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Diagouraga B, Tambones I, Carivenc C, Bechara C, Nadal M, de Massy B, le Maire A, Robert T. The TOPOVIBL meiotic DSB formation protein: new insights from its biochemical and structural characterization. Nucleic Acids Res 2024:gkae587. [PMID: 38966985 DOI: 10.1093/nar/gkae587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
The TOPOVIL complex catalyzes the formation of DNA double strand breaks (DSB) that initiate meiotic homologous recombination, an essential step for chromosome segregation and genetic diversity during gamete production. TOPOVIL is composed of two subunits (SPO11 and TOPOVIBL) and is evolutionarily related to the archaeal TopoVI topoisomerase complex. SPO11 is the TopoVIA subunit orthologue and carries the DSB formation catalytic activity. TOPOVIBL shares homology with the TopoVIB ATPase subunit. TOPOVIBL is essential for meiotic DSB formation, but its molecular function remains elusive, partly due to the lack of biochemical studies. Here, we purified TOPOVIBLΔC25 and characterized its structure and mode of action in vitro. Our structural analysis revealed that TOPOVIBLΔC25 adopts a dynamic conformation in solution and our biochemical study showed that the protein remains monomeric upon incubation with ATP, which correlates with the absence of ATP binding. Moreover, TOPOVIBLΔC25 interacted with DNA, with a preference for some geometries, suggesting that TOPOVIBL senses specific DNA architectures. Altogether, our study identified specific TOPOVIBL features that might help to explain how TOPOVIL function evolved toward a DSB formation activity in meiosis.
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Affiliation(s)
- Boubou Diagouraga
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Izabella Tambones
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Coralie Carivenc
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Chérine Bechara
- Institut de Génomique Fonctionnelle (IGF), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Marc Nadal
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France; Department of Life Sciences, Université Paris Cité, Paris, France
| | - Bernard de Massy
- Institut de Génétique Humaine (IGH), Univ Montpellier, CNRS, 34090 Montpellier, France
| | - Albane le Maire
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Thomas Robert
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, INSERM, 34090 Montpellier, France
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Hinsinger G, Du Trieu De Terdonck L, Urbach S, Salvetat N, Rival M, Galoppin M, Ripoll C, Cezar R, Laurent-Chabalier S, Demattei C, Agherbi H, Castelnovo G, Lehmann S, Rigau V, Marin P, Thouvenot E. CD138 as a Specific CSF Biomarker of Multiple Sclerosis. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2024; 11:e200230. [PMID: 38669615 PMCID: PMC11057439 DOI: 10.1212/nxi.0000000000200230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/30/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND AND OBJECTIVES The aim of this study was to identify novel biomarkers for multiple sclerosis (MS) diagnosis and prognosis, addressing the critical need for specific and prognostically valuable markers in the field. METHODS We conducted an extensive proteomic investigation, combining analysis of (1) CSF proteome from symptomatic controls, fast and slow converters after clinically isolated syndromes, and patients with relapsing-remitting MS (n = 10 per group) using label-free quantitative proteomics and (2) oligodendrocyte secretome changes under proinflammatory or proapoptotic conditions using stable isotope labeling by amino acids in cell culture. Proteins exhibiting differential abundance in both proteomic analyses were combined with other putative MS biomarkers, yielding a comprehensive list of 87 proteins that underwent quantification through parallel reaction monitoring (PRM) in a novel cohort, comprising symptomatic controls, inflammatory neurologic disease controls, and patients with MS at various disease stages (n = 10 per group). The 11 proteins that passed this qualification step were subjected to a new PRM assay within an expanded cohort comprising 158 patients with either MS at different disease stages or other inflammatory or noninflammatory neurologic disease controls. RESULTS This study unveiled a promising biomarker signature for MS, including previously established candidates, such as chitinase 3-like protein 1, chitinase 3-like protein 2, chitotriosidase, immunoglobulin kappa chain region C, neutrophil gelatinase-associated lipocalin, and CD27. In addition, we identified novel markers, namely cat eye syndrome critical region protein 1 (adenosine deaminase 2, a therapeutic target in multiple sclerosis) and syndecan-1, a proteoglycan, also known as plasma cell surface marker CD138 and acting as chitinase 3-like protein 1 receptor implicated in inflammation and cancer signaling. CD138 exhibited good diagnostic accuracy in distinguishing MS from inflammatory neurologic disorders (area under the curve [AUC] = 0.85, CI 0.75-0.95). CD138 immunostaining was also observed in the brains of patients with MS and cultured oligodendrocyte precursor cells but was absent in astrocytes. DISCUSSION These findings identify CD138 as a specific CSF biomarker for MS and suggest the selective activation of the chitinase 3-like protein 1/CD138 pathway within the oligodendrocyte lineage in MS. They offer promising prospects for improving MS diagnosis and prognosis by providing much-needed specificity and clinical utility. CLASSIFICATION OF EVIDENCE This study provides Class II evidence that CD138 distinguishes multiple sclerosis from other inflammatory neurologic disorders with an AUC of 0.85 (95% CI 0.75-0.95).
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Affiliation(s)
- Geoffrey Hinsinger
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Lucile Du Trieu De Terdonck
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Serge Urbach
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Nicolas Salvetat
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Manon Rival
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Manon Galoppin
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Chantal Ripoll
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Renaud Cezar
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Sabine Laurent-Chabalier
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Christophe Demattei
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Hanane Agherbi
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Giovanni Castelnovo
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Sylvain Lehmann
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Valérie Rigau
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Philippe Marin
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
| | - Eric Thouvenot
- From the IGF (G.H., L.D.T.D.T., S.U., M.R., M.G., C.R., P.M., E.T.), Université de Montpellier, CNRS, INSERM, Montpellier; Sys2Diag (N.S.), UMR 9005 CNRS / ALCEDIAG, Montpellier; Department of Neurology (M.R., H.A., G.C., E.T.), Nîmes University Hospital; IRMB (R.C.), Université de Montpellier, INSERM; Department of Immunology (R.C.), Nîmes University Hospital; Department of Biostatistics (S.L.-C., C.D.), Clinical Epidemiology, Public Health, and Innovation in Methodology, Nîmes University Hospital, Université de Montpellier; Biochemistry Department (S.L.), Hôpital Saint-Eloi; and Department of Pathology (V.R.), Montpellier University Hospital, France
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Sengupta S, Mondal M, Prasasvi KR, Mukherjee A, Magod P, Urbach S, Friedmann-Morvinski D, Marin P, Somasundaram K. Differentiated glioma cell-derived Fibromodulin activates Integrin-dependent Notch signaling in endothelial cells to promote tumor angiogenesis and growth. eLife 2022; 11:78972. [PMID: 35642785 PMCID: PMC9259034 DOI: 10.7554/elife.78972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/29/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer stem cells (CSCs) alone can initiate and maintain tumors, but the function of non-cancer stem cells (non-CSCs) that form the tumor bulk remains poorly understood. Proteomic analysis showed a higher abundance of the extracellular matrix small leucine-rich proteoglycan fibromodulin (FMOD) in the conditioned medium of differentiated glioma cells (DGCs), the equivalent of glioma non-CSCs, compared to that of glioma stem-like cells (GSCs). DGCs silenced for FMOD fail to cooperate with co-implanted GSCs to promote tumor growth. FMOD downregulation neither affects GSC growth and differentiation nor DGC growth and reprogramming in vitro. DGC-secreted FMOD promotes angiogenesis by activating integrin-dependent Notch signaling in endothelial cells. Furthermore, conditional silencing of FMOD in newly generated DGCs in vivo inhibits the growth of GSC-initiated tumors due to poorly developed vasculature and increases mouse survival. Collectively, these findings demonstrate that DGC-secreted FMOD promotes glioma tumor angiogenesis and growth through paracrine signaling in endothelial cells and identifies a DGC-produced protein as a potential therapeutic target in glioma.
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Affiliation(s)
- Shreoshi Sengupta
- Department of Microbiology and Cell Biology, Indian Institute of Science Bangalore, Bangalore, India
| | - Mainak Mondal
- Department of Microbiology and Cell Biology, Indian Institute of Science Bangalore, Bangalore, India
| | - Kaval Reddy Prasasvi
- Department of Microbiology and Cell Biology, Indian Institute of Science Bangalore, Bangalore, India
| | - Arani Mukherjee
- Department of Microbiology and Cell Biology, Indian Institute of Science Bangalore, Bangalore, India
| | - Prerna Magod
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
| | - Serge Urbach
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | | | - Philippe Marin
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Kumaravel Somasundaram
- Department of Microbiology and Cell Biology, Indian Institute of Science Bangalore, Bangalore, India
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Al Awabdh S, Donneger F, Goutierre M, Séveno M, Vigy O, Weinzettl P, Russeau M, Moutkine I, Lévi S, Marin P, Poncer JC. Gephyrin Interacts with the K-Cl Cotransporter KCC2 to Regulate Its Surface Expression and Function in Cortical Neurons. J Neurosci 2022; 42:166-182. [PMID: 34810232 PMCID: PMC8802937 DOI: 10.1523/jneurosci.2926-20.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 08/31/2021] [Accepted: 10/17/2021] [Indexed: 11/21/2022] Open
Abstract
The K+-Cl- cotransporter KCC2, encoded by the Slc12a5 gene, is a neuron-specific chloride extruder that tunes the strength and polarity of GABAA receptor-mediated transmission. In addition to its canonical ion transport function, KCC2 also regulates spinogenesis and excitatory synaptic function through interaction with a variety of molecular partners. KCC2 is enriched in the vicinity of both glutamatergic and GABAergic synapses, the activity of which in turn regulates its membrane stability and function. KCC2 interaction with the submembrane actin cytoskeleton via 4.1N is known to control its anchoring near glutamatergic synapses on dendritic spines. However, the molecular determinants of KCC2 clustering near GABAergic synapses remain unknown. Here, we used proteomics to identify novel KCC2 interacting proteins in the adult rat neocortex. We identified both known and novel candidate KCC2 partners, including some involved in neuronal development and synaptic transmission. These include gephyrin, the main scaffolding molecule at GABAergic synapses. Gephyrin interaction with endogenous KCC2 was confirmed by immunoprecipitation from rat neocortical extracts. We showed that gephyrin stabilizes plasmalemmal KCC2 and promotes its clustering in hippocampal neurons, mostly but not exclusively near GABAergic synapses, thereby controlling KCC2-mediated chloride extrusion. This study identifies gephyrin as a novel KCC2 anchoring molecule that regulates its membrane expression and function in cortical neurons.SIGNIFICANCE STATEMENT Fast synaptic inhibition in the brain is mediated by chloride-permeable GABAA receptors (GABAARs) and therefore relies on transmembrane chloride gradients. In neurons, these gradients are primarily maintained by the K/Cl cotransporter KCC2. Therefore, understanding the mechanisms controlling KCC2 expression and function is crucial to understand its physiological regulation and rescue its function in the pathology. KCC2 function depends on its membrane expression and clustering, but the underlying mechanisms remain unknown. We describe the interaction between KCC2 and gephyrin, the main scaffolding protein at inhibitory synapses. We show that gephyrin controls plasmalemmal KCC2 clustering and that loss of gephyrin compromises KCC2 function. Our data suggest functional units comprising GABAARs, gephyrin, and KCC2 act to regulate synaptic GABA signaling.
