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Zhan P, Peil A, Jiang Q, Wang D, Mousavi S, Xiong Q, Shen Q, Shang Y, Ding B, Lin C, Ke Y, Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem Rev 2023; 123:3976-4050. [PMID: 36990451 PMCID: PMC10103138 DOI: 10.1021/acs.chemrev.3c00028] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Indexed: 03/31/2023]
Abstract
DNA nanotechnology is a unique field, where physics, chemistry, biology, mathematics, engineering, and materials science can elegantly converge. Since the original proposal of Nadrian Seeman, significant advances have been achieved in the past four decades. During this glory time, the DNA origami technique developed by Paul Rothemund further pushed the field forward with a vigorous momentum, fostering a plethora of concepts, models, methodologies, and applications that were not thought of before. This review focuses on the recent progress in DNA origami-engineered nanomaterials in the past five years, outlining the exciting achievements as well as the unexplored research avenues. We believe that the spirit and assets that Seeman left for scientists will continue to bring interdisciplinary innovations and useful applications to this field in the next decade.
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Affiliation(s)
- Pengfei Zhan
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Andreas Peil
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
| | - Qiao Jiang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Dongfang Wang
- School
of Biomedical Engineering and Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Shikufa Mousavi
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Qiancheng Xiong
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
| | - Qi Shen
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, 266
Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Yingxu Shang
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Baoquan Ding
- National
Center for Nanoscience and Technology, No 11, BeiYiTiao Zhongguancun, Beijing 100190, China
| | - Chenxiang Lin
- Department
of Cell Biology, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, United States
- Nanobiology
Institute, Yale University, 850 West Campus Drive, West Haven, Connecticut 06516, United States
- Department
of Biomedical Engineering, Yale University, 17 Hillhouse Avenue, New Haven, Connecticut 06511, United States
| | - Yonggang Ke
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322, United States
| | - Na Liu
- 2nd Physics
Institute, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
- Max Planck
Institute for Solid State Research, Heisenbergstrasse 1, 70569 Stuttgart, Germany
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2
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Placidi G, Mattu C, Ciardelli G, Campa CC. Small molecules targeting endocytic uptake and recycling pathways. Front Cell Dev Biol 2023; 11:1125801. [PMID: 36968200 PMCID: PMC10036367 DOI: 10.3389/fcell.2023.1125801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/23/2023] [Indexed: 03/12/2023] Open
Abstract
Over the past years a growing number of studies highlighted the pivotal role of intracellular trafficking in cell physiology. Among the distinct transport itineraries connecting the endocytic system, both internalization (endocytosis) and recycling (endocytic recycling) pathways were found fundamental to ensure cellular sensing, cell-to-cell communication, cellular division, and collective cell migration in tissue specific-contexts. Consistently, the dysregulation of endocytic trafficking pathways is correlated with several human diseases including both cancers and neurodegeneration. Aimed at suppress specific intracellular trafficking routes involved in disease onset and progression, huge efforts have been made to identify small molecule inhibitors with suitable pharmacological properties for in vivo administration. Here, we review most used drugs and recently discovered small molecules able to block endocytosis and endocytic recycling pathways. We characterize such pharmacological inhibitors by emphasizing their target specificity, molecular affinity, biological activity and efficacy in both in vitro and in vivo experimental models.
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Affiliation(s)
- Giampaolo Placidi
- Italian Institute for Genomic Medicine, Candiolo, Italy
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Clara Mattu
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Gianluca Ciardelli
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
- Chemical-Physical Processes, National Research Council (CNR-IPCF), Pisa, Italy
| | - Carlo C. Campa
- Italian Institute for Genomic Medicine, Candiolo, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
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3
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Crook OM, Lilley KS, Gatto L, Kirk PD. Semi-Supervised Non-Parametric Bayesian Modelling of Spatial Proteomics. Ann Appl Stat 2022; 16:22-aoas1603. [PMID: 36507469 PMCID: PMC7613899 DOI: 10.1214/22-aoas1603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Understanding sub-cellular protein localisation is an essential component in the analysis of context specific protein function. Recent advances in quantitative mass-spectrometry (MS) have led to high resolution mapping of thousands of proteins to sub-cellular locations within the cell. Novel modelling considerations to capture the complex nature of these data are thus necessary. We approach analysis of spatial proteomics data in a non-parametric Bayesian framework, using K-component mixtures of Gaussian process regression models. The Gaussian process regression model accounts for correlation structure within a sub-cellular niche, with each mixture component capturing the distinct correlation structure observed within each niche. The availability of marker proteins (i.e. proteins with a priori known labelled locations) motivates a semi-supervised learning approach to inform the Gaussian process hyperparameters. We moreover provide an efficient Hamiltonian-within-Gibbs sampler for our model. Furthermore, we reduce the computational burden associated with inversion of covariance matrices by exploiting the structure in the covariance matrix. A tensor decomposition of our covariance matrices allows extended Trench and Durbin algorithms to be applied to reduce the computational complexity of inversion and hence accelerate computation. We provide detailed case-studies on Drosophila embryos and mouse pluripotent embryonic stem cells to illustrate the benefit of semi-supervised functional Bayesian modelling of the data.
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4
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Fasano G, Muto V, Radio FC, Venditti M, Mosaddeghzadeh N, Coppola S, Paradisi G, Zara E, Bazgir F, Ziegler A, Chillemi G, Bertuccini L, Tinari A, Vetro A, Pantaleoni F, Pizzi S, Conti LA, Petrini S, Bruselles A, Prandi IG, Mancini C, Chandramouli B, Barth M, Bris C, Milani D, Selicorni A, Macchiaiolo M, Gonfiantini MV, Bartuli A, Mariani R, Curry CJ, Guerrini R, Slavotinek A, Iascone M, Dallapiccola B, Ahmadian MR, Lauri A, Tartaglia M. Dominant ARF3 variants disrupt Golgi integrity and cause a neurodevelopmental disorder recapitulated in zebrafish. Nat Commun 2022; 13:6841. [PMID: 36369169 PMCID: PMC9652361 DOI: 10.1038/s41467-022-34354-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/24/2022] [Indexed: 11/13/2022] Open
Abstract
Vesicle biogenesis, trafficking and signaling via Endoplasmic reticulum-Golgi network support essential developmental processes and their disruption lead to neurodevelopmental disorders and neurodegeneration. We report that de novo missense variants in ARF3, encoding a small GTPase regulating Golgi dynamics, cause a developmental disease in humans impairing nervous system and skeletal formation. Microcephaly-associated ARF3 variants affect residues within the guanine nucleotide binding pocket and variably perturb protein stability and GTP/GDP binding. Functional analysis demonstrates variably disruptive consequences of ARF3 variants on Golgi morphology, vesicles assembly and trafficking. Disease modeling in zebrafish validates further the dominant behavior of the mutants and their differential impact on brain and body plan formation, recapitulating the variable disease expression. In-depth in vivo analyses traces back impaired neural precursors' proliferation and planar cell polarity-dependent cell movements as the earliest detectable effects. Our findings document a key role of ARF3 in Golgi function and demonstrate its pleiotropic impact on development.
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Affiliation(s)
- Giulia Fasano
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Valentina Muto
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Francesca Clementina Radio
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Martina Venditti
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Niloufar Mosaddeghzadeh
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Simona Coppola
- grid.416651.10000 0000 9120 6856National Center for Rare Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Graziamaria Paradisi
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy ,grid.12597.380000 0001 2298 9743Department for Innovation in Biological Agro-food and Forest systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
| | - Erika Zara
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy ,grid.7841.aDepartment of Biology and Biotechnology “Charles Darwin”, Università “Sapienza”, Rome, 00185 Italy
| | - Farhad Bazgir
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alban Ziegler
- grid.7252.20000 0001 2248 3363UFR Santé de l’Université d’Angers, INSERM U1083, CNRS UMR6015, MITOVASC, SFR ICAT, F-49000 Angers, France ,grid.411147.60000 0004 0472 0283Département de Génétique, CHU d’Angers, 49000 Angers, France
| | - Giovanni Chillemi
- grid.12597.380000 0001 2298 9743Department for Innovation in Biological Agro-food and Forest systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy ,grid.5326.20000 0001 1940 4177Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Centro Nazionale delle Ricerche, 70126 Bari, Italy
| | - Lucia Bertuccini
- grid.416651.10000 0000 9120 6856Servizio grandi strumentazioni e core facilities, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Antonella Tinari
- grid.416651.10000 0000 9120 6856Centro di riferimento per la medicina di genere, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Annalisa Vetro
- grid.8404.80000 0004 1757 2304Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, 50139 Florence, Italy
| | - Francesca Pantaleoni
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Simone Pizzi
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Libenzio Adrian Conti
- grid.414603.4Confocal Microscopy Core Facility, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Stefania Petrini
- grid.414603.4Confocal Microscopy Core Facility, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Alessandro Bruselles
- grid.416651.10000 0000 9120 6856Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Ingrid Guarnetti Prandi
- grid.12597.380000 0001 2298 9743Department for Innovation in Biological Agro-food and Forest systems (DIBAF), University of Tuscia, 01100 Viterbo, Italy
| | - Cecilia Mancini
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Balasubramanian Chandramouli
- grid.431603.30000 0004 1757 1950Super Computing Applications and Innovation, CINECA, 40033 Casalecchio di Reno, Italy
| | - Magalie Barth
- grid.411147.60000 0004 0472 0283Département de Génétique, CHU d’Angers, 49000 Angers, France
| | - Céline Bris
- grid.7252.20000 0001 2248 3363UFR Santé de l’Université d’Angers, INSERM U1083, CNRS UMR6015, MITOVASC, SFR ICAT, F-49000 Angers, France ,grid.411147.60000 0004 0472 0283Département de Génétique, CHU d’Angers, 49000 Angers, France
| | - Donatella Milani
- grid.414818.00000 0004 1757 8749Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Angelo Selicorni
- grid.512106.1Mariani Center for Fragile Children Pediatric Unit, Azienda Socio Sanitaria Territoriale Lariana, 22100 Como, Italy
| | - Marina Macchiaiolo
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Michaela V. Gonfiantini
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Andrea Bartuli
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Riccardo Mariani
- grid.414603.4Department of Laboratories Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Cynthia J. Curry
- grid.266102.10000 0001 2297 6811Genetic Medicine, Dept of Pediatrics, University of California San Francisco, Ca, Fresno, Ca, San Francisco, CA 94143 USA
| | - Renzo Guerrini
- grid.8404.80000 0004 1757 2304Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Meyer Children’s Hospital, University of Florence, 50139 Florence, Italy
| | - Anne Slavotinek
- grid.266102.10000 0001 2297 6811Genetic Medicine, Dept of Pediatrics, University of California San Francisco, Ca, Fresno, Ca, San Francisco, CA 94143 USA
| | - Maria Iascone
- grid.460094.f0000 0004 1757 8431Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Bruno Dallapiccola
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Mohammad Reza Ahmadian
- grid.411327.20000 0001 2176 9917Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Antonella Lauri
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Marco Tartaglia
- grid.414603.4Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
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5
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Angelotti T. Exploring the eukaryotic Yip and REEP/Yop superfamily of membrane-shaping adapter proteins (MSAPs): A cacophony or harmony of structure and function? Front Mol Biosci 2022; 9:912848. [PMID: 36060263 PMCID: PMC9437294 DOI: 10.3389/fmolb.2022.912848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Polytopic cargo proteins are synthesized and exported along the secretory pathway from the endoplasmic reticulum (ER), through the Golgi apparatus, with eventual insertion into the plasma membrane (PM). While searching for proteins that could enhance cell surface expression of olfactory receptors, a new family of proteins termed “receptor expression-enhancing proteins” or REEPs were identified. These membrane-shaping hairpin proteins serve as adapters, interacting with intracellular transport machinery, to regulate cargo protein trafficking. However, REEPs belong to a larger family of proteins, the Yip (Ypt-interacting protein) family, conserved in yeast and higher eukaryotes. To date, eighteen mammalian Yip family members, divided into four subfamilies (Yipf, REEP, Yif, and PRAF), have been identified. Yeast research has revealed many intriguing aspects of yeast Yip function, functions that have not completely been explored with mammalian Yip family members. This review and analysis will clarify the different Yip family nomenclature that have encumbered prior comparisons between yeast, plants, and eukaryotic family members, to provide a more complete understanding of their interacting proteins, membrane topology, organelle localization, and role as regulators of cargo trafficking and localization. In addition, the biological role of membrane shaping and sensing hairpin and amphipathic helical domains of various Yip proteins and their potential cellular functions will be described. Lastly, this review will discuss the concept of Yip proteins as members of a larger superfamily of membrane-shaping adapter proteins (MSAPs), proteins that both shape membranes via membrane-sensing and hairpin insertion, and well as act as adapters for protein-protein interactions. MSAPs are defined by their localization to specific membranes, ability to alter membrane structure, interactions with other proteins via specific domains, and specific interactions/effects on cargo proteins.
