1
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Forero SA, Liu S, Shetty N, Ophir AG. Re-wiring of the bonded brain: Gene expression among pair bonded female prairie voles changes as they transition to motherhood. GENES, BRAIN, AND BEHAVIOR 2024; 23:e12906. [PMID: 38861664 PMCID: PMC11166254 DOI: 10.1111/gbb.12906] [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: 01/25/2024] [Revised: 04/30/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024]
Abstract
Motherhood is a costly life-history transition accompanied by behavioral and neural plasticity necessary for offspring care. Motherhood in the monogamous prairie vole is associated with decreased pair bond strength, suggesting a trade-off between parental investment and pair bond maintenance. Neural mechanisms governing pair bonds and maternal bonds overlap, creating possible competition between the two. We measured mRNA expression of genes encoding receptors for oxytocin (oxtr), dopamine (d1r and d2r), mu-opioids (oprm1a), and kappa-opioids (oprk1a) within three brain areas processing salience of sociosensory cues (anterior cingulate cortex; ACC), pair bonding (nucleus accumbens; NAc), and maternal care (medial preoptic area; MPOA). We compared gene expression differences between pair bonded prairie voles that were never pregnant, pregnant (~day 16 of pregnancy), and recent mothers (day 3 of lactation). We found greater gene expression in the NAc (oxtr, d2r, oprm1a, and oprk1a) and MPOA (oxtr, d1r, d2r, oprm1a, and oprk1a) following the transition to motherhood. Expression for all five genes in the ACC was greatest for females that had been bonded for longer. Gene expression within each region was highly correlated, indicating that oxytocin, dopamine, and opioids comprise a complimentary gene network for social signaling. ACC-NAc gene expression correlations indicated that being a mother (oxtr and d1r) or maintaining long-term pair bonds (oprm1a) relies on the coordination of different signaling systems within the same circuit. Our study suggests the maternal brain undergoes changes that prepare females to face the trade-off associated with increased emotional investment in offspring, while also maintaining a pair bond.
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MESH Headings
- Animals
- Female
- Arvicolinae/genetics
- Receptors, Opioid, mu/genetics
- Receptors, Opioid, mu/metabolism
- Pair Bond
- Maternal Behavior/physiology
- Nucleus Accumbens/metabolism
- Pregnancy
- Receptors, Oxytocin/genetics
- Receptors, Oxytocin/metabolism
- Receptors, Opioid, kappa/genetics
- Receptors, Opioid, kappa/metabolism
- Gyrus Cinguli/metabolism
- Preoptic Area/metabolism
- Receptors, Dopamine D1/genetics
- Receptors, Dopamine D1/metabolism
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Affiliation(s)
| | - Sydney Liu
- Department of PsychologyCornell UniversityIthacaNew YorkUSA
| | - Netra Shetty
- Department of PsychologyCornell UniversityIthacaNew YorkUSA
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2
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Chen JJ, Kaufmann WA, Chen C, Arai I, Kim O, Shigemoto R, Jonas P. Developmental transformation of Ca 2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron 2024; 112:755-771.e9. [PMID: 38215739 DOI: 10.1016/j.neuron.2023.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 07/12/2023] [Accepted: 12/05/2023] [Indexed: 01/14/2024]
Abstract
The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission.
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Affiliation(s)
- Jing-Jing Chen
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Walter A Kaufmann
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Chong Chen
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Itaru Arai
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Olena Kim
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Ryuichi Shigemoto
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Peter Jonas
- Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria.
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3
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Lei J, Lin KZ. Bias-adjusted spectral clustering in multi-layer stochastic block models. J Am Stat Assoc 2022; 118:2433-2445. [PMID: 38532854 PMCID: PMC10963943 DOI: 10.1080/01621459.2022.2054817] [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: 03/10/2021] [Accepted: 03/04/2022] [Indexed: 12/31/2022]
Abstract
We consider the problem of estimating common community structures in multi-layer stochastic block models, where each single layer may not have sufficient signal strength to recover the full community structure. In order to efficiently aggregate signal across different layers, we argue that the sum-of-squared adjacency matrices contain sufficient signal even when individual layers are very sparse. Our method uses a bias-removal step that is necessary when the squared noise matrices may overwhelm the signal in the very sparse regime. The analysis of our method relies on several novel tail probability bounds for matrix linear combinations with matrix-valued coefficients and matrix-valued quadratic forms, which may be of independent interest. The performance of our method and the necessity of bias removal is demonstrated in synthetic data and in microarray analysis about gene co-expression networks.
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Affiliation(s)
- Jing Lei
- Department of Statistics and Data Science, Carnegie Mellon University, USA
| | - Kevin Z Lin
- Department of Statistics, Wharton School of Business, University of Pennsylvania, USA
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4
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Hommersom MP, Buijsen RAM, van Roon-Mom WMC, van de Warrenburg BPC, van Bokhoven H. Human Induced Pluripotent Stem Cell-Based Modelling of Spinocerebellar Ataxias. Stem Cell Rev Rep 2021; 18:441-456. [PMID: 34031815 PMCID: PMC8930896 DOI: 10.1007/s12015-021-10184-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/11/2021] [Indexed: 12/13/2022]
Abstract
Abstract Dominant spinocerebellar ataxias (SCAs) constitute a large group of phenotypically and genetically heterogeneous disorders that mainly present with dysfunction of the cerebellum as their main hallmark. Although animal and cell models have been highly instrumental for our current insight into the underlying disease mechanisms of these neurodegenerative disorders, they do not offer the full human genetic and physiological context. The advent of human induced pluripotent stem cells (hiPSCs) and protocols to differentiate these into essentially every cell type allows us to closely model SCAs in a human context. In this review, we systematically summarize recent findings from studies using hiPSC-based modelling of SCAs, and discuss what knowledge has been gained from these studies. We conclude that hiPSC-based models are a powerful tool for modelling SCAs as they contributed to new mechanistic insights and have the potential to serve the development of genetic therapies. However, the use of standardized methods and multiple clones of isogenic lines are essential to increase validity and reproducibility of the insights gained. Graphical Abstract ![]()
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Affiliation(s)
- Marina P Hommersom
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
| | - Ronald A M Buijsen
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Willeke M C van Roon-Mom
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Bart P C van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands.
