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Lin W, Phatarphekar A, Zhong Y, Liu L, Kwon HB, Gerwick WH, Wang Y, Mehta S, Zhang J. Light-gated integrator for highlighting kinase activity in living cells. Nat Commun 2024; 15:7804. [PMID: 39242543 PMCID: PMC11379911 DOI: 10.1038/s41467-024-51270-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 08/02/2024] [Indexed: 09/09/2024] Open
Abstract
Protein kinases are key signaling nodes that regulate fundamental biological and disease processes. Illuminating kinase signaling from multiple angles can provide deeper insights into disease mechanisms and improve therapeutic targeting. While fluorescent biosensors are powerful tools for visualizing live-cell kinase activity dynamics in real time, new molecular tools are needed that enable recording of transient signaling activities for post hoc analysis and targeted manipulation. Here, we develop a light-gated kinase activity coupled transcriptional integrator (KINACT) that converts dynamic kinase signals into "permanent" fluorescent marks. KINACT enables robust monitoring of kinase activity across scales, accurately recording subcellular PKA activity, highlighting PKA activity distribution in 3D cultures, and identifying PKA activators and inhibitors in high-throughput screens. We further leverage the ability of KINACT to drive signaling effector expression to allow feedback manipulation of the balance of GαsR201C-induced PKA and ERK activation and dissect the mechanisms of oncogenic G protein signaling.
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Affiliation(s)
- Wei Lin
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
| | | | - Yanghao Zhong
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Longwei Liu
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Hyung-Bae Kwon
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yingxiao Wang
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
- Shu Chien - Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
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2
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Foran G, Hallam RD, Megaly M, Turgambayeva A, Antfolk D, Li Y, Luca VC, Necakov A. Notch1 Phase Separation Coupled Percolation facilitates target gene expression and enhancer looping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.17.533124. [PMID: 39131356 PMCID: PMC11312450 DOI: 10.1101/2023.03.17.533124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
The Notch receptor is a pleiotropic signaling protein that translates intercellular ligand interactions into changes in gene expression via the nuclear localization of the Notch intracellular Domain (NICD). Using a combination of immunohistochemistry, RNA in situ, Optogenetics and super-resolution live imaging of transcription in human cells, we show that the N1ICD can form condensates that positively facilitate Notch target gene expression. We determined that N1ICD undergoes Phase Separation Coupled Percolation (PSCP) into transcriptional condensates, which recruit, enrich, and encapsulate a broad set of core transcriptional proteins. We show that the capacity for condensation is due to the intrinsically disordered transcriptional activation domain of the N1ICD. In addition, the formation of such transcriptional condensates acts to promote Notch-mediated super enhancer-looping and concomitant activation of the MYC protooncogene expression. Overall, we introduce a novel mechanism of Notch1 activity in which discrete changes in nuclear N1ICD abundance are translated into the assembly of transcriptional condensates that facilitate gene expression by enriching essential transcriptional machineries at target genomic loci.
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Affiliation(s)
- Gregory Foran
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Ryan Douglas Hallam
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Marvel Megaly
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Anel Turgambayeva
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Daniel Antfolk
- Department of Immunology, Moffitt Cancer Centre, Tampa, FL, USA
| | - Yifeng Li
- Department of Computer Science, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
| | - Vincent C. Luca
- Department of Immunology, Moffitt Cancer Centre, Tampa, FL, USA
| | - Aleksandar Necakov
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario, Canada, L2S 3A1
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3
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Brida KL, Jorgensen ET, Phillips RA, Newman CE, Tuscher JJ, Morring EK, Zipperly ME, Ianov L, Montgomery KD, Tippani M, Hyde TM, Maynard KR, Martinowich K, Day JJ. Reelin marks cocaine-activated striatal ensembles, promotes neuronal excitability, and regulates cocaine reward. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599348. [PMID: 38948801 PMCID: PMC11212904 DOI: 10.1101/2024.06.17.599348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Drugs of abuse activate defined neuronal ensembles in brain reward structures such as the nucleus accumbens (NAc), which are thought to promote the enduring synaptic, circuit, and behavioral consequences of drug exposure. While the molecular and cellular effects arising from experience with drugs like cocaine are increasingly well understood, the mechanisms that sculpt NAc ensemble participation are largely unknown. Here, we leveraged unbiased single-nucleus transcriptional profiling to identify expression of the secreted glycoprotein Reelin (encoded by the Reln gene) as a marker of cocaine-activated neuronal ensembles within the rat NAc. Multiplexed in situ detection confirmed selective expression of the immediate early gene Fos in Reln+ neurons after cocaine experience, and also revealed enrichment of Reln mRNA in Drd1 + medium spiny neurons (MSNs) in both the rat and human brain. Using a novel CRISPR interference strategy enabling selective Reln knockdown in the adult NAc, we observed altered expression of genes linked to calcium signaling, emergence of a transcriptional trajectory consistent with loss of cocaine sensitivity, and a striking decrease in MSN intrinsic excitability. At the behavioral level, loss of Reln prevented cocaine locomotor sensitization, abolished cocaine place preference memory, and decreased cocaine self-administration behavior. Together, these results identify Reelin as a critical mechanistic link between ensemble participation and cocaine-induced behavioral adaptations.
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4
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Xia X, Li Y. A new GRAB sensor reveals differences in the dynamics and molecular regulation between neuropeptide and neurotransmitter release. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595424. [PMID: 38826473 PMCID: PMC11142204 DOI: 10.1101/2024.05.22.595424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The co-existence and co-transmission of neuropeptides and small molecule neurotransmitters in the same neuron is a fundamental aspect of almost all neurons across various species. However, the differences regarding their in vivo spatiotemporal dynamics and underlying molecular regulation remain poorly understood. Here, we developed a GPCR-activation-based (GRAB) sensor for detecting short neuropeptide F (sNPF) with high sensitivity and spatiotemporal resolution. Furthermore, we explore the differences of in vivo dynamics and molecular regulation between sNPF and acetylcholine (ACh) from the same neurons. Interestingly, the release of sNPF and ACh shows different spatiotemporal dynamics. Notably, we found that distinct synaptotagmins (Syt) are involved in these two processes, as Syt7 and Sytα for sNPF release, while Syt1 for ACh release. Thus, this new GRAB sensor provides a powerful tool for studying neuropeptide release and providing new insights into the distinct release dynamics and molecular regulation between neuropeptides and small molecule neurotransmitters.
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Affiliation(s)
- Xiju Xia
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies (AAIS), and Peking University–Tsinghua University–National Institute of Biological Sciences Joint Graduate Program (PTN), Peking University, Beijing, 100871, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
- Academy for Advanced Interdisciplinary Studies (AAIS), and Peking University–Tsinghua University–National Institute of Biological Sciences Joint Graduate Program (PTN), Peking University, Beijing, 100871, China
- Chinese Institute for Brain Research, Beijing 102206, China
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5
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Zhang X, Mille-Fragoso LS, Kaseniit KE, Call CC, Zhang M, Hu Y, Xie Y, Gao XJ. Post-Transcriptional Modular Synthetic Receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592453. [PMID: 38746461 PMCID: PMC11092781 DOI: 10.1101/2024.05.03.592453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Inspired by the power of transcriptional synthetic receptors and hoping to complement them to expand the toolbox for cell engineering, we establish LIDAR (Ligand-Induced Dimerization Activating RNA editing), a modular post-transcriptional synthetic receptor platform that harnesses RNA editing by ADAR. LIDAR is compatible with various receptor architectures in different cellular contexts, and enables the sensing of diverse ligands and the production of functional outputs. Furthermore, LIDAR can sense orthogonal signals in the same cell and produce synthetic spatial patterns, potentially enabling the programming of complex multicellular behaviors. Finally, LIDAR is compatible with compact encoding and can be delivered by synthetic mRNA. Thus, LIDAR expands the family of synthetic receptors, holding the promise to empower basic research and therapeutic applications.
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6
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Kroning K, Gannot N, Li X, Putansu A, Zhou G, Sescil J, Shen J, Wilson A, Fiel H, Li P, Wang W. Single-chain fluorescent integrators for mapping G-protein-coupled receptor agonists. Proc Natl Acad Sci U S A 2024; 121:e2307090121. [PMID: 38648487 PMCID: PMC11067452 DOI: 10.1073/pnas.2307090121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 03/15/2024] [Indexed: 04/25/2024] Open
Abstract
G protein-coupled receptors (GPCRs) transduce the effects of many neuromodulators including dopamine, serotonin, epinephrine, acetylcholine, and opioids. The localization of synthetic or endogenous GPCR agonists impacts their action on specific neuronal pathways. In this paper, we show a series of single-protein chain integrator sensors that are highly modular and could potentially be used to determine GPCR agonist localization across the brain. We previously engineered integrator sensors for the mu- and kappa-opioid receptor agonists called M- and K-Single-chain Protein-based Opioid Transmission Indicator Tool (SPOTIT), respectively. Here, we engineered red versions of the SPOTIT sensors for multiplexed imaging of GPCR agonists. We also modified SPOTIT to create an integrator sensor design platform called SPOTIT for all GPCRs (SPOTall). We used the SPOTall platform to engineer sensors for the beta 2-adrenergic receptor (B2AR), the dopamine receptor D1, and the cholinergic receptor muscarinic 2 agonists. Finally, we demonstrated the application of M-SPOTIT and B2AR-SPOTall in detecting exogenously administered morphine, isoproterenol, and epinephrine in the mouse brain via locally injected viruses. The SPOTIT and SPOTall sensor design platform has the potential for unbiased agonist detection of many synthetic and endogenous neuromodulators across the brain.