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6
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Jung J, Khan MM, Landry J, Halavatyi A, Machado P, Reiss M, Pepperkok R. Regulation of the COPII secretory machinery via focal adhesions and extracellular matrix signaling. J Cell Biol 2022; 221:213351. [PMID: 35829701 PMCID: PMC9284426 DOI: 10.1083/jcb.202110081] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 05/10/2022] [Accepted: 06/24/2022] [Indexed: 12/19/2022] Open
Abstract
Proteins that enter the secretory pathway are transported from their place of synthesis in the endoplasmic reticulum to the Golgi complex by COPII-coated carriers. The networks of proteins that regulate these components in response to extracellular cues have remained largely elusive. Using high-throughput microscopy, we comprehensively screened 378 cytoskeleton-associated and related proteins for their functional interaction with the coat protein complex II (COPII) components SEC23A and SEC23B. Among these, we identified a group of proteins associated with focal adhesions (FERMT2, MACF1, MAPK8IP2, NGEF, PIK3CA, and ROCK1) that led to the downregulation of SEC23A when depleted by siRNA. Changes in focal adhesions induced by plating cells on ECM also led to the downregulation of SEC23A and decreases in VSVG transport from ER to Golgi. Both the expression of SEC23A and the transport defect could be rescued by treatment with a focal adhesion kinase inhibitor. Altogether, our results identify a network of cytoskeleton-associated proteins connecting focal adhesions and ECM-related signaling with the gene expression of the COPII secretory machinery and trafficking.
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Affiliation(s)
- Juan Jung
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Muzamil Majid Khan
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Translational Lung Research Center Heidelberg, German Center for Lung Research, Heidelberg, Germany
| | - Jonathan Landry
- Core Facilities Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Aliaksandr Halavatyi
- Core Facilities Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Pedro Machado
- Core Facilities Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Miriam Reiss
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rainer Pepperkok
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Core Facilities Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Translational Lung Research Center Heidelberg, German Center for Lung Research, Heidelberg, Germany
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7
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Barone MV, Auricchio R, Nanayakkara M, Greco L, Troncone R, Auricchio S. Pivotal Role of Inflammation in Celiac Disease. Int J Mol Sci 2022; 23:ijms23137177. [PMID: 35806180 PMCID: PMC9266393 DOI: 10.3390/ijms23137177] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 01/27/2023] Open
Abstract
Celiac disease (CD) is an immune-mediated enteropathy triggered in genetically susceptible individuals by gluten-containing cereals. A central role in the pathogenesis of CD is played by the HLA-restricted gliadin-specific intestinal T cell response generated in a pro-inflammatory environment. The mechanisms that generate this pro-inflammatory environment in CD is now starting to be addressed. In vitro study on CD cells and organoids, shows that constant low-grade inflammation is present also in the absence of gluten. In vivo studies on a population at risk, show before the onset of the disease and before the introduction of gluten in the diet, cellular and metabolic alterations in the absence of a T cell-mediated response. Gluten exacerbates these constitutive alterations in vitro and in vivo. Inflammation, may have a main role in CD, adding this disease tout court to the big family of chronic inflammatory diseases. Nutrients can have pro-inflammatory or anti-inflammatory effects, also mediated by intestinal microbiota. The intestine function as a crossroad for the control of inflammation both locally and at distance. The aim of this review is to discuss the recent literature on the main role of inflammation in the natural history of CD, supported by cellular fragility with increased sensitivity to gluten and other pro-inflammatory agents.
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Affiliation(s)
- Maria Vittoria Barone
- Department of Translational Medical Science, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (R.A.); (M.N.); (L.G.); (R.T.)
- European Laboratory for the Investigation of Food Induced Disease (ELFID), University Federico II, Via S. Pansini 5, 80131 Naples, Italy;
- Correspondence:
| | - Renata Auricchio
- Department of Translational Medical Science, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (R.A.); (M.N.); (L.G.); (R.T.)
- European Laboratory for the Investigation of Food Induced Disease (ELFID), University Federico II, Via S. Pansini 5, 80131 Naples, Italy;
| | - Merlin Nanayakkara
- Department of Translational Medical Science, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (R.A.); (M.N.); (L.G.); (R.T.)
- European Laboratory for the Investigation of Food Induced Disease (ELFID), University Federico II, Via S. Pansini 5, 80131 Naples, Italy;
| | - Luigi Greco
- Department of Translational Medical Science, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (R.A.); (M.N.); (L.G.); (R.T.)
- European Laboratory for the Investigation of Food Induced Disease (ELFID), University Federico II, Via S. Pansini 5, 80131 Naples, Italy;
| | - Riccardo Troncone
- Department of Translational Medical Science, University Federico II, Via S. Pansini 5, 80131 Naples, Italy; (R.A.); (M.N.); (L.G.); (R.T.)
- European Laboratory for the Investigation of Food Induced Disease (ELFID), University Federico II, Via S. Pansini 5, 80131 Naples, Italy;
| | - Salvatore Auricchio
- European Laboratory for the Investigation of Food Induced Disease (ELFID), University Federico II, Via S. Pansini 5, 80131 Naples, Italy;
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8
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Arslan T, Pan Y, Mermelekas G, Vesterlund M, Orre LM, Lehtiö J. SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry. Nat Protoc 2022; 17:1832-1867. [PMID: 35732783 DOI: 10.1038/s41596-022-00699-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/18/2022] [Indexed: 11/09/2022]
Abstract
The molecular functions of a protein are defined by its inherent properties in relation to its environment and interaction network. Within a cell, this environment and network are defined by the subcellular location of the protein. Consequently, it is crucial to know the localization of a protein to fully understand its functions. Recently, we have developed a mass spectrometry- (MS) and bioinformatics-based pipeline to generate a proteome-wide resource for protein subcellular localization across multiple human cancer cell lines ( www.subcellbarcode.org ). Here, we present a detailed wet-lab protocol spanning from subcellular fractionation to MS-sample preparation and analysis. A key feature of this protocol is that it includes all generated cell fractions without discarding any material during the fractionation process. We also describe the subsequent quantitative MS-data analysis, machine learning-based classification, differential localization analysis and visualization of the output. For broad applicability, we evaluated the pipeline by using MS data generated by two different peptide pre-fractionation approaches, namely high-resolution isoelectric focusing and high-pH reverse-phase fractionation, as well as direct analysis without pre-fractionation by using long-gradient liquid chromatography-MS. Moreover, an R package covering the dry-lab part of the method was developed and made available through Bioconductor. The method is straightforward and robust, and the entire protocol, from cell harvest to classification output, can be performed within 1-2 weeks. The protocol enables accurate classification of proteins to 15 compartments and 4 neighborhoods, visualization of the output data and differential localization analysis including treatment-induced protein relocalization, condition-dependent localization or cell type-specific localization. The SubCellBarCode package is freely available at https://bioconductor.org/packages/devel/bioc/html/SubCellBarCode.html .
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Affiliation(s)
- Taner Arslan
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Yanbo Pan
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Georgios Mermelekas
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Mattias Vesterlund
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Lukas M Orre
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden.
| | - Janne Lehtiö
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden.
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9
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Genetic disorders of cellular trafficking. Trends Genet 2022; 38:724-751. [DOI: 10.1016/j.tig.2022.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/11/2022] [Accepted: 02/28/2022] [Indexed: 02/06/2023]
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10
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Donkervoort S, Krause N, Dergai M, Yun P, Koliwer J, Gorokhova S, Geist Hauserman J, Cummings BB, Hu Y, Smith R, Uapinyoying P, Ganesh VS, Ghosh PS, Monaghan KG, Edassery SL, Ferle PE, Silverstein S, Chao KR, Snyder M, Ellingwood S, Bharucha‐Goebel D, Iannaccone ST, Dal Peraro M, Foley AR, Savas JN, Bolduc V, Fasshauer D, Bönnemann CG, Schwake M. BET1 variants establish impaired vesicular transport as a cause for muscular dystrophy with epilepsy. EMBO Mol Med 2021; 13:e13787. [PMID: 34779586 PMCID: PMC8649873 DOI: 10.15252/emmm.202013787] [Citation(s) in RCA: 9] [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: 12/04/2020] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 12/26/2022] Open
Abstract
BET1 is required, together with its SNARE complex partners GOSR2, SEC22b, and Syntaxin-5 for fusion of endoplasmic reticulum-derived vesicles with the ER-Golgi intermediate compartment (ERGIC) and the cis-Golgi. Here, we report three individuals, from two families, with severe congenital muscular dystrophy (CMD) and biallelic variants in BET1 (P1 p.(Asp68His)/p.(Ala45Valfs*2); P2 and P3 homozygous p.(Ile51Ser)). Due to aberrant splicing and frameshifting, the variants in P1 result in low BET1 protein levels and impaired ER-to-Golgi transport. Since in silico modeling suggested that p.(Ile51Ser) interferes with binding to interaction partners other than SNARE complex subunits, we set off and identified novel BET1 interaction partners with low affinity for p.(Ile51Ser) BET1 protein compared to wild-type, among them ERGIC-53. The BET1/ERGIC-53 interaction was validated by endogenous co-immunoprecipitation with both proteins colocalizing to the ERGIC compartment. Mislocalization of ERGIC-53 was observed in P1 and P2's derived fibroblasts; while in the p.(Ile51Ser) P2 fibroblasts specifically, mutant BET1 was also mislocalized along with ERGIC-53. Thus, we establish BET1 as a novel CMD/epilepsy gene and confirm the emerging role of ER/Golgi SNAREs in CMD.
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Affiliation(s)
- Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Niklas Krause
- Biochemistry III/Faculty of ChemistryBielefeld UniversityBielefeldGermany
| | - Mykola Dergai
- Department of Fundamental NeurosciencesUniversity of LausanneLausanneSwitzerland
| | - Pomi Yun
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Judith Koliwer
- Biochemistry III/Faculty of ChemistryBielefeld UniversityBielefeldGermany
| | - Svetlana Gorokhova
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
- Service de Génétique MédicaleHôpital de la Timone, APHMMarseilleFrance
- INSERM, U1251‐MMGAix‐Marseille UniversitéMarseilleFrance
| | - Janelle Geist Hauserman
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Beryl B Cummings
- Center for Mendelian GenomicsProgram in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMAUSA
| | - Ying Hu
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | | | - Prech Uapinyoying
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
- Research for Genetic MedicineChildren's National Medical CenterWashingtonDCUSA
| | - Vijay S Ganesh
- Center for Mendelian GenomicsProgram in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMAUSA
- Department of NeurologyBrigham & Women's HospitalHarvard Medical SchoolBostonMAUSA
| | - Partha S Ghosh
- Department of NeurologyBoston Children's HospitalBostonMAUSA
| | | | - Seby L Edassery
- Department of NeurologyFeinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Pia E Ferle
- Biochemistry III/Faculty of ChemistryBielefeld UniversityBielefeldGermany
| | - Sarah Silverstein
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
- Rutgers New Jersey School of MedicineNewarkNJUSA
- Undiagnosed Diseases ProgramNational Human Genome Research InstituteNational Institute of HealthBethesdaMDUSA
| | - Katherine R Chao
- Center for Mendelian GenomicsProgram in Medical and Population GeneticsBroad Institute of MIT and HarvardCambridgeMAUSA
| | - Molly Snyder
- Department of NeurologyChildren's HealthDallasTXUSA
| | | | - Diana Bharucha‐Goebel
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
- Division of NeurologyChildren’s National Medical CenterWashingtonDCUSA
| | - Susan T Iannaccone
- Division of Pediatric NeurologyDepartments of Pediatrics, Neurology and NeurotherapeuticsUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Matteo Dal Peraro
- Institute of BioengineeringSchool of Life SciencesÉcole Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
| | - A Reghan Foley
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Jeffrey N Savas
- Department of NeurologyFeinberg School of MedicineNorthwestern UniversityChicagoILUSA
| | - Véronique Bolduc
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Dirk Fasshauer
- Department of Fundamental NeurosciencesUniversity of LausanneLausanneSwitzerland
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood SectionNational Institute of Neurological Disorders and StrokeNational Institutes of HealthBethesdaMDUSA
| | - Michael Schwake
- Biochemistry III/Faculty of ChemistryBielefeld UniversityBielefeldGermany
- Department of NeurologyFeinberg School of MedicineNorthwestern UniversityChicagoILUSA
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11
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Choe CP, Choi SY, Kee Y, Kim MJ, Kim SH, Lee Y, Park HC, Ro H. Transgenic fluorescent zebrafish lines that have revolutionized biomedical research. Lab Anim Res 2021; 37:26. [PMID: 34496973 PMCID: PMC8424172 DOI: 10.1186/s42826-021-00103-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/26/2021] [Indexed: 12/22/2022] Open
Abstract
Since its debut in the biomedical research fields in 1981, zebrafish have been used as a vertebrate model organism in more than 40,000 biomedical research studies. Especially useful are zebrafish lines expressing fluorescent proteins in a molecule, intracellular organelle, cell or tissue specific manner because they allow the visualization and tracking of molecules, intracellular organelles, cells or tissues of interest in real time and in vivo. In this review, we summarize representative transgenic fluorescent zebrafish lines that have revolutionized biomedical research on signal transduction, the craniofacial skeletal system, the hematopoietic system, the nervous system, the urogenital system, the digestive system and intracellular organelles.