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Affiliation(s)
- Sana Al Awabdh
- INSERM UMR-S 1270, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
- Institut du Fer à Moulin, 75005 Paris, France
| | - Florian Donneger
- INSERM UMR-S 1270, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
- Institut du Fer à Moulin, 75005 Paris, France
| | - Marie Goutierre
- INSERM UMR-S 1270, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
- Institut du Fer à Moulin, 75005 Paris, France
| | - Martial Séveno
- BCM, Université de Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Oana Vigy
- IGF, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Pauline Weinzettl
- INSERM UMR-S 1270, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
- Institut du Fer à Moulin, 75005 Paris, France
- Institute of Biotechnology, University of Applied Sciences, Krems, Austria
| | - Marion Russeau
- INSERM UMR-S 1270, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
- Institut du Fer à Moulin, 75005 Paris, France
| | - Imane Moutkine
- INSERM UMR-S 1270, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
- Institut du Fer à Moulin, 75005 Paris, France
| | - Sabine Lévi
- INSERM UMR-S 1270, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
- Institut du Fer à Moulin, 75005 Paris, France
| | - Philippe Marin
- IGF, Université de Montpellier, CNRS, INSERM, 34090 Montpellier, France
| | - Jean Christophe Poncer
- INSERM UMR-S 1270, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
- Institut du Fer à Moulin, 75005 Paris, France
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Cline EN, Alvarez C, Duan J, Patrie SM. Online μSEC 2-nRPLC-MS for Improved Sensitivity of Intact Protein Detection of IEF-Separated Nonhuman Primate Cerebrospinal Fluid Proteins. Anal Chem 2021; 93:16741-16750. [PMID: 34881887 PMCID: PMC10476446 DOI: 10.1021/acs.analchem.1c00396] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteoform-resolved information, obtained by top-down (TD) "intact protein" proteomics, is expected to contribute substantially to the understanding of molecular pathogenic mechanisms and, in turn, identify novel therapeutic and diagnostic targets. However, the robustness of mass spectrometry (MS) analysis of intact proteins in complex biological samples is hindered by the high dynamic range in protein concentration and mass, protein instability, and buffer complexity. Here, we describe an evolutionary step for intact protein investigations through the online implementation of tandem microflow size-exclusion chromatography with nanoflow reversed-phase liquid chromatography and MS (μSEC2-nRPLC-MS). Online serial high-/low-pass SEC filtration overcomes the aforementioned hurdles to intact proteomic analysis through automated sample desalting/cleanup and enrichment of target mass ranges (5-155 kDa) prior to nRPLC-MS. The coupling of μSEC to nRPLC is achieved through a novel injection volume control (IVC) strategy of inserting protein trap columns, pre- and post-μSEC columns, to enable injection of dilute samples in high volumes without loss of sensitivity or resolution. Critical characteristics of the approach are tested via rigorous investigations on samples of varied complexity and chemical background. Application of the platform to cerebrospinal fluid (CSF) prefractionated by OFFGEL isoelectric focusing drastically increases the number of intact mass tags (IMTs) detected within the target mass range (5-30 kDa) in comparison to one-dimensional nRPLC-MS with approximately 100× less CSF than previous OFFGEL studies. Furthermore, the modular design of the μSEC2-nRPLC-MS platform is robust and promises significant flexibility for large-scale TDMS analysis of diverse samples either directly or in concert with other multidimensional fractionation steps.
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Affiliation(s)
- Erika N Cline
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Carina Alvarez
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Jiana Duan
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
| | - Steven M Patrie
- Department of Chemistry and the Proteomics Center of Excellence, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208, United States
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6
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Revisiting Ehrlichia ruminantium Replication Cycle Using Proteomics: The Host and the Bacterium Perspectives. Microorganisms 2021; 9:microorganisms9061144. [PMID: 34073568 PMCID: PMC8229282 DOI: 10.3390/microorganisms9061144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/28/2021] [Accepted: 05/07/2021] [Indexed: 12/16/2022] Open
Abstract
The Rickettsiales Ehrlichia ruminantium, the causal agent of the fatal tick-borne disease Heartwater, induces severe damage to the vascular endothelium in ruminants. Nevertheless, E. ruminantium-induced pathobiology remains largely unknown. Our work paves the way for understanding this phenomenon by using quantitative proteomic analyses (2D-DIGE-MS/MS, 1DE-nanoLC-MS/MS and biotin-nanoUPLC-MS/MS) of host bovine aorta endothelial cells (BAE) during the in vitro bacterium intracellular replication cycle. We detect 265 bacterial proteins (including virulence factors), at all time-points of the E. ruminantium replication cycle, highlighting a dynamic bacterium–host interaction. We show that E. ruminantium infection modulates the expression of 433 host proteins: 98 being over-expressed, 161 under-expressed, 140 detected only in infected BAE cells and 34 exclusively detected in non-infected cells. Cystoscape integrated data analysis shows that these proteins lead to major changes in host cell immune responses, host cell metabolism and vesicle trafficking, with a clear involvement of inflammation-related proteins in this process. Our findings led to the first model of E. ruminantium infection in host cells in vitro, and we highlight potential biomarkers of E. ruminantium infection in endothelial cells (such as ROCK1, TMEM16K, Albumin and PTPN1), which may be important to further combat Heartwater, namely by developing non-antibiotic-based strategies.
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7
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Voukali E, Veetil NK, Němec P, Stopka P, Vinkler M. Comparison of plasma and cerebrospinal fluid proteomes identifies gene products guiding adult neurogenesis and neural differentiation in birds. Sci Rep 2021; 11:5312. [PMID: 33674647 PMCID: PMC7935914 DOI: 10.1038/s41598-021-84274-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/10/2021] [Indexed: 11/27/2022] Open
Abstract
Cerebrospinal fluid (CSF) proteins regulate neurogenesis, brain homeostasis and participate in signalling during neuroinflammation. Even though birds represent valuable models for constitutive adult neurogenesis, current proteomic studies of the avian CSF are limited to chicken embryos. Here we use liquid chromatography-tandem mass spectrometry (nLC-MS/MS) to explore the proteomic composition of CSF and plasma in adult chickens (Gallus gallus) and evolutionarily derived parrots: budgerigar (Melopsittacus undulatus) and cockatiel (Nymphicus hollandicus). Because cockatiel lacks a complete genome information, we compared the cross-species protein identifications using the reference proteomes of three model avian species: chicken, budgerigar and zebra finch (Taeniopygia guttata) and found the highest identification rates when mapping against the phylogenetically closest species, the budgerigar. In total, we identified 483, 641 and 458 unique proteins consistently represented in the CSF and plasma of all chicken, budgerigar and cockatiel conspecifics, respectively. Comparative pathways analyses of CSF and blood plasma then indicated clusters of proteins involved in neurogenesis, neural development and neural differentiation overrepresented in CSF in each species. This study provides the first insight into the proteomics of adult avian CSF and plasma and brings novel evidence supporting the adult neurogenesis in birds.
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Affiliation(s)
- Eleni Voukali
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.
| | - Nithya Kuttiyarthu Veetil
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Pavel Němec
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Pavel Stopka
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 44, Prague, Czech Republic.
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8
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González-Calvo I, Iyer K, Carquin M, Khayachi A, Giuliani FA, Sigoillot SM, Vincent J, Séveno M, Veleanu M, Tahraoui S, Albert M, Vigy O, Bosso-Lefèvre C, Nadjar Y, Dumoulin A, Triller A, Bessereau JL, Rondi-Reig L, Isope P, Selimi F. Sushi domain-containing protein 4 controls synaptic plasticity and motor learning. eLife 2021; 10:65712. [PMID: 33661101 PMCID: PMC7972451 DOI: 10.7554/elife.65712] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/03/2021] [Indexed: 01/28/2023] Open
Abstract
Fine control of protein stoichiometry at synapses underlies brain function and plasticity. How proteostasis is controlled independently for each type of synaptic protein in a synapse-specific and activity-dependent manner remains unclear. Here, we show that Susd4, a gene coding for a complement-related transmembrane protein, is expressed by many neuronal populations starting at the time of synapse formation. Constitutive loss-of-function of Susd4 in the mouse impairs motor coordination adaptation and learning, prevents long-term depression at cerebellar synapses, and leads to misregulation of activity-dependent AMPA receptor subunit GluA2 degradation. We identified several proteins with known roles in the regulation of AMPA receptor turnover, in particular ubiquitin ligases of the NEDD4 subfamily, as SUSD4 binding partners. Our findings shed light on the potential role of SUSD4 mutations in neurodevelopmental diseases.
