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Cervone DT, Moreno-Justicia R, Quesada JP, Deshmukh AS. Mass spectrometry-based proteomics approaches to interrogate skeletal muscle adaptations to exercise. Scand J Med Sci Sports 2024; 34:e14334. [PMID: 36973869 DOI: 10.1111/sms.14334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 03/29/2023]
Abstract
Acute exercise and chronic exercise training elicit beneficial whole-body changes in physiology that ultimately depend on profound alterations to the dynamics of tissue-specific proteins. Since the work accomplished during exercise owes predominantly to skeletal muscle, it has received the majority of interest from exercise scientists that attempt to unravel adaptive mechanisms accounting for salutary metabolic effects and performance improvements that arise from training. Contemporary scientists are also beginning to use mass spectrometry-based proteomics, which is emerging as a powerful approach to interrogate the muscle protein signature in a more comprehensive manner. Collectively, these technologies facilitate the analysis of skeletal muscle protein dynamics from several viewpoints, including changes to intracellular proteins (expression proteomics), secreted proteins (secretomics), post-translational modifications as well as fiber-, cell-, and organelle-specific changes. This review aims to highlight recent literature that has leveraged new workflows and advances in mass spectrometry-based proteomics to further our understanding of training-related changes in skeletal muscle. We call attention to untapped areas in skeletal muscle proteomics research relating to exercise training and metabolism, as well as basic points of contention when applying mass spectrometry-based analyses, particularly in the study of human biology. We further encourage researchers to couple the hypothesis-generating and descriptive nature of omics data with functional analyses that propel our understanding of the complex adaptive responses in skeletal muscle that occur with acute and chronic exercise.
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Affiliation(s)
- Daniel T Cervone
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Roger Moreno-Justicia
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Júlia Prats Quesada
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Atul S Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
- Clinical Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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2
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Knecht S, Eberl HC, Kreisz N, Ugwu UJ, Starikova T, Kuster B, Wilhelm S. An Introduction to Analytical Challenges, Approaches, and Applications in Mass Spectrometry-Based Secretomics. Mol Cell Proteomics 2023; 22:100636. [PMID: 37597723 PMCID: PMC10518356 DOI: 10.1016/j.mcpro.2023.100636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/06/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023] Open
Abstract
The active release of proteins into the extracellular space and the proteolytic cleavage of cell surface proteins are key processes that coordinate and fine-tune a multitude of physiological functions. The entirety of proteins that fulfill these extracellular tasks are referred to as the secretome and are of special interest for the investigation of biomarkers of disease states and physiological processes related to cell-cell communication. LC-MS-based proteomics approaches are a valuable tool for the comprehensive and unbiased characterization of this important subproteome. This review discusses procedures, opportunities, and limitations of mass spectrometry-based secretomics to better understand and navigate the complex analytical landscape for studying protein secretion in biomedical science.
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Affiliation(s)
- Sascha Knecht
- Omics Sciences, Genomic Sciences, GlaxoSmithKline, Heidelberg, Germany; Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - H Christian Eberl
- Omics Sciences, Genomic Sciences, GlaxoSmithKline, Heidelberg, Germany
| | - Norbert Kreisz
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Ukamaka Juliet Ugwu
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Tatiana Starikova
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
| | - Stephanie Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany.
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Filippini F, Nola S, Zahraoui A, Roger K, Esmaili M, Sun J, Wojnacki J, Vlieghe A, Bun P, Blanchon S, Rain JC, Taymans JM, Chartier-Harlin MC, Guerrera C, Galli T. Secretion of VGF relies on the interplay between LRRK2 and post-Golgi v-SNAREs. Cell Rep 2023; 42:112221. [PMID: 36905628 DOI: 10.1016/j.celrep.2023.112221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/12/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
The neuropeptide VGF was recently proposed as a neurodegeneration biomarker. The Parkinson's disease-related protein leucine-rich repeat kinase 2 (LRRK2) regulates endolysosomal dynamics, a process that involves SNARE-mediated membrane fusion and could regulate secretion. Here we investigate potential biochemical and functional links between LRRK2 and v-SNAREs. We find that LRRK2 directly interacts with the v-SNAREs VAMP4 and VAMP7. Secretomics reveals VGF secretory defects in VAMP4 and VAMP7 knockout (KO) neuronal cells. In contrast, VAMP2 KO "regulated secretion-null" and ATG5 KO "autophagy-null" cells release more VGF. VGF is partially associated with extracellular vesicles and LAMP1+ endolysosomes. LRRK2 expression increases VGF perinuclear localization and impairs its secretion. Retention using selective hooks (RUSH) assays show that a pool of VGF traffics through VAMP4+ and VAMP7+ compartments, and LRRK2 expression delays its transport to the cell periphery. Overexpression of LRRK2 or VAMP7-longin domain impairs VGF peripheral localization in primary cultured neurons. Altogether, our results suggest that LRRK2 might regulate VGF secretion via interaction with VAMP4 and VAMP7.
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Affiliation(s)
- Francesca Filippini
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy & Diseased Brain, 75014 Paris, France
| | - Sébastien Nola
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy & Diseased Brain, 75014 Paris, France
| | - Ahmed Zahraoui
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy & Diseased Brain, 75014 Paris, France
| | - Kevin Roger
- Université Paris Cité, Proteomics Platform Necker, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, 75015 Paris, France
| | - Mansoore Esmaili
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ji Sun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - José Wojnacki
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy & Diseased Brain, 75014 Paris, France
| | - Anaïs Vlieghe
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy & Diseased Brain, 75014 Paris, France
| | - Philippe Bun
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, NeurImag Imaging Facility, 75014 Paris, France
| | | | | | - Jean-Marc Taymans
- Université de Lille, INSERM, CHU Lille, UMR-S1172, LilNCog - Lille Neuroscience & Cognition, Lille, France
| | | | - Chiara Guerrera
- Université Paris Cité, Proteomics Platform Necker, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, 75015 Paris, France
| | - Thierry Galli
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy & Diseased Brain, 75014 Paris, France; GHU Paris Psychiatrie & Neurosciences, Paris, France.
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Dijkstra J, Neikes HK, Rezaeifard S, Ma X, Voest EE, Tauriello DVF, Vermeulen M. Multiomics of Colorectal Cancer Organoids Reveals Putative Mediators of Cancer Progression Resulting from SMAD4 Inactivation. J Proteome Res 2023; 22:138-151. [PMID: 36450103 PMCID: PMC9830641 DOI: 10.1021/acs.jproteome.2c00551] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The development of metastasis severely reduces the life expectancy of patients with colorectal cancer (CRC). Although loss of SMAD4 is a key event in CRC progression, the resulting changes in biological processes in advanced disease and metastasis are not fully understood. Here, we applied a multiomics approach to a CRC organoid model that faithfully reflects the metastasis-supporting effects of SMAD4 inactivation. We show that loss of SMAD4 results in decreased differentiation and activation of pro-migratory and cell proliferation processes, which is accompanied by the disruption of several key oncogenic pathways, including the TGFβ, WNT, and VEGF pathways. In addition, SMAD4 inactivation leads to increased secretion of proteins that are known to be involved in a variety of pro-metastatic processes. Finally, we show that one of the factors that is specifically secreted by SMAD4-mutant organoids─DKK3─reduces the antitumor effects of natural killer cells (NK cells). Altogether, our data provide new insights into the role of SMAD4 perturbation in advanced CRC.
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Affiliation(s)
- Jelmer
J. Dijkstra
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular
Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, Geert Grooteplein 26−28, 6525
GA Nijmegen, The
Netherlands
| | - Hannah K. Neikes
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular
Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, Geert Grooteplein 26−28, 6525
GA Nijmegen, The
Netherlands
| | - Somayeh Rezaeifard
- Department
of Cell Biology, Radboud University Medical Center/Radboud Institute
for Molecular Life Sciences (RIMLS), Radboud
University Nijmegen, Geert Grooteplein 26−28, 6525
GA Nijmegen, The
Netherlands
| | - Xuhui Ma
- Department
of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Antoni van Leeuwenhoek
Hospital, 1066 CX Amsterdam, The Netherlands
| | - Emile E. Voest
- Department
of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Antoni van Leeuwenhoek
Hospital, 1066 CX Amsterdam, The Netherlands
| | - Daniele V. F. Tauriello
- Department
of Cell Biology, Radboud University Medical Center/Radboud Institute
for Molecular Life Sciences (RIMLS), Radboud
University Nijmegen, Geert Grooteplein 26−28, 6525
GA Nijmegen, The
Netherlands
| | - Michiel Vermeulen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular
Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, Geert Grooteplein 26−28, 6525
GA Nijmegen, The
Netherlands,
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Donnenberg VS, Luketich JD, Sultan I, Lister J, Bartlett DL, Ghosh S, Donnenberg AD. A maladaptive pleural environment suppresses preexisting anti-tumor activity of pleural infiltrating T cells. Front Immunol 2023; 14:1157697. [PMID: 37063842 PMCID: PMC10097923 DOI: 10.3389/fimmu.2023.1157697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/03/2023] [Indexed: 04/18/2023] Open
Abstract
Introduction Treatment options for patients with malignant pleural effusions (MPE) are limited due, at least in part, to the unique environment of the pleural space, which drives an aggressive tumor state and governs the behavior of infiltrating immune cells. Modulation of the pleural environment may be a necessary step toward the development of effective treatments. We examine immune checkpoint molecule (ICM) expression on pleural T cells, the secretomes of pleural fluid, pleural infiltrating T cells (PIT), and ability to activate PIT ex vivo. Methods ICM expression was determined on freshly drained and in vitro activated PIT from breast, lung and renal cell cancer. Secretomics (63 analytes) of activated PIT, primary tumor cultures and MPE fluid was determined using Luminex technology. Complementary digital spatial proteomic profiling (42 analytes) of CD45+ MPE cells was done using the Nanostring GeoMx platform. Cytolytic activity was measured against autologous tumor targets. Results ICM expression was low on freshy isolated PIT; regulatory T cells (T-reg) were not detectable by GeoMx. In vitro activated PIT coexpressed PD-1, LAG-3 and TIGIT but were highly cytotoxic against autologous tumor and uniquely secreted cytokines and chemokines in the > 100 pM range. These included CCL4, CCL3, granzyme B, IL-13, TNFα, IL-2 IFNγ, GM-CSF, and perforin. Activated PIT also secreted high levels of IL-6, IL-8 and sIL-6Rα, which contribute to polarization of the pleural environment toward wound healing and the epithelial to mesenchymal transition. Addition of IL-6Rα antagonist to cultures reversed tumor EMT but did not alter PIT activation, cytokine secretion or cytotoxicity. Discussion Despite the negative environment, immune effector cells are plentiful, persist in MPE in a quiescent state, and are easily activated and expanded in culture. Low expression of ICM on native PIT may explain reported lack of responsiveness to immune checkpoint blockade. The potent cytotoxic activity of activated PIT and a proof-of-concept clinical scale GMP-expansion experiment support their promise as a cellular therapeutic. We expect that a successful approach will require combining cellular therapy with pleural conditioning using immune checkpoint blockers together with inhibitors of upstream master cytokines such as the IL-6/IL-6R axis.
