Full Text Journal Articles by
Author Isabelle Fournier

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Alternative proteins are functional regulators in cell reprogramming by PKA activation.

Tristan Cardon, Julien Franck, Etienne Coyaud, Estelle M N Laurent, Marina Damato, Michele Maffia, Daniele Vergara, Isabelle Fournier, Michel Salzet,

It has been recently shown that many proteins are lacking from reference databases used in mass spectrometry analysis, due to their translation templated on alternative open reading frames. This questions our current understanding of gene annotation and drastically expands the theoretical proteome complexity. The functions of these alternative proteins (AltProts) ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2020, :]

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Reference and Ghost Proteins Identification in Rat C6 Glioma Extracellular Vesicles.

Adriana-Natalia Murgoci, Tristan Cardon, Soulaimane Aboulouard, Marie Duhamel, Isabelle Fournier, Dasa Cizkova, Michel Salzet,

Extracellular vesicles (EVs) mediate intercellular communication and regulate a broad range of biological processes. Novel therapeutic strategies have emerged based on the use of EVs as biological nanoparticles. To separate isolated EVs from protein aggregates and the external part of EVs membrane proteins, we performed a Trypsin/Lys C digestion treatment ... Read more >>

iScience (iScience)
[2020, 23(5):101045]

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Towards CNN Representations for Small Mass Spectrometry Data Classification: From Transfer Learning to Cumulative Learning

Khawla Seddiki, Philippe Saudemont, Frédéric Precioso, Nina Ogrinc, Maxence Wisztorski, Michel Salzet, Isabelle Fournier, Arnaud Droit,

Abstract Rapid and accurate clinical diagnosis of pathological conditions remains highly challenging. A very important component of diagnosis tool development is the design of effective classification models with Mass spectrometry (MS) data. Some popular Machine Learning (ML) approaches have been investigated for this purpose but these ML models require time-consuming ... Read more >>

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Meropenem vs standard of care for treatment of neonatal late onset sepsis (NeoMero1): A randomised controlled trial.

Irja Lutsar, Corine Chazallon, Ursula Trafojer, Vincent Meiffredy de Cabre, Cinzia Auriti, Chiara Bertaina, Francesca Ippolita Calo Carducci, Fuat Emre Canpolat, Susanna Esposito, Isabelle Fournier, Maarja Hallik, Paul T Heath, Mari-Liis Ilmoja, Elias Iosifidis, Jelena Kuznetsova, Laurence Meyer, Tuuli Metsvaht, George Mitsiakos, Zoi Dorothea Pana, Fabio Mosca, Lorenza Pugni, Emmanuel Roilides, Paolo Rossi, Kosmas Sarafidis, Laura Sanchez, Michael Sharland, Vytautas Usonis, Adilia Warris, Jean-Pierre Aboulker, Carlo Giaquinto, ,

BACKGROUND:The early use of broad-spectrum antibiotics remains the cornerstone for the treatment of neonatal late onset sepsis (LOS). However, which antibiotics should be used is still debatable, as relevant studies were conducted more than 20 years ago, recruited in single centres or countries, evaluated antibiotics not in clinical use anymore ... Read more >>

PLoS ONE (PloS one)
[2020, 15(3):e0229380]

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A Hidden Human Proteome Signature Characterizes the Epithelial Mesenchymal Transition Program.

Daniele Vergara, Tiziano Verri, Marina Damato, Marco Trerotola, Pasquale Simeone, Julien Franck, Isabelle Fournier, Michel Salzet, Michele Maffia,

BACKGROUND:Molecular changes associated with the initiation of the epithelial to mesenchymal transition (EMT) program involve alterations of large proteome-based networks. The role of protein products mapping to non-coding genomic regions is still unexplored. OBJECTIVE:The goal of this study was the identification of an alternative protein signature in breast cancer cellular ... Read more >>

Curr. Pharm. Des. (Current pharmaceutical design)
[2020, 26(3):372-375]

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Mechanisms of innate events during skin reaction following intradermal injection of seasonal influenza vaccine.

