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Meyer J, Yu K, Luna-Figueroa E, Deneen B, Noebels J. Glioblastoma disrupts cortical network activity at multiple spatial and temporal scales. Nat Commun 2024; 15:4503. [PMID: 38802334 PMCID: PMC11130179 DOI: 10.1038/s41467-024-48757-5] [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: 06/30/2023] [Accepted: 05/11/2024] [Indexed: 05/29/2024] Open
Abstract
The emergence of glioblastoma in cortical tissue initiates early and persistent neural hyperexcitability with signs ranging from mild cognitive impairment to convulsive seizures. The influence of peritumoral synaptic density, expansion dynamics, and spatial contours of excess glutamate upon higher order neuronal network modularity is unknown. We combined cellular and widefield imaging of calcium and glutamate fluorescent reporters in two glioblastoma mouse models with distinct synaptic microenvironments and infiltration profiles. Functional metrics of neural ensembles are dysregulated during tumor invasion depending on the stage of malignant progression and tumor cell proximity. Neural activity is differentially modulated during periods of accelerated and inhibited tumor expansion. Abnormal glutamate accumulation precedes and outpaces the spatial extent of baseline neuronal calcium signaling, indicating these processes are uncoupled in tumor cortex. Distinctive excitability homeostasis patterns and functional connectivity of local and remote neuronal populations support the promise of precision genetic diagnosis and management of this devastating brain disease.
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Affiliation(s)
- Jochen Meyer
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, USA.
| | - Kwanha Yu
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | | | - Benjamin Deneen
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey Noebels
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
- Center for Cancer Neuroscience, Baylor College of Medicine, Houston, TX, USA.
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA.
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2
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Sinopoulou E, Rosenzweig ES, Conner JM, Gibbs D, Weinholtz CA, Weber JL, Brock JH, Nout-Lomas YS, Ovruchesky E, Takashima Y, Biane JS, Kumamaru H, Havton LA, Beattie MS, Bresnahan JC, Tuszynski MH. Rhesus macaque versus rat divergence in the corticospinal projectome. Neuron 2022; 110:2970-2983.e4. [PMID: 35917818 PMCID: PMC9509478 DOI: 10.1016/j.neuron.2022.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 04/14/2022] [Accepted: 07/06/2022] [Indexed: 01/14/2023]
Abstract
We used viral intersectional tools to map the entire projectome of corticospinal neurons associated with fine distal forelimb control in Fischer 344 rats and rhesus macaques. In rats, we found an extraordinarily diverse set of collateral projections from corticospinal neurons to 23 different brain and spinal regions. Remarkably, the vast weighting of this "motor" projection was to sensory systems in both the brain and spinal cord, confirmed by optogenetic and transsynaptic viral intersectional tools. In contrast, rhesus macaques exhibited far heavier and narrower weighting of corticospinal outputs toward spinal and brainstem motor systems. Thus, corticospinal systems in macaques primarily constitute a final output system for fine motor control, whereas this projection in rats exerts a multi-modal integrative role that accesses far broader CNS regions. Unique structural-functional correlations can be achieved by mapping and quantifying a single neuronal system's total axonal output and its relative weighting across CNS targets.
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Affiliation(s)
- Eleni Sinopoulou
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Ephron S Rosenzweig
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - James M Conner
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Daniel Gibbs
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Chase A Weinholtz
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Janet L Weber
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - John H Brock
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Veterans Administration Medical Center, La Jolla, CA, USA
| | - Yvette S Nout-Lomas
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Eric Ovruchesky
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Yoshio Takashima
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Jeremy S Biane
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Hiromi Kumamaru
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Leif A Havton
- Departments of Neurology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Veterans Administration Medical Center, Bronx, NY, USA
| | - Michael S Beattie
- Department of Neurosurgery, University of California, San Francisco, CA, USA
| | | | - Mark H Tuszynski
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Veterans Administration Medical Center, La Jolla, CA, USA.