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Affiliation(s)
- Chong Pyo Choe
- Division of Life Science, Gyeongsang National University, Jinju, 52828, Republic of Korea.,Division of Applied Life Science, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Seok-Yong Choi
- Department of Biomedical Sciences, Chonnam National University Medical School, Hwasun, 58128, Republic of Korea
| | - Yun Kee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Min Jung Kim
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Seok-Hyung Kim
- Department of Marine Life Sciences and Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - Yoonsung Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Hae-Chul Park
- Department of Biomedical Sciences, College of Medicine, Korea University, Ansan, 15355, Republic of Korea
| | - Hyunju Ro
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
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12
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Quiros DN, Nieto F, Mayorga LS. From cartoons to quantitative models in Golgi transport. Biol Cell 2020; 113:146-164. [PMID: 33275796 DOI: 10.1111/boc.202000107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/29/2020] [Indexed: 11/29/2022]
Abstract
BACKGROUND Cell biology is evolving to become a more formal and quantitative science. In particular, several mathematical models have been proposed to address Golgi self-organisation and protein and lipid transport. However, most scientific articles about the Golgi apparatus are still using static cartoons that miss the dynamism of this organelle. RESULTS In this report, we show that schematic drawings of Golgi trafficking can be easily translated into an agent-based model using the Repast platform. The simulations generate an active interplay among cisternae and vesicles rendering quantitative predictions about Golgi stability and transport of soluble and membrane-associated cargoes. The models can incorporate complex networks of molecular interactions and chemical reactions by association with COPASI, a software that handles ordinary differential equations. CONCLUSIONS The strategy described provides a simple, flexible and multiscale support to analyse Golgi transport. The simulations can be used to address issues directly linked to the mechanism of transport or as a way to incorporate the complexity of trafficking to other cellular processes that occur in dynamic organelles. SIGNIFICANCE We show that the rules implicitly present in most schematic representations of intracellular trafficking can be used to build dynamic models with quantitative outputs that can be compared with experimental results.
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Affiliation(s)
- D Nicolas Quiros
- IHEM, Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Mendoza, Argentina
| | - Franco Nieto
- IHEM, Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina
| | - Luis S Mayorga
- IHEM, Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Mendoza, Argentina
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13
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Zhang C, Chen Y, Sun S, Zhang Y, Wang L, Luo Z, Liu M, Dong L, Dong N, Wu Q. A conserved LDL-receptor motif regulates corin and CD320 membrane targeting in polarized renal epithelial cells. eLife 2020; 9:56059. [PMID: 33136001 PMCID: PMC7605860 DOI: 10.7554/elife.56059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 10/19/2020] [Indexed: 12/27/2022] Open
Abstract
Selective protein distribution on distinct plasma membranes is important for epithelial cell function. To date, how proteins are directed to specific epithelial cell surface is not fully understood. Here we report a conserved DSSDE motif in LDL-receptor (LDLR) modules of corin (a transmembrane serine protease) and CD320 (a receptor for vitamin B12 uptake), which regulates apical membrane targeting in renal epithelial cells. Altering this motif prevents specific apical corin and CD320 expression in polarized Madin-Darby canine kidney (MDCK) cells. Mechanistic studies indicate that this DSSDE motif participates in a Rab11a-dependent mechanism that specifies apical sorting. In MDCK cells, inhibition of Rab11a, but not Rab11b, expression leads to corin and CD320 expression on both apical and basolateral membranes. Together, our results reveal a novel molecular recognition mechanism that regulates LDLR module-containing proteins in their specific apical expression in polarized renal epithelial cells.
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Affiliation(s)
- Ce Zhang
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China
| | - Yue Chen
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China
| | - Shijin Sun
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China.,MOH Key Laboratory of Thrombosis and Hemostasis, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yikai Zhang
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China.,MOH Key Laboratory of Thrombosis and Hemostasis, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Lina Wang
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China
| | - Zhipu Luo
- Institute of Molecular Enzymology, Soochow University, Suzhou, China
| | - Meng Liu
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China
| | - Liang Dong
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China
| | - Ningzheng Dong
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China.,MOH Key Laboratory of Thrombosis and Hemostasis, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Qingyu Wu
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Prevention, Soochow University, Suzhou, China.,Cardiovascular & Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, United States
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14
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Kumar A, Ahmad A, Vyawahare A, Khan R. Membrane Trafficking and Subcellular Drug Targeting Pathways. Front Pharmacol 2020; 11:629. [PMID: 32536862 PMCID: PMC7267071 DOI: 10.3389/fphar.2020.00629] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/21/2020] [Indexed: 12/29/2022] Open
Abstract
The movement of micro and macro molecules into and within a cell significantly governs several of their pharmacokinetic and pharmacodynamic parameters, thus regulating the cellular response to exogenous and endogenous stimuli. Trafficking of various pharmacological agents and other bioactive molecules throughout and within the cell is necessary for the fidelity of the cells but has been poorly investigated. Novel strategies against cancer and microbial infections need a deeper understanding of membrane as well as subcellular trafficking pathways and essentially regulate several aspects of the initiation and spread of anti-microbial and anti-cancer drug resistance. Furthermore, in order to avail the maximum possible bioavailability and therapeutic efficacy and to restrict the unwanted toxicity of pharmacological bioactives, these sometimes need to be functionalized with targeting ligands to regulate the subcellular trafficking and to enhance the localization. In the recent past the scenario drug targeting has primarily focused on targeting tissue components and cell vicinities, however, it is the membranous and subcellular trafficking system that directs the molecules to plausible locations. The effectiveness of the delivery platforms largely depends on their physicochemical nature, intracellular barriers, and biodistribution of the drugs, pharmacokinetics and pharmacodynamic paradigms. Most subcellular organelles possess some peculiar characteristics by which membranous and subcellular targeting can be manipulated, such as negative transmembrane potential in mitochondria, intraluminal delta pH in a lysosome, and many others. Many specialized methods, which positively promote the subcellular targeting and restrict the off-targeting of the bioactive molecules, exist. Recent advancements in designing the carrier molecules enable the handling of membrane trafficking to facilitate the delivery of active compounds to subcellular localizations. This review aims to cover membrane trafficking pathways which promote the delivery of the active molecule in to the subcellular locations, the associated pathways of the subcellular drug delivery system, and the role of the carrier system in drug delivery techniques.
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Affiliation(s)
- Ajay Kumar
- Department of Nano-Therapeutics, Institute of Nano Science and Technology, Mohali, India
| | - Anas Ahmad
- Department of Nano-Therapeutics, Institute of Nano Science and Technology, Mohali, India
| | - Akshay Vyawahare
- Department of Nano-Therapeutics, Institute of Nano Science and Technology, Mohali, India
| | - Rehan Khan
- Department of Nano-Therapeutics, Institute of Nano Science and Technology, Mohali, India
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15
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Di Martino R, Sticco L, Luini A. Regulation of cargo export and sorting at the trans‐Golgi network. FEBS Lett 2019; 593:2306-2318. [DOI: 10.1002/1873-3468.13572] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/02/2019] [Accepted: 08/06/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Rosaria Di Martino
- Institute of Biochemistry and Cell Biology (IBBC) Italian National Research Council (CNR) Naples Italy
| | - Lucia Sticco
- Institute of Biochemistry and Cell Biology (IBBC) Italian National Research Council (CNR) Naples Italy
| | - Alberto Luini
- Institute of Biochemistry and Cell Biology (IBBC) Italian National Research Council (CNR) Naples Italy
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16
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Saudubray JM, Mochel F, Lamari F, Garcia-Cazorla A. Proposal for a simplified classification of IMD based on a pathophysiological approach: A practical guide for clinicians. J Inherit Metab Dis 2019; 42:706-727. [PMID: 30883825 DOI: 10.1002/jimd.12086] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 03/13/2019] [Indexed: 12/14/2022]
Abstract
In view of the rapidly expanding number of IMD discovered by next generation sequencing, we propose a simplified classification of IMD that mixes elements from a clinical diagnostic perspective and a pathophysiological approach based on three large categories. We highlight the increasing importance of complex molecule metabolism and its connection with cell biology processes. Small molecule disorders have biomarkers and are divided in two subcategories: accumulation and deficiency. Accumulation of small molecules leads to acute or progressive postnatal "intoxication", present after a symptom-free interval, aggravated by catabolism and food intake. These treatable disorders must not be missed! Deficiency of small molecules is due to impaired synthesis of compounds distal to a block or altered transport of essential molecules. This subgroup shares many clinical characteristics with complex molecule disorders. Complex molecules (like glycogen, sphingolipids, phospholipids, glycosaminoglycans, glycolipids) are poorly diffusible. Accumulation of complex molecules leads to postnatal progressive storage like in glycogen and lysosomal storage disorders. Many are treatable. Deficiency of complex molecules is related to the synthesis and recycling of these molecules, which take place in organelles. They may interfere with fœtal development. Most present as neurodevelopmental or neurodegenerative disorders unrelated to food intake. Peroxisomal disorders, CDG defects of intracellular trafficking and processing, recycling of synaptic vesicles, and tRNA synthetases also belong to this category. Only few have biomarkers and are treatable. Disorders involving primarily energy metabolism encompass defects of membrane carriers of energetic molecules as well as cytoplasmic and mitochondrial metabolic defects. This oversimplified classification is connected to the most recent available nosology of IMD.
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Affiliation(s)
- Jean-Marie Saudubray
- Groupe de Recherche Clinique Neurométabolique, Université Pierre et Marie Curie, Paris, France
| | - Fanny Mochel
- Groupe de Recherche Clinique Neurométabolique, Université Pierre et Marie Curie, Paris, France
- Centre de Référence Neurométabolique Adulte, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Sorbonne Universités, UPMC-Paris 6, UMR S 1127 and Inserm U 1127, and CNRS UMR 7225, and ICM, F-75013, Paris, France
- Département de Génétique, Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Foudil Lamari
- Groupe de Recherche Clinique Neurométabolique, Université Pierre et Marie Curie, Paris, France
- Centre de Référence Neurométabolique Adulte, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Département de Biochimie, Assistance Publique-Hôpitaux de Paris, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Angeles Garcia-Cazorla
- Neurology Department, Neurometabolic Unit and Synaptic Metabolism Lab, Institut Pediàtric de Recerca, Hospital Sant Joan de Déu, metabERN and CIBERER-ISCIII, Barcelona, Spain
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17
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Cargo Sorting at the trans-Golgi Network for Shunting into Specific Transport Routes: Role of Arf Small G Proteins and Adaptor Complexes. Cells 2019; 8:cells8060531. [PMID: 31163688 PMCID: PMC6627992 DOI: 10.3390/cells8060531] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/29/2019] [Accepted: 05/30/2019] [Indexed: 01/27/2023] Open
Abstract
The trans-Golgi network (TGN) is responsible for selectively recruiting newly synthesized cargo into transport carriers for delivery to their appropriate destination. In addition, the TGN is responsible for receiving and recycling cargo from endosomes. The membrane organization of the TGN facilitates the sorting of cargoes into distinct populations of transport vesicles. There have been significant advances in defining the molecular mechanism involved in the recognition of membrane cargoes for recruitment into different populations of transport carriers. This machinery includes cargo adaptors of the adaptor protein (AP) complex family, and monomeric Golgi-localized γ ear-containing Arf-binding protein (GGA) family, small G proteins, coat proteins, as well as accessory factors to promote budding and fission of transport vesicles. Here, we review this literature with a particular focus on the transport pathway(s) mediated by the individual cargo adaptors and the cargo motifs recognized by these adaptors. Defects in these cargo adaptors lead to a wide variety of diseases.
