1
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Ercan H, Resch U, Hsu F, Mitulovic G, Bileck A, Gerner C, Yang JW, Geiger M, Miller I, Zellner M. A Practical and Analytical Comparative Study of Gel-Based Top-Down and Gel-Free Bottom-Up Proteomics Including Unbiased Proteoform Detection. Cells 2023; 12:747. [PMID: 36899884 PMCID: PMC10000902 DOI: 10.3390/cells12050747] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
Proteomics is an indispensable analytical technique to study the dynamic functioning of biological systems via different proteins and their proteoforms. In recent years, bottom-up shotgun has become more popular than gel-based top-down proteomics. The current study examined the qualitative and quantitative performance of these two fundamentally different methodologies by the parallel measurement of six technical and three biological replicates of the human prostate carcinoma cell line DU145 using its two most common standard techniques, label-free shotgun and two-dimensional differential gel electrophoresis (2D-DIGE). The analytical strengths and limitations were explored, finally focusing on the unbiased detection of proteoforms, exemplified by discovering a prostate cancer-related cleavage product of pyruvate kinase M2. Label-free shotgun proteomics quickly yields an annotated proteome but with reduced robustness, as determined by three times higher technical variation compared to 2D-DIGE. At a glance, only 2D-DIGE top-down analysis provided valuable, direct stoichiometric qualitative and quantitative information from proteins to their proteoforms, even with unexpected post-translational modifications, such as proteolytic cleavage and phosphorylation. However, the 2D-DIGE technology required almost 20 times as much time per protein/proteoform characterization with more manual work. Ultimately, this work should expose both techniques' orthogonality with their different contents of data output to elucidate biological questions.
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Affiliation(s)
- Huriye Ercan
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
- Immunology Outpatient Clinic, 1090 Vienna, Austria
| | - Ulrike Resch
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Felicia Hsu
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Goran Mitulovic
- Proteomics Core Facility, Clinical Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Andrea Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, 1090 Vienna, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
- Joint Metabolome Facility, University of Vienna and Medical University of Vienna, 1090 Vienna, Austria
| | - Jae-Won Yang
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Margarethe Geiger
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Ingrid Miller
- Institute of Medical Biochemistry, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Maria Zellner
- Centre for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
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2
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Ghanem MH, Shih AJ, Khalili H, Werth EG, Chakrabarty JK, Brown LM, Simpfendorfer KR, Gregersen PK. Proteomic and Single-Cell Transcriptomic Dissection of Human Plasmacytoid Dendritic Cell Response to Influenza Virus. Front Immunol 2022; 13:814627. [PMID: 35401570 PMCID: PMC8984281 DOI: 10.3389/fimmu.2022.814627] [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: 11/14/2021] [Accepted: 02/24/2022] [Indexed: 12/12/2022] Open
Abstract
Plasmacytoid dendritic cells [pDCs] represent a rare innate immune subset uniquely endowed with the capacity to produce substantial amounts of type-I interferons. This function of pDCs is critical for effective antiviral defenses and has been implicated in autoimmunity. While IFN-I and select cytokines have been recognized as pDC secreted products, a comprehensive agnostic profiling of the pDC secretome in response to a physiologic stimulus has not been reported. We applied LC-MS/MS to catalogue the repertoire of proteins secreted by pDCs in the unperturbed condition and in response to challenge with influenza H1N1. We report the identification of a baseline pDC secretome, and the repertoire of virus-induced proteins including most type-I interferons, various cytokines, chemokines and granzyme B. Additionally, using single-cell RNA-seq [scRNA-seq], we perform multidimensional analyses of pDC transcriptional diversity immediately ex vivo and following stimulation. Our data evidence preexisting pDC heterogeneity, with subsequent highly specialized roles within the pDC population upon stimulation ranging from dedicated cytokine super-producers to cells with APC-like traits. Dynamic expression of transcription factors and surface markers characterize subclusters within activated pDCs. Integrating the proteomic and transcriptomic datasets confirms the pDC-subcluster origin of the proteins identified in the secretome. Our findings represent the most comprehensive molecular characterization of primary human pDCs at baseline, and in response to influenza virus, reported to date.
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Affiliation(s)
- Mustafa H Ghanem
- Department of Molecular Medicine, Donald & Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States.,The Institute of Molecular Medicine at The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Andrew J Shih
- The Institute of Molecular Medicine at The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Houman Khalili
- The Institute of Molecular Medicine at The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Emily G Werth
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Jayanta K Chakrabarty
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Lewis M Brown
- Quantitative Proteomics and Metabolomics Center, Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Kim R Simpfendorfer
- Department of Molecular Medicine, Donald & Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States.,The Institute of Molecular Medicine at The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Peter K Gregersen
- Department of Molecular Medicine, Donald & Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, United States.,The Institute of Molecular Medicine at The Feinstein Institutes for Medical Research, Manhasset, NY, United States
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3
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Dihazi GH, Eltoweissy M, Jahn O, Tampe B, Zeisberg M, Wülfrath HS, Müller GA, Dihazi H. The Secretome Analysis of Activated Human Renal Fibroblasts Revealed Beneficial Effect of the Modulation of the Secreted Peptidyl-Prolyl Cis-Trans Isomerase A in Kidney Fibrosis. Cells 2020; 9:cells9071724. [PMID: 32708451 PMCID: PMC7407823 DOI: 10.3390/cells9071724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023] Open
Abstract
The secretome is an important mediator in the permanent process of reciprocity between cells and their environment. Components of secretome are involved in a large number of physiological mechanisms including differentiation, migration, and extracellular matrix modulation. Alteration in secretome composition may therefore trigger cell transformation, inflammation, and diseases. In the kidney, aberrant protein secretion plays a central role in cell activation and transition and in promoting renal fibrosis onset and progression. Using comparative proteomic analyses, we investigated in the present study the impact of cell transition on renal fibroblast cells secretome. Human renal cell lines were stimulated with profibrotic hormones and cytokines, and alterations in secretome were investigated using proteomic approaches. We identified protein signatures specific for the fibrotic phenotype and investigated the impact of modeling secretome proteins on extra cellular matrix accumulation. The secretion of peptidyl-prolyl cis-trans isomerase A (PPIA) was demonstrated to be associated with fibrosis phenotype. We showed that the in-vitro inhibition of PPIA with ciclosporin A (CsA) resulted in downregulation of PPIA and fibronectin (FN1) expression and significantly reduced their secretion. Knockdown studies of PPIA in a three-dimensional (3D) cell culture model significantly impaired the secretion and accumulation of the extracellular matrix (ECM), suggesting a positive therapeutic effect on renal fibrosis progression.
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Affiliation(s)
- Gry H. Dihazi
- Institute for Clinical Chemistry/UMG-Laboratories, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (G.H.D.); (H.S.W.)
| | - Marwa Eltoweissy
- Department of Zoology, Faculty of Science, Alexandria University, Alexandria 21500, Egypt;
| | - Olaf Jahn
- Proteomics Group, Max-Planck-Institute of Experimental Medicine, Hermann-Rein-Strasse 3, D-37075 Göttingen, Germany;
| | - Björn Tampe
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (B.T.); (M.Z.); (G.A.M.)
| | - Michael Zeisberg
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (B.T.); (M.Z.); (G.A.M.)
| | - Hauke S. Wülfrath
- Institute for Clinical Chemistry/UMG-Laboratories, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (G.H.D.); (H.S.W.)
| | - Gerhard A. Müller
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (B.T.); (M.Z.); (G.A.M.)
| | - Hassan Dihazi
- Clinic for Nephrology and Rheumatology, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany; (B.T.); (M.Z.); (G.A.M.)
- Center for Biostructural Imaging of Neurodegeneration (BIN), University Medical Center Göttingen, D-37075 Göttingen, Germany
- Correspondence: ; Tel.: +49-551-399-1221; Fax: +49-551-399-1039
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4
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Secretome Analysis of Mouse Dendritic Cells Interacting with a Probiotic Strain of Lactobacillus gasseri. Nutrients 2020; 12:nu12020555. [PMID: 32093322 PMCID: PMC7071482 DOI: 10.3390/nu12020555] [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: 01/20/2020] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 12/18/2022] Open
Abstract
Probiotics play a key role in the modulation of the gut immune system in health and disease and their action is mediated by molecules exposed on the microorganism surface or secreted probiotic-derived factors. In particular, Lactobacillus gasseri OLL2809, a probiotic microorganism isolated from human feces, has the potential to modulate various immune responses. The dendritic cells (DCs) are considered the main players in orchestrating the immune response, and their contact with intestinal microbiota is crucial for the development and homeostasis of gut immunity. To gain a perspective on the molecular mechanisms involved in the maturation process of DCs and investigate factors that could modulate these processes, a differential proteomic analysis was performed on the secretome of immature DCs, mature DCs (mDCs, induced by lipopolysaccharide (LPS)), and immature DCs challenged with L. gasseri OLL2809 before treatment with LPS (LGmDCs). The maturation process of DCs was associated to profound changes in the protein secretome and probiotic pre-treatment led to a dramatic modulation of several secreted proteins of mDC, not only classical immune mediators (i.e., cytokines, complement factors, T cell Receptor ligands) but also proteins involved in the contractile and desmosome machineries. The latter data highlight a novel mechanism by which L. gasseri can modulate the maturation process of DCs, reinforcing the concept of a protective anti-inflammatory role ascribed to this probiotic strain.