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3
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Steuer EL, Kemper LJ, Hlynialuk CJW, Leinonen-Wright K, Montonye ML, Lapcinski IP, Forster CL, Ashe KH, Liu P. Blocking Site-Specific Cleavage of Human Tau Delays Progression of Disease-Related Phenotypes in Genetically Matched Tau-Transgenic Mice Modeling Frontotemporal Dementia. J Neurosci 2022; 42:4737-4754. [PMID: 35508385 PMCID: PMC9186797 DOI: 10.1523/jneurosci.0543-22.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/22/2022] [Accepted: 04/28/2022] [Indexed: 11/21/2022] Open
Abstract
Studies have recently demonstrated that a caspase-2-mediated cleavage of human tau (htau) at asparate-314 (D314) is responsible for cognitive deficits and neurodegeneration in mice modeling frontotemporal dementia (FTD). However, these animal studies may be confounded by flaws in their model systems, such as endogenous functional gene disruption and inequivalent transgene expression. To avoid these weaknesses, we examined the pathogenic role of this site-specific htau cleavage in FTD using genetically matched htau targeted-insertion mouse lines: rT2 and rT3. Both male and female mice were included in this study. rT2 mice contain a single copy of the FTD-linked htau proline-to-leucine mutation at amino acid 301 (htau P301L), inserted into a neutral site to avoid dysregulation of host gene expression. The similarly constructed rT3 mice harbor an additional D314-to-glutamate (D314E) mutation that blocks htau cleavage. We demonstrate that htau transgene expression occurs primarily in the forebrain at similar levels in rT2 and rT3 mice. Importantly, expression of the cleavage-resistant D314E mutant delays transgene-induced tau accumulation in the postsynaptic density, brain atrophy, hippocampal neurodegeneration, and spatial memory impairment, without altering age-related progression of pathologic tau conformation and phosphorylation. Our comprehensive investigation of age-dependent disease phenotypes associated with the htau P301L variant in precisely engineered FTD-modeling mice unveils a transiently protective effect of blocking htau cleavage at D314. Findings of this study advance our understanding of the contribution of this tau cleavage to the pathogenesis of FTD, and aid the development of effective dementia-targeting therapies.SIGNIFICANCE STATEMENT A site-specific and caspase-2-mediated cleavage of human tau plays a pathologic role in dementia. In this study, we investigate the contribution of this cleavage to the pathogenesis of frontotemporal dementia (FTD) using two genetically matched, tau-transgene targeted-insertion mouse lines that differ only by a cleavage-resistant mutation. The use of these mice avoids confounding effects associated with the random integration of tau transgenes to the mouse genome and allows us to comprehensively evaluate the impact of the tau cleavage on FTD phenotypes. Our data reveal that blocking this tau cleavage delays memory impairment and neurodegeneration of FTD-modeling mice. These findings improve our understanding of the pathogenic mechanisms underlying FTD and will facilitate the development of effective therapeutics.
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Affiliation(s)
- Elizabeth L Steuer
- N. Bud Grossman Center for Memory Research and Care
- Department of Neurology
| | - Lisa J Kemper
- N. Bud Grossman Center for Memory Research and Care
- Department of Neurology
| | | | | | | | - Ian P Lapcinski
- N. Bud Grossman Center for Memory Research and Care
- Department of Neurology
| | - Colleen L Forster
- N. Bud Grossman Center for Memory Research and Care
- UMN Academic Health Center Biological Materials Procurement Network, University of Minnesota, Minneapolis, Minnesota 55455
| | - Karen H Ashe
- N. Bud Grossman Center for Memory Research and Care
- Department of Neurology
- Geriatric Research, Education, and Clinical Centers, Veterans Affairs Medical Center, Minneapolis, Minnesota 55417
| | - Peng Liu
- N. Bud Grossman Center for Memory Research and Care
- Department of Neurology
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4
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Wang J, Zhang L. Retrograde Axonal Transport Property of Adeno-Associated Virus and Its Possible Application in Future. Microbes Infect 2021; 23:104829. [PMID: 33878458 DOI: 10.1016/j.micinf.2021.104829] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/30/2021] [Accepted: 04/05/2021] [Indexed: 12/19/2022]
Abstract
Gene therapy has become a treatment method for many diseases. Adeno-associated virus (AAV) is one of the most common virus vectors, is also widely used in the gene therapy field. During the past 2 decades, the retrograde axonal transportability of AAV has been discovered and utilized. Many studies have worked on the retrograde axonal transportability of AAV, and more and more people are interested in this field. This review described the current application, influence factors, and mechanism of retrograde axonal transportability of AAV and predicted its potential use in disease treatment in near future.
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Affiliation(s)
- Jingjing Wang
- Department of Gastroenterology, The Third Central Hospital of Tianjin, 83 Jintang Road, Hedong District, Tianjin, 300170, China
| | - Liqin Zhang
- Department of Otolaryngology, Peking Union Medical College Hospital, Dongcheng Qu, Beijing, 100730, China.
