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Nekoua MP, Bertin A, Sane F, Gimeno JP, Fournier I, Salzet M, Engelmann I, Alidjinou EK, Hober D. Persistence of Coxsackievirus B4 in Pancreatic β Cells Disturbs Insulin Maturation, Pattern of Cellular Proteins, and DNA Methylation. Microorganisms 2021; 9:microorganisms9061125. [PMID: 34067388 PMCID: PMC8224704 DOI: 10.3390/microorganisms9061125] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/15/2022] Open
Abstract
Coxsackievirus-B4 (CV-B4) can persist in pancreatic cell lines and impair the phenoytpe and/or gene expressions in these cells; however, the models used to study this phenomenon did not produce insulin. Therefore, we investigated CV-B4 persistence and its consequences in insulin-producing pancreatic β cells. The insulin-secreting rat β cell line, INS-1, was infected with CV-B4. After lysis of a large part of the cell layer, the culture was still maintained and no additional cytopathic effect was observed. The amount of insulin in supernatants of cell cultures persistently infected with CV-B4 was not affected by the infection; in fact, a larger quantity of proinsulin was found. The mRNA expression of pro-hormone convertase 2, an enzyme involved in the maturation of proinsulin into insulin and studied using real-time reverse transcription-polymerase chain reaction, was inhibited in infected cultures. Further, the pattern of 47 cell proteins analyzed using Shotgun mass spectrometry was significantly modified. The DNA of persistently infected cell cultures was hypermethylated unlike that of controls. The persistent infection of INS-1 cells with CV-B4 had a deep impact on these cells, especially on insulin metabolism. Cellular changes caused by persistent CV-B4 infection of β cells can play a role in type 1 diabetes pathogenesis.
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Affiliation(s)
- Magloire Pandoua Nekoua
- Laboratoire de Virologie ULR3610, Université de Lille, CHU Lille, F-59000 Lille, France; (M.P.N.); (A.B.); (F.S.); (I.E.); (E.K.A.)
| | - Antoine Bertin
- Laboratoire de Virologie ULR3610, Université de Lille, CHU Lille, F-59000 Lille, France; (M.P.N.); (A.B.); (F.S.); (I.E.); (E.K.A.)
| | - Famara Sane
- Laboratoire de Virologie ULR3610, Université de Lille, CHU Lille, F-59000 Lille, France; (M.P.N.); (A.B.); (F.S.); (I.E.); (E.K.A.)
| | - Jean-Pascal Gimeno
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Inserm U1192, Université de Lille, F-59000 Lille, France; (J.-P.G.); (I.F.); (M.S.)
| | - Isabelle Fournier
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Inserm U1192, Université de Lille, F-59000 Lille, France; (J.-P.G.); (I.F.); (M.S.)
| | - Michel Salzet
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Inserm U1192, Université de Lille, F-59000 Lille, France; (J.-P.G.); (I.F.); (M.S.)
| | - Ilka Engelmann
- Laboratoire de Virologie ULR3610, Université de Lille, CHU Lille, F-59000 Lille, France; (M.P.N.); (A.B.); (F.S.); (I.E.); (E.K.A.)
| | - Enagnon Kazali Alidjinou
- Laboratoire de Virologie ULR3610, Université de Lille, CHU Lille, F-59000 Lille, France; (M.P.N.); (A.B.); (F.S.); (I.E.); (E.K.A.)
| | - Didier Hober
- Laboratoire de Virologie ULR3610, Université de Lille, CHU Lille, F-59000 Lille, France; (M.P.N.); (A.B.); (F.S.); (I.E.); (E.K.A.)
