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Fournier I, Caron C, McMurtry CM, Lapointe A, Giguere C, Doré-Bergeron MJ, Bergeron M. Comparison of Tympanostomy Tubes Under Local Anesthesia Versus General Anesthesia for Children. Laryngoscope 2024; 134:2422-2429. [PMID: 37800866 DOI: 10.1002/lary.31095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 10/07/2023]
Abstract
OBJECTIVE Tympanostomy tube insertion (TTI) is typically accomplished under general anesthesia (GA) in the operating room. We aimed to compare pain between GA and local anesthesia (LA) in surgically naïve children undergoing TTI. Secondary objectives examined patient's quality of life (QoL) and parent's satisfaction. STUDY DESIGN Prospective single-center study. SETTING Tertiary pediatric academic center. METHODS Consecutive children who underwent TTI under GA were compared to patients under LA. Pain standardized observational pain scales (Face, Legs, Activity, Cry, Consolability Scale [FLACC], Children's hospital of Eastern Ontario Pain Scale [CHEOPS]) were completed pre-procedure, during the first tympanostomy and second tympanostomy, and post-procedure, as well as 1 week postoperatively. General health-related QoL (PedsQL) and QoL specific to otitis media (OM-6) were measured before insertion and 1 month postoperatively. Parental satisfaction was also evaluated using a qualitative scale. RESULTS LA group had statistically significant higher pain levels at the beginning (7.3 vs. 0), during the first tympanostomy (7.8 vs. 0), during the second tympanostomy (7.7 vs. 0), and at end of the procedure (6.9 vs. 0) with the FLACC scale (all p < 0.01). Results were similar with the CHEOPS scale. No pain was noted 1 week after surgery in either group. Both groups had similar improvement in their QoL (p > 0.05). Minor complication occurred at a similar rate (p > 0.05). Parents were equally satisfied with their choice of anesthesia in both groups when initially questioned after the procedure (p > 0.05). CONCLUSIONS Children experienced significantly less pain under GA than LA. If LA is to be used, pain and distress-reducing strategies are critical. Shared decision-making with families is essential. LEVEL OF EVIDENCE 3 Laryngoscope, 134:2422-2429, 2024.
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Affiliation(s)
- Isabelle Fournier
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, Université de Montréal, Montreal, Quebec, Canada
| | - Camille Caron
- Faculty of Medecine, Université de Montréal, Montreal, Quebec, Canada
| | - C Meghan McMurtry
- Department of Psychology, University of Guelph, Guelph, Ontario, Canada
- Pediatric Chronic Pain Program, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Annie Lapointe
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, Université de Montréal, Montreal, Quebec, Canada
- Division of Pediatric Otolaryngology-Head and Neck Surgery, CHU Sainte-Justine, Montreal, Quebec, Canada
| | - Chantal Giguere
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, Université de Montréal, Montreal, Quebec, Canada
- Division of Pediatric Otolaryngology-Head and Neck Surgery, CHU Sainte-Justine, Montreal, Quebec, Canada
| | - Marie-Joëlle Doré-Bergeron
- Department of Paediatrics, Faculty of Medicine, Université de Montréal, Montreal, Quebec, Canada
- Department of Paediatrics, CHU Sainte-Justine, Montreal, Quebec, Canada
| | - Mathieu Bergeron
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, Université de Montréal, Montreal, Quebec, Canada
- Division of Pediatric Otolaryngology-Head and Neck Surgery, CHU Sainte-Justine, Montreal, Quebec, Canada
- CHU Sainte Justine Research Institute, CHU Sainte Justine, Montreal, Quebec, Canada
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Zirem Y, Ledoux L, Roussel L, Maurage CA, Tirilly P, Le Rhun É, Meresse B, Yagnik G, Lim MJ, Rothschild KJ, Duhamel M, Salzet M, Fournier I. Real-time glioblastoma tumor microenvironment assessment by SpiderMass for improved patient management. Cell Rep Med 2024; 5:101482. [PMID: 38552622 PMCID: PMC11031375 DOI: 10.1016/j.xcrm.2024.101482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 01/15/2024] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
Glioblastoma is a highly heterogeneous and infiltrative form of brain cancer associated with a poor outcome and limited therapeutic effectiveness. The extent of the surgery is related to survival. Reaching an accurate diagnosis and prognosis assessment by the time of the initial surgery is therefore paramount in the management of glioblastoma. To this end, we are studying the performance of SpiderMass, an ambient ionization mass spectrometry technology that can be used in vivo without invasiveness, coupled to our recently established artificial intelligence pipeline. We demonstrate that we can both stratify isocitrate dehydrogenase (IDH)-wild-type glioblastoma patients into molecular sub-groups and achieve an accurate diagnosis with over 90% accuracy after cross-validation. Interestingly, the developed method offers the same accuracy for prognosis. In addition, we are testing the potential of an immunoscoring strategy based on SpiderMass fingerprints, showing the association between prognosis and immune cell infiltration, to predict patient outcome.
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Affiliation(s)
- Yanis Zirem
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Léa Ledoux
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Lucas Roussel
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | | | - Pierre Tirilly
- Université de Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, 59000 Lille, France
| | - Émilie Le Rhun
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France; Departments of Neurosurgery and Neurology, Clinical Neuroscience Center, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Bertrand Meresse
- Université de Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, 59000 Lille, France
| | | | | | - Kenneth J Rothschild
- AmberGen, Inc., Billerica, MA, USA; Department of Physics and Photonics Center, Boston University, Boston, MA, USA
| | - Marie Duhamel
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Michel Salzet
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France; Institut Universitaire de France (IUF), Paris, France.
| | - Isabelle Fournier
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France; Institut Universitaire de France (IUF), Paris, France.
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Saliba I, Alshehri S, Fournier I, Altamami N. Large Vestibular Aqueduct-Associated Symptoms: Endolymphatic Duct Blockage as a Surgical Treatment. Audiol Res 2024; 14:304-316. [PMID: 38525688 PMCID: PMC10961693 DOI: 10.3390/audiolres14020027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/18/2024] [Accepted: 03/15/2024] [Indexed: 03/26/2024] Open
Abstract
OBJECTIVE This study aimed to evaluate the effectiveness of endolymphatic duct blockage (EDB) on dizziness control in patients with a large vestibular aqueduct (LVA) and to evaluate its effect on hearing. STUDY DESIGN This is a prospective nonrandomized study. SETTING Five adults and one child with dizziness and five children with progressive hearing loss were referred to our tertiary centers. METHODS The dizziness handicap inventory (DHI) and DHI-PC (dizziness handicap inventory-patient caregiver) questionnaires were used before and after surgery. All patients underwent a preoperative temporal bone HRCT scan and pure tone audiometry one day before surgery, then four and twelve months after surgery and at the last follow-up. The mean follow-up time was 5.6 years. Student's t-test was used to compare DHI/-PC results. RESULTS The DHI scores were 44, 24, 84, 59 and 56 before surgery, respectively, for Patients 1 to 5. The DHI scores at four months was significantly different, i.e., 4, 6, 0, 7 and 18 (p = 0.001). No differences were found between 4 and 12 months. Patient 6 (child) had Trisomy 21; their DHI-PC score dropped from 38 (preoperative score) to 8 (postoperative score), showing no activity limitations; clinical evaluation showed the complete resolution of symptoms. We found no significant differences between hearing loss before the surgery and at 1 and 12 months post operation for four adult patients. Our fifth adult patient's hearing changed from severe to profound SNHL. For 5 out of 6 pediatric patients, preoperative PTA and mean ABG were 63 dB and 20 dB, respectively; postoperatively, they improved to 42 dB and 16 dB, respectively. The hearing loss level for the sixth pediatric patient dropped from moderate (PTA = 42 dB) to severe (PTA = 85 dB) due to an opening of the endolymphatic sac and a sudden leak of the endolymph. CONCLUSIONS EDB, using two titanium clips, seems to be helpful for controlling vestibular symptoms and for stabilizing hearing or even to improve hearing in 82% of cases. Nevertheless, there is a risk of hearing worsening.
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Affiliation(s)
- Issam Saliba
- Division of Otorhinolaryngology and Head & Neck Surgery, University of Montreal, Montreal, QC H3C 3J7, Canada
- University of Montreal Health Center (CHUM), Department of Otorhinolaryngology and Head & Neck Surgery, Montreal, QC H2X 3E4, Canada
- University of Montreal Health Center Research Center (CRCHUM), Montreal, QC H2X 0A9, Canada
- Sainte-Justine University Hospital Center (CHU-SJ), Otorhinolaryngology and Head & Neck Surgery, Montreal, QC H3T 1C5, Canada
| | - Sarah Alshehri
- Division of Otorhinolaryngology and Head & Neck Surgery, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Isabelle Fournier
- Division of Otorhinolaryngology and Head & Neck Surgery, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Nasser Altamami
- Division of Otorhinolaryngology and Head & Neck Surgery, University of Montreal, Montreal, QC H3C 3J7, Canada
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Leblanc S, Yala F, Provencher N, Lucier JF, Levesque M, Lapointe X, Jacques JF, Fournier I, Salzet M, Ouangraoua A, Scott MS, Boisvert FM, Brunet MA, Roucou X. OpenProt 2.0 builds a path to the functional characterization of alternative proteins. Nucleic Acids Res 2024; 52:D522-D528. [PMID: 37956315 PMCID: PMC10767855 DOI: 10.1093/nar/gkad1050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/25/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
The OpenProt proteogenomic resource (https://www.openprot.org/) provides users with a complete and freely accessible set of non-canonical or alternative open reading frames (AltORFs) within the transcriptome of various species, as well as functional annotations of the corresponding protein sequences not found in standard databases. Enhancements in this update are largely the result of user feedback and include the prediction of structure, subcellular localization, and intrinsic disorder, using cutting-edge algorithms based on machine learning techniques. The mass spectrometry pipeline now integrates a machine learning-based peptide rescoring method to improve peptide identification. We continue to help users explore this cryptic proteome by providing OpenCustomDB, a tool that enables users to build their own customized protein databases, and OpenVar, a genomic annotator including genetic variants within AltORFs and protein sequences. A new interface improves the visualization of all functional annotations, including a spectral viewer and the prediction of multicoding genes. All data on OpenProt are freely available and downloadable. Overall, OpenProt continues to establish itself as an important resource for the exploration and study of new proteins.
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Affiliation(s)
- Sébastien Leblanc
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Feriel Yala
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Nicolas Provencher
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Jean-François Lucier
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Maxime Levesque
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Xavier Lapointe
- Department of Pediatrics, Medical Genetics Service, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Jean-Francois Jacques
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Isabelle Fournier
- INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
| | - Michel Salzet
- INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
| | - Aïda Ouangraoua
- Informatics Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Michelle S Scott
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC J1H 5N4, Canada
| | - François-Michel Boisvert
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC J1H 5N4, Canada
- Department of Immunology and Cellular Biology, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Marie A Brunet
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC J1H 5N4, Canada
- Department of Pediatrics, Medical Genetics Service, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC J1H 5N4, Canada
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de Oliveira Alves N, Dalmasso G, Nikitina D, Vaysse A, Ruez R, Ledoux L, Pedron T, Bergsten E, Boulard O, Autier L, Allam S, Motreff L, Sauvanet P, Letourneur D, Kashyap P, Gagnière J, Pezet D, Godfraind C, Salzet M, Lemichez E, Bonnet M, Najjar I, Malabat C, Monot M, Mestivier D, Barnich N, Yadav P, Fournier I, Kennedy S, Mettouchi A, Bonnet R, Sobhani I, Chamaillard M. The colibactin-producing Escherichia coli alters the tumor microenvironment to immunosuppressive lipid overload facilitating colorectal cancer progression and chemoresistance. Gut Microbes 2024; 16:2320291. [PMID: 38417029 PMCID: PMC10903627 DOI: 10.1080/19490976.2024.2320291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/14/2024] [Indexed: 03/01/2024] Open
Abstract
Intratumoral bacteria flexibly contribute to cellular and molecular tumor heterogeneity for supporting cancer recurrence through poorly understood mechanisms. Using spatial metabolomic profiling technologies and 16SrRNA sequencing, we herein report that right-sided colorectal tumors are predominantly populated with Colibactin-producing Escherichia coli (CoPEC) that are locally establishing a high-glycerophospholipid microenvironment with lowered immunogenicity. It coincided with a reduced infiltration of CD8+ T lymphocytes that produce the cytotoxic cytokines IFN-γ where invading bacteria have been geolocated. Mechanistically, the accumulation of lipid droplets in infected cancer cells relied on the production of colibactin as a measure to limit genotoxic stress to some extent. Such heightened phosphatidylcholine remodeling by the enzyme of the Land's cycle supplied CoPEC-infected cancer cells with sufficient energy for sustaining cell survival in response to chemotherapies. This accords with the lowered overall survival of colorectal patients at stage III-IV who were colonized by CoPEC when compared to patients at stage I-II. Accordingly, the sensitivity of CoPEC-infected cancer cells to chemotherapies was restored upon treatment with an acyl-CoA synthetase inhibitor. By contrast, such metabolic dysregulation leading to chemoresistance was not observed in human colon cancer cells that were infected with the mutant strain that did not produce colibactin (11G5∆ClbQ). This work revealed that CoPEC locally supports an energy trade-off lipid overload within tumors for lowering tumor immunogenicity. This may pave the way for improving chemoresistance and subsequently outcome of CRC patients who are colonized by CoPEC.
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Affiliation(s)
| | - Guillaume Dalmasso
- Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Darja Nikitina
- CNRS, Institute Pasteur, Paris, France
- Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Amaury Vaysse
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Plate-Forme Technologique Biomics, Paris, France
| | - Richard Ruez
- ONCOLille, INSERM, Phycell, University of Lille, Lille, France
| | - Lea Ledoux
- Réponse Inflammatoire et Spectrométrie de Masse-PRISM, University of Lille, Lille, France
| | | | - Emma Bergsten
- Institut Pasteur, Université Paris Cité, Paris, France
| | - Olivier Boulard
- ONCOLille, INSERM, Phycell, University of Lille, Lille, France
| | - Lora Autier
- ONCOLille, INSERM, Phycell, University of Lille, Lille, France
| | - Sofian Allam
- ONCOLille, INSERM, Phycell, University of Lille, Lille, France
| | - Laurence Motreff
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Plate-Forme Technologique Biomics, Paris, France
| | - Pierre Sauvanet
- Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, Université Clermont Auvergne, Clermont-Ferrand, France
| | | | - Pragya Kashyap
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, India
| | - Johan Gagnière
- Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Denis Pezet
- Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Catherine Godfraind
- Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Michel Salzet
- Réponse Inflammatoire et Spectrométrie de Masse-PRISM, University of Lille, Lille, France
| | | | - Mathilde Bonnet
- Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Imène Najjar
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Plate-Forme Technologique Biomics, Paris, France
| | - Christophe Malabat
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Plate-Forme Technologique Biomics, Paris, France
| | - Marc Monot
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Plate-Forme Technologique Biomics, Paris, France
| | | | - Nicolas Barnich
- Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Pankaj Yadav
- Department of Bioscience & Bioengineering, Indian Institute of Technology, Jodhpur, Rajasthan, India
| | - Isabelle Fournier
- Réponse Inflammatoire et Spectrométrie de Masse-PRISM, University of Lille, Lille, France
| | | | | | - Richard Bonnet
- Microbes, Intestin, Inflammation et Susceptibilité de l’Hôte (M2iSH), Centre de Recherche en Nutrition Humaine Auvergne, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Iradj Sobhani
- Université Paris Est Créteil, Créteil, France
- Service de Gastroentérologie CHU Henri Mondor, Assistance Publique des Hôpitaux de Paris-APHP, Créteil, France
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Capuz A, Osien S, Cardon T, Karnoub MA, Aboulouard S, Raffo-Romero A, Duhamel M, Cizkova D, Trerotola M, Devos D, Kobeissy F, F VA, Bonnefond A, Fournier I, Rodet F, Salzet M. Correction: Heimdall, an alternative protein issued from a ncRNA related to kappa light chain variable region of immunoglobulins from astrocytes: a new player in neural proteome. Cell Death Dis 2023; 14:677. [PMID: 37833264 PMCID: PMC10576076 DOI: 10.1038/s41419-023-06143-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Affiliation(s)
- Alice Capuz
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Sylvain Osien
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Tristan Cardon
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Mélodie Anne Karnoub
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Soulaimane Aboulouard
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Antonella Raffo-Romero
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Marie Duhamel
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Dasa Cizkova
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská cesta 9, 845 10, Bratislava, Slovakia
- Centre for Experimental and Clinical Regenerative Medicine, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Marco Trerotola
- Laboratory of Cancer Pathology, Center for Advanced Studies and Technology (CAST), University 'G. d'Annunzio', Chieti, Italy
- Department of Medical, Oral and Biotechnological Sciences, University 'G. d'Annunzio', Chieti, Italy
| | - David Devos
- Université de Lille, INSERM, U1172, CHU-Lille, Lille Neuroscience Cognition Research Centre, 1 place de Verdun, 59000, Lille, France
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Vanden Abeele F
- Université de Lille, INSERM U1003, Laboratory of Cell Physiology, 59650, Villeneuve d'Ascq, France
| | - Amélie Bonnefond
- Univ. Lille, Inserm UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, CHU de Lille, 1 place de Verdun, 59000, Lille, France
| | - Isabelle Fournier
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
- Institut Universitaire de France, 75005, Paris, France
| | - Franck Rodet
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France.
| | - Michel Salzet
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France.
