KCK, O’Toole CK, Conde Paredes ME, Yong HC, Varol E, Losonczy A, Spiegel I. 2P-NucTag: on-demand phototagging for molecular analysis of functionally identified cortical neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586118. [PMID: 38585980 PMCID: PMC10996538 DOI: 10.1101/2024.03.21.586118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Neural circuits are characterized by genetically and functionally diverse cell types. A mechanistic understanding of circuit function is predicated on linking the genetic and physiological properties of individual neurons. However, it remains highly challenging to map the functional properties of transcriptionally heterogeneous neuronal subtypes in mammalian cortical circuits in vivo. Here, we introduce a high-throughput two-photon nuclear phototagging (2P-NucTag) approach optimized for on-demand and indelible labeling of single neurons via a photoactivatable red fluorescent protein following in vivo functional characterization in behaving mice. We demonstrate the utility of this function-forward pipeline by selectively labeling and transcriptionally profiling previously inaccessible 'place' and 'silent' cells in the mouse hippocampus. Our results reveal unexpected differences in gene expression between these hippocampal pyramidal neurons with distinct spatial coding properties. Thus, 2P-NucTag opens a new way to uncover the molecular principles that govern the functional organization of neural circuits.
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Affiliation(s)
- Jingcheng Shi
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Doctoral Program in Neurobiology and Behavior, Columbia University, New York, NY, United States
| | - Boaz Nutkovich
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Dahlia Kushinsky
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Bovey Y. Rao
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Doctoral Program in Neurobiology and Behavior, Columbia University, New York, NY, United States
| | - Stephanie A. Herrlinger
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Tiberiu S. Mihaila
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Katayun Cohen-Kashi Malina
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Cliodhna K. O’Toole
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Margaret E. Conde Paredes
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Doctoral Program in Neurobiology and Behavior, Columbia University, New York, NY, United States
- Tandon School of Engineering, New York University, New York, NY, United States
| | - Hyun Choong Yong
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Erdem Varol
- Tandon School of Engineering, New York University, New York, NY, United States
| | - Attila Losonczy
- Department of Neuroscience, Columbia University, New York, NY, United States
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
| | - Ivo Spiegel
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
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5
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O'Toole SM, Oyibo HK, Keller GB. Molecularly targetable cell types in mouse visual cortex have distinguishable prediction error responses. Neuron 2023; 111:2918-2928.e8. [PMID: 37708892 DOI: 10.1016/j.neuron.2023.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 04/19/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Predictive processing postulates the existence of prediction error neurons in cortex. Neurons with both negative and positive prediction error response properties have been identified in layer 2/3 of visual cortex, but whether they correspond to transcriptionally defined subpopulations is unclear. Here we used the activity-dependent, photoconvertible marker CaMPARI2 to tag neurons in layer 2/3 of mouse visual cortex during stimuli and behaviors designed to evoke prediction errors. We performed single-cell RNA-sequencing on these populations and found that previously annotated Adamts2 and Rrad layer 2/3 transcriptional cell types were enriched when photolabeling during stimuli that drive negative or positive prediction error responses, respectively. Finally, we validated these results functionally by designing artificial promoters for use in AAV vectors to express genetically encoded calcium indicators. Thus, transcriptionally distinct cell types in layer 2/3 that can be targeted using AAV vectors exhibit distinguishable negative and positive prediction error responses.
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Affiliation(s)
- Sean M O'Toole
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Hassana K Oyibo
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg B Keller
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Science, University of Basel, Basel, Switzerland.