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5
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Logrip ML. Molecular tools to elucidate factors regulating alcohol use. Alcohol 2019; 74:3-9. [PMID: 30033149 DOI: 10.1016/j.alcohol.2018.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 03/15/2018] [Accepted: 03/15/2018] [Indexed: 12/20/2022]
Abstract
Alcohol use disorder (AUD) is a pervasive societal problem, marked by high levels of alcohol intake and recidivism. Despite these common disease traits, individuals diagnosed with AUD display a range of disordered drinking and alcohol-related behaviors. The diversity in disease presentation, as well as the established polygenic nature of the disorder and complex neurocircuitry, speaks to the variety of neurochemical changes resulting from alcohol intake that may differentially regulate alcohol-related behaviors. Investigations into the molecular adaptations responsible for maladaptive alcohol-related behavioral outcomes require an ever-evolving set of molecular tools to elucidate with increasing precision how alcohol alters behavior through neurochemical changes. This review highlights recent advances in molecular methodology, addressing how incorporation of these cutting-edge techniques not only may enhance current knowledge of the molecular bases of AUD, but also may facilitate identification of improved treatment targets that may be therapeutic in specific subpopulations of AUD individuals.
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6
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Considerations for the use of virally delivered genetic tools for in-vivo circuit analysis and behavior in mutant mice: a practical guide to optogenetics. Behav Pharmacol 2018; 28:598-609. [PMID: 29099403 DOI: 10.1097/fbp.0000000000000361] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Optogenetics was the method of the year in 2010 according to Nature Neuroscience. Since then, this method has become widespread, the use of virally delivered genetic tools has extended to other fields such as pharmacogenetics, and optogenetic techniques have become frequently applied in genetically manipulated animals for in-vivo circuit analysis and behavioral studies. However, several issues should be taken into consideration when planning such experiments. We aimed to summarize the critical points concerning optogenetic manipulation of a specific brain area in mutant mice. First, the appropriate vector should be chosen to allow optimal optogenetic manipulation. Adeno-associated viral vectors are the most common carriers with different available serotypes. Light-sensitive channels are available in many forms, and the expression of the delivered genetic material can be influenced in many ways. Second, selecting the adequate stimulation protocol is also essential. The pattern, intensity, and timing could be determinative parameters. Third, the mutant strain might have a phenotype that influences the observed behavior. In conclusion, detailed preliminary experiments and numerous control groups are required to choose the best vector and stimulation protocol and to ensure that the mutant animals do not have a specific phenotype that can influence the examined behavior.
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7
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In utero electroporation-based translating ribosome affinity purification identifies age-dependent mRNA expression in cortical pyramidal neurons. Neurosci Res 2018; 143:44-52. [PMID: 29857015 DOI: 10.1016/j.neures.2018.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/10/2018] [Accepted: 05/28/2018] [Indexed: 02/02/2023]
Abstract
We combined translating ribosome affinity purification (TRAP) with in utero electroporation (IUE), called iTRAP to identify the molecular profile of specific neuronal populations during neonatal development without the need for viral approaches and FACS sorting. We electroporated a plasmid encoding EGFP-tagged ribosomal protein L10a at embryonic day (E) 14-15 to target layer 2-4 cortical neurons of the somatosensory cortex. At three postnatal (P) ages-P0, P7, and P14-when morphogenesis occurs and synapses are forming, TRAP and molecular profiling was performed from electroporated regions. We found that ribosome bound (Ribo)-mRNAs from ∼7300 genes were significantly altered over time and included classical neuronal genes known to decrease (e.g., Tbr1, Dcx) or increase (e.g., Eno2, Camk2a, Syn1) as neurons mature. This approach led to the identification of specific developmental patterns for Ribo-mRNAs not previously reported to be developmentally regulated in neurons, providing rationale for future examination of their role in selective biological processes. These include upregulation of Lynx1, Nrn1, Cntnap1 over time; downregulation of St8sia2 and Draxin; and bidirectional changes to Fkbp1b. iTRAP is a versatile approach that allows researchers to easily assess the molecular profile of specific neuronal populations in selective brain regions under various conditions, including overexpression and knockdown of target genes, and in disease settings.
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8
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Medial preoptic circuit induces hunting-like actions to target objects and prey. Nat Neurosci 2018; 21:364-372. [DOI: 10.1038/s41593-018-0072-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 12/09/2017] [Indexed: 12/22/2022]
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9
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The Expanding Toolkit of Translating Ribosome Affinity Purification. J Neurosci 2018; 37:12079-12087. [PMID: 29237735 DOI: 10.1523/jneurosci.1929-17.2017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/16/2017] [Accepted: 11/03/2017] [Indexed: 01/23/2023] Open
Abstract
Translating ribosome affinity purification is a method initially developed for profiling mRNA from genetically defined cell types in complex tissues. It has been applied both to identify target molecules in cell types that are important for controlling a variety of behaviors in the brain, and to understand the molecular consequences on those cells due to experimental manipulations, ranging from drugs of abuse to disease-causing mutations. Since its inception, a variety of methodological advances are opening new avenues of investigation. These advances include a variety of new methods for targeting cells for translating ribosome affinity purification by features such as their projections or activity, additional tags and mouse reagents increasing the flexibility of the system, and new modifications of the method specifically focused on studying the regulation of translation. The latter includes methods to assess cell type-specific regulation of translation in specific subcellular compartments. Here, I provide a summary of these recent advances and resources, highlighting both new experimental opportunities and areas for future technical development.