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands. .,Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB, Nijmegen, Netherlands.
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5
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Carbonell AU, Cho CH, Tindi JO, Counts PA, Bates JC, Erdjument-Bromage H, Cvejic S, Iaboni A, Kvint I, Rosensaft J, Banne E, Anagnostou E, Neubert TA, Scherer SW, Molholm S, Jordan BA. Haploinsufficiency in the ANKS1B gene encoding AIDA-1 leads to a neurodevelopmental syndrome. Nat Commun 2019; 10:3529. [PMID: 31388001 PMCID: PMC6684583 DOI: 10.1038/s41467-019-11437-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 07/13/2019] [Indexed: 12/23/2022] Open
Abstract
Neurodevelopmental disorders, including autism spectrum disorder, have complex polygenic etiologies. Single-gene mutations in patients can help define genetic factors and molecular mechanisms underlying neurodevelopmental disorders. Here we describe individuals with monogenic heterozygous microdeletions in ANKS1B, a predicted risk gene for autism and neuropsychiatric diseases. Affected individuals present with a spectrum of neurodevelopmental phenotypes, including autism, attention-deficit hyperactivity disorder, and speech and motor deficits. Neurons generated from patient-derived induced pluripotent stem cells demonstrate loss of the ANKS1B-encoded protein AIDA-1, a brain-specific protein highly enriched at neuronal synapses. A transgenic mouse model of Anks1b haploinsufficiency recapitulates a range of patient phenotypes, including social deficits, hyperactivity, and sensorimotor dysfunction. Identification of the AIDA-1 interactome using quantitative proteomics reveals protein networks involved in synaptic function and the etiology of neurodevelopmental disorders. Our findings formalize a link between the synaptic protein AIDA-1 and a rare, previously undefined genetic disease we term ANKS1B haploinsufficiency syndrome.
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Affiliation(s)
- Abigail U Carbonell
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
| | - Chang Hoon Cho
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
| | - Jaafar O Tindi
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
| | - Pamela A Counts
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
| | - Juliana C Bates
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
| | - Hediye Erdjument-Bromage
- Department of Cell Biology and Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, 10016, NY, USA
| | - Svetlana Cvejic
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
| | - Alana Iaboni
- Autism Research Centre, Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, M46 1R8, ON, Canada
| | - Ifat Kvint
- Pediatric Neurology Clinic, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Jenny Rosensaft
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Ehud Banne
- Genetics Institute, Kaplan Medical Center, Hebrew University Hadassah Medical School, Rehovot, 76100, Israel
| | - Evdokia Anagnostou
- Autism Research Centre, Bloorview Research Institute, Holland Bloorview Kids Rehabilitation Hospital, Toronto, M46 1R8, ON, Canada
| | - Thomas A Neubert
- Department of Cell Biology and Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, 10016, NY, USA
- Department of Pharmacology, New York University School of Medicine, New York, 10016, NY, USA
| | - Stephen W Scherer
- Centre for Applied Genomics and McLaughlin Centre, Hospital for Sick Children and University of Toronto, Toronto, M56 0A4, ON, Canada
| | - Sophie Molholm
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, 10461, NY, USA
| | - Bryen A Jordan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, 10461, NY, USA.
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, Bronx, 10461, NY, USA.
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6
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Vogt D, Cho KKA, Shelton SM, Paul A, Huang ZJ, Sohal VS, Rubenstein JLR. Mouse Cntnap2 and Human CNTNAP2 ASD Alleles Cell Autonomously Regulate PV+ Cortical Interneurons. Cereb Cortex 2018; 28:3868-3879. [PMID: 29028946 PMCID: PMC6455910 DOI: 10.1093/cercor/bhx248] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 08/09/2017] [Accepted: 09/06/2017] [Indexed: 01/08/2023] Open
Abstract
Human mutations in CNTNAP2 are associated with an array of neuropsychiatric and neurological syndromes, including speech and language disorders, epilepsy, and autism spectrum disorder (ASD). We examined Cntnap2's expression and function in GABAergic cortical interneurons (CINs), where its RNA is present at highest levels in chandelier neurons, PV+ neurons and VIP+ neurons. In vivo functions were studied using both constitutive Cntnap2 null mice and a transplantation assay, the latter to assess cell autonomous phenotypes of medial ganglionic eminence (MGE)-derived CINs. We found that Cntnap2 constitutive null mutants had normal numbers of MGE-derived CINs, but had reduced PV+ CINs. Transplantation assays showed that Cntnap2 cell autonomously regulated the physiology of parvalbumin (PV)+, fast-spiking CINs; no phenotypes were observed in somatostatin+, regular spiking, CINs. We also tested the effects of 4 human CNTNAP2 ASD missense mutations in vivo, and found that they impaired PV+ CIN development. Together, these data reveal that reduced CNTNAP2 function impairs PV+ CINs, a cell type with important roles in regulating cortical circuits.