- Institut Universitaire de France, 75005, Paris, France.
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7
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Ledoux L, Zirem Y, Renaud F, Duponchel L, Salzet M, Ogrinc N, Fournier I. Comparing MS imaging of lipids by WALDI and MALDI: two technologies for evaluating a common ground truth in MS imaging. Analyst 2023; 148:4982-4986. [PMID: 37740342 DOI: 10.1039/d3an01096a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
In this study, we conducted a direct comparison of water-assisted laser desorption ionization (WALDI) and matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging, with MALDI serving as the benchmark for label-free molecular tissue analysis in biomedical research. Specifically, we investigated the lipidomic profiles of several biological samples and calculated the similarity of detected peaks and Pearson's correlation of spectral profile intensities between the two techniques. We show that, overall, MALDI MS and WALDI MS present very close lipidomic analyses and that the highest similarity is obtained for the norharmane MALDI matrix. Indeed, for norharmane in negative ion mode, the lipidomic spectra revealed 100% similarity of detected peaks and over 0.90 intensity correlation between both technologies for five samples. The MALDI-MSI positive ion lipid spectra displayed more than 83% similarity of detected peaks compared to those of WALDI-MSI. However, we observed a lower percentage (77%) of detected peaks when comparing WALDI-MSI with MALDI-MSI due to the rich WALDI-MSI lipid spectra. Despite this difference, the global lipidomic spectra showed high consistency between the two technologies, indicating that they are governed by similar processes. Thanks to this similarity, we can increase datasets by including data from both modalities to either co-train classification models or obtain cross-interrogation.
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Affiliation(s)
- Léa Ledoux
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
| | - Yanis Zirem
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
| | - Florence Renaud
- Unité mixte SIRIC CURAMUS et 938, Inserm. Université Paris Sorbonne, France
| | | | - Michel Salzet
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
- Institut Universitaire de France (IUF), Paris, France
| | - Nina Ogrinc
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
| | - Isabelle Fournier
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
- Institut Universitaire de France (IUF), Paris, France
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8
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Wisztorski M, Aboulouard S, Roussel L, Duhamel M, Saudemont P, Cardon T, Narducci F, Robin YM, Lemaire AS, Bertin D, Hajjaji N, Kobeissy F, Leblanc E, Fournier I, Salzet M. Fallopian tube lesions as potential precursors of early ovarian cancer: a comprehensive proteomic analysis. Cell Death Dis 2023; 14:644. [PMID: 37775701 PMCID: PMC10541450 DOI: 10.1038/s41419-023-06165-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/08/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
Ovarian cancer is the leading cause of death from gynecologic cancer worldwide. High-grade serous carcinoma (HGSC) is the most common and deadliest subtype of ovarian cancer. While the origin of ovarian tumors is still debated, it has been suggested that HGSC originates from cells in the fallopian tube epithelium (FTE), specifically the epithelial cells in the region of the tubal-peritoneal junction. Three main lesions, p53 signatures, STILs, and STICs, have been defined based on the immunohistochemistry (IHC) pattern of p53 and Ki67 markers and the architectural alterations of the cells, using the Sectioning and Extensively Examining the Fimbriated End Protocol. In this study, we performed an in-depth proteomic analysis of these pre-neoplastic epithelial lesions guided by mass spectrometry imaging and IHC. We evaluated specific markers related to each preneoplastic lesion. The study identified specific lesion markers, such as CAVIN1, Emilin2, and FBLN5. We also used SpiderMass technology to perform a lipidomic analysis and identified the specific presence of specific lipids signature including dietary Fatty acids precursors in lesions. Our study provides new insights into the molecular mechanisms underlying the progression of ovarian cancer and confirms the fimbria origin of HGSC.
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Affiliation(s)
- Maxence Wisztorski
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Soulaimane Aboulouard
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Lucas Roussel
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Marie Duhamel
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Philippe Saudemont
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Tristan Cardon
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
| | - Fabrice Narducci
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- Department of Gynecology Oncology, Oscar Lambret Cancer Center, 59020, Lille, France
| | - Yves-Marie Robin
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- Department of Gynecology Oncology, Oscar Lambret Cancer Center, 59020, Lille, France
| | - Anne-Sophie Lemaire
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- Department of Gynecology Oncology, Oscar Lambret Cancer Center, 59020, Lille, France
| | - Delphine Bertin
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- Department of Gynecology Oncology, Oscar Lambret Cancer Center, 59020, Lille, France
| | - Nawale Hajjaji
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France
- Medical Oncology Department, Oscar Lambret Cancer Center, 59020, Lille, France
| | - Firas Kobeissy
- Department of Neurobiology, Center for Neurotrauma, Multiomics & Biomarkers (CNMB), MorehouseSchool of Medicine, Atlanta, GA, 30310, USA
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Eric Leblanc
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France.
- Department of Gynecology Oncology, Oscar Lambret Cancer Center, 59020, Lille, France.
| | - Isabelle Fournier
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France.
- Institut Universitaire de France, 75000, Paris, France.
| | - Michel Salzet
- Univ.Lille, Inserm, CHU Lille, U-1192 - Laboratoire Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000, Lille, France.
- Institut Universitaire de France, 75000, Paris, France.
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9
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Garcia-Del Rio DF, Fournier I, Cardon T, Salzet M. Protocol to identify human subcellular alternative protein interactions using cross-linking mass spectrometry. STAR Protoc 2023; 4:102380. [PMID: 37384523 PMCID: PMC10511867 DOI: 10.1016/j.xpro.2023.102380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/04/2023] [Accepted: 05/24/2023] [Indexed: 07/01/2023] Open
Abstract
Since the start of mass-spectrometry-based proteomics, proteins from non-referenced open reading frames or alternative proteins (AltProts) have been overlooked. Here, we present a protocol to identify human subcellular AltProt and decipher some interactions using cross-linking mass spectrometry. We describe steps for cell culture, in cellulo cross-link, subcellular extraction, and sequential digestion. We then detail both liquid chromatography-tandem mass spectrometry and cross-link data analyses. The implementation of a single workflow allows the non-targeted identification of signaling pathways involving AltProts. For complete details on the use and execution of this protocol, please refer to Garcia-del Rio et al.1.
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Affiliation(s)
- Diego Fernando Garcia-Del Rio
- Université de Lille, Univ. Lille, CHU Lille, Inserm U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France; VIB Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent 9052, Belgium
| | - Isabelle Fournier
- Université de Lille, Univ. Lille, CHU Lille, Inserm U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
| | - Tristan Cardon
- Université de Lille, Univ. Lille, CHU Lille, Inserm U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
| | - Michel Salzet
- Université de Lille, Univ. Lille, CHU Lille, Inserm U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
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10
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Seddiki K, Precioso F, Sanabria M, Salzet M, Fournier I, Droit A. Early Diagnosis: End-to-End CNN-LSTM Models for Mass Spectrometry Data Classification. Anal Chem 2023; 95:13431-13437. [PMID: 37624777 PMCID: PMC10501374 DOI: 10.1021/acs.analchem.3c00613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 02/09/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) is a powerful method for cell profiling. The use of LC-MS technology is a tool of choice for cancer research since it provides molecular fingerprints of analyzed tissues. However, the ubiquitous presence of noise, the peaks shift between acquisitions, and the huge amount of information owing to the high dimensionality of the data make rapid and accurate cancer diagnosis a challenging task. Deep learning (DL) models are not only effective classifiers but are also well suited to jointly learn feature representation and classification tasks. This is particularly relevant when applied to raw LC-MS data and hence avoid the need for costly preprocessing and complicated feature selection. In this study, we propose a new end-to-end DL methodology that addresses all of the above challenges at once, while preserving the high potential of LC-MS data. Our DL model is designed to early discriminate between tumoral and normal tissues. It is a combination of a convolutional neural network (CNN) and a long short-term memory (LSTM) Network. The CNN network allows for significantly reducing the high dimensionality of the data while learning spatially relevant features. The LSTM network enables our model to capture temporal patterns. We show that our model outperforms not only benchmark models but also state-of-the-art models developed on the same data. Our framework is a promising strategy for improving early cancer detection during a diagnostic process.
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Affiliation(s)
- Khawla Seddiki
- Centre
de Recherche du CHU de Québec-Université Laval, Québec City, Québec G1V 4G2, Canada
- Univ.
Lille, Inserm, CHU Lille,
U1192-Protéomique Réponse Inflammatoire Spectrométrie
de Masse-PRISM, Lille F-59000, France
| | - Fŕed́eric Precioso
- Université
Ĉote d’Azur, CNRS, INRIA, I3S, Sophia Antipolis 06900, France
| | - Melissa Sanabria
- Université
Ĉote d’Azur, CNRS, INRIA, I3S, Sophia Antipolis 06900, France
| | - Michel Salzet
- Univ.
Lille, Inserm, CHU Lille,
U1192-Protéomique Réponse Inflammatoire Spectrométrie
de Masse-PRISM, Lille F-59000, France
| | - Isabelle Fournier
- Univ.
Lille, Inserm, CHU Lille,
U1192-Protéomique Réponse Inflammatoire Spectrométrie
de Masse-PRISM, Lille F-59000, France
| | - Arnaud Droit
- Centre
de Recherche du CHU de Québec-Université Laval, Québec City, Québec G1V 4G2, Canada
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11
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Diamantis D, Tsiailanis AD, Papaemmanouil C, Nika MC, Kanaki Z, Golic Grdadolnik S, Babic A, Tzakos EP, Fournier I, Salzet M, Kushwaha PP, Thomaidis NS, Rampias T, Shankar E, Karakurt S, Gupta S, Tzakos AG. Development of a novel apigenin prodrug programmed for alkaline-phosphatase instructed self-inhibition to combat cancer. J Biomol Struct Dyn 2023:1-22. [PMID: 37639498 DOI: 10.1080/07391102.2023.2247083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/05/2023] [Indexed: 08/31/2023]
Abstract
Elevated levels of alkaline phosphatase (ALP) in the tumor microenvironment (TME) are a hallmark of cancer progression and thus inhibition of ALP could serve as an effective approach against cancer. Herein, we developed a novel prodrug approach to tackle cancer that bears self-inhibiting alkaline phosphatase-responsiveness properties that can enhance at the same time the solubility of the parent compound. To probe this novel concept, we selected apigenin as the cytotoxic agent since we first unveiled, that it directly interacts and inhibits ALP activity. Consequently, we rationally designed and synthesized, using a self-immolative linker, an ALP responsive apigenin-based phosphate prodrug, phospho-apigenin. Phospho-apigenin markedly increased the stability of the parent compound apigenin. Furthermore, the prodrug exhibited enhanced antiproliferative effect in malignant cells with elevated ALP levels, compared to apigenin. This recorded potency of the developed prodrug was further confirmed in vivo where phospho-apigenin significantly suppressed by 52.8% the growth of PC-3 xenograft tumors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dimitrios Diamantis
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, Ioannina, Greece
| | - Antonios D Tsiailanis
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, Ioannina, Greece
| | - Christina Papaemmanouil
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, Ioannina, Greece
| | - Maria-Christina Nika
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Zoi Kanaki
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Simona Golic Grdadolnik
- Laboratory for Molecular Structural Dynamics, Theory Department, National Institute of Chemistry, Ljubljana, Slovenia
| | - Andrej Babic
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | | | - Isabelle Fournier
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Lille, France
- Institut Universitaire de France, Paris
| | - Michel Salzet
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Lille, France
- Institut Universitaire de France, Paris
| | - Prem Prakash Kushwaha
- Department of Urology, Case Western Reserve University & University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Nikolaos S Thomaidis
- Laboratory of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Eswar Shankar
- Department of Urology, Case Western Reserve University & University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Serdar Karakurt
- Department of Biochemistry, Selcuk University, Konya, Turkey
| | - Sanjay Gupta
- Department of Urology, Case Western Reserve University & University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Andreas G Tzakos
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, Ioannina, Greece
- Institute of Materials Science and Computing, University Research Center of Ioannina (URCI), Ioannina, Greece
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12
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Capuz A, Osien S, Cardon T, Karnoub MA, Aboulouard S, Raffo-Romero A, Duhamel M, Cizkova D, Trerotola M, Devos D, Kobeissy F, Vanden Abeele F, Bonnefond A, Fournier I, Rodet F, Salzet M. Heimdall, an alternative protein issued from a ncRNA related to kappa light chain variable region of immunoglobulins from astrocytes: a new player in neural proteome. Cell Death Dis 2023; 14:526. [PMID: 37587118 PMCID: PMC10432539 DOI: 10.1038/s41419-023-06037-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 07/27/2023] [Accepted: 08/02/2023] [Indexed: 08/18/2023]
Abstract
The dogma "One gene, one protein" is clearly obsolete since cells use alternative splicing and generate multiple transcripts which are translated into protein isoforms, but also use alternative translation initiation sites (TISs) and termination sites on a given transcript. Alternative open reading frames for individual transcripts give proteins originate from the 5'- and 3'-UTR mRNA regions, frameshifts of mRNA ORFs or from non-coding RNAs. Longtime considered as non-coding, recent in-silico translation prediction methods enriched the protein databases allowing the identification of new target structures that have not been identified previously. To gain insight into the role of these newly identified alternative proteins in the regulation of cellular functions, it is crucial to assess their dynamic modulation within a framework of altered physiological modifications such as experimental spinal cord injury (SCI). Here, we carried out a longitudinal proteomic study on rat SCI from 12 h to 10 days. Based on the alternative protein predictions, it was possible to identify a plethora of newly predicted protein hits. Among these proteins, some presented a special interest due to high homology with variable chain regions of immunoglobulins. We focus our interest on the one related to Kappa variable light chains which is similarly highly produced by B cells in the Bence jones disease, but here expressed in astrocytes. This protein, name Heimdall is an Intrinsically disordered protein which is secreted under inflammatory conditions. Immunoprecipitation experiments showed that the Heimdall interactome contained proteins related to astrocyte fate keepers such as "NOTCH1, EPHA3, IPO13" as well as membrane receptor protein including "CHRNA9; TGFBR, EPHB6, and TRAM". However, when Heimdall protein was neutralized utilizing a specific antibody or its gene knocked out by CRISPR-Cas9, sprouting elongations were observed in the corresponding astrocytes. Interestingly, depolarization assays and intracellular calcium measurements in Heimdall KO, established a depolarization effect on astrocyte membranes KO cells were more likely that the one found in neuroprogenitors. Proteomic analyses performed under injury conditions or under lipopolysaccharides (LPS) stimulation, revealed the expression of neuronal factors, stem cell proteins, proliferation, and neurogenesis of astrocyte convertor factors such as EPHA4, NOTCH2, SLIT3, SEMA3F, suggesting a role of Heimdall could regulate astrocytic fate. Taken together, Heimdall could be a novel member of the gatekeeping astrocyte-to-neuroprogenitor conversion factors.
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Affiliation(s)
- Alice Capuz
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Sylvain Osien
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Tristan Cardon
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Mélodie Anne Karnoub
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Soulaimane Aboulouard
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Antonella Raffo-Romero
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Marie Duhamel
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
| | - Dasa Cizkova
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská cesta 9, 845 10, Bratislava, Slovakia
- Centre for Experimental and Clinical Regenerative Medicine, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Marco Trerotola
- Laboratory of Cancer Pathology, Center for Advanced Studies and Technology (CAST), University 'G. d'Annunzio', Chieti, Italy
- Department of Medical, Oral and Biotechnological Sciences, University 'G. d'Annunzio', Chieti, Italy
| | - David Devos
- Université de Lille, INSERM, U1172, CHU-Lille, Lille Neuroscience Cognition Research Centre, 1 place de Verdun, 59000, Lille, France
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Fabien Vanden Abeele
- Université de Lille, INSERM U1003, Laboratory of Cell Physiology, 59650, Villeneuve d'Ascq, France
| | - Amélie Bonnefond
- Univ. Lille, Inserm UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, CHU de Lille, 1 place de Verdun, 59000, Lille, France
| | - Isabelle Fournier
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France
- Institut Universitaire de France, 75005, Paris, France
| | - Franck Rodet
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France.
| | - Michel Salzet
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, F-59000, Lille, France.
- Institut Universitaire de France, 75005, Paris, France.