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Affiliation(s)
- Inés González-Calvo
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France.,Institut des Neurosciences Cellulaires et Intégratives (INCI), CNRS, Université de Strasbourg, Strasbourg, France
| | - Keerthana Iyer
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Mélanie Carquin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Anouar Khayachi
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Fernando A Giuliani
- Institut des Neurosciences Cellulaires et Intégratives (INCI), CNRS, Université de Strasbourg, Strasbourg, France
| | - Séverine M Sigoillot
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Jean Vincent
- Institut Biology Paris Seine (IBPS), Neuroscience Paris Seine (NPS), CeZaMe, CNRS, Sorbonne University, INSERM, Paris, France
| | - Martial Séveno
- BioCampus Montpellier, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Maxime Veleanu
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Sylvana Tahraoui
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Mélanie Albert
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Oana Vigy
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Célia Bosso-Lefèvre
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
| | - Yann Nadjar
- École Normale Supérieure, Institut de Biologie de l'ENS, INSERM, CNRS, PSL Research University, Paris, France
| | - Andréa Dumoulin
- École Normale Supérieure, Institut de Biologie de l'ENS, INSERM, CNRS, PSL Research University, Paris, France
| | - Antoine Triller
- École Normale Supérieure, Institut de Biologie de l'ENS, INSERM, CNRS, PSL Research University, Paris, France
| | - Jean-Louis Bessereau
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut Neuromyogène, Lyon, France
| | - Laure Rondi-Reig
- Institut Biology Paris Seine (IBPS), Neuroscience Paris Seine (NPS), CeZaMe, CNRS, Sorbonne University, INSERM, Paris, France
| | - Philippe Isope
- Institut des Neurosciences Cellulaires et Intégratives (INCI), CNRS, Université de Strasbourg, Strasbourg, France
| | - Fekrije Selimi
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, PSL Research University, Paris, France
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9
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Fumagalli A, Heuninck J, Pizzoccaro A, Moutin E, Koenen J, Séveno M, Durroux T, Junier MP, Schlecht-Louf G, Bachelerie F, Schütz D, Stumm R, Smit MJ, Guérineau NC, Chaumont-Dubel S, Marin P. The atypical chemokine receptor 3 interacts with Connexin 43 inhibiting astrocytic gap junctional intercellular communication. Nat Commun 2020; 11:4855. [PMID: 32978390 PMCID: PMC7519114 DOI: 10.1038/s41467-020-18634-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/02/2020] [Indexed: 12/12/2022] Open
Abstract
The atypical chemokine receptor 3 (ACKR3) plays a pivotal role in directing the migration of various cellular populations and its over-expression in tumors promotes cell proliferation and invasiveness. The intracellular signaling pathways transducing ACKR3-dependent effects remain poorly characterized, an issue we addressed by identifying the interactome of ACKR3. Here, we report that recombinant ACKR3 expressed in HEK293T cells recruits the gap junction protein Connexin 43 (Cx43). Cx43 and ACKR3 are co-expressed in mouse brain astrocytes and human glioblastoma cells and form a complex in embryonic mouse brain. Functional in vitro studies show enhanced ACKR3 interaction with Cx43 upon ACKR3 agonist stimulation. Furthermore, ACKR3 activation promotes β-arrestin2- and dynamin-dependent Cx43 internalization to inhibit gap junctional intercellular communication in primary astrocytes. These results demonstrate a functional link between ACKR3 and gap junctions that might be of pathophysiological relevance. The atypical chemokine receptor 3 (ACKR3) is known to regulate cell migration, but the underlying mechanisms are unclear. Here, the authors show, from an interactome analysis, ACKR3 association with the gap junction protein Connexin 43 in vivo and ACKR3-mediated inhibition of astrocyte gap junctional communication.
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Affiliation(s)
- Amos Fumagalli
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Joyce Heuninck
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Anne Pizzoccaro
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Enora Moutin
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Joyce Koenen
- Université Paris-Saclay, Inserm, Inflammation, Microbiome and Immunosurveillance, 92140, Clamart, France.,Amsterdam Institute for Molecules Medicines and Systems, Division of Medicinal Chemistry, Faculty of Sciences, VU University Amsterdam, 1081, HV, Amsterdam, The Netherlands
| | - Martial Séveno
- Biocampus Montpellier, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Thierry Durroux
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Marie-Pierre Junier
- CNRS UMR8246, Inserm U1130, Neuroscience Paris Seine-IBPS, Sorbonne Universités, Paris, France
| | - Géraldine Schlecht-Louf
- Université Paris-Saclay, Inserm, Inflammation, Microbiome and Immunosurveillance, 92140, Clamart, France
| | - Francoise Bachelerie
- Université Paris-Saclay, Inserm, Inflammation, Microbiome and Immunosurveillance, 92140, Clamart, France
| | - Dagmar Schütz
- Institute of Pharmacology and Toxicology, Jena University Hospital, 07747, Jena, Germany
| | - Ralf Stumm
- Institute of Pharmacology and Toxicology, Jena University Hospital, 07747, Jena, Germany
| | - Martine J Smit
- Amsterdam Institute for Molecules Medicines and Systems, Division of Medicinal Chemistry, Faculty of Sciences, VU University Amsterdam, 1081, HV, Amsterdam, The Netherlands
| | - Nathalie C Guérineau
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Séverine Chaumont-Dubel
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Philippe Marin
- Institut de Génomique Fonctionnelle, Université de Montpellier, CNRS, INSERM, Montpellier, France.
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10
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Mitrofanova A, Drexler Y, Merscher S, Fornoni A. Role of Sphingolipid Signaling in Glomerular Diseases: Focus on DKD and FSGS. JOURNAL OF CELLULAR SIGNALING 2020; 1:56-69. [PMID: 32914148 PMCID: PMC7480905 DOI: 10.33696/signaling.1.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Sphingolipids are well-recognized as major players in the pathogenesis of many human diseases, including chronic kidney disease. The kidney is a very sensitive organ to alterations in sphingolipid metabolism. The critical issues to be addressed in this review relate to the role of sphingolipids and enzymes involved in sphingolipid metabolism in the pathogenesis of glomerular diseases with a special focus on podocytes, a key cellular component of the glomerular filtration barrier. Among several sphingolipids, we will highlight the role of ceramide, sphingosine, sphingosine-1-phosphate and ceramide-1-phosphate. Additionally, we will summarize the current knowledge with regard to the use of sphingolipids as therapeutic agents for the treatment of podocyte injury in kidney disease.
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Affiliation(s)
- Alla Mitrofanova
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, Florida, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, Florida, USA
- Department of Surgery, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Yelena Drexler
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, Florida, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Sandra Merscher
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, Florida, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, Florida, USA
| | - Alessia Fornoni
- Katz Family Division of Nephrology and Hypertension, Department of Medicine, University of Miami, Miller School of Medicine, Miami, Florida, USA
- Peggy and Harold Katz Family Drug Discovery Center, University of Miami, Miller School of Medicine, Miami, Florida, USA
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11
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Raynaud F, Homburger V, Seveno M, Vigy O, Moutin E, Fagni L, Perroy J. SNAP23-Kif5 complex controls mGlu1 receptor trafficking. J Mol Cell Biol 2019; 10:423-436. [PMID: 29762713 DOI: 10.1093/jmcb/mjy031] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/11/2018] [Indexed: 11/13/2022] Open
Abstract
Metabotropic glutamate receptors are expressed at excitatory synapses and control synaptic transmission in mammalian brain. These receptors are involved in numerous patho-physiological functions. However, little is known about the molecular determinants responsible for their intracellular transport and membrane targeting. Here we investigated the nature of the molecular motor and adaptor protein responsible for trafficking and membrane localization of the group I metabotropic glutamate mGlu1 postsynaptic receptor in cultured hippocampal neurons. In proteomic studies, we identified the synaptosome-associated protein 23 (SNAP23) and the molecular motor Kif5 kinesin as proteins interacting with mGlu1 receptor. We showed that SNAP23, but not Kif5, directly interacts with mGlu1 receptor carboxyl terminus. Using a recombination approach to impair or enhance the interaction between SNAP23 and Kif5, we found that the SNAP23-Kif5 complex controls the trafficking of mGlu1 receptor along microtubules. Additional fluorescence recovery after cleavage experiments allowed us to identify a role of the complex in the receptor cell surface targeting. In conclusion, our study indicates that along dendritic processes Kif5-SNAP23 complex contributes to proper mGlu1 receptor trafficking and cell surface expression.
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Affiliation(s)
| | | | - Martial Seveno
- BioCampus Montpellier, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Oana Vigy
- IGF, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Enora Moutin
- IGF, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Laurent Fagni
- IGF, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Julie Perroy
- IGF, CNRS, INSERM, Univ. Montpellier, Montpellier, France
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12
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Pigeyre L, Schatz M, Ravallec M, Gasmi L, Nègre N, Clouet C, Seveno M, El Koulali K, Decourcelle M, Guerardel Y, Cot D, Dupressoir T, Gosselin-Grenet AS, Ogliastro M. Interaction of a Densovirus with Glycans of the Peritrophic Matrix Mediates Oral Infection of the Lepidopteran Pest Spodoptera frugiperda. Viruses 2019; 11:v11090870. [PMID: 31533310 PMCID: PMC6783882 DOI: 10.3390/v11090870] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 01/01/2023] Open
Abstract
The success of oral infection by viruses depends on their capacity to overcome the gut epithelial barrier of their host to crossing over apical, mucous extracellular matrices. As orally transmitted viruses, densoviruses, are also challenged by the complexity of the insect gut barriers, more specifically by the chitinous peritrophic matrix, that lines and protects the midgut epithelium; how capsids stick to and cross these barriers to reach their final cell destination where replication goes has been poorly studied in insects. Here, we analyzed the early interaction of the Junonia coenia densovirus (JcDV) with the midgut barriers of caterpillars from the pest Spodoptera frugiperda. Using combination of imaging, biochemical, proteomic and transcriptomic analyses, we examined in vitro, ex vivo and in vivo the early interaction of the capsids with the peritrophic matrix and the consequence of early oral infection on the overall gut function. We show that the JcDV particle rapidly adheres to the peritrophic matrix through interaction with different glycans including chitin and glycoproteins, and that these interactions are necessary for oral infection. Proteomic analyses of JcDV binding proteins of the peritrophic matrix revealed mucins and non-mucins proteins including enzymes already known to act as receptors for several insect pathogens. In addition, we show that JcDV early infection results in an arrest of N-Acetylglucosamine secretion and a disruption in the integrity of the peritrophic matrix, which may help viral particles to pass through. Finally, JcDV early infection induces changes in midgut genes expression favoring an increased metabolism including an increased translational activity. These dysregulations probably participate to the overall dysfunction of the gut barrier in the early steps of viral pathogenesis. A better understanding of early steps of densovirus infection process is crucial to build biocontrol strategies against major insect pests.