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MESH Headings
- Animals
- Receptors, G-Protein-Coupled/agonists
- Receptors, G-Protein-Coupled/metabolism
- Humans
- Mice
- HEK293 Cells
- Receptors, Dopamine D1/agonists
- Receptors, Dopamine D1/metabolism
- Receptors, Adrenergic, beta-2/metabolism
- Receptors, Adrenergic, beta-2/genetics
- Receptor, Muscarinic M2/agonists
- Receptor, Muscarinic M2/metabolism
- Isoproterenol/pharmacology
- Receptors, Opioid, mu/agonists
- Receptors, Opioid, mu/metabolism
- Morphine/pharmacology
- Brain/metabolism
- Brain/drug effects
- Brain/diagnostic imaging
- Receptors, Opioid, kappa/agonists
- Receptors, Opioid, kappa/metabolism
- Biosensing Techniques/methods
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Affiliation(s)
- Kayla Kroning
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Noam Gannot
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
- Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan, Ann Arbor, MI48109
| | - Xingyu Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
- Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan, Ann Arbor, MI48109
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI48109
| | - Aubrey Putansu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Guanwei Zhou
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI48109
| | - Jennifer Sescil
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Jiaqi Shen
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Avery Wilson
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
| | - Hailey Fiel
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
| | - Peng Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
- Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan, Ann Arbor, MI48109
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI48109
| | - Wenjing Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI48109
- Department of Chemistry, University of Michigan, Ann Arbor, MI48109
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI48109
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7
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Wang W. Protein-Based Tools for Studying Neuromodulation. ACS Chem Biol 2024; 19:788-797. [PMID: 38581649 PMCID: PMC11129172 DOI: 10.1021/acschembio.4c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2024]
Abstract
Neuromodulators play crucial roles in regulating neuronal activity and affecting various aspects of brain functions, including learning, memory, cognitive functions, emotional states, and pain modulation. In this Account, we describe our group's efforts in designing sensors and tools for studying neuromodulation. Our lab focuses on developing new classes of integrators that can detect neuromodulators across the whole brain while leaving a mark for further imaging analysis at high spatial resolution. Our lab also designed chemical- and light-dependent protein switches for controlling peptide activity to potentially modulate the endogenous receptors of the neuromodulatory system in order to study the causal effects of selective neuronal pathways.
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Affiliation(s)
- Wenjing Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
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8
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Wang X, Kang L, Kong D, Wu X, Zhou Y, Yu G, Dai D, Ye H. A programmable protease-based protein secretion platform for therapeutic applications. Nat Chem Biol 2024; 20:432-442. [PMID: 37872400 DOI: 10.1038/s41589-023-01433-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 09/02/2023] [Indexed: 10/25/2023]
Abstract
Cell-based therapies represent potent enabling technologies in biomedical science. However, current genetic control systems for engineered-cell therapies are predominantly based on the transcription or translation of therapeutic outputs. Here we report a protease-based rapid protein secretion system (PASS) that regulates the secretion of pretranslated proteins retained in the endoplasmic reticulum (ER) owing to an ER-retrieval signal. Upon cleavage by inducible proteases, these proteins are secreted. Three PASS variants (chemPASS, antigenPASS and optoPASS) are developed. With chemPASS, we demonstrate the reversal of hyperglycemia in diabetic mice within minutes via drug-induced insulin secretion. AntigenPASS-equipped cells recognize the tumor antigen and secrete granzyme B and perforin, inducing targeted cell apoptosis. Finally, results from mouse models of diabetes, hypertension and inflammatory pain demonstrate light-induced, optoPASS-mediated therapeutic peptide secretion within minutes, conferring anticipated therapeutic benefits. PASS is a flexible platform for rapid delivery of therapeutic proteins that can facilitate the development and adoption of cell-based precision therapies.
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Affiliation(s)
- Xinyi Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Liping Kang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Deqiang Kong
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Xin Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yang Zhou
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
- Wuhu Hospital, Health Science Center, East China Normal University, Wuhu City, China
| | - Guiling Yu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Di Dai
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Haifeng Ye
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Biomedical Synthetic Biology Research Center, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
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9
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Eom K, Jung J, Kim B, Hyun JH. Molecular tools for recording and intervention of neuronal activity. Mol Cells 2024; 47:100048. [PMID: 38521352 PMCID: PMC11021360 DOI: 10.1016/j.mocell.2024.100048] [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: 12/15/2023] [Revised: 03/12/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024] Open
Abstract
Observing the activity of neural networks is critical for the identification of learning and memory processes, as well as abnormal activities of neural circuits in disease, particularly for the purpose of tracking disease progression. Methodologies for describing the activity history of neural networks using molecular biology techniques first utilized genes expressed by active neurons, followed by the application of recently developed techniques including optogenetics and incorporation of insights garnered from other disciplines, including chemistry and physics. In this review, we will discuss ways in which molecular biological techniques used to describe the activity of neural networks have evolved along with the potential for future development.
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Affiliation(s)
- Kisang Eom
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Jinhwan Jung
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Byungsoo Kim
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Jung Ho Hyun
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea; Center for Synapse Diversity and Specificity, DGIST, Daegu 42988, Republic of Korea.
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10
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Mohsenin H, Wagner HJ, Rosenblatt M, Kemmer S, Drepper F, Huesgen P, Timmer J, Weber W. Design of a Biohybrid Materials Circuit with Binary Decoder Functionality. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2308092. [PMID: 38118057 DOI: 10.1002/adma.202308092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/05/2023] [Indexed: 12/22/2023]
Abstract
Synthetic biology applies concepts from electrical engineering and information processing to endow cells with computational functionality. Transferring the underlying molecular components into materials and wiring them according to topologies inspired by electronic circuit boards has yielded materials systems that perform selected computational operations. However, the limited functionality of available building blocks is restricting the implementation of advanced information-processing circuits into materials. Here, a set of protease-based biohybrid modules the bioactivity of which can either be induced or inhibited is engineered. Guided by a quantitative mathematical model and following a design-build-test-learn (DBTL) cycle, the modules are wired according to circuit topologies inspired by electronic signal decoders, a fundamental motif in information processing. A 2-input/4-output binary decoder for the detection of two small molecules in a material framework that can perform regulated outputs in form of distinct protease activities is designed. The here demonstrated smart material system is strongly modular and can be used for biomolecular information processing for example in advanced biosensing or drug delivery applications.
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Affiliation(s)
- Hasti Mohsenin
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Hanna J Wagner
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104, Freiburg, Germany
| | - Marcus Rosenblatt
- Institute of Physics and Freiburg Center for Data Analysis and Modelling (FDM), University of Freiburg, Hermann-Herder-Straße 3, 79104, Freiburg, Germany
| | - Svenja Kemmer
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Institute of Physics and Freiburg Center for Data Analysis and Modelling (FDM), University of Freiburg, Hermann-Herder-Straße 3, 79104, Freiburg, Germany
| | - Friedel Drepper
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
| | - Pitter Huesgen
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
| | - Jens Timmer
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- Institute of Physics and Freiburg Center for Data Analysis and Modelling (FDM), University of Freiburg, Hermann-Herder-Straße 3, 79104, Freiburg, Germany
| | - Wilfried Weber
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestraße 18, 79104, Freiburg, Germany
- INM - Leibniz Institute for New Materials, Campus D2 2, 66123, Saarbrücken, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104, Freiburg, Germany
- Saarland University, Department of Materials Science and Engineering, Campus D2 2, 66123, Saarbrücken, Germany
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11
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Kise R, Inoue A. GPCR signaling bias: an emerging framework for opioid drug development. J Biochem 2024; 175:367-376. [PMID: 38308136 DOI: 10.1093/jb/mvae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/18/2024] [Accepted: 01/31/2024] [Indexed: 02/04/2024] Open
Abstract
Biased signaling, also known as functional selectivity, has emerged as an important concept in drug development targeting G-protein-coupled receptors (GPCRs). Drugs that provoke biased signaling are expected to offer an opportunity for enhanced therapeutic effectiveness with minimized side effects. Opioid analgesics, whilst exerting potent pain-relieving effects, have become a social problem owing to their serious side effects. For the development of safer pain medications, there has been extensive exploration of agonists with a distinct balance of G-protein and β-arrestin (βarr) signaling. Recently, several approaches based on protein-protein interactions have been developed to precisely evaluate individual signal pathways, paving the way for the comprehensive analysis of biased signals. In this review, we describe an overview of bias signaling in opioid receptors, especially the μ-opioid receptor (MOR), and how to evaluate signaling bias in the GPCR field. We also discuss future directions for rational drug development through the integration of diverse signal datasets.
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Affiliation(s)
- Ryoji Kise
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
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12
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Lin W, Phatarphekar A, Zhong Y, Liu L, Kwon HB, Gerwick WH, Wang Y, Mehta S, Zhang J. Light-gated Integrator for Highlighting Kinase Activity in Living Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585554. [PMID: 38562887 PMCID: PMC10983958 DOI: 10.1101/2024.03.18.585554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Protein kinases are key signaling nodes that regulate fundamental biological and disease processes. Illuminating kinase signaling from multiple angles can provide deeper insights into disease mechanisms and improve therapeutic targeting. While fluorescent biosensors are powerful tools for visualizing live-cell kinase activity dynamics in real time, new molecular tools are needed that enable recording of transient signaling activities for post hoc analysis and targeted manipulation. Here, we develop a light-gated kinase activity coupled transcriptional integrator (KINACT) that converts dynamic kinase signals into "permanent" fluorescent marks. KINACT enables robust monitoring of kinase activity across scales, accurately recording subcellular PKA activity, highlighting PKA signaling heterogeneity in 3D cultures, and identifying PKA activators and inhibitors in high-throughput screens. We further leverage the ability of KINACT to drive signaling effector expression to allow feedback manipulation of the balance of GαsR201C-induced PKA and ERK activation and dissect the mechanisms of oncogenic G protein signaling.
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Affiliation(s)
- Wei Lin
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | | | - Yanghao Zhong
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Longwei Liu
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Hyung-Bae Kwon
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yingxiao Wang
- Alfred E. Mann Department of Biomedical Engineering, University of Southern California, Los Angeles, CA, USA
| | - Sohum Mehta
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
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13
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Verbič A, Lebar T, Praznik A, Jerala R. Subunits of an E3 Ligase Complex as Degrons for Efficient Degradation of Cytosolic, Nuclear, and Membrane Proteins. ACS Synth Biol 2024; 13:792-803. [PMID: 38404221 PMCID: PMC10949250 DOI: 10.1021/acssynbio.3c00588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/27/2024]
Abstract
Protein degradation is a highly regulated cellular process crucial to enable the high dynamic range of the response to external and internal stimuli and to balance protein biosynthesis to maintain cell homeostasis. Within mammalian cells, hundreds of E3 ubiquitin ligases target specific protein substrates and could be repurposed for synthetic biology. Here, we present a systematic analysis of the four protein subunits of the multiprotein E3 ligase complex as scaffolds for the designed degrons. While all of them were functional, the fusion of a fragment of Skp1 with the target protein enabled the most effective degradation. Combination with heterodimerizing peptides, protease substrate sites, and chemically inducible dimerizers enabled the regulation of protein degradation. While the investigated subunits of E3 ligases showed variable degradation efficiency of the membrane and cytosolic and nuclear proteins, the bipartite SSD (SOCSbox-Skp1(ΔC111)) degron enabled fast degradation of protein targets in all tested cellular compartments, including the nucleus and plasma membrane, in different cell lines and could be chemically regulated. These subunits could be employed for research as well as for diverse applications, as demonstrated in the regulation of Cas9 and chimeric antigen receptor proteins.