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10
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Raam T, McAvoy KM, Besnard A, Veenema AH, Sahay A. Hippocampal oxytocin receptors are necessary for discrimination of social stimuli. Nat Commun 2017; 8:2001. [PMID: 29222469 PMCID: PMC5722862 DOI: 10.1038/s41467-017-02173-0] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 11/10/2017] [Indexed: 12/23/2022] Open
Abstract
Oxytocin receptor (Oxtr) signaling in neural circuits mediating discrimination of social stimuli and affiliation or avoidance behavior is thought to guide social recognition. Remarkably, the physiological functions of Oxtrs in the hippocampus are not known. Here we demonstrate using genetic and pharmacological approaches that Oxtrs in the anterior dentate gyrus (aDG) and anterior CA2/CA3 (aCA2/CA3) of mice are necessary for discrimination of social, but not non-social, stimuli. Further, Oxtrs in aCA2/CA3 neurons recruit a population-based coding mechanism to mediate social stimuli discrimination. Optogenetic terminal-specific attenuation revealed a critical role for aCA2/CA3 outputs to posterior CA1 for discrimination of social stimuli. In contrast, aCA2/CA3 projections to aCA1 mediate discrimination of non-social stimuli. These studies identify a role for an aDG-CA2/CA3 axis of Oxtr expressing cells in discrimination of social stimuli and delineate a pathway relaying social memory computations in the anterior hippocampus to the posterior hippocampus to guide social recognition.
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Affiliation(s)
- Tara Raam
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.,Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.,Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
| | - Kathleen M McAvoy
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.,Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Antoine Besnard
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.,Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Alexa H Veenema
- Department of Psychology, Michigan State University, East Lansing, MI, 48824, USA
| | - Amar Sahay
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA. .,Harvard Stem Cell Institute, Cambridge, MA, 02138, USA. .,Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA. .,Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
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11
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Allen WE, Kauvar IV, Chen MZ, Richman EB, Yang SJ, Chan K, Gradinaru V, Deverman BE, Luo L, Deisseroth K. Global Representations of Goal-Directed Behavior in Distinct Cell Types of Mouse Neocortex. Neuron 2017; 94:891-907.e6. [PMID: 28521139 PMCID: PMC5723385 DOI: 10.1016/j.neuron.2017.04.017] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 01/26/2017] [Accepted: 04/11/2017] [Indexed: 11/27/2022]
Abstract
The successful planning and execution of adaptive behaviors in mammals may require long-range coordination of neural networks throughout cerebral cortex. The neuronal implementation of signals that could orchestrate cortex-wide activity remains unclear. Here, we develop and apply methods for cortex-wide Ca2+ imaging in mice performing decision-making behavior and identify a global cortical representation of task engagement encoded in the activity dynamics of both single cells and superficial neuropil distributed across the majority of dorsal cortex. The activity of multiple molecularly defined cell types was found to reflect this representation with type-specific dynamics. Focal optogenetic inhibition tiled across cortex revealed a crucial role for frontal cortex in triggering this cortex-wide phenomenon; local inhibition of this region blocked both the cortex-wide response to task-initiating cues and the voluntary behavior. These findings reveal cell-type-specific processes in cortex for globally representing goal-directed behavior and identify a major cortical node that gates the global broadcast of task-related information.
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Affiliation(s)
- William E Allen
- Neurosciences Graduate Program, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Isaac V Kauvar
- Electrical Engineering Graduate Program, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Michael Z Chen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Ethan B Richman
- Neurosciences Graduate Program, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Samuel J Yang
- Electrical Engineering Graduate Program, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Ken Chan
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Viviana Gradinaru
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Benjamin E Deverman
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Liqun Luo
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA.
