1
|
Serra-Bardenys G, Blanco E, Escudero-Iriarte C, Serra-Camprubí Q, Querol J, Pascual-Reguant L, Morancho B, Escorihuela M, Tissera NS, Sabé A, Martín L, Segura-Bayona S, Verde G, Aiese Cigliano R, Millanes-Romero A, Jerónimo C, Cebrià-Costa JP, Nuciforo P, Simonetti S, Viaplana C, Dienstmann R, Oliveira M, Peg V, Stracker TH, Arribas J, Canals F, Villanueva J, Di Croce L, García de Herreros A, Tian TV, Peiró S. LOXL2-mediated chromatin compaction is required to maintain the oncogenic properties of triple-negative breast cancer cells. FEBS J 2024. [PMID: 38451841 DOI: 10.1111/febs.17112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 01/02/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Oxidation of histone H3 at lysine 4 (H3K4ox) is catalyzed by lysyl oxidase homolog 2 (LOXL2). This histone modification is enriched in heterochromatin in triple-negative breast cancer (TNBC) cells and has been linked to the maintenance of compacted chromatin. However, the molecular mechanism underlying this maintenance is still unknown. Here, we show that LOXL2 interacts with RuvB-Like 1 (RUVBL1), RuvB-Like 2 (RUVBL2), Actin-like protein 6A (ACTL6A), and DNA methyltransferase 1associated protein 1 (DMAP1), a complex involved in the incorporation of the histone variant H2A.Z. Our experiments indicate that this interaction and the active form of RUVBL2 are required to maintain LOXL2-dependent chromatin compaction. Genome-wide experiments showed that H2A.Z, RUVBL2, and H3K4ox colocalize in heterochromatin regions. In the absence of LOXL2 or RUVBL2, global levels of the heterochromatin histone mark H3K9me3 were strongly reduced, and the ATAC-seq signal in the H3K9me3 regions was increased. Finally, we observed that the interplay between these series of events is required to maintain H3K4ox-enriched heterochromatin regions, which in turn is key for maintaining the oncogenic properties of the TNBC cell line tested (MDA-MB-231).
Collapse
Affiliation(s)
- Gemma Serra-Bardenys
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Institut Bonanova FP Sanitaria, Consorci Mar Parc de Salut de Barcelona, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
| | | | | | - Jessica Querol
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Laura Pascual-Reguant
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
| | | | | | | | - Anna Sabé
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Luna Martín
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Gaetano Verde
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Alba Millanes-Romero
- Institute for Research in Biomedicine (IRB Barcelona) and Barcelona Institute of Science and Technology, Spain
| | - Celia Jerónimo
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
- Institut de Recherches Cliniques de Montréal, Canada
| | | | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sara Simonetti
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | | | - Mafalda Oliveira
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Vicente Peg
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), Barcelona, Spain
- Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Travis H Stracker
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD, USA
| | - Joaquín Arribas
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Francesc Canals
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | | | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Antonio García de Herreros
- Programa de Recerca en Càncer, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
- Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
| | - Tian V Tian
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Sandra Peiró
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| |
Collapse
|
2
|
Pujals M, Mayans C, Bellio C, Méndez O, Greco E, Fasani R, Alemany-Chavarria M, Zamora E, Padilla L, Mitjans F, Nuciforo P, Canals F, Nonell L, Abad M, Saura C, Tabernero J, Villanueva J. RAGE/SNAIL1 signaling drives epithelial-mesenchymal plasticity in metastatic triple-negative breast cancer. Oncogene 2023; 42:2610-2628. [PMID: 37468678 DOI: 10.1038/s41388-023-02778-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/29/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023]
Abstract
Epithelial/Mesenchymal (E/M) plasticity plays a fundamental role both in embryogenesis and during tumorigenesis. The receptor for advanced glycation end products (RAGE) is a driver of cell plasticity in fibrotic diseases; however, its role and molecular mechanism in triple-negative breast cancer (TNBC) remains unclear. Here, we demonstrate that RAGE signaling maintains the mesenchymal phenotype of aggressive TNBC cells by enforcing the expression of SNAIL1. Besides, we uncover a crosstalk mechanism between the TGF-β and RAGE pathways that is required for the acquisition of mesenchymal traits in TNBC cells. Consistently, RAGE inhibition elicits epithelial features that block migration and invasion capacities. Next, since RAGE is a sensor of the tumor microenvironment, we modeled acute acidosis in TNBC cells and showed it promotes enhanced production of RAGE ligands and the activation of RAGE-dependent invasive properties. Furthermore, acute acidosis increases SNAIL1 levels and tumor cell invasion in a RAGE-dependent manner. Finally, we demonstrate that in vivo inhibition of RAGE reduces metastasis incidence and expands survival, consistent with molecular effects that support the relevance of RAGE signaling in E/M plasticity. These results uncover new molecular insights on the regulation of E/M phenotypes in cancer metastasis and provide rationale for pharmacological intervention of this signaling axis.