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Affiliation(s)
- Anže Verbič
- Department of Synthetic Biology
and Immunology, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | | | - Arne Praznik
- Department of Synthetic Biology
and Immunology, National Institute of Chemistry, Ljubljana 1000, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology
and Immunology, National Institute of Chemistry, Ljubljana 1000, Slovenia
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14
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Cui M, Lee S, Ban SH, Ryu JR, Shen M, Yang SH, Kim JY, Choi SK, Han J, Kim Y, Han K, Lee D, Sun W, Kwon HB, Lee D. A single-component, light-assisted uncaging switch for endoproteolytic release. Nat Chem Biol 2024; 20:353-364. [PMID: 37973890 DOI: 10.1038/s41589-023-01480-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
Proteases function as pivotal molecular switches, initiating numerous biological events. Notably, potyviral protease, derived from plant viruses, has emerged as a trusted proteolytic switch in synthetic biological circuits. To harness their capabilities, we have developed a single-component photocleavable switch, termed LAUNCHER (Light-Assisted UNcaging switCH for Endoproteolytic Release), by employing a circularly permutated tobacco etch virus protease and a blue-light-gated substrate, which are connected by fine-tuned intermodular linkers. As a single-component system, LAUNCHER exhibits a superior signal-to-noise ratio compared with multi-component systems, enabling precise and user-controllable release of payloads. This characteristic renders LAUNCHER highly suitable for diverse cellular applications, including transgene expression, tailored subcellular translocation and optochemogenetics. Additionally, the plug-and-play integration of LAUNCHER into existing synthetic circuits facilitates the enhancement of circuit performance. The demonstrated efficacy of LAUNCHER in improving existing circuitry underscores its significant potential for expanding its utilization in various applications.
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Affiliation(s)
- Mingguang Cui
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seunghwan Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Sung Hwan Ban
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jae Ryun Ryu
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Meiying Shen
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Soo Hyun Yang
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jin Young Kim
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Seul Ki Choi
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
| | - Jaemin Han
- Korea University College of Medicine, Seoul, Republic of Korea
| | - Yoonhee Kim
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Kihoon Han
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
- Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Donghun Lee
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Woong Sun
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyung-Bae Kwon
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dongmin Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea.
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15
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Fenelon KD, Krause J, Koromila T. Opticool: Cutting-edge transgenic optical tools. PLoS Genet 2024; 20:e1011208. [PMID: 38517915 PMCID: PMC10959397 DOI: 10.1371/journal.pgen.1011208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024] Open
Abstract
Only a few short decades have passed since the sequencing of GFP, yet the modern repertoire of transgenically encoded optical tools implies an exponential proliferation of ever improving constructions to interrogate the subcellular environment. A myriad of tags for labeling proteins, RNA, or DNA have arisen in the last few decades, facilitating unprecedented visualization of subcellular components and processes. Development of a broad array of modern genetically encoded sensors allows real-time, in vivo detection of molecule levels, pH, forces, enzyme activity, and other subcellular and extracellular phenomena in ever expanding contexts. Optogenetic, genetically encoded optically controlled manipulation systems have gained traction in the biological research community and facilitate single-cell, real-time modulation of protein function in vivo in ever broadening, novel applications. While this field continues to explosively expand, references are needed to assist scientists seeking to use and improve these transgenic devices in new and exciting ways to interrogate development and disease. In this review, we endeavor to highlight the state and trajectory of the field of in vivo transgenic optical tools.
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Affiliation(s)
- Kelli D. Fenelon
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Julia Krause
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Theodora Koromila
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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16
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Huppertz MC, Wilhelm J, Grenier V, Schneider MW, Falt T, Porzberg N, Hausmann D, Hoffmann DC, Hai L, Tarnawski M, Pino G, Slanchev K, Kolb I, Acuna C, Fenk LM, Baier H, Hiblot J, Johnsson K. Recording physiological history of cells with chemical labeling. Science 2024; 383:890-897. [PMID: 38386755 DOI: 10.1126/science.adg0812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/22/2024] [Indexed: 02/24/2024]
Abstract
Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins that become labeled in the presence of both a specific cellular activity and a fluorescent substrate. The recording period is set by the presence of the substrate, whereas the cellular activity controls the degree of the labeling. The use of distinguishable substrates enabled the recording of successive periods of activity. We recorded protein-protein interactions, G protein-coupled receptor activation, and increases in intracellular calcium. Recordings of elevated calcium levels allowed selections of cells from heterogeneous populations for transcriptomic analysis and tracking of neuronal activities in flies and zebrafish.
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Affiliation(s)
- Magnus-Carsten Huppertz
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Jonas Wilhelm
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Vincent Grenier
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Martin W Schneider
- Department Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Tjalda Falt
- Active Sensing, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Nicola Porzberg
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - David Hausmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dirk C Hoffmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Ling Hai
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neurology and Neurooncology Program, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
- Bioinformatics and Omics Data Analytics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Miroslaw Tarnawski
- Protein Expression and Characterization Facility, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Gabriela Pino
- Chica and Heinz Schaller Foundation, Institute of Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany
| | - Krasimir Slanchev
- Department Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Ilya Kolb
- GENIE Project Team, Janelia Research Campus, Ashburn, VA 20147, USA
| | - Claudio Acuna
- Chica and Heinz Schaller Foundation, Institute of Anatomy and Cell Biology, Heidelberg University, Im Neuenheimer Feld 307, 69120 Heidelberg, Germany
| | - Lisa M Fenk
- Active Sensing, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Herwig Baier
- Department Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Julien Hiblot
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
| | - Kai Johnsson
- Department of Chemical Biology, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120 Heidelberg, Germany
- Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
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17
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Pang B, Wu X, Chen H, Yan Y, Du Z, Yu Z, Yang X, Wang W, Lu K. Exploring the memory: existing activity-dependent tools to tag and manipulate engram cells. Front Cell Neurosci 2024; 17:1279032. [PMID: 38259503 PMCID: PMC10800721 DOI: 10.3389/fncel.2023.1279032] [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: 08/17/2023] [Accepted: 10/17/2023] [Indexed: 01/24/2024] Open
Abstract
The theory of engrams, proposed several years ago, is highly crucial to understanding the progress of memory. Although it significantly contributes to identifying new treatments for cognitive disorders, it is limited by a lack of technology. Several scientists have attempted to validate this theory but failed. With the increasing availability of activity-dependent tools, several researchers have found traces of engram cells. Activity-dependent tools are based on the mechanisms underlying neuronal activity and use a combination of emerging molecular biological and genetic technology. Scientists have used these tools to tag and manipulate engram neurons and identified numerous internal connections between engram neurons and memory. In this review, we provide the background, principles, and selected examples of applications of existing activity-dependent tools. Using a combination of traditional definitions and concepts of engram cells, we discuss the applications and limitations of these tools and propose certain developmental directions to further explore the functions of engram cells.
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Affiliation(s)
- Bo Pang
- The Second Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Xiaoyan Wu
- The First Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Hailun Chen
- The Second Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Yiwen Yan
- School of Basic Medicine Science, Southern Medical University, Guangzhou, China
| | - Zibo Du
- The First Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Zihan Yu
- School of Basic Medicine Science, Southern Medical University, Guangzhou, China
| | - Xiai Yang
- Department of Neurology, Ankang Central Hospital, Ankang, China
| | - Wanshan Wang
- Laboratory Animal Management Center, Southern Medical University, Guangzhou, China
- Guangzhou Southern Medical Laboratory Animal Sci. and Tech. Co., Ltd., Guangzhou, China
| | - Kangrong Lu
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, Southern Medical University, Guangzhou, China
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18
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Teng F, Cui T, Zhou L, Gao Q, Zhou Q, Li W. Programmable synthetic receptors: the next-generation of cell and gene therapies. Signal Transduct Target Ther 2024; 9:7. [PMID: 38167329 PMCID: PMC10761793 DOI: 10.1038/s41392-023-01680-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/22/2023] [Accepted: 10/11/2023] [Indexed: 01/05/2024] Open
Abstract
Cell and gene therapies hold tremendous promise for treating a range of difficult-to-treat diseases. However, concerns over the safety and efficacy require to be further addressed in order to realize their full potential. Synthetic receptors, a synthetic biology tool that can precisely control the function of therapeutic cells and genetic modules, have been rapidly developed and applied as a powerful solution. Delicately designed and engineered, they can be applied to finetune the therapeutic activities, i.e., to regulate production of dosed, bioactive payloads by sensing and processing user-defined signals or biomarkers. This review provides an overview of diverse synthetic receptor systems being used to reprogram therapeutic cells and their wide applications in biomedical research. With a special focus on four synthetic receptor systems at the forefront, including chimeric antigen receptors (CARs) and synthetic Notch (synNotch) receptors, we address the generalized strategies to design, construct and improve synthetic receptors. Meanwhile, we also highlight the expanding landscape of therapeutic applications of the synthetic receptor systems as well as current challenges in their clinical translation.
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Affiliation(s)
- Fei Teng
- University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Tongtong Cui
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhou
- University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingqin Gao
- University of Chinese Academy of Sciences, Beijing, 101408, China
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zhou
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Wei Li
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- State Key Laboratory of Stem Cell and Regenerative Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
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19
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Farashi S, Sarihi A, Ramezani M, Shahidi S, Mazdeh M. Parkinson's disease tremor prediction using EEG data analysis-A preliminary and feasibility study. BMC Neurol 2023; 23:420. [PMID: 38001410 PMCID: PMC10668446 DOI: 10.1186/s12883-023-03468-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
PURPOSE Tremor is one of the hallmarks of Parkinson's disease (PD) that does not respond effectively to conventional medications. In this regard, as a complementary solution, methods such as deep brain stimulation have been proposed. To apply the intervention with minimal side effects, it is necessary to predict tremor initiation. The purpose of the current study was to propose a novel methodology for predicting resting tremors using analysis of EEG time-series. METHODS A modified algorithm for tremor onset detection from accelerometer data was proposed. Furthermore, a machine learning methodology for predicting PD hand tremors from EEG time-series was proposed. The most discriminative features extracted from EEG data based on statistical analyses and post-hoc tests were used to train the classifier for distinguishing pre-tremor conditions. RESULTS Statistical analyses with post-hoc tests showed that features such as form factor and statistical features were the most discriminative features. Furthermore, limited numbers of EEG channels (F3, F7, P4, CP2, FC6, and C4) and EEG bands (Delta and Gamma) were sufficient for an accurate tremor prediction based on EEG data. Based on the selected feature set, a KNN classifier obtained the best pre-tremor prediction performance with an accuracy of 73.67%. CONCLUSION This feasibility study was the first attempt to show the predicting ability of EEG time-series for PD hand tremor prediction. Considering the limitations of this study, future research with longer data, and different brain dynamics are needed for clinical applications.