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12
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Gracida X, Calarco JA. Cell type-specific transcriptome profiling in C. elegans using the Translating Ribosome Affinity Purification technique. Methods 2017. [PMID: 28648677 DOI: 10.1016/j.ymeth.2017.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Organs and specific cell types execute specialized functions in multicellular organisms, in large part through customized gene expression signatures. Thus, profiling the transcriptomes of specific cell and tissue types remains an important tool for understanding how cells become specialized. Methodological approaches to detect gene expression differences have utilized samples from whole animals, dissected tissues, and more recently single cells. Despite these advances, there is still a challenge and a need in most laboratories to implement less invasive yet powerful cell-type specific transcriptome profiling methods. Here, we describe the use of the Translating Ribosome Affinity Purification (TRAP) method for C. elegans to detect cell type-specific gene expression patterns at the level of translating mRNAs. In TRAP, a ribosomal protein is fused to a tag (GFP) and is expressed under cell type-specific promoters to mark genetically defined cell types in vivo. Affinity purification of lysates of animals expressing the tag enriches for ribosome-associated mRNAs of the targeted tissue. The purified mRNAs are used for making cDNA libraries subjected to high-throughput sequencing to obtain genome-wide profiles of transcripts from the targeted cell type. The ease of exposing C. elegans to diverse stimuli, coupled with available cell type specific promoters, makes TRAP a useful approach to enable the discovery of molecular components in response to external or genetic perturbations.
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Affiliation(s)
- Xicotencatl Gracida
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, United States; Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, MA 02138, United States.
| | - John A Calarco
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, United States; Department of Cell and Systems Biology, University of Toronto, Toronto M5S 3G5, Canada.
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13
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Zhao W, Yang W, Zheng S, Hu Q, Qiu P, Huang X, Hong X, Lan F. A new bioinformatic insight into the associated proteins in psychiatric disorders. SPRINGERPLUS 2016; 5:1967. [PMID: 27917343 PMCID: PMC5108746 DOI: 10.1186/s40064-016-3655-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 11/04/2016] [Indexed: 01/21/2023]
Abstract
BACKGROUND Psychiatric diseases severely affect the quality of patients' lives and bring huge economic pressure to their families. Also, the great phenotypic variability among these patients makes it difficult to investigate the pathogenesis. Nowadays, bioinformatics is hopeful to be used as an effective tool for the diagnosis of psychiatric disorders, which can identify sensitive biomarkers and explore associated signaling pathways. METHODS In this study, we performed an integrated bioinformatic analysis on 1945 mental-associated proteins including 91 secreted proteins and 593 membrane proteins, which were screened from the Universal Protein Resource (Uniport) database. Then the function and pathway enrichment analyses, ontological classification, and constructed PPI network were executed. RESULTS Our present study revealed that the majority of mental proteins were closely related to metabolic processes and cellular processes. We also identified some significant molecular biomarkers in the progression of mental disorders, such as HRAS, ALS2, SLC6A1, SLC39A12, SIL1, IDUA, NEPH2 and XPO1. Furthermore, it was found that hub proteins, such as COMT, POMC, NPS and BDNF, might be the potential targets for mental disorders therapy. Finally, we demonstrated that psychiatric disorders may share the same signaling pathways with cancers, involving ESR1, BCL2 and MAPK3. CONCLUSION Our data are expected to contribute to explaining the possible mechanisms of psychiatric diseases and providing a useful reference for the diagnosis and therapy of them.
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Affiliation(s)
- Wenlong Zhao
- Department of Neurology, Affiliated Dongfang Hospital of Xiamen University (Fuzhou General Hospital), Fuzhou, Fujian People's Republic of China
| | - Wenjing Yang
- Department of Neurology, Affiliated Dongfang Hospital of Xiamen University (Fuzhou General Hospital), Fuzhou, Fujian People's Republic of China
| | - Shuanglin Zheng
- Department of Neurology, Affiliated Dongfang Hospital of Xiamen University (Fuzhou General Hospital), Fuzhou, Fujian People's Republic of China
| | - Qiong Hu
- Department of Neurology, Affiliated Dongfang Hospital of Xiamen University (Fuzhou General Hospital), Fuzhou, Fujian People's Republic of China
| | - Ping Qiu
- Department of Neurology, Affiliated Dongfang Hospital of Xiamen University (Fuzhou General Hospital), Fuzhou, Fujian People's Republic of China
| | - Xinghua Huang
- Department of Clinical Genetics and Experimental Medicine, Fuzhou General Hospital, No. 156, Xier Huan Road, Gulou District, Fuzhou, 350025 Fujian People's Republic of China
| | - Xiaoqian Hong
- Department of Neurology, Affiliated Dongfang Hospital of Xiamen University (Fuzhou General Hospital), Fuzhou, Fujian People's Republic of China
| | - Fenghua Lan
- Department of Clinical Genetics and Experimental Medicine, Fuzhou General Hospital, No. 156, Xier Huan Road, Gulou District, Fuzhou, 350025 Fujian People's Republic of China
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