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5
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Burns J, Wilding CP, L Jones R, H Huang P. Proteomic research in sarcomas - current status and future opportunities. Semin Cancer Biol 2019; 61:56-70. [PMID: 31722230 PMCID: PMC7083238 DOI: 10.1016/j.semcancer.2019.11.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/04/2019] [Indexed: 02/07/2023]
Abstract
Sarcomas are a rare group of mesenchymal cancers comprising over 70 different histological subtypes. For the majority of these diseases, the molecular understanding of the basis of their initiation and progression remains unclear. As such, limited clinical progress in prognosis or therapeutic regimens have been made over the past few decades. Proteomics techniques are being increasingly utilised in the field of sarcoma research. Proteomic research efforts have thus far focused on histological subtype characterisation for the improvement of biological understanding, as well as for the identification of candidate diagnostic, predictive, and prognostic biomarkers for use in clinic. However, the field itself is in its infancy, and none of these proteomic research findings have been translated into the clinic. In this review, we provide a brief overview of the proteomic strategies that have been employed in sarcoma research. We evaluate key proteomic studies concerning several rare and ultra-rare sarcoma subtypes including, gastrointestinal stromal tumours, osteosarcoma, liposarcoma, leiomyosarcoma, malignant rhabdoid tumours, Ewing sarcoma, myxofibrosarcoma, and alveolar soft part sarcoma. Consequently, we illustrate how routine implementation of proteomics within sarcoma research, integration of proteomics with other molecular profiling data, and incorporation of proteomics into clinical trial studies has the potential to propel the biological and clinical understanding of this group of complex rare cancers moving forward.
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Affiliation(s)
- Jessica Burns
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Christopher P Wilding
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Robin L Jones
- Division of Clinical Studies, The Institute of Cancer Research, London SW3 6JB, UK; Sarcoma Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK.
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6
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da Cunha BR, Domingos C, Stefanini ACB, Henrique T, Polachini GM, Castelo-Branco P, Tajara EH. Cellular Interactions in the Tumor Microenvironment: The Role of Secretome. J Cancer 2019; 10:4574-4587. [PMID: 31528221 PMCID: PMC6746126 DOI: 10.7150/jca.21780] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/25/2019] [Indexed: 02/06/2023] Open
Abstract
Over the past years, it has become evident that cancer initiation and progression depends on several components of the tumor microenvironment, including inflammatory and immune cells, fibroblasts, endothelial cells, adipocytes, and extracellular matrix. These components of the tumor microenvironment and the neoplastic cells interact with each other providing pro and antitumor signals. The tumor-stroma communication occurs directly between cells or via a variety of molecules secreted, such as growth factors, cytokines, chemokines and microRNAs. This secretome, which derives not only from tumor cells but also from cancer-associated stromal cells, is an important source of key regulators of the tumorigenic process. Their screening and characterization could provide useful biomarkers to improve cancer diagnosis, prognosis, and monitoring of treatment responses.
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Affiliation(s)
- Bianca Rodrigues da Cunha
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP, Brazil
| | - Célia Domingos
- Department of Biomedical Sciences and Medicine, University of Algarve, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, Faro, Portugal
| | - Ana Carolina Buzzo Stefanini
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP, Brazil
| | - Tiago Henrique
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
| | - Giovana Mussi Polachini
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
| | - Pedro Castelo-Branco
- Department of Biomedical Sciences and Medicine, University of Algarve, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, Faro, Portugal
- Algarve Biomedical Center, Gambelas, Faro, Portugal
| | - Eloiza Helena Tajara
- Department of Molecular Biology, School of Medicine of São José do Rio Preto/FAMERP, São José do Rio Preto, SP, Brazil
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, SP, Brazil
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7
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Arya S, Wiatrek-Moumoulidis D, Synowsky SA, Shirran SL, Botting CH, Powis SJ, Stewart AJ. Quantitative proteomic changes in LPS-activated monocyte-derived dendritic cells: A SWATH-MS study. Sci Rep 2019; 9:4343. [PMID: 30867486 PMCID: PMC6416353 DOI: 10.1038/s41598-019-40773-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 02/22/2019] [Indexed: 01/20/2023] Open
Abstract
Dendritic cells are key immune cells that respond to pathogens and co-ordinate many innate and adaptive immune responses. Quantitative mass spectrometry using Sequential Window Acquisition of all THeoretical fragment-ion spectra-Mass Spectrometry (SWATH-MS) was performed here to determine the global alterations in monocyte-derived dendritic cells (moDCs) in response to stimulation with lipopolysaccharide (LPS). A moDC library of 4,666 proteins was generated and proteins were quantified at 0, 6 and 24 h post-LPS stimulation using SWATH-MS. At 6 h and 24 h post-LPS exposure, the relative abundance of 227 and 282 proteins was statistically significantly altered (p-value ≤ 0.05), respectively. Functional annotation of proteins exhibiting significant changes in expression between the various time points led to the identification of clusters of proteins implicated in distinct cellular processes including interferon and interleukin signalling, endocytosis, the ER-phagosome pathway and antigen-presentation. In SWATH-MS major histocompatibility complex (MHC) class I proteins were highly upregulated at 24 h, whilst MHC class II proteins exhibited comparatively fewer changes over this period. This study provides new detailed insight into the global proteomic changes that occur in moDCs during antigen processing and presentation and further demonstrates the potential of SWATH-MS for the quantitative study of proteins involved in cellular processes.
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Affiliation(s)
- Swati Arya
- School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK.,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Dagmara Wiatrek-Moumoulidis
- School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK.,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Silvia A Synowsky
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Sally L Shirran
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Catherine H Botting
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Simon J Powis
- School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK. .,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK.
| | - Alan J Stewart
- School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK. .,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK.
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8
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Liso A, Capitanio N, Gerli R, Conese M. From fever to immunity: A new role for IGFBP-6? J Cell Mol Med 2018; 22:4588-4596. [PMID: 30117676 PMCID: PMC6156343 DOI: 10.1111/jcmm.13738] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/22/2018] [Indexed: 12/12/2022] Open
Abstract
Fever is a fundamental response to infection and a hallmark of inflammatory disease, which has been conserved and shaped through millions of years of natural selection. Although fever is able to stimulate both innate and adaptive immune responses, the very nature of all the molecular thermosensors, the timing and the detailed mechanisms translating a physical trigger into a fundamental biological response are incompletely understood. Here we discuss the consequence of hyperthermic stress in dendritic cells (DCs), and how the sole physical input is sensed as an alert stimulus triggering a complex transition in a very narrow temporal window. Importantly, we review recent findings demonstrating the significant and specific changes discovered in gene expression and in the metabolic phenotype associated with hyperthermia in DCs. Furthermore, we discuss the results that support a model based on a thermally induced autocrine signalling, which rewires and sets a metabolism checkpoint linked to immune activation of dendritic cells. Importantly, in this context, we highlight the novel regulatory functions discovered for IGFBP‐6 protein: induction of chemotaxis; capacity to increase oxidative burst and degranulation of neutrophils, ability to induce metabolic changes in DCs. Finally, we discuss the role of IGFBP‐6 in autoimmune disease and how novel mechanistic insights could lead to exploit thermal stress‐related mechanisms in the context of cancer therapy.
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Affiliation(s)
- Arcangelo Liso
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Nazzareno Capitanio
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Roberto Gerli
- Department of Medicine, University of Perugia, Perugia, Italy
| | - Massimo Conese
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
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9
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Mass Spectrometry-based Structural Analysis and Systems Immunoproteomics Strategies for Deciphering the Host Response to Endotoxin. J Mol Biol 2018; 430:2641-2660. [PMID: 29949751 DOI: 10.1016/j.jmb.2018.06.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/23/2018] [Accepted: 06/15/2018] [Indexed: 02/06/2023]
Abstract
One cause of sepsis is systemic maladaptive immune response of the host to bacteria and specifically, to Gram-negative bacterial outer-membrane glycolipid lipopolysaccharide (LPS). On the host myeloid cell surface, proinflammatory LPS activates the innate immune system via Toll-like receptor-4/myeloid differentiation factor-2 complex. Intracellularly, LPS is also sensed by the noncanonical inflammasome through caspase-11 in mice and 4/5 in humans. The minimal functional determinant for innate immune activation is the membrane anchor of LPS called lipid A. Even subtle modifications to the lipid A scaffold can enable, diminish, or abolish immune activation. Bacteria are known to modify their LPS structure during environmental stress and infection of hosts to alter cellular immune phenotypes. In this review, we describe how mass spectrometry-based structural analysis of endotoxin helped uncover major determinations of molecular pathogenesis. Through characterization of LPS modifications, we now better understand resistance to antibiotics and cationic antimicrobial peptides, as well as how the environment impacts overall endotoxin structure. In addition, mass spectrometry-based systems immunoproteomics approaches can assist in elucidating the immune response against LPS. Many regulatory proteins have been characterized through proteomics and global/targeted analysis of protein modifications, enabling the discovery and characterization of novel endotoxin-mediated protein translational modifications.