Collapse
Affiliation(s)
- Mireia Pujals
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carla Mayans
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Chiara Bellio
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Olga Méndez
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Emanuela Greco
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Roberta Fasani
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Mercè Alemany-Chavarria
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Esther Zamora
- Medical Oncology Service, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Laura Padilla
- LEITAT Technological Center, 08028, Barcelona, Spain
| | | | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Francesc Canals
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Lara Nonell
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - María Abad
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Altos Labs Cambridge Institute of Science, Cambridge, UK
| | - Cristina Saura
- Medical Oncology Service, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Josep Tabernero
- Medical Oncology Service, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- IOB Institute of Oncology, Quiron Group (Quiron-IOB), Barcelona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Josep Villanueva
- Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
3
|
Lozano-Rabella M, Garcia-Garijo A, Palomero J, Yuste-Estevanez A, Erhard F, Farriol-Duran R, Martín-Liberal J, Ochoa-de-Olza M, Matos I, Gartner JJ, Ghosh M, Canals F, Vidal A, Piulats JM, Matías-Guiu X, Brana I, Muñoz-Couselo E, Garralda E, Schlosser A, Gros A. Exploring the Immunogenicity of Noncanonical HLA-I Tumor Ligands Identified through Proteogenomics. Clin Cancer Res 2023; 29:2250-2265. [PMID: 36749875 PMCID: PMC10261919 DOI: 10.1158/1078-0432.ccr-22-3298] [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: 10/24/2022] [Revised: 12/20/2022] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
PURPOSE Tumor antigens are central to antitumor immunity. Recent evidence suggests that peptides from noncanonical (nonC) aberrantly translated proteins can be presented on HLA-I by tumor cells. Here, we investigated the immunogenicity of nonC tumor HLA-I ligands (nonC-TL) to better understand their contribution to cancer immunosurveillance and their therapeutic applicability. EXPERIMENTAL DESIGN Peptides presented on HLA-I were identified in 9 patient-derived tumor cell lines from melanoma, gynecologic, and head and neck cancer through proteogenomics. A total of 507 candidate tumor antigens, including nonC-TL, neoantigens, cancer-germline, or melanocyte differentiation antigens, were tested for T-cell recognition of preexisting responses in patients with cancer. Donor peripheral blood lymphocytes (PBL) were in vitro sensitized against 170 selected nonC-TL to isolate antigen-specific T-cell receptors (TCR) and evaluate their therapeutic potential. RESULTS We found no recognition of the 507 nonC-TL tested by autologous ex vivo expanded tumor-reactive T-cell cultures while the same cultures demonstrated reactivity to mutated, cancer-germline, or melanocyte differentiation antigens. However, in vitro sensitization of donor PBL against 170 selected nonC-TL, led to the identification of TCRs specific to three nonC-TL, two of which mapped to the 5' UTR regions of HOXC13 and ZKSCAN1, and one mapping to a noncoding spliced variant of C5orf22C. T cells targeting these nonC-TL recognized cancer cell lines naturally presenting their corresponding antigens. Expression of the three immunogenic nonC-TL was shared across tumor types and barely or not detected in normal cells. CONCLUSIONS Our findings predict a limited contribution of nonC-TL to cancer immunosurveillance but demonstrate they may be attractive novel targets for widely applicable immunotherapies. See related commentary by Fox et al., p. 2173.
Collapse
Affiliation(s)
- Maria Lozano-Rabella
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Andrea Garcia-Garijo
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Jara Palomero
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Anna Yuste-Estevanez
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Roc Farriol-Duran
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Juan Martín-Liberal
- Early Drug Development Unit (UITM) Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - Maria Ochoa-de-Olza
- Early Drug Development Unit (UITM) Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - Ignacio Matos
- Early Drug Development Unit (UITM) Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - Jared J. Gartner
- Surgery Branch, National Cancer Institute (NCI), National Institutes of Health, Bethesda, Maryland
| | - Michael Ghosh
- Institute for Cell Biology Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Francesc Canals
- Proteomics, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - August Vidal
- Department of Pathology. Hospital Universitari de Bellvitge-IDIBELL, CIBERONC, Barcelona, Spain
| | - Josep Maria Piulats
- Medical Oncology, Catalan Institute of Cancer (ICO), IDIBELL-Oncobell, Hospitalet de Llobregat, Spain
| | - Xavier Matías-Guiu
- Department of Pathology. Hospital Universitari de Bellvitge-IDIBELL, CIBERONC, Barcelona, Spain
| | - Irene Brana
- Early Drug Development Unit (UITM) Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - Eva Muñoz-Couselo
- Melanoma and other skin tumors unit, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - Elena Garralda
- Early Drug Development Unit (UITM) Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital, Barcelona, Spain
| | - Andreas Schlosser
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Alena Gros
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| |
Collapse
|
4
|
McGrail K, Granado-Martínez P, Esteve-Puig R, García-Ortega S, Ding Y, Sánchez-Redondo S, Ferrer B, Hernandez-Losa J, Canals F, Manzano A, Navarro-Sabaté A, Bartrons R, Yanes O, Pérez-Alea M, Muñoz-Couselo E, Garcia-Patos V, Recio JA. BRAF activation by metabolic stress promotes glycolysis sensitizing NRAS Q61-mutated melanomas to targeted therapy. Nat Commun 2022; 13:7113. [PMID: 36402789 PMCID: PMC9675737 DOI: 10.1038/s41467-022-34907-0] [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: 09/11/2021] [Accepted: 11/08/2022] [Indexed: 11/21/2022] Open
Abstract
NRAS-mutated melanoma lacks a specific line of treatment. Metabolic reprogramming is considered a novel target to control cancer; however, NRAS-oncogene contribution to this cancer hallmark is mostly unknown. Here, we show that NRASQ61-mutated melanomas specific metabolic settings mediate cell sensitivity to sorafenib upon metabolic stress. Mechanistically, these cells are dependent on glucose metabolism, in which glucose deprivation promotes a switch from CRAF to BRAF signaling. This scenario contributes to cell survival and sustains glucose metabolism through BRAF-mediated phosphorylation of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-2/3 (PFKFB2/PFKFB3). In turn, this favors the allosteric activation of phosphofructokinase-1 (PFK1), generating a feedback loop that couples glycolytic flux and the RAS signaling pathway. An in vivo treatment of NRASQ61 mutant melanomas, including patient-derived xenografts, with 2-deoxy-D-glucose (2-DG) and sorafenib effectively inhibits tumor growth. Thus, we provide evidence for NRAS-oncogene contributions to metabolic rewiring and a proof-of-principle for the treatment of NRASQ61-mutated melanoma combining metabolic stress (glycolysis inhibitors) and previously approved drugs, such as sorafenib.