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Affiliation(s)
- Sajjad Farashi
- Neurophysiology Research Center, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Abdolrahman Sarihi
- Neurophysiology Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
- Department of Physiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mahdi Ramezani
- Department of Anatomical Sciences, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Siamak Shahidi
- Neurophysiology Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
- Department of Physiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mehrdokht Mazdeh
- Department of Neurology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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20
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Berndt A, Cai D, Cohen A, Juarez B, Iglesias JT, Xiong H, Qin Z, Tian L, Slesinger PA. Current Status and Future Strategies for Advancing Functional Circuit Mapping In Vivo. J Neurosci 2023; 43:7587-7598. [PMID: 37940594 PMCID: PMC10634581 DOI: 10.1523/jneurosci.1391-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 11/10/2023] Open
Abstract
The human brain represents one of the most complex biological systems, containing billions of neurons interconnected through trillions of synapses. Inherent to the brain is a biochemical complexity involving ions, signaling molecules, and peptides that regulate neuronal activity and allow for short- and long-term adaptations. Large-scale and noninvasive imaging techniques, such as fMRI and EEG, have highlighted brain regions involved in specific functions and visualized connections between different brain areas. A major shortcoming, however, is the need for more information on specific cell types and neurotransmitters involved, as well as poor spatial and temporal resolution. Recent technologies have been advanced for neuronal circuit mapping and implemented in behaving model organisms to address this. Here, we highlight strategies for targeting specific neuronal subtypes, identifying, and releasing signaling molecules, controlling gene expression, and monitoring neuronal circuits in real-time in vivo Combined, these approaches allow us to establish direct causal links from genes and molecules to the systems level and ultimately to cognitive processes.
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Affiliation(s)
| | - Denise Cai
- Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | | | | | | | | | - Zhenpeng Qin
- University of Texas-Dallas, Richardson, TX 75080
| | - Lin Tian
- University of California-Davis, Davis, CA 95616
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21
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Onodera K, Tsuno Y, Hiraoka Y, Tanaka K, Maejima T, Mieda M. In vivo recording of the circadian calcium rhythm in Prokineticin 2 neurons of the suprachiasmatic nucleus. Sci Rep 2023; 13:16974. [PMID: 37813987 PMCID: PMC10562406 DOI: 10.1038/s41598-023-44282-5] [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: 05/15/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023] Open
Abstract
Prokineticin 2 (Prok2) is a small protein expressed in a subpopulation of neurons in the suprachiasmatic nucleus (SCN), the primary circadian pacemaker in mammals. Prok2 has been implicated as a candidate output molecule from the SCN to control multiple circadian rhythms. Genetic manipulation specific to Prok2-producing neurons would be a powerful approach to understanding their function. Here, we report the generation of Prok2-tTA knock-in mice expressing the tetracycline transactivator (tTA) specifically in Prok2 neurons and an application of these mice to in vivo recording of Ca2+ rhythms in these neurons. First, the specific and efficient expression of tTA in Prok2 neurons was verified by crossing the mice with EGFP reporter mice. Prok2-tTA mice were then used to express a fluorescent Ca2+ sensor protein to record the circadian Ca2+ rhythm in SCN Prok2 neurons in vivo. Ca2+ in these cells showed clear circadian rhythms in both light-dark and constant dark conditions, with their peaks around midday. Notably, the hours of high Ca2+ nearly coincided with the rest period of the behavioral rhythm. These observations fit well with the predicted function of Prok2 neurons as a candidate output pathway of the SCN by suppressing locomotor activity during both daytime and subjective daytime.
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Affiliation(s)
- Kaito Onodera
- Department of Integrative Neurophysiology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
| | - Yusuke Tsuno
- Department of Integrative Neurophysiology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
| | - Yuichi Hiraoka
- Laboratory of Molecular Neuroscience, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kohichi Tanaka
- Laboratory of Molecular Neuroscience, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takashi Maejima
- Department of Integrative Neurophysiology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
| | - Michihiro Mieda
- Department of Integrative Neurophysiology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan.
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22
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Ricciardi F, Márquez C. The neural circuit that makes maternal mice respond to pups' cries. Nature 2023; 621:693-694. [PMID: 37735608 DOI: 10.1038/d41586-023-02545-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
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23
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Valtcheva S, Issa HA, Bair-Marshall CJ, Martin KA, Jung K, Zhang Y, Kwon HB, Froemke RC. Neural circuitry for maternal oxytocin release induced by infant cries. Nature 2023; 621:788-795. [PMID: 37730989 PMCID: PMC10639004 DOI: 10.1038/s41586-023-06540-4] [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: 10/15/2021] [Accepted: 08/15/2023] [Indexed: 09/22/2023]
Abstract
Oxytocin is a neuropeptide that is important for maternal physiology and childcare, including parturition and milk ejection during nursing1-6. Suckling triggers the release of oxytocin, but other sensory cues-specifically, infant cries-can increase the levels of oxytocin in new human mothers7, which indicates that cries can activate hypothalamic oxytocin neurons. Here we describe a neural circuit that routes auditory information about infant vocalizations to mouse oxytocin neurons. We performed in vivo electrophysiological recordings and photometry from identified oxytocin neurons in awake maternal mice that were presented with pup calls. We found that oxytocin neurons responded to pup vocalizations, but not to pure tones, through input from the posterior intralaminar thalamus, and that repetitive thalamic stimulation induced lasting disinhibition of oxytocin neurons. This circuit gates central oxytocin release and maternal behaviour in response to calls, providing a mechanism for the integration of sensory cues from the offspring in maternal endocrine networks to ensure modulation of brain state for efficient parenting.
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Affiliation(s)
- Silvana Valtcheva
- Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.
- Neuroscience Institute, New York University School of Medicine, New York, NY, USA.
- Department of Otolaryngology, New York University School of Medicine, New York, NY, USA.
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY, USA.
- Center for Neural Science, New York University, New York, NY, USA.
| | - Habon A Issa
- Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
- Neuroscience Institute, New York University School of Medicine, New York, NY, USA
- Department of Otolaryngology, New York University School of Medicine, New York, NY, USA
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY, USA
- Center for Neural Science, New York University, New York, NY, USA
| | - Chloe J Bair-Marshall
- Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
- Neuroscience Institute, New York University School of Medicine, New York, NY, USA
- Department of Otolaryngology, New York University School of Medicine, New York, NY, USA
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY, USA
- Center for Neural Science, New York University, New York, NY, USA
| | - Kathleen A Martin
- Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
- Neuroscience Institute, New York University School of Medicine, New York, NY, USA
- Department of Otolaryngology, New York University School of Medicine, New York, NY, USA
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY, USA
- Center for Neural Science, New York University, New York, NY, USA
| | - Kanghoon Jung
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yiyao Zhang
- Neuroscience Institute, New York University School of Medicine, New York, NY, USA
| | - Hyung-Bae Kwon
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert C Froemke
- Skirball Institute for Biomolecular Medicine, New York University School of Medicine, New York, NY, USA.
- Neuroscience Institute, New York University School of Medicine, New York, NY, USA.
- Department of Otolaryngology, New York University School of Medicine, New York, NY, USA.
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY, USA.
- Center for Neural Science, New York University, New York, NY, USA.
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24
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Jung K, Chang M, Steinecke A, Burke B, Choi Y, Oisi Y, Fitzpatrick D, Taniguchi H, Kwon HB. An adaptive behavioral control motif mediated by cortical axo-axonic inhibition. Nat Neurosci 2023; 26:1379-1393. [PMID: 37474640 PMCID: PMC10400431 DOI: 10.1038/s41593-023-01380-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/13/2023] [Indexed: 07/22/2023]
Abstract
Genetically defined subgroups of inhibitory interneurons are thought to play distinct roles in learning, but heterogeneity within these subgroups has limited our understanding of the scope and nature of their specific contributions. Here we reveal that the chandelier cell (ChC), an interneuron type that specializes in inhibiting the axon-initial segment (AIS) of pyramidal neurons, establishes cortical microcircuits for organizing neural coding through selective axo-axonic synaptic plasticity. We found that organized motor control is mediated by enhanced population coding of direction-tuned premotor neurons, with tuning refined through suppression of irrelevant neuronal activity. ChCs contribute to learning-dependent refinements by providing selective inhibitory control over individual pyramidal neurons rather than global suppression. Quantitative analysis of structural plasticity across axo-axonic synapses revealed that ChCs redistributed inhibitory weights to individual pyramidal neurons during learning. These results demonstrate an adaptive logic of the inhibitory circuit motif responsible for organizing distributed neural representations. Thus, ChCs permit efficient cortical computation in a targeted cell-specific manner.
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Affiliation(s)
- Kanghoon Jung
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Minhyeok Chang
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - André Steinecke
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | - Benjamin Burke
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Youngjin Choi
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yasuhiro Oisi
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
| | | | - Hiroki Taniguchi
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA
- Department of Pathology, Chronic Brain Injury program, Ohio State University, Columbus, OH, USA
| | - Hyung-Bae Kwon
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA.
- Max Planck Institute of Neurobiology, Martinsried, Germany.