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10
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Khan MM, Koppenol-Raab M, Kuriakose M, Manes NP, Goodlett DR, Nita-Lazar A. Host-pathogen dynamics through targeted secretome analysis of stimulated macrophages. J Proteomics 2018; 189:34-38. [PMID: 29572161 DOI: 10.1016/j.jprot.2018.03.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/26/2018] [Accepted: 03/19/2018] [Indexed: 12/17/2022]
Abstract
The pattern recognition receptors (PRRs) facilitate an organism's first line of defense against interlopers and shape the overall innate immune response through sensing and sampling pathogen-associated molecular patterns (PAMPs). The Toll-like receptor (TLR) family is the prototypic PRR family. Upon recognition of PAMPs, TLRs promote MyD88 dependent and independent responses. Understanding how different PAMPs are recognized by their specific TLRs and how pathogen recognition initiates immune activation is an intense area of research. Previously, we have reported the discovery of the temporal changes in signaling cascades of macrophage proteome and secretome post-stimulation with three different PAMPs. To extend our global proteomics approach to targeted protein abundance quantification, we describe the macrophage secretome targeted proteomics assay. We chose three different pathogens that specifically stimulate diverse TLRs (TLR2, TLR4, and TLR7). Using a simple targeted proteomics approach, combining data-dependent acquisition with an inclusion list, an array of cytokines, chemokines, and transcription factors can be profiled for their secretome abundance. This strategy facilitates the profiling and validation of pathogen-specific temporal changes in the macrophage secretome.
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Affiliation(s)
- Mohd M Khan
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Marijke Koppenol-Raab
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Minna Kuriakose
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David R Goodlett
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Baltimore, MD 21201, USA
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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11
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Menga M, Trotta R, Scrima R, Pacelli C, Silvestri V, Piccoli C, Capitanio N, Liso A. Febrile temperature reprograms by redox-mediated signaling the mitochondrial metabolic phenotype in monocyte-derived dendritic cells. Biochim Biophys Acta Mol Basis Dis 2017; 1864:685-699. [PMID: 29246446 DOI: 10.1016/j.bbadis.2017.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/15/2017] [Accepted: 12/08/2017] [Indexed: 02/06/2023]
Abstract
Fever-like hyperthermia is known to stimulate innate and adaptive immune responses. Hyperthermia-induced immune stimulation is also accompanied with, and likely conditioned by, changes in the cell metabolism and, in particular, mitochondrial metabolism is now recognized to play a pivotal role in this context, both as energy supplier and as signaling platform. In this study we asked if challenging human monocyte-derived dendritic cells with a relatively short-time thermal shock in the fever-range, typically observed in humans, caused alterations in the mitochondrial oxidative metabolism. We found that following hyperthermic stress (3h exposure at 39°C) TNF-α-releasing dendritic cells undergo rewiring of the oxidative metabolism hallmarked by decrease of the mitochondrial respiratory activity and of the oxidative phosphorylation and increase of lactate production. Moreover, enhanced production of reactive oxygen and nitrogen species and accumulation of mitochondrial Ca2+ was consistently observed in hyperthermia-conditioned dendritic cells and exhibited a reciprocal interplay. The hyperthermia-induced impairment of the mitochondrial respiratory activity was (i) irreversible following re-conditioning of cells to normothermia, (ii) mimicked by exposing normothermic cells to the conditioned medium of the hyperthermia-challenged cells, (iii) largely prevented by antioxidant and inhibitors of the nitric oxide synthase and of the mitochondrial calcium porter, which also inhibited release of TNF-α. These observations combined with gene expression analysis support a model based on a thermally induced autocrine signaling, which rewires and sets a metabolism checkpoint linked to immune activation of dendritic cells.
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Affiliation(s)
- Marta Menga
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Rosa Trotta
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Rosella Scrima
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Consiglia Pacelli
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Veronica Silvestri
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy
| | - Claudia Piccoli
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy
| | - Nazzareno Capitanio
- Department of Clinical and Experimental Medicine, University of Foggia, Foggia, Italy.
| | - Arcangelo Liso
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy.
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12
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Strasser L, Dang HH, Schwarz H, Asam C, Ferreira F, Horejs-Hoeck J, Huber CG. Unbiased Quantitative Proteomics Reveals a Crucial Role of the Allergen Context for the Activation of Human Dendritic Cells. Sci Rep 2017; 7:16638. [PMID: 29192156 PMCID: PMC5709417 DOI: 10.1038/s41598-017-16726-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 11/16/2017] [Indexed: 01/01/2023] Open
Abstract
Worldwide, more than 1 billion people suffer from allergic diseases. However, until now it is not fully understood how certain proteins can induce allergic immune responses, while others cannot. Studies suggest that allergenicity is a process not only determined by properties of the allergen itself but also by costimulatory factors, that are not classically associated with allergic reactions. To investigate the allergenicity of the major birch pollen allergen Bet v 1 and the impact of adjuvants associated with pollen, e.g. lipopolysaccharide (LPS), we performed quantitative proteome analysis to study the activation of monocyte-derived dendritic cells (moDCs). Thus, we treated cells with birch pollen extract (BPE), recombinant Bet v 1, and LPS followed by proteomic profiling via high-performance liquid chromatography and tandem mass spectrometry (HPLC-MS/MS) using isobaric labelling. Enrichment and pathway analysis revealed the influence of regulated proteins especially in cytokine signalling and dendritic cell activation. We found highly regulated, but differentially expressed proteins after treatment with BPE and LPS, whereas the cellular response to Bet v 1 was limited. Our findings lead to the conclusion that Bet v 1 needs a specific “allergen context” involving cofactors apart from LPS to induce an immune response in human moDCs.
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Affiliation(s)
- L Strasser
- Department of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria
| | - H-H Dang
- Department of Molecular Biology, Division of Allergy and Immunology, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria
| | - H Schwarz
- Department of Molecular Biology, Division of Allergy and Immunology, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria
| | - C Asam
- Department of Molecular Biology, Division of Allergy and Immunology, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria
| | - F Ferreira
- Department of Molecular Biology, Division of Allergy and Immunology, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria
| | - J Horejs-Hoeck
- Department of Molecular Biology, Division of Allergy and Immunology, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria
| | - C G Huber
- Department of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunner Straße 34, 5020, Salzburg, Austria.
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13
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Bochkov V, Gesslbauer B, Mauerhofer C, Philippova M, Erne P, Oskolkova OV. Pleiotropic effects of oxidized phospholipids. Free Radic Biol Med 2017; 111:6-24. [PMID: 28027924 DOI: 10.1016/j.freeradbiomed.2016.12.034] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 12/25/2022]
Abstract
Oxidized phospholipids (OxPLs) are increasingly recognized to play a role in a variety of normal and pathological states. OxPLs were implicated in regulation of inflammation, thrombosis, angiogenesis, endothelial barrier function, immune tolerance and other important processes. Rapidly accumulating evidence suggests that OxPLs are biomarkers of atherosclerosis and other pathologies. In addition, successful application of experimental drugs based on structural scaffold of OxPLs in animal models of inflammation was recently reported. This review briefly summarizes current knowledge on generation, methods of quantification and biological activities of OxPLs. Furthermore, receptor and cellular mechanisms of these effects are discussed. The goal of the review is to give a broad overview of this class of lipid mediators inducing pleiotropic biological effects.
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Affiliation(s)
- Valery Bochkov
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Austria.
| | - Bernd Gesslbauer
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Austria
| | - Christina Mauerhofer
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Austria
| | - Maria Philippova
- Signaling Laboratory, Department of Biomedicine, Basel University Hospital, Basel, Switzerland
| | - Paul Erne
- Signaling Laboratory, Department of Biomedicine, Basel University Hospital, Basel, Switzerland
| | - Olga V Oskolkova
- Institute of Pharmaceutical Sciences, Department of Pharmaceutical Chemistry, University of Graz, Austria.
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14
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Mohr T, Haudek-Prinz V, Slany A, Grillari J, Micksche M, Gerner C. Proteome profiling in IL-1β and VEGF-activated human umbilical vein endothelial cells delineates the interlink between inflammation and angiogenesis. PLoS One 2017; 12:e0179065. [PMID: 28617818 PMCID: PMC5472280 DOI: 10.1371/journal.pone.0179065] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/23/2017] [Indexed: 12/20/2022] Open
Abstract
Endothelial cells represent major effectors in inflammation and angiogenesis, processes that drive a multitude of pathological states such as atherosclerosis and cancer. Both inflammation and angiogenesis are interconnected with each other in the sense that many pro-inflammatory proteins possess proangiogenic properties and vice versa. To elucidate this interplay further, we present a comparative proteome study of inflammatory and angiogenic activated endothelial cells. HUVEC were stimulated with interleukin 1-β and VEGF, respectively. Cultured primary cells were fractionated into secreted, cytoplasmic and nuclear protein fractions and processed for subsequent LC-MS/MS analysis. Obtained protein profiles were filtered for fraction-specific proteins to address potential cross fractional contamination, subjected to comparative computational biology analysis (GO-Term enrichment analysis, weighted gene co-expression analysis) and compared to published mRNA profiles of IL-1β respectively VEGF stimulated HUVEC. GO Term enrichment analysis and comparative pathway analysis revealed features such as NOD and NfkB signaling for inflammatory activated HUVEC and VEGF and ErB signaling for VEGF-activated HUVEC with potential crosstalk via map kinases MAP2K2. Weighted protein co-expression network analysis revealed several potential hub genes so far not associated with driver function in inflammation or angiogenesis such as HSPG2, ANXA3, and GPI. "Classical" inflammation or angiogenesis markers such as IL6, CXCL8 or CST1 were found in a less central position within the co-expression networks. In conclusion, this study reports a framework for the computational biology based analysis of proteomics data applied to cytoplasmic, nucleic and extracellular fractions of quiescent, inflammatory and angiogenic activated HUVEC. Novel potential hub genes relevant for these processes were successfully identified.