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18
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Labruna G, Nanayakkara M, Pagliuca C, Nunziato M, Iaffaldano L, D'Argenio V, Colicchio R, Budelli AL, Nigro R, Salvatore P, Barone MV, Sacchetti L. Celiac disease-associated Neisseria flavescens decreases mitochondrial respiration in CaCo-2 epithelial cells: Impact of Lactobacillus paracasei CBA L74 on bacterial-induced cellular imbalance. Cell Microbiol 2019; 21:e13035. [PMID: 31042331 PMCID: PMC6618323 DOI: 10.1111/cmi.13035] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 04/10/2019] [Accepted: 04/22/2019] [Indexed: 12/16/2022]
Abstract
We previously identified a Neisseria flavescens strain in the duodenum of celiac disease (CD) patients that induced immune inflammation in ex vivo duodenal mucosal explants and in CaCo‐2 cells. We also found that vesicular trafficking was delayed after the CD‐immunogenic P31‐43 gliadin peptide‐entered CaCo‐2 cells and that Lactobacillus paracasei CBA L74 (L. paracasei‐CBA) supernatant reduced peptide entry. In this study, we evaluated if metabolism and trafficking was altered in CD‐N. flavescens‐infected CaCo‐2 cells and if any alteration could be mitigated by pretreating cells with L. paracasei‐CBA supernatant, despite the presence of P31‐43. We measured CaCo‐2 bioenergetics by an extracellular flux analyser, N. flavescens and P31‐43 intracellular trafficking by immunofluorescence, cellular stress by TBARS assay, and ATP by bioluminescence. We found that CD‐N. flavescens colocalised more than control N. flavescens with early endocytic vesicles and more escaped autophagy thereby surviving longer in infected cells. P31‐43 increased colocalisation of N. flavescens with early vesicles. Mitochondrial respiration was lower (P < .05) in CD‐N. flavescens‐infected cells versus not‐treated CaCo‐2 cells, whereas pretreatment with L. paracasei‐CBA reduced CD‐N. flavescens viability and improved cell bioenergetics and trafficking. In conclusion, CD‐N. flavescens induces metabolic imbalance in CaCo‐2 cells, and the L. paracasei‐CBA probiotic could be used to correct CD‐associated dysbiosis.
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Affiliation(s)
- Giuseppe Labruna
- IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) SDN, Naples, Italy
| | - Merlin Nanayakkara
- Dipartimento di Scienze Mediche Traslazionali and European Laboratory for the Investigation of Food Induced Disease (ELFID), Università degli Studi di Napoli Federico II, Naples, Italy
| | - Chiara Pagliuca
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Marcella Nunziato
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate SCarl, Naples, Italy
| | | | - Valeria D'Argenio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy.,CEINGE-Biotecnologie Avanzate SCarl, Naples, Italy.,Task Force on Microbiome Studies, Università degli Studi di Napoli Federico II and CEINGE-Biotecnologie Avanzate SCarl, Naples, Italy
| | - Roberta Colicchio
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | | | - Roberto Nigro
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Università di Napoli Federico II, Naples, Italy
| | - Paola Salvatore
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Maria Vittoria Barone
- Dipartimento di Scienze Mediche Traslazionali and European Laboratory for the Investigation of Food Induced Disease (ELFID), Università degli Studi di Napoli Federico II, Naples, Italy
| | - Lucia Sacchetti
- CEINGE-Biotecnologie Avanzate SCarl, Naples, Italy.,Task Force on Microbiome Studies, Università degli Studi di Napoli Federico II and CEINGE-Biotecnologie Avanzate SCarl, Naples, Italy
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19
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Lania G, Nanayakkara M, Maglio M, Auricchio R, Porpora M, Conte M, De Matteis MA, Rizzo R, Luini A, Discepolo V, Troncone R, Auricchio S, Barone MV. Constitutive alterations in vesicular trafficking increase the sensitivity of cells from celiac disease patients to gliadin. Commun Biol 2019; 2:190. [PMID: 31123714 PMCID: PMC6527696 DOI: 10.1038/s42003-019-0443-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 04/19/2019] [Indexed: 02/06/2023] Open
Abstract
Celiac Disease (CD) is an autoimmune disease characterized by inflammation of the intestinal mucosa due to an immune response to wheat gliadins. Some gliadin peptides (e.g., A-gliadin P57-68) induce an adaptive Th1 pro-inflammatory response. Other gliadin peptides (e.g., A-gliadin P31-43) induce a stress/innate immune response involving interleukin 15 (IL15) and interferon α (IFN-α). In the present study, we describe a stressed/inflamed celiac cellular phenotype in enterocytes and fibroblasts probably due to an alteration in the early-recycling endosomal system. Celiac cells are more sensitive to the gliadin peptide P31-43 and IL15 than controls. This phenotype is reproduced in control cells by inducing a delay in early vesicular trafficking. This constitutive lesion might mediate the stress/innate immune response to gliadin, which can be one of the triggers of the gliadin-specific T-cell response.
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Affiliation(s)
- Giuliana Lania
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Merlin Nanayakkara
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Mariantonia Maglio
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Renata Auricchio
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Monia Porpora
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Mariangela Conte
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Maria Antonietta De Matteis
- Department of Molecular Medicine and Medical Biotechnology, University of Napoli Federico II, Via S. Pansini 5, 80131 Naples, Italy
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Riccardo Rizzo
- Institute of Protein Biochemistry—IBP-CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Alberto Luini
- Institute of Protein Biochemistry—IBP-CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Valentina Discepolo
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Riccardo Troncone
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Salvatore Auricchio
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - Maria Vittoria Barone
- Department of Translational Medical Science (Section of Pediatrics), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- European Laboratory for the Investigation of Food Induced Diseases (ELFID), University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
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20
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Crook OM, Breckels LM, Lilley KS, Kirk PD, Gatto L. A Bioconductor workflow for the Bayesian analysis of spatial proteomics. F1000Res 2019; 8:446. [PMID: 31119032 PMCID: PMC6509962 DOI: 10.12688/f1000research.18636.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/25/2019] [Indexed: 02/02/2023] Open
Abstract
Knowledge of the subcellular location of a protein gives valuable insight into its function. The field of spatial proteomics has become increasingly popular due to improved multiplexing capabilities in high-throughput mass spectrometry, which have made it possible to systematically localise thousands of proteins per experiment. In parallel with these experimental advances, improved methods for analysing spatial proteomics data have also been developed. In this workflow, we demonstrate using `pRoloc` for the Bayesian analysis of spatial proteomics data. We detail the software infrastructure and then provide step-by-step guidance of the analysis, including setting up a pipeline, assessing convergence, and interpreting downstream results. In several places we provide additional details on Bayesian analysis to provide users with a holistic view of Bayesian analysis for spatial proteomics data.
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Affiliation(s)
- Oliver M. Crook
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- MRC Biostatistics Unit, Cambridge Institute for Public Health, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Lisa M. Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Paul D.W. Kirk
- MRC Biostatistics Unit, Cambridge Institute for Public Health, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Laurent Gatto
- Université catholique de Louvain, Brussels, 1200, Belgium
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21
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Westman J, Hube B, Fairn GD. Integrity under stress: Host membrane remodelling and damage by fungal pathogens. Cell Microbiol 2019; 21:e13016. [DOI: 10.1111/cmi.13016] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/30/2019] [Accepted: 02/05/2019] [Indexed: 12/28/2022]
Affiliation(s)
- Johannes Westman
- Program in Cell Biology The Hospital for Sick Children Toronto Ontario Canada
| | - Bernhard Hube
- Department Microbial Pathogenicity Mechanisms Hans Knoell Institute Jena Germany
- Institute of Microbiology Microbial Pathogenicity Friedrich Schiller University Jena Germany
| | - Gregory D. Fairn
- Keenan Research Centre for Biomedical Sciences St. Michael's Hospital Toronto Ontario Canada
- Department of Surgery University of Toronto Toronto Ontario Canada
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22
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Geladaki A, Kočevar Britovšek N, Breckels LM, Smith TS, Vennard OL, Mulvey CM, Crook OM, Gatto L, Lilley KS. Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics. Nat Commun 2019; 10:331. [PMID: 30659192 PMCID: PMC6338729 DOI: 10.1038/s41467-018-08191-w] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/18/2018] [Indexed: 01/09/2023] Open
Abstract
The study of protein localisation has greatly benefited from high-throughput methods utilising cellular fractionation and proteomic profiling. Hyperplexed Localisation of Organelle Proteins by Isotope Tagging (hyperLOPIT) is a well-established method in this area. It achieves high-resolution separation of organelles and subcellular compartments but is relatively time- and resource-intensive. As a simpler alternative, we here develop Localisation of Organelle Proteins by Isotope Tagging after Differential ultraCentrifugation (LOPIT-DC) and compare this method to the density gradient-based hyperLOPIT approach. We confirm that high-resolution maps can be obtained using differential centrifugation down to the suborganellar and protein complex level. HyperLOPIT and LOPIT-DC yield highly similar results, facilitating the identification of isoform-specific localisations and high-confidence localisation assignment for proteins in suborganellar structures, protein complexes and signalling pathways. By combining both approaches, we present a comprehensive high-resolution dataset of human protein localisations and deliver a flexible set of protocols for subcellular proteomics.
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Affiliation(s)
- Aikaterini Geladaki
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- Department of Genetics, University of Cambridge, 20 Downing Place, Cambridge, CB2 3EJ, UK
| | - Nina Kočevar Britovšek
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Tom S Smith
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Owen L Vennard
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Claire M Mulvey
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Oliver M Crook
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- MRC Biostatistics Unit, Cambridge Institute for Public Health, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK
| | - Laurent Gatto
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
- de Duve Institute, UC Louvain, Avenue Hippocrate 75, Brussels, 1200, Belgium
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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23
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The role of membrane trafficking in the processing of amyloid precursor protein and production of amyloid peptides in Alzheimer's disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:697-712. [PMID: 30639513 DOI: 10.1016/j.bbamem.2018.11.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/25/2018] [Accepted: 11/29/2018] [Indexed: 01/18/2023]
Abstract
Alzheimer's disease (AD) is characterized by progressive accumulation of misfolded proteins, which form senile plaques and neurofibrillary tangles, and the release of inflammatory mediators by innate immune responses. β-Amyloid peptide (Aβ) is derived from sequential processing of the amyloid precursor protein (APP) by membrane-bound proteases, namely the β-secretase, BACE1, and γ-secretase. Membrane trafficking plays a key role in the regulation of APP processing as both APP and the processing secretases traffic along distinct pathways. Genome wide sequencing studies have identified several AD susceptibility genes which regulate membrane trafficking events. To understand the pathogenesis of AD it is critical that the cell biology of APP and Aβ production in neurons is well defined. This review discusses recent advances in unravelling the membrane trafficking events associated with the production of Aβ, and how AD susceptible alleles may perturb the sorting and transport of APP and BACE1. Mechanisms whereby inflammation may influence APP processing are also considered.
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24
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Crook OM, Mulvey CM, Kirk PDW, Lilley KS, Gatto L. A Bayesian mixture modelling approach for spatial proteomics. PLoS Comput Biol 2018; 14:e1006516. [PMID: 30481170 PMCID: PMC6258510 DOI: 10.1371/journal.pcbi.1006516] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/17/2018] [Indexed: 01/01/2023] Open
Abstract
Analysis of the spatial sub-cellular distribution of proteins is of vital importance to fully understand context specific protein function. Some proteins can be found with a single location within a cell, but up to half of proteins may reside in multiple locations, can dynamically re-localise, or reside within an unknown functional compartment. These considerations lead to uncertainty in associating a protein to a single location. Currently, mass spectrometry (MS) based spatial proteomics relies on supervised machine learning algorithms to assign proteins to sub-cellular locations based on common gradient profiles. However, such methods fail to quantify uncertainty associated with sub-cellular class assignment. Here we reformulate the framework on which we perform statistical analysis. We propose a Bayesian generative classifier based on Gaussian mixture models to assign proteins probabilistically to sub-cellular niches, thus proteins have a probability distribution over sub-cellular locations, with Bayesian computation performed using the expectation-maximisation (EM) algorithm, as well as Markov-chain Monte-Carlo (MCMC). Our methodology allows proteome-wide uncertainty quantification, thus adding a further layer to the analysis of spatial proteomics. Our framework is flexible, allowing many different systems to be analysed and reveals new modelling opportunities for spatial proteomics. We find our methods perform competitively with current state-of-the art machine learning methods, whilst simultaneously providing more information. We highlight several examples where classification based on the support vector machine is unable to make any conclusions, while uncertainty quantification using our approach provides biologically intriguing results. To our knowledge this is the first Bayesian model of MS-based spatial proteomics data.