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6
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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] [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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7
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Li JZ, Dong LM, Zheng LL, Fu WL, Zhang JJ, Zhang L, Hu Q, Chen P, Gao ZF, Xia F. Molecular Visual Sensing, Boolean Logic Computing, and Data Security Using a Droplet-Based Superwetting Paradigm. ACS APPLIED MATERIALS & INTERFACES 2022; 14:40447-40459. [PMID: 36006781 DOI: 10.1021/acsami.2c11532] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Inspired by information processing and logic operations of life, many artificial biochemical systems have been designed for applications in molecular information processing. However, encoding the binary synergism between matter, energy, and information in a superwetting system remains challenging. Herein, a superwetting paradigm was proposed for multifunctional applications including molecular visual sensing and data security on a superhydrophobic surface. A Triton X-100-encapsulated gelatin (TeG) hydrogel was prepared and selectively decomposed by trypsin, releasing the surfactant to decrease the surface tension of a droplet. Integrating the droplet with the superhydrophobic surface, the superwetting behavior was utilized for visual detection and information encoding. Interestingly, the proposed TeG hydrogel can function as an artificial gelneuron for molecular-level logic computing, where the combination of matters (superhydrophobic surface, trypsin, and leupeptin) acts as inputs to interact with energy (liquid surface tension and solid surface energy) and information (binary character), resulting in superwettability transitions (droplet surface tension, contact angle, rolling angle, and bounce) as outputs. Impressively, the TeG gelneuron can be further developed as molecular-level double cryptographic steganography to encode, encrypt, and hide specific information (including the maze escape route and content of the classical literature) due to its programmability, stimuli responsive ability, and droplet concealment. This study will encourage the development of advanced molecular paradigms and their applications, such as superwetting visual sensing, molecular computing, interaction, and data security.
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Affiliation(s)
- Jin Ze Li
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Lu Ming Dong
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Lin Lin Zheng
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Wen Long Fu
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, P. R. China
| | - Jing Jing Zhang
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, P. R. China
| | - Lei Zhang
- Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L3G1, Canada
| | - Qiongzheng Hu
- School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, P. R. China
| | - Pu Chen
- Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L3G1, Canada
| | - Zhong Feng Gao
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, P. R. China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
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8
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Fluorescence imaging of large-scale neural ensemble dynamics. Cell 2022; 185:9-41. [PMID: 34995519 PMCID: PMC8849612 DOI: 10.1016/j.cell.2021.12.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/14/2022]
Abstract
Recent progress in fluorescence imaging allows neuroscientists to observe the dynamics of thousands of individual neurons, identified genetically or by their connectivity, across multiple brain areas and for extended durations in awake behaving mammals. We discuss advances in fluorescent indicators of neural activity, viral and genetic methods to express these indicators, chronic animal preparations for long-term imaging studies, and microscopes to monitor and manipulate the activity of large neural ensembles. Ca2+ imaging studies of neural activity can track brain area interactions and distributed information processing at cellular resolution. Across smaller spatial scales, high-speed voltage imaging reveals the distinctive spiking patterns and coding properties of targeted neuron types. Collectively, these innovations will propel studies of brain function and dovetail with ongoing neuroscience initiatives to identify new neuron types and develop widely applicable, non-human primate models. The optical toolkit's growing sophistication also suggests that "brain observatory" facilities would be useful open resources for future brain-imaging studies.
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9
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Autry AE, O'Connell LA. The Parental Dilemma: How Evolution of Diverse Strategies for Infant Care Informs Social Behavior Circuits. Front Neural Circuits 2021; 15:734474. [PMID: 34867211 PMCID: PMC8636452 DOI: 10.3389/fncir.2021.734474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/27/2021] [Indexed: 11/14/2022] Open
Affiliation(s)
- Anita E Autry
- Dominick P. Purpura Department of Neuroscience, Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, NY, United States
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10
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Corey EA, Zolotukhin S, Ache BW, Ukhanov K. Mixture interactions at mammalian olfactory receptors are dependent on the cellular environment. Sci Rep 2021; 11:9278. [PMID: 33927269 PMCID: PMC8085013 DOI: 10.1038/s41598-021-88601-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/07/2021] [Indexed: 02/02/2023] Open
Abstract
Functional characterization of mammalian olfactory receptors (ORs) remains a major challenge to ultimately understanding the olfactory code. Here, we compare the responses of the mouse Olfr73 ectopically expressed in olfactory sensory neurons using AAV gene delivery in vivo and expressed in vitro in cell culture. The response dynamics and concentration-dependence of agonists for the ectopically expressed Olfr73 were similar to those reported for the endogenous Olfr73, however the antagonism previously reported between its cognate agonist and several antagonists was not replicated in vivo. Expressing the OR in vitro reproduced the antagonism reported for short odor pulses, but not for prolonged odor exposure. Our findings suggest that both the cellular environment and the stimulus dynamics shape the functionality of Olfr73 and argue that characterizing ORs in 'native' conditions, rather than in vitro, provides a more relevant understanding of ligand-OR interactions.