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Affiliation(s)
- Thomas Mohr
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- ScienceConsult – DI Thomas Mohr KG, Guntramsdorf, Austria
| | - Verena Haudek-Prinz
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Astrid Slany
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Johannes Grillari
- Christian Doppler Laboratory on Biotechnology of Skin Aging, Department of Biotechnology, BOKU – University of Life Sciences, Vienna, Austria
- Evercyte GmbH, Vienna, Austria
| | - Michael Micksche
- Institute of Cancer Research, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
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15
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Koppenol-Raab M, Sjoelund V, Manes NP, Gottschalk RA, Dutta B, Benet ZL, Fraser IDC, Nita-Lazar A. Proteome and Secretome Analysis Reveals Differential Post-transcriptional Regulation of Toll-like Receptor Responses. Mol Cell Proteomics 2017; 16:S172-S186. [PMID: 28235783 PMCID: PMC5393387 DOI: 10.1074/mcp.m116.064261] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 02/24/2017] [Indexed: 12/27/2022] Open
Abstract
The innate immune system is the organism's first line of defense against pathogens. Pattern recognition receptors (PRRs) are responsible for sensing the presence of pathogen-associated molecules. The prototypic PRRs, the membrane-bound receptors of the Toll-like receptor (TLR) family, recognize pathogen-associated molecular patterns (PAMPs) and initiate an innate immune response through signaling pathways that depend on the adaptor molecules MyD88 and TRIF. Deciphering the differences in the complex signaling events that lead to pathogen recognition and initiation of the correct response remains challenging. Here we report the discovery of temporal changes in the protein signaling components involved in innate immunity. Using an integrated strategy combining unbiased proteomics, transcriptomics and macrophage stimulations with three different PAMPs, we identified differences in signaling between individual TLRs and revealed specifics of pathway regulation at the protein level.
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Affiliation(s)
- Marijke Koppenol-Raab
- From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892
| | - Virginie Sjoelund
- From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892
| | - Nathan P Manes
- From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892
| | - Rachel A Gottschalk
- From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892
| | - Bhaskar Dutta
- From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892
| | - Zachary L Benet
- From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892
| | - Iain D C Fraser
- From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892
| | - Aleksandra Nita-Lazar
- From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892
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16
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Tahir A, Bileck A, Muqaku B, Niederstaetter L, Kreutz D, Mayer RL, Wolrab D, Meier SM, Slany A, Gerner C. Combined Proteome and Eicosanoid Profiling Approach for Revealing Implications of Human Fibroblasts in Chronic Inflammation. Anal Chem 2017; 89:1945-1954. [DOI: 10.1021/acs.analchem.6b04433] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Ammar Tahir
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Andrea Bileck
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Besnik Muqaku
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Laura Niederstaetter
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Dominique Kreutz
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Rupert L. Mayer
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Denise Wolrab
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Samuel M. Meier
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Astrid Slany
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Christopher Gerner
- Department of Analytical
Chemistry, Faculty of Chemistry, University of Vienna, 1090 Vienna, Austria
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17
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Herath TDK, Darveau RP, Seneviratne CJ, Wang CY, Wang Y, Jin L. Heterogeneous Porphyromonas gingivalis LPS modulates immuno-inflammatory response, antioxidant defense and cytoskeletal dynamics in human gingival fibroblasts. Sci Rep 2016; 6:29829. [PMID: 27538450 PMCID: PMC4990928 DOI: 10.1038/srep29829] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 06/22/2016] [Indexed: 12/30/2022] Open
Abstract
Periodontal (gum) disease is a highly prevalent infection and inflammation accounting for the majority of tooth loss in adult population worldwide. Porphyromonas gingivalis is a keystone periodontal pathogen and its lipopolysaccharide (PgLPS) acts as a major virulence attribute to the disease. Herein, we deciphered the overall host response of human gingival fibroblasts (HGFs) to two featured isoforms of tetra-acylated PgLPS1435/1449 and penta-acylated PgLPS1690 with reference to E. coli LPS through quantitative proteomics. This study unraveled differentially expressed novel biomarkers of immuno-inflammatory response, antioxidant defense and cytoskeletal dynamics in HGFs. PgLPS1690 greatly upregulated inflammatory proteins (e.g. cyclophilin, inducible nitric oxide synthase, annexins, galectin, cathepsins and heat shock proteins), whereas the anti-inflammatory proteins (e.g. Annexin A2 and Annexin A6) were significantly upregulated by PgLPS1435/1449. Interestingly, the antioxidants proteins such as mitochondrial manganese-containing superoxide dismutase and peroxiredoxin 5 were only upregulated by PgLPS1690. The cytoskeletal rearrangement-related proteins like myosin were differentially regulated by these PgLPS isoforms. The present study gives new insight into the biological properties of P. gingivalis LPS lipid A moiety that could critically modulate immuno-inflammatory response, antioxidant defense and cytoskeletal dynamics in HGFs, and thereby enhances our understanding of periodontal pathogenesis.
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Affiliation(s)
- Thanuja D K Herath
- National Dental Centre Singapore, Singapore.,Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | | | | | - Cun-Yu Wang
- School of Dentistry, University of California Los Angeles, Los Angeles, USA
| | - Yu Wang
- Department of Pharmacology &Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Lijian Jin
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
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18
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Zhang Y, Bottinelli D, Lisacek F, Luban J, Strambio-De-Castillia C, Varesio E, Hopfgartner G. Optimization of human dendritic cell sample preparation for mass spectrometry-based proteomic studies. Anal Biochem 2015; 484:40-50. [PMID: 25983236 PMCID: PMC4732721 DOI: 10.1016/j.ab.2015.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/04/2015] [Accepted: 05/06/2015] [Indexed: 12/11/2022]
Abstract
Dendritic cells (DCs) are specialized leukocytes that orchestrate the adaptive immune response. Mass spectrometry (MS)-based proteomic study of these cells presents technical challenges, especially when the DCs are human in origin due to the paucity of available biological material. Here, to maximize MS coverage of the global human DC proteome, different cell disruption methods, lysis conditions, protein precipitation, and protein pellet solubilization and denaturation methods were compared. Mechanical disruption of DC cell pellets under cryogenic conditions, coupled with the use of RIPA (radioimmunoprecipitation assay) buffer, was shown to be the method of choice based on total protein extraction and on the solubilization and identification of nuclear proteins. Precipitation by acetone was found to be more efficient than that by 10% trichloroacetic acid (TCA)/acetone, allowing in excess of 28% more protein identifications. Although being an effective strategy to eliminate the detergent residue, the acetone wash step caused a loss of protein identifications. However, this potential drawback was overcome by adding 1% sodium deoxycholate into the dissolution buffer, which enhanced both solubility of the precipitated proteins and digestion efficiency. This in turn resulted in 6 to 11% more distinct peptides and 14 to 19% more total proteins identified than using 0.5M triethylammonium bicarbonate alone, with the greatest increase (34%) for hydrophobic proteins.
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Affiliation(s)
- Ying Zhang
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Dario Bottinelli
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1211 Geneva 4, Switzerland; Faculty of Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | | | - Emmanuel Varesio
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, CH-1211 Geneva 4, Switzerland.
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19
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Autonomous inhibition of apoptosis correlates with responsiveness of colon carcinoma cell lines to ciglitazone. PLoS One 2014; 9:e114158. [PMID: 25502518 PMCID: PMC4263530 DOI: 10.1371/journal.pone.0114158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 11/04/2014] [Indexed: 01/05/2023] Open
Abstract
Colorectal cancer is a leading cause of mortality worldwide. Resistance to therapy is common and often results in patients succumbing to the disease. The mechanisms of resistance are poorly understood. Cells basically have two possibilities to survive a treatment with potentially apoptosis-inducing substances. They can make use of their existing proteins to counteract the induced reactions or quickly upregulate protective factors to evade the apoptotic signal. To identify protein patterns involved in resistance to apoptosis, we studied two colorectal adenocarcinoma cell lines with different growth responses to low-molar concentrations of the thiazolidinedione Ciglitazone: HT29 cells underwent apoptosis, whereas SW480 cells increased cell number. Fluorescence detection and autoradiography scans of 2D-PAGE gels were performed in both cell lines to assess protein synthesis and turnover, respectively. To verify the data we performed shotgun analysis using the same treatment procedure as in 2D-experiments. Biological functions of the identified proteins were mainly associated with apoptosis regulation, chaperoning, intrinsic inflammation, and DNA repair. The present study suggests that different growth response of two colorectal carcinoma cell lines after treatment with Ciglitazone results from cell-specific protein synthesis and differences in protein regulation.