- Correspondence: ; Tel.: +33-(0)-3-2044-6688
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Bauzone M, Souidi M, Dessein AF, Wisztorski M, Vincent A, Gimeno JP, Monté D, Van Seuningen I, Gespach C, Huet G. Cross-talk between YAP and RAR-RXR Drives Expression of Stemness Genes to Promote 5-FU Resistance and Self-Renewal in Colorectal Cancer Cells. Mol Cancer Res 2021; 19:612-622. [PMID: 33472949 DOI: 10.1158/1541-7786.mcr-20-0462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 11/10/2020] [Accepted: 01/12/2021] [Indexed: 12/15/2022]
Abstract
The mechanisms whereby the Hippo pathway effector YAP regulates cancer cell stemness, plasticity, and chemoresistance are not fully understood. We previously showed that in 5-fluorouracil (5-FU)-resistant colorectal cancer cells, the transcriptional coactivator YAP is differentially regulated at critical transitions connected with reversible quiescence/dormancy to promote metastasis. Here, we found that experimental YAP activation in 5-FU-sensitive and 5-FU-resistant HT29 colorectal cancer cells enhanced nuclear YAP localization and the transcript levels of the retinoic acid (RA) receptors RARα/γ and RAR target genes CYP26A1, ALDH1A3, and LGR5 through RA Response Elements (RARE). In these two cell models, constitutive YAP activation reinforced the expression of the stemness biomarkers and regulators ALDH1A3, LGR5, and OCT4. Conversely, YAP silencing, RAR/RXR inhibition by the pan-RAR antagonist BMS493, and vitamin A depletion downregulated stemness traits and self-renewal. Regarding the mechanisms engaged, proximity-dependent labeling, nuclear YAP pulldown coupled with mass spectrometry, and chromatin immunoprecipitation (ChIP)/re-ChIP experiments revealed: (i) the nuclear colocalization/interaction of YAP with RARγ and RXRs; and (ii) combined genomic co-occupancy of YAP, RARα/γ, and RXRα interactomes at proximal RAREs of LGR5 and ALDH1A3 promoters. Moreover, activation of the YAP/RAR-RXR cross-talk in colorectal cancer cells promoted RAR self-activation loops via vitamin A metabolism, RA, and active RAR ligands generated by ALDH1A3. Together, our data identify YAP as a bona fide RAR-RXR transcriptional coactivator that acts through RARE-activated stemness genes. IMPLICATIONS: Targeting the newly identified YAP/RAR-RXR cross-talk implicated in cancer cell stemness maintenance may lead to multitarget combination therapies for patients with colorectal cancer.
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Affiliation(s)
- Marjolaine Bauzone
- Université Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
| | - Mouloud Souidi
- Université Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
| | - Anne-Frédérique Dessein
- Université Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France.,Centre de Biopathologie, Lille CHU, Lille, France
| | - Maxence Wisztorski
- Université Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, France
| | - Audrey Vincent
- Université Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
| | - Jean-Pascal Gimeno
- Université Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, France
| | - Didier Monté
- CNRS ERL9002 Integrative Structural Biology, Lille, France.,Université Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
| | - Isabelle Van Seuningen
- Université Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
| | - Christian Gespach
- Sorbonne Université, Inserm U938, Team TGFβ Signaling in Cellular Plasticity and Cancer, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Guillemette Huet
- Université Lille, CNRS, Inserm, CHU Lille, UMR9020-UMR1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France. .,Centre de Biopathologie, Lille CHU, Lille, France
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Gross-Amat O, Guillen M, Gimeno JP, Salzet M, Lebonvallet N, Misery L, Auxenfans C, Nataf S. Molecular Mapping of Hydrogen Sulfide Targets in Normal Human Keratinocytes. Int J Mol Sci 2020; 21:E4648. [PMID: 32629886 PMCID: PMC7369889 DOI: 10.3390/ijms21134648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/17/2020] [Accepted: 06/26/2020] [Indexed: 12/11/2022] Open
Abstract
Although sulfur-rich thermal waters have ancestrally been used in the context of dermatological conditions, a global mapping of the molecular effects exerted by H2S on human keratinocytes is still lacking. To fill this knowledge gap, we subjected cultured human keratinocytes to distinct amounts of the non-gaseous hydrogen sulfur donor NaHS. We first checked that H2S accumulated in the cytoplasm of keratinocytes under our experimental conditions andused a combination of proteomics, genomics and biochemical approaches to unravel functionally relevant H2S targets in human keratinocytes. We found that the identified targets fall into two main categories: (i) the oxidative stress response molecules superoxide dismutase 2 (SOD2), NAD(P)H quinone dehydrogenase 1 (NQO1) and culin 3 (CUL3) and (ii) the chemokines interleukin-8 (IL-8) and CXCL2. Interestingly, NaHS also stimulated the caspase-1 inflammasome pathway, leading to increased secretion of the pro-inflammatory molecule interleukin-18 (IL-18). Interestingly, the secretion of interleukin-1 beta (IL-1β) was only modestly impacted by NaHS exposure despite a significant accumulation of IL-1β pro-form. Finally, we observed that NaHS significantly hampered the growth of human keratinocyte progenitors and stem cells cultured under clonogenic conditions or as epidermal cell sheets. We conclude that H2S exerts specific molecular effects on normal human keratinocytes.