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Affiliation(s)
- Vera S. Donnenberg
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- University of Pittsburgh Medical Center (UPMC) Hillman Cancer Centers, Pittsburgh, PA, United States
- McGowan Institute for Regenerative Medicine, Pittsburgh, PA, United States
- *Correspondence: Albert D. Donnenberg, ; Vera S. Donnenberg,
| | - James D. Luketich
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- University of Pittsburgh Medical Center (UPMC) Hillman Cancer Centers, Pittsburgh, PA, United States
| | - Ibrahim Sultan
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- McGowan Institute for Regenerative Medicine, Pittsburgh, PA, United States
| | - John Lister
- Department of Medicine, Division of Hematology and Cellular Therapy, Allegheny Health Network Cancer Institute, Pittsburgh, PA, United States
- Drexel University College of Medicine, Philadelphia, PA, United States
| | - David L. Bartlett
- Drexel University College of Medicine, Philadelphia, PA, United States
- Department of Surgery, Division of Surgical Oncology, Allegheny Health Network Cancer Institute, Pittsburgh, PA, United States
| | - Sohini Ghosh
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Allegheny Health Network, Pittsburgh, PA, United States
| | - Albert D. Donnenberg
- University of Pittsburgh Medical Center (UPMC) Hillman Cancer Centers, Pittsburgh, PA, United States
- McGowan Institute for Regenerative Medicine, Pittsburgh, PA, United States
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- *Correspondence: Albert D. Donnenberg, ; Vera S. Donnenberg,
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Knecht S, Eberl HC, Bantscheff M. Interval-Based Secretomics Unravels Acute-Phase Response in Hepatocyte Model Systems. Mol Cell Proteomics 2022; 21:100241. [PMID: 35525403 PMCID: PMC9184749 DOI: 10.1016/j.mcpro.2022.100241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 11/21/2022] Open
Abstract
Mass spectrometry-based secretomics approaches frequently utilize serum-free culture conditions to circumvent serum-induced interference and to increase analytical depth. However, this can negatively affect a wide range of cellular functions and cell viability. These effects become particularly apparent when investigating transcriptionally regulated secretion events and feedback-loops in response to perturbations that require 48 h or more to fully manifest. We present an “interval-based” secretomics workflow, which determines protein secretion rates in short serum-free time windows. Relative quantification using tandem mass tags enables precise monitoring of time-dependent changes. We applied this approach to determine temporal profiles of protein secretion in the hepatocyte model cell lines HepG2 and HepaRG after stimulation of the acute-phase response (APR) by the cytokines IL1b and IL6. While the popular hepatocarcinoma cell line HepG2 showed an incomplete APR, secretion patterns derived from differentiated HepaRG cells recapitulated the expected APR more comprehensively. For several APR response proteins, substantial secretion was only observed after 72 h, a time window at which cell fitness is substantially impaired under serum-free cell culture conditions. The interval-based secretomics approach enabled the first comprehensive analysis of time-dependent secretion of liver cell models in response to these proinflammatory cytokines. The extended time range facilitated the observation of distinct chronological phases and cytokine-dependent secretion phenotypes of the APR. IL1b directed the APR toward pathogen defense over three distinct phases—chemotaxis, effector, clearance—while IL6 directed the APR toward regeneration. Protein shedding on the cell surface was pronounced upon IL1b stimulation, and small molecule inhibition of ADAM and matrix metalloproteases identified induced as well as constitutive shedding events. Inhibition of ADAM proteases with TAPI-0 resulted in reduced shedding of the sorting receptor SORT1, and an attenuated cytokine response suggesting a direct link between cell surface shedding and cytokine secretion rates. Interval-based secretomics enables extended time course analysis. Time-resolved acute phase response in liver model systems HepG2 and HepaRG. IL1b response clusters in three phases. Cell surface shedding is amplified during acute-phase response. ADAM inhibition dampens secretion of inflammatory cytokines.
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Affiliation(s)
- Sascha Knecht
- Cellzome GmbH, GlaxoSmithKline (GSK), Heidelberg, Germany
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Ribeaucourt D, Saker S, Navarro D, Bissaro B, Drula E, Correia LO, Haon M, Grisel S, Lapalu N, Henrissat B, O'Connell RJ, Lambert F, Lafond M, Berrin JG. Identification of Copper-Containing Oxidoreductases in the Secretomes of Three Colletotrichum Species with a Focus on Copper Radical Oxidases for the Biocatalytic Production of Fatty Aldehydes. Appl Environ Microbiol 2021; 87:e0152621. [PMID: 34613753 DOI: 10.1128/AEM.01526-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Copper radical alcohol oxidases (CRO-AlcOx), which have been recently discovered among fungal phytopathogens, are attractive for the production of fragrant fatty aldehydes. With the initial objective to investigate the secretion of CRO-AlcOx by natural fungal strains, we undertook time course analyses of the secretomes of three Colletotrichum species (C. graminicola, C. tabacum, and C. destructivum) using proteomics. The addition of a copper-manganese-ethanol mixture in the absence of any plant-biomass mimicking compounds to Colletotrichum cultures unexpectedly induced the secretion of up to 400 proteins, 29 to 52% of which were carbohydrate-active enzymes (CAZymes), including a wide diversity of copper-containing oxidoreductases from the auxiliary activities (AA) class (AA1, AA3, AA5, AA7, AA9, AA11, AA12, AA13, and AA16). Under these specific conditions, while a CRO-glyoxal oxidase from the AA5_1 subfamily was among the most abundantly secreted proteins, the targeted AA5_2 CRO-AlcOx were secreted at lower levels, suggesting heterologous expression as a more promising strategy for CRO-AlcOx production and utilization. C. tabacum and C. destructivum CRO-AlcOx were thus expressed in Pichia pastoris, and their preference toward both aromatic and aliphatic primary alcohols was assessed. The CRO-AlcOx from C. destructivum was further investigated in applied settings, revealing a full conversion of C6 and C8 alcohols into their corresponding fragrant aldehydes. IMPORTANCE In the context of the industrial shift toward greener processes, the biocatalytic production of aldehydes is of utmost interest owing to their importance for their use as flavor and fragrance ingredients. Copper radical alcohol oxidases (CRO-AlcOx) have the potential to become platform enzymes for the oxidation of alcohols to aldehydes. However, the secretion of CRO-AlcOx by natural fungal strains has never been explored, while the use of crude fungal secretomes is an appealing approach for industrial applications to alleviate various costs pertaining to biocatalyst production. While investigating this primary objective, the secretomics studies revealed unexpected results showing that under the oxidative stress conditions we probed, Colletotrichum species can secrete a broad diversity of copper-containing enzymes (laccases, sugar oxidoreductases, and lytic polysaccharide monooxygenases [LPMOs]) usually assigned to "plant cell wall degradation," despite the absence of any plant-biomass mimicking compound. However, in these conditions, only small amounts of CRO-AlcOx were secreted, pointing out recombinant expression as the most promising path for their biocatalytic application.