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Affiliation(s)
- Oliver M. Crook
- Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Cambridge, UK
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, Cambridge Institute for Public Health, Cambridge, UK
| | - Claire M. Mulvey
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Paul D. W. Kirk
- MRC Biostatistics Unit, Cambridge Institute for Public Health, Cambridge, UK
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Laurent Gatto
- Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Cambridge, UK
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- * E-mail:
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25
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García-Cazorla À, Saudubray JM. Cellular neurometabolism: a tentative to connect cell biology and metabolism in neurology. J Inherit Metab Dis 2018; 41:1043-1054. [PMID: 30014209 PMCID: PMC6326994 DOI: 10.1007/s10545-018-0226-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/12/2018] [Accepted: 06/26/2018] [Indexed: 12/19/2022]
Abstract
It has become increasingly evident that inborn errors of metabolism (IEMs) are particularly prevalent as diseases of the nervous system and that a broader, more inclusive definition of IEM is necessary. In fact, as long as biochemistry is involved, any kind of monogenic disease can become an IEM. This new, extended definition includes new categories and mechanisms, and as a general trend will go beyond a single biochemical pathway and/or organelle, and will appear as a connection of multiple crossroads in a system biology approach.From one side, a simplified and updated classification of IEM is presented that mixes elements from the diagnostic approach with pathophysiological considerations into three large categories based on the size of molecules ("small and simple" or "large and complex") and their implication in energy metabolism. But from another side, whatever their size, metabolites involved in IEM may behave in the brain as signalling molecules, structural components and fuels, and many metabolites have more than one role. Neurometabolism is becoming more relevant, not only in relation to these new categories of diseases but also as a necessary way to explain the mechanisms of brain damage in classically defined categories of IEM. Brain metabolism, which has been largely disregarded in the traditional approach to investigating and treating neurological diseases, is a major clue and probably the next imminent "revolution" in neurology and neuroscience. Biochemistry (metabolism) and cell neurobiology need to meet. Additionally, the brain should be studied as a system (connecting different levels of complexity).
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Affiliation(s)
- Àngels García-Cazorla
- Neurometabolic Unit and Synaptic Metabolism Lab (Department of Neurology), Institut Pediàtric de Recerca. Hospital Sant Joan de Déu and CIBERER (ISCIII), Barcelona, Spain
| | - Jean-Marie Saudubray
- Department of Neurology, Neurometabolic Unit, Hopital Pitié Salpétrière, 47-83 Boulevard de l’Hopital, 75651 Paris Cedex 13, France
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26
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Alimohamadi H, Rangamani P. Modeling Membrane Curvature Generation due to Membrane⁻Protein Interactions. Biomolecules 2018; 8:E120. [PMID: 30360496 PMCID: PMC6316661 DOI: 10.3390/biom8040120] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 01/03/2023] Open
Abstract
To alter and adjust the shape of the plasma membrane, cells harness various mechanisms of curvature generation. Many of these curvature generation mechanisms rely on the interactions between peripheral membrane proteins, integral membrane proteins, and lipids in the bilayer membrane. Mathematical and computational modeling of membrane curvature generation has provided great insights into the physics underlying these processes. However, one of the challenges in modeling these processes is identifying the suitable constitutive relationships that describe the membrane free energy including protein distribution and curvature generation capability. Here, we review some of the commonly used continuum elastic membrane models that have been developed for this purpose and discuss their applications. Finally, we address some fundamental challenges that future theoretical methods need to overcome to push the boundaries of current model applications.
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Affiliation(s)
- Haleh Alimohamadi
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, CA 92093, USA.
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, CA 92093, USA.
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27
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Editorial for the special issue on "Golgi-related human disorders". Tissue Cell 2018; 49:131-132. [PMID: 28342448 DOI: 10.1016/j.tice.2017.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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28
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Ramirez-Macias I, Barlow LD, Anton C, Spang A, Roncero C, Dacks JB. Evolutionary cell biology traces the rise of the exomer complex in Fungi from an ancient eukaryotic component. Sci Rep 2018; 8:11154. [PMID: 30042439 PMCID: PMC6057913 DOI: 10.1038/s41598-018-29416-4] [Citation(s) in RCA: 5] [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: 12/20/2017] [Accepted: 07/11/2018] [Indexed: 11/22/2022] Open
Abstract
Cargo is transported from the trans-Golgi Network to the plasma membrane by adaptor complexes, which are pan-eukaryotic components. However, in yeast, cargo can also be exported by the exomer complex, a heterotetrameric protein complex consisting of two copies of Chs5, and any two members of four paralogous proteins (ChAPs). To understand the larger relevance of exomer, its phylogenetic distribution and function outside of yeast need to be explored. We find that the four ChAP proteins are derived from gene duplications after the divergence of Yarrowia from the remaining Saccharomycotina, with BC8 paralogues (Bch2 and Chs6) being more diverged relative to the BB8 paralogues (Bch1 and Bud7), suggesting neofunctionalization. Outside Ascomycota, a single preduplicate ChAP is present in nearly all Fungi and in diverse eukaryotes, but has been repeatedly lost. Chs5, however, is a fungal specific feature, appearing coincidentally with the loss of AP-4. In contrast, the ChAP protein is a wide-spread, yet uncharacterized, membrane-trafficking component, adding one more piece to the increasingly complex machinery deduced as being present in our ancient eukaryotic ancestor.
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Affiliation(s)
- Inmaculada Ramirez-Macias
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Lael D Barlow
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Carlos Anton
- Instituto de Biología Funcional y Genómica (IBFG) and Departamento de Microbiología y Genética, CSIC-Universidad de Salamanca, 37007, Salamanca, Spain
| | - Anne Spang
- Biozentrum, University of Basel, Basel, Switzerland
| | - Cesar Roncero
- Instituto de Biología Funcional y Genómica (IBFG) and Departamento de Microbiología y Genética, CSIC-Universidad de Salamanca, 37007, Salamanca, Spain
| | - Joel B Dacks
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada.
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29
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Ashikov A, Abu Bakar N, Wen XY, Niemeijer M, Rodrigues Pinto Osorio G, Brand-Arzamendi K, Hasadsri L, Hansikova H, Raymond K, Vicogne D, Ondruskova N, Simon MEH, Pfundt R, Timal S, Beumers R, Biot C, Smeets R, Kersten M, Huijben K, Linders PTA, van den Bogaart G, van Hijum SAFT, Rodenburg R, van den Heuvel LP, van Spronsen F, Honzik T, Foulquier F, van Scherpenzeel M, Lefeber DJ, Mirjam W, Han B, Helen M, Helen M, Peter VH, Jiddeke VDK, Diego M, Lars M, Katja BH, Jozef H, Majid A, Kevin C, Johann TWN. Integrating glycomics and genomics uncovers SLC10A7 as essential factor for bone mineralization by regulating post-Golgi protein transport and glycosylation. Hum Mol Genet 2018; 27:3029-3045. [DOI: 10.1093/hmg/ddy213] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/29/2018] [Indexed: 01/13/2023] Open
Affiliation(s)
- Angel Ashikov
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Nurulamin Abu Bakar
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Xiao-Yan Wen
- Zebrafish Centre for Advanced Drug Discovery & Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St Michael’s Hospital, Toronto, ON, Canada
- Department of Medicine, Physiology & Institute of Medical Science, Faculty of Medicine, University of Toronto, ON, Canada
| | - Marco Niemeijer
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Glentino Rodrigues Pinto Osorio
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Koroboshka Brand-Arzamendi
- Zebrafish Centre for Advanced Drug Discovery & Keenan Research Centre for Biomedical Science, Li Ka Shing Knowledge Institute, St Michael’s Hospital, Toronto, ON, Canada
- Department of Medicine, Physiology & Institute of Medical Science, Faculty of Medicine, University of Toronto, ON, Canada
| | - Linda Hasadsri
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Hana Hansikova
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Kimiyo Raymond
- Division of Laboratory Genetics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Dorothée Vicogne
- CNRS-UMR 8576, Structural and Functional Glycobiology Unit, FRABIO, University of Lille, 59655 Villeneuve d’Ascq, France
| | - Nina Ondruskova
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Marleen E H Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Sharita Timal
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Roel Beumers
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Christophe Biot
- CNRS-UMR 8576, Structural and Functional Glycobiology Unit, FRABIO, University of Lille, 59655 Villeneuve d’Ascq, France
| | - Roel Smeets
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Marjan Kersten
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Karin Huijben
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Peter T A Linders
- Department of Tumor Immunology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Geert van den Bogaart
- Department of Tumor Immunology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Sacha A F T van Hijum
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- NIZO, 6710 BA Ede, The Netherlands
| | - Richard Rodenburg
- Radboud Center for Mitochondrial Disorders, Translational Metabolic Laboratory, Department of Pediatrics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | | | - Francjan van Spronsen
- Division of Metabolic Diseases, Beatrix Children’s Hospital, University Medical Center Groningen, PO BOX 30.001, 9700 RB Groningen, The Netherlands
| | - Tomas Honzik
- Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Francois Foulquier
- CNRS-UMR 8576, Structural and Functional Glycobiology Unit, FRABIO, University of Lille, 59655 Villeneuve d’Ascq, France
| | - Monique van Scherpenzeel
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Dirk J Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Translational Metabolic Laboratory, Department Laboratory Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Wamelink Mirjam
- Department of Clinical Chemistry, VU University Medical Center, Amsterdam, The Netherlands
| | - Brunner Han
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Mundy Helen
- Centre for Inherited Metabolic Disease, Evelina Children's Hospital, Guys and St Thomas NHS Foundation Trust, London SE1 7EH, UK
| | - Michelakakis Helen
- Department of Enzymology and Cellular Function, Institute of Child Health, Athens, Greece
| | - van Hasselt Peter
- Department of Metabolic Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | - van de Kamp Jiddeke
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Martinelli Diego
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Research Hospital, Rome, Italy
| | - Morkrid Lars
- Department of Medical Biochemistry, Oslo University Hospital, and Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | - Alfadhel Majid
- King Abdullah International Medical Research Centre, King Saud bin Abdul Aziz University for Health Sciences, Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdul Aziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Carpenter Kevin
- NSW Biochemical Genetics Service, The Children's Hospital at Westmead, Disciplines of Genetic Medicine & Child and Adolescent Health, The University of Sydney, NSW 2145, Australia
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30
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Zappa F, Failli M, De Matteis MA. The Golgi complex in disease and therapy. Curr Opin Cell Biol 2018; 50:102-116. [PMID: 29614425 DOI: 10.1016/j.ceb.2018.03.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 03/02/2018] [Accepted: 03/11/2018] [Indexed: 10/17/2022]
Abstract
The Golgi complex occupies a strategic position in the endomembrane system and acts not only as a key trafficking and sorting station and a vital biosynthetic center for glycoproteins and lipids, but also as an active signaling hub. As such, the Golgi complex participates in the establishment and maintenance of cell compartmentalization and in general, cell processes such as cell growth and apoptosis. The different functions of the Golgi complex are executed by composite molecular machineries that have been exhaustively dissected over the last three decades. These machineries can become dysfunctional as a result of mutations in the respective encoding genes or may be hijacked by infectious agents or misregulated in the course of multifactorial diseases such as neurodegeneration and cancer. Small molecules targeting components of these machineries have been instrumental in dissecting their functions in in vitro studies and some of them have been developed or are currently under development for clinical use.
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Affiliation(s)
- Francesca Zappa
- Telethon Institute of Genetics and Medicine, Pozzuoli (Naples), Italy
| | - Mario Failli
- Telethon Institute of Genetics and Medicine, Pozzuoli (Naples), Italy
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, Pozzuoli (Naples), Italy; Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy.
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31
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Pierson CR. Gene therapy strategies for X-linked myotubular myopathy. Expert Opin Orphan Drugs 2018. [DOI: 10.1080/21678707.2018.1443807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Christopher R. Pierson
- Department of Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH, USA
- Departments of Pathology and Biomedical Education & Anatomy, The Ohio State University College of Medicine, Columbus, OH, USA
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32
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Jani P, Liu C, Zhang H, Younes K, Benson MD, Qin C. The role of bone morphogenetic proteins 2 and 4 in mouse dentinogenesis. Arch Oral Biol 2018. [PMID: 29529483 DOI: 10.1016/j.archoralbio.2018.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
OBJECTIVE The bone morphogenetic proteins (BMPs) play crucial roles in tooth development. However, several BMPs retain expression in the dentin of the fully patterned and differentiated tooth. We hypothesized that BMP signaling therefore plays a role in the function of the differentiated odontoblast, the job of which is to lay down and mineralize the dentin matrix. DESIGN We generated mice deficient in Bmp2 and 4 using a dentin matrix protein 1 (Dmp1) promoter-driven cre recombinase that was expressed in differentiated odontoblasts. RESULTS The first and second molars of these Bmp2 and Bmp4 double conditional knockout (DcKO) mice displayed reduced dentin and enlarged pulp chambers compared to cre-negative littermate controls. DcKO mouse dentin in first molars was characterized by small, disorganized dentinal fibers, a wider predentin layer, and reduced expression of dentin sialophosphoprotein (DSPP), dentin matrix protein 1 (DMP1), and bone sialoprotein (BSP). DcKO mouse odontoblasts demonstrated increased type I collagen mRNA production, indicating that the loss of BMP signaling altered the rate of collagen gene expression in these cells. Bmp2 and Bmp4 single Dmp1-cre knockout mice displayed no discernable dentin phenotype. CONCLUSIONS These data demonstrate that BMP signaling in differentiated odontoblasts is necessary for proper dentin production in mature teeth.