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25
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Tsuno Y, Peng Y, Horike SI, Wang M, Matsui A, Yamagata K, Sugiyama M, Nakamura TJ, Daikoku T, Maejima T, Mieda M. In vivo recording of suprachiasmatic nucleus dynamics reveals a dominant role of arginine vasopressin neurons in circadian pacesetting. PLoS Biol 2023; 21:e3002281. [PMID: 37643163 PMCID: PMC10465001 DOI: 10.1371/journal.pbio.3002281] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 07/28/2023] [Indexed: 08/31/2023] Open
Abstract
The central circadian clock of the suprachiasmatic nucleus (SCN) is a network consisting of various types of neurons and glial cells. Individual cells have the autonomous molecular machinery of a cellular clock, but their intrinsic periods vary considerably. Here, we show that arginine vasopressin (AVP) neurons set the ensemble period of the SCN network in vivo to control the circadian behavior rhythm. Artificial lengthening of cellular periods by deleting casein kinase 1 delta (CK1δ) in the whole SCN lengthened the free-running period of behavior rhythm to an extent similar to CK1δ deletion specific to AVP neurons. However, in SCN slices, PER2::LUC reporter rhythms of these mice only partially and transiently recapitulated the period lengthening, showing a dissociation between the SCN shell and core with a period instability in the shell. In contrast, in vivo calcium rhythms of both AVP and vasoactive intestinal peptide (VIP) neurons in the SCN of freely moving mice demonstrated stably lengthened periods similar to the behavioral rhythm upon AVP neuron-specific CK1δ deletion, without changing the phase relationships between each other. Furthermore, optogenetic activation of AVP neurons acutely induced calcium increase in VIP neurons in vivo. These results indicate that AVP neurons regulate other SCN neurons, such as VIP neurons, in vivo and thus act as a primary determinant of the SCN ensemble period.
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Affiliation(s)
- Yusuke Tsuno
- Department of Integrative Neurophysiology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Yubo Peng
- Department of Integrative Neurophysiology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Shin-ichi Horike
- Division of Integrated Omics Research, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | - Mohan Wang
- Department of Integrative Neurophysiology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Ayako Matsui
- Department of Integrative Neurophysiology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kanato Yamagata
- Child Brain Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Mizuki Sugiyama
- Laboratory of Animal Physiology, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Takahiro J. Nakamura
- Laboratory of Animal Physiology, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Takiko Daikoku
- Division of Animal Disease Model, Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Japan
| | - Takashi Maejima
- Department of Integrative Neurophysiology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Michihiro Mieda
- Department of Integrative Neurophysiology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
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26
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Zheng Y, Li Y. Past, present, and future of tools for dopamine detection. Neuroscience 2023:S0306-4522(23)00295-6. [PMID: 37419404 DOI: 10.1016/j.neuroscience.2023.06.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 07/09/2023]
Abstract
Dopamine (DA) is a critical neuromodulator involved in various brain functions. To understand how DA regulates neural circuits and behaviors in the physiological and pathological conditions, it is essential to have tools that enable the direct detection of DA dynamics in vivo. Recently, genetically encoded DA sensors based on G protein-coupled receptors revolutionized this field, as it allows us to track in vivo DA dynamic with unprecedented spatial-temporal resolution, high molecular specificity, and sub-second kinetics. In this review, we first summarize traditional DA detection methods. Then we focus on the development of genetically encoded DA sensors and feature its significance to understanding dopaminergic neuromodulation across diverse behaviors and species. Finally, we present our perspectives about the future direction of the next-generation DA sensors and extend their potential applications. Overall, this review offers a comprehensive perspective on the past, present, and future of DA detection tools, with important implications for the study of DA functions in health and disease.
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Affiliation(s)
- Yu Zheng
- Peking-Tsinghua Center for Life Sciences, 100871 Beijing, China
| | - Yulong Li
- Peking-Tsinghua Center for Life Sciences, 100871 Beijing, China; State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, 100871 Beijing, China; PKU-IDG/McGovern Institute for Brain Research, 100871 Beijing, China; National Biomedical Imaging Center, Peking University, 100871 Beijing, China.
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27
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Kroning K, Gannot N, Li X, Zhou G, Sescil J, Putansu A, Shen J, Wilson A, Fiel H, Li P, Wang W. Single-chain fluorescent integrators for mapping G-protein-coupled receptor agonists. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.543062. [PMID: 37398137 PMCID: PMC10312536 DOI: 10.1101/2023.05.31.543062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
GPCRs transduce the effects of many neuromodulators including dopamine, serotonin, epinephrine, acetylcholine, and opioids. The localization of synthetic or endogenous GPCR agonists impacts their action on specific neuronal pathways. In this paper, we show a series of single-protein chain integrator sensors to determine GPCR agonist localization in the whole brain. We previously engineered integrator sensors for the mu and kappa opioid receptor agonists called M- and K-SPOTIT, respectively. Here, we show a new integrator sensor design platform called SPOTall that we used to engineer sensors for the beta-2-adrenergic receptor (B2AR), the dopamine receptor D1, and the cholinergic receptor muscarinic 2 agonists. For multiplexed imaging of SPOTIT and SPOTall, we engineered a red version of the SPOTIT sensors. Finally, we used M-SPOTIT and B2AR-SPOTall to detect morphine, isoproterenol, and epinephrine in the mouse brain. The SPOTIT and SPOTall sensor design platform can be used to design a variety of GPCR integrator sensors for unbiased agonist detection of many synthetic and endogenous neuromodulators across the whole brain.
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Affiliation(s)
- Kayla Kroning
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Chemistry, University of Michigan, Ann Arbor, MI
| | - Noam Gannot
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan, Ann Arbor, MI
| | - Xingyu Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan, Ann Arbor, MI
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI
| | - Guanwei Zhou
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI
| | - Jennifer Sescil
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Chemistry, University of Michigan, Ann Arbor, MI
| | - Aubrey Putansu
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Chemistry, University of Michigan, Ann Arbor, MI
| | - Jiaqi Shen
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Chemistry, University of Michigan, Ann Arbor, MI
| | - Avery Wilson
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Hailey Fiel
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Peng Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan, Ann Arbor, MI
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI
| | - Wenjing Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI
- Department of Chemistry, University of Michigan, Ann Arbor, MI
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI
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28
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Lee SY, Cheah JS, Zhao B, Xu C, Roh H, Kim CK, Cho KF, Udeshi ND, Carr SA, Ting AY. Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells. Nat Methods 2023; 20:908-917. [PMID: 37188954 PMCID: PMC10539039 DOI: 10.1038/s41592-023-01880-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
The incorporation of light-responsive domains into engineered proteins has enabled control of protein localization, interactions and function with light. We integrated optogenetic control into proximity labeling, a cornerstone technique for high-resolution proteomic mapping of organelles and interactomes in living cells. Through structure-guided screening and directed evolution, we installed the light-sensitive LOV domain into the proximity labeling enzyme TurboID to rapidly and reversibly control its labeling activity with low-power blue light. 'LOV-Turbo' works in multiple contexts and dramatically reduces background in biotin-rich environments such as neurons. We used LOV-Turbo for pulse-chase labeling to discover proteins that traffic between endoplasmic reticulum, nuclear and mitochondrial compartments under cellular stress. We also showed that instead of external light, LOV-Turbo can be activated by bioluminescence resonance energy transfer from luciferase, enabling interaction-dependent proximity labeling. Overall, LOV-Turbo increases the spatial and temporal precision of proximity labeling, expanding the scope of experimental questions that can be addressed with proximity labeling.
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Affiliation(s)
- Song-Yi Lee
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Joleen S Cheah
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Boxuan Zhao
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Charles Xu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Heegwang Roh
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Christina K Kim
- Department of Genetics, Stanford University, Stanford, CA, USA
- Center for Neuroscience and Department of Neurology, University of California, Davis, CA, USA
| | - Kelvin F Cho
- Department of Genetics, Stanford University, Stanford, CA, USA
- Amgen Research, South San Francisco, CA, USA
| | | | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Alice Y Ting
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Biology, Stanford University, Stanford, CA, USA.
- Department of Chemistry, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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29
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Townson JM, Gomez-Lamarca MJ, Santa Cruz Mateos C, Bray SJ. OptIC-Notch reveals mechanism that regulates receptor interactions with CSL. Development 2023; 150:dev201785. [PMID: 37294169 PMCID: PMC10309584 DOI: 10.1242/dev.201785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/03/2023] [Indexed: 05/13/2023]
Abstract
Active Notch signalling is elicited through receptor-ligand interactions that result in release of the Notch intracellular domain (NICD), which translocates into the nucleus. NICD activates transcription at target genes, forming a complex with the DNA-binding transcription factor CSL [CBF1/Su(H)/LAG-1] and co-activator Mastermind. However, CSL lacks its own nuclear localisation sequence, and it remains unclear where the tripartite complex is formed. To probe the mechanisms involved, we designed an optogenetic approach to control NICD release (OptIC-Notch) and monitored the subsequent complex formation and target gene activation. Strikingly, we observed that, when uncleaved, OptIC-Notch sequestered CSL in the cytoplasm. Hypothesising that exposure of a juxta membrane ΦWΦP motif is key to sequestration, we masked this motif with a second light-sensitive domain (OptIC-Notch{ω}), which was sufficient to prevent CSL sequestration. Furthermore, NICD produced by light-induced cleavage of OptIC-Notch or OptIC-Notch{ω} chaperoned CSL into the nucleus and induced target gene expression, showing efficient light-controlled activation. Our results demonstrate that exposure of the ΦWΦP motif leads to CSL recruitment and suggest this can occur in the cytoplasm prior to nuclear entry.
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Affiliation(s)
- Jonathan M. Townson
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Maria J. Gomez-Lamarca
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Carmen Santa Cruz Mateos
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
| | - Sarah J. Bray
- Department of Physiology Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK
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30
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Ding J, Lu J, Zhang Q, Xu Y, Song B, Wu Y, Shi H, Chu B, Wang H, He Y. Camouflage Nanoparticles Enable in Situ Bioluminescence-Driven Optogenetic Therapy of Retinoblastoma. ACS NANO 2023; 17:7750-7764. [PMID: 37022677 DOI: 10.1021/acsnano.3c00470] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Optogenetic therapy has emerged as a promising technique for the treatment of ocular diseases; however, most optogenetic tools rely on external blue light to activate the photoswitch, whose relatively strong phototoxicity may induce retinal damage. Herein, we present the demonstration of camouflage nanoparticle-based vectors for in situ bioluminescence-driven optogenetic therapy of retinoblastoma. In biomimetic vectors, the photoreceptor CRY2 and its interacting partner CIB1 plasmid are camouflaged with folic acid ligands and luciferase NanoLuc-modified macrophage membranes. To conduct proof-of-concept research, this study employs a mouse model of retinoblastoma. In comparison to external blue light irradiation, the developed system enables an in situ bioluminescence-activated apoptotic pathway to inhibit tumor growth with greater therapeutic efficacy, resulting in a significant reduction in ocular tumor size. Furthermore, unlike external blue light irradiation, which causes retinal damage and corneal neovascularization, the camouflage nanoparticle-based optogenetic system maintains retinal structural integrity while avoiding corneal neovascularization.