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20
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Slany A, Meshcheryakova A, Beer A, Ankersmit HJ, Paulitschke V, Gerner C. Plasticity of fibroblasts demonstrated by tissue-specific and function-related proteome profiling. Clin Proteomics 2014; 11:41. [PMID: 26029019 PMCID: PMC4448269 DOI: 10.1186/1559-0275-11-41] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 10/17/2014] [Indexed: 01/15/2023] Open
Abstract
Background Fibroblasts are mesenchymal stromal cells which occur in all tissue types. While their main function is related to ECM production and physical support, they are also important players in wound healing, and have further been recognized to be able to modulate inflammatory processes and support tumor growth. Fibroblasts can display distinct phenotypes, depending on their tissue origin, as well as on their functional state. Results In order to contribute to the proteomic characterization of fibroblasts, we have isolated primary human fibroblasts from human skin, lung and bone marrow and generated proteome profiles of these cells by LC-MS/MS. Comparative proteome profiling revealed characteristic differences therein, which seemed to be related to the cell’s tissue origin. Furthermore, the cells were treated in vitro with the pro-inflammatory cytokine IL-1beta. While all fibroblasts induced the secretion of Interleukins IL-6 and IL-8 and the chemokine GRO-alpha, other inflammation-related proteins were up-regulated in an apparently tissue-dependent manner. Investigating fibroblasts from tumorous tissues of skin, lung and bone marrow with respect to such inflammation-related proteins revealed hardly any conformity but rather individual and tumor type-related variations. However, apparent up-regulation of IGF-II, PAI-1 and PLOD2 was observed in melanoma-, lung adenocarcinoma- and multiple myeloma-associated fibroblasts, as well as in hepatocellular carcinoma-associated fibroblasts. Conclusions Inflammation-related proteome alterations of primary human fibroblasts were determined by the analysis of IL-1beta treated cells. Tumor-associated fibroblasts from different tissue types hardly showed signs of acute inflammation but displayed characteristic functional aberrations potentially related to chronic inflammation. The present data suggest that the state of the tumor microenvironment is relevant for tumor progression and targeted treatment of tumor-associated fibroblasts may support anti-cancer strategies. Electronic supplementary material The online version of this article (doi:10.1186/1559-0275-11-41) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Astrid Slany
- Faculty of Chemistry, Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Anastasia Meshcheryakova
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Vienna, Austria ; Christian Doppler Laboratory for the Diagnosis and Regeneration of Cardiac and Thoracic Diseases, Medical University Vienna, Vienna, Austria
| | - Agnes Beer
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Vienna, Austria ; Christian Doppler Laboratory for the Diagnosis and Regeneration of Cardiac and Thoracic Diseases, Medical University Vienna, Vienna, Austria
| | - Hendrik Jan Ankersmit
- Department of Thoracic Surgery, Division of Surgery, Medical University Vienna, Vienna, Austria ; Christian Doppler Laboratory for the Diagnosis and Regeneration of Cardiac and Thoracic Diseases, Medical University Vienna, Vienna, Austria
| | - Verena Paulitschke
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Christopher Gerner
- Faculty of Chemistry, Department of Analytical Chemistry, University of Vienna, Vienna, Austria ; Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Vienna, Austria ; Christian Doppler Laboratory for the Diagnosis and Regeneration of Cardiac and Thoracic Diseases, Medical University Vienna, Vienna, Austria
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21
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Kim HS, Kang D, Moon MH, Kim HJ. Identification of pancreatic cancer-associated tumor antigen from HSP-enriched tumor lysate-pulsed human dendritic cells. Yonsei Med J 2014; 55:1014-27. [PMID: 24954332 PMCID: PMC4075362 DOI: 10.3349/ymj.2014.55.4.1014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 10/23/2013] [Accepted: 11/04/2013] [Indexed: 11/27/2022] Open
Abstract
PURPOSE Vaccine strategies utilizing dendritic cells (DCs) to elicit anti-tumor immunity are the subject of intense research. Although we have shown that DCs pulsed with heat-treated tumor lysate (HTL) induced more potent anti-tumor immunity than DCs pulsed with conventional tumor lysate (TL), the underlying molecular mechanism is unclear. In order to explore the molecular basis of this approach and to identify potential antigenic peptides from pancreatic cancer, we analyzed and compared the major histocompatibility complex (MHC) ligands derived from TL- and HTL-pulsed dendritic cells by mass spectrophotometry. MATERIALS AND METHODS Human monocyte-derived dendritic cells were pulsed with TL or HTL prior to maturation induction. To delineate differences of MHC-bound peptide repertoire eluted from DCs pulsed with TL or HTL, nanoflow liquid chromatography-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS-MS) was employed. RESULTS HTL, but not TL, significantly induced DC function, assessed by phenotypic maturation, allostimulation capacity and IFN-γ secretion by stimulated allogeneic T cells. DCs pulsed with TL or HTL displayed pancreas or pancreatic cancer-related peptides in context of MHC class I and II molecules. Some of the identified peptides had not been previously reported as expressed in pancreatic cancer or cancer of other tissue types. CONCLUSION Our partial lists of MHC-associated peptides revealed the differences between peptide profiles eluted from HTL-and TL-loaded DCs, implying that induced heat shock proteins in HTL chaperone tumor-derived peptides enhanced their delivery to DCs and promoted cross-presentation by DC. These findings may aid in identifying novel tumor antigens or biomarkers and in designing future vaccination strategies.
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Affiliation(s)
- Han-Soo Kim
- Innovative Cell and Gene Therapy Center, International St. Mary's Hospital, Incheon, Korea
| | - Dukjin Kang
- Center for Bioanalysis, Division of Metrology for Quality of Life, Korea Research Institute of Standards and Science, Daejeon, Korea
| | | | - Hyung Jik Kim
- Department of Internal Medicine, Hallym University College of Medicine, Chuncheon, Korea.
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22
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Slany A, Paulitschke V, Haudek-Prinz V, Meshcheryakova A, Gerner C. Determination of cell type-specific proteome signatures of primary human leukocytes, endothelial cells, keratinocytes, hepatocytes, fibroblasts and melanocytes by comparative proteome profiling. Electrophoresis 2014; 35:1428-38. [PMID: 24644141 DOI: 10.1002/elps.201300581] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/04/2014] [Accepted: 02/05/2014] [Indexed: 12/25/2022]
Abstract
Cells gain their functional specialization by different protein synthesis. A lot of knowledge with respect to cell type-specific proteins has been collected during the last thirty years. This knowledge was built mainly by using antibodies. Nowadays, modern MS, which supports comprehensive proteome analyses of biological samples, may render possible the search for cell type-specific proteins as well. However, a therefore necessary systematic MS study comprising many different cell types has not been performed until now. Here we present a proteome analysis strategy supporting the automated and meaningful comparison of any biological samples. We have presently applied this strategy to six different primary human cell types, namely leukocytes, endothelial cells, keratinocytes, hepatocytes, fibroblasts, and melanocytes. Comparative analysis of the resulting proteome profiles allowed us to select proteins specifically identified in one of the six cell types and not in any of the five others. Based on these results, we designated cell type-specific proteome signatures consisting each of six such characteristic proteins. These signatures independently reproduced well-known marker proteins already established for FACS analyses in addition to novel candidate marker proteins. We applied these signatures for the interpretation of proteome profiles obtained from the analyses of hepatocellular carcinoma-associated tissue homogenates and normal liver tissue homogenates. The identification of members of the above described signatures gave us an indication of the presence of characteristic cells in the diseased tissues and thus supported the interpretation of the proteomics data of these complex biological samples.
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Affiliation(s)
- Astrid Slany
- Institute of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Austria; Department of Medicine I, Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Austria
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23
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Kroeker AL, Coombs KM. Systems biology unravels interferon responses to respiratory virus infections. World J Biol Chem 2014; 5:12-25. [PMID: 24600511 PMCID: PMC3942539 DOI: 10.4331/wjbc.v5.i1.12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/11/2013] [Accepted: 01/06/2014] [Indexed: 02/05/2023] Open
Abstract
Interferon production is an important defence against viral replication and its activation is an attractive therapeutic target. However, it has long been known that viruses perpetually evolve a multitude of strategies to evade these host immune responses. In recent years there has been an explosion of information on virus-induced alterations of the host immune response that have resulted from data-rich omics technologies. Unravelling how these systems interact and determining the overall outcome of the host response to viral infection will play an important role in future treatment and vaccine development. In this review we focus primarily on the interferon pathway and its regulation as well as mechanisms by which respiratory RNA viruses interfere with its signalling capacity.
