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Díez P, Pérez-Andrés M, Bøgsted M, Azkargorta M, García-Valiente R, Dégano RM, Blanco E, Mateos-Gomez S, Bárcena P, Santa Cruz S, Góngora R, Elortza F, Landeira-Viñuela A, Juanes-Velasco P, Segura V, Manzano-Román R, Almeida J, Dybkaer K, Orfao A, Fuentes M. Dynamic Intracellular Metabolic Cell Signaling Profiles During Ag-Dependent B-Cell Differentiation. Front Immunol 2021; 12:637832. [PMID: 33859640 PMCID: PMC8043114 DOI: 10.3389/fimmu.2021.637832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/10/2021] [Indexed: 11/23/2022] Open
Abstract
Human B-cell differentiation has been extensively investigated on genomic and transcriptomic grounds; however, no studies have accomplished so far detailed analysis of antigen-dependent maturation-associated human B-cell populations from a proteomic perspective. Here, we investigate for the first time the quantitative proteomic profiles of B-cells undergoing antigen-dependent maturation using a label-free LC-MS/MS approach applied on 5 purified B-cell subpopulations (naive, centroblasts, centrocytes, memory and plasma B-cells) from human tonsils (data are available via ProteomeXchange with identifier PXD006191). Our results revealed that the actual differences among these B-cell subpopulations are a combination of expression of a few maturation stage-specific proteins within each B-cell subset and maturation-associated changes in relative protein expression levels, which are related with metabolic regulation. The considerable overlap of the proteome of the 5 studied B-cell subsets strengthens the key role of the regulation of the stoichiometry of molecules associated with metabolic regulation and programming, among other signaling cascades (such as antigen recognition and presentation and cell survival) crucial for the transition between each B-cell maturation stage.
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Affiliation(s)
- Paula Díez
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Martín Pérez-Andrés
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Martin Bøgsted
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Derio, Spain
| | | | - Rosa M Dégano
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Elena Blanco
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Sheila Mateos-Gomez
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Paloma Bárcena
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Santiago Santa Cruz
- Service of Otolaryngology and Cervical Facial Pathology, University Hospital of Salamanca, Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Félix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Derio, Spain
| | - Alicia Landeira-Viñuela
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Pablo Juanes-Velasco
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Victor Segura
- Division of Hepatology and Gene Therapy, Proteomics and BioInformatics Unit, Centre for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Raúl Manzano-Román
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Julia Almeida
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Karen Dybkaer
- Department of Haematology, Aalborg University Hospital, Aalborg, Denmark
| | - Alberto Orfao
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.,Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
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2
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Filareti M, Luotti S, Pasetto L, Pignataro M, Paolella K, Messina P, Pupillo E, Filosto M, Lunetta C, Mandrioli J, Fuda G, Calvo A, Chiò A, Corbo M, Bendotti C, Beghi E, Bonetto V. Decreased Levels of Foldase and Chaperone Proteins Are Associated with an Early-Onset Amyotrophic Lateral Sclerosis. Front Mol Neurosci 2017; 10:99. [PMID: 28428745 PMCID: PMC5382314 DOI: 10.3389/fnmol.2017.00099] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/23/2017] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by a progressive upper and lower motor neuron degeneration. One of the peculiar clinical characteristics of ALS is the wide distribution in age of onset, which is probably caused by different combinations of intrinsic and exogenous factors. We investigated whether these modifying factors are converging into common pathogenic pathways leading either to an early or a late disease onset. This would imply the identification of phenotypic biomarkers, that can distinguish the two populations of ALS patients, and of relevant pathways to consider in a therapeutic intervention. Toward this aim a differential proteomic analysis was performed in peripheral blood mononuclear cells (PBMC) from a group of 16 ALS patients with an age of onset ≤55 years and a group of 16 ALS patients with an age of onset ≥75 years, and matched healthy controls. We identified 43 differentially expressed proteins in the two groups of patients. Gene ontology analysis revealed that there was a significant enrichment in annotations associated with protein folding and response to stress. We next validated a selected number of proteins belonging to this functional group in 85 patients and 83 age- and sex-matched healthy controls using immunoassays. The results of the validation study confirmed that there was a decreased level of peptidyl-prolyl cis-trans isomerase A (also known as cyclophilin A), heat shock protein HSP 90-alpha, 78 kDa glucose-regulated protein (also known as BiP) and protein deglycase DJ-1 in PBMC of ALS patients with an early onset. Similar results were obtained in PBMC and spinal cord from two SOD1G93A mouse models with an early and late disease onset. This study suggests that a different ability to upregulate proteins involved in proteostasis, such as foldase and chaperone proteins, may be at the basis of a different susceptibility to ALS, putting forward the development of therapeutic approaches aiming at boosting the protein quality control system.