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Affiliation(s)
- Daniel Vogt
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen K A Cho
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | - Samantha M Shelton
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | - Anirban Paul
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Vikaas S Sohal
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
| | - John L R Rubenstein
- Department of Psychiatry, University of California San Francisco, San Francisco, CA, USA
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7
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Völker LA, Maar BA, Pulido Guevara BA, Bilkei-Gorzo A, Zimmer A, Brönneke H, Dafinger C, Bertsch S, Wagener JR, Schweizer H, Schermer B, Benzing T, Hoehne M. Neph2/Kirrel3 regulates sensory input, motor coordination, and home-cage activity in rodents. GENES BRAIN AND BEHAVIOR 2018; 17:e12516. [DOI: 10.1111/gbb.12516] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 07/22/2018] [Accepted: 08/17/2018] [Indexed: 11/30/2022]
Affiliation(s)
- Linus A. Völker
- Department II of Internal Medicine and Center for Molecular Medicine Cologne; University of Cologne; Cologne Germany
| | - Barbara A. Maar
- Department II of Internal Medicine and Center for Molecular Medicine Cologne; University of Cologne; Cologne Germany
| | - Barbara A. Pulido Guevara
- Department II of Internal Medicine and Center for Molecular Medicine Cologne; University of Cologne; Cologne Germany
| | - Andras Bilkei-Gorzo
- Institute of Molecular Psychiatry; Medical Faculty of the University of Bonn; Bonn Germany
| | - Andreas Zimmer
- Institute of Molecular Psychiatry; Medical Faculty of the University of Bonn; Bonn Germany
| | - Hella Brönneke
- Mouse Phenotyping Core Facility; Cologne Excellence Cluster on Cellular Stress Responses (CECAD); 50931 Cologne Germany
| | - Claudia Dafinger
- Department II of Internal Medicine and Center for Molecular Medicine Cologne; University of Cologne; Cologne Germany
| | - Sabine Bertsch
- Department II of Internal Medicine and Center for Molecular Medicine Cologne; University of Cologne; Cologne Germany
| | - Jan-Robin Wagener
- Institute for Neuroanatomy, Universitätsmedizin Göttingen; Georg-August-University Göttingen; Göttingen Germany
| | - Heiko Schweizer
- Renal Division; University Hospital Freiburg; Freiburg Germany
| | - Bernhard Schermer
- Department II of Internal Medicine and Center for Molecular Medicine Cologne; University of Cologne; Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
- Systems Biology of Ageing Cologne (Sybacol); University of Cologne; Cologne Germany
| | - Thomas Benzing
- Department II of Internal Medicine and Center for Molecular Medicine Cologne; University of Cologne; Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
- Systems Biology of Ageing Cologne (Sybacol); University of Cologne; Cologne Germany
| | - Martin Hoehne
- Department II of Internal Medicine and Center for Molecular Medicine Cologne; University of Cologne; Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
- Systems Biology of Ageing Cologne (Sybacol); University of Cologne; Cologne Germany
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8
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Chen C, Satterfield R, Young SM, Jonas P. Triple Function of Synaptotagmin 7 Ensures Efficiency of High-Frequency Transmission at Central GABAergic Synapses. Cell Rep 2018; 21:2082-2089. [PMID: 29166601 PMCID: PMC5863544 DOI: 10.1016/j.celrep.2017.10.122] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/06/2017] [Accepted: 10/29/2017] [Indexed: 12/21/2022] Open
Abstract
Synaptotagmin 7 (Syt7) is thought to be a Ca2+ sensor that mediates asynchronous transmitter release and facilitation at synapses. However, Syt7 is strongly expressed in fast-spiking, parvalbumin-expressing GABAergic interneurons, and the output synapses of these neurons produce only minimal asynchronous release and show depression rather than facilitation. To resolve this apparent contradiction, we examined the effects of genetic elimination of Syt7 on synaptic transmission at the GABAergic basket cell (BC)-Purkinje cell (PC) synapse in cerebellum. Our results indicate that at the BC-PC synapse, Syt7 contributes to asynchronous release, pool replenishment, and facilitation. In combination, these three effects ensure efficient transmitter release during high-frequency activity and guarantee frequency independence of inhibition. Our results identify a distinct function of Syt7: ensuring the efficiency of high-frequency inhibitory synaptic transmission.
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Affiliation(s)
- Chong Chen
- IST Austria (Institute of Science and Technology Austria), Am Campus 1, A-3400 Klosterneuburg, Austria
| | - Rachel Satterfield
- Max Planck Florida Institute for Neuroscience, Research Group Molecular Mechanisms of Synaptic Function, Jupiter, FL 33458, USA
| | - Samuel M Young
- Max Planck Florida Institute for Neuroscience, Research Group Molecular Mechanisms of Synaptic Function, Jupiter, FL 33458, USA; Department of Anatomy and Cell Biology, Department of Otolaryngology, Iowa Neuroscience Institute, Aging Mind Brain Initiative, University of Iowa, Iowa City, IA 52242, USA
| | - Peter Jonas
- IST Austria (Institute of Science and Technology Austria), Am Campus 1, A-3400 Klosterneuburg, Austria.
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9
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Mostafavi S, Gaiteri C, Sullivan SE, White CC, Tasaki S, Xu J, Taga M, Klein HU, Patrick E, Komashko V, McCabe C, Smith R, Bradshaw EM, Root DE, Regev A, Yu L, Chibnik LB, Schneider JA, Young-Pearse TL, Bennett DA, De Jager PL. A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer's disease. Nat Neurosci 2018; 21:811-819. [PMID: 29802388 PMCID: PMC6599633 DOI: 10.1038/s41593-018-0154-9] [Citation(s) in RCA: 315] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/20/2018] [Indexed: 02/07/2023]
Abstract
There is a need for new therapeutic targets with which to prevent Alzheimer’s disease (AD), a major contributor to aging-related cognitive decline. Here, we report the construction and validation of a molecular network of the aging human frontal cortex. Using RNA sequence data from 478 individuals, we first build a molecular network using modules of coexpressed genes and then relate these modules to AD and its neuropathologic and cognitive endophenotypes. We confirm these associations in two independent AD datasets as well as in epigenomic data. We also illustrate the use of the network in prioritizing amyloid-associated genes for in vitro validation in human neurons and astrocytes. These analyses based on unique cohorts enable us to resolve the role of distinct cortical modules that have a direct effect on the accumulation of AD pathology from those that have a direct effect on cognitive decline, exemplifying a network approach to complex diseases. Systems biology analysis of RNA sequencing data from the aging human cortex identifies a molecular network which prioritizes groups of genes that influence cognitive decline or neuropathology in Alzheimer’s disease.