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13
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Capuz A, Osien S, Karnoub MA, Aboulouard S, Laurent E, Coyaud E, Raffo-Romero A, Duhamel M, Bonnefond A, Derhourhi M, Trerotola M, El Yazidi-Belkoura I, Devos D, Zilkova M, Kobeissy F, Vanden Abeele F, Fournier I, Cizkova D, Rodet F, Salzet M. Astrocytes express aberrant immunoglobulins as putative gatekeeper of astrocytes to neuronal progenitor conversion. Cell Death Dis 2023; 14:237. [PMID: 37015912 PMCID: PMC10073301 DOI: 10.1038/s41419-023-05737-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/24/2023] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Using multi-omics analyses including RNAseq, RT-PCR, RACE-PCR, and shotgun proteomic with enrichment strategies, we demonstrated that newborn rat astrocytes produce neural immunoglobulin constant and variable heavy chains as well as light chains. However, their edification is different from the ones found in B cells and they resemble aberrant immunoglobulins observed in several cancers. Moreover, the complete enzymatic V(D)J recombination complex has also been identified in astrocytes. In addition, the constant heavy chain is also present in adult rat astrocytes, whereas in primary astrocytes from human fetus we identified constant and variable kappa chains as well as the substitution lambda chains known to be involved in pre-B cells. To gather insights into the function of these neural IgGs, CRISPR-Cas9 of IgG2B constant heavy chain encoding gene (Igh6), IgG2B overexpression, proximal labeling of rat astrocytes IgG2B and targets identification through 2D gels were performed. In Igh6 KO astrocytes, overrepresentation of factors involved in hematopoietic cells, neural stem cells, and the regulation of neuritogenesis have been identified. Moreover, overexpression of IgG2B in astrocytes induces the CRTC1-CREB-BDNF signaling pathway known to be involved in gliogenesis, whereas Igh6 KO triggers the BMP/YAP1/TEAD3 pathway activated in astrocytes dedifferentiation into neural progenitors. Proximal labeling experiments revealed that IgG2B is N-glycosylated by the OST complex, addressed to vesicle membranes containing the ATPase complex, and behaves partially like CD98hc through its association with LAT1. These experiments also suggest that proximal IgG2B-LAT1 interaction occurs concomitantly with MACO-1 and C2CD2L, at the heart of a potentially novel cell signaling platform. Finally, we demonstrated that these chains are synthesized individually and associated to recognize specific targets. Indeed, intermediate filaments Eif4a2 and Pdia6 involved in astrocyte fate constitute targets for these neural IgGs. Taken together, we hypothese that neural aberrant IgG chains may act as gatekeepers of astrocytes' fate.
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Affiliation(s)
- Alice Capuz
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, 59655, Villeneuve d'Ascq, France
| | - Sylvain Osien
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, 59655, Villeneuve d'Ascq, France
| | - Mélodie Anne Karnoub
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, 59655, Villeneuve d'Ascq, France
| | - Soulaimane Aboulouard
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, 59655, Villeneuve d'Ascq, France
| | - Estelle Laurent
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, 59655, Villeneuve d'Ascq, France
| | - Etienne Coyaud
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, 59655, Villeneuve d'Ascq, France
| | - Antonella Raffo-Romero
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, 59655, Villeneuve d'Ascq, France
| | - Marie Duhamel
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, 59655, Villeneuve d'Ascq, France
| | - Amélie Bonnefond
- Univ. Lille, Inserm UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, CHU de Lille, 1 place de Verdun, 59000, Lille, France
| | - Mehdi Derhourhi
- Univ. Lille, Inserm UMR1283, CNRS UMR8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, CHU de Lille, 1 place de Verdun, 59000, Lille, France
| | - Marco Trerotola
- Laboratory of Cancer Pathology, Center for Advanced Studies and Technology (CAST), University 'G. D'Annunzio', Chieti, Italy
- Department of Medical, Oral and Biotechnological Sciences, University 'G. D'Annunzio', Chieti, Italy
| | - Ikram El Yazidi-Belkoura
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, 59655, Villeneuve d'Ascq, France
| | - David Devos
- Université de Lille, INSERM, U1172, CHU-Lille, Lille Neuroscience Cognition Research Centre, 1 place de Verdun, 59000, Lille, France
| | - Monika Zilkova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská cesta 9, 84510, Bratislava, Slovakia
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Fabien Vanden Abeele
- Université de Lille, INSERM U1003, Laboratory of Cell Physiology, 59655, Villeneuve d'Ascq, France
| | - Isabelle Fournier
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, 59655, Villeneuve d'Ascq, France
- Institut Universitaire de France, 75005, Paris, France
| | - Dasa Cizkova
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, 59655, Villeneuve d'Ascq, France
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská cesta 9, 84510, Bratislava, Slovakia
- Centre for Experimental and Clinical Regenerative Medicine, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
| | - Franck Rodet
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, 59655, Villeneuve d'Ascq, France.
| | - Michel Salzet
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, 59655, Villeneuve d'Ascq, France.
- Institut Universitaire de France, 75005, Paris, France.
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14
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Bikfalvi A, da Costa CA, Avril T, Barnier JV, Bauchet L, Brisson L, Cartron PF, Castel H, Chevet E, Chneiweiss H, Clavreul A, Constantin B, Coronas V, Daubon T, Dontenwill M, Ducray F, Entz-Werlé N, Figarella-Branger D, Fournier I, Frenel JS, Gabut M, Galli T, Gavard J, Huberfeld G, Hugnot JP, Idbaih A, Junier MP, Mathivet T, Menei P, Meyronet D, Mirjolet C, Morin F, Mosser J, Moyal ECJ, Rousseau V, Salzet M, Sanson M, Seano G, Tabouret E, Tchoghandjian A, Turchi L, Vallette FM, Vats S, Verreault M, Virolle T. Challenges in glioblastoma research: focus on the tumor microenvironment. Trends Cancer 2023:S2405-8033(23)00029-8. [PMID: 36997420 DOI: 10.1016/j.trecan.2023.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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15
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Raffo-Romero A, Aboulouard S, Bouchaert E, Rybicka A, Tierny D, Hajjaji N, Fournier I, Salzet M, Duhamel M. Establishment and characterization of canine mammary tumoroids for translational research. BMC Biol 2023; 21:23. [PMID: 36737789 PMCID: PMC9898911 DOI: 10.1186/s12915-023-01516-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 01/17/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Cancer heterogeneity is a main obstacle for the development of effective therapies, as its replication in in vitro preclinical models is challenging. Around 96% of developed drugs are estimated to fail from discovery to the clinical trial phase probably because of the unsuitability and unreliability of current preclinical models (Front Pharmacol 9:6, 2018; Nat Rev Cancer 8: 147-56, 2008) in replicating the overall biology of tumors, for instance the tumor microenvironment. Breast cancer is the most frequent cancer among women causing the greatest number of cancer-related deaths. Breast cancer can typically be modeled in vitro through the use of tumoroids; however, current approaches using mouse tumoroids fail to reproduce crucial aspect of human breast cancer, while access to human cells is limited and the focus of ethical concerns. New models of breast cancer, such as companion dogs, have emerged given the resemblance of developed spontaneous mammary tumors to human breast cancer in many clinical and molecular aspects; however, they have so far failed to replicate the tumor microenvironment. The present work aimed at developing a robust canine mammary tumor model in the form of tumoroids which recapitulate the tumor diversity and heterogeneity. RESULTS We conducted a complete characterization of canine mammary tumoroids through histologic, molecular, and proteomic analysis, demonstrating their strong similarity to the primary tumor. We demonstrated that these tumoroids can be used as a drug screening model. In fact, we showed that paclitaxel, a human chemotherapeutic, could kill canine tumoroids with the same efficacy as human tumoroids with 0.1 to 1 μM of drug needed to kill 50% of the cells. Due to easy tissue availability, canine tumoroids can be produced at larger scale and cryopreserved to constitute a biobank. We have demonstrated that cryopreserved tumoroids keep the same histologic and molecular features (ER, PR, and HER2 expression) as fresh tumoroids. Furthermore, two cryopreservation techniques were compared from a proteomic point of view which showed that tumoroids made from frozen material allowed to maintain the same molecular diversity as from freshly dissociated tumor. CONCLUSIONS These findings revealed that canine mammary tumoroids can be easily generated and may provide an adequate and more reliable preclinical model to investigate tumorigenesis mechanisms and develop new treatments for both veterinary and human medicine.
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Affiliation(s)
- Antonella Raffo-Romero
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France
| | - Soulaimane Aboulouard
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France
| | - Emmanuel Bouchaert
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France ,grid.487385.50000 0004 1789 0046OCR (Oncovet Clinical Research), Parc Eurasanté Lille Métropole, 80 Rue du Dr Yersin, 59120 Loos, France
| | - Agata Rybicka
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France ,grid.487385.50000 0004 1789 0046OCR (Oncovet Clinical Research), Parc Eurasanté Lille Métropole, 80 Rue du Dr Yersin, 59120 Loos, France
| | - Dominique Tierny
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France ,grid.487385.50000 0004 1789 0046OCR (Oncovet Clinical Research), Parc Eurasanté Lille Métropole, 80 Rue du Dr Yersin, 59120 Loos, France
| | - Nawale Hajjaji
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France ,grid.452351.40000 0001 0131 6312Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Isabelle Fournier
- grid.410463.40000 0004 0471 8845Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France ,grid.440891.00000 0001 1931 4817Institut Universitaire de France, Paris, France
| | - Michel Salzet
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France. .,Institut Universitaire de France, Paris, France.
| | - Marie Duhamel
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire Et Spectrométrie de Masse (PRISM), Lille, France.
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16
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Galmiche A, Saidak Z, Babin E, Brenet E, Davrou J, Fournier I, Devauchelle B, Testelin S, Dakpe S, Pellet A, Thariat J, Bastit V, Clatot F, Saintigny P, Bouaoud J, Foy JP. From precise surgery to precision surgery: The multiple dimensions of therapeutic precision for head and neck cancer. J Stomatol Oral Maxillofac Surg 2023; 124:101342. [PMID: 36423829 DOI: 10.1016/j.jormas.2022.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 11/23/2022]
Affiliation(s)
- Antoine Galmiche
- UR7516 CHIMERE (Chirurgie, imagerie et régénération tissulaire de l'extrémité céphalique), université de Picardie Jules Verne, Amiens, France; Institut Faire Face, CHU Amiens, 80054 Amiens, France; Centre de Biologie Humaine, CHU Amiens, 80054 Amiens, France.
| | - Zuzana Saidak
- UR7516 CHIMERE (Chirurgie, imagerie et régénération tissulaire de l'extrémité céphalique), université de Picardie Jules Verne, Amiens, France; Institut Faire Face, CHU Amiens, 80054 Amiens, France; Centre de Biologie Humaine, CHU Amiens, 80054 Amiens, France
| | - Emmanuel Babin
- Service d'ORL-CCF, laboratoire Anticipe Inserm U1086, CHU de Caen, Normandie université France, 14033 Caen, France
| | - Esteban Brenet
- Department of Otorhinolaryngology and Head and neck surgery, CHU Reims, Hôpital Robert Debré, Rue du Général Koenig, 51100, Reims, France ; Faculty of Medicine, Reims Champagne Ardenne University, 51100, Reims, France
| | - Julien Davrou
- Sorbonne Université, Paris, France; Department of Maxillo-Facial Surgery, Hôpital Pitié-Salpêtrière, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Isabelle Fournier
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Inserm U1192, Université de Lille, F-59000 Lille, France ; Institut Universitaire de France (IUF), F-75000 Paris, France
| | - Bernard Devauchelle
- UR7516 CHIMERE (Chirurgie, imagerie et régénération tissulaire de l'extrémité céphalique), université de Picardie Jules Verne, Amiens, France; Institut Faire Face, CHU Amiens, 80054 Amiens, France; Department of Maxillofacial Surgery and Stomatology, University Hospital of Amiens, Amiens, France
| | - Sylvie Testelin
- UR7516 CHIMERE (Chirurgie, imagerie et régénération tissulaire de l'extrémité céphalique), université de Picardie Jules Verne, Amiens, France; Institut Faire Face, CHU Amiens, 80054 Amiens, France; Department of Maxillofacial Surgery and Stomatology, University Hospital of Amiens, Amiens, France
| | - Stephanie Dakpe
- UR7516 CHIMERE (Chirurgie, imagerie et régénération tissulaire de l'extrémité céphalique), université de Picardie Jules Verne, Amiens, France; Institut Faire Face, CHU Amiens, 80054 Amiens, France; Department of Maxillofacial Surgery and Stomatology, University Hospital of Amiens, Amiens, France
| | - Adrien Pellet
- Sorbonne Université, Paris, France ; Department of Maxillo-Facial Surgery, Hôpital Pitié-Salpêtrière, Assistance Publique des Hôpitaux de Paris, 47-83 boulevard de l'Hôpital, Paris 75013, France ; Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon 69008, France
| | - Juliette Thariat
- Department of Radiation Oncology, Centre François Baclesse, Caen, France; Laboratoire de Physique Corpusculaire UMR6534 IN2P3 ENSICAEN CNRS, Normandy University, Caen, France
| | - Vianney Bastit
- Department of Head and Neck Surgery, Centre François Baclesse, Caen, France
| | - Florian Clatot
- Normandie Univ, UNIROUEN, Inserm U1245, Rouen, France; Department of Medical Oncology, Centre Henri Becquerel, Rouen, France
| | - Pierre Saintigny
- Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon 69008, France ; Department of Medical Oncology, Centre Léon Bérard, 28 rue Laennec, 69373 Lyon cedex 08, Lyon 69008, France; Department of Translational Medicine, Centre Léon Bérard, Lyon 69008, France
| | - Jebrane Bouaoud
- Sorbonne Université, Paris, France ; Department of Maxillo-Facial Surgery, Hôpital Pitié-Salpêtrière, Assistance Publique des Hôpitaux de Paris, 47-83 boulevard de l'Hôpital, Paris 75013, France ; Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon 69008, France
| | - Jean-Philippe Foy
- Sorbonne Université, Paris, France ; Department of Maxillo-Facial Surgery, Hôpital Pitié-Salpêtrière, Assistance Publique des Hôpitaux de Paris, 47-83 boulevard de l'Hôpital, Paris 75013, France ; Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon 69008, France
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17
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Mallah K, Zibara K, Kerbaj C, Eid A, Khoshman N, Ousseily Z, Kobeissy A, Cardon T, Cizkova D, Kobeissy F, Fournier I, Salzet M. Neurotrauma investigation through spatial omics guided by mass spectrometry imaging: Target identification and clinical applications. Mass Spectrom Rev 2023; 42:189-205. [PMID: 34323300 DOI: 10.1002/mas.21719] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/04/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
Traumatic brain injury (TBI) represents one of the major public health concerns worldwide due to the increase in TBI incidence as a result of injuries from daily life accidents such as sports and motor vehicle transportation as well as military-related practices. This type of central nervous system trauma is known to predispose patients to several neurological disorders such as Parkinson's disease, Alzheimer's disease, chronic trauamatic encephalopathy, and age-related Dementia. Recently, several proteomic and lipidomic platforms have been applied on different TBI studies to investigate TBI-related mechanisms that have broadened our understanding of its distinct neuropathological complications. In this study, we provide an updated comprehensive overview of the current knowledge and novel perspectives of the spatially resolved microproteomics and microlipidomics approaches guided by mass spectrometry imaging used in TBI studies and its applications in the neurotrauma field. In this regard, we will discuss the use of the spatially resolved microproteomics and assess the different microproteomic sampling methods such as laser capture microdissection, parafilm assisted microdissection, and liquid microjunction extraction as accurate and precise techniques in the field of neuroproteomics. Additionally, we will highlight lipid profiling applications and their prospective potentials in characterizing molecular processes involved in the field of TBI. Specifically, we will discuss the phospholipid metabolism acting as a precursor for proinflammatory molecules such as eicosanoids. Finally, we will survey the current state of spatial neuroproteomics and microproteomics applications and present the various studies highlighting their findings in these fields.
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Affiliation(s)
- Khalil Mallah
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina, USA
- PRASE, Lebanese University, Beirut, Lebanon
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Kazem Zibara
- PRASE, Lebanese University, Beirut, Lebanon
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Coline Kerbaj
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Ali Eid
- Department of Basic Medical Sciences, QU Health, Qatar University, Doha, Qatar
| | - Nour Khoshman
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Zahraa Ousseily
- Department of Biology, Faculty of Sciences-I, Lebanese University, Beirut, Lebanon
| | - Abir Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Tristan Cardon
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Dasa Cizkova
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
- Center for Experimental and Clinical Regenerative Medicine, University of Veterinary Medicine and Pharmacy in Košice, Košice, Slovakia
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Isabelle Fournier
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
- Institut Universitaire de France, Paris, France
| | - Michel Salzet
- Univ.Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
- Institut Universitaire de France, Paris, France
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18
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Ogrinc N, Chaillou P, Kruszewski A, Duriez C, Salzet M, Fournier I. Ambient Mass Spectrometry Imaging by Water-Assisted Laser Desorption/Ionization for Ex Vivo and in Vivo Applications. Methods Mol Biol 2023; 2688:83-94. [PMID: 37410286 DOI: 10.1007/978-1-0716-3319-9_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Water-assisted laser desorption/ionization mass spectrometry (WALDI-MS), also known as SpiderMass, is an emerging ambient ionization technique for in vivo and real-time analysis. It employs a remote infrared (IR) laser tuned to excite the most intense vibrational band (O-H) of water. The water molecules act as an endogenous matrix leading to the desorption/ionization of a variety of biomolecules from tissues, particularly metabolites and lipids. WALDI-MS was recently advanced into an imaging modality for ex vivo 2D sections and 3D in vivo real-time imaging. Here, we describe the methodological aspects for performing 2D and 3D imaging experiments with WALDI-MSI and the parameters for optimizing the image acquisition.
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Affiliation(s)
- Nina Ogrinc
- Université de Lille, Inserm, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, France
| | - Paul Chaillou
- Université de Lille, Inserm, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, France
| | - Alexandre Kruszewski
- Université de Lille, Inserm, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, France
| | - Cristian Duriez
- Université de Lille, Inserm, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, France
| | - Michel Salzet
- Université de Lille, Inserm, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, France
| | - Isabelle Fournier
- Université de Lille, Inserm, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, France.