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24
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Fabrik I, Link M, Härtlova A, Dankova V, Rehulka P, Stulik J. Application of SILAC labeling to primary bone marrow-derived dendritic cells reveals extensive GM-CSF-dependent arginine metabolism. J Proteome Res 2013; 13:752-62. [PMID: 24308431 DOI: 10.1021/pr4007798] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Although dendritic cells (DCs) control the priming of the adaptive immunity response, a comprehensive description of their behavior at the protein level is missing. The introduction of the quantitative proteomic technique of metabolic labeling (SILAC) into the field of DC research would therefore be highly beneficial. To achieve this, we applied SILAC labeling to primary bone marow-derived DCs (BMDCs). These cells combine both biological relevance and experimental feasibility, as their in vitro generation permits the use of (13)C/(15)N-labeled amino acids. Interestingly, BMDCs appear to exhibit a very active arginine metabolism. Using standard cultivation conditions, ∼20% of all protein-incorporated proline was a byproduct of heavy arginine degradation. In addition, the dissipation of (15)N from labeled arginine to the whole proteome was observed. The latter decreased the mass accuracy in MS and affected the natural isotopic distribution of peptides. SILAC-connected metabolic issues were shown to be enhanced by GM-CSF, which is used for the differentiation of DC progenitors. Modifications of the cultivation procedure suppressed the arginine-related effects, yielding cells with a proteome labeling efficiency of ≥90%. Importantly, BMDCs generated according to the new cultivation protocol preserved their resemblance to inflammatory DCs in vivo, as evidenced by their response to LPS treatment.
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Affiliation(s)
- Ivo Fabrik
- Institute of Molecular Pathology, Faculty of Military Health Sciences, University of Defence , Trebesska 1575, 500 01 Hradec Kralove, Czech Republic
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Slany A, Haudek-Prinz V, Meshcheryakova A, Bileck A, Lamm W, Zielinski C, Gerner C, Drach J. Extracellular matrix remodeling by bone marrow fibroblast-like cells correlates with disease progression in multiple myeloma. J Proteome Res 2013; 13:844-54. [PMID: 24256566 DOI: 10.1021/pr400881p] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The pathogenesis of multiple myeloma (MM) is regarded as a multistep process, in which an asymptomatic stage of monoclonal gammopathy of undetermined significance (MGUS) precedes virtually all cases of MM. Molecular events characteristic for the transition from MGUS to MM are still poorly defined. We hypothesized that fibroblast-like cells in the tumor microenvironment are critically involved in the pathogenesis of MM. Therefore, we performed a comparative proteome profiling study, analyzing primary human fibroblast-like cells isolated from the bone marrow of MM, of MGUS, as well as of non-neoplastic control patients. Thereby, a group of extracellular matrix (ECM) proteins, ECM receptors, and ECM-modulating enzymes turned out to be progressively up-regulated in MGUS and MM. These proteins include laminin α4, lysyl-hydroxylase 2, prolyl 4-hydroxylase 1, nidogen-2, integrin α5β5, c-type mannose receptor 2, PAI-1, basigin, and MMP-2, in addition to PDGF-receptor β and the growth factor periostin, which are likewise involved in ECM activities. Our results indicate that ECM remodeling by fibroblast-like cells may take place already at the level of MGUS and may become even more pronounced in MM. The identified proteins which indicate the stepwise progression from MGUS to MM may offer new tools for therapeutic strategies.
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Affiliation(s)
- Astrid Slany
- Faculty of Chemistry, Institute of Analytical Chemistry, University of Vienna , Währingerstraße 38, A-1090 Vienna, Austria
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Haudek-Prinz VJ, Klepeisz P, Slany A, Griss J, Meshcheryakova A, Paulitschke V, Mitulovic G, Stöckl J, Gerner C. Proteome signatures of inflammatory activated primary human peripheral blood mononuclear cells. J Proteomics 2012; 76 Spec No.:150-62. [PMID: 22813876 PMCID: PMC3509337 DOI: 10.1016/j.jprot.2012.07.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 06/29/2012] [Accepted: 07/04/2012] [Indexed: 02/02/2023]
Abstract
Proteome profiling is the method of choice to identify marker proteins whose expression may be characteristic for certain diseases. The formation of such marker proteins results from disease-related pathophysiologic processes. In healthy individuals, peripheral blood mononuclear cells (PBMCs) circulate in a quiescent cell state monitoring potential immune-relevant events, but have the competence to respond quickly and efficiently in an inflammatory manner to any invasion of potential pathogens. Activation of these cells is most plausibly accompanied by characteristic proteome alterations. Therefore we investigated untreated and inflammatory activated primary human PBMCs by proteome profiling using a 'top down' 2D-PAGE approach in addition to a 'bottom up' LC-MS/MS-based shotgun approach. Furthermore, we purified primary human T-cells and monocytes and activated them separately. Comparative analysis allowed us to characterize a robust proteome signature including NAMPT and PAI2 which indicates the activation of PBMCs. The T-cell specific inflammation signature included IRF-4, GBP1 and the previously uncharacterized translation product of GBP5; the corresponding monocyte signature included PDCD5, IL1RN and IL1B. The involvement of inflammatory activated PBMCs in certain diseases as well as the responsiveness of these cells to anti-inflammatory drugs may be evaluated by quantification of these marker proteins. This article is part of a Special Issue entitled: Integrated omics.
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Fík Z, Valach J, Chovanec M, Mazánek J, Kodet R, Kodet O, Tachezy R, Foltynová E, André S, Kaltner H, Gabius HJ, Smetana K. Loss of adhesion/growth-regulatory galectin-9 from squamous cell epithelium in head and neck carcinomas. J Oral Pathol Med 2012; 42:166-73. [PMID: 22650413 DOI: 10.1111/j.1600-0714.2012.01185.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Galectins are potent effectors of cell adhesion and growth regulation. Their expression as comples network necessitates systematic study of each member of this family. Toward this aim, we here focus on the tandem-repeat-type galectin-9. Its presence is monitored in normal squamous epithelium of the head and neck, the surgical margin, and four types of squamous cell carcinoma. Lectin presence was detected in cells of the basal layer of the epithelium. All galectin-9-negative epithelia showed aberrant positivity for keratins 14 and 19. The surgical margin presented either a normal pattern of galectin-9 and keratin presence or a mosaic-like presence/absence of galectin-9 and aberrant expression of both keratins 14 and 19. All studied specimens of squamous cell carcinoma were negative for galectin-9. When biotinylated galectin-9, or its N-terminal domain, was tested, no significant tissue reactivity for both probes was observed. Neuraminidase treatment generated reactivity to the N-domain. In conclusion, galectin-9 is expressed in the majority of samples of normal epithelium, along with regular presence of keratins 14 or 19. This lectin can represent a potential marker of normality in the cases of the studied squamous cell epithelia.
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Affiliation(s)
- Zdeněk Fík
- Institute of Anatomy, 1st Faculty of Medicine, Charles University, U Nemocnice, Prague, Czech Republic
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Santinha DR, Marques DR, Maciel EA, Simões CSO, Rosa S, Neves BM, Macedo B, Domingues P, Cruz MT, Domingues MRM. Profiling changes triggered during maturation of dendritic cells: a lipidomic approach. Anal Bioanal Chem 2012; 403:457-71. [PMID: 22402731 DOI: 10.1007/s00216-012-5843-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 01/11/2012] [Accepted: 02/06/2012] [Indexed: 12/11/2022]
Abstract
Lipids are important in several biological processes because they act as signalling and regulating molecules, or, locally, as membrane components that modulate protein function. This paper reports the pattern of lipid composition of dendritic cells (DCs), a cell type of critical importance in inflammatory and immune responses. After activation by antigens, DCs undergo drastic phenotypical and functional transformations, in a process known as maturation. To better characterize this process, changes of lipid profile were evaluated by use of a lipidomic approach. As an experimental model of DCs, we used a foetal skin-derived dendritic cell line (FSDC) induced to mature by treatment with lipopolysaccharide (LPS). The results showed that LPS treatment increased ceramide (Cer) and phosphatidylcholine (PC) levels and reduced sphingomyelin (SM) and phosphatidylinositol (PI) content. Mass spectrometric analysis of a total lipid extract and of each class of lipids revealed that maturation promoted clear changes in ceramide profile. Quantitative analysis enabled identification of an increase in the total ceramide content and enhanced Cer at m/z 646.6, identified as Cer(d18:1/24:1), and at m/z 648.6, identified as Cer(d18:1/24:0). The pattern of change of these lipids give an extremely rich source of data for evaluating modulation of specific lipid species triggered during DC maturation.