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Affiliation(s)
- Sara Mostafavi
- Department of Statistics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Canadian Institute for Advanced Research, Toronto, ON, Canada
| | - Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Sarah E Sullivan
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Shinya Tasaki
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Jishu Xu
- Broad Institute, Cambridge, MA, USA
| | - Mariko Taga
- Broad Institute, Cambridge, MA, USA.,Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Hans-Ulrich Klein
- Broad Institute, Cambridge, MA, USA.,Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | | | - Vitalina Komashko
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | | | - Robert Smith
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth M Bradshaw
- Broad Institute, Cambridge, MA, USA.,Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | | | | | - Lei Yu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Lori B Chibnik
- Broad Institute, Cambridge, MA, USA.,Harvard Medical School, Boston, MA, USA.,Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Tracy L Young-Pearse
- Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA.
| | - Philip L De Jager
- Broad Institute, Cambridge, MA, USA. .,Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA.
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10
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Mancarci BO, Toker L, Tripathy SJ, Li B, Rocco B, Sibille E, Pavlidis P. Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data. eNeuro 2017; 4:ENEURO.0212-17.2017. [PMID: 29204516 PMCID: PMC5707795 DOI: 10.1523/eneuro.0212-17.2017] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/25/2017] [Accepted: 10/31/2017] [Indexed: 12/13/2022] Open
Abstract
Establishing the molecular diversity of cell types is crucial for the study of the nervous system. We compiled a cross-laboratory database of mouse brain cell type-specific transcriptomes from 36 major cell types from across the mammalian brain using rigorously curated published data from pooled cell type microarray and single-cell RNA-sequencing (RNA-seq) studies. We used these data to identify cell type-specific marker genes, discovering a substantial number of novel markers, many of which we validated using computational and experimental approaches. We further demonstrate that summarized expression of marker gene sets (MGSs) in bulk tissue data can be used to estimate the relative cell type abundance across samples. To facilitate use of this expanding resource, we provide a user-friendly web interface at www.neuroexpresso.org.
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Affiliation(s)
- B. Ogan Mancarci
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver V6T 1Z4, Canada
- Department of Psychiatry, University of British Columbia, Vancouver V6T 2A1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Lilah Toker
- Department of Psychiatry, University of British Columbia, Vancouver V6T 2A1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Shreejoy J. Tripathy
- Department of Psychiatry, University of British Columbia, Vancouver V6T 2A1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Brenna Li
- Department of Psychiatry, University of British Columbia, Vancouver V6T 2A1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Brad Rocco
- Campbell Family Mental Health Research Institute of CAMH
- Department of Psychiatry and the Department of Pharmacology and Toxicology, University of Toronto, Vancouver M5S 1A8, Canada
| | - Etienne Sibille
- Campbell Family Mental Health Research Institute of CAMH
- Department of Psychiatry and the Department of Pharmacology and Toxicology, University of Toronto, Vancouver M5S 1A8, Canada
| | - Paul Pavlidis
- Department of Psychiatry, University of British Columbia, Vancouver V6T 2A1, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
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11
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Transcriptomic correlates of neuron electrophysiological diversity. PLoS Comput Biol 2017; 13:e1005814. [PMID: 29069078 PMCID: PMC5673240 DOI: 10.1371/journal.pcbi.1005814] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/06/2017] [Accepted: 10/09/2017] [Indexed: 12/19/2022] Open
Abstract
How neuronal diversity emerges from complex patterns of gene expression remains poorly understood. Here we present an approach to understand electrophysiological diversity through gene expression by integrating pooled- and single-cell transcriptomics with intracellular electrophysiology. Using neuroinformatics methods, we compiled a brain-wide dataset of 34 neuron types with paired gene expression and intrinsic electrophysiological features from publically accessible sources, the largest such collection to date. We identified 420 genes whose expression levels significantly correlated with variability in one or more of 11 physiological parameters. We next trained statistical models to infer cellular features from multivariate gene expression patterns. Such models were predictive of gene-electrophysiological relationships in an independent collection of 12 visual cortex cell types from the Allen Institute, suggesting that these correlations might reflect general principles relating expression patterns to phenotypic diversity across very different cell types. Many associations reported here have the potential to provide new insights into how neurons generate functional diversity, and correlations of ion channel genes like Gabrd and Scn1a (Nav1.1) with resting potential and spiking frequency are consistent with known causal mechanisms. Our work highlights the promise and inherent challenges in using cell type-specific transcriptomics to understand the mechanistic origins of neuronal diversity.