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Affiliation(s)
- Jiali Ding
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano and Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou 215123, China
| | - Jianping Lu
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano and Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou 215123, China
| | - Qian Zhang
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano and Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou 215123, China
| | - Yanan Xu
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano and Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou 215123, China
| | - Bin Song
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano and Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou 215123, China
| | - Yuqi Wu
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano and Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou 215123, China
| | - Haoliang Shi
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano and Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou 215123, China
| | - Binbin Chu
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano and Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou 215123, China
| | - Houyu Wang
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano and Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou 215123, China
| | - Yao He
- Suzhou Key Laboratory of Nanotechnology and Biomedicine, Institute of Functional Nano and Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology (NANO-CIC), Soochow University, Suzhou 215123, China
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31
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Lee S, Cui M, Lee D, Han K, Sun W, Lee D. A rationally designed optochemogenetic switch for activating canonical Wnt signaling. iScience 2023; 26:106233. [PMID: 36915690 PMCID: PMC10006827 DOI: 10.1016/j.isci.2023.106233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/10/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Accurate spatiotemporal control of multicellular self-organization by various signaling pathways is essential for developmental stages. In particular, evolutionarily conserved Wnt signaling serves as a major morphogenetic switch to determine the anteroposterior axis of the embryo. Here, we developed a genetically encoded optochemogenetic Wnt switch, named optochemoWnt, by coupling a blue light-inducible CRY2olig and rapamycin-inducible LRP6c clustering. The rationally designed optochemoWnt successfully modulated Wnt signaling with AND-gated patterns and demonstrated an improved signal-to-noise ratio (SNR). The dual-triggered switch provides a safeguard to prevent signal leakage resulting from ambient light sources under general laboratory conditions. OptochemoWnt expands the molecular toolbox available for the fields of developmental biology and tissue engineering. In addition, the AND-gated strategy of optochemoWnt may be used for other biomedical applications that integrate user defined switch elements with Boolean logic gates.
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Affiliation(s)
- Seunghwan Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.,BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Mingguang Cui
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.,BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Donghun Lee
- Department of Physics, Korea University, Seoul, Republic of Korea
| | - Kihoon Han
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea.,Department of Neuroscience, Korea University College of Medicine, Seoul, Republic of Korea
| | - Woong Sun
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.,BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Dongmin Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea.,BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
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32
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Jung K, Chang M, Steinecke A, Berke B, Choi Y, Oisi Y, Fitzpatrick D, Taniguchi H, Kwon HB. An adaptive behavioral control motif mediated by cortical axo-axonic inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.10.531767. [PMID: 36945592 PMCID: PMC10029003 DOI: 10.1101/2023.03.10.531767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Neural circuits are reorganized with specificity during learning. Genetically-defined subgroups of inhibitory interneurons are thought to play distinct roles in learning, but heterogeneity within these subgroups has limited our understanding of the scope and nature of their specific contributions to learning. Here we reveal that the chandelier cell (ChC), an interneuron type that specializes in inhibiting the axon-initial segment (AIS) of pyramidal neurons, establishes cortical microcircuits for organizing neural coding through selective axo-axonic synaptic plasticity. We find that organized motor control is mediated by enhanced population coding of direction-tuned premotor neurons, whose tuning is refined through suppression of irrelevant neuronal activity. ChCs are required for learning-dependent refinements via providing selective inhibitory control over pyramidal neurons rather than global suppression. Quantitative analysis on structural plasticity of axo-axonic synapses revealed that ChCs redistributed inhibitory weights to individual pyramidal neurons during learning. These results demonstrate an adaptive logic of the inhibitory circuit motif responsible for organizing distributed neural representations. Thus, ChCs permit efficient cortical computation in a target cell specific manner, which highlights the significance of interneuron diversity.
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33
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Lee SY, Cheah JS, Zhao B, Xu C, Roh H, Kim CK, Cho KF, Udeshi ND, Carr SA, Ting AY. Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.09.531939. [PMID: 36945504 PMCID: PMC10028978 DOI: 10.1101/2023.03.09.531939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
The incorporation of light-responsive domains into engineered proteins has enabled control of protein localization, interactions, and function with light. We integrated optogenetic control into proximity labeling (PL), a cornerstone technique for high-resolution proteomic mapping of organelles and interactomes in living cells. Through structure-guided screening and directed evolution, we installed the light-sensitive LOV domain into the PL enzyme TurboID to rapidly and reversibly control its labeling activity with low-power blue light. "LOV-Turbo" works in multiple contexts and dramatically reduces background in biotin-rich environments such as neurons. We used LOV-Turbo for pulse-chase labeling to discover proteins that traffick between endoplasmic reticulum, nuclear, and mitochondrial compartments under cellular stress. We also showed that instead of external light, LOV-Turbo can be activated by BRET from luciferase, enabling interaction-dependent PL. Overall, LOV-Turbo increases the spatial and temporal precision of PL, expanding the scope of experimental questions that can be addressed with PL.
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34
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Day-Cooney J, Dalangin R, Zhong H, Mao T. Genetically encoded fluorescent sensors for imaging neuronal dynamics in vivo. J Neurochem 2023; 164:284-308. [PMID: 35285522 PMCID: PMC11322610 DOI: 10.1111/jnc.15608] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 11/29/2022]
Abstract
The brain relies on many forms of dynamic activities in individual neurons, from synaptic transmission to electrical activity and intracellular signaling events. Monitoring these neuronal activities with high spatiotemporal resolution in the context of animal behavior is a necessary step to achieve a mechanistic understanding of brain function. With the rapid development and dissemination of highly optimized genetically encoded fluorescent sensors, a growing number of brain activities can now be visualized in vivo. To date, cellular calcium imaging, which has been largely used as a proxy for electrical activity, has become a mainstay in systems neuroscience. While challenges remain, voltage imaging of neural populations is now possible. In addition, it is becoming increasingly practical to image over half a dozen neurotransmitters, as well as certain intracellular signaling and metabolic activities. These new capabilities enable neuroscientists to test previously unattainable hypotheses and questions. This review summarizes recent progress in the development and delivery of genetically encoded fluorescent sensors, and highlights example applications in the context of in vivo imaging.
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Affiliation(s)
- Julian Day-Cooney
- Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Rochelin Dalangin
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA
| | - Haining Zhong
- Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA
| | - Tianyi Mao
- Vollum Institute, Oregon Health and Science University, Portland, Oregon, USA
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35
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Shen J, Geng L, Li X, Emery C, Kroning K, Shingles G, Lee K, Heyden M, Li P, Wang W. A general method for chemogenetic control of peptide function. Nat Methods 2023; 20:112-122. [PMID: 36481965 PMCID: PMC10069916 DOI: 10.1038/s41592-022-01697-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 10/21/2022] [Indexed: 12/13/2022]
Abstract
Natural or engineered peptides serve important biological functions. A general approach to achieve chemical-dependent activation of short peptides will be valuable for spatial and temporal control of cellular processes. Here we present a pair of chemically activated protein domains (CAPs) for controlling the accessibility of both the N- and C-terminal portion of a peptide. CAPs were developed through directed evolution of an FK506-binding protein. By fusing a peptide to one or both CAPs, the function of the peptide is blocked until a small molecule displaces them from the FK506-binding protein ligand-binding site. We demonstrate that CAPs are generally applicable to a range of short peptides, including a protease cleavage site, a dimerization-inducing heptapeptide, a nuclear localization signal peptide, and an opioid peptide, with a chemical dependence up to 156-fold. We show that the CAPs system can be utilized in cell cultures and multiple organs in living animals.
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Affiliation(s)
- Jiaqi Shen
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Lequn Geng
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Xingyu Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Catherine Emery
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, USA
| | - Kayla Kroning
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Gwendolyn Shingles
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Kerry Lee
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Peng Li
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Biologic and Materials Sciences & Prosthodontics, University of Michigan, Ann Arbor, MI, USA.
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA.
| | - Wenjing Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA.
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36
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Zhou G, Wan WW, Wang W. Modular Peroxidase-Based Reporters for Detecting Protease Activity and Protein Interactions with Temporal Gating. J Am Chem Soc 2022; 144:22933-22940. [PMID: 36511757 PMCID: PMC10026560 DOI: 10.1021/jacs.2c08280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Enzymatic reporters have been widely applied to study various biological processes because they can amplify signal through enzymatic reactions and provide good sensitivity. However, there is still a need for modular motifs for designing a series of enzymatic reporters. Here, we report a modular peroxidase-based motif, named CLAPon, that features acid-base coil-caged enhanced ascorbate peroxidase (APEX). We demonstrate the modularity of CLAPon by designing a series of reporters for detecting protease activity and protein-protein interactions (PPIs). CLAPon for protease activity showed a 390-fold fluorescent signal increase upon tobacco etch virus protease cleavage. CLAPon for PPI detection (PPI-CLAPon) has two variants, PPI-CLAPon1.0 and 1.1. PPI-CLAPon1.0 showed a signal-to-noise ratio (SNR) of up to 107 for high-affinity PPI pairs and enabled imaging with sub-cellular spatial resolution. However, the more sensitive PPI-CLAPon1.1 is required for detecting low-affinity PPI pairs. PPI-CLAPon1.0 was further engineered to a reporter with light-dependent temporal gating, called LiPPI-CLAPon1.0, which can detect a 3-min calcium-dependent PPI with an SNR of 17. LiPPI-CLAPon enables PPI detection within a specific time window with rapid APEX activation and diverse readout. Lastly, PPI-CLAPon1.0 was designed to have chemical gating, providing more versatility to complement the LiPPI-CLAPon. These CLAPon-based reporter designs can be broadly applied to study various signaling processes that involve protease activity and PPIs and provide a versatile platform to design various genetically encoded reporters.