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Affiliation(s)
- Olivia Gross-Amat
- Lyon-Est School of Medicine, University Claude Bernard Lyon-1, 69100 Villeurbanne, France; (M.G.); (S.N.)
- Bank of Tissues and Cells, Lyon University Hospital (Hospices Civils de Lyon), 69003 Lyon, France;
- CarMeN Laboratory, INSERM U1060, INRA U1397, INSA de Lyon, 69600 Oullins, France
| | - Marine Guillen
- Lyon-Est School of Medicine, University Claude Bernard Lyon-1, 69100 Villeurbanne, France; (M.G.); (S.N.)
| | - Jean-Pascal Gimeno
- Inserm, CHRU Lille, U-1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, University of Lille, F-59000 Lille, France; (J.-P.G.); (M.S.)
| | - Michel Salzet
- Inserm, CHRU Lille, U-1192-Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, University of Lille, F-59000 Lille, France; (J.-P.G.); (M.S.)
| | - Nicolas Lebonvallet
- Laboratory of Epithelial-Neural Interactions, University of Brest, LIEN, 29200 Brest, France; (N.L.); (L.M.)
| | - Laurent Misery
- Laboratory of Epithelial-Neural Interactions, University of Brest, LIEN, 29200 Brest, France; (N.L.); (L.M.)
- Department of dermatology, Brest University Hospital (CHU de Brest), 29200 Brest, France
| | - Céline Auxenfans
- Bank of Tissues and Cells, Lyon University Hospital (Hospices Civils de Lyon), 69003 Lyon, France;
- Tissue Biology and Therapeutic Engineering Laboratory, UMR 5305, 69007 Lyon, France
| | - Serge Nataf
- Lyon-Est School of Medicine, University Claude Bernard Lyon-1, 69100 Villeurbanne, France; (M.G.); (S.N.)
- Bank of Tissues and Cells, Lyon University Hospital (Hospices Civils de Lyon), 69003 Lyon, France;
- CarMeN Laboratory, INSERM U1060, INRA U1397, INSA de Lyon, 69600 Oullins, France
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Lemaire Q, Raffo-Romero A, Arab T, Van Camp C, Drago F, Forte S, Gimeno JP, Begard S, Colin M, Vizioli J, Sautière PE, Salzet M, Lefebvre C. Isolation of microglia-derived extracellular vesicles: towards miRNA signatures and neuroprotection. J Nanobiotechnology 2019; 17:119. [PMID: 31801555 PMCID: PMC6894150 DOI: 10.1186/s12951-019-0551-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/20/2019] [Indexed: 12/18/2022] Open
Abstract
The functional preservation of the central nervous system (CNS) is based on the neuronal plasticity and survival. In this context, the neuroinflammatory state plays a key role and involves the microglial cells, the CNS-resident macrophages. In order to better understand the microglial contribution to the neuroprotection, microglia-derived extracellular vesicles (EVs) were isolated and molecularly characterized to be then studied in neurite outgrowth assays. The EVs, mainly composed of exosomes and microparticles, are an important cell-to-cell communication process as they exhibit different types of mediators (proteins, lipids, nucleic acids) to recipient cells. The medicinal leech CNS was initially used as an interesting model of microglia/neuron crosstalk due to their easy collection for primary cultures. After the microglia-derived EV isolation following successive methods, we developed their large-scale and non-targeted proteomic analysis to (i) detect as many EV protein markers as possible, (ii) better understand the biologically active proteins in EVs and (iii) evaluate the resulting protein signatures in EV-activated neurons. The EV functional properties were also evaluated in neurite outgrowth assays on rat primary neurons and the RNAseq analysis of the microglia-derived EVs was performed to propose the most representative miRNAs in microglia-derived EVs. This strategy allowed validating the EV isolation, identify major biological pathways in EVs and corroborate the regenerative process in EV-activated neurons. In parallel, six different miRNAs were originally identified in microglia-derived EVs including 3 which were only known in plants until now. The analysis of the neuronal proteins under the microglial EV activation suggested possible miRNA-dependent regulation mechanisms. Taken together, this combination of methodologies showed the leech microglial EVs as neuroprotective cargos across species and contributed to propose original EV-associated miRNAs whose functions will have to be evaluated in the EV-dependent dialog between microglia and neurons.