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12
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Using c-kit to genetically target cerebellar molecular layer interneurons in adult mice. PLoS One 2017; 12:e0179347. [PMID: 28658323 PMCID: PMC5489153 DOI: 10.1371/journal.pone.0179347] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 05/26/2017] [Indexed: 11/19/2022] Open
Abstract
The cerebellar system helps modulate and fine-tune motor action. Purkinje cells (PCs) provide the sole output of the cerebellar cortex, therefore, any cerebellar involvement in motor activity must be driven by changes in PC firing rates. Several different cell types influence PC activity including excitatory input from parallel fibers and inhibition from molecular layer interneurons (MLIs). Similar to PCs, MLI activity is driven by parallel fibers, therefore, MLIs provide feed-forward inhibition onto PCs. To aid in the experimental assessment of how molecular layer inhibition contributes to cerebellar function and motor behavior, we characterized a new knock-in mouse line with Cre recombinase expression under control of endogenous c-kit transcriptional machinery. Using these engineered c-Kit mice, we were able to obtain high levels of conditional MLI transduction in adult mice using Cre-dependent viral vectors without any PC or granule cell labeling. We then used the mouse line to target MLIs for activity perturbation in vitro using opto- and chemogenetics.
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13
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Baker MW, Macagno ER. Gap junction proteins and the wiring (Rewiring) of neuronal circuits. Dev Neurobiol 2017; 77:575-586. [PMID: 27512961 DOI: 10.1002/dneu.22429] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/01/2016] [Accepted: 08/08/2016] [Indexed: 11/11/2022]
Abstract
The unique morphology and pattern of synaptic connections made by a neuron during development arise in part by an extended period of growth in which cell-cell interactions help to sculpt the arbor into its final shape, size, and participation in different synaptic networks. Recent experiments highlight a guiding role played by gap junction proteins in controlling this process. Ectopic and overexpression studies in invertebrates have revealed that the selective expression of distinct gap junction genes in neurons and glial cells is sufficient to establish selective new connections in the central nervous systems of the leech (Firme et al. [2012]: J Neurosci 32:14265-14270), the nematode (Rabinowitch et al. [2014]: Nat Commun 5:4442), and the fruit fly (Pézier et al., 2016: PLoS One 11:e0152211). We present here an overview of this work and suggest that gap junction proteins, in addition to their synaptic/communicative functions, have an instructive role as recognition and adhesion factors. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 575-586, 2017.
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Affiliation(s)
- Michael W Baker
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, 92093
| | - Eduardo R Macagno
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, California, 92093
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14
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Lin YS, Wang HY, Huang DF, Hsieh PF, Lin MY, Chou CH, Wu IJ, Huang GJ, Gau SSF, Huang HS. Neuronal Splicing Regulator RBFOX3 (NeuN) Regulates Adult Hippocampal Neurogenesis and Synaptogenesis. PLoS One 2016; 11:e0164164. [PMID: 27701470 PMCID: PMC5049801 DOI: 10.1371/journal.pone.0164164] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/20/2016] [Indexed: 11/18/2022] Open
Abstract
Dysfunction of RBFOX3 has been identified in neurodevelopmental disorders such as autism spectrum disorder, cognitive impairments and epilepsy and a causal relationship with these diseases has been previously demonstrated with Rbfox3 homozygous knockout mice. Despite the importance of RBFOX3 during neurodevelopment, the function of RBFOX3 regarding neurogenesis and synaptogenesis remains unclear. To address this critical question, we profiled the developmental expression pattern of Rbfox3 in the brain of wild-type mice and analyzed brain volume, disease-relevant behaviors, neurogenesis, synaptic plasticity, and synaptogenesis in Rbfox3 homozygous knockout mice and their corresponding wild-type counterparts. Here we report that expression of Rbfox3 differs developmentally for distinct brain regions. Moreover, Rbfox3 homozygous knockout mice exhibited cold hyperalgesia and impaired cognitive abilities. Focusing on hippocampal phenotypes, we found Rbfox3 homozygous knockout mice displayed deficits in neurogenesis, which was correlated with cognitive impairments. Furthermore, RBFOX3 regulates the exons of genes with synapse-related function. Synaptic plasticity and density, which are related to cognitive behaviors, were altered in the hippocampal dentate gyrus of Rbfox3 homozygous knockout mice; synaptic plasticity decreased and the density of synapses increased. Taken together, our results demonstrate the important role of RBFOX3 during neural development and maturation. In addition, abnormalities in synaptic structure and function occur in Rbfox3 homozygous knockout mice. Our findings may offer mechanistic explanations for human brain diseases associated with dysfunctional RBFOX3.
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Affiliation(s)
- Yi-Sian Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Han-Ying Wang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - De-Fong Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Pei-Fen Hsieh
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Meng-Ying Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chih-Hsuan Chou
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - I-Ju Wu
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Guo-Jen Huang
- Department of Biomedical Sciences, Chang Gung University, Tao-Yuan, Taiwan
| | - Susan Shur-Fen Gau
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Psychiatry, College of Medicine, National Taiwan University, Taipei, Taiwan
- Clinical Center for Neuroscience and Behavior, National Taiwan University Hospital, Taipei, Taiwan
- Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
| | - Hsien-Sung Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, Taiwan
- Clinical Center for Neuroscience and Behavior, National Taiwan University Hospital, Taipei, Taiwan
- Neurobiology and Cognitive Science Center, National Taiwan University, Taipei, Taiwan
- Ph.D. Program in Translational Medicine, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Neurodevelopment Club in Taiwan, Taipei, Taiwan
- * E-mail:
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15
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Zhou FC, Resendiz M, Lo CL, Chen Y. Cell-Wide DNA De-Methylation and Re-Methylation of Purkinje Neurons in the Developing Cerebellum. PLoS One 2016; 11:e0162063. [PMID: 27583369 PMCID: PMC5008790 DOI: 10.1371/journal.pone.0162063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/16/2016] [Indexed: 01/15/2023] Open
Abstract
Global DNA de-methylation is thought to occur only during pre-implantation and gametogenesis in mammals. Scalable, cell-wide de-methylation has not been demonstrated beyond totipotent stages. Here, we observed a large scale de-methylation and subsequent re-methylation (CDR) (including 5-methylcytosine (5mC) and 5-hydroxylmethylcytosine (5hmC)) in post-mitotic cerebellar Purkinje cells (PC) through the course of normal development. Through single cell immuno-identification and cell-specific quantitative methylation assays, we demonstrate that the CDR event is an intrinsically scheduled program, occurring in nearly every PC. Meanwhile, cerebellar granule cells and basket interneurons adopt their own DNA methylation program, independent of PCs. DNA de-methylation was further demonstrated at the gene level, on genes pertinent to PC development. The PC, being one of the largest neurons in the brain, may showcase an amplified epigenetic cycle which may mediate stage transformation including cell cycle arrest, vast axonal-dendritic growth, and synaptogenesis at the onset of neuronal specificity. This discovery is a key step toward better understanding the breadth and role of DNA methylation and de-methylation during neural ontology.