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Affiliation(s)
- Guanwei Zhou
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wei Wei Wan
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wenjing Wang
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Corresponding Author: Wenjing Wang,
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Abstract
Verifying causal effects of neural circuits is essential for proving a direct circuit-behavior relationship. However, techniques for tagging only active neurons with high spatiotemporal precision remain at the beginning stages. Here we develop the soma-targeted Cal-Light (ST-Cal-Light) which selectively converts somatic calcium rise triggered by action potentials into gene expression. Such modification simultaneously increases the signal-to-noise ratio of reporter gene expression and reduces the light requirement for successful labeling. Because of the enhanced efficacy, the ST-Cal-Light enables the tagging of functionally engaged neurons in various forms of behaviors, including context-dependent fear conditioning, lever-pressing choice behavior, and social interaction behaviors. We also target kainic acid-sensitive neuronal populations in the hippocampus which subsequently suppress seizure symptoms, suggesting ST-Cal-Light's applicability in controlling disease-related neurons. Furthermore, the generation of a conditional ST-Cal-Light knock-in mouse provides an opportunity to tag active neurons in a region- or cell-type specific manner via crossing with other Cre-driver lines. Thus, the versatile ST-Cal-Light system links somatic action potentials to behaviors with high temporal precision, and ultimately allows functional circuit dissection at a single cell resolution.
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38
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Kroning KE, Wang W. Genetically encoded tools for in vivo G-protein-coupled receptor agonist detection at cellular resolution. Clin Transl Med 2022; 12:e1124. [PMID: 36446954 PMCID: PMC9708909 DOI: 10.1002/ctm2.1124] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/10/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) are the most abundant receptor type in the human body and are responsible for regulating many physiological processes, such as sensation, cognition, muscle contraction and metabolism. Further, GPCRs are widely expressed in the brain where their agonists make up a large number of neurotransmitters and neuromodulators. Due to the importance of GPCRs in human physiology, genetically encoded sensors have been engineered to detect GPCR agonists at cellular resolution in vivo. These sensors can be placed into two main categories: those that offer real-time information on the signalling dynamics of GPCR agonists and those that integrate the GPCR agonist signal into a permanent, quantifiable mark that can be used to detect GPCR agonist localisation in a large brain area. In this review, we discuss the various designs of real-time and integration sensors, their advantages and limitations, and some in vivo applications. We also discuss the potential of using real-time and integrator sensors together to identify neuronal circuits affected by endogenous GPCR agonists and perform detailed characterisations of the spatiotemporal dynamics of GPCR agonist release in those circuits. By using these sensors together, the overall knowledge of GPCR-mediated signalling can be expanded.
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Affiliation(s)
- Kayla E. Kroning
- Life Sciences Institute, University of MichiganAnn ArborMichiganUSA
- Department of ChemistryUniversity of MichiganAnn ArborMichiganUSA
| | - Wenjing Wang
- Life Sciences Institute, University of MichiganAnn ArborMichiganUSA
- Department of ChemistryUniversity of MichiganAnn ArborMichiganUSA
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39
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A red light-responsive photoswitch for deep tissue optogenetics. Nat Biotechnol 2022; 40:1672-1679. [PMID: 35697806 DOI: 10.1038/s41587-022-01351-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/04/2022] [Indexed: 12/30/2022]
Abstract
Red light penetrates deep into mammalian tissues and has low phototoxicity, but few optogenetic tools that use red light have been developed. Here we present MagRed, a red light-activatable photoswitch that consists of a red light-absorbing bacterial phytochrome incorporating a mammalian endogenous chromophore, biliverdin and a photo-state-specific binder that we developed using Affibody library selection. Red light illumination triggers the binding of the two components of MagRed and the assembly of split-proteins fused to them. Using MagRed, we developed a red light-activatable Cre recombinase, which enables light-activatable DNA recombination deep in mammalian tissues. We also created red light-inducible transcriptional regulators based on CRISPR-Cas9 that enable an up to 378-fold activation (average, 135-fold induction) of multiple endogenous target genes. MagRed will facilitate optogenetic applications deep in mammalian organisms in a variety of biological research areas.
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40
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Cleveland JD, Taslimi A, Liu Q, Van Keuren AM, Churchill MEA, Tucker CL. Reprogramming the Cleavage Specificity of Botulinum Neurotoxin Serotype B1. ACS Synth Biol 2022; 11:3318-3329. [PMID: 36153971 PMCID: PMC9907380 DOI: 10.1021/acssynbio.2c00235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Proteases with reprogrammed specificity for nonnative substrates are highly desired in synthetic biology and biomedicine. However, generating reprogrammed proteases that are orthogonal and highly specific for a new target has been a major challenge. In this work, we sought to expand the versatility of protease systems by engineering an orthogonal botulinum neurotoxin serotype B (BoNT/B) protease that recognizes an orthogonal substrate. We designed and validated an orthogonal BoNT/B protease system in mammalian cells, combining mutations in the protease with compensatory mutations in the protease substrate and incorporating a truncated target sequence and then demonstrated use of this orthogonal BoNT/B protease-substrate combination to regulate complex transcriptional circuitry in mammalian cells. Transposing this platform into yeast, we demonstrated utility of this approach for in vivo protease evolution. We tested this platform with the newly designed orthogonal protease and then used it in a high-throughput screen to identify novel orthogonal protease/protease substrate combinations. While carrying out this work, we also generated new cleavage reporters that could be used to report botulinum toxin protease activity in mammalian cells using simple fluorescent readouts. We envision that these approaches will expand the applications of botulinum protease in new directions and aid in the development of new reprogrammed proteases.
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Affiliation(s)
- Joseph D. Cleveland
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Amir Taslimi
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Qi Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Anna M. Van Keuren
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Mair E. A. Churchill
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
| | - Chandra L. Tucker
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045 USA
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41
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Bickle J, De Sousa AF, Silva AJ. New research tools suggest a “levels-less” image of the behaving organism and dissolution of the reduction vs. anti-reduction dispute. Front Psychol 2022; 13:990316. [PMID: 36110269 PMCID: PMC9470241 DOI: 10.3389/fpsyg.2022.990316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
A kind of “ruthless reductionism” characterized the experimental practices of the first two decades of molecular and cellular cognition (MCC). More recently, new research tools have expanded experimental practices in this field, enabling researchers to image and manipulate individual molecular mechanisms in behaving organisms with an unprecedented temporal, sub-cellular, cellular, and even circuit-wide specificity. These tools dramatically expand the range and reach of experiments in MCC, and in doing so they may help us transcend the worn-out and counterproductive debates about “reductionism” and “emergence” that divide neuroscientists and philosophers alike. We describe examples of these new tools and illustrate their practical power by presenting an exemplary recent case of MCC research using them. From these tools and results, we provide an initial sketch of a new image of the behaving organism in its full causal-interactive complexity, with its molecules, cells, and circuits combined within the single system that it is. This new image stands in opposition to the traditional “levels” image of the behaving organism, and even the initial sketch we provide of it here offers hope for avoiding the dreary metaphysical debates about “emergence” and “downward causation,” and even the reduction vs. anti-reduction dispute, all dependent upon the familiar “levels” image.
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Affiliation(s)
- John Bickle
- Department of Philosophy and Religion, Shackouls Honors College, Mississippi State University, Starkville, MS, United States
- Department of Advanced Biomedical Education, University of Mississippi Medical Center, Jackson, MS, United States
- *Correspondence: John Bickle,
| | - André F. De Sousa
- Department of Neurobiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Alcino J. Silva
- Department of Neurobiology, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Psychiatry and Integrative Center for Learning and Memory, UCLA, Los Angeles, CA, United States
- Department of Psychology and Integrative Center for Learning and Memory, UCLA, Los Angeles, CA, United States
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42
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Fink T, Jerala R. Designed protease-based signaling networks. Curr Opin Chem Biol 2022; 68:102146. [DOI: 10.1016/j.cbpa.2022.102146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/09/2022] [Accepted: 03/14/2022] [Indexed: 12/27/2022]
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43
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Shen Y, Zhou M, Cai D, Filho DA, Fernandes G, Cai Y, de Sousa AF, Tian M, Kim N, Lee J, Necula D, Zhou C, Li S, Salinas S, Liu A, Kang X, Kamata M, Lavi A, Huang S, Silva T, Heo WD, Silva AJ. CCR5 closes the temporal window for memory linking. Nature 2022; 606:146-152. [PMID: 35614219 PMCID: PMC9197199 DOI: 10.1038/s41586-022-04783-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/20/2022] [Indexed: 11/09/2022]
Abstract
Real-world memories are formed in a particular context and are often not acquired or recalled in isolation1-5. Time is a key variable in the organization of memories, as events that are experienced close in time are more likely to be meaningfully associated, whereas those that are experienced with a longer interval are not1-4. How the brain segregates events that are temporally distinct is unclear. Here we show that a delayed (12-24 h) increase in the expression of C-C chemokine receptor type 5 (CCR5)-an immune receptor that is well known as a co-receptor for HIV infection6,7-after the formation of a contextual memory determines the duration of the temporal window for associating or linking that memory with subsequent memories. This delayed expression of CCR5 in mouse dorsal CA1 neurons results in a decrease in neuronal excitability, which in turn negatively regulates neuronal memory allocation, thus reducing the overlap between dorsal CA1 memory ensembles. Lowering this overlap affects the ability of one memory to trigger the recall of the other, and therefore closes the temporal window for memory linking. Our findings also show that an age-related increase in the neuronal expression of CCR5 and its ligand CCL5 leads to impairments in memory linking in aged mice, which could be reversed with a Ccr5 knockout and a drug approved by the US Food and Drug Administration (FDA) that inhibits this receptor, a result with clinical implications. Altogether, the findings reported here provide insights into the molecular and cellular mechanisms that shape the temporal window for memory linking.
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Affiliation(s)
- Yang Shen
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA
| | - Miou Zhou
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA.
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, USA.
| | - Denise Cai
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA
- Neuroscience Department, Icahn School of Medicine, New York, NY, USA
| | - Daniel Almeida Filho
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA
| | - Giselle Fernandes
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA
| | - Ying Cai
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA
| | - André F de Sousa
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA
| | - Min Tian
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Nury Kim
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jinsu Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Deanna Necula
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA
| | - Chengbin Zhou
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA
| | - Shuoyi Li
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA
| | - Shelbi Salinas
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, USA
| | - Andy Liu
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA
| | - Xiaoman Kang
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA
| | - Masakazu Kamata
- Department of Hematology and Oncology, University of California Los Angeles, Los Angeles, CA, USA
| | - Ayal Lavi
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA
| | - Shan Huang
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA
| | - Tawnie Silva
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA
| | - Won Do Heo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Alcino J Silva
- Neurobiology, Psychiatry and Psychology Departments and Integrative Center for Learning and Memory, University of California Los Angeles, Los Angeles, CA, USA.