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Affiliation(s)
- Elizabeth A Corey
- Whitney Laboratory, University of Florida, Gainesville, FL, USA
- Center for Smell and Taste, University of Florida, Gainesville, FL, USA
| | - Sergei Zolotukhin
- Department of Pediatrics, University of Florida, Gainesville, FL, USA
- Center for Smell and Taste, University of Florida, Gainesville, FL, USA
| | - Barry W Ache
- Whitney Laboratory, University of Florida, Gainesville, FL, USA
- Department of Biology and Neuroscience, University of Florida, Gainesville, FL, USA
- Center for Smell and Taste, University of Florida, Gainesville, FL, USA
- McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Kirill Ukhanov
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL, USA.
- Center for Smell and Taste, University of Florida, Gainesville, FL, USA.
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11
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Serrano-Saiz E, Isogai Y. Single-cell molecular and developmental perspectives of sexually dimorphic circuits underlying innate social behaviors. Curr Opin Neurobiol 2021; 68:159-166. [PMID: 33915498 DOI: 10.1016/j.conb.2021.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/10/2021] [Accepted: 03/16/2021] [Indexed: 12/21/2022]
Abstract
While single-cell transcriptomics in the brain has uncovered a vast diversity of neural cell types in unprecedented detail, it is becoming increasingly urgent to address what exactly their functional roles are in the context of circuits and behavior. In this review, we discuss the molecular profiling of cell types in circuits underlying social behaviors in mice as a prominent case study. We first highlight key roles of molecularly identified sensory and downstream neurons involved in sexually dimorphic behaviors. We then propose future opportunities to define cell types using multimodal criteria, especially gene expression, physiology, as well as the developmental origin, to advance our understanding of these circuits.
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Affiliation(s)
| | - Yoh Isogai
- Sainsbury Wellcome Centre for Neural Circuits and Behaviour, University College London, London, United Kingdom.
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12
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Fowler BE, Macpherson LJ. In vivo Calcium Imaging of Mouse Geniculate Ganglion Neuron Responses to Taste Stimuli. J Vis Exp 2021. [PMID: 33645563 DOI: 10.3791/62172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Within the last ten years, advances in genetically encoded calcium indicators (GECIs) have promoted a revolution in in vivo functional imaging. Using calcium as a proxy for neuronal activity, these techniques provide a way to monitor the responses of individual cells within large neuronal ensembles to a variety of stimuli in real time. We, and others, have applied these techniques to image the responses of individual geniculate ganglion neurons to taste stimuli applied to the tongues of live anesthetized mice. The geniculate ganglion is comprised of the cell bodies of gustatory neurons innervating the anterior tongue and palate as well as some somatosensory neurons innervating the pinna of the ear. Imaging the taste-evoked responses of individual geniculate ganglion neurons with GCaMP has provided important information about the tuning profiles of these neurons in wild-type mice as well as a way to detect peripheral taste miswiring phenotypes in genetically manipulated mice. Here we demonstrate the surgical procedure to expose the geniculate ganglion, GCaMP fluorescence image acquisition, initial steps for data analysis, and troubleshooting. This technique can be used with transgenically encoded GCaMP, or with AAV-mediated GCaMP expression, and can be modified to image particular genetic subsets of interest (i.e., Cre-mediated GCaMP expression). Overall, in vivo calcium imaging of geniculate ganglion neurons is a powerful technique for monitoring the activity of peripheral gustatory neurons and provides complementary information to more traditional whole-nerve chorda tympani recordings or taste behavior assays.
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Affiliation(s)
- Bryan E Fowler
- Department of Biology, The University of Texas at San Antonio
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13
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von Buchholtz LJ, Ghitani N, Lam RM, Licholai JA, Chesler AT, Ryba NJP. Decoding Cellular Mechanisms for Mechanosensory Discrimination. Neuron 2021; 109:285-298.e5. [PMID: 33186546 PMCID: PMC9909446 DOI: 10.1016/j.neuron.2020.10.028] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/27/2020] [Accepted: 10/20/2020] [Indexed: 01/29/2023]
Abstract
Single-cell RNA-sequencing and in vivo functional imaging provide expansive but disconnected views of neuronal diversity. Here, we developed a strategy for linking these modes of classification to explore molecular and cellular mechanisms responsible for detecting and encoding touch. By broadly mapping function to neuronal class, we uncovered a clear transcriptomic logic responsible for the sensitivity and selectivity of mammalian mechanosensory neurons. Notably, cell types with divergent gene-expression profiles often shared very similar properties, but we also discovered transcriptomically related neurons with specialized and divergent functions. Applying our approach to knockout mice revealed that Piezo2 differentially tunes all types of mechanosensory neurons with marked cell-class dependence. Together, our data demonstrate how mechanical stimuli recruit characteristic ensembles of transcriptomically defined neurons, providing rules to help explain the discriminatory power of touch. We anticipate a similar approach could expose fundamental principles governing representation of information throughout the nervous system.