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Affiliation(s)
- Quentin Lemaire
- Laboratoire de Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000, Lille, France
| | - Antonella Raffo-Romero
- Laboratoire de Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000, Lille, France
| | - Tanina Arab
- Laboratoire de Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000, Lille, France
| | - Christelle Van Camp
- Laboratoire de Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000, Lille, France
| | - Francesco Drago
- Department of Biomedical and Biotechnological Sciences, Section of Pharmacology, University of Catania, Catania, Italy
| | | | - Jean-Pascal Gimeno
- Laboratoire de Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000, Lille, France
| | - Séverine Begard
- Centre de Recherche Jean-Pierre AUBERT (JPArc), INSERM U1172, Université de Lille, 59000, Lille, France
| | - Morvane Colin
- Centre de Recherche Jean-Pierre AUBERT (JPArc), INSERM U1172, Université de Lille, 59000, Lille, France
| | - Jacopo Vizioli
- Laboratoire de Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000, Lille, France
| | - Pierre-Eric Sautière
- Laboratoire de Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000, Lille, France
| | - Michel Salzet
- Laboratoire de Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000, Lille, France
| | - Christophe Lefebvre
- Laboratoire de Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000, Lille, France.
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Ogrinc N, Saudemont P, Balog J, Robin YM, Gimeno JP, Pascal Q, Tierny D, Takats Z, Salzet M, Fournier I. Water-assisted laser desorption/ionization mass spectrometry for minimally invasive in vivo and real-time surface analysis using SpiderMass. Nat Protoc 2019; 14:3162-3182. [PMID: 31597965 DOI: 10.1038/s41596-019-0217-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 06/14/2019] [Indexed: 11/09/2022]
Abstract
Rapid, sensitive, precise and accurate analysis of samples in their native in vivo environment is critical to better decipher physiological and physiopathological mechanisms. SpiderMass is an ambient mass spectrometry (MS) system designed for mobile in vivo and real-time surface analyses of biological tissues. The system uses a fibered laser, which is tuned to excite the most intense vibrational band of water, resulting in a process termed water-assisted laser desorption/ionization (WALDI). The water molecules act as an endogenous matrix in a matrix-assisted laser desorption ionization (MALDI)-like scenario, leading to the desorption/ionization of biomolecules (lipids, metabolites and proteins). The ejected material is transferred to the mass spectrometer through an atmospheric interface and a transfer line that is several meters long. Here, we formulate a three-stage procedure that includes (i) a laser system setup coupled to a Waters Q-TOF or Thermo Fisher Q Exactive mass analyzer, (ii) analysis of specimens and (iii) data processing. We also describe the optimal setup for the analysis of cell cultures, fresh-frozen tissue sections and in vivo experiments on skin. With proper optimization, the system can be used for a variety of different targets and applications. The entire procedure takes 1-2 d for complex samples.