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A fluorescent nanosensor paint detects dopamine release at axonal varicosities with high spatiotemporal resolution. Proc Natl Acad Sci U S A 2022; 119:e2202842119. [PMID: 35613050 DOI: 10.1073/pnas.2202842119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
SignificanceThe neurotransmitter dopamine controls normal behavior and dopaminergic dysfunction is prevalent in multiple brain diseases. To reach a detailed understanding of how dopamine release and signaling are regulated at the subcellular level, we developed a near infrared fluorescent dopamine nanosensor 'paint' (AndromeDA) to directly image dopamine release and its spatiotemporal characteristics. With AndromeDA, we can ascribe discrete DA release events to defined axonal varicosities, directly assess the heterogeneity of DA release events across such release sites, and determine the molecular components of the DA release machinery. AndromeDA thus provides a new method for gaining fundamental insights into the core mechanisms of dopamine release, which with greatly benefit our knowledge of dopamine biology and pathobiology.
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45
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Barykina NV, Karasev MM, Verkhusha VV, Shcherbakova DM. Technologies for large-scale mapping of functional neural circuits active during a user-defined time window. Prog Neurobiol 2022; 216:102290. [PMID: 35654210 DOI: 10.1016/j.pneurobio.2022.102290] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/15/2022] [Accepted: 05/25/2022] [Indexed: 11/25/2022]
Abstract
The mapping of neural circuits activated during behavior down to individual neurons is crucial for decoding how the brain processes information. Technologies allowing activity-dependent labeling of neurons during user-defined restricted time windows are rapidly developing. Precise marking of the time window with light, in addition to chemicals, is now possible. In these technologies, genetically encoded molecules integrate molecular events resulting from neuronal activity with light/drug-dependent events. The outputs are either changes in fluorescence or activation of gene expression. Molecular reporters allow labeling of activated neurons for visualization and cell-type identification. The transcriptional readout also allows further control of activated neuronal populations using optogenetic tools as reporters. Here we review the design of these technologies and discuss their demonstrated applications to reveal previously unknown connections in the mammalian brain. We also consider the strengths and weaknesses of the current approaches and provide a perspective for the future.
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Affiliation(s)
- Natalia V Barykina
- P.K. Anokhin Institute of Normal Physiology, Moscow 125315, Russia; Medicum, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Maksim M Karasev
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Vladislav V Verkhusha
- Department of Genetics, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Medicum, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Daria M Shcherbakova
- Department of Genetics, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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46
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Sokhadze G, Campbell PW, Charalambakis N, Govindaiah G, Guido W, McGee AW. Cre driver mouse lines for thalamocortical circuit mapping. J Comp Neurol 2022; 530:1049-1063. [PMID: 34545582 PMCID: PMC9891227 DOI: 10.1002/cne.25248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 08/16/2021] [Accepted: 09/07/2021] [Indexed: 02/04/2023]
Abstract
Subpopulations of neurons and associated neural circuits can be targeted in mice with genetic tools in a highly selective manner for visualization and manipulation. However, there are not well-defined Cre "driver" lines that target the expression of Cre recombinase to thalamocortical (TC) neurons. Here, we characterize three Cre driver lines for the nuclei of the dorsal thalamus: Oligodendrocyte transcription factor 3 (Olig3)-Cre, histidine decarboxylase (HDC)-Cre, and corticotropin-releasing hormone (CRH)-Cre. We examined the postnatal distribution of Cre expression for each of these lines with the Cre-dependent reporter CAG-tdTomato (Ai9). Cre-dependent expression of tdTomato reveals that Olig3-Cre expresses broadly within the thalamus, including TC neurons and interneurons, while HDC-Cre and CRH-Cre each have unique patterns of expression restricted to TC neurons within and across the sensory relay nuclei of the dorsal thalamus. Cre expression is present by the time of natural birth in all three lines, underscoring their utility for developmental studies. To demonstrate the utility of these Cre drivers for studying sensory TC circuitry, we targeted the expression of channelrhodopsin-2 to thalamus from the CAG-COP4*H134R/EYFP (Ai32) allele with either HDC-Cre or CRH-Cre. Optogenetic activation of TC afferents in primary visual cortex was sufficient to measure frequency-dependent depression. Thus, these Cre drivers provide selective Cre-dependent gene expression in thalamus suitable for both anatomical and functional studies.
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Affiliation(s)
- Guela Sokhadze
- Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Louisville Kentucky USA
| | - Peter W. Campbell
- Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Louisville Kentucky USA
| | - Naomi Charalambakis
- Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Louisville Kentucky USA
| | - Gubbi Govindaiah
- Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Louisville Kentucky USA
| | - William Guido
- Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Louisville Kentucky USA
| | - Aaron W. McGee
- Department of Anatomical Sciences and Neurobiology University of Louisville School of Medicine Louisville Kentucky USA
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47
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Wu Z, Lin D, Li Y. Pushing the frontiers: tools for monitoring neurotransmitters and neuromodulators. Nat Rev Neurosci 2022; 23:257-274. [PMID: 35361961 PMCID: PMC11163306 DOI: 10.1038/s41583-022-00577-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2022] [Indexed: 12/26/2022]
Abstract
Neurotransmitters and neuromodulators have a wide range of key roles throughout the nervous system. However, their dynamics in both health and disease have been challenging to assess, owing to the lack of in vivo tools to track them with high spatiotemporal resolution. Thus, developing a platform that enables minimally invasive, large-scale and long-term monitoring of neurotransmitters and neuromodulators with high sensitivity, high molecular specificity and high spatiotemporal resolution has been essential. Here, we review the methods available for monitoring the dynamics of neurotransmitters and neuromodulators. Following a brief summary of non-genetically encoded methods, we focus on recent developments in genetically encoded fluorescent indicators, highlighting how these novel indicators have facilitated advances in our understanding of the functional roles of neurotransmitters and neuromodulators in the nervous system. These studies present a promising outlook for the future development and use of tools to monitor neurotransmitters and neuromodulators.
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Affiliation(s)
- Zhaofa Wu
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Dayu Lin
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, China.
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- Chinese Institute for Brain Research, Beijing, China.
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China.
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48
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Manhas J, Edelstein HI, Leonard JN, Morsut L. The evolution of synthetic receptor systems. Nat Chem Biol 2022; 18:244-255. [PMID: 35058646 PMCID: PMC9041813 DOI: 10.1038/s41589-021-00926-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 10/18/2021] [Indexed: 12/15/2022]
Abstract
Receptors enable cells to detect, process and respond to information about their environments. Over the past two decades, synthetic biologists have repurposed physical parts and concepts from natural receptors to engineer synthetic receptors. These technologies implement customized sense-and-respond programs that link a cell's interaction with extracellular and intracellular cues to user-defined responses. When combined with tools for information processing, these advances enable programming of sophisticated customized functions. In recent years, the library of synthetic receptors and their capabilities has substantially evolved-a term we employ here to mean systematic improvement and expansion. Here, we survey the existing mammalian synthetic biology toolkit of protein-based receptors and signal-processing components, highlighting efforts to evolve and integrate some of the foundational synthetic receptor systems. We then propose a generalized strategy for engineering and improving receptor systems to meet defined functional objectives called a 'metric-enabled approach for synthetic receptor engineering' (MEASRE).
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Affiliation(s)
- Janvie Manhas
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hailey I Edelstein
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Joshua N Leonard
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA.
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL, USA.
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, USA.
| | - Leonardo Morsut
- The Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
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49
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Alachkar A, Alhassan S, Senel M. Lab-In-A-Syringe: A Novel Electrochemical Biosensor for On-Site and Real-Time Monitoring of Dopamine in Freely Behaving Mice. ACS Sens 2022; 7:331-337. [PMID: 35006681 DOI: 10.1021/acssensors.1c02525] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There is a growing demand for real-time analysis and sampling of biofluids on a single low-cost platform in ultralow fluid volumes with robustness. In this study, a microfluidic sensor was developed, manufactured through an additive manufacturing technique, and used for dopamine (DA) measurements. We implemented a biosensing system using pencil graphites (PGEs) integrated into a three-dimensional (3D) printed microfluidic syringe-type device (μSyringe). The amperometry technique was used to monitor the current changes associated with the electrooxidation of DA. The sensing signal was stable and linear in a concentration range of DA between the limit of quantification (0.1 nM) and the upper limit of linearity (500 nM). The μSyringe sensing device is simple, robust, and stable, making it suitable for real-time measurement of DA in cerebrospinal fluid (CSF) from freely moving mice.
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Affiliation(s)
- Amal Alachkar
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-4625, United States
- Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California-Irvine, Irvine, California 92697-4625, United States
- Center for the Neurobiology of Learning and Memory, University of California-Irvine, Irvine, California 92697-4625, United States
| | - Sammy Alhassan
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-4625, United States
| | - Mehmet Senel
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-4625, United States
- Department of Biochemistry, Faculty of Pharmacy, Biruni University, Istanbul 34010, Turkey
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50
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Lee D, Kwon HB. Current and future techniques for detecting oxytocin: Focusing on genetically-encoded GPCR sensors. J Neurosci Methods 2022; 366:109407. [PMID: 34763021 DOI: 10.1016/j.jneumeth.2021.109407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 10/12/2021] [Accepted: 11/03/2021] [Indexed: 10/19/2022]
Abstract
Oxytocin is a neuropituitary hormone that is involved in a wide range of psychosocial behaviors. Despite its psychophysiological importance as a neuromodulator in the CNS, effective techniques capable of monitoring oxytocin dynamics or testing related behavioral consequences are limited. Along with an explosive advancement in synthetic biology, high-performance genetically-encoded neuromodulator sensors are being developed. Here we comprehensively review the current methodologies available for detecting oxytocin in neuroscience. Their strengths and weaknesses are discussed, and a graphical summary is plotted for better comparison of techniques. We also suggest future directions for next generation oxytocin sensor development and their working principles.
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Affiliation(s)
- Dongmin Lee
- Department of Anatomy, Korea University College of Medicine, Seoul, Republic of Korea; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Hyung-Bae Kwon
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, 733N Broadway, Baltimore, MD 21205, USA.
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