Jessica Gonnet, Lauranne Poncelet, Celine Meriaux, Elena Gonçalves, Lina Weiss, Nicolas Tchitchek, Eric Pedruzzi, Angele Soria, David Boccara, Annika Vogt, Olivia Bonduelle, Gregory Hamm, Rima Ait-Belkacem, Jonathan Stauber, Isabelle Fournier, Maxence Wisztorski, Behazine Combadiere,

The skin plays a crucial role in host defences against microbial attack and the innate cells must provide the immune system with sufficient information to organize these defences. This unique feature makes the skin a promising site for vaccine administration. Although cellular innate immune events during vaccination have been widely ... Read more >>

J Proteomics (Journal of proteomics)
[2020, 216:103670]

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Carbonic Anhydrase XII Expression Is Modulated during Epithelial Mesenchymal Transition and Regulated through Protein Kinase C Signaling.

Daniele Vergara, Sara Ravaioli, Eugenio Fonzi, Loredaria Adamo, Marina Damato, Sara Bravaccini, Francesca Pirini, Antonio Gaballo, Raffaela Barbano, Barbara Pasculli, Julien Franck, Isabelle Fournier, Michel Salzet, Michele Maffia,

Members of the carbonic anhydrase family are functionally involved in the regulation of intracellular and extracellular pH in physiological and pathological conditions. Their expression is finely regulated to maintain a strict control on cellular homeostasis, and it is dependent on the activation of extracellular and intracellular signaling pathways. Combining RNA ... Read more >>

Int J Mol Sci (International journal of molecular sciences)
[2020, 21(3):]

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Optimized Sample Preparation Workflow for Improved Identification of Ghost Proteins.

Tristan Cardon, Flore Hervé, Vivian Delcourt, Xavier Roucou, Michel Salzet, Julien Franck, Isabelle Fournier,

Large scale proteomic strategies rely on database interrogation. Thus, only referenced proteins can be identified. Recently, Alternative Proteins (AltProts) translated from nonannotated Alternative Open reading frame (AltORFs) were discovered using customized databases. Because of their small size which confers them peptide-like physicochemical properties, they are more difficult to detect using ... Read more >>

Anal. Chem. (Analytical chemistry)
[2020, 92(1):1122-1129]

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Water-assisted laser desorption/ionization mass spectrometry for minimally invasive in vivo and real-time surface analysis using SpiderMass.

Nina Ogrinc, Philippe Saudemont, Julia Balog, Yves-Marie Robin, Jean-Pascal Gimeno, Quentin Pascal, Dominique Tierny, Zoltan Takats, Michel Salzet, Isabelle Fournier,

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 ... Read more >>

Nat Protoc (Nature protocols)
[2019, 14(11):3162-3182]

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Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging of Lipids in Experimental Model of Traumatic Brain Injury Detecting Acylcarnitines as Injury Related Markers.

Khalil Mallah, Jusal Quanico, Antonella Raffo-Romero, Tristan Cardon, Soulaimane Aboulouard, David Devos, Firas Kobeissy, Kazem Zibara, Michel Salzet, Isabelle Fournier,

Identifying new lipid markers linked to traumatic brain injury (TBI) is of major importance in characterizing their central role in the regeneration process and inflammatory response in such an injury model. In the present study, an advanced lipidomics analysis using high spectral resolution matrix-assisted laser desorption/ionization-mass spectrometry imaging was performed ... Read more >>

Anal. Chem. (Analytical chemistry)
[2019, 91(18):11879-11887]

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A Treatment-Decision Score for HIV-Infected Children With Suspected Tuberculosis.