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Affiliation(s)
- Lars J. von Buchholtz
- National Institute of Dental and Craniofacial Research, NIH, Bethesda MD 20892, USA,These authors contributed equally
| | - Nima Ghitani
- National Center for Integrative and Complementary Health, Bethesda MD 20892, USA,These authors contributed equally
| | - Ruby M. Lam
- National Center for Integrative and Complementary Health, Bethesda MD 20892, USA,Brown-National Institutes of Health Graduate Partnerships Program, Brown University, Providence, RI, USA
| | - Julia A. Licholai
- National Institute of Dental and Craniofacial Research, NIH, Bethesda MD 20892, USA,Brown-National Institutes of Health Graduate Partnerships Program, Brown University, Providence, RI, USA
| | - Alexander T. Chesler
- National Center for Integrative and Complementary Health, Bethesda MD 20892, USA,Lead contact: ,Correspondence: or
| | - Nicholas J. P. Ryba
- National Institute of Dental and Craniofacial Research, NIH, Bethesda MD 20892, USA,Correspondence: or
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14
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Tirindelli R. Coding of pheromones by vomeronasal receptors. Cell Tissue Res 2021; 383:367-386. [PMID: 33433690 DOI: 10.1007/s00441-020-03376-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/02/2020] [Indexed: 01/11/2023]
Abstract
Communication between individuals is critical for species survival, reproduction, and expansion. Most terrestrial species, with the exception of humans who predominantly use vision and phonation to create their social network, rely on the detection and decoding of olfactory signals, which are widely known as pheromones. These chemosensory cues originate from bodily fluids, causing attractive or avoidance behaviors in subjects of the same species. Intraspecific pheromone signaling is then crucial to identify sex, social ranking, individuality, and health status, thus establishing hierarchies and finalizing the most efficient reproductive strategies. Indeed, all these features require fine tuning of the olfactory systems to detect molecules containing this information. To cope with this complexity of signals, tetrapods have developed dedicated olfactory subsystems that refer to distinct peripheral sensory detectors, called the main olfactory and the vomeronasal organ, and two minor structures, namely the septal organ of Masera and the Grueneberg ganglion. Among these, the vomeronasal organ plays the most remarkable role in pheromone coding by mediating several behavioral outcomes that are critical for species conservation and amplification. In rodents, this organ is organized into two segregated neuronal subsets that express different receptor families. To some extent, this dichotomic organization is preserved in higher projection areas of the central nervous system, suggesting, at first glance, distinct functions for these two neuronal pathways. Here, I will specifically focus on this issue and discuss the role of vomeronasal receptors in mediating important innate behavioral effects through the recognition of pheromones and other biological chemosignals.
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Affiliation(s)
- Roberto Tirindelli
- Department of Medicine and Surgery, University of Parma, Via Volturno, 39, 43125, Parma, Italy.
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15
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Kim CK, Sanchez MI, Hoerbelt P, Fenno LE, Malenka RC, Deisseroth K, Ting AY. A Molecular Calcium Integrator Reveals a Striatal Cell Type Driving Aversion. Cell 2020; 183:2003-2019.e16. [PMID: 33308478 PMCID: PMC9839359 DOI: 10.1016/j.cell.2020.11.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 09/18/2020] [Accepted: 11/06/2020] [Indexed: 01/17/2023]
Abstract
The ability to record transient cellular events in the DNA or RNA of cells would enable precise, large-scale analysis, selection, and reprogramming of heterogeneous cell populations. Here, we report a molecular technology for stable genetic tagging of cells that exhibit activity-related increases in intracellular calcium concentration (FLiCRE). We used FLiCRE to transcriptionally label activated neural ensembles in the nucleus accumbens of the mouse brain during brief stimulation of aversive inputs. Using single-cell RNA sequencing, we detected FLiCRE transcripts among the endogenous transcriptome, providing simultaneous readout of both cell-type and calcium activation history. We identified a cell type in the nucleus accumbens activated downstream of long-range excitatory projections. Taking advantage of FLiCRE's modular design, we expressed an optogenetic channel selectively in this cell type and showed that direct recruitment of this otherwise genetically inaccessible population elicits behavioral aversion. The specificity and minute resolution of FLiCRE enables molecularly informed characterization, manipulation, and reprogramming of activated cellular ensembles.