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Affiliation(s)
- Laetitia Pigeyre
- Ecole Pratique des Hautes Etudes (EPHE), PSL Research Univ, DGIMI, Univ Montpellier, INRA, 34095 Montpellier, France.
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
| | - Malvina Schatz
- Ecole Pratique des Hautes Etudes (EPHE), PSL Research Univ, DGIMI, Univ Montpellier, INRA, 34095 Montpellier, France.
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
| | - Marc Ravallec
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
| | - Leila Gasmi
- Estructura de Recerca Interdisciplinar en Biotecnologia I Biomedicina (ERI-BIOTECMED, Deaprtment of Genetics Faculty of Biological Sciences Univ Valencia, 46100 Burjassot, Spain.
| | - Nicolas Nègre
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
| | - Cécile Clouet
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
| | - Martial Seveno
- BioCampus, Univ Montpellier, CNRS, INSERM, 34000 Montpellier, France.
| | | | | | - Yann Guerardel
- Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) Univ Lille, CNRS, UMR 8576-UGSF, 59000 Lille, France.
| | - Didier Cot
- Institut Européen des Membranes (IEM), Univ Montpellier, CBRS, ENSCM, 34095 Montpellier, France.
| | - Thierry Dupressoir
- Ecole Pratique des Hautes Etudes (EPHE), PSL Research Univ, DGIMI, Univ Montpellier, INRA, 34095 Montpellier, France.
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
| | - Anne-Sophie Gosselin-Grenet
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
| | - Mylène Ogliastro
- Diversité des Génomes et Interactions Microorganismes Insectes (DGIMI), Univ Montpellier, INRA, 34095 Montpellier, France.
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13
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Rodrigues V, Fernandez B, Vercoutere A, Chamayou L, Andersen A, Vigy O, Demettre E, Seveno M, Aprelon R, Giraud-Girard K, Stachurski F, Loire E, Vachiéry N, Holzmuller P. Immunomodulatory Effects of Amblyomma variegatum Saliva on Bovine Cells: Characterization of Cellular Responses and Identification of Molecular Determinants. Front Cell Infect Microbiol 2018; 7:521. [PMID: 29354598 PMCID: PMC5759025 DOI: 10.3389/fcimb.2017.00521] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 12/07/2017] [Indexed: 12/25/2022] Open
Abstract
The tropical bont tick, Amblyomma variegatum, is a tick species of veterinary importance and is considered as one of major pest of ruminants in Africa and in the Caribbean. It causes direct skin lesions, transmits heartwater, and reactivates bovine dermatophilosis. Tick saliva is reported to affect overall host responses through immunomodulatory and anti-inflammatory molecules, among other bioactive molecules. The general objective of this study was to better understand the role of saliva in interaction between the Amblyomma tick and the host using cellular biology approaches and proteomics, and to discuss its impact on disease transmission and/or activation. We first focused on the immuno-modulating effects of semi-fed A. variegatum female saliva on bovine peripheral blood mononuclear cells (PBMC) and monocyte-derived macrophages in vitro. We analyzed its immuno-suppressive properties by measuring the effect of saliva on PBMC proliferation, and observed a significant decrease in ConA-stimulated PBMC lymphoproliferation. We then studied the effect of saliva on bovine macrophages using flow cytometry to analyze the expression of MHC-II and co-stimulation molecules (CD40, CD80, and CD86) and by measuring the production of nitric oxide (NO) and pro- or anti-inflammatory cytokines. We observed a significant decrease in the expression of MHC-II, CD40, and CD80 molecules, associated with decreased levels of IL-12-p40 and TNF-α and increased level of IL-10, which could explain the saliva-induced modulation of NO. To elucidate these immunomodulatory effects, crude saliva proteins were analyzed using proteomics with an Orbitrap Elite mass spectrometer. Among the 336 proteins identified in A. variegatum saliva, we evidenced bioactive molecules exhibiting anti-inflammatory, immuno-modulatory, and anti-oxidant properties (e.g., serpins, phospholipases A2, heme lipoprotein). We also characterized an intriguing ubiquitination complex that could be involved in saliva-induced immune modulation of the host. We propose a model for the interaction between A. variegatum saliva and host immune cells that could have an effect during tick feeding by favoring pathogen dissemination or activation by reducing the efficiency of host immune response to the corresponding tick-borne diseases.
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Affiliation(s)
- Valérie Rodrigues
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
| | - Bernard Fernandez
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
| | - Arthur Vercoutere
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
| | - Léo Chamayou
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
| | - Alexandre Andersen
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
| | - Oana Vigy
- Institut de Génomique Fonctionnelle, Centre Nationnal de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Edith Demettre
- BioCampus Montpellier, Centre Nationnal de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Martial Seveno
- BioCampus Montpellier, Centre Nationnal de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université de Montpellier, Montpellier, France
| | - Rosalie Aprelon
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,CIRAD, UMR ASTRE, Petit-Bourg, Guadeloupe, France
| | - Ken Giraud-Girard
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,CIRAD, UMR ASTRE, Petit-Bourg, Guadeloupe, France
| | - Frédéric Stachurski
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
| | - Etienne Loire
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
| | - Nathalie Vachiéry
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France.,CIRAD, UMR ASTRE, Petit-Bourg, Guadeloupe, France
| | - Philippe Holzmuller
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR ASTRE "Animal, Santé, Territoire, Risques et Ecosystèmes,"Montpellier, France.,ASTRE, Université de Montpellier (I-MUSE), CIRAD, Institut National de la Recherche Agronomique, Montpellier, France
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14
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Kupniewska A, Szymanska K, Demkow U. Proteomics in the Diagnosis of Inborn Encephalopathies of Unknown Origin: A Myth or Reality. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1040:83-99. [PMID: 28983862 DOI: 10.1007/5584_2017_104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2023]
Abstract
Synaptopathy underlies a great variety of neurological or neurodevelopmental disorders, including neurodegenerative diseases and the highly complex neuropsychiatric syndromes. Standard diagnostic assays in the majority of synaptopathies are insufficient to make an appropriate and fast diagnosis, which has spurred a search for more accurate diagnostic methods using recent technological advances. As synaptopathy phenotypes strictly depend on genetics and environmental factors, the best way to approach these diseases is the investigation of entire sets of protein characteristics. Thus, proteomics has emerged as a mainstay in the studies on synaptopathies, with mass spectrometry as a technology of choice. This review is an update on the proteomic methods and achievements in the understanding, diagnostics, and novel biomarkers of synaptopathies. The article also provides a critical point of view and future perspectives on the application of neuroproteomics in clinical practice.
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Affiliation(s)
- Anna Kupniewska
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, 63A Zwirki and Wigury Street, 02-091, Warsaw, Poland.
| | - Krystyna Szymanska
- Department of Clinical and Experimental Neuropathology, The Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawińskiego Street, 02-106, Warsaw, Poland
- Department of Child Psychiatry, Warsaw Medical University, Warsaw, 24 Marszalkowska Street, 00-576, Warsaw, Poland
| | - Urszula Demkow
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, 63A Zwirki and Wigury Street, 02-091, Warsaw, Poland
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15
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Sinnaeve J, Mobley BC, Ihrie RA. Space Invaders: Brain Tumor Exploitation of the Stem Cell Niche. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 188:29-38. [PMID: 29024634 DOI: 10.1016/j.ajpath.2017.08.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 07/22/2017] [Accepted: 08/17/2017] [Indexed: 12/20/2022]
Abstract
Increasing evidence indicates that the adult neurogenic niche of the ventricular-subventricular zone (V-SVZ), beyond serving as a potential site of origin, affects the outcome of malignant brain cancers. Glioma contact with this niche predicts worse prognosis, suggesting a supportive role for the V-SVZ environment in tumor initiation or progression. In this review, we describe unique components of the V-SVZ that may permit or promote tumor growth within the region. Cell-cell interactions, soluble factors, and extracellular matrix composition are discussed, and the role of the niche in future therapies is explored. The purpose of this review is to highlight niche intrinsic factors that may promote or support malignant cell growth and maintenance, and point out how we might leverage these features to improve patient outcome.
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Affiliation(s)
- Justine Sinnaeve
- Departments of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Bret C Mobley
- Departments of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Rebecca A Ihrie
- Departments of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee; Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, Tennessee.
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16
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Abstract
SIGNIFICANCE Secreted proteins are important both as signaling molecules and potential biomarkers. Recent Advances: Protein can undergo different types of oxidation, both in physiological conditions or under oxidative stress. Several redox proteomics techniques have been successfully applied to the identification of glutathionylated proteins, an oxidative post-translational modification consisting in the formation of a mixed disulfide between a protein cysteine and glutathione. Redox proteomics has also been used to study other forms of protein oxidation. CRITICAL ISSUES Because of the highest proportion of free cysteines in the cytosol, redox proteomics of protein thiols has focused, so far, on intracellular proteins. However, plasma proteins, such as transthyretin and albumin, have been described as glutathionylated or cysteinylated. The present review discusses the redox state of protein cysteines in relation to their cellular distribution. We describe the various approaches used to detect secreted glutathionylated proteins, the only thiol modification studied so far in secreted proteins, and the specific problems presented in the study of the secretome. FUTURE DIRECTIONS This review focusses on glutathionylated proteins secreted under inflammatory conditions and that may act as soluble mediators (cytokines). Future studies on the redox secretome (including other forms of oxidation) might identify new soluble mediators and biomarkers of oxidative stress. Antioxid. Redox Signal. 26, 299-312.
