PICK1 Interacts with PACSIN to Regulate AMPA Receptor Internalization and Cerebellar Long-Term Depression
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Defining Functional Interactions During Biogenesis of Epithelial Junctions
ARTICLE Received 11 Dec 2015 | Accepted 13 Oct 2016 | Published 6 Dec 2016 | Updated 5 Jan 2017 DOI: 10.1038/ncomms13542 OPEN Defining functional interactions during biogenesis of epithelial junctions J.C. Erasmus1,*, S. Bruche1,*,w, L. Pizarro1,2,*, N. Maimari1,3,*, T. Poggioli1,w, C. Tomlinson4,J.Lees5, I. Zalivina1,w, A. Wheeler1,w, A. Alberts6, A. Russo2 & V.M.M. Braga1 In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases. 1 National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. 2 Computing Department, Imperial College London, London SW7 2AZ, UK. 3 Bioengineering Department, Faculty of Engineering, Imperial College London, London SW7 2AZ, UK. 4 Department of Surgery & Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK. -
4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4). -
Supplementary Table 1
Supplementary Table 1. 492 genes are unique to 0 h post-heat timepoint. The name, p-value, fold change, location and family of each gene are indicated. Genes were filtered for an absolute value log2 ration 1.5 and a significance value of p ≤ 0.05. Symbol p-value Log Gene Name Location Family Ratio ABCA13 1.87E-02 3.292 ATP-binding cassette, sub-family unknown transporter A (ABC1), member 13 ABCB1 1.93E-02 −1.819 ATP-binding cassette, sub-family Plasma transporter B (MDR/TAP), member 1 Membrane ABCC3 2.83E-02 2.016 ATP-binding cassette, sub-family Plasma transporter C (CFTR/MRP), member 3 Membrane ABHD6 7.79E-03 −2.717 abhydrolase domain containing 6 Cytoplasm enzyme ACAT1 4.10E-02 3.009 acetyl-CoA acetyltransferase 1 Cytoplasm enzyme ACBD4 2.66E-03 1.722 acyl-CoA binding domain unknown other containing 4 ACSL5 1.86E-02 −2.876 acyl-CoA synthetase long-chain Cytoplasm enzyme family member 5 ADAM23 3.33E-02 −3.008 ADAM metallopeptidase domain Plasma peptidase 23 Membrane ADAM29 5.58E-03 3.463 ADAM metallopeptidase domain Plasma peptidase 29 Membrane ADAMTS17 2.67E-04 3.051 ADAM metallopeptidase with Extracellular other thrombospondin type 1 motif, 17 Space ADCYAP1R1 1.20E-02 1.848 adenylate cyclase activating Plasma G-protein polypeptide 1 (pituitary) receptor Membrane coupled type I receptor ADH6 (includes 4.02E-02 −1.845 alcohol dehydrogenase 6 (class Cytoplasm enzyme EG:130) V) AHSA2 1.54E-04 −1.6 AHA1, activator of heat shock unknown other 90kDa protein ATPase homolog 2 (yeast) AK5 3.32E-02 1.658 adenylate kinase 5 Cytoplasm kinase AK7 -
Weighted Burden Analysis of Exome-Sequenced Case-Control Sample Implicates Synaptic Genes in Schizophrenia Aetiology
Behavior Genetics (2018) 48:198–208 https://doi.org/10.1007/s10519-018-9893-3 ORIGINAL RESEARCH Weighted Burden Analysis of Exome-Sequenced Case-Control Sample Implicates Synaptic Genes in Schizophrenia Aetiology David Curtis1,2 · Leda Coelewij1 · Shou‑Hwa Liu1 · Jack Humphrey1,3 · Richard Mott1 Received: 22 November 2017 / Accepted: 13 March 2018 / Published online: 21 March 2018 © The Author(s) 2018 Abstract A previous study of exome-sequenced schizophrenia cases and controls reported an excess of singleton, gene-disruptive vari- ants among cases, concentrated in particular gene sets. The dataset included a number of subjects with a substantial Finnish contribution to ancestry. We have reanalysed the same dataset after removal of these subjects and we have also included non- singleton variants of all types using a weighted burden test which assigns higher weights to variants predicted to have a greater effect on protein function. We investigated the same 31 gene sets as previously and also 1454 GO gene sets. The reduced dataset consisted of 4225 cases and 5834 controls. No individual variants or genes were significantly enriched in cases but 13 out of the 31 gene sets were significant after Bonferroni correction and the “FMRP targets” set produced a signed log p value (SLP) of 7.1. The gene within this set with the highest SLP, equal to 3.4, was FYN, which codes for a tyrosine kinase which phosphorylates glutamate metabotropic receptors and ionotropic NMDA receptors, thus modulating their trafficking, subcellular distribution and function. In the most recent GWAS of schizophrenia it was identified as a “prioritized candidate gene”. -