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Affiliation(s)
- Christina K. Kim
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,These authors contributed equally to this work
| | - Mateo I. Sanchez
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.,These authors contributed equally to this work
| | - Paul Hoerbelt
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Lief E. Fenno
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford University, Stanford, CA 94035, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Robert C. Malenka
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Karl Deisseroth
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford University, Stanford, CA 94035, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.,Correspondence to: or
| | - Alice Y. Ting
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA.,Lead contact:
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16
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Xu S, Yang H, Menon V, Lemire AL, Wang L, Henry FE, Turaga SC, Sternson SM. Behavioral state coding by molecularly defined paraventricular
hypothalamic cell type ensembles. Science 2020; 370:370/6514/eabb2494. [DOI: 10.1126/science.abb2494] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 08/18/2020] [Indexed: 12/11/2022]
Abstract
Brains encode behaviors using neurons amenable to systematic
classification by gene expression. The contribution of molecular identity to
neural coding is not understood because of the challenges involved with
measuring neural dynamics and molecular information from the same cells. We
developed CaRMA (calcium and RNA multiplexed activity) imaging based on
recording in vivo single-neuron calcium dynamics followed by gene expression
analysis. We simultaneously monitored activity in hundreds of neurons in
mouse paraventricular hypothalamus (PVH). Combinations of cell-type marker
genes had predictive power for neuronal responses across 11 behavioral
states. The PVH uses combinatorial assemblies of molecularly defined neuron
populations for grouped-ensemble coding of survival behaviors. The
neuropeptide receptor neuropeptide Y receptor type 1 (Npy1r) amalgamated
multiple cell types with similar responses. Our results show that
molecularly defined neurons are important processing units for brain
function.
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Affiliation(s)
- Shengjin Xu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Hui Yang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Vilas Menon
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Andrew L. Lemire
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Lihua Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Fredrick E. Henry
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Srinivas C. Turaga
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Scott M. Sternson
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
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17
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Wong WM, Cao J, Zhang X, Doyle WI, Mercado LL, Gautron L, Meeks JP. Physiology-forward identification of bile acid-sensitive vomeronasal receptors. SCIENCE ADVANCES 2020; 6:eaaz6868. [PMID: 32523992 PMCID: PMC7259934 DOI: 10.1126/sciadv.aaz6868] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
The mouse accessory olfactory system (AOS) supports social and reproductive behavior through the sensation of environmental chemosignals. A growing number of excreted steroids have been shown to be potent AOS cues, including bile acids (BAs) found in feces. As is still the case with most AOS ligands, the specific receptors used by vomeronasal sensory neurons (VSNs) to detect BAs remain unknown. To identify VSN BA receptors, we first performed a deep analysis of VSN BA tuning using volumetric GCaMP6f/s Ca2+ imaging. These experiments revealed multiple populations of BA-receptive VSNs with submicromolar sensitivities. We then developed a new physiology-forward approach for identifying AOS ligand-receptor interactions, which we call Fluorescence Live Imaging for Cell Capture and RNA sequencing, or FLICCR-seq. FLICCR-seq analysis revealed five specific V1R family receptors enriched in BA-sensitive VSNs. These studies introduce a powerful new approach for ligand-receptor matching and reveal biological mechanisms underlying mammalian BA chemosensation.
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Affiliation(s)
- Wen Mai Wong
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA
| | - Jie Cao
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA
| | - Xingjian Zhang
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA
| | - Wayne I. Doyle
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA
| | - Luis L. Mercado
- Division of Hypothalamic Research and Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA
| | - Laurent Gautron
- Division of Hypothalamic Research and Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA
| | - Julian P. Meeks
- Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, USA
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18
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Isolating neurons on the basis of function. Nat Methods 2020; 17:131. [DOI: 10.1038/s41592-020-0744-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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Renninger SL. Cell types exposed by social scent. Science 2019; 366:1311-1312. [PMID: 31831656 DOI: 10.1126/science.aaz8969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Sabine L Renninger
- Champalimaud Research, Champalimaud Centre for the Unknown, 1400-038 Lisbon, Portugal.
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