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Affiliation(s)
- Deolinda R Santinha
- Faculty of Pharmacy and Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
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Weichhart T, Kopecky C, Kubicek M, Haidinger M, Döller D, Katholnig K, Suarna C, Eller P, Tölle M, Gerner C, Zlabinger GJ, van der Giet M, Hörl WH, Stocker R, Säemann MD. Serum amyloid A in uremic HDL promotes inflammation. J Am Soc Nephrol 2012; 23:934-47. [PMID: 22282592 DOI: 10.1681/asn.2011070668] [Citation(s) in RCA: 163] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Uremia impairs the atheroprotective properties of HDL, but the mechanisms underlying why this occurs are unknown. Here, we observed that HDL isolated from healthy individuals inhibited the production of inflammatory cytokines by peripheral monocytes stimulated with a Toll-like receptor 2 agonist. In contrast, HDL isolated from the majority of patients with ESRD did not show this anti-inflammatory property; many HDL samples even promoted the production of inflammatory cytokines. To investigate this difference, we used shotgun proteomics to identify 49 HDL-associated proteins in a uremia-specific pattern. Proteins enriched in HDL from patients with ESRD (ESRD-HDL) included surfactant protein B (SP-B), apolipoprotein C-II, serum amyloid A (SAA), and α-1-microglobulin/bikunin precursor. In addition, we detected some ESRD-enriched proteins in earlier stages of CKD. We did not detect a difference in oxidation status between HDL isolated from uremic and healthy patients. Regarding function of these uremia-specific proteins, only SAA mimicked ESRD-HDL by promoting inflammatory cytokine production. Furthermore, SAA levels in ESRD-HDL inversely correlated with its anti-inflammatory potency. In conclusion, HDL has anti-inflammatory activities that are defective in uremic patients as a result of specific changes in its molecular composition. These data suggest a potential link between the high levels of inflammation and cardiovascular mortality in uremia.
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Affiliation(s)
- Thomas Weichhart
- Department of Internal Medicine III, Division of Nephrology and Dialysis, Medical University of Vienna, Austria.
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Analytical constraints for the analysis of human cell line secretomes by shotgun proteomics. J Proteomics 2011; 75:1043-54. [PMID: 22079246 DOI: 10.1016/j.jprot.2011.10.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 09/16/2011] [Accepted: 10/22/2011] [Indexed: 01/21/2023]
Abstract
Human cell line secretome represents a valuable source of therapeutic targets and candidate biomarkers. Secreted proteins found in biological fluids or culture media are by essence highly diluted. Secretome investigation with proteomic approaches is hardly compatible with the high content of proteins found in complete cell culture media. Therefore, many studies are currently done with media containing few or no protein. Such conditions may perturb cell metabolism and proliferation. Here, we compared seventeen different compositions of culture media for the human bronchial epithelial BEAS-2B cell line. Cell viability, proliferation rate and initial protein charge were systematically compared. We have shown that an important difficulty for the proteomic analysis is due to the presence of detergents such as Pluronic F-68 which hinders peptide mass spectrometry. The high glucose containing DMEM medium which is free of proteins was shown to preserve a good viability and proliferation of cells. With this conditioning medium, we identified 81 extracellular proteins in the secretome of BEAS-2B cells. Moreover, to illustrate this approach, we exposed BEAS-2B cells to a low toxic dose of CoCl(2,) and found 24 extracellular proteins modulated by cobalt. This study highlights the possible contribution of such proteomic approach in the field of toxicology.
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Di Caro V, D'Anneo A, Phillips B, Engman C, Harnaha J, Trucco M, Giannoukakis N. Phosphatidylinositol-3-kinase activity during in vitro dendritic cell generation determines suppressive or stimulatory capacity. Immunol Res 2011; 50:130-52. [PMID: 21476100 DOI: 10.1007/s12026-011-8206-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Modulating PI3K at different stages of dendritic cells (DC) generation could be a novel means to balance the generation of immunosuppressive versus immunostimulatory DC. We show that PI3K inhibition during mouse DC generation in vitro results in cells that are potently immunosuppressive and characteristic of CD8alpha- CD11c+ CD11b+ DC. These DC exhibited low surface class I and class II MHC, CD40, and CD86 and did not produce TNF-alpha. In allogeneic MLR, these DC were suppressive. Although in these mixed cultures, there was no increase in the frequency of CD4+ CD25+ Foxp3+ cells, the Foxp3 content on a per cell basis was significantly increased. Sustained TLR9 signaling in the presence of PI3K inhibition during DC generation overrode the cells' suppressive phenotype.
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Affiliation(s)
- Valentina Di Caro
- Department of Pediatrics, Division of Immunogenetics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, 4401 Penn Avenue, Pittsburgh, PA 15224, USA
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Plasma membrane proteomes of differentially matured dendritic cells identified by LC-MS/MS combined with iTRAQ labelling. J Proteomics 2011; 75:938-48. [PMID: 22040742 PMCID: PMC3444755 DOI: 10.1016/j.jprot.2011.10.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 10/07/2011] [Accepted: 10/17/2011] [Indexed: 01/21/2023]
Abstract
Dendritic cells (DCs) play a pivotal role in polarising Th lymphocyte subsets but it is unclear what molecular events occur when DCs generate Th2-type responses. Here, we analysed plasma membrane-enriched fractions from immature, pro-Th1 and pro-Th2 DCs and used a combination of iTRAQ labelling and LC–MS/MS to quantify changes in the proteomes. Analysis was performed on triplicate biological samples and changes verified by flow cytometry. MHC class II molecules and CD29 were up-regulated in pro-Th1 DCs whilst CD18 and CD44 were up-regulated in pro-Th2 DCs. One of the most down-regulated molecules in pro-Th1 DCs was YM-1 whilst the greatest decrease in pro-Th2 DCs was NAP-22. Other molecules up-regulated in pro-Th2 DC compared to pro-Th1 DCs included some potentially involved in protein folding during antigen processing (clathrin and Rab-7), whilst other non-membrane proteins such as enzymes/transporters related to cell metabolism (malate dehydrogenase, pyruvate kinase, and ATPase Na+/K+) were also recorded. This suggests that pro-Th2 DCs are more metabolically active while pro-Th1 DCs have a mature ‘end state’. Overall, although several molecules were preferentially expressed on pro-Th2 DCs, our proteomics data support the view of a ‘limited maturation’ of pro-Th2 DCs compared to pro-Th1 DCs.
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Da Riva L, Bozzi F, Mondellini P, Miccichè F, Fumagalli E, Vaghi E, Tarantino E, Huber V, Gronchi A, Tamborini E, Pierotti MA, Pilotti S, Bongarzone I. Proteomic detection of a large amount of SCGFα in the stroma of GISTs after imatinib therapy. J Transl Med 2011; 9:158. [PMID: 21943129 PMCID: PMC3192683 DOI: 10.1186/1479-5876-9-158] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 09/23/2011] [Indexed: 01/24/2023] Open
Abstract
Background Gastrointestinal stromal tumors (GISTs) are the most frequent mesenchymal tumors to develop in the digestive tract. These tumors are highly resistant to conventional chemotherapy and only the introduction of imatinib mesylate has improved the prognosis of patients. However, Response Evaluation Criteria in Solid Tumors are inappropriate for assessing tumor response, and the histological/pathological response to imatinib is variable, heterogeneous, and does not associate with clinical response. The effects of imatinib on responding GISTs are still being explored, and few studies correlate the clinical response with the histological response after pharmacological treatment. Recently, apoptosis and autophagy were suggested as possible alternative mechanisms of pharmacological response. Methods Here, we used a proteomic approach, combined with other analyses, to identify some molecular stromal components related to the response/behavior of resected, high-risk GISTs after neoadiuvant imatinib therapy. Results Our proteomic results indicate an elevated concentration of Stem Cell Growth Factor (SCGF), a hematopoietic growth factor having a role in the development of erythroid and myeloid progenitors, in imatinib-responsive tumor areas. SCGFα expression was detected by mass spectrometry, immunohistochemistry and/or western blot and attributed to acellular matrix of areas scored negative for KIT (CD117). RT-PCR results indicated that GIST samples did not express SCGF transcripts. The recently reported demonstration by Gundacker et al. [1] of the secretion of SCGF in mature pro-inflammatory dendritic cells would indicate a potential importance of SCGF in tissue inflammatory response. Accordingly, inflammatory infiltrates were detected in imatinib-affected areas and the CD68-positivity of the SCGF-positive and KIT-negative areas suggested previous infiltration of monocytes/macrophages into these regions. Thus, chronic inflammation subsequent to imatinib treatment may determine monocyte/macrophage recruitment in imatinib-damaged areas; these areas also feature prominent tumor-cell loss that is replaced by dense hyalinization and fibrosis. Conclusions Our studies highlight a possible role of SCGFα in imatinib-induced changes of GIST structure, consistent with a therapeutic response.
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Affiliation(s)
- Luca Da Riva
- Proteomics Laboratory, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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Caccia D, Zanetti Domingues L, Miccichè F, De Bortoli M, Carniti C, Mondellini P, Bongarzone I. Secretome compartment is a valuable source of biomarkers for cancer-relevant pathways. J Proteome Res 2011; 10:4196-207. [PMID: 21751813 DOI: 10.1021/pr200344n] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In principle, targeted therapies have optimal activity against a specific subset of tumors that depend upon the targeted molecule or pathway for growth, survival, or metastasis. Consequently, it is important in drug development and clinical practice to have predictive biomarkers that can reliably identify patients who will benefit from a given therapy. We analyzed tumor cell-line secretomes (conditioned cell media) to look for predictive biomarkers; secretomes represent a potential source for potential biomarkers that are expressed in intracellular signaling and therefore may reflect changes induced by targeted therapy. Using Gene Ontology, we classified by function the secretome proteins of 12 tumor cell lines of different histotypes. Representations and hierarchical relationships among the functional groups differed among the cell lines. Using bioinformatics tools, we identified proteins involved in intracellular signaling pathways. For example, we found that secretome proteins related to TGF-beta signaling in thyroid cancer cells, such as vasorin, CD109, and βIG-H3 (TGFBI), were sensitive to RPI-1 and dasatinib treatments, which have been previously demonstrated to be effective in blocking cell proliferation. The secretome may be a valuable source of potential biomarkers for detecting cancer and measuring the effectiveness of cancer therapies.