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Affiliation(s)
- Pietro Ghezzi
- 1 Brighton & Sussex Medical School , Brighton, United Kingdom
| | - Philippe Chan
- 2 PISSARO Proteomic Platform, Institute for Research and Innovation in Biomedicine, University of Rouen , Rouen, France
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17
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Gorelik A, Heinz LX, Illes K, Superti-Furga G, Nagar B. Crystal Structure of the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3B Provides Insights into Determinants of Substrate Specificity. J Biol Chem 2016; 291:24054-24064. [PMID: 27687724 DOI: 10.1074/jbc.m116.755801] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 09/18/2016] [Indexed: 01/24/2023] Open
Abstract
The enzyme acid sphingomyelinase-like phosphodiesterase 3B (SMPDL3B) was shown to act as a negative regulator of innate immune signaling, affecting cellular lipid composition and membrane fluidity. Furthermore, several reports identified this enzyme as an off target of the therapeutic antibody rituximab, with implications in kidney disorders. However, structural information for this protein is lacking. Here we present the high resolution crystal structure of murine SMPDL3B, which reveals a substrate binding site strikingly different from its paralogs. The active site is located in a narrow boot-shaped cavity. We identify a unique loop near the active site that appears to impose size constraints on incoming substrates. A structure in complex with phosphocholine indicates that the protein recognizes this head group via an aromatic box, a typical choline-binding motif. Although a potential substrate for SMPDL3B is sphingomyelin, we identify other possible substrates such as CDP-choline, ATP, and ADP. Functional experiments employing structure-guided mutagenesis in macrophages highlight amino acid residues potentially involved in recognition of endogenous substrates. Our study is an important step toward elucidating the specific function of this poorly characterized enzyme.
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Affiliation(s)
- Alexei Gorelik
- From the Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Leonhard X Heinz
- the CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, 1090 Vienna, Austria, and
| | - Katalin Illes
- From the Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Giulio Superti-Furga
- the CeMM Research Center for Molecular Medicine, Austrian Academy of Sciences, 1090 Vienna, Austria, and.,the Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Bhushan Nagar
- From the Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines, McGill University, Montreal, Quebec H3G 0B1, Canada,
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18
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Xing C, Lo EH. Help-me signaling: Non-cell autonomous mechanisms of neuroprotection and neurorecovery. Prog Neurobiol 2016; 152:181-199. [PMID: 27079786 DOI: 10.1016/j.pneurobio.2016.04.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 04/06/2016] [Accepted: 04/09/2016] [Indexed: 12/11/2022]
Abstract
Self-preservation is required for life. At the cellular level, this fundamental principle is expressed in the form of molecular mechanisms for preconditioning and tolerance. When the cell is threatened, internal cascades of survival signaling become triggered to protect against cell death and defend against future insults. Recently, however, emerging findings suggest that this principle of self-preservation may involve not only intracellular signals; the release of extracellular signals may provide a way to recruit adjacent cells into an amplified protective program. In the central nervous system where multiple cell types co-exist, this mechanism would allow threatened neurons to "ask for help" from glial and vascular compartments. In this review, we describe this new concept of help-me signaling, wherein damaged or diseased neurons release signals that may shift glial and vascular cells into potentially beneficial phenotypes, and help remodel the neurovascular unit. Understanding and dissecting these non-cell autonomous mechanisms of self-preservation in the CNS may lead to novel opportunities for neuroprotection and neurorecovery.
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Affiliation(s)
- Changhong Xing
- Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
| | - Eng H Lo
- Departments of Radiology and Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
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19
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Proteomic analysis of mouse choroid plexus cell line ECPC-4 treated with lipid A. Inflamm Res 2016; 65:295-302. [PMID: 26794622 DOI: 10.1007/s00011-016-0916-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 12/17/2015] [Accepted: 01/05/2016] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVES Choroid plexus (CP) epithelial cells have multiple functions in the cerebral ventricles, including cerebrospinal fluid (CSF) production and forming part of the blood-CSF barrier. They are also responsible for producing inflammatory mediators involved in meningitis. The present study aimed to elucidate the functions of the CP epithelial cells during CNS inflammation. MATERIALS AND METHODS We analyzed the proteome and phosphoproteome in lipid A-treated ECPC-4 mouse CP cells by gel electrophoresis and mass spectrometry. RESULTS Levels of 10 proteins and seven phosphoproteins were significantly altered by lipid A in time-dependent manners, including V-type proton ATPase subunit B (ATP6V), protein 40 kD, elongation factor-1δ, coatomer subunit ε (COPE), vimentin (isoform CRA a), purine nucleoside phosphorylase, eukaryotic initiation factor-4F splicing variant, put. β-actin, peroxiredoxin-6 isoform 1, and immunoglobulin heavy chain variable region. These proteins could be classified as having cytoskeleton/intermediate filament, protein-folding, signal-transduction, cell-growth, metabolism, and redox-regulation functions. The identified phosphoproteins were HSP 84, γ-actin, HSP 70 cognate, vimentin, tubulin β-4B chain, protein disulfide-isomerase A6 precursor, and heterogenous nuclear ribonucleoprotein, which could be classified as having cytoskeleton/intermediate filament, protein-folding, and metabolism functions. CONCLUSIONS These results indicate that lipid A can change the levels of proteins and phosphoproteins in ECPC-4 cells, suggesting that the identified proteins and phosphoproteins may play important roles in inflammation of the CP.
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20
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Kwasnik A, Tonry C, Ardle AM, Butt AQ, Inzitari R, Pennington SR. Proteomes, Their Compositions and Their Sources. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:3-21. [DOI: 10.1007/978-3-319-41448-5_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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21
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Woo J, Han D, Park J, Kim SJ, Kim Y. In-depth characterization of the secretome of mouse CNS cell lines by LC-MS/MS without prefractionation. Proteomics 2015; 15:3617-22. [PMID: 26227174 DOI: 10.1002/pmic.201400623] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 05/19/2015] [Accepted: 07/21/2015] [Indexed: 11/07/2022]
Abstract
Microglia, astrocytes, and neurons, which have important functions in the central nervous system (CNS), communicate mutually to generate a signal through secreted proteins or small molecules, but many of which have not been identified. Because establishing a reference for the secreted proteins from CNS cells could be invaluable in examining cell-to-cell communication in the brain, we analyzed the secretome of three murine CNS cell lines without prefractionation by high-resolution mass spectrometry. In this study, 2795 proteins were identified from conditioned media of the three cell lines, and 2125 proteins were annotated as secreted proteins by bioinformatics analysis. Further, approximately 500 secreted proteins were quantifiable as differentially expressed proteins by label-free quantitation. As a result, our secretome references are useful datasets for the future study of neuronal diseases. All MS data have been deposited in the ProteomeXchange with identifier PXD001597 (http://proteomecentral.proteomexchange.org/dataset/PXD001597).
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Affiliation(s)
- Jongmin Woo
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea
| | - Dohyun Han
- Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - Joonho Park
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, Korea
| | - Sang Jeong Kim
- Department of Physiology, Seoul National University College of Medicine, Seoul, Korea
| | - Youngsoo Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.,Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University College of Medicine, Seoul, Korea.,Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, Korea
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22
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Nijaguna MB, Patil V, Urbach S, Shwetha SD, Sravani K, Hegde AS, Chandramouli BA, Arivazhagan A, Marin P, Santosh V, Somasundaram K. Glioblastoma-derived Macrophage Colony-stimulating Factor (MCSF) Induces Microglial Release of Insulin-like Growth Factor-binding Protein 1 (IGFBP1) to Promote Angiogenesis. J Biol Chem 2015; 290:23401-15. [PMID: 26245897 DOI: 10.1074/jbc.m115.664037] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 01/08/2023] Open
Abstract
Glioblastoma (grade IV glioma/GBM) is the most common primary adult malignant brain tumor with poor prognosis. To characterize molecular determinants of tumor-stroma interaction in GBM, we profiled 48 serum cytokines and identified macrophage colony-stimulating factor (MCSF) as one of the elevated cytokines in sera from GBM patients. Both MCSF transcript and protein were up-regulated in GBM tissue samples through a spleen tyrosine kinase (SYK)-dependent activation of the PI3K-NFκB pathway. Ectopic overexpression and silencing experiments revealed that glioma-secreted MCSF has no role in autocrine functions and M2 polarization of macrophages. In contrast, silencing expression of MCSF in glioma cells prevented tube formation of human umbilical vein endothelial cells elicited by the supernatant from monocytes/microglial cells treated with conditioned medium from glioma cells. Quantitative proteomics based on stable isotope labeling by amino acids in cell culture showed that glioma-derived MCSF induces changes in microglial secretome and identified insulin-like growth factor-binding protein 1 (IGFBP1) as one of the MCSF-regulated proteins secreted by microglia. Silencing IGFBP1 expression in microglial cells or its neutralization by an antibody reduced the ability of supernatants derived from microglial cells treated with glioma cell-conditioned medium to induce angiogenesis. In conclusion, this study shows up-regulation of MCSF in GBM via a SYK-PI3K-NFκB-dependent mechanism and identifies IGFBP1 released by microglial cells as a novel mediator of MCSF-induced angiogenesis, of potential interest for developing targeted therapy to prevent GBM progression.