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Affiliation(s)
- Feng C. Zhou
- Department of Anatomy & Cell Biology, Indiana University School of Medicine, Indianapolis, Indiana, 46202, United States of America
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, 46202, United States of America
- * E-mail:
| | - Marisol Resendiz
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, Indiana, 46202, United States of America
| | - Chiao-Ling Lo
- Department of Anatomy & Cell Biology, Indiana University School of Medicine, Indianapolis, Indiana, 46202, United States of America
| | - Yuanyuan Chen
- Department of Anatomy & Cell Biology, Indiana University School of Medicine, Indianapolis, Indiana, 46202, United States of America
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16
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Kloth AD, Badura A, Li A, Cherskov A, Connolly SG, Giovannucci A, Bangash MA, Grasselli G, Peñagarikano O, Piochon C, Tsai PT, Geschwind DH, Hansel C, Sahin M, Takumi T, Worley PF, Wang SSH. Cerebellar associative sensory learning defects in five mouse autism models. eLife 2015; 4:e06085. [PMID: 26158416 PMCID: PMC4512177 DOI: 10.7554/elife.06085] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 07/03/2015] [Indexed: 12/17/2022] Open
Abstract
Sensory integration difficulties have been reported in autism, but their underlying brain-circuit mechanisms are underexplored. Using five autism-related mouse models, Shank3+/ΔC, Mecp2(R308/Y), Cntnap2-/-, L7-Tsc1 (L7/Pcp2(Cre)::Tsc1(flox/+)), and patDp(15q11-13)/+, we report specific perturbations in delay eyeblink conditioning, a form of associative sensory learning requiring cerebellar plasticity. By distinguishing perturbations in the probability and characteristics of learned responses, we found that probability was reduced in Cntnap2-/-, patDp(15q11-13)/+, and L7/Pcp2(Cre)::Tsc1(flox/+), which are associated with Purkinje-cell/deep-nuclear gene expression, along with Shank3+/ΔC. Amplitudes were smaller in L7/Pcp2(Cre)::Tsc1(flox/+) as well as Shank3+/ΔC and Mecp2(R308/Y), which are associated with granule cell pathway expression. Shank3+/ΔC and Mecp2(R308/Y) also showed aberrant response timing and reduced Purkinje-cell dendritic spine density. Overall, our observations are potentially accounted for by defects in instructed learning in the olivocerebellar loop and response representation in the granule cell pathway. Our findings indicate that defects in associative temporal binding of sensory events are widespread in autism mouse models.
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Affiliation(s)
- Alexander D Kloth
- Department of Molecular Biology and Princeton Neuroscience Institute, Princeton University, Princeton, United States
| | - Aleksandra Badura
- Department of Molecular Biology and Princeton Neuroscience Institute, Princeton University, Princeton, United States
| | - Amy Li
- Department of Molecular Biology and Princeton Neuroscience Institute, Princeton University, Princeton, United States
| | - Adriana Cherskov
- Department of Molecular Biology and Princeton Neuroscience Institute, Princeton University, Princeton, United States
| | - Sara G Connolly
- Department of Molecular Biology and Princeton Neuroscience Institute, Princeton University, Princeton, United States
| | - Andrea Giovannucci
- Department of Molecular Biology and Princeton Neuroscience Institute, Princeton University, Princeton, United States
| | - M Ali Bangash
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Giorgio Grasselli
- Department of Neurobiology, University of Chicago, Chicago, United States
| | - Olga Peñagarikano
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States
| | - Claire Piochon
- Department of Neurobiology, University of Chicago, Chicago, United States
| | - Peter T Tsai
- The F.M. Kirby Neurobiology Center, Department of Neurology, Children's Hospital Boston, Harvard Medical School, Boston, United States
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, United States
| | - Christian Hansel
- Department of Neurobiology, University of Chicago, Chicago, United States
| | - Mustafa Sahin
- The F.M. Kirby Neurobiology Center, Department of Neurology, Children's Hospital Boston, Harvard Medical School, Boston, United States
| | | | - Paul F Worley
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Samuel S-H Wang
- Department of Molecular Biology and Princeton Neuroscience Institute, Princeton University, Princeton, United States
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17
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Developmental gene expression profile of axon guidance cues in Purkinje cells during cerebellar circuit formation. THE CEREBELLUM 2014; 13:307-17. [PMID: 24550128 DOI: 10.1007/s12311-014-0548-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The establishment of precise neural circuits during development involves a variety of contact-mediated and secreted guidance molecules that are expressed in a complementary fashion by different cell types. To build a functional circuit, each cell type must first trigger an intrinsic genetic program that is led by their environment at a key time point. It is therefore essential to identify the different cell-specific and stage-specific transcriptional profiles expressed by neurons. However, very few studies have been done to address this issue thus far. Herein, we have carried out a large-scale quantitative real-time PCR analysis of all classical axon guidance molecules (i.e., Semaphorins, Netrins, Ephrins, and Slits) and their receptors expressed by Purkinje cells (PCs) at specific stages of postnatal cerebellar development in vivo. Most cerebellar connections are setup in a well-characterized sequential manner during postnatal development and lead to the fine regulation of the PC, the sole output of the structure. Our analysis of the relative expression of these guidance cues has uncovered a dynamic expression pattern corresponding to specific stages of cerebellar development, thus providing a starting point for studying the role of these axon guidance molecules in cerebellar wiring.