Collapse
Affiliation(s)
- Kimberley McGrail
- grid.430994.30000 0004 1763 0287Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Vall d’Hebron Research Institute (VHIR), Vall d’Hebron Hospital Barcelona-UAB, Barcelona, 08035 Spain
| | - Paula Granado-Martínez
- grid.430994.30000 0004 1763 0287Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Vall d’Hebron Research Institute (VHIR), Vall d’Hebron Hospital Barcelona-UAB, Barcelona, 08035 Spain
| | - Rosaura Esteve-Puig
- grid.430994.30000 0004 1763 0287Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Vall d’Hebron Research Institute (VHIR), Vall d’Hebron Hospital Barcelona-UAB, Barcelona, 08035 Spain ,Present Address: MAJ3 Capital S.L, Barcelona, 08018 Spain
| | - Sara García-Ortega
- grid.430994.30000 0004 1763 0287Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Vall d’Hebron Research Institute (VHIR), Vall d’Hebron Hospital Barcelona-UAB, Barcelona, 08035 Spain
| | - Yuxin Ding
- grid.430994.30000 0004 1763 0287Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Vall d’Hebron Research Institute (VHIR), Vall d’Hebron Hospital Barcelona-UAB, Barcelona, 08035 Spain
| | - Sara Sánchez-Redondo
- grid.430994.30000 0004 1763 0287Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Vall d’Hebron Research Institute (VHIR), Vall d’Hebron Hospital Barcelona-UAB, Barcelona, 08035 Spain ,grid.7719.80000 0000 8700 1153Present Address: Microenvironment & Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Berta Ferrer
- grid.430994.30000 0004 1763 0287Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Vall d’Hebron Research Institute (VHIR), Vall d’Hebron Hospital Barcelona-UAB, Barcelona, 08035 Spain ,grid.411083.f0000 0001 0675 8654Anatomy Pathology Department, Vall d’Hebron Hospital Barcelona-UAB, Barcelona, 08035 Spain
| | - Javier Hernandez-Losa
- grid.411083.f0000 0001 0675 8654Anatomy Pathology Department, Vall d’Hebron Hospital Barcelona-UAB, Barcelona, 08035 Spain
| | - Francesc Canals
- grid.411083.f0000 0001 0675 8654Proteomics Laboratory, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, 08035 Spain
| | - Anna Manzano
- grid.418284.30000 0004 0427 2257Department of Physiological Sciences, University of Barcelona, Bellvitge Biomedical Research Institute, Barcelona, Spain
| | - Aura Navarro-Sabaté
- grid.418284.30000 0004 0427 2257Department of Physiological Sciences, University of Barcelona, Bellvitge Biomedical Research Institute, Barcelona, Spain
| | - Ramón Bartrons
- grid.418284.30000 0004 0427 2257Department of Physiological Sciences, University of Barcelona, Bellvitge Biomedical Research Institute, Barcelona, Spain
| | - Oscar Yanes
- grid.410367.70000 0001 2284 9230Universitat Rovira i Virgili, Department of Electronic Engineering, IISPV, Tarragona, Spain ,grid.413448.e0000 0000 9314 1427CIBER on Diabetes and Associated Metabolic Diseases (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Mileidys Pérez-Alea
- grid.430994.30000 0004 1763 0287Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Vall d’Hebron Research Institute (VHIR), Vall d’Hebron Hospital Barcelona-UAB, Barcelona, 08035 Spain ,Present Address: Advance Biodesign, 69800 Saint-Priest, France
| | - Eva Muñoz-Couselo
- grid.430994.30000 0004 1763 0287Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Vall d’Hebron Research Institute (VHIR), Vall d’Hebron Hospital Barcelona-UAB, Barcelona, 08035 Spain ,grid.411083.f0000 0001 0675 8654Clinical Oncology Program, Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron Hospital Barcelona-UAB, Barcelona, 08035 Spain
| | - Vicenç Garcia-Patos
- grid.430994.30000 0004 1763 0287Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Vall d’Hebron Research Institute (VHIR), Vall d’Hebron Hospital Barcelona-UAB, Barcelona, 08035 Spain ,grid.411083.f0000 0001 0675 8654Dermatology Department, Vall d’Hebron Hospital Barcelona-UAB, Barcelona, 08035 Spain
| | - Juan A. Recio
- grid.430994.30000 0004 1763 0287Biomedical Research in Melanoma-Animal Models and Cancer Laboratory, Vall d’Hebron Research Institute (VHIR), Vall d’Hebron Hospital Barcelona-UAB, Barcelona, 08035 Spain
| |
Collapse
|
5
|