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19
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Bikfalvi A, da Costa CA, Avril T, Barnier JV, Bauchet L, Brisson L, Cartron PF, Castel H, Chevet E, Chneiweiss H, Clavreul A, Constantin B, Coronas V, Daubon T, Dontenwill M, Ducray F, Enz-Werle N, Figarella-Branger D, Fournier I, Frenel JS, Gabut M, Galli T, Gavard J, Huberfeld G, Hugnot JP, Idbaih A, Junier MP, Mathivet T, Menei P, Meyronet D, Mirjolet C, Morin F, Mosser J, Moyal ECJ, Rousseau V, Salzet M, Sanson M, Seano G, Tabouret E, Tchoghandjian A, Turchi L, Vallette FM, Vats S, Verreault M, Virolle T. Challenges in glioblastoma research: focus on the tumor microenvironment. Trends Cancer 2023; 9:9-27. [PMID: 36400694 DOI: 10.1016/j.trecan.2022.09.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 09/20/2022] [Accepted: 09/30/2022] [Indexed: 11/17/2022]
Abstract
Glioblastoma (GBM) is the most deadly type of malignant brain tumor, despite extensive molecular analyses of GBM cells. In recent years, the tumor microenvironment (TME) has been recognized as an important player and therapeutic target in GBM. However, there is a need for a full and integrated understanding of the different cellular and molecular components involved in the GBM TME and their interactions for the development of more efficient therapies. In this review, we provide a comprehensive report of the GBM TME, which assembles the contributions of physicians and translational researchers working on brain tumor pathology and therapy in France. We propose a holistic view of the subject by delineating the specific features of the GBM TME at the cellular, molecular, and therapeutic levels.
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Affiliation(s)
- Andreas Bikfalvi
- Bordeaux University, INSERM, U1312 BRIC, Tumor and Vascular Biology Laboratory, F-33600, Pessac, France.
| | - Cristine Alves da Costa
- Côte d'Azur University, INSERM, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Team "Laboratory of Excellence (LABEX) Distalz", F-06560 Nice, France
| | - Tony Avril
- Rennes University, Inserm U1242, Centre de Lutte contre le Cancer Eugène Marquis, F- 35000 Rennes, France
| | - Jean-Vianney Barnier
- Institute of Neuroscience Paris-Saclay, UMR9197, CNRS, Univ. Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Luc Bauchet
- Montpellier University Medical Center, Department of Neurosurgery, INSERM U1191, F-34090 Montpellier, France
| | - Lucie Brisson
- Bordeaux University, INSERM, U1312 BRIC, Tumor and Vascular Biology Laboratory, F-33600, Pessac, France
| | | | - Hélène Castel
- Normandie University, INSERM U1239, DC2N, Institute for Research and Innovation in Biomedicine (IRIB), F-76000 Rouen, France
| | - Eric Chevet
- Rennes University, Inserm U1242, Centre de Lutte contre le Cancer Eugène Marquis, F- 35000 Rennes, France
| | - Hervé Chneiweiss
- Sorbonne University, CNRS UMR8246, Inserm U1130, IBPS-Neuroscience Paris Seine, F- 75005 Paris, France
| | - Anne Clavreul
- Angers University, CHU d'Angers, CRCINA, F-49000 Angers, France
| | - Bruno Constantin
- Poitiers University, CNRS UMR 6041, Laboratory Channels & Connexins in Cancers and Cell Stemness, F-86000 Poitiers, France
| | - Valérie Coronas
- Poitiers University, CNRS UMR 6041, Laboratory Channels & Connexins in Cancers and Cell Stemness, F-86000 Poitiers, France
| | - Thomas Daubon
- Bordeaux University, CNRS, IBGC, UMR 5095, F-33 077 Bordeaux, France
| | - Monique Dontenwill
- Strasbourg University, Laboratoire de Bioimagerie et Pathologie, UMR7021 CNRS, F-67401 Illkirch-Graffenstaden, France
| | - Francois Ducray
- Lyon I University, Cancer Research Centre of Lyon (CRCL) INSERM 1052&CNRS UMR5286, Centre Léon Bérard, Lyon 69008, France., F-69622 Villeurbanne, France
| | - Natacha Enz-Werle
- Strasbourg University, Laboratoire de Bioimagerie et Pathologie, UMR7021 CNRS, F-67401 Illkirch-Graffenstaden, France
| | - Dominique Figarella-Branger
- Aix-Marseille University, Service d'Anatomie Pathologique et de Neuropathologie, Hôpital de la Timone, F-13385 Marseille, France
| | - Isabelle Fournier
- Lille University, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Jean-Sébastien Frenel
- Normandie University, INSERM U1239, DC2N, Institute for Research and Innovation in Biomedicine (IRIB), F-76000 Rouen, France
| | - Mathieu Gabut
- Lyon I University, Cancer Research Centre of Lyon (CRCL) INSERM 1052&CNRS UMR5286, Centre Léon Bérard, Lyon 69008, France., F-69622 Villeurbanne, France
| | - Thierry Galli
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Membrane Traffic in Healthy & Diseased Brain, GHU PARIS Psychiatrie & Neurosciences, F-75014 Paris, France
| | - Julie Gavard
- CRCI2NA, INSERM U1307, CNRS UMR6075, Nantes Universite, 44007 Nantes, France
| | - Gilles Huberfeld
- College de France, Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Université PSL, Paris 75005, France
| | - Jean-Philippe Hugnot
- Montpellier University, Institut de Génomique Fonctionnelle, CNRS, INSERM, F-34094 Montpellier, France
| | - Ahmed Idbaih
- Sorbonne University, AP-HP, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, F-75013, Paris, France
| | - Marie-Pierre Junier
- Sorbonne University, CNRS UMR8246, Inserm U1130, IBPS-Neuroscience Paris Seine, F- 75005 Paris, France
| | - Thomas Mathivet
- Bordeaux University, INSERM, U1312 BRIC, Tumor and Vascular Biology Laboratory, F-33600, Pessac, France
| | - Philippe Menei
- Angers University, CHU d'Angers, CRCINA, F-49000 Angers, France
| | - David Meyronet
- Institute of Neuropathology, Hospices Civils de Lyon, F-69008, Lyon, France
| | - Céline Mirjolet
- Centre Georges-François Leclerc, UNICANCER, Dijon, France. Inserm U1231, Equipe Cadir, F-21000 Dijon, France
| | - Fabrice Morin
- Normandie University, INSERM U1239, DC2N, Institute for Research and Innovation in Biomedicine (IRIB), F-76000 Rouen, France
| | - Jean Mosser
- Rennes University, Inserm U1242, Centre de Lutte contre le Cancer Eugène Marquis, F- 35000 Rennes, France
| | - Elisabeth Cohen-Jonathan Moyal
- Institut Claudius Regaud, NSERM 1037, CRCT Team RADOPT, Département de Radiothérapie, IUCT-Oncopole, F-31100 Toulouse, France
| | - Véronique Rousseau
- Institute of Neuroscience Paris-Saclay, UMR9197, CNRS, Univ. Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Michel Salzet
- Lille University, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Marc Sanson
- Sorbonne University, AP-HP, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, F-75013, Paris, France
| | - Giorgio Seano
- Curie Institute Research Center, Tumor Microenvironment Laboratory, PSL Research University, Inserm U1021, CNRS UMR3347, F-91898 Orsay, France
| | - Emeline Tabouret
- Aix-Marseille University, CNRS, INP, Inst Neurophysiopathol, F-13005 Marseille, France
| | - Aurélie Tchoghandjian
- Aix-Marseille University, CNRS, INP, Inst Neurophysiopathol, F-13005 Marseille, France
| | - Laurent Turchi
- Côte D'Azur University, CNRS, INSERM, Institut de Biologie Valrose, Team INSERM "Cancer Stem Cell Plasticity and Functional Intra-tumor Heterogeneity", F-06108 Nice, France
| | - Francois M Vallette
- CRCI2NA, INSERM U1307, CNRS UMR6075, Nantes Universite, 44007 Nantes, France
| | - Somya Vats
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Membrane Traffic in Healthy & Diseased Brain, GHU PARIS Psychiatrie & Neurosciences, F-75014 Paris, France
| | - Maité Verreault
- Sorbonne University, AP-HP, Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, F-75013, Paris, France
| | - Thierry Virolle
- Côte D'Azur University, CNRS, INSERM, Institut de Biologie Valrose, Team INSERM "Cancer Stem Cell Plasticity and Functional Intra-tumor Heterogeneity", F-06108 Nice, France
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20
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Capuz A, Karnoub MA, Osien S, Rose M, Mériaux C, Fournier I, Devos D, Vanden Abeele F, Rodet F, Cizkova D, Salzet M. The Antibody Dependant Neurite Outgrowth Modulation Response Involvement in Spinal Cord Injury. Front Immunol 2022; 13:882830. [PMID: 35784350 PMCID: PMC9245426 DOI: 10.3389/fimmu.2022.882830] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/02/2022] [Indexed: 12/25/2022] Open
Abstract
Spinal cord injury (SCI) represents a major medical challenge. At present, there is still no cure to treat it efficiently and enable functional recovery below the injury site. Previously, we demonstrated that inflammation determines the fate of the physiopathology. To decipher the molecular mechanisms involved in this process, we performed a meta-analysis of our spatio-temporal proteomic studies in the time course of SCI. This highlighted the presence of IgG isotypes in both spinal cord explants and their secretomes. These IgGs were detected in the spinal cord even if no SCI occurred. However, during the time course following SCI, abundance of IgG1 and IgG2 subclasses (a, b, c) varied according to the spatial repartition. IgG1 was clearly mostly abundant at 12 h, and a switch to IgG2a was observed after 24 h. This IgG stayed predominant 3, 7, and 10 days after SCI. A protein related to IgM as well as a variable heavy chain were only detected 12 h after lesion. Interestingly, treatment with RhoA inhibitor influenced the abundance of the various IgG isotypes and a preferential switch to IgG2c was observed. By data reuse of rat dorsal root ganglion (DRG) neurons RNAseq datasets and RT-PCR experiments performed on cDNA from DRG sensory neurons ND7/23 and N27 dopaminergic neural cell lines, we confirmed expression of immunoglobulin heavy and light chains (constant and variable) encoding genes in neurons. We then identified CD16 and CD32b as their specific receptors in sensory neuron cell line ND7/23 and their activation regulated neurites outgrowth. These results suggest that during SCI, neuronal IgG isotypes are released to modulate neurites outgrowth. Therefore, we propose a new view of the SCI response involving an antibody dependent neurite outgrowth modulation (ADNM) which could be a precursor to the neuroinflammatory response in pathological conditions.
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Affiliation(s)
- Alice Capuz
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Mélodie-Anne Karnoub
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Sylvain Osien
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Mélanie Rose
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Céline Mériaux
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Isabelle Fournier
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
- Institut Universitaire de France, Paris, France
| | - David Devos
- Université de Lille, Inserm U1172, CHU-Lille, Lille Neuroscience Cognition Research Centre, Lille, France
| | - Fabien Vanden Abeele
- Université de Lille, Inserm U1003, Laboratory of Cell Physiology, Villeneuve d’Ascq, France
| | - Franck Rodet
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Dasa Cizkova
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
- Centre for Experimental and Clinical Regenerative Medicine, University of Veterinary Medicine and Pharmacy in Kosice, Kosice, Slovakia
- *Correspondence: Michel Salzet, ; Dasa Cizkova,
| | - Michel Salzet
- Université de Lille, Inserm U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
- Institut Universitaire de France, Paris, France
- *Correspondence: Michel Salzet, ; Dasa Cizkova,
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21
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Ogrinc N, Schneider S, Bourmaud A, Gengler N, Salzet M, Fournier I. Direct In Vivo Analysis of CBD- and THC-Acid Cannabinoids and Classification of Cannabis Cultivars Using SpiderMass. Metabolites 2022; 12:metabo12060480. [PMID: 35736414 PMCID: PMC9227750 DOI: 10.3390/metabo12060480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/27/2021] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 02/01/2023] Open
Abstract
In recent years, cannabis and hemp-based products have become increasingly popular for recreational use, edibles, beverages, health care products, and medicines. The rapid detection and differentiation of phytocannabinoids is, therefore, essential to assess the potency and the therapeutic and nutritional values of cannabis cultivars. Here, we implemented SpiderMass technology for in vivo detection of cannabidiolic acid (CBDA) and ∆9-tetrahydrocannabinolicacid (∆9-THCA), and other endogenous organic plant compounds, to access distribution gradients within the plants and differentiate between cultivars. The SpiderMass system is composed of an IR-laser handheld microsampling probe connected to a mass spectrometer through a transfer tube. The analysis was performed on different plant organs from freshly cultivated cannabis plants in only a few seconds. SpiderMass analysis easily discriminated the two acid phytocannabinoid isomers via MS/MS, and the built statistical models differentiated between four cannabis cultivars. Different abundancies of the two acid phytocannabinoids were found along the plant as well as between different cultivars. Overall, these results introduce direct analysis by SpiderMass as a compelling analytical alternative for rapid hemp analysis.
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Affiliation(s)
- Nina Ogrinc
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Inserm U1192, Université de Lille, F-59000 Lille, France; (N.O.); (M.S.)
| | - Serge Schneider
- Service de Toxicologie Analytique–Chimie Pharmaceutique, Laboratoire National de Santé (LNS), Dudelange, L-3555 Luxembourg, Luxembourg; (S.S.); (A.B.); (N.G.)
| | - Adèle Bourmaud
- Service de Toxicologie Analytique–Chimie Pharmaceutique, Laboratoire National de Santé (LNS), Dudelange, L-3555 Luxembourg, Luxembourg; (S.S.); (A.B.); (N.G.)
| | - Nicolas Gengler
- Service de Toxicologie Analytique–Chimie Pharmaceutique, Laboratoire National de Santé (LNS), Dudelange, L-3555 Luxembourg, Luxembourg; (S.S.); (A.B.); (N.G.)
| | - Michel Salzet
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Inserm U1192, Université de Lille, F-59000 Lille, France; (N.O.); (M.S.)
- Institut Universitaire de France (IUF), F-75000 Paris, France
| | - Isabelle Fournier
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Inserm U1192, Université de Lille, F-59000 Lille, France; (N.O.); (M.S.)
- Institut Universitaire de France (IUF), F-75000 Paris, France
- Correspondence:
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22
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Jarduli-Maciel LR, de Azevedo JTC, Clave E, Costa TCDM, Arruda LCM, Fournier I, Palma PVB, Lima KC, Elias JB, Stracieri ABP, Pieroni F, Cunha R, Darrigo-Júnior LG, Grecco CES, Covas DT, Silva-Pinto AC, De Santis GC, Simões BP, Oliveira MC, Toubert A, Malmegrim KCR. Allogeneic haematopoietic stem cell transplantation resets T- and B-cell compartments in sickle cell disease patients. Clin Transl Immunology 2022; 11:e1389. [PMID: 35474905 PMCID: PMC9035210 DOI: 10.1002/cti2.1389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 11/12/2022] Open
Abstract
Objectives Allogeneic haematopoietic stem cell transplantation (allo-HSCT) is the only currently available curative treatment for sickle cell disease (SCD). Here, we comprehensively evaluated the reconstitution of T- and B-cell compartments in 29 SCD patients treated with allo-HSCT and how it correlated with the development of acute graft-versus-host disease (aGvHD). Methods T-cell neogenesis was assessed by quantification of signal-joint and β-chain TCR excision circles. B-cell neogenesis was evaluated by quantification of signal-joint and coding-joint K-chain recombination excision circles. T- and B-cell peripheral subset numbers were assessed by flow cytometry. Results Before allo-HSCT (baseline), T-cell neogenesis was normal in SCD patients compared with age-, gender- and ethnicity-matched healthy controls. Following allo-HSCT, T-cell neogenesis declined but was fully restored to healthy control levels at one year post-transplantation. Peripheral T-cell subset counts were fully restored only at 24 months post-transplantation. Occurrence of acute graft-versus-host disease (aGvHD) transiently affected T- and B-cell neogenesis and overall reconstitution of T- and B-cell peripheral subsets. B-cell neogenesis was significantly higher in SCD patients at baseline than in healthy controls, remaining high throughout the follow-up after allo-HSCT. Notably, after transplantation SCD patients showed increased frequencies of IL-10-producing B-regulatory cells and IgM+ memory B-cell subsets compared with baseline levels and with healthy controls. Conclusion Our findings revealed that the T- and B-cell compartments were normally reconstituted in SCD patients after allo-HSCT. In addition, the increase of IL-10-producing B-regulatory cells may contribute to improve immune regulation and homeostasis after transplantation.