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Affiliation(s)
- Melania Filareti
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy.,Department of Neurorehabilitation Sciences, Casa Cura PoliclinicoMilan, Italy
| | - Silvia Luotti
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Laura Pasetto
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Mauro Pignataro
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Katia Paolella
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Paolo Messina
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Elisabetta Pupillo
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Massimiliano Filosto
- Center for Neuromuscular Diseases and Neuropathies, Unit of Neurology, ASST Spedali Civili and University of BresciaBrescia, Italy
| | | | - Jessica Mandrioli
- Department of Neuroscience, Azienda Ospedaliero Universitaria di Modena, Ospedale Civile S. Agostino-EstenseModena, Italy
| | - Giuseppe Fuda
- ALS Center, Department of Neuroscience Rita Levi Montalcini, University of TorinoTorino, Italy
| | - Andrea Calvo
- ALS Center, Department of Neuroscience Rita Levi Montalcini, University of TorinoTorino, Italy
| | - Adriano Chiò
- ALS Center, Department of Neuroscience Rita Levi Montalcini, University of TorinoTorino, Italy
| | - Massimo Corbo
- Department of Neurorehabilitation Sciences, Casa Cura PoliclinicoMilan, Italy
| | - Caterina Bendotti
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Ettore Beghi
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
| | - Valentina Bonetto
- Istituto Di Ricerche Farmacologiche Mario Negri, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS)Milan, Italy
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3
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Giuliano S, Agresta AM, De Palma A, Viglio S, Mauri P, Fumagalli M, Iadarola P, Montalbetti L, Salvini R, Bardoni A. Proteomic analysis of lymphoblastoid cells from Nasu-Hakola patients: a step forward in our understanding of this neurodegenerative disorder. PLoS One 2014; 9:e110073. [PMID: 25470616 PMCID: PMC4254282 DOI: 10.1371/journal.pone.0110073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 09/05/2014] [Indexed: 12/31/2022] Open
Abstract
Nasu-Hakola disease (NHD) is a recessively inherited rare disorder characterized by a combination of neuropsychiatric and bone symptoms which, while being unique to this disease, do not provide a rationale for the unambiguous identification of patients. These individuals, in fact, are likely to go unrecognized either because they are considered to be affected by other kinds of dementia or by fibrous dysplasia of bone. Given that dementia in NHD has much in common with Alzheimer’s disease and other neurodegenerative disorders, it cannot be expected to achieve the differential diagnosis of this disease without performing a genetic analysis. Under this scenario, the availability of protein biomarkers would indeed provide a novel context to facilitate interpretation of symptoms and to make the precise identification of this disease possible. The work here reported was designed to generate, for the first time, protein profiles of lymphoblastoid cells from NHD patients. Two-dimensional electrophoresis (2-DE) and nano liquid chromatography-tandem mass spectrometry (nLC-MS/MS) have been applied to all components of an Italian family (seven subjects) and to five healthy subjects included as controls. Comparative analyses revealed differences in the expression profile of 21 proteins involved in glucose metabolism and information pathways as well as in stress responses.