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Affiliation(s)
- Nina Ogrinc
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France
| | - Philippe Saudemont
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France
- SATT-Nord, Immeuble Central Gare, Lille, France
| | - Julia Balog
- Department of Surgery and Cancer, St Mary's Hospital, Imperial College London, London, UK
| | - Yves-Marie Robin
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France
- Unité de Pathologie Morphologique et Moléculaire, Centre Oscar Lambret, Lille, France
| | - Jean-Pascal Gimeno
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France
| | - Quentin Pascal
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France
- OCR (Oncovet Clinical Research), Eurasanté, Loos, France
| | - Dominique Tierny
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France
- OCR (Oncovet Clinical Research), Eurasanté, Loos, France
| | - Zoltan Takats
- Department of Surgery and Cancer, St Mary's Hospital, Imperial College London, London, UK
| | - Michel Salzet
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France.
| | - Isabelle Fournier
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Villeneuve d'Ascq, France.
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Delcourt V, Franck J, Quanico J, Gimeno JP, Wisztorski M, Raffo-Romero A, Kobeissy F, Roucou X, Salzet M, Fournier I. Spatially-Resolved Top-down Proteomics Bridged to MALDI MS Imaging Reveals the Molecular Physiome of Brain Regions. Mol Cell Proteomics 2017; 17:357-372. [PMID: 29122912 PMCID: PMC5795397 DOI: 10.1074/mcp.m116.065755] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 10/11/2017] [Indexed: 12/14/2022] Open
Abstract
Tissue spatially-resolved proteomics was performed on 3 brain regions, leading to the characterization of 123 reference proteins. Moreover, 8 alternative proteins from alternative open reading frames (AltORF) were identified. Some proteins display specific post-translational modification profiles or truncation linked to the brain regions and their functions. Systems biology analysis performed on the proteome identified in each region allowed to associate sub-networks with the functional physiology of each brain region. Back correlation of the proteins identified by spatially-resolved proteomics at a given tissue localization with the MALDI MS imaging data, was then performed. As an example, mapping of the distribution of the matrix metallopeptidase 3-cleaved C-terminal fragment of α-synuclein (aa 95–140) identified its specific distribution along the hippocampal dentate gyrus. Taken together, we established the molecular physiome of 3 rat brain regions through reference and hidden proteome characterization.
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Affiliation(s)
- Vivian Delcourt
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France.,§Département de Biochimie Lab. Z8-2001, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Julien Franck
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France
| | - Jusal Quanico
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France
| | - Jean-Pascal Gimeno
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France
| | - Maxence Wisztorski
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France
| | - Antonella Raffo-Romero
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France
| | - Firas Kobeissy
- ¶Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Xavier Roucou
- §Département de Biochimie Lab. Z8-2001, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Michel Salzet
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France;
| | - Isabelle Fournier
- From the ‡Laboratoire Proteomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM) - INSERM U1192, Université Lille 1, Bât SN3, 1 étage, Cité Scientifique, F-59655 Villeneuve d'Ascq Cedex, France;
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Delcourt V, Franck J, Leblanc E, Narducci F, Robin YM, Gimeno JP, Quanico J, Wisztorski M, Kobeissy F, Jacques JF, Roucou X, Salzet M, Fournier I. Combined Mass Spectrometry Imaging and Top-down Microproteomics Reveals Evidence of a Hidden Proteome in Ovarian Cancer. EBioMedicine 2017. [PMID: 28629911 PMCID: PMC5514399 DOI: 10.1016/j.ebiom.2017.06.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Recently, it was demonstrated that proteins can be translated from alternative open reading frames (altORFs), increasing the size of the actual proteome. Top-down mass spectrometry-based proteomics allows the identification of intact proteins containing post-translational modifications (PTMs) as well as truncated forms translated from reference ORFs or altORFs. METHODS Top-down tissue microproteomics was applied on benign, tumor and necrotic-fibrotic regions of serous ovarian cancer biopsies, identifying proteins exhibiting region-specific cellular localization and PTMs. The regions of interest (ROIs) were determined by MALDI mass spectrometry imaging and spatial segmentation. FINDINGS Analysis with a customized protein sequence database containing reference and alternative proteins (altprots) identified 15 altprots, including alternative G protein nucleolar 1 (AltGNL1) found in the tumor, and translated from an altORF nested within the GNL1 canonical coding sequence. Co-expression of GNL1 and altGNL1 was validated by transfection in HEK293 and HeLa cells with an expression plasmid containing a GNL1-FLAG(V5) construct. Western blot and immunofluorescence experiments confirmed constitutive co-expression of altGNL1-V5 with GNL1-FLAG. CONCLUSIONS Taken together, our approach provides means to evaluate protein changes in the case of serous ovarian cancer, allowing the detection of potential markers that have never been considered.