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Affiliation(s)
- Luciana Ribeiro Jarduli-Maciel
- Graduate Program in Biosciences Applied to Pharmacy School of Pharmaceutical Sciences of Ribeirão Preto University of São Paulo Ribeirão Preto SP Brazil.,Center for Cell-Based Therapy Regional Blood Center of Ribeirão Preto University of São Paulo Ribeirão Preto SP Brazil
| | - Júlia Teixeira Cottas de Azevedo
- Center for Cell-Based Therapy Regional Blood Center of Ribeirão Preto University of São Paulo Ribeirão Preto SP Brazil.,Graduate Program in Basic and Applied Immunology Ribeirão Preto Medical School University of São Paulo Ribeirão Preto SP Brazil
| | | | - Thalita Cristina de Mello Costa
- Center for Cell-Based Therapy Regional Blood Center of Ribeirão Preto University of São Paulo Ribeirão Preto SP Brazil.,University Hospital of Ribeirão Preto Medical School University of São Paulo Ribeirão Preto SP Brazil
| | | | - Isabelle Fournier
- Laboratoire d'Immunologie et d'Histocompatibilité Hôpital Saint-Louis AP-HP Paris France
| | - Patrícia Vianna Bonini Palma
- Center for Cell-Based Therapy Regional Blood Center of Ribeirão Preto University of São Paulo Ribeirão Preto SP Brazil
| | - Keli Cristina Lima
- Graduate Program in Biosciences Applied to Pharmacy School of Pharmaceutical Sciences of Ribeirão Preto University of São Paulo Ribeirão Preto SP Brazil.,Center for Cell-Based Therapy Regional Blood Center of Ribeirão Preto University of São Paulo Ribeirão Preto SP Brazil
| | | | | | - Fabiano Pieroni
- Ribeirão Preto Medical School University of São Paulo São Paulo SP Brazil
| | - Renato Cunha
- Center for Cell-Based Therapy Regional Blood Center of Ribeirão Preto University of São Paulo Ribeirão Preto SP Brazil.,Ribeirão Preto Medical School University of São Paulo São Paulo SP Brazil
| | | | | | - Dimas Tadeu Covas
- Center for Cell-Based Therapy Regional Blood Center of Ribeirão Preto University of São Paulo Ribeirão Preto SP Brazil.,Ribeirão Preto Medical School University of São Paulo São Paulo SP Brazil
| | - Ana Cristina Silva-Pinto
- Center for Cell-Based Therapy Regional Blood Center of Ribeirão Preto University of São Paulo Ribeirão Preto SP Brazil.,University Hospital of Ribeirão Preto Medical School University of São Paulo Ribeirão Preto SP Brazil
| | - Gil Cunha De Santis
- Center for Cell-Based Therapy Regional Blood Center of Ribeirão Preto University of São Paulo Ribeirão Preto SP Brazil.,University Hospital of Ribeirão Preto Medical School University of São Paulo Ribeirão Preto SP Brazil
| | - Belinda Pinto Simões
- Center for Cell-Based Therapy Regional Blood Center of Ribeirão Preto University of São Paulo Ribeirão Preto SP Brazil.,Ribeirão Preto Medical School University of São Paulo São Paulo SP Brazil
| | - Maria Carolina Oliveira
- Center for Cell-Based Therapy Regional Blood Center of Ribeirão Preto University of São Paulo Ribeirão Preto SP Brazil.,Ribeirão Preto Medical School University of São Paulo São Paulo SP Brazil
| | - Antoine Toubert
- Université de Paris INSERM UMR 1160 IRSL Paris France.,Laboratoire d'Immunologie et d'Histocompatibilité Hôpital Saint-Louis AP-HP Paris France
| | - Kelen Cristina Ribeiro Malmegrim
- Center for Cell-Based Therapy Regional Blood Center of Ribeirão Preto University of São Paulo Ribeirão Preto SP Brazil.,Department of Clinical Analysis, Toxicology and Food Sciences School of Pharmaceutical Sciences of Ribeirão Preto University of São Paulo Ribeirão Preto SP Brazil
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23
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Ogrinc N, Attencourt C, Colin E, Boudahi A, Tebbakha R, Salzet M, Testelin S, Dakpé S, Fournier I. Mass Spectrometry-Based Differentiation of Oral Tongue Squamous Cell Carcinoma and Nontumor Regions With the SpiderMass Technology. Front Oral Health 2022; 3:827360. [PMID: 35309279 PMCID: PMC8929397 DOI: 10.3389/froh.2022.827360] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 12/01/2021] [Accepted: 01/26/2022] [Indexed: 12/14/2022] Open
Abstract
Oral cavity cancers are the 15th most common cancer with more than 350,000 new cases and ~178,000 deaths each year. Among them, squamous cell carcinoma (SCC) accounts for more than 90% of tumors located in the oral cavity and on oropharynx. For the oral cavity SCC, the surgical resection remains the primary course of treatment. Generally, surgical margins are defined intraoperatively using visual and tactile elements. However, in 15–30% of cases, positive margins are found after histopathological examination several days postsurgery. Technologies based on mass spectrometry (MS) were recently developed to help guide surgical resection. The SpiderMass technology is designed for in-vivo real-time analysis under minimally invasive conditions. This instrument achieves tissue microsampling and real-time molecular analysis with the combination of a laser microprobe and a mass spectrometer. It ultimately acts as a tool to support histopathological decision-making and diagnosis. This pilot study included 14 patients treated for tongue SCC (T1 to T4) with the surgical resection as the first line of treatment. Samples were first analyzed by a pathologist to macroscopically delineate the tumor, dysplasia, and peritumoral areas. The retrospective and prospective samples were sectioned into three consecutive sections and thaw-mounted on slides for H&E staining (7 μm), SpiderMass analysis (20 μm), and matrix-assisted laser desorption ionization (MALDI) MS imaging (12 μm). The SpiderMass microprobe collected lipidometabolic profiles of the dysplasia, tumor, and peritumoral regions annotated by the pathologist. The MS spectra were then subjected to the multivariate statistical analysis. The preliminary data demonstrate that the lipidometabolic molecular profiles collected with the SpiderMass are significantly different between the tumor and peritumoral regions enabling molecular classification to be established by linear discriminant analysis (LDA). MALDI images of the different samples were submitted to segmentation for cross instrument validation and revealed additional molecular discrimination within the tumor and nontumor regions. These very promising preliminary results show the applicability of the SpiderMass to SCC of the tongue and demonstrate its interest in the surgical treatment of head and neck cancers.
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Affiliation(s)
- Nina Ogrinc
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse – PRISM, Lille, France
- *Correspondence: Nina Ogrinc
| | - Christophe Attencourt
- Department of Pathology, CHU Amiens-Picardie, Amiens, France
- UR7516 CHIMERE, Université de Picardie Jules Verne, Amiens, France
| | - Emilien Colin
- UR7516 CHIMERE, Université de Picardie Jules Verne, Amiens, France
- Department of Maxillofacial Surgery, CHU Amiens-Picardie, Amiens, France
- Institut Faire Faces, Amiens, France
| | - Ahmed Boudahi
- Department of Pathology, CHU Amiens-Picardie, Amiens, France
| | - Riad Tebbakha
- Tumorothèque de Picardie, CHU Amiens-Picardie, Amiens, France
| | - Michel Salzet
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse – PRISM, Lille, France
- Institut Universitaire de France (IUF), Paris, France
| | - Sylvie Testelin
- UR7516 CHIMERE, Université de Picardie Jules Verne, Amiens, France
- Department of Maxillofacial Surgery, CHU Amiens-Picardie, Amiens, France
- Institut Faire Faces, Amiens, France
| | - Stéphanie Dakpé
- UR7516 CHIMERE, Université de Picardie Jules Verne, Amiens, France
- Department of Maxillofacial Surgery, CHU Amiens-Picardie, Amiens, France
- Institut Faire Faces, Amiens, France
- Stéphanie Dakpé
| | - Isabelle Fournier
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse – PRISM, Lille, France
- Institut Universitaire de France (IUF), Paris, France
- Isabelle Fournier
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24
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Hajjaji N, Aboulouard S, Cardon T, Bertin D, Robin YM, Fournier I, Salzet M. Path to Clonal Theranostics in Luminal Breast Cancers. Front Oncol 2022; 11:802177. [PMID: 35096604 PMCID: PMC8793283 DOI: 10.3389/fonc.2021.802177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 10/26/2021] [Accepted: 12/06/2021] [Indexed: 12/18/2022] Open
Abstract
Integrating tumor heterogeneity in the drug discovery process is a key challenge to tackle breast cancer resistance. Identifying protein targets for functionally distinct tumor clones is particularly important to tailor therapy to the heterogeneous tumor subpopulations and achieve clonal theranostics. For this purpose, we performed an unsupervised, label-free, spatially resolved shotgun proteomics guided by MALDI mass spectrometry imaging (MSI) on 124 selected tumor clonal areas from early luminal breast cancers, tumor stroma, and breast cancer metastases. 2868 proteins were identified. The main protein classes found in the clonal proteome dataset were enzymes, cytoskeletal proteins, membrane-traffic, translational or scaffold proteins, or transporters. As a comparison, gene-specific transcriptional regulators, chromatin related proteins or transmembrane signal receptor were more abundant in the TCGA dataset. Moreover, 26 mutated proteins have been identified. Similarly, expanding the search to alternative proteins databases retrieved 126 alternative proteins in the clonal proteome dataset. Most of these alternative proteins were coded mainly from non-coding RNA. To fully understand the molecular information brought by our approach and its relevance to drug target discovery, the clonal proteomic dataset was further compared to the TCGA breast cancer database and two transcriptomic panels, BC360 (nanoString®) and CDx (Foundation One®). We retrieved 139 pathways in the clonal proteome dataset. Only 55% of these pathways were also present in the TCGA dataset, 68% in BC360 and 50% in CDx. Seven of these pathways have been suggested as candidate for drug targeting, 22 have been associated with breast cancer in experimental or clinical reports, the remaining 19 pathways have been understudied in breast cancer. Among the anticancer drugs, 35 drugs matched uniquely with the clonal proteome dataset, with only 7 of them already approved in breast cancer. The number of target and drug interactions with non-anticancer drugs (such as agents targeting the cardiovascular system, metabolism, the musculoskeletal or the nervous systems) was higher in the clonal proteome dataset (540 interactions) compared to TCGA (83 interactions), BC360 (419 interactions), or CDx (172 interactions). Many of the protein targets identified and drugs screened were clinically relevant to breast cancer and are in clinical trials. Thus, we described the non-redundant knowledge brought by this clone-tailored approach compared to TCGA or transcriptomic panels, the targetable proteins identified in the clonal proteome dataset, and the potential of this approach for drug discovery and repurposing through drug interactions with antineoplastic agents and non-anticancer drugs.
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Affiliation(s)
- Nawale Hajjaji
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Soulaimane Aboulouard
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Tristan Cardon
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Delphine Bertin
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Yves-Marie Robin
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Isabelle Fournier
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Institut universitaire de France, Paris, France
| | - Michel Salzet
- Univ. Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Institut universitaire de France, Paris, France
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25
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Malaker SA, Quanico J, Raffo-Romero A, Kobeissy F, Aboulouard S, Tierny D, Bertozzi CR, Fournier I, Salzet M. On-tissue spatially resolved glycoproteomics guided by N-glycan imaging reveal global dysregulation of canine glioma glycoproteomic landscape. Cell Chem Biol 2022; 29:30-42.e4. [PMID: 34102146 PMCID: PMC8617081 DOI: 10.1016/j.chembiol.2021.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 04/06/2021] [Accepted: 05/10/2021] [Indexed: 01/22/2023]
Abstract
Here, we present an approach to identify N-linked glycoproteins and deduce their spatial localization using a combination of matrix-assisted laser desorption ionization (MALDI) N-glycan mass spectrometry imaging (MSI) and spatially resolved glycoproteomics. We subjected glioma biopsies to on-tissue PNGaseF digestion and MALDI-MSI and found that the glycan HexNAc4-Hex5-NeuAc2 was predominantly expressed in necrotic regions of high-grade canine gliomas. To determine the underlying sialo-glycoprotein, various regions in adjacent tissue sections were subjected to microdigestion and manual glycoproteomic analysis. Results identified haptoglobin as the protein associated with HexNAc4-Hex5-NeuAc2, thus directly linking glycan imaging with intact glycopeptide identification. In total, our spatially resolved glycoproteomics technique identified over 400 N-, O-, and S- glycopeptides from over 30 proteins, demonstrating the diverse array of glycosylation present on the tissue slices and the sensitivity of our technique. Ultimately, this proof-of-principle work demonstrates that spatially resolved glycoproteomics greatly complement MALDI-MSI in understanding dysregulated glycosylation.
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Affiliation(s)
- Stacy Alyse Malaker
- Université de Lille 1, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000 Lille, France,Department of Chemistry and ChEM-H, Stanford University, Stanford, CA 94035, USA,Present address: Department of Chemistry, Yale University, New Haven, CT 06511, USA,These authors contributed equally
| | - Jusal Quanico
- Université de Lille 1, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000 Lille, France,Present address: Center for Proteomics, Antwerp University,Campus Groenenborger, Groenenborgerlaan 171, 2020 Antwerp, Belgium,These authors contributed equally
| | - Antonella Raffo-Romero
- Université de Lille 1, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000 Lille, France
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Lebanon
| | - Soulaimane Aboulouard
- Université de Lille 1, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000 Lille, France
| | - Dominique Tierny
- OCR (Oncovet Clinical Research), Parc Eurasanté Lille Métropole, 80 rue du Dr Yersin, 59120 Loos, France
| | - Carolyn Ruth Bertozzi
- Department of Chemistry and ChEM-H, Stanford University, Stanford, CA 94035, USA,Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Isabelle Fournier
- Université de Lille 1, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000 Lille, France,Correspondence: (I.F.), (M.S.)
| | - Michel Salzet
- Université de Lille 1, INSERM, U1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), 59000 Lille, France,Lead contact,Correspondence: (I.F.), (M.S.)
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Abstract
Glioblastoma is the most common brain cancer in adults. Nevertheless, the median survival time is 15 months, if treated with at least a near total resection and followed by radiotherapy in association with temozolomide. In glioblastoma (GBM), variations of non-coding ribonucleic acid (ncRNA) expression have been demonstrated in tumor processes, especially in the regulation of major signaling pathways. Moreover, many ncRNAs present in their sequences an Open Reading Frame (ORF) allowing their translations into proteins, so-called alternative proteins (AltProt) and constituting the “ghost proteome.” This neglected world in GBM has been shown to be implicated in protein–protein interaction (PPI) with reference proteins (RefProt) reflecting involvement in signaling pathways linked to cellular mobility and transfer RNA regulation. More recently, clinical studies have revealed that AltProt is also involved in the patient’s survival and bad prognosis. We thus propose to review the ncRNAs involved in GBM and highlight their function in the disease.
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Affiliation(s)
- Tristan Cardon
- University of Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Isabelle Fournier
- University of Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,Institut Universitaire de France, Paris, France
| | - Michel Salzet
- University of Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,Institut Universitaire de France, Paris, France
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Ogrinc N, Kruszewski A, Chaillou P, Saudemont P, Lagadec C, Salzet M, Duriez C, Fournier I. Robot-Assisted SpiderMass for In Vivo Real-Time Topography Mass Spectrometry Imaging. Anal Chem 2021; 93:14383-14391. [PMID: 34670081 DOI: 10.1021/acs.analchem.1c01692] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Mass spectrometry imaging (MSI) has shown to bring invaluable information for biological and clinical applications. However, conventional MSI is generally performed ex vivo from tissue sections. Here, we developed a novel MS-based method for in vivo mass spectrometry imaging. By coupling the SpiderMass technology, that provides in vivo minimally invasive analysis-to a robotic arm of high accuracy, we demonstrate that images can be acquired from any surface by moving the laser probe above the surface. By equipping the robotic arm with a sensor, we are also able to both get the topography image of the sample surface and the molecular distribution, and then and plot back the molecular data, directly to the 3D topographical image without the need for image fusion. This is shown for the first time with the 3D topographic MS-based whole-body imaging of a mouse. Enabling fast in vivo MSI bridged to topography paves the way for surgical applications to excision margins.
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Affiliation(s)
- Nina Ogrinc
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Alexandre Kruszewski
- UMR 9189 - CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille, University of Lille, INRIA, CNRS, F-59000 Lille, France
| | - Paul Chaillou
- UMR 9189 - CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille, University of Lille, INRIA, CNRS, F-59000 Lille, France
| | - Philippe Saudemont
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Chann Lagadec
- University of Lille, CNRS, Inserm, CHU Lille, Centre Oscar Lambret, UMR9020 - UMR-S 1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Michel Salzet
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.,Institut Universitaire de France (IUF), Paris 75231, France
| | - Christian Duriez
- UMR 9189 - CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille, University of Lille, INRIA, CNRS, F-59000 Lille, France
| | - Isabelle Fournier
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.,Institut Universitaire de France (IUF), Paris 75231, France
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28
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Ogrinc N, Caux PD, Robin YM, Bouchaert E, Fatou B, Ziskind M, Focsa C, Bertin D, Tierny D, Takats Z, Salzet M, Fournier I. Direct Water-Assisted Laser Desorption/Ionization Mass Spectrometry Lipidomic Analysis and Classification of Formalin-Fixed Paraffin-Embedded Sarcoma Tissues without Dewaxing. Clin Chem 2021; 67:1513-1523. [PMID: 34586394 DOI: 10.1093/clinchem/hvab160] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Formalin-fixed paraffin-embedded (FFPE) tissue has been the gold standard for routine pathology for general and cancer postoperative diagnostics. Despite robust histopathology, immunohistochemistry, and molecular methods, accurate diagnosis remains difficult for certain cases. Overall, the entire process can be time consuming, labor intensive, and does not reach over 90% diagnostic sensitivity and specificity. There is a growing need in onco-pathology for adjunct novel rapid, accurate, reliable, diagnostically sensitive, and specific methods for high-throughput biomolecular identification. Lipids have long been considered only as building blocks of cell membranes or signaling molecules, but have recently been introduced as central players in cancer. Due to sample processing, which limits their detection, lipid analysis directly from unprocessed FFPE tissues has never been reported. METHODS We present a proof-of-concept with direct analysis of tissue-lipidomic signatures from FFPE tissues without dewaxing and minimal sample preparation using water-assisted laser desorption ionization mass spectrometry and deep-learning. RESULTS On a cohort of difficult canine and human sarcoma cases, classification for canine sarcoma subtyping was possible with 99.1% accuracy using "5-fold" and 98.5% using "leave-one-patient out," and 91.2% accuracy for human sarcoma using 5-fold and 73.8% using leave-one-patient out. The developed classification model enabled stratification of blind samples in <5 min and showed >95% probability for discriminating 2 human sarcoma blind samples. CONCLUSION It is possible to create a rapid diagnostic platform to screen clinical FFPE tissues with minimal sample preparation for molecular pathology.