Barbero F, Michelini S, Moriones OH, Patarroyo J, Rosell J, F. Gusta M, Vitali M, Martín L, Canals F, Duschl A, Horejs-Hoeck J, Mondragón L, Bastús NG, Puntes V. Role of Common Cell Culture Media Supplements on Citrate-Stabilized Gold Nanoparticle Protein Corona Formation, Aggregation State, and the Consequent Impact on Cellular Uptake. Bioconjug Chem 2022; 33:1505-1514. [DOI: 10.1021/acs.bioconjchem.2c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Francesco Barbero
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- Universitat Autònoma de Barcelona (UAB), Campus
UAB, Bellaterra, 08193 Barcelona, Spain
| | - Sara Michelini
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Oscar H. Moriones
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- Universitat Autònoma de Barcelona (UAB), Campus
UAB, Bellaterra, 08193 Barcelona, Spain
| | - Javier Patarroyo
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Jordi Rosell
- Vall d’Hebron Institut de Recerca (VHIR), 08035 Barcelona, Spain
| | - Muriel F. Gusta
- Vall d’Hebron Institut de Recerca (VHIR), 08035 Barcelona, Spain
| | - Michele Vitali
- Vall d’Hebron Institut de Recerca (VHIR), 08035 Barcelona, Spain
| | - Luna Martín
- Proteomics Laboratory, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Francesc Canals
- Proteomics Laboratory, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Albert Duschl
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Jutta Horejs-Hoeck
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Laura Mondragón
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- Vall d’Hebron Institut de Recerca (VHIR), 08035 Barcelona, Spain
| | - Neus G. Bastús
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Víctor Puntes
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- Universitat Autònoma de Barcelona (UAB), Campus
UAB, Bellaterra, 08193 Barcelona, Spain
- Vall d’Hebron Institut de Recerca (VHIR), 08035 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), P. Lluís Companys 23, 08010 Barcelona, Spain
| |
Collapse
|
6
|
Colomé N, Abian J, Aloria K, Arizmendi JM, Barceló-Batllori S, Braga-Lagache S, Burlet-Schiltz O, Carrascal M, Casal JI, Chicano-Gálvez E, Chiva C, Clemente LF, Elortza F, Estanyol JM, Fernandez-Irigoyen J, Fernández-Puente P, Fidalgo MJ, Froment C, Fuentes M, Fuentes-Almagro C, Gay M, Hainard A, Heller M, Hernández ML, Ibarrola N, Iloro I, Kieselbach T, Lario A, Locard-Paulet M, Marina-Ramírez A, Martín L, Morato-López E, Muñoz J, Navajas R, Odena MA, Odriozola L, de Oliveira E, Paradela A, Pasquarello C, de Los Rios V, Ruiz-Romero C, Sabidó E, Sánchez Del Pino M, Sancho J, Santamaría E, Schaeffer-Reiss C, Schneider J, de la Torre C, Valero ML, Vilaseca M, Wu S, Wu L, Ximénez de Embún P, Canals F, Corrales FJ. Multi-laboratory experiment PME11 for the standardization of phosphoproteome analysis. J Proteomics 2022; 251:104409. [PMID: 34758407 DOI: 10.1016/j.jprot.2021.104409] [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: 10/01/2021] [Revised: 10/12/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022]
Abstract
Global analysis of protein phosphorylation by mass spectrometry proteomic techniques has emerged in the last decades as a powerful tool in biological and biomedical research. However, there are several factors that make the global study of the phosphoproteome more challenging than measuring non-modified proteins. The low stoichiometry of the phosphorylated species and the need to retrieve residue specific information require particular attention on sample preparation, data acquisition and processing to ensure reproducibility, qualitative and quantitative robustness and ample phosphoproteome coverage in phosphoproteomic workflows. Aiming to investigate the effect of different variables in the performance of proteome wide phosphoprotein analysis protocols, ProteoRed-ISCIII and EuPA launched the Proteomics Multicentric Experiment 11 (PME11). A reference sample consisting of a yeast protein extract spiked in with different amounts of a phosphomix standard (Sigma/Merck) was distributed to 31 laboratories around the globe. Thirty-six datasets from 23 laboratories were analyzed. Our results indicate the suitability of the PME11 reference sample to benchmark and optimize phosphoproteomics strategies, weighing the influence of different factors, as well as to rank intra and inter laboratory performance.