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18
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Hollins SL, Goldie BJ, Carroll AP, Mason EA, Walker FR, Eyles DW, Cairns MJ. Ontogeny of small RNA in the regulation of mammalian brain development. BMC Genomics 2014; 15:777. [PMID: 25204312 PMCID: PMC4171549 DOI: 10.1186/1471-2164-15-777] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/04/2014] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) play a pivotal role in coordinating messenger RNA (mRNA) transcription and stability in almost all known biological processes, including the development of the central nervous system. Despite our broad understanding of their involvement, we still have a very sparse understanding of specifically how miRNA contribute to the strict regional and temporal regulation of brain development. Accordingly, in the current study we have examined the contribution of miRNA in the developing rat telencephalon and mesencephalon from just after neural tube closure till birth using a genome-wide microarray strategy. RESULTS We identified temporally distinct expression patterns in both the telencephalon and mesencephalon for both miRNAs and their target genes. We demonstrate direct miRNA targeting of several genes involved with the migration, differentiation and maturation of neurons. CONCLUSIONS Our findings suggest that miRNA have significant implications for the development of neural structure and support important mechanisms that if disrupted, may contribute to or drive neurodevelopmental disorders.
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Affiliation(s)
- Sharon L Hollins
- />School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, the University of Newcastle, University Drive, Callaghan, NSW 2308 Australia
- />Centre for Translational Neuroscience and Mental Health, Hunter Medical Research Institute, Newcastle, NSW 2305 Australia
| | - Belinda J Goldie
- />School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, the University of Newcastle, University Drive, Callaghan, NSW 2308 Australia
- />Centre for Translational Neuroscience and Mental Health, Hunter Medical Research Institute, Newcastle, NSW 2305 Australia
- />Schizophrenia Research Institute, Sydney, NSW Australia
| | - Adam P Carroll
- />School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, the University of Newcastle, University Drive, Callaghan, NSW 2308 Australia
- />Centre for Translational Neuroscience and Mental Health, Hunter Medical Research Institute, Newcastle, NSW 2305 Australia
| | - Elizabeth A Mason
- />Queensland Brain Institute, University of Queensland, Brisbane, Qld 4072 Australia
| | - Frederick R Walker
- />School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, the University of Newcastle, University Drive, Callaghan, NSW 2308 Australia
- />Centre for Translational Neuroscience and Mental Health, Hunter Medical Research Institute, Newcastle, NSW 2305 Australia
| | - Darryl W Eyles
- />Queensland Brain Institute, University of Queensland, Brisbane, Qld 4072 Australia
- />Queensland Centre for Mental Health Research, Wacol, Qld, 4076 Australia
| | - Murray J Cairns
- />School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, the University of Newcastle, University Drive, Callaghan, NSW 2308 Australia
- />Centre for Translational Neuroscience and Mental Health, Hunter Medical Research Institute, Newcastle, NSW 2305 Australia
- />Schizophrenia Research Institute, Sydney, NSW Australia
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19
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Pollock JD, Wu DY, Satterlee JS. Molecular neuroanatomy: a generation of progress. Trends Neurosci 2014; 37:106-23. [PMID: 24388609 PMCID: PMC3946666 DOI: 10.1016/j.tins.2013.11.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 11/08/2013] [Accepted: 11/14/2013] [Indexed: 11/22/2022]
Abstract
The neuroscience research landscape has changed dramatically over the past decade. Specifically, an impressive array of new tools and technologies have been generated, including but not limited to: brain gene expression atlases, genetically encoded proteins to monitor and manipulate neuronal activity, and new methods for imaging and mapping circuits. However, despite these technological advances, several significant challenges must be overcome to enable a better understanding of brain function and to develop cell type-targeted therapeutics to treat brain disorders. This review provides an overview of some of the tools and technologies currently being used to advance the field of molecular neuroanatomy, and also discusses emerging technologies that may enable neuroscientists to address these crucial scientific challenges over the coming decade.
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Affiliation(s)
- Jonathan D Pollock
- Division of Basic Neurobiology and Behavioral Research, Genetics and Molecular Neurobiology Research Branch, National Institute on Drug Abuse/National Institutes of Health (NIH), 6001 Executive Boulevard, Bethesda, MD 20850, USA.