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Gonzalez-Franquesa A, Peijs L, Cervone DT, Koçana C, Zierath JR, Deshmukh AS. Insulin and 5-Aminoimidazole-4-Carboxamide Ribonucleotide (AICAR) Differentially Regulate the Skeletal Muscle Cell Secretome. Proteomes 2021; 9:37. [PMID: 34449730 PMCID: PMC8396280 DOI: 10.3390/proteomes9030037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/09/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022] Open
Abstract
Skeletal muscle is a major contributor to whole-body glucose homeostasis and is an important endocrine organ. To date, few studies have undertaken the large-scale identification of skeletal muscle-derived secreted proteins (myokines), particularly in response to stimuli that activate pathways governing energy metabolism in health and disease. Whereas the AMP-activated protein kinase (AMPK) and insulin-signaling pathways have received notable attention for their ability to independently regulate skeletal muscle substrate metabolism, little work has examined their ability to re-pattern the secretome. The present study coupled the use of high-resolution MS-based proteomics and bioinformatics analysis of conditioned media derived from 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR-an AMPK activator)- and insulin-treated differentiated C2C12 myotubes. We quantified 858 secreted proteins, including cytokines and growth factors such as fibroblast growth factor-21 (Fgf21). We identified 377 and 118 proteins that were significantly altered by insulin and AICAR treatment, respectively. Notably, the family of insulin growth factor binding-proteins (Igfbp) was differentially regulated by each treatment. Insulin- but not AICAR-induced conditioned media increased the mitochondrial respiratory capacity of myotubes, potentially via secreted factors. These findings may serve as an important resource to elucidate secondary metabolic effects of insulin and AICAR stimulation in skeletal muscle.
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Affiliation(s)
- Alba Gonzalez-Franquesa
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark; (A.G.-F.); (L.P.); (D.T.C.); (C.K.); (J.R.Z.)
| | - Lone Peijs
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark; (A.G.-F.); (L.P.); (D.T.C.); (C.K.); (J.R.Z.)
| | - Daniel T. Cervone
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark; (A.G.-F.); (L.P.); (D.T.C.); (C.K.); (J.R.Z.)
| | - Ceren Koçana
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark; (A.G.-F.); (L.P.); (D.T.C.); (C.K.); (J.R.Z.)
| | - Juleen R. Zierath
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark; (A.G.-F.); (L.P.); (D.T.C.); (C.K.); (J.R.Z.)
- Integrative Physiology, Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Atul S. Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark; (A.G.-F.); (L.P.); (D.T.C.); (C.K.); (J.R.Z.)
- Clinical Proteomics, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
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Souibgui E, Bruel C, Choquer M, de Vallée A, Dieryckx C, Dupuy JW, Latorse MP, Rascle C, Poussereau N. Clathrin Is Important for Virulence Factors Delivery in the Necrotrophic Fungus Botrytis cinerea. Front Plant Sci 2021; 12:668937. [PMID: 34220891 PMCID: PMC8244658 DOI: 10.3389/fpls.2021.668937] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/19/2021] [Indexed: 06/13/2023]
Abstract
Fungi are the most prevalent plant pathogens, causing annually important damages. To infect and colonize their hosts, they secrete effectors including hydrolytic enzymes able to kill and macerate plant tissues. These secreted proteins are transported from the Endoplasmic Reticulum and the Golgi apparatus to the extracellular space through intracellular vesicles. In pathogenic fungi, intracellular vesicles were described but their biogenesis and their role in virulence remain unclear. In this study, we report the essential role of clathrin heavy chain (CHC) in the pathogenicity of Botrytis cinerea, the agent of gray mold disease. To investigate the importance of this protein involved in coat vesicles formation in eukaryotic cells, a T-DNA insertional mutant reduced in the expression of the CHC-encoding gene, and a mutant expressing a dominant-negative form of CHC were studied. Both mutants were strongly affected in pathogenicity. Characterization of the mutants revealed altered infection cushions and an important defect in protein secretion. This study demonstrates the essential role of clathrin in the infectious process of a plant pathogenic fungus and more particularly its role in virulence factors delivery.
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Affiliation(s)
- Eytham Souibgui
- UMR 5240, CNRS MAP, INSA Lyon, Bayer SAS, UCBL, University Lyon, Lyon, France
| | - Christophe Bruel
- UMR 5240, CNRS MAP, INSA Lyon, Bayer SAS, UCBL, University Lyon, Lyon, France
| | - Mathias Choquer
- UMR 5240, CNRS MAP, INSA Lyon, Bayer SAS, UCBL, University Lyon, Lyon, France
| | - Amélie de Vallée
- UMR 5240, CNRS MAP, INSA Lyon, Bayer SAS, UCBL, University Lyon, Lyon, France
| | - Cindy Dieryckx
- UMR 5240, CNRS MAP, INSA Lyon, Bayer SAS, UCBL, University Lyon, Lyon, France
| | - Jean William Dupuy
- Plateforme Protéome, Centre de Génomique Fonctionnelle, Université de Bordeaux, Bordeaux, France
| | | | - Christine Rascle
- UMR 5240, CNRS MAP, INSA Lyon, Bayer SAS, UCBL, University Lyon, Lyon, France
| | - Nathalie Poussereau
- UMR 5240, CNRS MAP, INSA Lyon, Bayer SAS, UCBL, University Lyon, Lyon, France
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10
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Cirksena K, Hütte HJ, Shcherbakova A, Thumberger T, Sakson R, Weiss S, Jensen LR, Friedrich A, Todt D, Kuss AW, Ruppert T, Wittbrodt J, Bakker H, Buettner FFR. The C-Mannosylome of Human Induced Pluripotent Stem Cells Implies a Role for ADAMTS16 C-Mannosylation in Eye Development. Mol Cell Proteomics 2021; 20:100092. [PMID: 33975020 PMCID: PMC8256286 DOI: 10.1016/j.mcpro.2021.100092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/22/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022] Open
Abstract
C-mannosylation is a modification of tryptophan residues with a single mannose and can affect protein folding, secretion, and/or function. To date, only a few proteins have been demonstrated to be C-mannosylated, and studies that globally assess protein C-mannosylation are scarce. To interrogate the C-mannosylome of human induced pluripotent stem cells, we compared the secretomes of CRISPR–Cas9 mutants lacking either the C-mannosyltransferase DPY19L1 or DPY19L3 to WT human induced pluripotent stem cells using MS-based quantitative proteomics. The secretion of numerous proteins was reduced in these mutants, including that of A Disintegrin And Metalloproteinase with ThromboSpondin Motifs 16 (ADAMTS16), an extracellular protease that was previously reported to be essential for optic fissure fusion in zebrafish eye development. To test the functional relevance of this observation, we targeted dpy19l1 or dpy19l3 in embryos of the Japanese rice fish medaka (Oryzias latipes) by CRISPR–Cas9. We observed that targeting of dpy19l3 partially caused defects in optic fissure fusion, called coloboma. We further showed in a cellular model that DPY19L1 and DPY19L3 mediate C-mannosylation of a recombinantly expressed thrombospondin type 1 repeat of ADAMTS16 and thereby support its secretion. Taken together, our findings imply that DPY19L3-mediated C-mannosylation is involved in eye development by assisting secretion of the extracellular protease ADAMTS16. TSR1 of ADAMTS16 can be C-mannosylated. Deletion of DPY19L1 or DPY19L3 in hiPSCs caused reduced secretion of ADAMTS16. Targeting of dpy19l3 in medaka occasionally led to coloboma.
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Affiliation(s)
- Karsten Cirksena
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Hermann J Hütte
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | | | - Thomas Thumberger
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Roman Sakson
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany; HBIGS, Heidelberg Biosciences International Graduate School, Heidelberg University, Heidelberg, Germany; Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Stefan Weiss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Lars Riff Jensen
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Alina Friedrich
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Daniel Todt
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany; European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Andreas W Kuss
- Human Molecular Genetics Group, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Hans Bakker
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Falk F R Buettner
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany.
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11
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Abstract
Outbreaks and deaths related to Foodborne Diseases (FBD) occur constantly in the world, as a result of the consumption of contaminated foodstuffs with pathogens such as Listeria monocytogenes, Escherichia coli, Staphylococcus aureus, Salmonella spp, Clostridium spp. and Campylobacter spp. The purpose of this review is to discuss the main omic techniques applied in foodborne pathogen and to demonstrate their functionalities through the food chain and to guarantee the food safety. The main techniques presented are genomic, transcriptomic, secretomic, proteomic, and metabolomic, which together, in the field of food and nutrition, are known as "Foodomics." This review had highlighted the potential of omics to integrate variables that contribute to food safety and to enable us to understand their application on foodborne diseases. The appropriate use of these techniques had driven the definition of critical parameters to achieve successful results in the improvement of consumers health, costs and to obtain safe and high-quality products.
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Affiliation(s)
| | | | | | - Emmanuel Barboza
- Health Sciences Faculty, University of Western Sao Paulo, Presidente Prudente, Sao Paulo, Brazil
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12
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Tesei D, Chiang AJ, Kalkum M, Stajich JE, Mohan GBM, Sterflinger K, Venkateswaran K. Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus Knufia chersonesos. Front Genet 2021; 12:638708. [PMID: 33815472 PMCID: PMC8012687 DOI: 10.3389/fgene.2021.638708] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/19/2021] [Indexed: 11/13/2022] Open
Abstract
Black fungi are a group of melanotic microfungi characterized by remarkable polyextremotolerance. Due to a broad ecological plasticity and adaptations at the cellular level, it is predicted that they may survive in a variety of extreme environments, including harsh niches on Earth and Mars, and in outer space. However, the molecular mechanisms aiding survival, especially in space, are yet to be fully elucidated. Based on these premises, the rock-inhabiting black fungus Knufia chersonesos (Wt) and its non-melanized mutant (Mut) were exposed to simulated microgravity-one of the prevalent features characterizing space conditions-by growing the cultures in high-aspect-ratio vessels (HARVs). Qualitative and quantitative proteomic analyses were performed on the mycelia and supernatant of culture medium (secretome) to assess alterations in cell physiology in response to low-shear simulated microgravity (LSSMG) and to ultimately evaluate the role of cell-wall melanization in stress survival. Differential expression was observed for proteins involved in carbohydrate and lipid metabolic processes, transport, and ribosome biogenesis and translation via ribosomal translational machinery. However, no evidence of significant activation of stress components or starvation response was detected, except for the scytalone dehydratase, enzyme involved in the synthesis of dihydroxynaphthalene (DNH) melanin, which was found to be upregulated in the secretome of the wild type and downregulated in the mutant. Differences in protein modulation were observed between K. chersonesos Wt and Mut, with several proteins being downregulated under LSSMG in the Mut when compared to the Wt. Lastly, no major morphological alterations were observed following exposure to LSSMG. Similarly, the strains' survivability was not negatively affected. This study is the first to characterize the response to simulated microgravity in black fungi, which might have implications on future astrobiological missions.