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Affiliation(s)
- Vivian Delcourt
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Département de Biochimie Lab. Z8-2001, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Julien Franck
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Eric Leblanc
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Centre Oscar-Lambret, 3 Rue Frédéric Combemale, 59000 Lille, France
| | - Fabrice Narducci
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Centre Oscar-Lambret, 3 Rue Frédéric Combemale, 59000 Lille, France
| | - Yves-Marie Robin
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Centre Oscar-Lambret, 3 Rue Frédéric Combemale, 59000 Lille, France
| | - Jean-Pascal Gimeno
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; ONCOLille, Maison Régionale de la Recherche Clinique, Lille, France
| | - Jusal Quanico
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Maxence Wisztorski
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Lebanon
| | - Jean-François Jacques
- Département de Biochimie Lab. Z8-2001, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Xavier Roucou
- Département de Biochimie Lab. Z8-2001, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Canada
| | - Michel Salzet
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Isabelle Fournier
- Université de Lille 1, INSERM, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
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Le Rhun E, Duhamel M, Wisztorski M, Gimeno JP, Zairi F, Escande F, Reyns N, Kobeissy F, Maurage CA, Salzet M, Fournier I. Evaluation of non-supervised MALDI mass spectrometry imaging combined with microproteomics for glioma grade III classification. Biochim Biophys Acta Proteins Proteom 2016; 1865:875-890. [PMID: 27890679 DOI: 10.1016/j.bbapap.2016.11.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 11/17/2016] [Accepted: 11/20/2016] [Indexed: 10/20/2022]
Abstract
An integrated diagnosis using molecular features is recommended in the 2016 World Health Organization (WHO) classification. Our aim was to explore non-targeted molecular classification using MALDI mass spectrometry imaging (MALDI MSI) associated to microproteomics in order to classify anaplastic glioma by integration of clinical data. We used fresh-frozen tissue sections to perform MALDI MSI of proteins based on their digestion peptides after in-situ trypsin digestion of the tissue sections and matrix deposition by micro-spraying. The generated 70μm spatial resolution image datasets were further processed by individual or global segmentation in order to cluster the tissues according to their molecular protein signature. The clustering gives 3 main distinct groups. Within the tissues the ROIs (regions of interest) defined by these groups were used for microproteomics by micro-extraction of the tryptic peptides after on-tissue enzymatic digestion. More than 2500 proteins including 22 alternative proteins (AltProt) are identified by the Shotgun microproteomics. Statistical analysis on the basis of the label free quantification of the proteins shows a similar classification to the MALDI MSI segmentation into 3 groups. Functional analysis performed on each group reveals sub-networks related to neoplasia for group 1, glioma with inflammation for group 2 and neurogenesis for group 3. This demonstrates the interest on these new non-targeted large molecular data combining both MALDI MSI and microproteomics data, for tumor classification. This analysis provides new insights into grade III glioma organization. This specific information could allow a more accurate classification of the biopsies according to the prognosis and the identification of potential new targeted therapeutic options. This article is part of a Special Issue entitled: MALDI Imaging, edited by Dr. Corinna Henkel and Prof. Peter Hoffmann.
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Affiliation(s)
- Emilie Le Rhun
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Lille University Hospital, Neuro-Oncology, Department of Neurosurgery, F-59000 Lille, France; Breast Unit, Department of Medical Oncology, Oscar Lambret Center, Lille, France.
| | - Marie Duhamel
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Maxence Wisztorski
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Jean-Pascal Gimeno
- ONCOLille, Maison Régionale de la Recherche Clinique, F-59000 Lille, France.
| | - Fahed Zairi
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France; Lille University Hospital, Department of Neurosurgery, F-59000 Lille, France.
| | - Fabienne Escande
- Lille University Hospital, Pôle Pathologie Biologique, Service Anatomie Pathologique, F-59000 Lille, France.
| | - Nicolas Reyns
- Lille University Hospital, Department of Neurosurgery, F-59000 Lille, France.