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Affiliation(s)
- Dario Caccia
- Proteomics Laboratory, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
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Griss J, Haudek-Prinz V, Gerner C. GPDE: A biological proteomic database for biomarker discovery and evaluation. Proteomics 2011; 11:1000-4. [PMID: 21337704 DOI: 10.1002/pmic.201000507] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Revised: 10/25/2010] [Accepted: 12/05/2010] [Indexed: 11/06/2022]
Abstract
Clinical proteomics faces extremely complex and variable data. Here, we present an updated version of the Griss Proteomics Database Engine (GPDE): A free biological proteomic database specifically designed for clinical proteomics and biomarker discovery (http://gpde.sourceforge.net). It combines experiments based on investigated cell types thereby supporting customizable biological meta-analyses. Through the new features described here, the GPDE now became a powerful yet easy-to-use tool to support the fast identification and reliable evaluation of biomarker candidates.
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Affiliation(s)
- Johannes Griss
- Department of Medicine I, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
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36
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Dowling P, Clynes M. Conditioned media from cell lines: a complementary model to clinical specimens for the discovery of disease-specific biomarkers. Proteomics 2011; 11:794-804. [PMID: 21229588 DOI: 10.1002/pmic.201000530] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 09/08/2010] [Accepted: 09/16/2010] [Indexed: 12/13/2022]
Abstract
In the strictest sense, the cell secretome (conditioned media) refers to the collection of proteins that contain a signal peptide and are processed via the endoplasmic reticulum and Golgi apparatus through the classical secretion pathway. More generally, the secretome also encompasses proteins shed from the cell surface and intracellular proteins released through non-classical secretion pathway or exosomes. These secreted proteins include numerous enzymes, growth factors, cytokines and hormones or other soluble mediators. They are fundamental in the processes of cell growth, differentiation, invasion and angiogenesis by regulating cell-to-cell and cell-to-extracellular matrix interactions. The main aim of this review is to provide a synopsis of findings from the analysis of the secretome taking diabetes, cancer and neurodegenerative diseases as examples. We will also discuss the preparation of conditioned media and on the main proteomic-based methodological approaches that have been developed for the study of secreted/shed proteins.
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Affiliation(s)
- Paul Dowling
- National Institute for Cellular Biotechnology, Dublin City University, Dublin, Ireland.
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37
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Gerner C, Haudek-Prinz VJ, Lackner A, Losert A, Peter-Vörösmarty B, Lorenz O, Grusch M. Indications for cell stress in response to adenoviral and baculoviral gene transfer observed by proteome profiling of human cancer cells. Electrophoresis 2010; 31:1822-32. [PMID: 20446292 DOI: 10.1002/elps.200900753] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Gene transfer to cultured cells is an important tool for functional studies in many areas of biomedical research and vector systems derived from adenoviruses and baculoviruses are frequently used for this purpose. In order to characterize how viral gene transfer vectors affect the functional state of transduced cells, we applied 2-D PAGE allowing quantitative determination of protein amounts and synthesis rates of metabolically labeled cells and shotgun proteomics. Using HepG2 human hepatoma cells we show that both vector types can achieve efficient expression of green fluorescent protein, which accounted for about 0.1% of total cellular protein synthesis 72 h after transduction. No evidence in contrast was found for expression of proteins from the viral backbones. With respect to the host cell response, both vectors induced a general increase in protein synthesis of about 50%, which was independent of green fluorescent protein expression. 2-D PAGE autoradiographs identified a 3.6-fold increase of gamma-actin synthesis in adenovirus transduced cells. In addition shotgun proteomics of cytoplasmic and nuclear extract fractions identified a slight induction of several proteins related to inflammatory activation, cell survival and chromatin function by both virus types. These data demonstrate that commonly used gene transfer vectors induce a response reminiscent of stress activation in host cells, which needs to be taken into account when performing functional assays with transduced cells.
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Affiliation(s)
- Christopher Gerner
- Department of Medicine I, Division: Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
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38
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Buschow SI, Lasonder E, van Deutekom HWM, Oud MM, Beltrame L, Huynen MA, de Vries IJM, Figdor CG, Cavalieri D. Dominant processes during human dendritic cell maturation revealed by integration of proteome and transcriptome at the pathway level. J Proteome Res 2010; 9:1727-37. [PMID: 20131907 DOI: 10.1021/pr9008546] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Gene expression is commonly used to study the activation of dendritic cells (DCs) to identify proteins that determine whether these cells induce an immunostimulatory or tolerogenic immune response. RNA expression, however, does not necessarily predict protein abundance and often requires large numbers of experiments for statistical significance. Proteomics provides a direct view on protein expression but is costly and time consuming. Here, we combined a comprehensive quantitative proteome and transcriptome analysis on a single batch of immature and cytokine cocktail matured human DCs and integrated resulting data sets at the pathway level. Although overall correlation between differential mRNA and protein expression was low, correlation between components of DC relevant pathways was significantly higher. Differentially expressed proteins and genes partly mapped to identical but also to different pathway components demonstrating that RNA and protein data not only supported but also complemented each other. We identified 5 dominant pathways, which confirmed the importance of cytokines, cell adhesion, and migration in DC maturation and also indicated a fundamental role for lipid metabolism. From these pathways we extracted novel maturation markers that might improve DC vaccine design. For several of the candidate markers we confirmed widespread significance examining DCs from multiple individuals, underscoring the validity of our approach. We conclude that integration of different but related data sets at the pathway level can significantly increase the predictive power of multi "omics" analyses.
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Affiliation(s)
- Sonja I Buschow
- Department of Tumor Immunology and CMBI at the Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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Slany A, Haudek VJ, Zwickl H, Gundacker NC, Grusch M, Weiss TS, Seir K, Rodgarkia-Dara C, Hellerbrand C, Gerner C. Cell characterization by proteome profiling applied to primary hepatocytes and hepatocyte cell lines Hep-G2 and Hep-3B. J Proteome Res 2010; 9:6-21. [PMID: 19678649 DOI: 10.1021/pr900057t] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hepatocytes are known to express a large number of characteristic proteins. Transformed and cultured hepatocytes only partially maintain functional cell differentiation characteristics, which can be assessed by proteome profiling. Here, we applied 2D-PAGE analysis in addition to shotgun proteomics to assess the functional cell state of primary human hepatocytes (PHH), HepG2 and Hep3B cells. Out of a total of 1995 proteins identified in the cytoplasm of these cells, we filtered 107 proteins which are characteristic for hepatocytes. A total of 104 of those were identified in primary human hepatocytes, 20 in HepG2, and only 6 in Hep3B. Forty-six out of 72 proteins identified in the secretome of PHH, 55 out of 139 in HepG2, and only 24 out of 72 in Hep3B were plasma proteins characteristic for hepatocytes. Beside other biomarker candidates presently identified, 11 proteins of the HepG2 secretome have been described previously as biomarkers for hepatocellular carcinoma. Because of indications that epithelial to mesenchymal transition (EMT) may have occurred in the cultured hepatoma cells, we included the analysis of fibroblasts representative for mesenchymal cells. Hep3B, but not HepG2, secreted five proteins including follistatin-related protein 1 which are characteristic for mesenchymal cells and may be marker proteins for EMT. Our data demonstrate that HepG2 show more features characteristic for hepatocytes than Hep3B, while Hep3B express more mesenchymal proteins indicative for EMT. Proteome profiling thus proved to enable comprehensive assessment of functional cell states and cell differentiation states of cultured hepatocytes and enabled the identification of numerous biomarkers for hepatocellular carcinoma and EMT.
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Affiliation(s)
- Astrid Slany
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Austria
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40
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Ferreira GB, Mathieu C, Overbergh L. Understanding dendritic cell biology and its role in immunological disorders through proteomic profiling. Proteomics Clin Appl 2009; 4:190-203. [PMID: 21137043 DOI: 10.1002/prca.200900162] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Revised: 10/08/2009] [Accepted: 10/19/2009] [Indexed: 01/10/2023]
Abstract
Dendritic cells (DC) have always been present on the bright spot of immune research. They have been extensively studied for the last 35 years, and much is known about their different phenotypes, stimulatory capacity, and role in the immune system. During the last 15 years, great attention has been given to studies on global gene and protein expression profiles during the differentiation and maturation processes of these cells. It is well understood that studying the proteome, together with information on the role of protein post-translational modifications (PTM), will reveal the real dynamics of a living cell. The rapid increase of proteomic studies during the last decade describing the differentiation and maturation process in DCs, as well as modifications brought by the use of different compounds that either increase or decrease their immunogenicity, reflects the importance of understanding the molecular processes behind the functional properties of these cells. In the present review, we will give an overview of proteomic studies focusing on DCs. Thereby we will concentrate on the importance of these studies in understanding DC behavior from a molecular point of view and how these findings have aided in understanding the differences in functional properties of these cells.
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