Native KCC2 Interactome Reveals PACSIN1 As a Critical Regulator of Synaptic Inhibition
bioRxiv preprint doi: https://doi.org/10.1101/142265; this version posted May 25, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Native KCC2 interactome reveals PACSIN1 as a critical regulator of synaptic inhibition Vivek Mahadevan1, 2, C. Sahara Khademullah1, #, Zahra Dargaei1, #, Jonah Chevrier1,, Pavel Uvarov3, Julian Kwan4, Richard D. Bagshaw5, Tony Pawson5, §, Andrew Emili4, Yves DeKoninck6, Victor Anggono7, Matti S. Airaksinen3, Melanie A. Woodin1* 1 Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario, M5S 3G5, Canada 2 Present address: Section on Cellular and Synaptic Physiology, NICHD, Bethesda, Maryland, USA 3 Department of Anatomy, Faculty of Medicine, University of Helsinki, Finland 4 Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada 5 Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada 6 Institut Universitaire en Santé Mentale de Québec, Québec, QC G1J 2G3, Canada; Department of Psychiatry and Neuroscience, Université Laval, Québec, QC, G1V 0A6, Canada 7 Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, QLD 4072, Australia # Equal contribution § Deceased August 7, 2013 * Corresponding author: [email protected], 416-978-8646 bioRxiv preprint doi: https://doi.org/10.1101/142265; this version posted May 25, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Lineage-Specific Effector Signatures of Invariant NKT Cells Are Shared Amongst Δγ T, Innate Lymphoid, and Th Cells
Downloaded from http://www.jimmunol.org/ by guest on September 26, 2021 δγ is online at: average * The Journal of Immunology , 10 of which you can access for free at: 2016; 197:1460-1470; Prepublished online 6 July from submission to initial decision 4 weeks from acceptance to publication 2016; doi: 10.4049/jimmunol.1600643 http://www.jimmunol.org/content/197/4/1460 Lineage-Specific Effector Signatures of Invariant NKT Cells Are Shared amongst T, Innate Lymphoid, and Th Cells You Jeong Lee, Gabriel J. Starrett, Seungeun Thera Lee, Rendong Yang, Christine M. Henzler, Stephen C. Jameson and Kristin A. Hogquist J Immunol cites 41 articles Submit online. Every submission reviewed by practicing scientists ? is published twice each month by Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://jimmunol.org/subscription http://www.jimmunol.org/content/suppl/2016/07/06/jimmunol.160064 3.DCSupplemental This article http://www.jimmunol.org/content/197/4/1460.full#ref-list-1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* Why • • • Material References Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2016 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of September 26, 2021. The Journal of Immunology Lineage-Specific Effector Signatures of Invariant NKT Cells Are Shared amongst gd T, Innate Lymphoid, and Th Cells You Jeong Lee,* Gabriel J. -
Epigenetic Trajectories to Childhood Asthma
Epigenetic Trajectories to Childhood Asthma Item Type text; Electronic Dissertation Authors DeVries, Avery Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction, presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 04/10/2021 09:24:24 Link to Item http://hdl.handle.net/10150/630233 1 EPIGENETIC TRAJECTORIES TO CHILDHOOD ASTHMA by Avery DeVries __________________________ Copyright © Avery DeVries 2018 A Dissertation Submitted to the Faculty of the DEPARTMENT OF CELLULAR AND MOLECULAR MEDICINE In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY In the Graduate College THE UNIVERSITY OF ARIZONA 2018 2 3 STATEMENT BY AUTHOR This dissertation has been submitted in partial fulfillment of the requirements for an advanced degree at the University of Arizona and is deposited in the University Library to be made available to borrowers under rules of the Library. Brief quotations from this dissertation are allowable without special permission, provided that an accurate acknowledgement of the source is made. Requests for permission for extended quotation from or reproduction of this manuscript in whole or in part may be granted by the head of the major department or the Dean of the Graduate College when in his or her judgment the proposed use of the material is in the interests of scholarship. In all other instances, however, permission must be obtained from the author. SIGNED: Avery DeVries 4 ACKNOWLEDGEMENTS I would like to thank my dissertation mentor, Donata Vercelli, for endless support throughout this journey and for always encouraging and challenging me to be a better scientist. -