Collapse
Affiliation(s)
- Núria Colomé
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | - Joaquín Abian
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, 08036 Barcelona, Spain
| | - Kerman Aloria
- ProteoRed-ISCIII, Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jesús M Arizmendi
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | | | - Sophie Braga-Lagache
- Department for BioMedical Research (DBMR), Proteomics and Mass Spectrometry Core Facility, University of Bern, CH-3010 Bern, Switzerland
| | - Odile Burlet-Schiltz
- Proteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | - Montse Carrascal
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, 08036 Barcelona, Spain
| | - J Ignacio Casal
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Eduard Chicano-Gálvez
- ProteoRed-ISCIII, Proteomics Unit, IMIBIC/UCO/HURS, IMIBIC Building Fl.3, 14004 Córdoba, Spain
| | - Cristina Chiva
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; ProteoRed ISCIII, Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Felix Elortza
- ProteoRed-ISCIII, CIC bioGUNE, Proteomics Platform, Basque Research & Technology Alliance (BRTA), CIBERehd,Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Josep M Estanyol
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, 08036 Barcelona, Spain
| | - Joaquín Fernandez-Irigoyen
- Proteored-ISCIII. Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain
| | - Patricia Fernández-Puente
- Grupo de Investigación de Reumatología (GIR), Agrupación CICA-INIBIC, Universidad de A Coruña, A Coruña, Spain
| | - María José Fidalgo
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, 08036 Barcelona, Spain
| | - Carine Froment
- Proteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Proteomics Unit, CIBERONC, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca, Spain
| | - Carlos Fuentes-Almagro
- Proteomics Unit, SCAI, University of Córdoba, Ramón y Cajal Building, Rabanales Campus, 14071, Córdoba, Spain
| | - Marina Gay
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), BIST (The Barcelona Institute of Science and Technology), Baldiri i Reixac 10, 08028 Barcelona, Spain
| | | | - Manfred Heller
- Department for BioMedical Research (DBMR), Proteomics and Mass Spectrometry Core Facility, University of Bern, CH-3010 Bern, Switzerland
| | | | - Nieves Ibarrola
- ProteoRed-ISCIII, Proteomics Unit. Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Universidad de Salamanca-CSIC, Salamanca, Spain
| | - Ibon Iloro
- ProteoRed-ISCIII, CIC bioGUNE, Proteomics Platform, Basque Research & Technology Alliance (BRTA), CIBERehd,Bizkaia Science and Technology Park, 48160 Derio, Spain
| | | | | | - Marie Locard-Paulet
- Proteomics and Mass Spectrometry of Biomolecules, Proteomics Infrastructure of Toulouse, Proteomics French Infrastructure, ProFI. Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, UPS, CNRS, Toulouse, France
| | | | - Luna Martín
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | | | - Javier Muñoz
- ProteoRed-ISCIII, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Rosana Navajas
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain
| | - M Antonia Odena
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, 08028, Barcelona, Spain
| | - Leticia Odriozola
- ProteoRed-ISCIII, CIMA, University of Navarra, 31008, Pamplona, Spain
| | - Eliandre de Oliveira
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, 08028, Barcelona, Spain
| | - Alberto Paradela
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain
| | | | - Vivian de Los Rios
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Cristina Ruiz-Romero
- Grupo de Investigación de Reumatología (GIR) - ProteoRed-ISCIII, Unidad de Proteómica, INIBIC-Complejo Hospitalario Universitario de A Coruña, SERGAS, A Coruña, Spain
| | - Eduard Sabidó
- Proteomics Unit, Center for Genomics Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; ProteoRed ISCIII, Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Manuel Sánchez Del Pino
- Biotechnology and Biomedicine Interdisciplinary Research Unit (ERI BIOTECMED), University of Valencia, 46100 Burjassot, Spain
| | - Jaime Sancho
- ProteoRed-ISCIII, IPBLN -CSIC, 18016 Granada, Spain
| | - Enrique Santamaría
- Proteored-ISCIII. Proteomics Unit, Clinical Neuroproteomics Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, 31008 Pamplona, Spain
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
| | - Justine Schneider
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France
| | - Carolina de la Torre
- ProteoRed-ISCIII, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - M Luz Valero
- ProteoRed-ISCIII, Proteomics Unit, Central Service for Experimental Research (SCSIE), University of Valencia, 46100, Burjassot, Spain
| | - Marta Vilaseca
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), BIST (The Barcelona Institute of Science and Technology), Baldiri i Reixac 10, 08028 Barcelona, Spain
| | - Shuai Wu
- Agilent Technologies, Inc., Santa Clara, CA 95051, USA
| | - Linfeng Wu
- Agilent Technologies, Inc., Santa Clara, CA 95051, USA
| | | | - Francesc Canals
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain.
| | - Fernando J Corrales
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain; ProteoRed-ISCIII, CIMA, University of Navarra, 31008, Pamplona, Spain.
| | -
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain; ProteoRed-ISCIII-PRB3, Spanish Proteomics Networked Platform, Centro Nacional de Biotecnología (CSIC), 28049, Madrid, Spain
| | -
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), 28049, Madrid, Spain; European Proteomics Association, Standardization Initiative, , Centro Nacional de Biotecnología (CSIC), 28049, Madrid, Spain
| |
Collapse
|
7
|
Lozano-Rabella M, Garcia-Garijo A, Palomero J, Erhard F, Martín-Liberal J, Matos I, Gartner J, Rosenberg S, Ghosh M, Canals F, Vidal A, Piulats JM, Matias-Guiu X, Braña I, Muñoz E, Garralda E, Schlosser A, Gros A. 912 Preferential recognition of neoantigens over non-canonical peptides in cancer patients. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BackgroundDespite recent advances in exome and RNA sequencing to identify tumor-rejection antigens including neoantigens, the existing techniques fail to identify the vast majority of antigens targeted by tumor-reactive cells. A growing number of studies suggest that HLA-I peptides derived from non-canonical (nonC) open reading frames or derived from allegedly non-coding regions can contribute to tumor immunogenicity. Here we use proteogenomics to identify personalized candidate canonical and non-canonical tumor-rejection antigens and to evaluate their contribution to cancer immune surveillance in patients.MethodsWhole exome sequencing was performed to identify the non-synonymous somatic mutations (NSM) and immunopeptidomics to identify the HLA-I presented peptides (pHLA) in 9 patient-derived tumor cell lines (TCL). Peptid-PRISM proteogenomics pipeline was used to identify both canonical and non-canonical pHLA, including those derived from NSM in coding regions. All peptides containing mutations and derived from either cancer-testis (CTA) or tumor-associated antigens (TAA) were selected as candidate tumor antigens. For nonC peptides, an immunopeptidomics healthy dataset containing several tissues and HLA-allotypes was used to eliminate those derived from normal ORFs and select nonC peptides preferentially expressed in tumor cells (nonC-TE). The selected candidate peptides were synthesized, pulsed onto autologous APCs and co-cultured with tumor-reactive ex vivo expanded lymphocytes to assess immune recognition (figure 1).ResultsNonC-TE peptides were identified in all TCL studied, ranging from 0.5% to 5.4% of the total HLA-I presented peptides (n= 506). As described previoulsy, 5’UTR were the main source. Of note, the tumor type did not have an impact on the frequency of presented nonC peptides, but rather the presence of HLA-A*11:01 and HLA-A*03:01 was a major determinant. T cell responses were detected against at least 13/33 putative neoantigens, 2/24 CTA and 2/61 TAA. On the contrary, none of the 471 nonC-TE candidate peptides tested thus far, including one containing a NSM were able to elicit a recall immune response. Nevertheless, T cells recognizing at least 3 of them were detected through in vitro sensitization of non-autologous PBMCs.Abstract 912 Figure 1Workflow diagramTumor biopsies and blood samples are obtained from cancer patients (left panel). Patient-derived tumor cell lines are generated in vitro, the peptides presented on HLA molecules are further isolated and analyzed in a mass-spectrometer (top panel). Whole exome sequencing (WES) from matched tumor and healthy tissue is performed to identify the non-synonymous somatic mutations (NSM) (middle panel). Peptide-PRISM proteogenomics pipeline combines the information from the immunopeptidomics data and WES to identify pHLA sequences from both canonical and non-canonical candidate tumor antigens (top right panel). Lymphocyte populations either TILs or sorted PBMCs are expanded and further screened for pre-existing T cell responses (bottom panel) against the candidate epitopes by co-culturing the T cells with peptide-pulsed autologous APC. The recognition is assessed by measuring IFNg release by elispot and the upregulation of activation surface markers by FACS (bottom right panel).ConclusionsOur results show that although HLA-I nonC peptides were frequently presented in all TCLs studied and they can be immunogenic, neoantigens derived from mutations in canonical coding regions were preferentially recognized by tumor-reactive lymphocytes, suggesting T cells targeting the latter are primed more efficiently. The identification of mutated nonC antigens using whole genome sequencing to identify mutations in non-coding regions warrants further examination. Still, the specificity of many tumor-reactive TILs remains unknown.Ethics Approval”This study was approved by the ”Comité de Ética de Investigación con Medicamentos del Hospital Universitario Vall d’Hebron” institution’s Ethics Board; approval number PR(AG)537/2019.”
Collapse
|
8
|
Simats A, Ramiro L, García-Berrocoso T, Briansó F, Gonzalo R, Martín L, Sabé A, Gill N, Penalba A, Colomé N, Sánchez A, Canals F, Bustamante A, Rosell A, Montaner J. A Mouse Brain-based Multi-omics Integrative Approach Reveals Potential Blood Biomarkers for Ischemic Stroke. Mol Cell Proteomics 2020; 19:1921-1936. [PMID: 32868372 PMCID: PMC7710142 DOI: 10.1074/mcp.ra120.002283] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 08/10/2020] [Indexed: 12/14/2022] Open
Abstract
Stroke remains a leading cause of death and disability worldwide. Despite continuous advances, the identification of key molecular signatures in the hyper-acute phase of ischemic stroke is still a primary interest for translational research on stroke diagnosis, prognosis, and treatment. Data integration from high-throughput -omics techniques has become crucial to unraveling key interactions among different molecular elements in complex biological contexts, such as ischemic stroke. Thus, we used advanced data integration methods for a multi-level joint analysis of transcriptomics and proteomics data sets obtained from mouse brains at 2 h after cerebral ischemia. By modeling net-like correlation structures, we identified an integrated network of genes and proteins that are differentially expressed at a very early stage after stroke. We validated 10 of these deregulated elements in acute stroke, and changes in their expression pattern over time after cerebral ischemia were described. Of these, CLDN20, GADD45G, RGS2, BAG5, and CTNND2 were next evaluated as blood biomarkers of cerebral ischemia in mice and human blood samples, which were obtained from stroke patients and patients presenting stroke-mimicking conditions. Our findings indicate that CTNND2 levels in blood might potentially be useful for distinguishing ischemic strokes from stroke-mimicking conditions in the hyper-acute phase of the disease. Furthermore, circulating GADD45G content within the first 6 h after stroke could also play a key role in predicting poor outcomes in stroke patients. For the first time, we have used an integrative biostatistical approach to elucidate key molecules in the initial stages of stroke pathophysiology and highlight new notable molecules that might be further considered as blood biomarkers of ischemic stroke.
Collapse
Affiliation(s)
- Alba Simats
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Ramiro
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Teresa García-Berrocoso
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ferran Briansó
- Bioinformatics and Biostatistics Unit, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain; Genetics, Microbiology and Statistics Dept., Universitat de Barcelona, Barcelona, Spain
| | - Ricardo Gonzalo
- Bioinformatics and Biostatistics Unit, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Luna Martín
- Proteomics Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anna Sabé
- Proteomics Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Natalia Gill
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anna Penalba
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Nuria Colomé
- Proteomics Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alex Sánchez
- Bioinformatics and Biostatistics Unit, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain; Genetics, Microbiology and Statistics Dept., Universitat de Barcelona, Barcelona, Spain
| | - Francesc Canals
- Proteomics Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alejandro Bustamante
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anna Rosell
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Joan Montaner
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.