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Affiliation(s)
- Donatella Tesei
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Abby J. Chiang
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Markus Kalkum
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Ganesh Babu Malli Mohan
- Department of Biotechnology, Centre for Research and Infectious Diseases, SASTRA Deemed University, Thanjavur, India
| | - Katja Sterflinger
- Institute for Natural Sciences and Technology in the Arts, Academy of Fine Arts Vienna, Vienna, Austria
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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13
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Neik TX, Amas J, Barbetti M, Edwards D, Batley J. Understanding Host-Pathogen Interactions in Brassica napus in the Omics Era. Plants (Basel) 2020; 9:E1336. [PMID: 33050509 PMCID: PMC7599536 DOI: 10.3390/plants9101336] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
Brassica napus (canola/oilseed rape/rapeseed) is an economically important crop, mostly found in temperate and sub-tropical regions, that is cultivated widely for its edible oil. Major diseases of Brassica crops such as Blackleg, Clubroot, Sclerotinia Stem Rot, Downy Mildew, Alternaria Leaf Spot and White Rust have caused significant yield and economic losses in rapeseed-producing countries worldwide, exacerbated by global climate change, and, if not remedied effectively, will threaten global food security. To gain further insights into the host-pathogen interactions in relation to Brassica diseases, it is critical that we review current knowledge in this area and discuss how omics technologies can offer promising results and help to push boundaries in our understanding of the resistance mechanisms. Omics technologies, such as genomics, proteomics, transcriptomics and metabolomics approaches, allow us to understand the host and pathogen, as well as the interaction between the two species at a deeper level. With these integrated data in multi-omics and systems biology, we are able to breed high-quality disease-resistant Brassica crops in a more holistic, targeted and accurate way.
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Affiliation(s)
- Ting Xiang Neik
- Sunway College Kuala Lumpur, Bandar Sunway 47500, Selangor, Malaysia;
| | - Junrey Amas
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
| | - Martin Barbetti
- School of Agriculture and Environment and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia;
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
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14
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Tüshaus J, Müller SA, Kataka ES, Zaucha J, Sebastian Monasor L, Su M, Güner G, Jocher G, Tahirovic S, Frishman D, Simons M, Lichtenthaler SF. An optimized quantitative proteomics method establishes the cell type-resolved mouse brain secretome. EMBO J 2020; 39:e105693. [PMID: 32954517 PMCID: PMC7560198 DOI: 10.15252/embj.2020105693] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 12/21/2022] Open
Abstract
To understand how cells communicate in the nervous system, it is essential to define their secretome, which is challenging for primary cells because of large cell numbers being required. Here, we miniaturized secretome analysis by developing the “high‐performance secretome protein enrichment with click sugars” (hiSPECS) method. To demonstrate its broad utility, hiSPECS was used to identify the secretory response of brain slices upon LPS‐induced neuroinflammation and to establish the cell type‐resolved mouse brain secretome resource using primary astrocytes, microglia, neurons, and oligodendrocytes. This resource allowed mapping the cellular origin of CSF proteins and revealed that an unexpectedly high number of secreted proteins in vitro and in vivo are proteolytically cleaved membrane protein ectodomains. Two examples are neuronally secreted ADAM22 and CD200, which we identified as substrates of the Alzheimer‐linked protease BACE1. hiSPECS and the brain secretome resource can be widely exploited to systematically study protein secretion and brain function and to identify cell type‐specific biomarkers for CNS diseases.
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Affiliation(s)
- Johanna Tüshaus
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Stephan A Müller
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Evans Sioma Kataka
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technical University of Munich, Freising, Germany
| | - Jan Zaucha
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technical University of Munich, Freising, Germany
| | | | - Minhui Su
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany
| | - Gökhan Güner
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Georg Jocher
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Sabina Tahirovic
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technical University of Munich, Freising, Germany
| | - Mikael Simons
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Institute of Neuronal Cell Biology, Technical University Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.,Neuroproteomics, School of Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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15
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Dettmer R, Cirksena K, Münchhoff J, Kresse J, Diekmann U, Niwolik I, Buettner FFR, Naujok O. FGF2 Inhibits Early Pancreatic Lineage Specification during Differentiation of Human Embryonic Stem Cells. Cells 2020; 9:cells9091927. [PMID: 32825270 PMCID: PMC7565644 DOI: 10.3390/cells9091927] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/12/2020] [Accepted: 08/18/2020] [Indexed: 02/07/2023] Open
Abstract
Growth factors are important regulators during organ development. For many vertebrates (but not humans) it is known how they contribute to the formation and expansion of PDX1-positive cells during pancreas organogenesis. Here, the effects of the fibroblast growth factors FGF2, FGF7, FGF10, and epidermal growth factor (EGF) on pancreas development in humans were assessed by using human pluripotent stem cells (hPSCs). During this, FGF2 was identified as a potent anti-pancreatic factor whereas FGF7, FGF10, and EGF increased the cell mass while retaining PDX1-positivity. FGF2 increased the expression of the anti-pancreatic factor sonic hedgehog (SHH) while suppressing PDX1 in a dose-dependent manner. Differentiating cells secreted SHH to the medium and we interrogated the cells’ secretome during differentiation to globally examine the composition of secreted signaling factors. Members of the TGF-beta-, Wnt-, and FGF-pathways were detected. FGF17 showed a suppressive anti-pancreatic effect comparable to FGF2. By inhibition of specific branches of FGF-receptor signaling, we allocated the SHH-induction by FGF2 to MEK/ERK-signaling and the anti-pancreatic effect of FGF2 to the receptor variant FGFR1c or 3c. Altogether, we report findings on the paracrine activity of differentiating hPSCs during generation of pancreatic progenitors. These observations suggest a different role for FGF2 in humans compared to animal models of pancreas organogenesis.
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16
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Beumer J, Puschhof J, Bauzá-Martinez J, Martínez-Silgado A, Elmentaite R, James KR, Ross A, Hendriks D, Artegiani B, Busslinger GA, Ponsioen B, Andersson-Rolf A, Saftien A, Boot C, Kretzschmar K, Geurts MH, Bar-Ephraim YE, Pleguezuelos-Manzano C, Post Y, Begthel H, van der Linden F, Lopez-Iglesias C, van de Wetering WJ, van der Linden R, Peters PJ, Heck AJR, Goedhart J, Snippert H, Zilbauer M, Teichmann SA, Wu W, Clevers H. High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells. Cell 2020; 181:1291-1306.e19. [PMID: 32407674 DOI: 10.1016/j.cell.2020.04.036] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/10/2020] [Accepted: 04/21/2020] [Indexed: 12/11/2022]
Abstract
Enteroendocrine cells (EECs) sense intestinal content and release hormones to regulate gastrointestinal activity, systemic metabolism, and food intake. Little is known about the molecular make-up of human EEC subtypes and the regulated secretion of individual hormones. Here, we describe an organoid-based platform for functional studies of human EECs. EEC formation is induced in vitro by transient expression of NEUROG3. A set of gut organoids was engineered in which the major hormones are fluorescently tagged. A single-cell mRNA atlas was generated for the different EEC subtypes, and their secreted products were recorded by mass-spectrometry. We note key differences to murine EECs, including hormones, sensory receptors, and transcription factors. Notably, several hormone-like molecules were identified. Inter-EEC communication is exemplified by secretin-induced GLP-1 secretion. Indeed, individual EEC subtypes carry receptors for various EEC hormones. This study provides a rich resource to study human EEC development and function.
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Affiliation(s)
- Joep Beumer
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Jens Puschhof
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Julia Bauzá-Martinez
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Adriana Martínez-Silgado
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Kylie R James
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Alexander Ross
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Delilah Hendriks
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Benedetta Artegiani
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Georg A Busslinger
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Bas Ponsioen
- Oncode Institute, Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Amanda Andersson-Rolf
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Aurelia Saftien
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Charelle Boot
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Kai Kretzschmar
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Maarten H Geurts
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Yotam E Bar-Ephraim
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Cayetano Pleguezuelos-Manzano
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Yorick Post
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Harry Begthel
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Franka van der Linden
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, the Netherlands
| | - Carmen Lopez-Iglesias
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6229 ER Maastricht, the Netherlands
| | - Willine J van de Wetering
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6229 ER Maastricht, the Netherlands
| | - Reinier van der Linden
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, 6229 ER Maastricht, the Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Joachim Goedhart
- Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Amsterdam, the Netherlands
| | - Hugo Snippert
- Oncode Institute, Center for Molecular Medicine, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands; The Princess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands.