120409 Thesis
Mechanisms of Specificity in Neuronal Activity-regulated Gene Transcription by Michelle Renée Lyons Department of Neurobiology Duke University Date:_______________________ Approved: ___________________________ Anne West, Supervisor ___________________________ Dona Chikaraishi, Chair ___________________________ James O. McNamara ___________________________ Geoffrey Pitt ___________________________ Scott Soderling Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Neurobiology in the Graduate School of Duke University 2012 i v ABSTRACT Mechanisms of Specificity in Neuronal Activity-regulated Gene Transcription by Michelle Renée Lyons Department of Neurobiology Duke University Date:_______________________ Approved: ___________________________ Anne West, Supervisor ___________________________ Dona Chikaraishi, Chair ___________________________ James O. McNamara ___________________________ Geoffrey Pitt ___________________________ Scott Soderling An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Neurobiology in the Graduate School of Duke University 2012 Copyright by Michelle Renée Lyons 2012 Abstract In the nervous system, activity-regulated gene transcription is one of the fundamental processes responsible for orchestrating proper brain development – a process that in humans takes over 20 years. Moreover, activity-dependent regulation of gene expression continues to be important -
The Scrib1 Interactome and Its Relevance for Synaptic Plasticity & Neurodevelopmental Disorders Vera Margarido Pinheiro
The Scrib1 Interactome and its relevance for synaptic plasticity & neurodevelopmental disorders Vera Margarido Pinheiro To cite this version: Vera Margarido Pinheiro. The Scrib1 Interactome and its relevance for synaptic plasticity & neurode- velopmental disorders. Neurons and Cognition [q-bio.NC]. Université de Bordeaux, 2014. English. NNT : 2014BORD0318. tel-01435921 HAL Id: tel-01435921 https://tel.archives-ouvertes.fr/tel-01435921 Submitted on 16 Jan 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE PRÉSENTÉE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITÉ DE BORDEAUX ÉCOLE DOCTORALE: SCIENCES DE LA VIE ET DE LA SANTE SPÉCIALITÉ: NEUROSCIENCES Par Vera PINHEIRO L’interactome de Scrib1 et son importance pour la plasticitè synaptique & les troubles de neurodéveloppement Sous la direction de : Nathalie SANS Soutenue le 4 Décembre 2014 Membres du jury : M. GARRET, Maurice CNRS, Bordeaux Président Mme CARVALHO, Ana Luisa Uni. Coimbra, Portugal rapporteur M. HENLEY, Jeremy Uni. Bristol, Royaume Uni rapporteur M. THOUMINE, Olivier CNRS, Bordeaux -
Proteomic Landscape of the Human Choroid–Retinal Pigment Epithelial Complex
Supplementary Online Content Skeie JM, Mahajan VB. Proteomic landscape of the human choroid–retinal pigment epithelial complex. JAMA Ophthalmol. Published online July 24, 2014. doi:10.1001/jamaophthalmol.2014.2065. eFigure 1. Choroid–retinal pigment epithelial (RPE) proteomic analysis pipeline. eFigure 2. Gene ontology (GO) distributions and pathway analysis of human choroid– retinal pigment epithelial (RPE) protein show tissue similarity. eMethods. Tissue collection, mass spectrometry, and analysis. eTable 1. Complete table of proteins identified in the human choroid‐RPE using LC‐ MS/MS. eTable 2. Top 50 signaling pathways in the human choroid‐RPE using MetaCore. eTable 3. Top 50 differentially expressed signaling pathways in the human choroid‐RPE using MetaCore. eTable 4. Differentially expressed proteins in the fovea, macula, and periphery of the human choroid‐RPE. eTable 5. Differentially expressed transcription proteins were identified in foveal, macular, and peripheral choroid‐RPE (p<0.05). eTable 6. Complement proteins identified in the human choroid‐RPE. eTable 7. Proteins associated with age related macular degeneration (AMD). This supplementary material has been provided by the authors to give readers additional information about their work. © 2014 American Medical Association. All rights reserved. 1 Downloaded From: https://jamanetwork.com/ on 09/25/2021 eFigure 1. Choroid–retinal pigment epithelial (RPE) proteomic analysis pipeline. A. The human choroid‐RPE was dissected into fovea, macula, and periphery samples. B. Fractions of proteins were isolated and digested. C. The peptide fragments were analyzed using multi‐dimensional LC‐MS/MS. D. X!Hunter, X!!Tandem, and OMSSA were used for peptide fragment identification. E. Proteins were further analyzed using bioinformatics. -