| |
Collapse
|
9
|
Vitali M, Casals E, Canals F, Colomé N, Puntes V. Simple spectroscopic determination of the hard protein corona composition in AuNPs: albumin at 75. Nanoscale 2020; 12:15832-15844. [PMID: 32692793 DOI: 10.1039/d0nr02379e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We analyzed the different spectroscopic profiles of nanoparticle hard protein corona formation using two model proteins, albumin and immunoglobulin. When compared to serum, this served for the analysis of the hard protein corona main components. To do that, we employed time-resolved UV-Visible light absorption spectroscopy, dynamic light scattering, and zeta potential measurements during nanoparticle-protein incubation. Under the tested experimental conditions, the expected evolution from a non-stable (soft) to a stable (hard) protein corona was confirmed for serum and albumin. At the same time, immunoglobulin incubation inevitably failed to form a corona and led to nanoparticle aggregation. The formation profiles of the protein corona were similar in the case of albumin and serum, indicating the dominance of albumin coating the nanoparticle surface when exposed to plasma. This was confirmed by mass spectrometry. Chemical digestion of the nanoparticles bearing different protein coronas gave indications of the density of the different protein coatings. Overall, this study of the protein corona by determining the adsorption kinetics finger-print enables the development of precise nanotechnologies avoiding cumbersome processes and delaying proteomics analysis.
Collapse
Affiliation(s)
- Michele Vitali
- Vall d'Hebron Institut de Recerca (VHIR), 08035, Barcelona, Spain.
| | | | | | | | | |
Collapse
|
10
|
Granado-Martínez P, Garcia-Ortega S, González-Sánchez E, McGrail K, Selgas R, Grueso J, Gil R, Naldaiz-Gastesi N, Rhodes AC, Hernandez-Losa J, Ferrer B, Canals F, Villanueva J, Méndez O, Espinosa-Gil S, Lizcano JM, Muñoz-Couselo E, García-Patos V, Recio JA. STK11 (LKB1) missense somatic mutant isoforms promote tumor growth, motility and inflammation. Commun Biol 2020; 3:366. [PMID: 32647375 PMCID: PMC7347935 DOI: 10.1038/s42003-020-1092-0] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 06/19/2020] [Indexed: 02/07/2023] Open
Abstract
Elucidating the contribution of somatic mutations to cancer is essential for personalized medicine. STK11 (LKB1) appears to be inactivated in human cancer. However, somatic missense mutations also occur, and the role/s of these alterations to this disease remain unknown. Here, we investigated the contribution of four missense LKB1 somatic mutations in tumor biology. Three out of the four mutants lost their tumor suppressor capabilities and showed deficient kinase activity. The remaining mutant retained the enzymatic activity of wild type LKB1, but induced increased cell motility. Mechanistically, LKB1 mutants resulted in differential gene expression of genes encoding vesicle trafficking regulating molecules, adhesion molecules and cytokines. The differentially regulated genes correlated with protein networks identified through comparative secretome analysis. Notably, three mutant isoforms promoted tumor growth, and one induced inflammation-like features together with dysregulated levels of cytokines. These findings uncover oncogenic roles of LKB1 somatic mutations, and will aid in further understanding their contributions to cancer development and progression. Paula Granado-Martínez, Sara Ortega, Elena González-Sánchez et al. report a functional analysis of four cancer-associated mutant isoforms of the gene STK11 using cell-based and animal models. They find the mutant isoforms no longer show tumor suppressor activity, promote tumor growth, and affect the regulation of cytokines and genes involved in vesicle trafficking.
Collapse
Affiliation(s)
- Paula Granado-Martínez
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory- Vall d'Hebron Research Institute VHIR-Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain
| | - Sara Garcia-Ortega
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory- Vall d'Hebron Research Institute VHIR-Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain
| | - Elena González-Sánchez
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory- Vall d'Hebron Research Institute VHIR-Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain
| | - Kimberley McGrail
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory- Vall d'Hebron Research Institute VHIR-Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain
| | - Rafael Selgas
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory- Vall d'Hebron Research Institute VHIR-Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain
| | - Judit Grueso
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory- Vall d'Hebron Research Institute VHIR-Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain.,Experimental Therapeutics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, 08035, Spain
| | - Rosa Gil
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory- Vall d'Hebron Research Institute VHIR-Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain
| | - Neia Naldaiz-Gastesi
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory- Vall d'Hebron Research Institute VHIR-Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain.,Biodonostia, Neurosciences Area, Group of Neuromuscular Diseases, San Sebastian, 20014, Spain
| | - Ana C Rhodes
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory- Vall d'Hebron Research Institute VHIR-Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain.,Barcelona Clinic Liver Cancer (BCLC) Group, Liver Unit, Hospital Clínic of Barcelona, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, 08036, Spain
| | - Javier Hernandez-Losa
- Anatomy Pathology Department, Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain
| | - Berta Ferrer
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory- Vall d'Hebron Research Institute VHIR-Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain.,Anatomy Pathology Department, Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain
| | - Francesc Canals
- Proteomics Laboratory, Vall d'Hebron Institute of Oncology (VHIO, Barcelona, 08035, Spain
| | - Josep Villanueva
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO, Barcelona, 08035, Spain
| | - Olga Méndez
- Preclinical Research Program, Vall d'Hebron Institute of Oncology (VHIO, Barcelona, 08035, Spain
| | - Sergio Espinosa-Gil
- Protein Kinases and Signal Transduction Laboratory, Neuroscience Institute and Molecular Biology and Biochemistry Department, UAB, Bellaterra, Barcelona, 08193, Spain
| | - José M Lizcano
- Protein Kinases and Signal Transduction Laboratory, Neuroscience Institute and Molecular Biology and Biochemistry Department, UAB, Bellaterra, Barcelona, 08193, Spain
| | - Eva Muñoz-Couselo
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory- Vall d'Hebron Research Institute VHIR-Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain.,Clinical Oncology Program, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Hospital, Barcelona-UAB, Barcelona, 08035, Spain
| | - Vicenç García-Patos
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory- Vall d'Hebron Research Institute VHIR-Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain.,Dermatology Department, Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain
| | - Juan A Recio
- Biomedical Research in Melanoma-Animal Models and Cancer Laboratory- Vall d'Hebron Research Institute VHIR-Vall d'Hebron Hospital Barcelona-UAB, Barcelona, 08035, Spain.