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17
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Molloy K, Cagney G, Dillon ET, Wynne K, Greene CM, McElvaney NG. Impaired Airway Epithelial Barrier Integrity in Response to Stenotrophomonas maltophilia Proteases, Novel Insights Using Cystic Fibrosis Bronchial Epithelial Cell Secretomics. Front Immunol 2020; 11:198. [PMID: 32161586 PMCID: PMC7053507 DOI: 10.3389/fimmu.2020.00198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/27/2020] [Indexed: 11/13/2022] Open
Abstract
Stenotrophomonas maltophilia is a Gram-negative opportunistic pathogen that can chronically colonize the lungs of people with cystic fibrosis (CF) and is associated with lethal pulmonary hemorrhage in immunocompromised patients. Its secreted virulence factors include the extracellular serine proteases StmPR1, StmPR2, and StmPR3. To explore the impact of secreted virulence determinants on pulmonary mucosal defenses in CF, we examined the secretome of human CFBE41o- bronchial epithelial cells in response to treatment with S. maltophilia K279a cell culture supernatant (CS) using a liquid-chromatography-tandem mass spectrometry (LC-MS/MS) based label-free quantitative (LFQ) shotgun proteomics approach for global profiling of the cell secretome. Secretome analysis identified upregulated pathways mainly relating to biological adhesion and epithelial cell signaling in infection, whereas no specific pathways relating to the immune response were enriched. Further exploration of the potentially harmful effects of K279a CS on CF bronchial epithelial cells, demonstrated that K279a CS caused CFBE41o- cell condensation and detachment, reversible by the serine protease inhibitor PMSF. K279a CS also decreased trans-epithelial electrical resistance in CFBE41o- cell monolayers suggestive of disruption of tight junction complexes (TJC). This finding was corroborated by an observed increase in fluorescein isothiocyanate (FITC) dextran permeability and by demonstrating PMSF-sensitive degradation of the tight junction proteins ZO-1 and occludin, but not JAM-A or claudin-1. These observations demonstrating destruction of the CFBE41o- TJC provide a novel insight regarding the virulence of S. maltophilia and may explain the possible injurious effects of this bacterium on the CF bronchial epithelium and the pathogenic mechanism leading to lethal pulmonary hemorrhage.
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Affiliation(s)
- Kevin Molloy
- Department of Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Eugene T Dillon
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Catherine M Greene
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Noel G McElvaney
- Department of Medicine, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
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18
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de Vallée A, Bally P, Bruel C, Chandat L, Choquer M, Dieryckx C, Dupuy JW, Kaiser S, Latorse MP, Loisel E, Mey G, Morgant G, Rascle C, Schumacher J, Simon A, Souibgui E, Viaud M, Villalba F, Poussereau N. A Similar Secretome Disturbance as a Hallmark of Non-pathogenic Botrytis cinerea ATMT-Mutants? Front Microbiol 2019; 10:2829. [PMID: 31866989 PMCID: PMC6908482 DOI: 10.3389/fmicb.2019.02829] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/21/2019] [Indexed: 12/31/2022] Open
Abstract
The gray mold fungus Botrytis cinerea is a necrotrophic pathogen able to infect hundreds of host plants, including high-value crops such as grapevine, strawberry and tomato. In order to decipher its infectious strategy, a library of 2,144 mutants was generated by random insertional mutagenesis using Agrobacterium tumefaciens-mediated transformation (ATMT). Twelve mutants exhibiting total loss of virulence toward different host plants were chosen for detailed analyses. Their molecular characterization revealed a single T-DNA insertion in different loci. Using a proteomics approach, the secretome of four of these strains was compared to that of the parental strain and a common profile of reduced lytic enzymes was recorded. Significant variations in this profile, notably deficiencies in the secretion of proteases and hemicellulases, were observed and validated by biochemical tests. They were also a hallmark of the remaining eight non-pathogenic strains, suggesting the importance of these secreted proteins in the infection process. In the twelve non-pathogenic mutants, the differentiation of infection cushions was also impaired, suggesting a link between the penetration structures and the secretion of proteins involved in the virulence of the pathogen.
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Affiliation(s)
- Amélie de Vallée
- Microbiologie, Adaptation et Pathogénie, UMR 5240, Univ Lyon, Université Lyon 1, Bayer SAS, Lyon, France
| | - Pascal Bally
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Christophe Bruel
- Microbiologie, Adaptation et Pathogénie, UMR 5240, Univ Lyon, Université Lyon 1, Bayer SAS, Lyon, France
| | - Lucie Chandat
- Centre de Recherche La Dargoire, Bayer SAS, Lyon, France
| | - Mathias Choquer
- Microbiologie, Adaptation et Pathogénie, UMR 5240, Univ Lyon, Université Lyon 1, Bayer SAS, Lyon, France
| | - Cindy Dieryckx
- Microbiologie, Adaptation et Pathogénie, UMR 5240, Univ Lyon, Université Lyon 1, Bayer SAS, Lyon, France
| | - Jean William Dupuy
- Plateforme Protéome, Centre de Génomique Fonctionnelle, Université de Bordeaux, Bordeaux, France
| | - Sophie Kaiser
- Microbiologie, Adaptation et Pathogénie, UMR 5240, Univ Lyon, Université Lyon 1, Bayer SAS, Lyon, France
| | | | - Elise Loisel
- Microbiologie, Adaptation et Pathogénie, UMR 5240, Univ Lyon, Université Lyon 1, Bayer SAS, Lyon, France
| | - Géraldine Mey
- Microbiologie, Adaptation et Pathogénie, UMR 5240, Univ Lyon, Université Lyon 1, Bayer SAS, Lyon, France
| | - Guillaume Morgant
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Christine Rascle
- Microbiologie, Adaptation et Pathogénie, UMR 5240, Univ Lyon, Université Lyon 1, Bayer SAS, Lyon, France
| | - Julia Schumacher
- Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| | - Adeline Simon
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Eytham Souibgui
- Microbiologie, Adaptation et Pathogénie, UMR 5240, Univ Lyon, Université Lyon 1, Bayer SAS, Lyon, France
| | - Muriel Viaud
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | | | - Nathalie Poussereau
- Microbiologie, Adaptation et Pathogénie, UMR 5240, Univ Lyon, Université Lyon 1, Bayer SAS, Lyon, France
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Deshmukh AS, Peijs L, Beaudry JL, Jespersen NZ, Nielsen CH, Ma T, Brunner AD, Larsen TJ, Bayarri-Olmos R, Prabhakar BS, Helgstrand C, Severinsen MCK, Holst B, Kjaer A, Tang-Christensen M, Sanfridson A, Garred P, Privé GG, Pedersen BK, Gerhart-Hines Z, Nielsen S, Drucker DJ, Mann M, Scheele C. Proteomics-Based Comparative Mapping of the Secretomes of Human Brown and White Adipocytes Reveals EPDR1 as a Novel Batokine. Cell Metab 2019; 30:963-975.e7. [PMID: 31668873 DOI: 10.1016/j.cmet.2019.10.001] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 04/26/2019] [Accepted: 10/02/2019] [Indexed: 10/25/2022]
Abstract
Adipokines secreted from white adipose tissue play a role in metabolic crosstalk and homeostasis, whereas the brown adipose secretome is less explored. We performed high-sensitivity mass-spectrometry-based proteomics on the cell media of human adipocytes derived from the supraclavicular brown adipose and from the subcutaneous white adipose depots of adult humans. We identified 471 potentially secreted proteins covering interesting categories such as hormones, growth factors, extracellular matrix proteins, and proteins of the complement system, which were differentially regulated between brown and white adipocytes. A total of 101 proteins were exclusively quantified in brown adipocytes, and among these was ependymin-related protein 1 (EPDR1). EPDR1 was detected in human plasma, and functional studies suggested a role for EPDR1 in thermogenic determination during adipogenesis. In conclusion, we report substantial differences between the secretomes of brown and white human adipocytes and identify novel candidate batokines that can be important regulators of human metabolism.
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Affiliation(s)
- Atul S Deshmukh
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Lone Peijs
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen 2100, Denmark
| | - Jacqueline L Beaudry
- The Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Department of Medicine, University of Toronto, Toronto, ON M5G 1X5, Canada
| | - Naja Z Jespersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen 2100, Denmark
| | - Carsten H Nielsen
- Department of Clinical Physiology, Nuclear Medicine and PET and Cluster for Molecular Imaging, Department of Biomedical Sciences, Rigshospitalet and University of Copenhagen, Copenhagen 2200, Denmark; Minerva Imaging ApS, Copenhagen 2200, Denmark
| | - Tao Ma
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Andreas D Brunner
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Therese J Larsen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen 2100, Denmark
| | - Rafael Bayarri-Olmos
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen 2100, Denmark
| | - Bhargav S Prabhakar
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | | | - Mai C K Severinsen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen 2100, Denmark
| | - Birgitte Holst
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Andreas Kjaer
- Department of Clinical Physiology, Nuclear Medicine and PET and Cluster for Molecular Imaging, Department of Biomedical Sciences, Rigshospitalet and University of Copenhagen, Copenhagen 2200, Denmark
| | | | | | - Peter Garred
- Laboratory of Molecular Medicine, Department of Clinical Immunology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen 2100, Denmark
| | - Gilbert G Privé
- Princess Margaret Cancer Centre, Toronto, ON M5G 1L7, Canada
| | - Bente K Pedersen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen 2100, Denmark
| | - Zachary Gerhart-Hines
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark
| | - Søren Nielsen
- The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen 2100, Denmark
| | - Daniel J Drucker
- The Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Department of Medicine, University of Toronto, Toronto, ON M5G 1X5, Canada
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark.
| | - Camilla Scheele
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2200, Denmark; The Centre of Inflammation and Metabolism and the Centre for Physical Activity Research, Rigshospitalet, University of Copenhagen, Copenhagen 2100, Denmark.