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Affiliation(s)
- Serena Giuliano
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy; Laboratoire d'excellence-Ion channel science and therapeutics, UMR, CNRS, Nice, France
| | - Anna Maria Agresta
- Institute for Biochemical Technologies, Proteomics and Metabolomics Unit, National Research Council, Segrate (Milano), Italy
| | - Antonella De Palma
- Institute for Biochemical Technologies, Proteomics and Metabolomics Unit, National Research Council, Segrate (Milano), Italy
| | - Simona Viglio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Pierluigi Mauri
- Institute for Biochemical Technologies, Proteomics and Metabolomics Unit, National Research Council, Segrate (Milano), Italy
| | - Marco Fumagalli
- Department of Biology and Biotechnologies, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Paolo Iadarola
- Department of Biology and Biotechnologies, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Lorenza Montalbetti
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Roberta Salvini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
| | - Anna Bardoni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Pavia, Italy
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Salonen J, Rönnholm G, Kalkkinen N, Vihinen M. Proteomic changes during B cell maturation: 2D-DIGE approach. PLoS One 2013; 8:e77894. [PMID: 24205016 PMCID: PMC3812168 DOI: 10.1371/journal.pone.0077894] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 09/06/2013] [Indexed: 11/18/2022] Open
Abstract
B cells play a pivotal role in adaptive immune system, since they maintain a delicate balance between recognition and clearance of foreign pathogens and tolerance to self. During maturation, B cells progress through a series of developmental stages defined by specific phenotypic surface markers and the rearrangement and expression of immunoglobulin (Ig) genes. To get insight into B cell proteome during the maturation pathway, we studied differential protein expression in eight human cell lines, which cover four distinctive developmental stages; early pre-B, pre-B, plasma cell and immature B cell upon anti-IgM stimulation. Our two-dimensional differential gel electrophoresis (2D-DIGE) and mass spectrometry based proteomic study indicates the involvement of large number of proteins with various functions. Notably, proteins related to cytoskeleton were relatively highly expressed in early pre-B and pre-B cells, whereas plasma cell proteome contained endoplasmic reticulum and Golgi system proteins. Our long time series analysis in anti-IgM stimulated Ramos B cells revealed the dynamic regulation of cytoskeleton organization, gene expression and metabolic pathways, among others. The findings are related to cellular processes in B cells and are discussed in relation to experimental information for the proteins and pathways they are involved in. Representative 2D-DIGE maps of different B cell maturation stages are available online at http://structure.bmc.lu.se/BcellProteome/.
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Affiliation(s)
- Johanna Salonen
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
- BioMediTech, Tampere, Finland
- Research Unit, Tampere University Hospital, Tampere, Finland
| | - Gunilla Rönnholm
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Nisse Kalkkinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Mauno Vihinen
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
- BioMediTech, Tampere, Finland
- Research Unit, Tampere University Hospital, Tampere, Finland
- Department of Experimental Medical Science, Lund University, Lund, Sweden
- * E-mail:
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5
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Korte J, Fröhlich T, Kohn M, Kaspers B, Arnold GJ, Härtle S. 2D DIGE analysis of the bursa of Fabricius reveals characteristic proteome profiles for different stages of chicken B-cell development. Proteomics 2012; 13:119-33. [PMID: 23135993 DOI: 10.1002/pmic.201200177] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 09/14/2012] [Accepted: 10/05/2012] [Indexed: 11/09/2022]
Abstract
Antibody producing B-cells are an essential component of the immune system. In contrast to human and mice where B-cells develop in the bone marrow, chicken B-cells develop in defined stages in the bursa of Fabricius, a gut associated lymphoid tissue. In order to gain a better understanding of critical biological processes like immigration of B-cell precursors into the bursa anlage, their differentiation and final emigration from the bursa we analyzed the proteome dynamics of this organ during embryonic and posthatch development. Samples were taken from four representative developmental stages (embryonic day (ED) 10, ED18, day 2, and day 28) and compared in an extensive 2D DIGE approach comprising six biological replicates per time point. Cluster analysis and PCA demonstrated high reliability and reproducibility of the obtained data set and revealed distinctive proteome profiles for the selected time points, which precisely reflect the differentiation processes. One hundred fifty three protein spots with significantly different intensities were identified by MS. We detected alterations in the abundance of several proteins assigned to retinoic acid metabolism (e.g. retinal-binding protein 5) and the actin-cytoskeleton (e.g. vinculin and gelsolin). By immunohistochemistry, desmin was identified as stromal cell protein associated with the maturation of B-cell follicles. Strongest protein expression difference (10.8-fold) was observed for chloride intracellular channel 2. This protein was thus far not associated with B-cell biology but our data suggest an important function in bursa B-cell development.