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Affiliation(s)
- Priyam Jani
- Department of Biomedical Sciences and Center for Craniofacial Research and Diagnosis, Texas A&M University College of Dentistry, Dallas, TX 75246, USA
| | - Chao Liu
- Department of Biomedical Sciences and Center for Craniofacial Research and Diagnosis, Texas A&M University College of Dentistry, Dallas, TX 75246, USA
| | - Hua Zhang
- Department of Biomedical Sciences and Center for Craniofacial Research and Diagnosis, Texas A&M University College of Dentistry, Dallas, TX 75246, USA
| | - Khaled Younes
- Department of Biomedical Sciences and Center for Craniofacial Research and Diagnosis, Texas A&M University College of Dentistry, Dallas, TX 75246, USA
| | - M Douglas Benson
- Department of Biomedical Sciences and Center for Craniofacial Research and Diagnosis, Texas A&M University College of Dentistry, Dallas, TX 75246, USA.
| | - Chunlin Qin
- Department of Biomedical Sciences and Center for Craniofacial Research and Diagnosis, Texas A&M University College of Dentistry, Dallas, TX 75246, USA.
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Amnionless-mediated glycosylation is crucial for cell surface targeting of cubilin in renal and intestinal cells. Sci Rep 2018; 8:2351. [PMID: 29402915 PMCID: PMC5799345 DOI: 10.1038/s41598-018-20731-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/23/2018] [Indexed: 11/10/2022] Open
Abstract
Mutations in either cubilin (CUBN) or amnionless (AMN) genes cause Imerslund–Gräsbeck syndrome (IGS), a hereditary disease characterised by anaemia attributed to selective intestinal malabsorption of cobalamin and low-molecular weight proteinuria. Although cubilin protein does not have a transmembrane segment, it functions as a multi-ligand receptor by binding to the transmembrane protein, amnionless. We established a system to quantitatively analyse membrane targeting of the protein complex in cultured renal and intestinal cells and analysed the pathogenic mechanisms of mutations found in IGS patients. A novel CUBN mutation, several previously reported CUBN missense mutations and all previously reported AMN missense mutations resulted in endoplasmic reticulum (ER) retention and completely inhibited amnionless-dependent plasma membrane expression of cubilin. The ER retention of cubilin and amnionless was confirmed in renal proximal tubular cells of a patient with IGS. Notably, the interaction between cubilin and amnionless was not sufficient, but amnionless-mediated glycosylation of cubilin was necessary for their surface expression. Quantitative mass spectrometry and mutagenesis demonstrated that N-linked glycosylation of at least 4 residues of cubilin protein was required for its surface targeting. These results delineated the molecular mechanisms of membrane trafficking of cubilin in renal and intestinal cells.
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34
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Nbeal2 interacts with Dock7, Sec16a, and Vac14. Blood 2017; 131:1000-1011. [PMID: 29187380 DOI: 10.1182/blood-2017-08-800359] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/21/2017] [Indexed: 12/11/2022] Open
Abstract
Mutations in NBEAL2, the gene encoding the scaffolding protein Nbeal2, are causal of gray platelet syndrome (GPS), a rare recessive bleeding disorder characterized by platelets lacking α-granules and progressive marrow fibrosis. We present here the interactome of Nbeal2 with additional validation by reverse immunoprecipitation of Dock7, Sec16a, and Vac14 as interactors of Nbeal2. We show that GPS-causing mutations in its BEACH domain have profound and possible effects on the interaction with Dock7 and Vac14, respectively. Proximity ligation assays show that these 2 proteins are physically proximal to Nbeal2 in human megakaryocytes. In addition, we demonstrate that Nbeal2 is primarily localized in the cytoplasm and Dock7 on the membrane of or in α-granules. Interestingly, platelets from GPS cases and Nbeal2-/- mice are almost devoid of Dock7, resulting in a profound dysregulation of its signaling pathway, leading to defective actin polymerization, platelet activation, and shape change. This study shows for the first time proteins interacting with Nbeal2 and points to the dysregulation of the canonical signaling pathway of Dock7 as a possible cause of the aberrant formation of platelets in GPS cases and Nbeal2-deficient mice.
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35
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Yin X, Kang JH, Andrianifahanana M, Wang Y, Jung MY, Hernandez DM, Leof EB. Basolateral delivery of the type I transforming growth factor beta receptor is mediated by a dominant-acting cytoplasmic motif. Mol Biol Cell 2017; 28:2701-2711. [PMID: 28768825 PMCID: PMC5620377 DOI: 10.1091/mbc.e17-05-0334] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 12/25/2022] Open
Abstract
A novel motif within the cytoplasmic tail of the type I TGF-β receptor (TβRI) controls basolateral delivery. While this element functions independent of TβRI recycling and heteromeric TGF-β receptor trafficking, it can dominantly direct an apically expressed receptor to the basolateral membrane in polarized epithelial cells. Delivery of biomolecules to the correct subcellular locales is critical for proper physiological function. To that end, we have previously determined that type I and II transforming growth factor beta (TGF-β) receptors (TβRI and TβRII, respectively) localize to the basolateral domain in polarized epithelia. While TβRII targeting was shown to be regulated by sequences between amino acids 529 and 538, the analogous region(s) within TβRI is unknown. To address that question, sequential cytoplasmic TβRI truncations and point mutations identified a targeting motif between residues 158 and 163 (VxxEED) required for basolateral TβRI expression. Further studies documented that receptor internalization, down-regulation, direct recycling, or Smad signaling were unaffected by motif mutations that caused TβRI mislocalization. However, inclusion of amino acids 148–217 containing the targeting motif was able to direct basolateral expression of the apically sorted nerve growth factor receptor (NGFR, p75; extracellular and transmembrane regions) in a dominant manner. Finally, coexpression of apically targeted type I and type II TGF-β receptors mediated Smad3 signaling from the apical membrane of polarized epithelial cells. These findings demonstrate that the absence of apical TGF-β signaling in normal epithelia is primarily a reflection of domain-specific receptor expression and not an inability to couple with the signaling machinery.
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Affiliation(s)
- Xueqian Yin
- Thoracic Diseases Research Unit, Department of Pulmonary and Critical Care Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905
| | - Jeong-Han Kang
- Thoracic Diseases Research Unit, Department of Pulmonary and Critical Care Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905
| | - Mahefatiana Andrianifahanana
- Thoracic Diseases Research Unit, Department of Pulmonary and Critical Care Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905
| | - Youli Wang
- Division of Nephrology, Augusta University, Augusta, GA 30904
| | - Mi-Yeon Jung
- Thoracic Diseases Research Unit, Department of Pulmonary and Critical Care Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905
| | - Danielle M Hernandez
- Thoracic Diseases Research Unit, Department of Pulmonary and Critical Care Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905
| | - Edward B Leof
- Thoracic Diseases Research Unit, Department of Pulmonary and Critical Care Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905
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36
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Abstract
The organization of eukaryotic cells into distinct subcompartments is vital for all functional processes, and aberrant protein localization is a hallmark of many diseases. Microscopy methods, although powerful, are usually low-throughput and dependent on the availability of fluorescent fusion proteins or highly specific and sensitive antibodies. One method that provides a global picture of the cell is localization of organelle proteins by isotope tagging (LOPIT), which combines biochemical cell fractionation using density gradient ultracentrifugation with multiplexed quantitative proteomics mass spectrometry, allowing simultaneous determination of the steady-state distribution of hundreds of proteins within organelles. Proteins are assigned to organelles based on the similarity of their gradient distribution to those of well-annotated organelle marker proteins. We have substantially re-developed our original LOPIT protocol (published by Nature Protocols in 2006) to enable the subcellular localization of thousands of proteins per experiment (hyperLOPIT), including spatial resolution at the suborganelle and large protein complex level. This Protocol Extension article integrates all elements of the hyperLOPIT pipeline, including an additional enrichment strategy for chromatin, extended multiplexing capacity of isobaric mass tags, state-of-the-art mass spectrometry methods and multivariate machine-learning approaches for analysis of spatial proteomics data. We have also created an open-source infrastructure to support analysis of quantitative mass-spectrometry-based spatial proteomics data (http://bioconductor.org/packages/pRoloc) and an accompanying interactive visualization framework (http://www. bioconductor.org/packages/pRolocGUI). The procedure we outline here is applicable to any cell culture system and requires ∼1 week to complete sample preparation steps, ∼2 d for mass spectrometry data acquisition and 1-2 d for data analysis and downstream informatics.
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37
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Tsuruta F, Okajima T, Yano S, Chiba T. Quantification of Endosome and Lysosome Motilities in Cultured Neurons Using Fluorescent Probes. J Vis Exp 2017. [PMID: 28570534 DOI: 10.3791/55488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
In the brain, membrane trafficking systems play important roles in regulating neuronal functions, such as neuronal morphology, synaptic plasticity, survival, and glial communications. To date, numerous studies have reported that defects in these systems cause various neuronal diseases. Thus, understanding the mechanisms underlying vesicle dynamics may provide influential clues that could aid in the treatment of several neuronal disorders. Here, we describe a method for quantifying vesicle motilities, such as motility distance and rate of movement, using a software plug-in for the ImageJ platform. To obtain images for quantification, we labeled neuronal endosome-lysosome structures with EGFP-tagged vesicle marker proteins and observed the movement of vesicles using a time-lapse microscopy. This method is highly useful and simplify measuring vesicle motility in neurites, such as axons and dendrites, as well as in the soma of both neurons and glial cells. Furthermore, this method can be applied to other cell lines, such as fibroblasts and endothelial cells. This approach could provide a valuable advancement of our understanding of membrane trafficking.
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Affiliation(s)
- Fuminori Tsuruta
- Graduate School of Life and Environmental Sciences, University of Tsukuba; PhD Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba; Life Science Center of Tsukuba Advanced Research Alliance (TARA), University of Tsukuba;
| | - Tomomi Okajima
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Sarasa Yano
- Graduate School of Life and Environmental Sciences, University of Tsukuba
| | - Tomoki Chiba
- Graduate School of Life and Environmental Sciences, University of Tsukuba; PhD Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba; Life Science Center of Tsukuba Advanced Research Alliance (TARA), University of Tsukuba
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38
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Wang PJ, Lin ST, Liu SH, Kuo KT, Hsu CH, Knepper MA, Yu MJ. Vasopressin-induced serine 269 phosphorylation reduces Sipa1l1 (signal-induced proliferation-associated 1 like 1)-mediated aquaporin-2 endocytosis. J Biol Chem 2017; 292:7984-7993. [PMID: 28336531 DOI: 10.1074/jbc.m117.779611] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/14/2017] [Indexed: 11/06/2022] Open
Abstract
The abundance of integral membrane proteins in the plasma membrane is determined by a dynamic balance between exocytosis and endocytosis, which can often be regulated by physiological stimuli. Here, we describe a mechanism that accounts for the ability of the peptide hormone vasopressin to regulate water excretion via a phosphorylation-dependent modulation of the PDZ domain-ligand interaction involving the water channel protein aquaporin-2. We discovered that the PDZ domain-containing protein Sipa1l1 (signal-induced proliferation-associated 1 like 1) binds to the cytoplasmic PDZ-ligand motif of aquaporin-2 and accelerates its endocytosis in the absence of vasopressin. Vasopressin-induced aquaporin-2 phosphorylation within the type I PDZ-ligand motif disrupted the interaction, in association with reduced aquaporin-2 endocytosis and prolonged plasma membrane aquaporin-2 retention. This phosphorylation-dependent alteration in the PDZ domain-ligand interaction was explained by 3D structural models, which showed a hormone-regulated mechanism that controls osmotic water transport and systemic water balance in mammals.