Olivier Marcy, Laurence Borand, Vibol Ung, Philippe Msellati, Mathurin Tejiokem, Khanh Truong Huu, Viet Do Chau, Duong Ngoc Tran, Francis Ateba-Ndongo, Suzie Tetang-Ndiang, Boubacar Nacro, Bintou Sanogo, Leakhena Neou, Sophie Goyet, Bunnet Dim, Polidy Pean, Catherine Quillet, Isabelle Fournier, Laureline Berteloot, Guislaine Carcelain, Sylvain Godreuil, Stéphane Blanche, Christophe Delacourt, ,

BACKGROUND:Diagnosis of tuberculosis should be improved in children infected with HIV to reduce mortality. We developed prediction scores to guide antituberculosis treatment decision in HIV-infected children with suspected tuberculosis. METHODS:HIV-infected children with suspected tuberculosis enrolled in Burkina Faso, Cambodia, Cameroon, and Vietnam (ANRS 12229 PAANTHER 01 Study), underwent clinical assessment, ... Read more >>

Pediatrics (Pediatrics)
[2019, 144(3):]

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Canine Bone Marrow-derived Mesenchymal Stem Cells: Genomics, Proteomics and Functional Analyses of Paracrine Factors.

Filip Humenik, Dasa Cizkova, Stefan Cikos, Lenka Luptakova, Aladar Madari, Dagmar Mudronova, Maria Kuricova, Jana Farbakova, Alexandra Spirkova, Eva Petrovova, Martin Cente, Zuzana Mojzisova, Soulaimane Aboulouard, Adriana-Natalia Murgoci, Isabelle Fournier, Michel Salzet,

Adult stem cells have become prominent candidates for treating various diseases in veterinary practice. The main goal of our study was therefore to provide a comprehensive study of canine bone marrow-derived mesenchymal stem cells (BMMSC) and conditioned media, isolated from healthy adult dogs of different breeds. Under well-defined standardized isolation ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2019, 18(9):1824-1835]

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Mass spectrometry-based intraoperative tumor diagnostics: a letter in reply.

Isabelle Fournier, Michel Salzet,

Future Sci OA (Future science OA)
[2019, 5(7):FSO403]

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The Brain Origin of Neonatal Microglia Determines the Content of Exosomes and Biological Function

Adriana-Natalia Murgoci, Khalil Mallah, Soulaimane Aboulouard, Christophe Lefebvre, Milan Cizek, Isabelle Fournier, Dasa Cizkova, Michel Salzet,

Using a combination of pan proteomic platform associated with systemic biology analyses, we demonstrate that neonatal microglial cells derived from cortex and spinal cord expressed different phenotypes upon the physiological or pathological conditions. They also highlight great variability in protein production on both cellular and exosome levels. Bioinformatics data indicate ... Read more >>

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Distinct Protein Expression Networks are Activated in Microglia Cells after Stimulation with IFN-γ and IL-4.

Daniele Vergara, Annamaria Nigro, Alessandro Romano, Stefania De Domenico, Marina Damato, Julien Franck, Chiara Coricciati, Maxence Wistorski, Tristan Cardon, Isabelle Fournier, Angelo Quattrini, Michel Salzet, Roberto Furlan, Michele Maffia,

Microglia cells are the primary immune population of the central nervous system with a role in the regulation of several physiological and pathological conditions. Upon appropriate stimulation, microglia cells can be polarized in a pro-inflammatory M1-like or anti-inflammatory M2-like status. Biological processes and pathways engaged in microglia polarization are starting ... Read more >>

Cells (Cells)
[2019, 8(6):]

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Mapping Spatiotemporal Microproteomics Landscape in Experimental Model of Traumatic Brain Injury Unveils a link to Parkinson's Disease.

Khalil Mallah, Jusal Quanico, Antonella Raffo-Romero, Tristan Cardon, Soulaimane Aboulouard, David Devos, Firas Kobeissy, Kazem Zibara, Michel Salzet, Isabelle Fournier,

Traumatic brain injury (TBI) represents a major health concerns with no clinically-approved FDA drug available for therapeutic intervention. Several genomics and neuroproteomics studies have been employed to decipher the underlying pathological mechanisms involved that can serve as potential neurotherapeutic targets and unveil a possible underlying relation of TBI to other ... Read more >>

Mol. Cell Proteomics (Molecular & cellular proteomics : MCP)
[2019, 18(8):1669-1682]

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Nuclei of HeLa cells interactomes unravel a network of ghost proteins involved in proteins translation.