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Affiliation(s)
- Mamatha Bangalore Nijaguna
- From the Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Vikas Patil
- From the Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Serge Urbach
- the Institut de Génomique Fonctionnelle, CNRS UMR 5203, F-34094 Montpellier, France, INSERM U1191, F-34094 Montpellier, France, the Université de Montpellier, F-34094 Montpellier, France
| | | | | | - Alangar S Hegde
- the Sri Satya Sai Institute of Higher Medical Sciences, Bangalore 560066, India
| | | | | | - Philippe Marin
- the Institut de Génomique Fonctionnelle, CNRS UMR 5203, F-34094 Montpellier, France, INSERM U1191, F-34094 Montpellier, France, the Université de Montpellier, F-34094 Montpellier, France
| | | | - Kumaravel Somasundaram
- From the Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India,
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23
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Percy AJ, Yang J, Chambers AG, Simon R, Hardie DB, Borchers CH. Multiplexed MRM with Internal Standards for Cerebrospinal Fluid Candidate Protein Biomarker Quantitation. J Proteome Res 2014; 13:3733-3747. [DOI: 10.1021/pr500317d] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Andrew J. Percy
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Juncong Yang
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Andrew G. Chambers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Romain Simon
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Darryl B. Hardie
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
| | - Christoph H. Borchers
- University of
Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Vancouver Island Technology Park, 3101-4464 Markham Street, Victoria, BC V8Z
7X8, Canada
- Department
of Biochemistry and Microbiology, University of Victoria, Petch Building
Room 207, 3800 Finnerty Road, Victoria, BC V8P 5C2, Canada
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24
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Jha MK, Suk K. Glia-based biomarkers and their functional role in the CNS. Expert Rev Proteomics 2014; 10:43-63. [DOI: 10.1586/epr.12.70] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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25
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Angiogenin induces modifications in the astrocyte secretome: Relevance to amyotrophic lateral sclerosis. J Proteomics 2013; 91:274-85. [DOI: 10.1016/j.jprot.2013.07.028] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 07/18/2013] [Accepted: 07/26/2013] [Indexed: 11/19/2022]
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26
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Shank3-Rich2 interaction regulates AMPA receptor recycling and synaptic long-term potentiation. J Neurosci 2013; 33:9699-715. [PMID: 23739967 DOI: 10.1523/jneurosci.2725-12.2013] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Synaptic long-term potentiation (LTP) is a key mechanism involved in learning and memory, and its alteration is associated with mental disorders. Shank3 is a major postsynaptic scaffolding protein that orchestrates dendritic spine morphogenesis, and mutations of this protein lead to mental retardation and autism spectrum disorders. In the present study we investigated the role of a new Shank3-associated protein in LTP. We identified the Rho-GAP interacting CIP4 homolog 2 (Rich2) as a new Shank3 partner by proteomic screen. Using single-cell bioluminescence resonance energy transfer microscopy, we found that Rich2-Shank3 interaction is increased in dendritic spines of mouse cultured hippocampal neurons during LTP. We further characterized Rich2 as an endosomal recycling protein that controls AMPA receptor GluA1 subunit exocytosis and spine morphology. Knock-down of Rich2 with siRNA, or disruption of the Rich2-Shank3 complex using an interfering mimetic peptide, inhibited the dendritic spine enlargement and the increase in GluA1 subunit exocytosis typical of LTP. These results identify Rich2-Shank3 as a new postsynaptic protein complex involved in synaptic plasticity.
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27
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Duarte ST, Armstrong J, Roche A, Ortez C, Pérez A, O'Callaghan MDM, Pereira A, Sanmartí F, Ormazábal A, Artuch R, Pineda M, García-Cazorla A. Abnormal expression of cerebrospinal fluid cation chloride cotransporters in patients with Rett syndrome. PLoS One 2013; 8:e68851. [PMID: 23894354 PMCID: PMC3716803 DOI: 10.1371/journal.pone.0068851] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 06/05/2013] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE Rett Syndrome is a progressive neurodevelopmental disorder caused mainly by mutations in the gene encoding methyl-CpG-binding protein 2. The relevance of MeCP2 for GABAergic function was previously documented in animal models. In these models, animals show deficits in brain-derived neurotrophic factor, which is thought to contribute to the pathogenesis of this disease. Neuronal Cation Chloride Cotransporters (CCCs) play a key role in GABAergic neuronal maturation, and brain-derived neurotrophic factor is implicated in the regulation of CCCs expression during development. Our aim was to analyse the expression of two relevant CCCs, NKCC1 and KCC2, in the cerebrospinal fluid of Rett syndrome patients and compare it with a normal control group. METHODS The presence of bumetanide sensitive NKCC1 and KCC2 was analysed in cerebrospinal fluid samples from a control pediatric population (1 day to 14 years of life) and from Rett syndrome patients (2 to 19 years of life), by immunoblot analysis. RESULTS Both proteins were detected in the cerebrospinal fluid and their levels are higher in the early postnatal period. However, Rett syndrome patients showed significantly reduced levels of KCC2 and KCC2/NKCC1 ratio when compared to the control group. CONCLUSIONS Reduced KCC2/NKCC1 ratio in the cerebrospinal fluid of Rett Syndrome patients suggests a disturbed process of GABAergic neuronal maturation and open up a new therapeutic perspective.
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Affiliation(s)
- Sofia Temudo Duarte
- Department of Neurology, Hospital Sant Joan de Déu (HSJD), Barcelona, Spain.
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28
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Häggmark A, Byström S, Ayoglu B, Qundos U, Uhlén M, Khademi M, Olsson T, Schwenk JM, Nilsson P. Antibody-based profiling of cerebrospinal fluid within multiple sclerosis. Proteomics 2013; 13:2256-67. [PMID: 23696371 DOI: 10.1002/pmic.201200580] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/19/2013] [Accepted: 04/09/2013] [Indexed: 12/11/2022]
Abstract
Antibody suspension bead arrays have proven to enable multiplexed and high-throughput protein profiling in unfractionated plasma and serum samples through a direct labeling approach. We here describe the development and application of an assay for protein profiling of cerebrospinal fluid (CSF). While setting up the assay, systematic intensity differences between sample groups were observed that reflected inherent sample specific total protein amounts. Supplementing the labeling reaction with BSA and IgG diminished these differences without impairing the apparent sensitivity of the assay. We also assessed the effects of heat treatment on the analysis of CSF proteins and applied the assay to profile 43 selected proteins by 101 antibodies in 339 CSF samples from a multiple sclerosis (MS) cohort. Two proteins, GAP43 and SERPINA3 were found to have a discriminating potential with altered intensity levels between sample groups. GAP43 was detected at significantly lower levels in secondary progressive MS compared to early stages of MS and the control group of other neurological diseases. SERPINA3 instead was detected at higher levels in all MS patients compared to controls. The developed assay procedure now offers new possibilities for broad-scale protein profiling of CSF within neurological disorders.
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Affiliation(s)
- Anna Häggmark
- SciLifeLab Stockholm, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
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Jaros JAJ, Guest PC, Bahn S, Martins-de-Souza D. Affinity depletion of plasma and serum for mass spectrometry-based proteome analysis. Methods Mol Biol 2013; 1002:1-11. [PMID: 23625390 DOI: 10.1007/978-1-62703-360-2_1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Protein biomarker discovery in blood plasma and serum is severely hampered by the vast dynamic range of the proteome. With protein concentrations spanning 12 orders of magnitude, conventional mass spectrometric analysis allows for detection of only a few low-abundance proteins. Prior depletion of high-abundant proteins from the sample can increase analytical depth considerably and has become a widely used practice. We describe in detail an affinity depletion method that selectively removes 14 of the most abundant proteins in plasma and serum.
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Thouvenot E, Urbach S, Vigy O, Séveno M, Galéotti N, Nguyen G, Bockaert J, Marin P. Quantitative proteomic analysis reveals protein expression changes in the murine neuronal secretome during apoptosis. J Proteomics 2012; 77:394-405. [DOI: 10.1016/j.jprot.2012.09.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 08/24/2012] [Accepted: 09/12/2012] [Indexed: 01/08/2023]
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Fanara P, Wong PYA, Husted KH, Liu S, Liu VM, Kohlstaedt LA, Riiff T, Protasio JC, Boban D, Killion S, Killian M, Epling L, Sinclair E, Peterson J, Price RW, Cabin DE, Nussbaum RL, Brühmann J, Brandt R, Christine CW, Aminoff MJ, Hellerstein MK. Cerebrospinal fluid-based kinetic biomarkers of axonal transport in monitoring neurodegeneration. J Clin Invest 2012; 122:3159-69. [PMID: 22922254 DOI: 10.1172/jci64575] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 07/12/2012] [Indexed: 12/14/2022] Open
Abstract
Progress in neurodegenerative disease research is hampered by the lack of biomarkers of neuronal dysfunction. We here identified a class of cerebrospinal fluid-based (CSF-based) kinetic biomarkers that reflect altered neuronal transport of protein cargo, a common feature of neurodegeneration. After a pulse administration of heavy water (2H2O), distinct, newly synthesized 2H-labeled neuronal proteins were transported to nerve terminals and secreted, and then appeared in CSF. In 3 mouse models of neurodegeneration, distinct 2H-cargo proteins displayed delayed appearance and disappearance kinetics in the CSF, suggestive of aberrant transport kinetics. Microtubule-modulating pharmacotherapy normalized CSF-based kinetics of affected 2H-cargo proteins and ameliorated neurodegenerative symptoms in mice. After 2H2O labeling, similar neuronal transport deficits were observed in CSF of patients with Parkinson's disease (PD) compared with non-PD control subjects, which indicates that these biomarkers are translatable and relevant to human disease. Measurement of transport kinetics may provide a sensitive method to monitor progression of neurodegeneration and treatment effects.