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Affiliation(s)
- Po-Jen Wang
- From the Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei 10051, Taiwan
| | - Shu-Ting Lin
- From the Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei 10051, Taiwan
| | - Shao-Hsuan Liu
- From the Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei 10051, Taiwan
| | - Kuang-Ting Kuo
- From the Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei 10051, Taiwan
| | - Chun-Hua Hsu
- the Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan, and
| | - Mark A Knepper
- the Systems Biology Center, NHLBI, National Institutes of Health, Bethesda, Maryland 20892-1603
| | - Ming-Jiun Yu
- From the Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei 10051, Taiwan,
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39
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Zigdon H, Meshcheriakova A, Farfel-Becker T, Volpert G, Sabanay H, Futerman AH. Altered lysosome distribution is an early neuropathological event in neurological forms of Gaucher disease. FEBS Lett 2017; 591:774-783. [PMID: 28186340 DOI: 10.1002/1873-3468.12591] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 02/01/2017] [Accepted: 02/01/2017] [Indexed: 11/08/2022]
Abstract
In the lysosomal storage disorder Gaucher disease (GD), glucosylceramide (GlcCer) accumulates due to the defective activity of glucocerebrosidase. A subset of GD patients develops neuropathology. We now show mislocalization of Limp2-positive puncta and a large reduction in the number of Lamp1-positive puncta, which are associated with impaired tubulin. These changes occur at an early stage in animal models of GD, prior to development of overt symptoms and considerably earlier than neuronal loss. Altered lysosomal localization and cytoskeleton disruption precede the neuroinflammatory pathways, axonal dystrophy and neuronal loss previously characterized in neuronal forms of GD.
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Affiliation(s)
- Hila Zigdon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Meshcheriakova
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Farfel-Becker
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Giora Volpert
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Helena Sabanay
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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40
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Gabriel SS, Belge H, Gassama A, Debaix H, Luciani A, Fehr T, Devuyst O. Bone marrow transplantation improves proximal tubule dysfunction in a mouse model of Dent disease. Kidney Int 2017; 91:842-855. [PMID: 28143656 DOI: 10.1016/j.kint.2016.11.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 11/01/2016] [Accepted: 11/23/2016] [Indexed: 01/02/2023]
Abstract
Dent disease is a rare X-linked tubulopathy caused by mutations in the endosomal chloride-proton exchanger (ClC-5) resulting in defective receptor-mediated endocytosis and severe proximal tubule dysfunction. Bone marrow transplantation has recently been shown to preserve kidney function in cystinosis, a lysosomal storage disease causing proximal tubule dysfunction. Here we test the effects of bone marrow transplantation in Clcn5Y/- mice, a faithful model for Dent disease. Transplantation of wild-type bone marrow in Clcn5Y/- mice significantly improved proximal tubule dysfunction, with decreased low-molecular-weight proteinuria, glycosuria, calciuria, and polyuria four months after transplantation, compared to Clcn5Y/- mice transplanted with ClC-5 knockout bone marrow. Bone marrow-derived cells engrafted in the interstitium, surrounding proximal tubule cells, which showed a rescue of the apical expression of ClC-5 and megalin receptors. The improvement of proximal tubule dysfunction correlated with Clcn5 gene expression in kidneys of mice transplanted with wild-type bone marrow cells. Coculture of Clcn5Y/- proximal tubule cells with bone marrow-derived cells confirmed rescue of ClC-5 and megalin, resulting in improved endocytosis. Nanotubular extensions between the engrafted bone marrow-derived cells and proximal tubule cells were observed in vivo and in vitro. No rescue was found when the formation of the tunneling nanotubes was prevented by actin depolymerization or when cells were physically separated by transwell inserts. Thus, bone marrow transplantation may rescue the epithelial phenotype due to an inherited endosomal defect. Direct contacts between bone marrow-derived cells and diseased tubular cells play a key role in the rescue mechanism.
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Affiliation(s)
- Sarah S Gabriel
- Institute of Physiology, University of Zürich, Zürich, Switzerland; Division of Nephrology, University Hospital Zürich, Zürich, Switzerland
| | - Hendrica Belge
- Institute of Physiology, University of Zürich, Zürich, Switzerland
| | - Alkaly Gassama
- Institute of Physiology, University of Zürich, Zürich, Switzerland
| | - Huguette Debaix
- Institute of Physiology, University of Zürich, Zürich, Switzerland
| | | | - Thomas Fehr
- Institute of Physiology, University of Zürich, Zürich, Switzerland; Division of Nephrology, University Hospital Zürich, Zürich, Switzerland; Department of Internal Medicine, Cantonal Hospital Graubünden, Chur, Switzerland
| | - Olivier Devuyst
- Institute of Physiology, University of Zürich, Zürich, Switzerland.
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41
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Klayman LM, Wedegaertner PB. Inducible Inhibition of Gβγ Reveals Localization-dependent Functions at the Plasma Membrane and Golgi. J Biol Chem 2016; 292:1773-1784. [PMID: 27994056 DOI: 10.1074/jbc.m116.750430] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 12/16/2016] [Indexed: 01/28/2023] Open
Abstract
Heterotrimeric G proteins signal at a variety of endomembrane locations, in addition to their canonical function at the cytoplasmic surface of the plasma membrane (PM), where they are activated by cell surface G protein-coupled receptors. Here we focus on βγ signaling at the Golgi, where βγ activates a signaling cascade, ultimately resulting in vesicle fission from the trans-Golgi network (TGN). To develop a novel molecular tool for inhibiting endogenous βγ in a spatial-temporal manner, we take advantage of a lipid association mutant of the widely used βγ inhibitor GRK2ct (GRK2ct-KERE) and the FRB/FKBP heterodimerization system. We show that GRK2ct-KERE cannot inhibit βγ function when expressed in cells, but recruitment to a specific membrane location recovers the ability of GRK2ct-KERE to inhibit βγ signaling. PM-recruited GRK2ct-KERE inhibits lysophosphatidic acid-induced phosphorylation of Akt, whereas Golgi-recruited GRK2ct-KERE inhibits cargo transport from the TGN to the PM. Moreover, we show that Golgi-recruited GRK2ct-KERE inhibits model basolaterally targeted but not apically targeted cargo delivery, for both PM-destined and secretory cargo, providing the first evidence of selectivity in terms of cargo transport regulated by βγ. Last, we show that Golgi fragmentation induced by ilimaquinone and nocodazole is blocked by βγ inhibition, demonstrating that βγ is a key regulator of multiple pathways that impact Golgi morphology. Thus, we have developed a new molecular tool, recruitable GRK2ct-KERE, to modulate βγ signaling at specific subcellular locations, and we demonstrate novel cargo selectivity for βγ regulation of TGN to PM transport and a novel role for βγ in mediating Golgi fragmentation.
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Affiliation(s)
- Lauren M Klayman
- From the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Philip B Wedegaertner
- From the Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107.
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42
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Egorov MV, Polishchuk RS. Emerging role of Cdc42-specific guanine nucleotide exchange factors as regulators of membrane trafficking in health and disease. Tissue Cell 2016; 49:157-162. [PMID: 28029388 DOI: 10.1016/j.tice.2016.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/20/2016] [Accepted: 10/18/2016] [Indexed: 01/10/2023]
Abstract
It is widely accepted that the Golgi complex operates as a main sorting station in the biosynthetic pathway. On the other hand, the Golgi complex harbors numerous signaling molecules that generate the platform for the coordination of the transduction of specific signals and of membrane transport events. A part of these processes, which require the complex integration of transport-, cytoskeleton- and polarity-associated mechanisms, is tightly regulated by molecular machineries comprising guanine nucleotide exchange factors (GEF) and their down-stream effectors, such as the small GTPase Cdc42. Dysfunction of several Cdc42-specific GEFs has been shown to cause a number of human diseases, which are associated with impaired intracellular trafficking at the level of the Golgi complex as well as in other compartments. Here we briefly overview how mutations in Cdc42-specific GEFs have an impact on the organization of intracellular trafficking fluxes and how such trafficking aberrations could be associated with a number of human disorders.
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Affiliation(s)
- M V Egorov
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy.
| | - R S Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy.
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43
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Groot-Kormelink PJ, Ferrand S, Kelley N, Bill A, Freuler F, Imbert PE, Marelli A, Gerwin N, Sivilotti LG, Miraglia L, Orth AP, Oakeley EJ, Schopfer U, Siehler S. High Throughput Random Mutagenesis and Single Molecule Real Time Sequencing of the Muscle Nicotinic Acetylcholine Receptor. PLoS One 2016; 11:e0163129. [PMID: 27649498 PMCID: PMC5029940 DOI: 10.1371/journal.pone.0163129] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/03/2016] [Indexed: 12/15/2022] Open
Abstract
High throughput random mutagenesis is a powerful tool to identify which residues are important for the function of a protein, and gain insight into its structure-function relation. The human muscle nicotinic acetylcholine receptor was used to test whether this technique previously used for monomeric receptors can be applied to a pentameric ligand-gated ion channel. A mutant library for the α1 subunit of the channel was generated by error-prone PCR, and full length sequences of all 2816 mutants were retrieved using single molecule real time sequencing. Each α1 mutant was co-transfected with wildtype β1, δ, and ε subunits, and the channel function characterized by an ion flux assay. To test whether the strategy could map the structure-function relation of this receptor, we attempted to identify mutations that conferred resistance to competitive antagonists. Mutant hits were defined as receptors that responded to the nicotinic agonist epibatidine, but were not inhibited by either α-bungarotoxin or tubocurarine. Eight α1 subunit mutant hits were identified, six of which contained mutations at position Y233 or V275 in the transmembrane domain. Three single point mutations (Y233N, Y233H, and V275M) were studied further, and found to enhance the potencies of five channel agonists tested. This suggests that the mutations made the channel resistant to the antagonists, not by impairing antagonist binding, but rather by producing a gain-of-function phenotype, e.g. increased agonist sensitivity. Our data show that random high throughput mutagenesis is applicable to multimeric proteins to discover novel functional mutants, and outlines the benefits of using single molecule real time sequencing with regards to quality control of the mutant library as well as downstream mutant data interpretation.
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Affiliation(s)
- Paul J. Groot-Kormelink
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Sandrine Ferrand
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Nicholas Kelley
- Analytical Sciences and Imaging, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Anke Bill
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Felix Freuler
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Pierre-Eloi Imbert
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Anthony Marelli
- Genomics Institute of the Novartis Research Foundation, Novartis Institutes for BioMedical Research, San Diego, California, United States of America
| | - Nicole Gerwin
- Musculoskeletal Disease Area, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Lucia G. Sivilotti
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, United Kingdom
| | - Loren Miraglia
- Genomics Institute of the Novartis Research Foundation, Novartis Institutes for BioMedical Research, San Diego, California, United States of America
| | - Anthony P. Orth
- Genomics Institute of the Novartis Research Foundation, Novartis Institutes for BioMedical Research, San Diego, California, United States of America
| | - Edward J. Oakeley
- Analytical Sciences and Imaging, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Ulrich Schopfer
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Sandra Siehler
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Basel, Switzerland
- * E-mail:
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Jansen J, Timal S, van Scherpenzeel M, Michelakakis H, Vicogne D, Ashikov A, Moraitou M, Hoischen A, Huijben K, Steenbergen G, van den Boogert M, Porta F, Calvo P, Mavrikou M, Cenacchi G, van den Bogaart G, Salomon J, Holleboom A, Rodenburg R, Drenth J, Huynen M, Wevers R, Morava E, Foulquier F, Veltman J, Lefeber D. TMEM199 Deficiency Is a Disorder of Golgi Homeostasis Characterized by Elevated Aminotransferases, Alkaline Phosphatase, and Cholesterol and Abnormal Glycosylation. Am J Hum Genet 2016; 98:322-30. [PMID: 26833330 DOI: 10.1016/j.ajhg.2015.12.011] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 12/14/2015] [Indexed: 01/01/2023] Open
Abstract
Congenital disorders of glycosylation (CDGs) form a genetically and clinically heterogeneous group of diseases with aberrant protein glycosylation as a hallmark. A subgroup of CDGs can be attributed to disturbed Golgi homeostasis. However, identification of pathogenic variants is seriously complicated by the large number of proteins involved. As part of a strategy to identify human homologs of yeast proteins that are known to be involved in Golgi homeostasis, we identified uncharacterized transmembrane protein 199 (TMEM199, previously called C17orf32) as a human homolog of yeast V-ATPase assembly factor Vph2p (also known as Vma12p). Subsequently, we analyzed raw exome-sequencing data from families affected by genetically unsolved CDGs and identified four individuals with different mutations in TMEM199. The adolescent individuals presented with a mild phenotype of hepatic steatosis, elevated aminotransferases and alkaline phosphatase, and hypercholesterolemia, as well as low serum ceruloplasmin. Affected individuals showed abnormal N- and mucin-type O-glycosylation, and mass spectrometry indicated reduced incorporation of galactose and sialic acid, as seen in other Golgi homeostasis defects. Metabolic labeling of sialic acids in fibroblasts confirmed deficient Golgi glycosylation, which was restored by lentiviral transduction with wild-type TMEM199. V5-tagged TMEM199 localized with ERGIC and COPI markers in HeLa cells, and electron microscopy of a liver biopsy showed dilated organelles suggestive of the endoplasmic reticulum and Golgi apparatus. In conclusion, we have identified TMEM199 as a protein involved in Golgi homeostasis and show that TMEM199 deficiency results in a hepatic phenotype with abnormal glycosylation.