Tristan Cardon, Michel Salzet, Julien Franck, Isabelle Fournier,

Ghost proteins are issued from alternative Open Reading Frames (ORFs) and are missing a genome annotation. Indeed, historical filters applied for the detection of putative translated ORFs led to a wrong classification of transcripts considered as non-coding although translated proteins can be detected by proteomics. This Ghost (also called Alternative) ... Read more >>

Biochim Biophys Acta Gen Subj (Biochimica et biophysica acta. General subjects)
[2019, 1863(10):1458-1470]

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Spinal Cord Injury: Animal Models, Imaging Tools and the Treatment Strategies.

Dasa Cizkova, Adriana-Natalia Murgoci, Veronika Cubinkova, Filip Humenik, Zuzana Mojzisova, Marcela Maloveska, Milan Cizek, Isabelle Fournier, Michel Salzet,

Spinal cord injury (SCI) often leads to irreversible neuro-degenerative changes with life-long consequences. While there is still no effective therapy available, the results of past research have led to improved quality of life for patients suffering from partial or permanent paralysis. In this review we focus on the need, importance ... Read more >>

Neurochem. Res. (Neurochemical research)
[2020, 45(1):134-143]

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Prevalence of pretreatment HIV drug resistance in West African and Southeast Asian countries.

Nicole Ngo-Giang-Huong, Thu H K Huynh, Anoumou Y Dagnra, Thomas-d'Aquin Toni, Almoustapha I Maiga, Dramane Kania, Sabrina Eymard-Duvernay, Martine Peeters, Cathia Soulie, Gilles Peytavin, Claire Rekacewicz, Marie-Laure Chaix, Avelin F Aghokeng, ,

Background:ART in the developing world has moved to a new era with the WHO recommendation to test and immediately treat HIV-positive individuals. A high frequency of pretreatment HIV drug resistance (PDR) can compromise ART efficacy. Our study presents updated estimates of PDR in seven countries from West Africa (Burkina Faso, ... Read more >>

J. Antimicrob. Chemother. (The Journal of antimicrobial chemotherapy)
[2019, 74(2):462-467]

Cited: 3 times

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OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes.

Marie A Brunet, Mylène Brunelle, Jean-François Lucier, Vivian Delcourt, Maxime Levesque, Frédéric Grenier, Sondos Samandi, Sébastien Leblanc, Jean-David Aguilar, Pascal Dufour, Jean-Francois Jacques, Isabelle Fournier, Aida Ouangraoua, Michelle S Scott, François-Michel Boisvert, Xavier Roucou,

Advances in proteomics and sequencing have highlighted many non-annotated open reading frames (ORFs) in eukaryotic genomes. Genome annotations, cornerstones of today's research, mostly rely on protein prior knowledge and on ab initio prediction algorithms. Such algorithms notably enforce an arbitrary criterion of one coding sequence (CDS) per transcript, leading to ... Read more >>

Nucleic Acids Res. (Nucleic acids research)
[2019, 47(D1):D403-D410]

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A specific lipid metabolic profile is associated with the epithelial mesenchymal transition program.