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Affiliation(s)
- Nina Ogrinc
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Pierre-Damien Caux
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Yves-Marie Robin
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,Unité de Pathologie Morphologique et Moléculaire, Centre Oscar Lambret, Lille, France
| | - Emmanuel Bouchaert
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,OCR (Oncovet Clinical Research), Parc Eurasante Lille Metropole, Loos, France
| | - Benoit Fatou
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Michael Ziskind
- University of Lille, CNRS, UMR 8523, PhLAM-Physique des Lasers, Atomes et Molécules, Lille, France
| | - Cristian Focsa
- University of Lille, CNRS, UMR 8523, PhLAM-Physique des Lasers, Atomes et Molécules, Lille, France
| | - Delphine Bertin
- Unité de Pathologie Morphologique et Moléculaire, Centre Oscar Lambret, Lille, France
| | - Dominique Tierny
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,OCR (Oncovet Clinical Research), Parc Eurasante Lille Metropole, Loos, France
| | - Zoltan Takats
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Michel Salzet
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,Institut Universitaire de France (IUF), Paris, France
| | - Isabelle Fournier
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,Institut Universitaire de France (IUF), Paris, France
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Faure MC, Khoueiry R, Quanico J, Acloque H, Guerquin MJ, Bertoldo MJ, Chevaleyre C, Ramé C, Fournier I, Salzet M, Dupont J, Froment P. In Utero Exposure to Metformin Reduces the Fertility of Male Offspring in Adulthood. Front Endocrinol (Lausanne) 2021; 12:750145. [PMID: 34745014 PMCID: PMC8565088 DOI: 10.3389/fendo.2021.750145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/17/2021] [Indexed: 12/11/2022] Open
Abstract
Metformin is a drug used for the treatment of type 2 diabetes and disorders associated with insulin resistance. Metformin is also used in the treatment of pregnancy disorders such as gestational diabetes. However, the consequences of foetal exposure to metformin on the fertility of exposed offspring remain poorly documented. In this study, we investigated the effect of in utero metformin exposure on the fertility of female and male offspring. We observed that metformin is detectable in the blood of the mother and in amniotic fluid and blood of the umbilical cord. Metformin was not measurable in any tissues of the embryo, including the gonads. The effect of metformin exposure on offspring was sex specific. The adult females that had been exposed to metformin in utero presented no clear reduction in fertility. However, the adult males that had been exposed to metformin during foetal life exhibited a 30% reduction in litter size compared with controls. The lower fertility was not due to a change in sperm production or the motility of sperm. Rather, the phenotype was due to lower sperm head quality - significantly increased spermatozoa head abnormality with greater DNA damage - and hypermethylation of the genomic DNA in the spermatozoa associated with lower expression of the ten-eleven translocation methylcytosine dioxygenase 1 (TET1) protein. In conclusion, while foetal metformin exposure did not dramatically alter gonad development, these results suggest that metabolic modification by metformin during the foetal period could change the expression of epigenetic regulators such as Tet1 and perturb the genomic DNA in germ cells, changes that might contribute to a reduced fertility.
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Affiliation(s)
- Mélanie C. Faure
- l’Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), UMR85 Physiologie de la Reproduction et des Comportements/Centre national de la Recherche Scientifique (CNRS), UMR7247/Université François Rabelais de Tours/Institut français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Rita Khoueiry
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Jusal Quanico
- Université Lille 1, INSERM U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), Villeneuve d’Ascq, France
| | - Hervé Acloque
- Université Paris-Saclay, INRAE, AgroParisTech, Génétique Animale et Biologie Intégrative (GABI), Jouy-en-Josas, France
| | - Marie-Justine Guerquin
- UMR967 INSERM, Commissariat à l'Énergie Atomique (CEA)/Direction de la Recherche Fondamentale (DRF)/Institut de Radiobiologie Cellulaire et Moléculaire (iRCM)/Service Cellules Souches et Radiation (SCSR)/LDG, Université Paris Diderot, Sorbonne Paris Cité, Université Paris-Sud, Université Paris-Saclay, Laboratory of Development of the Gonads, Fontenay aux Roses, France
| | - Michael J. Bertoldo
- Fertility and Research Centre, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Claire Chevaleyre
- l’Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), UMR85 Physiologie de la Reproduction et des Comportements/Centre national de la Recherche Scientifique (CNRS), UMR7247/Université François Rabelais de Tours/Institut français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Christelle Ramé
- l’Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), UMR85 Physiologie de la Reproduction et des Comportements/Centre national de la Recherche Scientifique (CNRS), UMR7247/Université François Rabelais de Tours/Institut français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Isabelle Fournier
- Université Lille 1, INSERM U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), Villeneuve d’Ascq, France
| | - Michel Salzet
- Université Lille 1, INSERM U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), Villeneuve d’Ascq, France
| | - Joëlle Dupont
- l’Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), UMR85 Physiologie de la Reproduction et des Comportements/Centre national de la Recherche Scientifique (CNRS), UMR7247/Université François Rabelais de Tours/Institut français du Cheval et de l'Équitation (IFCE), Nouzilly, France
| | - Pascal Froment
- l’Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), UMR85 Physiologie de la Reproduction et des Comportements/Centre national de la Recherche Scientifique (CNRS), UMR7247/Université François Rabelais de Tours/Institut français du Cheval et de l'Équitation (IFCE), Nouzilly, France
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Rose M, Cardon T, Aboulouard S, Hajjaji N, Kobeissy F, Duhamel M, Fournier I, Salzet M. Surfaceome Proteomic of Glioblastoma Revealed Potential Targets for Immunotherapy. Front Immunol 2021; 12:746168. [PMID: 34646273 PMCID: PMC8503648 DOI: 10.3389/fimmu.2021.746168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/08/2021] [Indexed: 12/21/2022] Open
Abstract
Glioblastoma (GBM) is the most common and devastating malignant brain tumor in adults. The mortality rate is very high despite different treatments. New therapeutic targets are therefore highly needed. Cell-surface proteins represent attractive targets due to their accessibility, their involvement in essential signaling pathways, and their dysregulated expression in cancer. Moreover, they are potential targets for CAR-based immunotherapy or mRNA vaccine strategies. In this context, we investigated the GBM-associated surfaceome by comparing it to astrocytes cell line surfaceome to identify new specific targets for GBM. For this purpose, biotinylation of cell surface proteins has been carried out in GBM and astrocytes cell lines. Biotinylated proteins were purified on streptavidin beads and analyzed by shotgun proteomics. Cell surface proteins were identified with Cell Surface Proteins Atlas (CSPA) and Gene Ontology enrichment. Among all the surface proteins identified in the different cell lines we have confirmed the expression of 66 of these in patient’s glioblastoma using spatial proteomic guided by MALDI-mass spectrometry. Moreover, 87 surface proteins overexpressed or exclusive in GBM cell lines have been identified. Among these, we found 11 specific potential targets for GBM including 5 mutated proteins such as RELL1, CYBA, EGFR, and MHC I proteins. Matching with drugs and clinical trials databases revealed that 7 proteins were druggable and under evaluation, 3 proteins have no known drug interaction yet and none of them are the mutated form of the identified proteins. Taken together, we discovered potential targets for immune therapy strategies in GBM.
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Affiliation(s)
- Mélanie Rose
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Tristan Cardon
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Soulaimane Aboulouard
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Nawale Hajjaji
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Marie Duhamel
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Isabelle Fournier
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Institut Universitaire de France, Paris, France
| | - Michel Salzet
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Institut Universitaire de France, Paris, France
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31
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Drelich L, Aboulouard S, Franck J, Salzet M, Fournier I, Wisztorski M. Toward High Spatially Resolved Proteomics Using Expansion Microscopy. Anal Chem 2021; 93:12195-12203. [PMID: 34449217 DOI: 10.1021/acs.analchem.0c05372] [Citation(s) in RCA: 2] [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] [Indexed: 12/31/2022]
Abstract
Expansion microscopy (EM) is an emerging approach for morphological examination of biological specimens at nanoscale resolution using conventional optical microscopy. To achieve physical separation of cell structures, tissues are embedded in a swellable polymer and expanded several fold in an isotropic manner. This work shows the development and optimization of physical tissue expansion as a new method for spatially resolved large-scale proteomics. Herein we established a novel method to enlarge the tissue section to be compatible with manual microdissection on regions of interest and MS-based proteomic analysis. A major issue in expansion microscopy is the loss of protein information during the mechanical homogenization phase due to the use of proteinase K. For isotropic expansion, different homogenization agents were investigated, both to maximize protein identification and to minimize protein diffusion. Best results were obtained with SDS for homogenization. Using our modified protocol, we were able to enlarge a tissue section more than 3-fold and identified up to 655 proteins from 1 mm in size after expansion, equivalent to 330 μm in their real size corresponding thus to an average of 260 cells. This approach can be performed easily without any expensive sampling instrument. We demonstrated the compatibility of sample preparation for expansion microscopy and proteomic study in a spatial context.
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Affiliation(s)
- Lauranne Drelich
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France
| | - Soulaimane Aboulouard
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France
| | - Julien Franck
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France
| | - Michel Salzet
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France.,Institut Universitaire de France (IUF), Paris, 75000, France
| | - Isabelle Fournier
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France.,Institut Universitaire de France (IUF), Paris, 75000, France
| | - Maxence Wisztorski
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, 59000, France
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32
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Fournier I, Beck SR, Droit-Volet S, Brogniart J, Osiurak F. Learning versus reasoning to use tools in children. J Exp Child Psychol 2021; 211:105232. [PMID: 34252753 DOI: 10.1016/j.jecp.2021.105232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 05/31/2021] [Accepted: 06/23/2021] [Indexed: 11/27/2022]
Abstract
Tool behavior might be based on two strategies associated with specific cognitive mechanisms: cued-learning and technical-reasoning strategies. We aimed to explore whether these strategies coexist in young children and whether they are manifest differently through development. We presented 216 3- to 9-year-olds with a vertical maze task consisting in moving a ball from the top to the bottom of a maze. Two tool-use/mechanical actions were possible: rotating action and sliding action. Three conditions were tested, each focused on a different strategy. In the Opaque-Cue condition (cued-learning strategy), children could not see the mechanical action of each tool. Nevertheless, a cue was provided according to the tool needed to solve the problem. In the Transparent-No Cue condition (technical-reasoning strategy), no cue was presented. However, children could see the mechanical actions associated with each tool. In the Transparent-Cue condition (cued-learning and/or technical-reasoning strategies) children saw both the mechanical actions and the cues. Results indicated that the Opaque-Cue and Transparent-Cue conditions were easier than the Transparent-No-Cue condition in all children. These findings stress that children can use either cued learning or technical reasoning to use tools, according to the available information. The behavioral pattern observed in the Transparent-Cue condition suggests that children might be inclined to use technical reasoning even when the task can be solved through cued learning.
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Affiliation(s)
- Isabelle Fournier
- Laboratoire d'Étude des Mécanismes Cognitifs (EA 3082), Institut de Psychologie, Université Lyon 2, 69676 Bron Cedex, France
| | - Sarah R Beck
- School of Psychology, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Sylvie Droit-Volet
- Université Clermont Auvergne, CNRS, LAPSCO, F-63000, Clermont-Ferrand, France
| | - Joël Brogniart
- Laboratoire d'Étude des Mécanismes Cognitifs (EA 3082), Institut de Psychologie, Université Lyon 2, 69676 Bron Cedex, France
| | - François Osiurak
- Laboratoire d'Étude des Mécanismes Cognitifs (EA 3082), Institut de Psychologie, Université Lyon 2, 69676 Bron Cedex, France; Institut Universitaire de France, 75005 Paris, France.
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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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Ogrinc N, Saudemont P, Takats Z, Salzet M, Fournier I. Cancer Surgery 2.0: Guidance by Real-Time Molecular Technologies. Trends Mol Med 2021; 27:602-615. [PMID: 33965341 DOI: 10.1016/j.molmed.2021.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 12/14/2022]
Abstract
In vivo cancer margin delineation during surgery remains a major challenge. Despite the availability of several image guidance techniques and intraoperative assessment, clear surgical margins and debulking efficiency remain scarce. For this reason, there is particular interest in developing rapid intraoperative tools with high sensitivity and specificity to help guide cancer surgery in vivo. Recently, several emerging technologies including intraoperative mass spectrometry have paved the way for molecular guidance in a clinical setting. We evaluate these techniques and assess their relevance for intraoperative surgical guidance and how they can transform the future of molecular cancer surgery, diagnostics, patient management and care.
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Affiliation(s)
- Nina Ogrinc
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Philippe Saudemont
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Zoltan Takats
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Michel Salzet
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France; Institut Universitaire de France (IUF), Paris, France.
| | - Isabelle Fournier
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France; Institut Universitaire de France (IUF), Paris, France.
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Gascon L, Fournier I, Chiesa-Estomba C, Russo G, Fakhry N, Lechien JR, Burnell L, Vergez S, Metwaly O, Capasso P, Ayad T. Systematic review of international guidelines for head and neck oncology management in COVID-19 patients. Eur Arch Otorhinolaryngol 2021; 279:907-943. [PMID: 33891167 PMCID: PMC8062612 DOI: 10.1007/s00405-021-06823-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 04/11/2021] [Indexed: 11/28/2022]
Abstract
Purpose The coronavirus pandemic has redefined the practice of head and neck surgeons in the management of oncology patients. Several countries have issued practice recommendations in that context. This review is a collaboration of the YO-IFOS (Young Otolaryngologists of the International Federation of Otolaryngological Societies) group in order to summarize, in a systematic way, all available guidelines and provide clear guidelines for the management of head and neck cancer patients in the COVID-19 pandemic. Methods This systematic review was performed according to the PRISMA statements. Inclusion criteria for the systematic review were based on the population, intervention, comparison, and outcomes according to (PICO) framework. The AGREE II (Appraisal of Guidelines for Research and Evaluation II) instrument was used to assess quality of all practice guidelines included in this review. Results Recommendations include adjustments regarding new patients’ referral such as performing a pre-appointment triage and working in telemedicine when possible. Surgical prioritization must be adjusted in order to respect pandemic requirements. High-grade malignancies should, howeve,r not be delayed, due to potential serious consequences. Many head and neck interventions being aerosol-generating procedures, COVID-19 testing prior to a surgery and adequate PPE precautions are essential in operating rooms. Conclusion These recommendations for head and neck oncology patients serve as a guide for physicians in the pandemic. Adjustments and updates are necessary as the pandemic evolves.
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Affiliation(s)
- Laurence Gascon
- Task Force COVID-19 of the Young-Otolaryngologists of the International Federations of Oto-rhino-laryngological Societies (YO-IFOS), Paris, France.,Division of Otolaryngology-Head and Neck Surgery, Centre Hospitalier de l'Université de Montréal, 1051, rue Sanguinet, Montréal, QC, H2X 0C1, Canada
| | - Isabelle Fournier
- Task Force COVID-19 of the Young-Otolaryngologists of the International Federations of Oto-rhino-laryngological Societies (YO-IFOS), Paris, France.,Division of Otolaryngology-Head and Neck Surgery, Centre Hospitalier de l'Université de Montréal, 1051, rue Sanguinet, Montréal, QC, H2X 0C1, Canada
| | - Carlos Chiesa-Estomba
- Task Force COVID-19 of the Young-Otolaryngologists of the International Federations of Oto-rhino-laryngological Societies (YO-IFOS), Paris, France.,Department of Otorhinolaryngology-Head and Neck Surgery, Hospital Universitario Donostia, San Sebastián, Spain
| | - Gennaro Russo
- Task Force COVID-19 of the Young-Otolaryngologists of the International Federations of Oto-rhino-laryngological Societies (YO-IFOS), Paris, France.,Otolaryngology Head and Neck Surgery Unit of "Azienda Ospedaliera di Rilievo Nazionale dei Colli, Ospedale Monaldi", Naples, Italy
| | - Nicolas Fakhry
- Task Force COVID-19 of the Young-Otolaryngologists of the International Federations of Oto-rhino-laryngological Societies (YO-IFOS), Paris, France.,Otolaryngology-Head and Neck Surgery Department, University Hospital of la Conception, APHM, Aix-Marseille Univ, Marseille, France
| | - Jérôme R Lechien
- Task Force COVID-19 of the Young-Otolaryngologists of the International Federations of Oto-rhino-laryngological Societies (YO-IFOS), Paris, France.,Department of Otolaryngology-Head and Neck Surgery, School of Medicine, Foch Hospital, UFR Simone Veil, Université Versailles Saint-Quentin-en-Yvelines (Paris Saclay University), Paris, France
| | - Lisa Burnell
- Task Force COVID-19 of the Young-Otolaryngologists of the International Federations of Oto-rhino-laryngological Societies (YO-IFOS), Paris, France.,ENT Morningside, Morningside Mediclinic Sandton, Johannesburg, South Africa
| | - Sebastien Vergez
- Task Force COVID-19 of the Young-Otolaryngologists of the International Federations of Oto-rhino-laryngological Societies (YO-IFOS), Paris, France.,Head and Neck Surgery Department, University Cancer Institute of Toulouse-Oncopole, Toulouse University Hospital, Toulouse, France
| | - Osama Metwaly
- Task Force COVID-19 of the Young-Otolaryngologists of the International Federations of Oto-rhino-laryngological Societies (YO-IFOS), Paris, France.,Kasr Alainy School of Medicine, Cairo University, Cairo, Egypt
| | - Pasquale Capasso
- Task Force COVID-19 of the Young-Otolaryngologists of the International Federations of Oto-rhino-laryngological Societies (YO-IFOS), Paris, France.,Otolaryngology Head and Neck Surgery Unit of "Azienda Ospedaliera di Rilievo Nazionale dei Colli, Ospedale Monaldi", Naples, Italy
| | - Tareck Ayad
- Task Force COVID-19 of the Young-Otolaryngologists of the International Federations of Oto-rhino-laryngological Societies (YO-IFOS), Paris, France. .,Division of Otolaryngology-Head and Neck Surgery, Centre Hospitalier de l'Université de Montréal, 1051, rue Sanguinet, Montréal, QC, H2X 0C1, Canada.