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Endo-lysosomal dysfunction in human proximal tubular epithelial cells deficient for lysosomal cystine transporter cystinosin. PLoS One 2015; 10:e0120998. [PMID: 25811383 PMCID: PMC4374958 DOI: 10.1371/journal.pone.0120998] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 02/09/2015] [Indexed: 12/11/2022] Open
Abstract
Nephropathic cystinosis is a lysosomal storage disorder caused by mutations in the CTNS gene encoding cystine transporter cystinosin that results in accumulation of amino acid cystine in the lysosomes throughout the body and especially affects kidneys. Early manifestations of the disease include renal Fanconi syndrome, a generalized proximal tubular dysfunction. Current therapy of cystinosis is based on cystine-lowering drug cysteamine that postpones the disease progression but offers no cure for the Fanconi syndrome. We studied the mechanisms of impaired reabsorption in human proximal tubular epithelial cells (PTEC) deficient for cystinosin and investigated the endo-lysosomal compartments of cystinosin-deficient PTEC by means of light and electron microscopy. We demonstrate that cystinosin-deficient cells had abnormal shape and distribution of the endo-lysosomal compartments and impaired endocytosis, with decreased surface expression of multiligand receptors and delayed lysosomal cargo processing. Treatment with cysteamine improved surface expression and lysosomal cargo processing but did not lead to a complete restoration and had no effect on the abnormal morphology of endo-lysosomal compartments. The obtained results improve our understanding of the mechanism of proximal tubular dysfunction in cystinosis and indicate that impaired protein reabsorption can, at least partially, be explained by abnormal trafficking of endosomal vesicles.
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Protein traffic disorders: an effective high-throughput fluorescence microscopy pipeline for drug discovery. Sci Rep 2015; 5:9038. [PMID: 25762484 PMCID: PMC4356983 DOI: 10.1038/srep09038] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/13/2015] [Indexed: 12/12/2022] Open
Abstract
Plasma membrane proteins are essential molecules in the cell which mediate interactions with the exterior milieu, thus representing key drug targets for present pharma. Not surprisingly, protein traffic disorders include a large range of diseases sharing the common mechanism of failure in the respective protein to reach the plasma membrane. However, specific therapies for these diseases are remarkably lacking. Herein, we report a robust platform for drug discovery applied to a paradigmatic genetic disorder affecting intracellular trafficking – Cystic Fibrosis. This platform includes (i) two original respiratory epithelial cellular models incorporating an inducible double-tagged traffic reporter; (ii) a plasma membrane protein traffic assay for high-throughput microscopy screening; and (iii) open-source image analysis software to quantify plasma membrane protein traffic. By allowing direct scoring of compounds rescuing the basic traffic defect, this platform enables an effective drug development pipeline, which can be promptly adapted to any traffic disorder-associated protein and leverage therapy development efforts.
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Enrich C, Rentero C, Hierro A, Grewal T. Role of cholesterol in SNARE-mediated trafficking on intracellular membranes. J Cell Sci 2015; 128:1071-81. [PMID: 25653390 DOI: 10.1242/jcs.164459] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The cell surface delivery of extracellular matrix (ECM) and integrins is fundamental for cell migration in wound healing and during cancer cell metastasis. This process is not only driven by several soluble NSF attachment protein (SNAP) receptor (SNARE) proteins, which are key players in vesicle transport at the cell surface and intracellular compartments, but is also tightly modulated by cholesterol. Cholesterol-sensitive SNAREs at the cell surface are relatively well characterized, but it is less well understood how altered cholesterol levels in intracellular compartments impact on SNARE localization and function. Recent insights from structural biology, protein chemistry and cell microscopy have suggested that a subset of the SNAREs engaged in exocytic and retrograde pathways dynamically 'sense' cholesterol levels in the Golgi and endosomal membranes. Hence, the transport routes that modulate cellular cholesterol distribution appear to trigger not only a change in the location and functioning of SNAREs at the cell surface but also in endomembranes. In this Commentary, we will discuss how disrupted cholesterol transport through the Golgi and endosomal compartments ultimately controls SNARE-mediated delivery of ECM and integrins to the cell surface and, consequently, cell migration.
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Affiliation(s)
- Carlos Enrich
- Departament de Biologia Cellular, Immunologia i Neurociències, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS). Facultat de Medicina, Universitat de Barcelona, 08036-Barcelona, Spain
| | - Carles Rentero
- Departament de Biologia Cellular, Immunologia i Neurociències, Centre de Recerca Biomèdica CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS). Facultat de Medicina, Universitat de Barcelona, 08036-Barcelona, Spain
| | - Aitor Hierro
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio; IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Thomas Grewal
- Faculty of Pharmacy, University of Sydney, Sydney, NSW 2006, Australia
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Ravenscroft G, Laing NG, Bönnemann CG. Pathophysiological concepts in the congenital myopathies: blurring the boundaries, sharpening the focus. ACTA ACUST UNITED AC 2014; 138:246-68. [PMID: 25552303 DOI: 10.1093/brain/awu368] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The congenital myopathies are a diverse group of genetic skeletal muscle diseases, which typically present at birth or in early infancy. There are multiple modes of inheritance and degrees of severity (ranging from foetal akinesia, through lethality in the newborn period to milder early and later onset cases). Classically, the congenital myopathies are defined by skeletal muscle dysfunction and a non-dystrophic muscle biopsy with the presence of one or more characteristic histological features. However, mutations in multiple different genes can cause the same pathology and mutations in the same gene can cause multiple different pathologies. This is becoming ever more apparent now that, with the increasing use of next generation sequencing, a genetic diagnosis is achieved for a greater number of patients. Thus, considerable genetic and pathological overlap is emerging, blurring the classically established boundaries. At the same time, some of the pathophysiological concepts underlying the congenital myopathies are moving into sharper focus. Here we explore whether our emerging understanding of disease pathogenesis and underlying pathophysiological mechanisms, rather than a strictly gene-centric approach, will provide grounds for a different and perhaps complementary grouping of the congenital myopathies, that at the same time could help instil the development of shared potential therapeutic approaches. Stemming from recent advances in the congenital myopathy field, five key pathophysiology themes have emerged: defects in (i) sarcolemmal and intracellular membrane remodelling and excitation-contraction coupling; (ii) mitochondrial distribution and function; (iii) myofibrillar force generation; (iv) atrophy; and (v) autophagy. Based on numerous emerging lines of evidence from recent studies in cell lines and patient tissues, mouse models and zebrafish highlighting these unifying pathophysiological themes, here we review the congenital myopathies in relation to these emerging pathophysiological concepts, highlighting both areas of overlap between established entities, as well as areas of distinction within single gene disorders.
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Affiliation(s)
- Gianina Ravenscroft
- 1 Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, Western Australia, Australia
| | - Nigel G Laing
- 1 Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, Western Australia, Australia
| | - Carsten G Bönnemann
- 2 National Institute of Neurological Disorders and Stroke/NIH, Porter Neuroscience Research Centre, Bethesda, MD, USA
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Luini A, Mavelli G, Jung J, Cancino J. Control systems and coordination protocols of the secretory pathway. F1000PRIME REPORTS 2014; 6:88. [PMID: 25374666 PMCID: PMC4191269 DOI: 10.12703/p6-88] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Like other cellular modules, the secretory pathway and the Golgi complex are likely to be supervised by control systems that support homeostasis and optimal functionality under all conditions, including external and internal perturbations. Moreover, the secretory apparatus must be functionally connected with other cellular modules, such as energy metabolism and protein degradation, via specific rules of interaction, or “coordination protocols”. These regulatory devices are of fundamental importance for optimal function; however, they are generally “hidden” at steady state. The molecular components and the architecture of the control systems and coordination protocols of the secretory pathway are beginning to emerge through studies based on the use of controlled transport-specific perturbations aimed specifically at the detection and analysis of these internal regulatory devices.
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Affiliation(s)
- Alberto Luini
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Biochimica delle Proteine (IBP)Via Pietro Castellino 111, 80131 NapoliItaly
- Telethon Institute of Genetics and Medicine (TIGEM)Via Pietro Castellino 111, 80131 NapoliItaly
| | - Gabriella Mavelli
- Istituto di Analisi dei Sistemi ed Informatica Antonio Ruberti, Consiglio Nazionale delle RicercheViale Manzoni 30, 00185 RomaItaly
| | - Juan Jung
- Istituto di Ricovero e Cura a Carattere Scientifico-SDN80143 NapoliItaly
| | - Jorge Cancino
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Biochimica delle Proteine (IBP)Via Pietro Castellino 111, 80131 NapoliItaly
- Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andrés BelloQuillota 980, 2520000 Viña del MarChile
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Kanagaraj P, Gautier-Stein A, Riedel D, Schomburg C, Cerdà J, Vollack N, Dosch R. Souffle/Spastizin controls secretory vesicle maturation during zebrafish oogenesis. PLoS Genet 2014; 10:e1004449. [PMID: 24967841 PMCID: PMC4072560 DOI: 10.1371/journal.pgen.1004449] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 05/02/2014] [Indexed: 12/20/2022] Open
Abstract
During oogenesis, the egg prepares for fertilization and early embryogenesis. As a consequence, vesicle transport is very active during vitellogenesis, and oocytes are an outstanding system to study regulators of membrane trafficking. Here, we combine zebrafish genetics and the oocyte model to identify the molecular lesion underlying the zebrafish souffle (suf) mutation. We demonstrate that suf encodes the homolog of the Hereditary Spastic Paraplegia (HSP) gene SPASTIZIN (SPG15). We show that in zebrafish oocytes suf mutants accumulate Rab11b-positive vesicles, but trafficking of recycling endosomes is not affected. Instead, we detect Suf/Spastizin on cortical granules, which undergo regulated secretion. We demonstrate genetically that Suf is essential for granule maturation into secretion competent dense-core vesicles describing a novel role for Suf in vesicle maturation. Interestingly, in suf mutants immature, secretory precursors accumulate, because they fail to pinch-off Clathrin-coated buds. Moreover, pharmacological inhibition of the abscission regulator Dynamin leads to an accumulation of immature secretory granules and mimics the suf phenotype. Our results identify a novel regulator of secretory vesicle formation in the zebrafish oocyte. In addition, we describe an uncharacterized cellular mechanism for Suf/Spastizin activity during secretion, which raises the possibility of novel therapeutic avenues for HSP research. Oocytes of egg laying animals frequently represent the biggest cell type of a species. The size of the egg is a consequence of active transport processes, e.g. the import of yolk proteins, which results in the massive storage of vesicles. In addition, secretory vesicles termed cortical granules are stored in the oocyte to be discharged right after fertilization during cortical reaction, which also occurs in mammals. Their secretion leads to chorion expansion, which prevents the lethal entry of additional sperm and protects the developing embryo against physical damage. Mutants with a defect in membrane transport are successful tools to discover genes regulating vesicle formation. We molecularly identify the disrupted gene in the recessive maternal-effect mutation souffle, which encodes a homolog of human SPASTIZIN. SPASTIZIN was previously implicated in endocytosis, but our cellular analysis of mutant oocytes connects this gene also with the regulation of cortical granule exocytosis. More precisely, we show that Suf/Spastizin is crucial for the maturation of cortical granules into secretion competent vesicles describing a novel role for this protein. Since SPASITIZN causes the disease Hereditary Spastic Paraplegia in humans, our results will help to decipher the pathogenesis of this neurodegenerative disorder.
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Affiliation(s)
- Palsamy Kanagaraj
- Institut fuer Entwicklungsbiochemie, Georg-August Universitaet Goettingen, Goettingen, Germany
| | | | - Dietmar Riedel
- Max-Planck Institut fuer Biophysikalische Chemie, Goettingen, Germany
| | - Christoph Schomburg
- Institut fuer Entwicklungsbiochemie, Georg-August Universitaet Goettingen, Goettingen, Germany
| | - Joan Cerdà
- IRTA-Institute of Marine Sciences, CSIC, Barcelona, Spain
| | - Nadine Vollack
- Institut fuer Entwicklungsbiochemie, Georg-August Universitaet Goettingen, Goettingen, Germany
| | - Roland Dosch
- Institut fuer Entwicklungsbiochemie, Georg-August Universitaet Goettingen, Goettingen, Germany
- Departement de Zoologie et Biologie Animale, Universite de Geneve, Geneva, Switzerland
- * E-mail:
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