Anna Maria Giudetti, Stefania De Domenico, Andrea Ragusa, Paola Lunetti, Antonio Gaballo, Julien Franck, Pasquale Simeone, Giuseppe Nicolardi, Francesco De Nuccio, Angelo Santino, Loredana Capobianco, Paola Lanuti, Isabelle Fournier, Michel Salzet, Michele Maffia, Daniele Vergara,

Several studies have identified a specific metabolic program that is associated with the process of epithelial-mesenchymal transition (EMT). Whereas much is known about the association between glucose metabolism and EMT, the contribution of lipid metabolism is not still completely understood. Here, we studied epithelial and mesenchymal breast cancer cells by ... Read more >>

Biochim Biophys Acta Mol Cell Biol Lipids (Biochimica et biophysica acta. Molecular and cell biology of lipids)
[2019, 1864(3):344-357]

Cited: 3 times

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The multiverse nature of epithelial to mesenchymal transition.

Pasquale Simeone, Marco Trerotola, Julien Franck, Tristan Cardon, Marco Marchisio, Isabelle Fournier, Michel Salzet, Michele Maffia, Daniele Vergara,

The epithelial mesenchymal transition (EMT) program is defined as a cellular transition from an epithelial to a mesenchymal state. This process occurs to provide the cell with new phenotypic assets and new skills to perform complex processes. EMT is regulated at multilayer levels, including transcriptional control of gene expression, regulation ... Read more >>

Semin. Cancer Biol. (Seminars in cancer biology)
[2019, 58:1-10]

Cited: 12 times

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Meropenem vs standard of care for treatment of neonatal late onset sepsis (NeoMero1): a randomised controlled trial

Irja Lutsar, Corine Chazallon, Ursula Trafojer, Vincent Meiffredy de Cabre, Cinzia Auriti, Chiara Bertaina, Francesca Ippolita Calo Carducci, Fuat Emre Canpolat, Susanna Esposito, Isabelle Fournier, Maarja Hallik, Paul Heath Frcpch, Mari-Liis Ilmoja, Elias Iosifidis, Jelena Kuznetsova, Laurence Meyer, Tuuli Metsvaht, George Mitsiakos, Zoi Dorothea Pana, Fabio Mosca, Lorenza Pugni, Emmanuel Roilides, Paolo Rossi, Kosmas Sarafidis, Laura Sanchez, Michael Sharland, Vytautas Usonis, Adilia Warris, Jean-Pierre Aboulker, Carlo Giaquinto, ,

Abstract Background The early use of broad-spectrum antibiotics remains the cornerstone for the treatment of neonatal late onset sepsis (LOS). However, which antibiotics should be used is still debatable, as relevant studies were conducted more than 20 years ago, were single centre or country, insufficiently powered, evaluated antibiotics not in ... Read more >>

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Real-Time Molecular Diagnosis of Tumors Using Water-Assisted Laser Desorption/Ionization Mass Spectrometry Technology.

Philippe Saudemont, Jusal Quanico, Yves-Marie Robin, Anna Baud, Julia Balog, Benoit Fatou, Dominique Tierny, Quentin Pascal, Kevin Minier, Mélissa Pottier, Cristian Focsa, Michael Ziskind, Zoltan Takats, Michel Salzet, Isabelle Fournier,

Histopathological diagnosis of biopsy samples and margin assessment of surgical specimens are challenging aspects in sarcoma. Using dog patient tissues, we assessed the performance of a recently developed technology for fast ex vivo molecular lipid-based diagnosis of sarcomas. The instrument is based on mass spectrometry (MS) molecular analysis through a laser ... Read more >>

Cancer Cell (Cancer cell)
[2018, 34(5):840-851.e4]

Cited: 4 times

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Lipid Changes Associated with Traumatic Brain Injury Revealed by 3D MALDI-MSI.

Khalil Mallah, Jusal Quanico, Dennis Trede, Firas Kobeissy, Kazem Zibara, Michel Salzet, Isabelle Fournier,

Traumatic brain injury (TBI) is a major cause of death and disability in children and young adults worldwide according to the World Health Organization (WHO). The emergence of mass-spectrometry-based techniques, such as MALDI-MSI, has allowed the monitoring and visualization of changes post injury, providing a global picture of the impact ... Read more >>

Anal. Chem. (Analytical chemistry)
[2018, 90(17):10568-10576]

Cited: 1 time

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