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Affiliation(s)
- Julia Korte
- Department for Veterinary Science, Institute for Animal Physiology, Ludwig-Maximilians-Universität München, Munich, Germany
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6
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Vettermann C, Castor D, Mekker A, Gerrits B, Karas M, Jäck HM. Proteome profiling suggests a pro-inflammatory role for plasma cells through release of high-mobility group box 1 protein. Proteomics 2011; 11:1228-37. [PMID: 21319304 DOI: 10.1002/pmic.201000491] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 11/07/2010] [Accepted: 12/13/2010] [Indexed: 02/06/2023]
Abstract
The final step of B-cell maturation is to differentiate into plasma cells, a process that is accompanied by gross changes in subcellular organization to enable antibody secretion. To better understand this critical step in mounting a humoral immune response, we analyzed proteome dynamics during plasma cell differentiation with combined 2-DE/MS. Thirty-two identified protein spots changed in relative abundance when lipopolysaccharide (LPS)-stimulated primary B cells differentiated into antibody-secreting plasma cells. A correlative analysis of protein and transcript abundance suggested that one third of these proteins are post-transcriptionally regulated. Apart from ER-resident chaperones, lipid metabolic enzymes, and translation initiation factors, we identified several proteins that had not been previously studied in plasma cells. Among them is the transiently upregulated proteasome activator (PA) 28γ, a component of the putative nuclear proteasome. Additionally, we discovered that the non-canonical inflammatory cytokine high-mobility group box 1 (HMG1) was released from plasma cells into the extracellular milieu. This suggests a novel role for plasma cells as pro-inflammatory mediators, which has important implications for various autoimmune diseases and chronic inflammation.
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Affiliation(s)
- Christian Vettermann
- Division of Molecular Immunology, Department of Internal Medicine, Nikolaus-Fiebiger-Center for Molecular Medicine, University of Erlangen-Nürnberg, Erlangen, Germany
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7
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Blood-related proteomics. J Proteomics 2009; 73:483-507. [PMID: 19567275 DOI: 10.1016/j.jprot.2009.06.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 06/17/2009] [Accepted: 06/20/2009] [Indexed: 12/12/2022]
Abstract
Blood-related proteomics is an emerging field, recently gaining momentum. Indeed, a wealth of data is now available and a plethora of groups has contributed to add pieces to the jigsaw puzzle of protein complexity within plasma and blood cells. In this review article we purported to sail across the mare magnum of the actual knowledge in this research endeavour. The main strides in proteomic investigations on red blood cells, platelets, plasma and white blood cells are hereby presented in a chronological order. Moreover, a glance is given at prospective studies which promise to shift the focus of attention from the end product to its provider, the donor, in a sort of Kantian "Copernican revolution". A well-rounded portrait of the usefulness of proteomics in blood-related research is accurately given. In particular, proteomic tools could be adopted to follow the main steps of the blood-banking production processes (a comparison of collection methods, pathogen inactivation techniques, storage protocols). Thus proteomics has been recently transformed from a mere basic-research extremely-expensive toy into a dramatically-sensitive and efficient eye-lens to either delve into the depths of the molecular mechanisms of blood and blood components or to establish quality parameters in the blood-banking production chain totally anew.
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8
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Miguet L, Béchade G, Fornecker L, Zink E, Felden C, Gervais C, Herbrecht R, van Dorsselaer A, Mauvieux L, Sanglier-Cianferani S. Proteomic Analysis of Malignant B-Cell Derived Microparticles Reveals CD148 as a Potentially Useful Antigenic Biomarker for Mantle Cell Lymphoma Diagnosis. J Proteome Res 2009; 8:3346-54. [DOI: 10.1021/pr801102c] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laurent Miguet
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, UDS, CNRS, UMR7178, ECPM 25 rue Becquerel, 67087 Strasbourg, France, Laboratoire d’Hématologie cellulaire EA 3948, Institut d’Hématologie, Strasbourg, France, and Pôle d’Onco-Hématologie - Hôpitaux Universitaires de Strasbourg, France