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Lebanon; Department of Psychiatry, Center of Neuroproteomics and Biomarkers Research, University of Florida, Gainesville, FL, USA.
| | - Claude-Alain Maurage
- Lille University Hospital, Pôle Pathologie Biologique, Service Anatomie Pathologique, F-59000 Lille, France.
| | - Michel Salzet
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
| | - Isabelle Fournier
- Univ. Lille, INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France.
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Caron J, Chataigné G, Gimeno JP, Duhal N, Goossens JF, Dhulster P, Cudennec B, Ravallec R, Flahaut C. Food peptidomics ofin vitrogastrointestinal digestions of partially purified bovine hemoglobin: low-resolution versus high-resolution LC-MS/MS analyses. Electrophoresis 2016; 37:1814-22. [DOI: 10.1002/elps.201500559] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/09/2016] [Accepted: 03/04/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Juliette Caron
- Univ. Lille, Univ. Artois; EA 7394 - ICV - Institut Charles Viollette; Lille France
| | - Gabrielle Chataigné
- Univ. Lille, Univ. Artois; EA 7394 - ICV - Institut Charles Viollette; Lille France
| | - Jean-Pascal Gimeno
- Laboratoire PRISM/clic imaging-U 1192 INSERM Protéomique, réponse inflammatoire et spectrométrie de masse; Université Lille 1; Villeneuve d'Ascq France
| | | | | | - Pascal Dhulster
- Univ. Lille, Univ. Artois; EA 7394 - ICV - Institut Charles Viollette; Lille France
| | - Benoit Cudennec
- Univ. Lille, Univ. Artois; EA 7394 - ICV - Institut Charles Viollette; Lille France
| | - Rozenn Ravallec
- Univ. Lille, Univ. Artois; EA 7394 - ICV - Institut Charles Viollette; Lille France
| | - Christophe Flahaut
- Univ. Lille, Univ. Artois; EA 7394 - ICV - Institut Charles Viollette; Lille France
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Wisztorski M, Desmons A, Quanico J, Fatou B, Gimeno JP, Franck J, Salzet M, Fournier I. Spatially-resolved protein surface microsampling from tissue sections using liquid extraction surface analysis. Proteomics 2016; 16:1622-32. [DOI: 10.1002/pmic.201500508] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/29/2016] [Accepted: 02/24/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Maxence Wisztorski
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
| | - Annie Desmons
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
| | - Jusal Quanico
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
| | - Benoit Fatou
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
| | - Jean-Pascal Gimeno
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
- ONCOLille; Maison Régionale de la Recherche Clinique; Lille France
| | - Julien Franck
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
| | - Michel Salzet
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
| | - Isabelle Fournier
- Univ. Lille, Inserm; U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM; Lille France
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Mercier C, Truntzer C, Pecqueur D, Gimeno JP, Belz G, Roy P. Mixed-model of ANOVA for measurement reproducibility in proteomics. J Proteomics 2009; 72:974-81. [PMID: 19481188 DOI: 10.1016/j.jprot.2009.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2008] [Revised: 05/07/2009] [Accepted: 05/18/2009] [Indexed: 10/20/2022]
Abstract
This work is a statistical analysis of reproducibility of a MALDI-TOF mass spectrometry experiment. Its aim is to evaluate measurement variability and compare peak intensities from two types of MALDI-TOF platforms. We compared and commented on the abilities of Principal Component Analysis and mixed-model analysis of variance to evaluate the biological variability and the technical variability of peak intensities in different patients. The properties and hypotheses of both methods are summarized and applied to spectra from plasma of patients with Hodgkin lymphoma. Principal Component Analysis checks rapidly the balance between the two variabilities; however, a mixed-model analysis of variance is necessary to quantify the biological and technical components of the experimental variance as well as their interactions and to split the total variance into between-subjects and within-subject components. The latter method helped to assess the reproducibility of measurements from two MALDI-TOF platforms and to decompose the technical variability according to the experimental design.
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