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20
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Song P, Kwon Y, Joo JY, Kim DG, Yoon JH. Secretomics to Discover Regulators in Diseases. Int J Mol Sci 2019; 20:ijms20163893. [PMID: 31405033 PMCID: PMC6720857 DOI: 10.3390/ijms20163893] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/01/2019] [Accepted: 08/08/2019] [Indexed: 01/03/2023] Open
Abstract
Secretory proteins play important roles in the cross-talk of individual functional units, including cells. Since secretory proteins are essential for signal transduction, they are closely related with disease development, including metabolic and neural diseases. In metabolic diseases, adipokines, myokines, and hepatokines are secreted from respective organs under specific environmental conditions, and play roles in glucose homeostasis, angiogenesis, and inflammation. In neural diseases, astrocytes and microglia cells secrete cytokines and chemokines that play roles in neurotoxic and neuroprotective responses. Mass spectrometry-based secretome profiling is a powerful strategy to identify and characterize secretory proteins. This strategy involves stepwise processes such as the collection of conditioned medium (CM) containing secretome proteins and concentration of the CM, peptide preparation, mass analysis, database search, and filtering of secretory proteins; each step requires certain conditions to obtain reliable results. Proteomic analysis of extracellular vesicles has become a new research focus for understanding the additional extracellular functions of intracellular proteins. Here, we provide a review of the insights obtained from secretome analyses with regard to disease mechanisms, and highlight the future prospects of this technology. Continued research in this field is expected to provide valuable information on cell-to-cell communication and uncover new pathological mechanisms.
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Affiliation(s)
- Parkyong Song
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan 50612, Korea
| | - Yonghoon Kwon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Jae-Yeol Joo
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu 41062, Korea
| | - Do-Geun Kim
- Dementia Research Group, Korea Brain Research Institute, Daegu 41062, Korea
| | - Jong Hyuk Yoon
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu 41062, Korea.
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Yoon JH, Kim D, Kim J, Lee H, Ghim J, Kang BJ, Song P, Suh PG, Ryu SH, Lee TG. NOTUM Is Involved in the Progression of Colorectal Cancer. Cancer Genomics Proteomics 2018; 15:485-497. [PMID: 30343282 DOI: 10.21873/cgp.20107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND There are limitations to current colorectal cancer (CRC)-specific diagnostic methods and therapies. Tumorigenesis proceeds because of interaction between cancer cells and various surrounding cells; discovering new molecular mediators through studies of the CRC secretome is a promising approach for the development of CRC diagnostics and therapies. MATERIALS AND METHODS A comparative secretomic analysis was performed using primary and metastatic human isogenic CRC cells. Proliferation was determined by MTT and thymidine incorporation assay, migration was determined by wound-healing assay (ELISA). The level of palmitoleoyl-protein carboxylesterase (NOTUM) in plasma from patients with CRC was determined by enzyme-linked immunosorbent assay. RESULTS NOTUM expression was increased in metastatic cells. Proliferation was suppressed by inhibiting expression of NOTUM. Knockdown of NOTUM genes inhibited proliferation as well as migration, with possible involvement of p38 and c-JUN N-terminal kinase in this process. The result was verified in patients with CRC. CONCLUSION NOTUM may be a new candidate for diagnostics and therapy of CRC.
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Affiliation(s)
- Jong Hyuk Yoon
- Department of Neural Development and Disease, Korea Brain Research Institute, Daegu, Republic of Korea
| | - Dayea Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - Jaeyoon Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.,NovaCell Technology, Inc., Pohang, Republic of Korea
| | - Hyeongjoo Lee
- NovaCell Technology, Inc., Pohang, Republic of Korea
| | - Jaewang Ghim
- NovaCell Technology, Inc., Pohang, Republic of Korea
| | - Byung Jun Kang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Parkyong Song
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Pann-Ghill Suh
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Sung Ho Ryu
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Taehoon G Lee
- NovaCell Technology, Inc., Pohang, Republic of Korea
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22
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Rebets Y, Tsolis KC, Guðmundsdóttir EE, Koepff J, Wawiernia B, Busche T, Bleidt A, Horbal L, Myronovskyi M, Ahmed Y, Wiechert W, Rückert C, Hamed MB, Bilyk B, Anné J, Friðjónsson Ó, Kalinowski J, Oldiges M, Economou A, Luzhetskyy A. Characterization of Sigma Factor Genes in Streptomyces lividans TK24 Using a Genomic Library-Based Approach for Multiple Gene Deletions. Front Microbiol 2018; 9:3033. [PMID: 30619125 PMCID: PMC6295645 DOI: 10.3389/fmicb.2018.03033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 11/23/2018] [Indexed: 12/15/2022] Open
Abstract
Alternative sigma factors control numerous aspects of bacterial life, including adaptation to physiological stresses, morphological development, persistence states and virulence. This is especially true for the physiologically complex actinobacteria. Here we report the development of a robust gene deletions system for Streptomyces lividans TK24 based on a BAC library combined with the λ-Red recombination technique. The developed system was validated by systematically deleting the most highly expressed genes encoding alternative sigma factors and several other regulatory genes within the chromosome of S. lividans TK24. To demonstrate the possibility of large scale genomic manipulations, the major part of the undecylprodigiosin gene cluster was deleted as well. The resulting mutant strains were characterized in terms of morphology, growth parameters, secondary metabolites production and response to thiol-oxidation and cell-wall stresses. Deletion of SLIV_12645 gene encoding S. coelicolor SigR1 ortholog has the most prominent phenotypic effect, resulted in overproduction of actinorhodin and coelichelin P1 and increased sensitivity to diamide. The secreted proteome analysis of SLIV_12645 mutant revealed SigR1 influence on trafficking of proteins involved in cell wall biogenesis and refactoring. The reported here gene deletion system will further facilitate work on S. lividans strain improvement as a host for either secondary metabolites or protein production and will contribute to basic research in streptomycetes physiology, morphological development, secondary metabolism. On the other hand, the systematic deletion of sigma factors encoding genes demonstrates the complexity and conservation of regulatory processes conducted by sigma factors in streptomycetes.
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Affiliation(s)
- Yuriy Rebets
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | | | | | - Joachim Koepff
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | | | - Tobias Busche
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Arne Bleidt
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Liliya Horbal
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Maksym Myronovskyi
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Yousra Ahmed
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Wolfgang Wiechert
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | | | - Mohamed B. Hamed
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Department of Molecular Biology, National Research Centre, Giza, Egypt
| | - Bohdan Bilyk
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
| | - Jozef Anné
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | | | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Marco Oldiges
- IBG-1: Biotechnology, Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Anastassios Economou
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Andriy Luzhetskyy
- Pharmazeutische Biotechnologie, Universität des Saarlandes, Saarbrücken, Germany
- Actinobacteria Metabolic Engineering Group, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany
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Li JM, Tseng CW, Lin CC, Law CH, Chien YA, Kuo WH, Chou HC, Wang WC, Chan HL. Upregulation of LGALS1 is associated with oral cancer metastasis. Ther Adv Med Oncol 2018; 10:1758835918794622. [PMID: 30159048 PMCID: PMC6109855 DOI: 10.1177/1758835918794622] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/04/2018] [Indexed: 12/12/2022] Open
Abstract
Background Oral cancer metastasis is a devastating process that contributes to poor prognosis and high mortality, yet its detailed underlying mechanisms remain unclear. Here, we aimed to evaluate metastasis-specific markers in oral cancer and to provide comprehensive recognition concerning functional roles of the specific target in oral cancer metastasis. Methods Lectin, galactoside-binding, soluble, 1 (LGALS1) was identified by secretomic analysis. LGALS1 expression of patient samples with oral cancer on the tissue microarray were examined by immunochemical (IHC) staining. Small interfering RNA (siRNA)-mediated knockdown of LGALS1 revealed the role of LGALS1 in oral cancer metastasis in vitro and in vivo. Results LGALS1 was observed to be upregulated in highly invasive oral cancer cells, and elevated LGALS1 expression was correlated with cancer progression and lymph node metastasis in oral cancer tissue specimens. Functionally, silencing LGALS1 resulted in suppressed cell growth, wound healing, cell migration, and cell invasion in oral cancer cells in vitro. Knockdown of LGALS1 in highly invasive oral cancer cells dramatically inhibited lung metastasis in an in vivo mouse model. Mechanistic studies suggested p38 mitogen-activated protein kinase (MAPK) phosphorylation, upregulated MMP-9, and mesenchymal phenotypes of epithelial-mesenchymal transition (EMT) in highly invasive oral cancer cells, whereas siRNA against LGALS1 resulted in the inactivation of p38 MAPK pathway, downregulated MMP-9, and EMT inhibition. Conclusions These findings demonstrate that elevated LGALS1 is strongly correlated with oral cancer progression and metastasis, and that it could potentially serve as a prognostic biomarker and an innovative target for oral cancer therapy.