| | - Guillaume Béchade
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, UDS, CNRS, UMR7178, ECPM 25 rue Becquerel, 67087 Strasbourg, France, Laboratoire d’Hématologie cellulaire EA 3948, Institut d’Hématologie, Strasbourg, France, and Pôle d’Onco-Hématologie - Hôpitaux Universitaires de Strasbourg, France
| | - Luc Fornecker
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, UDS, CNRS, UMR7178, ECPM 25 rue Becquerel, 67087 Strasbourg, France, Laboratoire d’Hématologie cellulaire EA 3948, Institut d’Hématologie, Strasbourg, France, and Pôle d’Onco-Hématologie - Hôpitaux Universitaires de Strasbourg, France
| | - Estelle Zink
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, UDS, CNRS, UMR7178, ECPM 25 rue Becquerel, 67087 Strasbourg, France, Laboratoire d’Hématologie cellulaire EA 3948, Institut d’Hématologie, Strasbourg, France, and Pôle d’Onco-Hématologie - Hôpitaux Universitaires de Strasbourg, France
| | - Claire Felden
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, UDS, CNRS, UMR7178, ECPM 25 rue Becquerel, 67087 Strasbourg, France, Laboratoire d’Hématologie cellulaire EA 3948, Institut d’Hématologie, Strasbourg, France, and Pôle d’Onco-Hématologie - Hôpitaux Universitaires de Strasbourg, France
| | - Carine Gervais
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, UDS, CNRS, UMR7178, ECPM 25 rue Becquerel, 67087 Strasbourg, France, Laboratoire d’Hématologie cellulaire EA 3948, Institut d’Hématologie, Strasbourg, France, and Pôle d’Onco-Hématologie - Hôpitaux Universitaires de Strasbourg, France
| | - Raoul Herbrecht
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, UDS, CNRS, UMR7178, ECPM 25 rue Becquerel, 67087 Strasbourg, France, Laboratoire d’Hématologie cellulaire EA 3948, Institut d’Hématologie, Strasbourg, France, and Pôle d’Onco-Hématologie - Hôpitaux Universitaires de Strasbourg, France
| | - Alain van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, UDS, CNRS, UMR7178, ECPM 25 rue Becquerel, 67087 Strasbourg, France, Laboratoire d’Hématologie cellulaire EA 3948, Institut d’Hématologie, Strasbourg, France, and Pôle d’Onco-Hématologie - Hôpitaux Universitaires de Strasbourg, France
| | - Laurent Mauvieux
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, UDS, CNRS, UMR7178, ECPM 25 rue Becquerel, 67087 Strasbourg, France, Laboratoire d’Hématologie cellulaire EA 3948, Institut d’Hématologie, Strasbourg, France, and Pôle d’Onco-Hématologie - Hôpitaux Universitaires de Strasbourg, France
| | - Sarah Sanglier-Cianferani
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC-DSA, UDS, CNRS, UMR7178, ECPM 25 rue Becquerel, 67087 Strasbourg, France, Laboratoire d’Hématologie cellulaire EA 3948, Institut d’Hématologie, Strasbourg, France, and Pôle d’Onco-Hématologie - Hôpitaux Universitaires de Strasbourg, France
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9
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Alex P, Gucek M, Li X. Applications of proteomics in the study of inflammatory bowel diseases: Current status and future directions with available technologies. Inflamm Bowel Dis 2009; 15:616-29. [PMID: 18844215 PMCID: PMC2667948 DOI: 10.1002/ibd.20652] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inflammatory bowel diseases (IBD) are chronic, heterogeneous, and multifactorial intestinal inflammatory disorders. Major challenges in IBD research include identification of major pathogenic alterations of genes/proteins as well as effective biomarkers for early diagnosis, prognosis, and prediction of therapeutic response. Since proteins govern cellular structure and biological function, a wide selection of proteomic approaches enables effective characterization of IBD pathogenesis by investigating the dynamic nature of protein expression, cellular and subcellular distribution, posttranslational modifications, and interactions at both the cellular and subcellular levels. The aims of this review are to 1) highlight the current status of proteomic studies of IBD, and 2) introduce the available and emerging proteomic technologies that have potential applications in the study of IBD. These technologies include various mass spectrometry technologies, quantitative proteomics (2D-PAGE, ICAT, SILAC, iTRAQ), protein/antibody arrays, and multi-epitope-ligand cartography. This review also presents information and methodologies, from sample selection and enrichment to protein identification, that are not only essential but also particularly relevant to IBD research. The potential future application of these technologies is expected to have a significant impact on the discovery of novel biomarkers and key pathogenic factors for IBD.