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Hölttä M, Zetterberg H, Mirgorodskaya E, Mattsson N, Blennow K, Gobom J. Peptidome analysis of cerebrospinal fluid by LC-MALDI MS. PLoS One 2012; 7:e42555. [PMID: 22880031 PMCID: PMC3412831 DOI: 10.1371/journal.pone.0042555] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 07/10/2012] [Indexed: 12/18/2022] Open
Abstract
We report on the analysis of endogenous peptides in cerebrospinal fluid (CSF) by mass spectrometry. A method was developed for preparation of peptide extracts from CSF. Analysis of the extracts by offline LC-MALDI MS resulted in the detection of 3,000–4,000 peptide-like features. Out of these, 730 peptides were identified by MS/MS. The majority of these peptides have not been previously reported in CSF. The identified peptides were found to originate from 104 proteins, of which several have been reported to be involved in different disorders of the central nervous system. These results support the notion that CSF peptidomics may be viable complement to proteomics in the search of biomarkers of CNS disorders.
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Affiliation(s)
- Mikko Hölttä
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Ekaterina Mirgorodskaya
- Department of Occupational and Environmental Medicine, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Niklas Mattsson
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Kaj Blennow
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Johan Gobom
- Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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Secretome protein enrichment identifies physiological BACE1 protease substrates in neurons. EMBO J 2012; 31:3157-68. [PMID: 22728825 DOI: 10.1038/emboj.2012.173] [Citation(s) in RCA: 255] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Accepted: 06/05/2012] [Indexed: 12/23/2022] Open
Abstract
Cell surface proteolysis is essential for communication between cells and results in the shedding of membrane-protein ectodomains. However, physiological substrates of the contributing proteases are largely unknown. We developed the secretome protein enrichment with click sugars (SPECS) method, which allows proteome-wide identification of shedding substrates and secreted proteins from primary cells, even in the presence of serum proteins. SPECS combines metabolic glycan labelling and click chemistry-mediated biotinylation and distinguishes between cellular and serum proteins. SPECS identified 34, mostly novel substrates of the Alzheimer protease BACE1 in primary neurons, making BACE1 a major sheddase in the nervous system. Selected BACE1 substrates-seizure-protein 6, L1, CHL1 and contactin-2-were validated in brains of BACE1 inhibitor-treated and BACE1 knock-out mice. For some substrates, BACE1 was the major sheddase, whereas for other substrates additional proteases contributed to total substrate shedding. The new substrates point to a central function of BACE1 in neurite outgrowth and synapse formation. SPECS is also suitable for quantitative secretome analyses of primary cells and may be used for the discovery of biomarkers secreted from tumour or stem cells.
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Morales DM, Townsend RR, Malone JP, Ewersmann CA, Macy EM, Inder TE, Limbrick DD. Alterations in protein regulators of neurodevelopment in the cerebrospinal fluid of infants with posthemorrhagic hydrocephalus of prematurity. Mol Cell Proteomics 2011; 11:M111.011973. [PMID: 22186713 DOI: 10.1074/mcp.m111.011973] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Neurological outcomes of preterm infants with posthemorrhagic hydrocephalus are among the worst in newborn medicine. There remains no consensus regarding the diagnosis or treatment of posthemorrhagic hydrocephalus, and the pathological pathways leading to the adverse neurological sequelae are poorly understood. In the current study, we developed an innovative approach to simultaneously identify potential diagnostic markers of posthemorrhagic hydrocephalus and investigate novel pathways of posthemorrhagic hydrocephalus-related neurological disability. Tandem multi-affinity fractionation for specific removal of plasma proteins from the hemorrhagic cerebrospinal fluid samples was combined with high resolution label-free quantitative proteomics. Analysis of cerebrospinal fluid obtained from infants with posthemorrhagic hydrocephalus demonstrated marked differences in the levels of 438 proteins when compared with cerebrospinal fluid from age-matched control infants. Amyloid precursor protein, neural cell adhesion molecule-L1, neural cell adhesion molecule-1, brevican and other proteins with important roles in neurodevelopment showed profound elevations in posthemorrhagic hydrocephalus cerebrospinal fluid compared with control. Initiation of neurosurgical treatment of posthemorrhagic hydrocephalus resulted in resolution of these elevations. The results from this foundational study demonstrate the significant promise of tandem multi-affinity fractionation-proteomics in the identification and quantitation of protein mediators of neurodevelopment and neurological injury. More specifically, our results suggest that cerebrospinal fluid levels of proteins such as amyloid precursor protein or neural cell adhesion molecule-L1 should be investigated as potential diagnostic markers of posthemorrhagic hydrocephalus. Notably, dysregulation of the levels these and other proteins may directly affect ongoing neurodevelopmental processes in these preterm infants, providing an entirely new hypothesis for the developmental disability associated with posthemorrhagic hydrocephalus.
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Affiliation(s)
- Diego M Morales
- Department of Neurological Surgery, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri 63110, USA.
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Ramírez-Boo M, Núnez E, Jorge I, Navarro P, Fernandes LT, Segalés J, Garrido JJ, Vázquez J, Moreno Á. Quantitative proteomics by 2-DE, 16O/18O labelling and linear ion trap mass spectrometry analysis of lymph nodes from piglets inoculated by porcine circovirus type 2. Proteomics 2011; 11:3452-69. [DOI: 10.1002/pmic.201000610] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 05/18/2011] [Accepted: 05/30/2011] [Indexed: 12/13/2022]
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Borg J, Campos A, Diema C, Omeñaca N, de Oliveira E, Guinovart J, Vilaseca M. Spectral counting assessment of protein dynamic range in cerebrospinal fluid following depletion with plasma-designed immunoaffinity columns. Clin Proteomics 2011; 8:6. [PMID: 21906361 PMCID: PMC3167203 DOI: 10.1186/1559-0275-8-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 06/03/2011] [Indexed: 01/25/2023] Open
Abstract
Background In cerebrospinal fluid (CSF), which is a rich source of biomarkers for neurological diseases, identification of biomarkers requires methods that allow reproducible detection of low abundance proteins. It is therefore crucial to decrease dynamic range and improve assessment of protein abundance. Results We applied LC-MS/MS to compare the performance of two CSF enrichment techniques that immunodeplete either albumin alone (IgYHSA) or 14 high-abundance proteins (IgY14). In order to estimate dynamic range of proteins identified, we measured protein abundance with APEX spectral counting method. Both immunodepletion methods improved the number of low-abundance proteins detected (3-fold for IgYHSA, 4-fold for IgY14). The 10 most abundant proteins following immunodepletion accounted for 41% (IgY14) and 46% (IgYHSA) of CSF protein content, whereas they accounted for 64% in non-depleted samples, thus demonstrating significant enrichment of low-abundance proteins. Defined proteomics experiment metrics showed overall good reproducibility of the two immunodepletion methods and MS analysis. Moreover, offline peptide fractionation in IgYHSA sample allowed a 4-fold increase of proteins identified (520 vs. 131 without fractionation), without hindering reproducibility. Conclusions The novelty of this study was to show the advantages and drawbacks of these methods side-to-side. Taking into account the improved detection and potential loss of non-target proteins following extensive immunodepletion, it is concluded that both depletion methods combined with spectral counting may be of interest before further fractionation, when searching for CSF biomarkers. According to the reliable identification and quantitation obtained with APEX algorithm, it may be considered as a cheap and quick alternative to study sample proteomic content.
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Affiliation(s)
- Jacques Borg
- Laboratoire de Neurobiochimie, Université Jean Monnet, Saint-Etienne, France.
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Duarte ST, Ortez C, Pérez A, Artuch R, García-Cazorla A. Analysis of synaptic proteins in the cerebrospinal fluid as a new tool in the study of inborn errors of neurotransmission. J Inherit Metab Dis 2011; 34:523-8. [PMID: 21229320 DOI: 10.1007/s10545-010-9256-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Revised: 11/22/2010] [Accepted: 11/25/2010] [Indexed: 11/25/2022]
Abstract
In a few rare diseases, specialised studies in cerebrospinal fluid (CSF) are required to identify the underlying metabolic disorder. We aimed to explore the possibility of detecting key synaptic proteins in the CSF, in particular dopaminergic and gabaergic, as new procedures that could be useful for both pathophysiological and diagnostic purposes in investigation of inherited disorders of neurotransmission. Dopamine receptor type 2 (D2R), dopamine transporter (DAT) and vesicular monoamine transporter type 2 (VMAT2) were analysed in CSF samples from 30 healthy controls (11 days to 17 years) by western blot analysis. Because VMAT2 was the only protein with intracellular localisation, and in order to compare results, GABA vesicular transporter, which is another intracellular protein, was also studied. Spearman's correlation and Student's t tests were applied to compare optical density signals between different proteins. All these synaptic proteins could be easily detected and quantified in the CSF. DAT, D2R and GABA VT expression decrease with age, particularly in the first months of life, reflecting the expected intense synaptic activity and neuronal circuitry formation. A statistically significant relationship was found between D2R and DAT expression, reinforcing the previous evidence of DAT regulation by D2R. To our knowledge, there are no previous studies on human CSF reporting a reliable analysis of these proteins. These kinds of studies could help elucidate new causes of disturbed dopaminergic and gabaergic transmission as well as understanding different responses to L-dopa in inherited disorders affecting dopamine metabolism. Moreover, this approach to synaptic activity in vivo can be extended to different groups of proteins and diseases.