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Affiliation(s)
- Ji-Min Li
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chien-Wei Tseng
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan
| | - Chi-Chen Lin
- Department of Life Sciences, Institute of Biomedical Science, National Chung Hsing University, Taichung, Taiwan
| | - Ching-Hsuan Law
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Yu-An Chien
- Department of Applied Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | - Wen-Hung Kuo
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Hsiu-Chuan Chou
- Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan
| | - Wen-Ching Wang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Hong-Lin Chan
- Institute of Bioinformatics and Structural Biology and Department of Medical Sciences, National Tsing Hua University, No. 101, Kuang-Fu Rd. Sec. 2, Hsinchu, 30013, Taiwan
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Vincent D, Plummer KM, Solomon PS, Lebrun MH, Job D, Rafiqi M. Editorial: How Can Secretomics Help Unravel the Secrets of Plant-Microbe Interactions? Front Plant Sci 2016; 7:1777. [PMID: 27965687 PMCID: PMC5127848 DOI: 10.3389/fpls.2016.01777] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/11/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Delphine Vincent
- Department of Economic Development, Jobs, Transport and Resources, AgriBio, La Trobe UniversityBundoora, VIC, Australia
| | - Kim M. Plummer
- Animal, Plant and Soil Sciences Department, AgriBio, La Trobe UniversityBundoora, VIC, Australia
| | - Peter S. Solomon
- Plant Sciences Division, Research School of Biology, The Australian National UniversityCanberra, ACT, Australia
| | - Marc-Henri Lebrun
- Institut National de la Recherche Agronomique-AgroParisTech, UMR INRA1290, Biologie et Gestion des Risques en Agriculture - Champignons Pathogènes des PlantesThiverval-Grignon, France
| | - Dominique Job
- Centre National de la Recherche-Scientifique, UMR5240 Centre Nationnal de la Recherche Scientifique/University Claude Bernard Lyon 1/INSA/Bayer CropScience Joint Laboratory, Bayer CropScienceLyon, France
| | - Maryam Rafiqi
- Jodrell Laboratory, Royal Botanic GardensKew, London, UK
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Garcia K, Ané JM. Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins. Front Microbiol 2016; 7:1734. [PMID: 27853454 PMCID: PMC5089978 DOI: 10.3389/fmicb.2016.01734] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 10/17/2016] [Indexed: 12/25/2022] Open
Affiliation(s)
- Kevin Garcia
- Department of Bacteriology, University of Wisconsin-Madison , Madison, WI, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; Department of Agronomy, University of Wisconsin-Madison, Madison, WI, USA
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Kaihola H, Yaldir FG, Hreinsson J, Hörnaeus K, Bergquist J, Olivier JDA, Åkerud H, Sundström-Poromaa I. Effects of Fluoxetine on Human Embryo Development. Front Cell Neurosci 2016; 10:160. [PMID: 27378857 PMCID: PMC4909759 DOI: 10.3389/fncel.2016.00160] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/01/2016] [Indexed: 02/05/2023] Open
Abstract
The use of antidepressant treatment during pregnancy is increasing, and selective serotonin reuptake inhibitors (SSRIs) are the most widely prescribed antidepressants in pregnant women. Serotonin plays a role in embryogenesis, and serotonin transporters are expressed in two-cell mouse embryos. Thus, the aim of the present study was to evaluate whether fluoxetine, one of the most prescribed SSRI antidepressant world-wide, exposure influences the timing of different embryo developmental stages, and furthermore, to analyze what protein, and protein networks, are affected by fluoxetine in the early embryo development. Human embryos (n = 48) were randomly assigned to treatment with 0.25 or 0.5 μM fluoxetine in culture medium. Embryo development was evaluated by time-lapse monitoring. The fluoxetine-induced human embryo proteome was analyzed by shotgun mass spectrometry. Protein secretion from fluoxetine-exposed human embryos was analyzed by use of high-multiplex immunoassay. The lower dose of fluoxetine had no influence on embryo development. A trend toward reduced time between thawing and start of cavitation was noted in embryos treated with 0.5 μM fluoxetine (p = 0.065). Protein analysis by shotgun mass spectrometry detected 45 proteins that were uniquely expressed in fluoxetine-treated embryos. These proteins are involved in cell growth, survival, proliferation, and inflammatory response. Culturing with 0.5 μM, but not 0.25 μM fluoxetine, caused a significant increase in urokinase-type plasminogen activator (uPA) in the culture medium. In conclusion, fluoxetine has marginal effects on the timing of developmental stages in embryos, but induces expression and secretion of several proteins in a manner that depends on dose. For these reasons, and in line with current guidelines, the lowest possible dose of SSRI should be used in pregnant women who need to continue treatment.
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Affiliation(s)
- Helena Kaihola
- Department of Women's and Children's Health, Uppsala University Uppsala, Sweden
| | - Fatma G Yaldir
- Centre of Reproduction, Uppsala University Hospital Uppsala, Sweden
| | | | - Katarina Hörnaeus
- Analytical Chemistry, Department of Chemistry - BMC and Science for Life Laboratory, Uppsala University Uppsala, Sweden
| | - Jonas Bergquist
- Analytical Chemistry, Department of Chemistry - BMC and Science for Life Laboratory, Uppsala University Uppsala, Sweden
| | - Jocelien D A Olivier
- Unit Behavioural Neuroscience, Department of Neurobiology, Groningen Institute for Evolutionary Life Sciences, University of Groningen Groningen, Netherlands
| | - Helena Åkerud
- Department of Women's and Children's Health, Uppsala University Uppsala, Sweden
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Pellegrin C, Morin E, Martin FM, Veneault-Fourrey C. Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins. Front Microbiol 2015; 6:1278. [PMID: 26635749 PMCID: PMC4649063 DOI: 10.3389/fmicb.2015.01278] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/31/2015] [Indexed: 12/20/2022] Open
Abstract
Fungi are major players in the carbon cycle in forest ecosystems due to the wide range of interactions they have with plants either through soil degradation processes by litter decayers or biotrophic interactions with pathogenic and ectomycorrhizal symbionts. Secretion of fungal proteins mediates these interactions by allowing the fungus to interact with its environment and/or host. Ectomycorrhizal (ECM) symbiosis independently appeared several times throughout evolution and involves approximately 80% of trees. Despite extensive physiological studies on ECM symbionts, little is known about the composition and specificities of their secretomes. In this study, we used a bioinformatics pipeline to predict and analyze the secretomes of 49 fungal species, including 11 ECM fungi, wood and soil decayers and pathogenic fungi to tackle the following questions: (1) Are there differences between the secretomes of saprophytic and ECM fungi? (2) Are small-secreted proteins (SSPs) more abundant in biotrophic fungi than in saprophytic fungi? and (3) Are there SSPs shared between ECM, saprotrophic and pathogenic fungi? We showed that the number of predicted secreted proteins is similar in the surveyed species, independently of their lifestyle. The secretome from ECM fungi is characterized by a restricted number of secreted CAZymes, but their repertoires of secreted proteases and lipases are similar to those of saprotrophic fungi. Focusing on SSPs, we showed that the secretome of ECM fungi is enriched in SSPs compared with other species. Most of the SSPs are coded by orphan genes with no known PFAM domain or similarities to known sequences in databases. Finally, based on the clustering analysis, we identified shared- and lifestyle-specific SSPs between saprotrophic and ECM fungi. The presence of SSPs is not limited to fungi interacting with living plants as the genome of saprotrophic fungi also code for numerous SSPs. ECM fungi shared lifestyle-specific SSPs likely involved in symbiosis that are good candidates for further functional analyses.
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Affiliation(s)
- Clement Pellegrin
- UMR 1136 Interactions Arbres/Microorganismes, Université de LorraineVandoeuvre-lès-Nancy, France
- UMR 1136 Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Institut National de la Recherche Agronomique, INRA-NancyChampenoux, France
| | - Emmanuelle Morin
- UMR 1136 Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Institut National de la Recherche Agronomique, INRA-NancyChampenoux, France
| | - Francis M. Martin
- UMR 1136 Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Institut National de la Recherche Agronomique, INRA-NancyChampenoux, France
| | - Claire Veneault-Fourrey
- UMR 1136 Interactions Arbres/Microorganismes, Université de LorraineVandoeuvre-lès-Nancy, France
- UMR 1136 Interactions Arbres/Microorganismes, Laboratoire d'Excellence ARBRE, Institut National de la Recherche Agronomique, INRA-NancyChampenoux, France
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Abstract
Proteomics of secretory granules is an emerging strategy for identifying secreted proteins, including potentially novel candidate biomarkers and peptide hormones. In addition, proteomics can provide information about the abundance, localization and structure (post-translational modification) of granule proteins and peptides. Analytical strategies within this research line include so-called 'subtractive proteomics', 'peptidomics' and granule purification by the use of multiple gradient centrifugations. Here we review the literature, and describe the challenges and opportunities in proteomics of secretory granules.
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Affiliation(s)
- Jakob Albrethsen
- Department of Clinical Biochemistry (KB3014), Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
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Dieryckx C, Gaudin V, Dupuy JW, Bonneu M, Girard V, Job D. Beyond plant defense: insights on the potential of salicylic and methylsalicylic acid to contain growth of the phytopathogen Botrytis cinerea. Front Plant Sci 2015; 6:859. [PMID: 26528317 PMCID: PMC4607878 DOI: 10.3389/fpls.2015.00859] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 09/29/2015] [Indexed: 05/27/2023]
Abstract
Using Botrytis cinerea we confirmed in the present work several previous studies showing that salicylic acid, a main plant hormone, inhibits fungal growth in vitro. Such an inhibitory effect was also observed for the two salicylic acid derivatives, methylsalicylic and acetylsalicylic acid. In marked contrast, 5-sulfosalicylic acid was totally inactive. Comparative proteomics from treated vs. control mycelia showed that both the intracellular and extracellular proteomes were affected in the presence of salicylic acid or methylsalicylic acid. These data suggest several mechanisms that could potentially account for the observed fungal growth inhibition, notably pH regulation, metal homeostasis, mitochondrial respiration, ROS accumulation and cell wall remodeling. The present observations support a role played by the phytohormone SA and derivatives in directly containing the pathogen. Data are available via ProteomeXchange with identifier PXD002873.