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Affiliation(s)
- Philip Alex
- Division of Gastroenterology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA
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10
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In pursuit of a super producer-alternative paths to high producing recombinant mammalian cells. Curr Opin Biotechnol 2007; 18:557-64. [PMID: 18082393 DOI: 10.1016/j.copbio.2007.10.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Revised: 10/23/2007] [Accepted: 10/29/2007] [Indexed: 01/14/2023]
Abstract
Recombinant mammalian cells are used to produce numerous, high-value protein therapeutics. Generating hyper-producing cell lines is crucial for delivery of products to ailing patients. Better understanding of the complex trait of hyperproductivity can facilitate the creation of hyper-producing cell lines. Ruminating over the reported transcriptomic and proteomic studies, we attempt to assess whether high productivity response is a result of minute changes occurring globally or large alterations observed locally at the molecular level. We present here our philosophical perspective on the alternative routes to high productivity. We contend that given the advances in genome-scale technologies and data analysis approaches, insights gained from elucidating the gene-trait relationship underlying hyperproductivity will accelerate the development of hyperproductive processes.
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Gasser B, Sauer M, Maurer M, Stadlmayr G, Mattanovich D. Transcriptomics-based identification of novel factors enhancing heterologous protein secretion in yeasts. Appl Environ Microbiol 2007; 73:6499-507. [PMID: 17766460 PMCID: PMC2075068 DOI: 10.1128/aem.01196-07] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Efficient production of heterologous proteins with yeasts and other eukaryotic hosts is often hampered by inefficient secretion of the product. Limitation of protein secretion has been attributed to a low folding rate, and a rational solution is the overexpression of proteins supporting folding, like protein disulfide isomerase (Pdi), or the unfolded protein response transcription factor Hac1. Assuming that other protein factors which are not directly involved in protein folding may also support secretion of heterologous proteins, we set out to analyze the differential transcriptome of a Pichia pastoris strain overexpressing human trypsinogen versus that of a nonexpressing strain. Five hundred twenty-four genes were identified to be significantly regulated. Excluding those genes with totally divergent functions (like, e.g., core metabolism), we reduced this number to 13 genes which were upregulated in the expression strain having potential function in the secretion machinery and in stress regulation. The respective Saccharomyces cerevisiae homologs of these genes, including the previously characterized secretion helpers PDI1, ERO1, SSO2, KAR2/BiP, and HAC1 as positive controls, were cloned and overexpressed in a P. pastoris strain expressing a human antibody Fab fragment. All genes except one showed a positive effect on Fab fragment secretion, as did the controls. Six out of these novel secretion helper factors, more precisely Bfr2 and Bmh2 (involved in protein transport), the chaperones Ssa4 and Sse1, the vacuolar ATPase subunit Cup5, and Kin2 (a protein kinase connected to exocytosis), proved their benefits for practical application in laboratory-scale production processes by increasing both specific production rates and the volumetric productivity of an antibody fragment up to 2.5-fold in fed-batch fermentations of P. pastoris.
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Affiliation(s)
- Brigitte Gasser
- Institute of Applied Microbiology, Department of Biotechnology, University of Natural Resources and Applied Life Sciences Vienna, Muthgasse 18, A-1190 Vienna, Austria
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Ollila J, Vihinen M. Immunological systems biology: Gene expression analysis of B-cell development in Ramos B-cells. Mol Immunol 2007; 44:3537-51. [PMID: 17485117 DOI: 10.1016/j.molimm.2007.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Accepted: 03/14/2007] [Indexed: 12/22/2022]
Abstract
B-cell development into antibody producing cells is a complex process that relies on the tightly controlled production of hundreds of genes and proteins. A B-cell is activated through the B-cell receptor (BCR) and this activation is modified by different co-stimulatory or inhibitory co-receptors. The concerted action of signals from BCR and from co-receptors decides the fate of the B-cells. The majority of B-cells enter apoptosis, while some of them progress through the cell cycle and become, for example, antibody producing plasma cells. We studied BCR stimulated Ramos B-cells to explore the expression of BCR pathway, cell cycle and apoptosis related genes. We followed, using microarrays, the gene expression for several days after BCR engagement. Several bioinformatics methods were used to investigate the properties and common features of co-expressed genes. Certain gene ontologies have statistically significant enrichment into clusters of similarly expressed genes. The cell signaling pathways and gene expression data were combined to reveal detailed information about biological processes and B-cell systems biology. The results provide knowledge of the development of adaptive immunity and clues about how the pathways are affected by regulation of the expression of genes.
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Affiliation(s)
- Juha Ollila
- Department of Biological and Environmental Sciences, Division of Biochemistry, University of Helsinki, Finland
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