Utilizing an Animal Model to Identify Brain Neurodegeneration-Related Biomarkers in Aging
International Journal of Molecular Sciences Article Utilizing an Animal Model to Identify Brain Neurodegeneration-Related Biomarkers in Aging Ming-Hui Yang 1 , Yi-Ming Arthur Chen 2, Shan-Chen Tu 3, Pei-Ling Chi 1, Kuo-Pin Chuang 4,5,6,7, Chin-Chuan Chang 7,8,9,10,11 , Chiang-Hsuan Lee 12 , Yi-Ling Chen 8, Che-Hsin Lee 13 , Cheng-Hui Yuan 14 and Yu-Chang Tyan 3,6,7,11,15,16,17,18,19,* 1 Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan; [email protected] (M.-H.Y.); [email protected] (P.-L.C.) 2 Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City 242, Taiwan; [email protected] 3 Department of Medical Imaging and Radiological Sciences, Kaohsiung Medical University, Kaohsiung 807, Taiwan; [email protected] 4 International Degree Program in Animal Vaccine Technology, International College, National Pingtung University of Science and Technology, Pingtung 912, Taiwan; [email protected] 5 Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung 912, Taiwan 6 Graduate Institute of Animal Vaccine Technology, College of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 912, Taiwan 7 School of Medicine, College of Medicine, Kaoshiung Medical University, Kaoshiung 807, Taiwan; [email protected] 8 Department of Nuclear Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan; [email protected] 9 Citation: Yang, M.-H.; Chen, Y.-M.A.; Department of Electrical Engineering, I-Shou University, Kaohsiung 840, Taiwan 10 School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan Tu, S.-C.; Chi, P.-L.; Chuang, K.-P.; 11 Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan Chang, C.-C.; Lee, C.-H.; Chen, Y.-L.; 12 Department of Nuclear Medicine, Chi Mei Medical Center, Tainan 710, Taiwan; [email protected] Lee, C.-H.; Yuan, C.-H.; et al. -
Identification of Neuronal Substrates Implicates Pak5 in Synaptic Vesicle Trafficking
Identification of neuronal substrates implicates Pak5 in synaptic vesicle trafficking Todd I. Strochlica, Susanna Concilioa, Julien Viaudb, Ryan A. Eberwinea, Lisa Epstein Wongc, Audrey Mindenc, Benjamin E. Turkd, Markus Plomanne, and Jeffrey R. Petersona,1 aCancer Biology Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111; bInstitut National de la Sante et de la Recherche Medicale U1048 Equipe B. Payrastre Bâtiment B, Pavillon Lefebvre, BP 3028, 31024 Toulouse, France; cSusan Lehman Cullman Laboratory for Cancer Research, Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, 164 Frelinghuysen Road, Piscataway, NJ 08854; dDepartment of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520; and eCenter for Biochemistry, Medical Faculty of the University of Cologne, Joseph-Stelzmann-Strasse 52 50931 Cologne, Germany Edited by Pietro De Camilli, Yale University and Howard Hughes Medical Institute, New Haven, CT, and approved January 17, 2012 (received for review October 7, 2011) Synaptic transmission is mediated by a complex set of molecular in the brain (14, 15). Consistent with some level of functional re- events that must be coordinated in time and space. While many dundancy between these Pak isoforms, no phenotype has been proteins that function at the synapse have been identified, the reported for PAK5 or PAK6 single knockout mice (10, 16), but signaling pathways regulating these molecules are poorly under- PAK5/PAK6 double knockout mice exhibit defects in behavior, stood. Pak5 (p21-activated kinase 5) is a brain-specific isoform of memory, and learning (16). The molecular mechanisms underly- the group II Pak kinases whose substrates and roles within the ing these cognitive defects, however, have yet to be determined.