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Affiliation(s)
- Cindy Dieryckx
- Laboratoire Mixte UMR 5240, Plateforme de Protéomique, Centre National de la Recherche ScientifiqueLyon, France
| | - Vanessa Gaudin
- Laboratoire Mixte UMR 5240, Plateforme de Protéomique, Centre National de la Recherche ScientifiqueLyon, France
| | - Jean-William Dupuy
- Plateforme Protéome, Centre de Génomique Fonctionnelle, Université de BordeauxBordeaux, France
| | - Marc Bonneu
- Plateforme Protéome, Centre de Génomique Fonctionnelle, Université de BordeauxBordeaux, France
| | - Vincent Girard
- Laboratoire Mixte UMR 5240, Plateforme de Protéomique, Centre National de la Recherche ScientifiqueLyon, France
| | - Dominique Job
- Laboratoire Mixte UMR 5240, Plateforme de Protéomique, Centre National de la Recherche ScientifiqueLyon, France
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González-Fernández R, Valero-Galván J, Gómez-Gálvez FJ, Jorrín-Novo JV. Unraveling the in vitro secretome of the phytopathogen Botrytis cinerea to understand the interaction with its hosts. Front Plant Sci 2015; 6:839. [PMID: 26500673 PMCID: PMC4598570 DOI: 10.3389/fpls.2015.00839] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/24/2015] [Indexed: 05/09/2023]
Abstract
Botrytis cinerea is a necrotrophic fungus with high adaptability to different environments and hosts. It secretes a large number of extracellular proteins, which favor plant tissue penetration and colonization, thus contributing to virulence. Secretomics is a proteomics sub-discipline which study the secreted proteins and their secretion mechanisms, so-called secretome. By using proteomics as experimental approach, many secreted proteins by B. cinerea have been identified from in vitro experiments, and belonging to different functional categories: (i) cell wall-degrading enzymes such as pectinesterases and endo-polygalacturonases; (ii) proteases involved in host protein degradation such as an aspartic protease; (iii) proteins related to the oxidative burst such as glyoxal oxidase; (iv) proteins which may induce the plant hypersensitive response such as a cerato-platanin domain-containing protein; and (v) proteins related to production and secretion of toxins such as malate dehydrogenase. In this mini-review, we made an overview of the proteomics contribution to the study and knowledge of the B. cinerea extracellular secreted proteins based on our current work carried out from in vitro experiments, and recent published papers both in vitro and in planta studies on this fungi. We hypothesize on the putative functions of these secreted proteins, and their connection to the biology of the B. cinerea interaction with its hosts.
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Affiliation(s)
- Raquel González-Fernández
- Department of Chemical and Biological Science, Biomedicine Science Institute, Autonomous University of Ciudad JuárezCiudad Juárez, México
- *Correspondence: Raquel González-Fernández,
| | - José Valero-Galván
- Department of Chemical and Biological Science, Biomedicine Science Institute, Autonomous University of Ciudad JuárezCiudad Juárez, México
| | - Francisco J. Gómez-Gálvez
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba, Agrifood Campus of International Excellence (ceiA3)Córdoba, Spain
| | - Jesús V. Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba, Agrifood Campus of International Excellence (ceiA3)Córdoba, Spain
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Palomäki J, Sund J, Vippola M, Kinaret P, Greco D, Savolainen K, Puustinen A, Alenius H. A secretomics analysis reveals major differences in the macrophage responses towards different types of carbon nanotubes. Nanotoxicology 2014; 9:719-28. [PMID: 25325160 DOI: 10.3109/17435390.2014.969346] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Certain types of carbon nanotubes (CNT) can evoke inflammation, fibrosis and mesothelioma in vivo, raising concerns about their potential health effects. It has been recently postulated that NLRP3 inflammasome activation is important in the CNT-induced toxicity. However, more comprehensive studies of the protein secretion induced by CNT can provide new information about their possible pathogenic mechanisms. Here, we studied protein secretion from human macrophages with a proteomic approach in an unbiased way. Human monocyte-derived macrophages (MDM) were exposed to tangled or rigid, long multi-walled CNT (MWCNT) or crocidolite asbestos for 6 h. The growth media was concentrated and secreted proteins were analyzed using 2D-DIGE and DeCyder software. Subsequently, significantly up- or down-regulated protein spots were in-gel digested and identified with an LC-MS/MS approach. Bioinformatics analysis was performed to reveal the different patterns of protein secretion induced by these materials. The results show that both long rigid MWCNT and asbestos elicited ample and highly similar protein secretion. In contrast, exposure to long tangled MWCNT induced weaker protein secretion with a more distinct profile. Secretion of lysosomal proteins followed the exposure to all materials, suggesting lysosomal damage. However, only long rigid MWCNT was associated with apoptosis. This analysis suggests that the CNT toxicity in human MDM is mediated via vigorous secretion of inflammation-related proteins and apoptosis. This study provides new insights into the mechanisms of toxicity of high aspect ratio nanomaterials and indicates that not all types of CNT are as hazardous as asbestos fibers.
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Affiliation(s)
- Jaana Palomäki
- Nanosafety Research Centre, Finnish Institute of Occupational Health , Helsinki , Finland
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Carloni V, Luong TV, Rombouts K. Hepatic stellate cells and extracellular matrix in hepatocellular carcinoma: more complicated than ever. Liver Int 2014; 34:834-43. [PMID: 24397349 DOI: 10.1111/liv.12465] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 01/02/2014] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide and the third leading cause of cancer death. Recent epidemiological data indicate that the mortality rate of HCC will double over the next decades in the USA and Europe. Liver cancer progresses in a large percentage of cases during the clinical course of chronic fibro-inflammatory liver diseases leading to cirrhosis. Therefore, HCC development is regarded as the result of different environmental risk factors each involving different genetic, epigenetic- and chromosomal alterations and gene mutations. During tumour progression, the malignant hepatocytes and the activated hepatic stellate cells are accompanied by cancer-associated fibroblasts, myofibroblasts and immune cells generally called tumour stromal cells. This new and dynamic milieu further enhances the responsiveness of tumour cells towards soluble mediators secreted by tumour stromal cells, thus directly affecting the malignant hepatocytes. This results in altered molecular pathways with cell proliferation as the most important mechanism of liver cancer progression. Given this contextual complexity, it is of utmost importance to characterize the molecular pathogenesis of HCC, and to identify the dominant pathways/drivers and aberrant signalling pathways. This will allow an effective therapy for HCC that should combine strategies affecting both cancer and the tumour stromal cells. This review provides an overview of the recent challenges and issues regarding hepatic stellate cells, extracellular matrix dynamics, liver fibrosis/cirrhosis and therapy, tumour microenvironment and HCC.
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Affiliation(s)
- Vinicio Carloni
- Department of Experimental and Clinical Medicine, Center for Research, Transfer and High Education, DENOthe, University of Florence, Florence, Italy
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Lange L, Bech L, Busk PK, Grell MN, Huang Y, Lange M, Linde T, Pilgaard B, Roth D, Tong X. The importance of fungi and of mycology for a global development of the bioeconomy. IMA Fungus 2012; 3:87-92. [PMID: 23155503 PMCID: PMC3399105 DOI: 10.5598/imafungus.2012.03.01.09] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 06/12/2012] [Indexed: 11/16/2022] Open
Abstract
The vision of the European common research programme for 2014–2020, called Horizon 2020, is to create a smarter, more sustainable and more inclusive society. However, this is a global endeavor, which is important for mycologists all over the world because it includes a special role for fungi and fungal products. After ten years of research on industrial scale conversion of biowaste, the conclusion is that the most efficient and gentle way of converting recalcitrant lignocellulosic materials into high value products for industrial purposes, is through the use of fungal enzymes. Moreover, fungi and fungal products are also instrumental in producing fermented foods, to give storage stability and improved health. Climate change will lead to increasingly severe stress on agricultural production and productivity, and here the solution may very well be that fungi will be brought into use as a new generation of agricultural inoculants to provide more robust, more nutrient efficient, and more drought tolerant crop plants. However, much more knowledge is required in order to be able to fully exploit the potentials of fungi, to deliver what is needed and to address the major global challenges through new biological processes, products, and solutions. This knowledge can be obtained by studying the fungal proteome and metabolome; the biology of fungal RNA and epigenetics; protein expression, homologous as well as heterologous; fungal host/substrate relations; physiology, especially of extremophiles; and, not the least, the extent of global fungal biodiversity. We also need much more knowledge and understanding of how fungi degrade biomass in nature. The projects in our group in Aalborg University are examples of the basic and applied research going on to increase the understanding of the biology of the fungal secretome and to discover new enzymes and new molecular/bioinformatics tools. However, we need to put Mycology higher up on global agendas, e.g. by positioning Mycology as a candidate for an OECD Excellency Program. This could pave the way for increased funding of international collaboration, increased global visibility, and higher priority among decision makers all over the world.
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Affiliation(s)
- Lene Lange
- Institute of Biotechnology and Chemistry, Faculty of Science and Technology, Aalborg University, Denmark
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