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Colin F, Schauer K, Hamiche A, Martineau P, Borg JP, Bednar J, Bertolin G, Camoin L, Collette Y, Dimitrov S, Fournier I, Hyenne V, Mendoza-Parra MA, Morelli X, Rondé P, Sumara I, Tramier M, Schultz P, Goetz JG. The NANOTUMOR consortium - Towards the Tumor Cell Atlas. Biol Cell 2021; 113:272-280. [PMID: 33554340 DOI: 10.1111/boc.202000135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/25/2021] [Indexed: 02/06/2023]
Abstract
Cancer is a multi-step disease where an initial tumour progresses through critical steps shaping, in most cases, life-threatening secondary foci called metastases. The oncogenic cascade involves genetic, epigenetic, signalling pathways, intracellular trafficking and/or metabolic alterations within cancer cells. In addition, pre-malignant and malignant cells orchestrate complex and dynamic interactions with non-malignant cells and acellular matricial components or secreted factors within the tumour microenvironment that is instrumental in the progression of the disease. As our aptitude to effectively treat cancer mostly depends on our ability to decipher, properly diagnose and impede cancer progression and metastasis formation, full characterisation of molecular complexes and cellular processes at play along the metastasis cascade is crucial. For many years, the scientific community lacked adapted imaging and molecular technologies to accurately dissect, at the highest resolution possible, tumour and stromal cells behaviour within their natural microenvironment. In that context, the NANOTUMOR consortium is a French national multi-disciplinary workforce which aims at a providing a multi-scale characterisation of the oncogenic cascade, from the atomic level to the dynamic organisation of the cell in response to genetic mutations, environmental changes or epigenetic modifications. Ultimately, this program aims at identifying new therapeutic targets using innovative drug design.
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Affiliation(s)
- Florent Colin
- INSERM UMR_S1109, Tumor Biomechanics Lab, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), CNRS SNC5055, Strasbourg, France
| | - Kristine Schauer
- CNRS UMR144, Molecular Mechanisms of Intracellular Transport group, Institut Curie, 75005 Paris, France, PSL Research University, Paris, France, Sorbonne Université, Paris, France, Inserm U1279, Gustave Roussy Institute, Université Paris-Saclay, Villejuif, France
| | - Ali Hamiche
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch, France
| | - Pierre Martineau
- Institut de Recherche en Cancérologie de Montpellier (IRCM), INSERM U1194, Université de Montpellier, Institut régional du Cancer de Montpellier (ICM), Montpellier, France
| | - Jean-Paul Borg
- Aix Marseille Univ, CNRS UMR7258, INSERM UMR1068, Institut Paoli Calmettes, CRCM, Marseille, 13009, France.,Institut Universitaire de France (IUF), Paris, France
| | - Jan Bednar
- Institute for Advanced Biosciences (IAB), Université Grenoble Alpes, CNRS UMR5309, INSERM U1209, La Tronche, France
| | - Giulia Bertolin
- CNRS, Univ Rennes, IGDR (Genetics and Development Institute of Rennes), UMR 6290, Rennes, F-35000, France
| | - Luc Camoin
- Aix Marseille Univ, CNRS UMR7258, INSERM UMR1068, Institut Paoli Calmettes, CRCM, Marseille, 13009, France
| | - Yves Collette
- Aix Marseille Univ, CNRS UMR7258, INSERM UMR1068, Institut Paoli Calmettes, CRCM, Marseille, 13009, France
| | - Stephan Dimitrov
- Institute for Advanced Biosciences (IAB), Université Grenoble Alpes, CNRS UMR5309, INSERM U1209, La Tronche, France
| | - Isabelle Fournier
- Institut Universitaire de France (IUF), Paris, France.,Univ. Lille, INSERM, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, F-59000, France
| | - Vincent Hyenne
- INSERM UMR_S1109, Tumor Biomechanics Lab, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), CNRS SNC5055, Strasbourg, France
| | - Marco A Mendoza-Parra
- UMR8030 Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, University of Evry-val-d'Essonne, University Paris-Saclay, Evry, France
| | - Xavier Morelli
- Aix Marseille Univ, CNRS UMR7258, INSERM UMR1068, Institut Paoli Calmettes, CRCM, Marseille, 13009, France
| | - Philippe Rondé
- Faculté de Pharmacie, Université de Strasbourg, Illkirch, France.,CNRS UMR7021, Laboratoire de Bioimagerie et Pathologies, Illkirch, France
| | - Izabela Sumara
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch, France
| | - Marc Tramier
- CNRS, Univ Rennes, IGDR (Genetics and Development Institute of Rennes), UMR 6290, Rennes, F-35000, France
| | - Patrick Schultz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR7104, INSERM U1258, Université de Strasbourg, Illkirch, France
| | - Jacky G Goetz
- INSERM UMR_S1109, Tumor Biomechanics Lab, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg (FMTS), CNRS SNC5055, Strasbourg, France
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Hajjaji N, Aboulouard S, Bertin D, Robin YM, Fournier I, Salzet M. Abstract PS18-36: Proteomic profiling of specific tumor clones using spatially resolved mass spectrometry technologies for precision oncology. Cancer Res 2021. [DOI: 10.1158/1538-7445.sabcs20-ps18-36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background
Breast cancer (BC) remains a leading cause of cancer-related death among women worldwide. The complexity of this disease, especially its heterogeneity, have prevented its eradication and driven resistance to treatments. To reach precision oncology to eradicate BC, therapy needs to be specific to each tumor clone. Yielding enough molecular information from tumor clones to identify new drug targets represents a technical challenge due to sample size limitation or loss of spatial resolution. Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry combined with microproteomics enables a spatially-resolved unlabeled tumor imaging of its protein distribution, thus revealing proteomic clones. Our aims were to analyze the clonal proteome of luminal breast cancers, and explore its potential to expand new drug target discovery and drug repurposing.
Methods
A retrospective study at the Comprehensive Cancer Centre Oscar Lambret (Lille, France) was conducted to analyze 76 FFPE luminal HER2 negative tumors: 52 primary tumors from patients with early BC and 24 BC metastases. Patients gave their informed consent and the study was approved by the local institutional review board. MALDI mass spectrometry imaging and spatially-resolved on-tissue shotgun microproteomics were performed on FFPE slides of tumor tissue to determine the proteomic profile of selected clones using nanoLC-MS & MS/MS. Protein identification was performed using MaxQuant software against the Uniprot database. Functional annotation and characterization of the identified proteins were performed using Panther software. Candidate druggable targets were searched using DrugCentral druggable genome database, and their druggability level was assessed using the classification by the Illuminating the Druggable Genome Knowledge Management Center. The clonal proteome dataset was compared to publically available TCGA, BC360, and CDx datasets.
Results
The clonal proteome analysis identified a total of 2868 different proteins; 780 proteins were found in more than 50% of the patients. Panther analysis showed that 22% of the proteins were classified as enzymes, 15% were related to DNA processes, 6% were structural proteins, and less than 2% were related to immunity. Panther identified 139 pathways in the clonal proteome dataset. The clonal proteome analysis yielded the highest number of pathways compared to TCGA, BC360, and CDx datasets. 41 pathways (mainly metabolic pathways) were exclusive to the clonal proteome dataset. 1495 proteins of this dataset had an entry and were druggable in DrugCentral database, with 52% of them with known mechanisms of action and drug interaction. The main target classes were enzymes (60%), kinases (23%) and transporters (7%), whereas kinases were dominant in TCGA, BC360, and CDx datasets (46% to 77%). To explore the clonal proteome potential for repurposing anticancer drugs in luminal breast cancers, protein targets matching approved antineoplastic agents were searched using DrugCentral database. 97 approved anticancer drugs were identified, mostly chemotherapy (33%) or protein kinase inhibitors (28%), of whom only 17 were approved for breast cancer treatment. Compared to publically available TCGA, BC360, and CDx datasets, the clonal proteome analysis yielded the highest number of drug target candidate.
Conclusion
Mass spectrometry-based analysis of BC proteomic clones provides the technological means to access large functional molecular information at a clonal level to develop clone specific strategies for drug target discovery and drug repurposing in BC.
Citation Format: Nawale Hajjaji, Soulaimane Aboulouard, Delphine Bertin, Yves Marie Robin, Isabelle Fournier, Michel Salzet. Proteomic profiling of specific tumor clones using spatially resolved mass spectrometry technologies for precision oncology [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS18-36.
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Affiliation(s)
| | | | | | | | | | - Michel Salzet
- 2PRISM Laboratory Inserm U1192, University of Lille, Lille, France
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Brunet MA, Lucier JF, Levesque M, Leblanc S, Jacques JF, Al-Saedi HRH, Guilloy N, Grenier F, Avino M, Fournier I, Salzet M, Ouangraoua A, Scott M, Boisvert FM, Roucou X. OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes. Nucleic Acids Res 2021; 49:D380-D388. [PMID: 33179748 PMCID: PMC7779043 DOI: 10.1093/nar/gkaa1036] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
OpenProt (www.openprot.org) is the first proteogenomic resource supporting a polycistronic annotation model for eukaryotic genomes. It provides a deeper annotation of open reading frames (ORFs) while mining experimental data for supporting evidence using cutting-edge algorithms. This update presents the major improvements since the initial release of OpenProt. All species support recent NCBI RefSeq and Ensembl annotations, with changes in annotations being reported in OpenProt. Using the 131 ribosome profiling datasets re-analysed by OpenProt to date, non-AUG initiation starts are reported alongside a confidence score of the initiating codon. From the 177 mass spectrometry datasets re-analysed by OpenProt to date, the unicity of the detected peptides is controlled at each implementation. Furthermore, to guide the users, detectability statistics and protein relationships (isoforms) are now reported for each protein. Finally, to foster access to deeper ORF annotation independently of one's bioinformatics skills or computational resources, OpenProt now offers a data analysis platform. Users can submit their dataset for analysis and receive the results from the analysis by OpenProt. All data on OpenProt are freely available and downloadable for each species, the release-based format ensuring a continuous access to the data. Thus, OpenProt enables a more comprehensive annotation of eukaryotic genomes and fosters functional proteomic discoveries.
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Affiliation(s)
- Marie A Brunet
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada
| | - Jean-François Lucier
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Biology Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Maxime Levesque
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Biology Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Sébastien Leblanc
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada
| | - Jean-Francois Jacques
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada
| | - Hassan R H Al-Saedi
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Noé Guilloy
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada
| | - Frederic Grenier
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Biology Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Mariano Avino
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - Isabelle Fournier
- INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
| | - Michel Salzet
- INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
| | - Aïda Ouangraoua
- Informatics Department, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Michelle S Scott
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
| | - François-Michel Boisvert
- Department of Immunology and Cellular Biology, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean Mignault, Sherbrooke, QC J1E 4K8, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université Laval, Quebec City, QC G1V0A6, Canada
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Cardon T, Fournier I, Salzet M. SARS-Cov-2 Interactome with Human Ghost Proteome: A Neglected World Encompassing a Wealth of Biological Data. Microorganisms 2020; 8:E2036. [PMID: 33352703 PMCID: PMC7766365 DOI: 10.3390/microorganisms8122036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 11/17/2022] Open
Abstract
Conventionally, eukaryotic mRNAs were thought to be monocistronic, leading to the translation of a single protein. However, large-scale proteomics have led to a massive identification of proteins translated from mRNAs of alternative ORF (AltORFs), in addition to the predicted proteins issued from the reference ORF or from ncRNAs. These alternative proteins (AltProts) are not represented in the conventional protein databases and this "ghost proteome" was not considered until recently. Some of these proteins are functional and there is growing evidence that they are involved in central functions in physiological and physiopathological context. Based on our experience with AltProts, we were interested in finding out their interaction with the viral protein coming from the SARS-CoV-2 virus, responsible for the 2020 COVID-19 outbreak. Thus, we have scrutinized the recently published data by Krogan and coworkers (2020) on the SARS-CoV-2 interactome with host cells by affinity purification in co-immunoprecipitation (co-IP) in the perspective of drug repurposing. The initial work revealed the interaction between 332 human cellular reference proteins (RefProts) with the 27 viral proteins. Re-interrogation of this data using 23 viral targets and including AltProts, followed by enrichment of the interaction networks, leads to identify 218 RefProts (in common to initial study), plus 56 AltProts involved in 93 interactions. This demonstrates the necessity to take into account the ghost proteome for discovering new therapeutic targets, and establish new therapeutic strategies. Missing the ghost proteome in the drug metabolism and pharmacokinetic (DMPK) drug development pipeline will certainly be a major limitation to the establishment of efficient therapies.
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Affiliation(s)
- Tristan Cardon
- Inserm U1192, University Lille, CHU Lille, Laboratory Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Isabelle Fournier
- Inserm U1192, University Lille, CHU Lille, Laboratory Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
- Institut Universitaire de France, 75000 Paris, France
| | - Michel Salzet
- Inserm U1192, University Lille, CHU Lille, Laboratory Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
- Institut Universitaire de France, 75000 Paris, France
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Osiurak F, Cretel C, Duhau-Marmon N, Fournier I, Marignier L, De Oliveira E, Navarro J, Reynaud E. The Pedagogue, the Engineer, and the Friend : From Whom Do We Learn? Hum Nat 2020; 31:462-482. [PMID: 33420606 DOI: 10.1007/s12110-020-09379-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/06/2020] [Indexed: 06/12/2023]
Abstract
Humans can follow different social learning strategies, sometimes oriented toward the models' characteristics (i.e., who-strategies). The goal of the present study was to explore which who-strategy is preferentially followed in the technological context based on the models' psychological characteristics. We identified three potential who-strategies: Copy the pedagogue (a model with high theory-of-mind skills), copy the engineer (a model with high technical-reasoning skills), and copy the friend (a model with high level of prosocialness). We developed a closed-group micro-society paradigm in which participants had to build the highest possible towers. Participants began with an individual building phase. Then, they were gathered to discuss the best solutions to increase tower height. After this discussion phase, they had to make a new building attempt, followed by another discussion phase, and so forth for a total of six building phases and five discussion rounds. This methodology allowed us to create an attraction score for each participant (the more an individual was copied in a group, the greater the attraction score). We also assessed participants' theory-of-mind skills, technical-reasoning skills, and prosocialness to predict participants' attraction scores based on these measures. Results show that we learn from engineers (high technical-reasoning skills) because they are the most successful. Their attraction power is not immediate, but after they have been identified as attractors, their technique is copied irrespective of their pedagogy (theory-of-mind skills) or friendliness (prosocialness). These findings open avenues for the study of the cognitive bases of human technological culture.
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Affiliation(s)
- François Osiurak
- Laboratoire d'Etude des Mécanismes Cognitifs, Université de Lyon, 5, avenue Pierre Mendès-France, 69676, Bron Cedex, France.
- Institut Universitaire de France, Paris, France.
| | - Caroline Cretel
- Laboratoire d'Etude des Mécanismes Cognitifs, Université de Lyon, 5, avenue Pierre Mendès-France, 69676, Bron Cedex, France
| | - Naomi Duhau-Marmon
- Laboratoire d'Etude des Mécanismes Cognitifs, Université de Lyon, 5, avenue Pierre Mendès-France, 69676, Bron Cedex, France
| | - Isabelle Fournier
- Laboratoire d'Etude des Mécanismes Cognitifs, Université de Lyon, 5, avenue Pierre Mendès-France, 69676, Bron Cedex, France
| | - Lucie Marignier
- Laboratoire d'Etude des Mécanismes Cognitifs, Université de Lyon, 5, avenue Pierre Mendès-France, 69676, Bron Cedex, France
| | - Emmanuel De Oliveira
- Laboratoire d'Etude des Mécanismes Cognitifs, Université de Lyon, 5, avenue Pierre Mendès-France, 69676, Bron Cedex, France
| | - Jordan Navarro
- Laboratoire d'Etude des Mécanismes Cognitifs, Université de Lyon, 5, avenue Pierre Mendès-France, 69676, Bron Cedex, France
- Institut Universitaire de France, Paris, France
| | - Emanuelle Reynaud
- Laboratoire d'Etude des Mécanismes Cognitifs, Université de Lyon, 5, avenue Pierre Mendès-France, 69676, Bron Cedex, France
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Beauvais D, Andrianne C, Aubrun C, Berquier M, Bole S, Caulier A, Courbon C, Delorme J, Fournier I, François G, Jaivenois MF, Le Bars L, Mussot I, Vercasson M, Wallart Brejaud A, Yakoub-Agha I, Lacroix D. Le parcours de soins du patient dans le cadre des CAR T-cell : recommandations de la Société francophone de greffe de moelle et de thérapie cellulaire (SFGM-TC). Bull Cancer 2020; 107:S170-S177. [DOI: 10.1016/j.bulcan.2020.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 11/28/2022]
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Cardon T, Fournier I, Salzet M. Shedding Light on the Ghost Proteome. Trends Biochem Sci 2020; 46:239-250. [PMID: 33246829 DOI: 10.1016/j.tibs.2020.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 01/19/2023]
Abstract
Conventionally, eukaryotic mRNAs were thought to be monocistronic, leading to the translation of a single protein. However, large-scale proteomics has led to the identification of proteins translated from alternative open reading frames (AltORFs) in mRNAs. AltORFs are found in addition to predicted reference ORFs and noncoding RNA. Alternative proteins are not represented in the conventional protein databases, and this 'Ghost proteome' was not considered until recently. Some of these proteins are functional, and there is growing evidence that they are involved in central functions in physiological and physiopathological contexts. Here, we review how this Ghost proteome fills the gap in our understanding of signaling pathways, establishes new markers of pathologies, and highlights therapeutic targets.