| | - Da-Yu Wu
- Division of Basic Neurobiology and Behavioral Research, Genetics and Molecular Neurobiology Research Branch, National Institute on Drug Abuse/National Institutes of Health (NIH), 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - John S Satterlee
- Division of Basic Neurobiology and Behavioral Research, Genetics and Molecular Neurobiology Research Branch, National Institute on Drug Abuse/National Institutes of Health (NIH), 6001 Executive Boulevard, Bethesda, MD 20850, USA
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20
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Neman J, Termini J, Wilczynski S, Vaidehi N, Choy C, Kowolik CM, Li H, Hambrecht AC, Roberts E, Jandial R. Human breast cancer metastases to the brain display GABAergic properties in the neural niche. Proc Natl Acad Sci U S A 2014; 111:984-9. [PMID: 24395782 PMCID: PMC3903266 DOI: 10.1073/pnas.1322098111] [Citation(s) in RCA: 227] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dispersion of tumors throughout the body is a neoplastic process responsible for the vast majority of deaths from cancer. Despite disseminating to distant organs as malignant scouts, most tumor cells fail to remain viable after their arrival. The physiologic microenvironment of the brain must become a tumor-favorable microenvironment for successful metastatic colonization by circulating breast cancer cells. Bidirectional interplay of breast cancer cells and native brain cells in metastasis is poorly understood and rarely studied. We had the rare opportunity to investigate uncommonly available specimens of matched fresh breast-to-brain metastases tissue and derived cells from patients undergoing neurosurgical resection. We hypothesized that, to metastasize, breast cancers may escape their normative genetic constraints by accommodating and coinhabiting the neural niche. This acquisition or expression of brain-like properties by breast cancer cells could be a malignant adaptation required for brain colonization. Indeed, we found breast-to-brain metastatic tissue and cells displayed a GABAergic phenotype similar to that of neuronal cells. The GABAA receptor, GABA transporter, GABA transaminase, parvalbumin, and reelin were all highly expressed in breast cancer metastases to the brain. Proliferative advantage was conferred by the ability of breast-to-brain metastases to take up and catabolize GABA into succinate with the resultant formation of NADH as a biosynthetic source through the GABA shunt. The results suggest that breast cancers exhibit neural characteristics when occupying the brain microenvironment and co-opt GABA as an oncometabolite.
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Affiliation(s)
| | | | | | | | - Cecilia Choy
- Divisions of Neurosurgery and
- Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010; and
| | | | - Hubert Li
- Immunology, and
- Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010; and
| | - Amanda C. Hambrecht
- Divisions of Neurosurgery and
- Department of Biology, University of Southern California, Los Angeles, CA 90089
| | | | - Rahul Jandial
- Divisions of Neurosurgery and
- Department of Biology, University of Southern California, Los Angeles, CA 90089
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21
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Taguchi YH. MicroRNA-mediated regulation of target genes in several brain regions is correlated to both microRNA-targeting-specific promoter methylation and differential microRNA expression. BioData Min 2013; 6:11. [PMID: 23725297 PMCID: PMC3693885 DOI: 10.1186/1756-0381-6-11] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 05/23/2013] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Public domain databases nowadays provide multiple layers of genome-wide data e.g., promoter methylation, mRNA expression, and miRNA expression and should enable integrative modeling of the mechanisms of regulation of gene expression. However, researches along this line were not frequently executed. RESULTS Here, the public domain dataset of mRNA expression, microRNA (miRNA) expression and promoter methylation patterns in four regions, the frontal cortex, temporal cortex, pons and cerebellum, of human brain were sourced from the National Center for Biotechnology Informations gene expression omnibus, and reanalyzed computationally. A large number of miRNA-mediated regulation of target genes and miRNA-targeting-specific promoter methylation were identified in the six pairwise comparisons among the four brain regions. The miRNA-mediated regulation of target genes was found to be highly correlated with one or both of miRNA-targeting-specific promoter methylation and differential miRNA expression. Genes enriched for Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were related to brain function and/or development were found among the target genes of miRNAs whose differential expression patterns were highly correlated with the miRNA-mediated regulation of their target genes. CONCLUSIONS The combinatorial analysis of miRNA-mediated regulation of target genes, miRNA-targeting-specific promoter methylation and differential miRNA expression can help reveal the brain region-specific contributions of miRNAs to brain function and development.
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Affiliation(s)
- Y-H Taguchi
- Department of Physics, Chuo University, Tokyo 112-8551, Japan.
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22
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Aboukhalil R, Fendler B, Atwal GS. Kerfuffle: a web tool for multi-species gene colocalization analysis. BMC Bioinformatics 2013; 14:22. [PMID: 23327649 PMCID: PMC3598493 DOI: 10.1186/1471-2105-14-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 01/11/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The evolutionary pressures that underlie the large-scale functional organization of the genome are not well understood in eukaryotes. Recent evidence suggests that functionally similar genes may colocalize (cluster) in the eukaryotic genome, suggesting the role of chromatin-level gene regulation in shaping the physical distribution of coordinated genes. However, few of the bioinformatic tools currently available allow for a systematic study of gene colocalization across several, evolutionarily distant species. Furthermore, most tools require the user to input manually curated lists of gene position information, DNA sequence or gene homology relations between species. With the growing number of sequenced genomes, there is a need to provide new comparative genomics tools that can address the analysis of multi-species gene colocalization. RESULTS Kerfuffle is a web tool designed to help discover, visualize, and quantify the physical organization of genomes by identifying significant gene colocalization and conservation across the assembled genomes of available species (currently up to 47, from humans to worms). Kerfuffle only requires the user to specify a list of human genes and the names of other species of interest. Without further input from the user, the software queries the e!Ensembl BioMart server to obtain positional information and discovers homology relations in all genes and species specified. Using this information, Kerfuffle performs a multi-species clustering analysis, presents downloadable lists of clustered genes, performs Monte Carlo statistical significance calculations, estimates how conserved gene clusters are across species, plots histograms and interactive graphs, allows users to save their queries, and generates a downloadable visualization of the clusters using the Circos software. These analyses may be used to further explore the functional roles of gene clusters by interrogating the enriched molecular pathways associated with each cluster. CONCLUSIONS Kerfuffle is a new, easy-to-use and publicly available tool to aid our understanding of functional genomics and comparative genomics. This software allows for flexibility and quick investigations of a user-defined set of genes, and the results may be saved online for further analysis. Kerfuffle is freely available at http://atwallab.org/kerfuffle, is implemented in JavaScript (using jQuery and jsCharts libraries) and PHP 5.2, runs on an Apache server, and stores data in flat files and an SQLite database.
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