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Affiliation(s)
- Sofia T Duarte
- Department of Neurology, Hospital Sant Joan de Déu, Barcelona, and CIBER-ER (Biomedical Network Research Centre on Rare Diseases, Instituto de Salud Carlos III, Madrid, Spain
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Jeon H, Lee S, Lee WH, Suk K. Analysis of glial secretome: The long pentraxin PTX3 modulates phagocytic activity of microglia. J Neuroimmunol 2010; 229:63-72. [DOI: 10.1016/j.jneuroim.2010.07.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 07/01/2010] [Accepted: 07/04/2010] [Indexed: 11/25/2022]
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Polaskova V, Kapur A, Khan A, Molloy MP, Baker MS. High-abundance protein depletion: comparison of methods for human plasma biomarker discovery. Electrophoresis 2010; 31:471-82. [PMID: 20119956 DOI: 10.1002/elps.200900286] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Affinity depletion of abundant proteins from human plasma has become a routine sample preparation strategy in proteomics used prior to protein identification and quantitation. To date, there have been limited published studies comparing the performance of commercially available depletion products. We conducted a thorough evaluation of six depletion columns using 2-DE combined with sophisticated image analysis software, examining the following criteria: (i) efficiency of high-abundance protein depletion, (ii) non-specific removal of other than the targeted proteins and (iii) total number of protein spots detected on the gels following depletion. From all the products investigated, the Seppro IgY system provided the best results. It displayed the greatest number of protein spots on the depleted plasma gels, minimal non-specific binding and high efficiency of abundant protein removal. Nevertheless, the increase in the number of detected spots compared with the second best performing and cheaper multiple affinity removal column (MARC) was not shown to be statistically significant. The ProteoPrep spin column, considered to be the "deepest" depletion technique available at the time of conducting the study, surprisingly displayed significantly fewer spots on the flow-through fraction gels compared with both the Seppro and the MARC. The spin column format and low plasma capacity were also found to be impractical for 2-DE. To conclude, we succeeded in providing an overview of the depletion columns performances with regard to the three examined areas. Our study will serve as a reference to other scientists when deciding on the optimal product for their particular projects.
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Affiliation(s)
- Veronika Polaskova
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW, Australia
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Wetterhall M, Zuberovic A, Hanrieder J, Bergquist J. Assessment of the partitioning capacity of high abundant proteins in human cerebrospinal fluid using affinity and immunoaffinity subtraction spin columns. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:1519-30. [PMID: 20444656 DOI: 10.1016/j.jchromb.2010.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 04/01/2010] [Accepted: 04/01/2010] [Indexed: 11/18/2022]
Abstract
The performance of three different affinity and immunoaffinity subtraction spin columns was investigated for the removal of the most abundant proteins in human cerebrospinal fluid (CSF). A pool of human CSF was processed with the spin columns and both the bound and flow through fractions were compared with each other and with intact CSF using 1D gel electrophoresis and nanoLC-MALDI-TOF/TOF-MS analysis. MASCOT MS/MS ionscores were compared before and after processing with the columns. The non-specific co-removal of proteins bound to the high abundant proteins, so called "sponge effect" was also examined for each spin column. The reproducibility of one of the spin columns, ProteomeLab IgY-12 proteome partitioning spin column, was further investigated by isobaric tags for relative and absolute quantification (iTRAQ) labeling and MS/MS analysis. Overall, 173 unique proteins were identified on a 95% MudPIT confidence scoring level. For all three spin columns, the number of proteins identified and their MASCOT scores were increased up to 10 times. The largest degree of non-specific protein removal was observed for a purely affinity based albumin removal column, where 28 other proteins also were present. The ProteomeLab IgY-12 proteome partitioning spin column showed very high reproducibility when combined with iTRAQ labeling and MS/MS analysis. The combined relative standard deviation (R.S.D.) for the high abundant protein removal, iTRAQ labeling and nanoLC-MALDI-TOF/TOF-MS analysis was less than 17.5%.
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Affiliation(s)
- Magnus Wetterhall
- Department of Physical and Analytical Chemistry, Analytical Chemistry, Uppsala University, Uppsala, Sweden
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Suk K. Combined analysis of the glia secretome and the CSF proteome: neuroinflammation and novel biomarkers. Expert Rev Proteomics 2010; 7:263-274. [DOI: 10.1586/epr.10.6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Pendyala G, Fox HS. Proteomic and metabolomic strategies to investigate HIV-associated neurocognitive disorders. Genome Med 2010; 2:22. [PMID: 20353544 PMCID: PMC2873800 DOI: 10.1186/gm143] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Diagnosing neurodegenerative diseases, monitoring their progression and assessing responses to treatments will all be aided by the identification of molecular markers of different stages of pathology. Protein biomarkers for HIV-associated neurocognitive disorders that have been discovered using proteomics include complement C3, soluble superoxide dismutase and a prostaglandin synthase. Metabolomics has not yet been widely used for biomarker discovery, but early work shows that it has great potential.
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Affiliation(s)
- Gurudutt Pendyala
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, 985800 Nebraska Medical Center, Omaha, NE 68198, USA.
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Pendyala G, Trauger SA, Kalisiak E, Ellis RJ, Siuzdak G, Fox HS. Cerebrospinal fluid proteomics reveals potential pathogenic changes in the brains of SIV-infected monkeys. J Proteome Res 2009; 8:2253-60. [PMID: 19281240 DOI: 10.1021/pr800854t] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The HIV-1-associated neurocognitive disorder occurs in approximately one-third of infected individuals. It has persisted in the current era of antiretroviral therapy, and its study is complicated by the lack of biomarkers for this condition. Since the cerebrospinal fluid is the most proximal biofluid to the site of pathology, we studied the cerebrospinal fluid in a nonhuman primate model for HIV-1-associated neurocognitive disorder. Here we present a simple and efficient liquid chromatography-coupled mass spectrometry-based proteomics approach that utilizes small amounts of cerebrospinal fluid. First, we demonstrate the validity of the methodology using human cerebrospinal fluid. Next, using the simian immunodeficiency virus-infected monkey model, we show its efficacy in identifying proteins such as alpha-1-antitrypsin, complement C3, hemopexin, IgM heavy chain, and plasminogen, whose increased expression is linked to disease. Finally, we find that the increase in cerebrospinal fluid proteins is linked to increased expression of their genes in the brain parenchyma, revealing that the cerebrospinal fluid alterations identified reflect changes in the brain itself and not merely leakage of the blood-brain or blood-cerebrospinal fluid barriers. This study reveals new central nervous system alterations in lentivirus-induced neurological disease, and this technique can be applied to other systems in which limited amounts of biofluids can be obtained.
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Affiliation(s)
- Gurudutt Pendyala
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska 68198-5800, USA
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Roche S, Tiers L, Provansal M, Seveno M, Piva MT, Jouin P, Lehmann S. Depletion of one, six, twelve or twenty major blood proteins before proteomic analysis: the more the better? J Proteomics 2009; 72:945-51. [PMID: 19341827 DOI: 10.1016/j.jprot.2009.03.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 03/16/2009] [Accepted: 03/24/2009] [Indexed: 10/20/2022]
Abstract
Depletion of major blood proteins is one of the most promising approaches to access low abundant biomarkers using proteomics. Immunocapture columns often used for this purpose exist in different formats depending on the number of major proteins removed. In this article, we compared the relative interest of depleting either one (albumin), six (albumin, IgG, IgA, transferrin, alpha1-antitrypsin, and haptoglobin), twelve (the previous six and apo A-I and -II, orosomucoid, alpha2-macroglobulin, fibrinogen, IgM) or twenty blood proteins (the previous twelve and IgD, ceruloplasmin, apo B, complement C1q, C3, C4, plasminogen, and prealbumin). Such study raises interesting issues related to the reproducibility, practicability, specificity of the immunocapture, and to the impact of removing not only the selected molecules, but also associated peptides and proteins. Depleted sera were here analysed using different proteomic approaches, including two dimensional electrophoresis and SELDI-TOF. Altogether, our results clearly confirmed the interest of depleting major blood proteins for the proteomic detection of low abundant components. However, we observed that increasing the number of depleted proteins from twelve to twenty had a limited beneficial impact and might increase drawbacks in removing associated peptides and proteins. This conclusion is however related to the technologies that we have used, and we believe that it is necessary to adapt the immunocapture to the analytical method employed, and to the ratio between wanted and unwanted proteins removed.
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Affiliation(s)
- Stéphane Roche
- CHU Montpellier, Biochimie Saint Eloi, Plateforme de Protéomique Clinique 80 av A. Fliche, Montpellier, France
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Bernay B, Gaillard MC, Guryca V, Emadali A, Kuhn L, Bertrand A, Detraz I, Carcenac C, Savasta M, Brouillet E, Garin J, Elalouf JM. Discovering new bioactive neuropeptides in the striatum secretome using in vivo microdialysis and versatile proteomics. Mol Cell Proteomics 2009; 8:946-58. [PMID: 19164277 DOI: 10.1074/mcp.m800501-mcp200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The striatum, a major component of the brain basal nuclei, is central for planning and executing voluntary movements and undergoes lesions in neurodegenerative disorders such as Huntington disease. To perform highly integrated tasks, the striatum relies on a complex network of communication within and between brain regions with a key role devoted to secreted molecules. To characterize the rat striatum secretome, we combined in vivo microdialysis together with proteomics analysis of trypsin digests and peptidomics studies of native fragments. This versatile approach, carried out using different microdialysis probes and mass spectrometer devices, allowed evidencing with high confidence the expression of 88 proteins and 100 processed peptides. Their secretory pathways were predicted by in silico analysis. Whereas high molecular weight proteins were mainly secreted by the classical mode (94%), low molecular weight proteins equally used classical and non-classical modes (53 and 47%, respectively). In addition, our results suggested alternative secretion mechanisms not predicted by bioinformatics tools. Based on spectrum counting, we performed a relative quantification of secreted proteins and peptides in both basal and neuronal depolarization conditions. This allowed detecting a series of neuropeptide precursors and a 6-fold increase for neurosecretory protein VGF and proenkephalin (PENK) levels. A focused investigation and a long peptide experiment led to the identification of new secreted non-opioid PENK peptides, referred to as PENK 114-133, PENK 239-260, and PENK 143-185. Moreover we showed that injecting synthetic PENK 114-133 and PENK 239-260 into the striatum robustly increased glutamate release in this region. Thus, the combination of microdialysis and versatile proteomics methods shed new light on the secreted protein repertoire and evidenced novel neuropeptide transmitters.
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Affiliation(s)
- Benoît Bernay
- Laboratoire de PhysioGénomique, Service de Biologie Intégrative et Génétique Moléculaire (SBIGeM), Institut de Biologie et de Technologies de Saclay (iBiTec-S), Commissariat à l'Energie Atomique (CEA), F-91191 Gif-sur-Yvette, France.
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