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Affiliation(s)
- Tristan Cardon
- Laboratoire Protéomique, Réponse Inflammatoire Spectrométrie de Masse (PRISM), Inserm U1192, University of Lille, CHU Lille, F-59000 Lille, France.
| | - Isabelle Fournier
- Laboratoire Protéomique, Réponse Inflammatoire Spectrométrie de Masse (PRISM), Inserm U1192, University of Lille, CHU Lille, F-59000 Lille, France; Institut Universitaire de France, Paris, France.
| | - Michel Salzet
- Laboratoire Protéomique, Réponse Inflammatoire Spectrométrie de Masse (PRISM), Inserm U1192, University of Lille, CHU Lille, F-59000 Lille, France; Institut Universitaire de France, Paris, France.
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43
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Cardon T, Ozcan B, Aboulouard S, Kobeissy F, Duhamel M, Rodet F, Fournier I, Salzet M. Epigenetic Studies Revealed a Ghost Proteome in PC1/3 KD Macrophages under Antitumoral Resistance Induced by IL-10. ACS Omega 2020; 5:27774-27782. [PMID: 33163760 PMCID: PMC7643081 DOI: 10.1021/acsomega.0c02530] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/18/2020] [Indexed: 06/11/2023]
Abstract
Our previous investigation on macrophages has allowed us to show that the inhibition of the enzyme proprotein convertase (PC1/3) controls the activation of macrophages. We demonstrated that PC1/3 knockdown (KD) in macrophages exhibits an increased secretion of proinflammatory and antitumoral factors. In this biological context, we assessed the presence of histone modifications and the presence and contribution of a "ghost proteome" in these macrophages. We identified a set of alternative proteins (AltProts) that have a key role in the regulation of various signaling pathways. In this study, to further investigate the underlying mechanisms involved in the resistance of PC1/3-KD macrophages to anti-inflammatory stimuli, we have conducted a proteomic system biology study to assess the epigenome variation, focusing on histone modifications. Results from our study have indicated the presence of significant variations in histone modifications along with the identification of 28 AltProts, which can be correlated with antitumoral resistance under IL-10 stimulation. These findings highlight a key role of altered epigenome histone modifications in driving resistance and indicate that like the reference proteins, AltProts can have a major impact in the field of epigenetics and regulation of gene expression, as shown in our results.
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Affiliation(s)
- Tristan Cardon
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Bilgehan Ozcan
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Soulaimane Aboulouard
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Firas Kobeissy
- Department
of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611, United States
| | - Marie Duhamel
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Franck Rodet
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Isabelle Fournier
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
- Institut
Universitaire de France, Paris 75000, France
| | - Michel Salzet
- Inserm,
CHRU Lille, University Lille, U-1192—Laboratoire Protéomique,
Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
- Institut
Universitaire de France, Paris 75000, France
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Vergara D, Verri T, Damato M, Trerotola M, Simeone P, Franck J, Fournier I, Salzet M, Maffia M. A Hidden Human Proteome Signature Characterizes the Epithelial Mesenchymal Transition Program. Curr Pharm Des 2020; 26:372-375. [PMID: 31995001 DOI: 10.2174/1381612826666200129091610] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 01/27/2020] [Indexed: 12/14/2022]
Abstract
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 models with a distinct expression of EMT markers. METHODS We profiled MCF-7 and MDA-MB-231 cells using liquid-chromatography mass/spectrometry (LCMS/ MS) and interrogated the OpenProt database to identify novel predicted isoforms and novel predicted proteins from alternative open reading frames (AltProts). RESULTS Our analysis revealed an AltProt and isoform protein signature capable of classifying the two breast cancer cell lines. Among the most highly expressed alternative proteins, we observed proteins potentially associated with inflammation, metabolism and EMT. CONCLUSION Here, we present an AltProts signature associated with EMT. Further studies will be needed to define their role in cancer progression.
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Affiliation(s)
- Daniele Vergara
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Tiziano Verri
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Marina Damato
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Marco Trerotola
- Department of Medical, Oral and Biotechnological Sciences, "G.d'Annunzio" University of Chieti-Pescara, Italy
| | - Pasquale Simeone
- Department of Medicine and Aging Sciences, "G.d'Annunzio" University of Chieti-Pescara, Italy; Laboratory of Cytomorphology, Center for Advanced Studies and Technology (CAST), "G.d'Annunzio" University of Chieti-Pescara, Italy
| | - Julien Franck
- University of Lille, Inserm, U-1192, Laboratoire Proteomique, Reponse Inflammatoire et Spectrometrie de Masse-PRISM, F-59000, Lille, France
| | - Isabelle Fournier
- University of Lille, Inserm, U-1192, Laboratoire Proteomique, Reponse Inflammatoire et Spectrometrie de Masse-PRISM, F-59000, Lille, France
| | - Michel Salzet
- University of Lille, Inserm, U-1192, Laboratoire Proteomique, Reponse Inflammatoire et Spectrometrie de Masse-PRISM, F-59000, Lille, France
| | - Michele Maffia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
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Cardon T, Franck J, Coyaud E, Laurent EMN, Damato M, Maffia M, Vergara D, Fournier I, Salzet M. Alternative proteins are functional regulators in cell reprogramming by PKA activation. Nucleic Acids Res 2020; 48:7864-7882. [PMID: 32324228 PMCID: PMC7641301 DOI: 10.1093/nar/gkaa277] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 08/09/2019] [Revised: 04/06/2020] [Accepted: 04/21/2020] [Indexed: 12/28/2022] Open
Abstract
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) still remain largely unknown. We have developed a large-scale and unsupervised approach based on cross-linking mass spectrometry (XL-MS) followed by shotgun proteomics to gather information on the functional role of AltProts by mapping them back into known signalling pathways through the identification of their reference protein (RefProt) interactors. We have identified and profiled AltProts in a cancer cell reprogramming system: NCH82 human glioma cells after 0, 16, 24 and 48 h Forskolin stimulation. Forskolin is a protein kinase A activator inducing cell differentiation and epithelial–mesenchymal transition. Our data show that AltMAP2, AltTRNAU1AP and AltEPHA5 interactions with tropomyosin 4 are downregulated under Forskolin treatment. In a wider perspective, Gene Ontology and pathway enrichment analysis (STRING) revealed that RefProts associated with AltProts are enriched in cellular mobility and transfer RNA regulation. This study strongly suggests novel roles of AltProts in multiple essential cellular functions and supports the importance of considering them in future biological studies.
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Affiliation(s)
- Tristan Cardon
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Julien Franck
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Etienne Coyaud
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Estelle M N Laurent
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France
| | - Marina Damato
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France.,Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Michele Maffia
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Daniele Vergara
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Isabelle Fournier
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France.,Institut Universitaire de France (IUF),75005 Paris, France
| | - Michel Salzet
- Univ. Lille, Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), F-59000 Lille, France.,Institut Universitaire de France (IUF),75005 Paris, France
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Hajjaji N, Abbouchi M, Nguyen LA, Charles S, Leclercq S, Bertin D, Robin YM, Fournier I, Salzet M. A novel proteomic mass spectrometry-based approach to reveal functionally heterogeneous tumor clones in breast cancer metastases and identify clone-specific drug targets. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e13063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e13063 Background: Breast cancer mortality is expected to rise by almost 30% by 2030 worldwide, mainly due to the occurrence of distant metastases. The development of drugs specifically targeted at tumor drivers has not yet curbed resistance to treatment, which prevents metastases curability. There is a need for new molecular approaches to tackle metastases complex biology, particularly tumor heterogeneity, a main determinant of resistance. The aim of this study was to use a proteomic mass spectrometry-based approach to reveal functionally heterogeneous’ tumor subpopulations in breast cancer metastases, and identify clone specific drug targets. Methods: Metastasis biopsies (n = 21) were collected retrospectively from patients with advanced breast cancer treated at Oscar Lambret Cancer Center (Lille, France). Tumor heterogeneity was analyzed directly on FFPE tissue sections using MALDI mass spectrometry imaging (MSI) on a RapifleX Tissuetyper. Unsupervised spatial segmentation was performed to reveal tumor subpopulations with distinct proteomic profiles within each metastasis. The full proteomic characterization of these tumor clones was further performed with spatially resolved proteomic mass spectrometry. Results: MSI revealed that breast cancer metastases contained 2 to 5 functionally distinct tumor clones (proteomic clones). Although the clone profiles within a metastasis were correlated, unsupervised hierarchical clustering showed a clear distinction between them and specific proteomic signatures. Enrichment analysis showed that differentially expressed proteins were involved in a variety of biological processes or pathways including regulation of histone acetylation, extracellular matrix degradation, DNA repair, NOTCH pathway, estrogen-responsive target genes or exocytosis. The evolution of the proteomic clones profile during disease progression was also determined by comparison of paired biopsies. To identify the candidate treatments best fitted to metastasis heterogeneity, the specific proteomic signatures of the clones were matched against a druggable genome database. It was possible to unveil candidate drug targets personalized to each metastasis functional clone. Conclusions: MALDI mass spectrometry imaging combined with spatially resolved proteomics has the potential to tackle breast cancer metastases heterogeneity, and identify candidate drug targets specific to functional clones to personalize treatments.
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Affiliation(s)
| | - Mira Abbouchi
- PRISM Laboratory Inserm U1192 University of Lille, Lille, France
| | | | - Samuel Charles
- PRISM Laboratory Inserm U1192 University of Lille, Lille, France
| | - Sarah Leclercq
- PRISM Laboratory Inserm U1192 University of Lille, Lille, France
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Brunet MA, Brunelle M, Lucier JF, Delcourt V, Levesque M, Grenier F, Samandi S, Leblanc S, Aguilar JD, Dufour P, Jacques JF, Fournier I, Ouangraoua A, Scott MS, Boisvert FM, Roucou X. OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes. Nucleic Acids Res 2020; 47:D403-D410. [PMID: 30299502 PMCID: PMC6323990 DOI: 10.1093/nar/gky936] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [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: 07/19/2018] [Accepted: 10/04/2018] [Indexed: 01/06/2023] Open
Abstract
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 a substantial underestimation of the coding potential of eukaryotes. Here, we present OpenProt, the first database fully endorsing a polycistronic model of eukaryotic genomes to date. OpenProt contains all possible ORFs longer than 30 codons across 10 species, and cumulates supporting evidence such as protein conservation, translation and expression. OpenProt annotates all known proteins (RefProts), novel predicted isoforms (Isoforms) and novel predicted proteins from alternative ORFs (AltProts). It incorporates cutting-edge algorithms to evaluate protein orthology and re-interrogate publicly available ribosome profiling and mass spectrometry datasets, supporting the annotation of thousands of predicted ORFs. The constantly growing database currently cumulates evidence from 87 ribosome profiling and 114 mass spectrometry studies from several species, tissues and cell lines. All data is freely available and downloadable from a web platform (www.openprot.org) supporting a genome browser and advanced queries for each species. Thus, OpenProt enables a more comprehensive landscape of eukaryotic genomes’ coding potential.
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Affiliation(s)
- Marie A Brunet
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec, Canada.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université de Lille, F-59000 Lille, France
| | - Mylène Brunelle
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec, Canada.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université de Lille, F-59000 Lille, France
| | - Jean-François Lucier
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, Québec, Canada.,Biology Department, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Vivian Delcourt
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec, Canada.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université de Lille, F-59000 Lille, France.,INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
| | - Maxime Levesque
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, Québec, Canada.,Biology Department, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Frédéric Grenier
- Center for Computational Science, Université de Sherbrooke, Sherbrooke, Québec, Canada.,Biology Department, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Sondos Samandi
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec, Canada.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université de Lille, F-59000 Lille, France
| | - Sébastien Leblanc
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-David Aguilar
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Pascal Dufour
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jean-Francois Jacques
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec, Canada.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université de Lille, F-59000 Lille, France
| | - Isabelle Fournier
- INSERM U1192, Laboratoire Protéomique, Réponse Inflammatoire & Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
| | - Aida Ouangraoua
- Informatics Department, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Michelle S Scott
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Xavier Roucou
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, Québec, Canada.,PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Université de Lille, F-59000 Lille, France
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Murgoci AN, Cardon T, Aboulouard S, Duhamel M, Fournier I, Cizkova D, Salzet M. Reference and Ghost Proteins Identification in Rat C6 Glioma Extracellular Vesicles. iScience 2020; 23:101045. [PMID: 32334413 PMCID: PMC7182720 DOI: 10.1016/j.isci.2020.101045] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/23/2020] [Accepted: 04/03/2020] [Indexed: 01/08/2023] Open
Abstract
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 of EVs pellets, followed by Amicon filtration. After these steps, all the fractions have been subjected to proteomic analyses. Comparison between 6 h Trypsin/Lys C treatment or non-treated EVs revealed a quantitative variation of the surface proteins. Some surface proteins have been demasked after 6 h enzymatic digestion like CD81, CD82, Ust, Vcan, Lamp 1, Rab43, Annexin A2, Synthenin, and VSP37b. Moreover, six ghost proteins have also been identified and one corresponds to a long noncoding RNA. We thus demonstrate the presence of ghost proteins in EVs produced by glioma cells that can contribute to tumorigenesis. Glioma C6 extracellular vesicle protein mapping Quick steps protocols to map outer/inner membrane EV membrane proteins C6 glioma cell line EVs contain ghost proteins
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Affiliation(s)
- Adriana-Natalia Murgoci
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava 84510, Slovakia
| | - Tristan Cardon
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Soulaimane Aboulouard
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Marie Duhamel
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Isabelle Fournier
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France
| | - Dasa Cizkova
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava 84510, Slovakia; Department of Anatomy, Histology and Physiology, University of Veterinary Medicine and Pharmacy in Košice, Košice 04181, Slovakia.
| | - Michel Salzet
- Univ. Lille, Inserm, U-1192 - Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse-PRISM, Lille 59000, France.
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Rose M, Duhamel M, Aboulouard S, Kobeissy F, Le Rhun E, Desmons A, Tierny D, Fournier I, Rodet F, Salzet M. The Role of a Proprotein Convertase Inhibitor in Reactivation of Tumor-Associated Macrophages and Inhibition of Glioma Growth. Mol Ther Oncolytics 2020; 17:31-46. [PMID: 32300641 PMCID: PMC7152595 DOI: 10.1016/j.omto.2020.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/20/2020] [Indexed: 02/07/2023]
Abstract
Tumors are characterized by the presence of malignant and non-malignant cells, such as immune cells including macrophages, which are preponderant. Macrophages impact the efficacy of chemotherapy and may lead to drug resistance. In this context and based on our previous work, we investigated the ability to reactivate macrophages by using a proprotein convertases inhibitor. Proprotein convertases process immature proteins into functional proteins, with several of them having a role in immune cell activation and tumorigenesis. Macrophages were treated with a peptidomimetic inhibitor targeting furin, PC1/3, PC4, PACE4, and PC5/6. Their anti-glioma activity was analyzed by mass spectrometry-based proteomics and viability assays in 2D and 3D in vitro cultures. Comparison with temozolomide, the drug used for glioma therapy, established that the inhibitor was more efficient for the reduction of cancer cell density. The inhibitor was also able to reactivate macrophages through the secretion of several immune factors with antitumor properties. Moreover, two proteins considered as good glioma patient survival indicators were also identified in 3D cultures treated with the inhibitor. Finally, we established that the proprotein convertases inhibitor has a dual role as an anti-glioma drug and anti-tumoral macrophage reactivation drug. This strategy could be used together with chemotherapy to increase therapy efficacy in glioma.
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Affiliation(s)
- Mélanie Rose
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France.,Oncovet Clinical Research (OCR), SIRIC ONCOLille, 59650 Villeneuve d'Ascq, France
| | - Marie Duhamel
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France
| | - Soulaimane Aboulouard
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France
| | - Firas Kobeissy
- Department of Psychiatry, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Emilie Le Rhun
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France
| | - Annie Desmons
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France
| | - Dominique Tierny
- Oncovet Clinical Research (OCR), SIRIC ONCOLille, 59650 Villeneuve d'Ascq, France
| | - Isabelle Fournier
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France
| | - Franck Rodet
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France
| | - Michel Salzet
- Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), INSERM U1192, Université de Lille, 59000 Lille, France
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