| |
Collapse
|
11
|
Martínez-Torró C, Torres-Puig S, Monge M, Sánchez-Alba L, González-Martín M, Marcos-Silva M, Perálvarez-Marín A, Canals F, Querol E, Piñol J, Pich OQ. Transcriptional response to metal starvation in the emerging pathogen Mycoplasma genitalium is mediated by Fur-dependent and -independent regulatory pathways. Emerg Microbes Infect 2019; 9:5-19. [PMID: 31859607 PMCID: PMC6968530 DOI: 10.1080/22221751.2019.1700762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Transition metals participate in numerous enzymatic reactions and they are essential for survival in all living organisms. For this reason, bacterial pathogens have evolved dedicated machineries to effectively compete with their hosts and scavenge metals at the site of infection. In this study, we investigated the mechanisms controlling metal acquisition in the emerging human pathogen Mycoplasma genitalium. We observed a robust transcriptional response to metal starvation, and many genes coding for predicted lipoproteins and ABC-transporters were significantly up-regulated. Transcriptional analysis of a mutant strain lacking a metalloregulator of the Fur family revealed the activation of a full operon encoding a putative metal transporter system and a gene coding for a Histidine-rich lipoprotein (Hrl). We recognized a conserved sequence with dyad symmetry within the promoter region of the Fur-regulated genes. Mutagenesis of the predicted Fur operator within the hrl promoter abrogated Fur- and metal-dependent expression of a reporter gene. Metal starvation still impelled a strong transcriptional response in the fur mutant, demonstrating the existence of Fur-independent regulatory pathways controlling metal homeostasis. Finally, analysis of metal accumulation in the wild-type strain and the fur mutant by ICP-MS revealed an important role of Fur in nickel acquisition.
Collapse
Affiliation(s)
- Carlos Martínez-Torró
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sergi Torres-Puig
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marta Monge
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Lucía Sánchez-Alba
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Miguel González-Martín
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marina Marcos-Silva
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alex Perálvarez-Marín
- Biophysics Unit, Department of Biochemistry and Molecular Biology, School of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Francesc Canals
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Enrique Querol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jaume Piñol
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Oscar Q Pich
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| |
Collapse
|
12
|
Garcia-Puig A, Mosquera JL, Jiménez-Delgado S, García-Pastor C, Jorba I, Navajas D, Canals F, Raya A. Proteomics Analysis of Extracellular Matrix Remodeling During Zebrafish Heart Regeneration. Mol Cell Proteomics 2019; 18:1745-1755. [PMID: 31221719 PMCID: PMC6731076 DOI: 10.1074/mcp.ra118.001193] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 06/03/2019] [Indexed: 12/13/2022] Open
Abstract
Adult zebrafish, in contrast to mammals, are able to regenerate their hearts in response to injury or experimental amputation. Our understanding of the cellular and molecular bases that underlie this process, although fragmentary, has increased significantly over the last years. However, the role of the extracellular matrix (ECM) during zebrafish heart regeneration has been comparatively rarely explored. Here, we set out to characterize the ECM protein composition in adult zebrafish hearts, and whether it changed during the regenerative response. For this purpose, we first established a decellularization protocol of adult zebrafish ventricles that significantly enriched the yield of ECM proteins. We then performed proteomic analyses of decellularized control hearts and at different times of regeneration. Our results show a dynamic change in ECM protein composition, most evident at the earliest (7 days postamputation) time point analyzed. Regeneration associated with sharp increases in specific ECM proteins, and with an overall decrease in collagens and cytoskeletal proteins. We finally tested by atomic force microscopy that the changes in ECM composition translated to decreased ECM stiffness. Our cumulative results identify changes in the protein composition and mechanical properties of the zebrafish heart ECM during regeneration.
Collapse
Affiliation(s)
- Anna Garcia-Puig
- ‡Center of Regenerative Medicine in Barcelona (CMRB), 3rd Floor Hospital Duran i Reynals, Avinguda de la Gran Via 199-203, 08908 Hospitalet de Llobregat (Barcelona), Spain; §Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 08908 Hospitalet de Llobregat (Barcelona), Spain
| | - Jose Luis Mosquera
- ¶Bioinformatics Unit, Institut d'Investigació Biomèdica de Bellvitge IDIBELL), 3rd Floor Hospital Duran i Reynals, Avinguda de la Gran Via 199-203, 08908 Hospitalet de Llobregat (Barcelona), Spain
| | - Senda Jiménez-Delgado
- ‡Center of Regenerative Medicine in Barcelona (CMRB), 3rd Floor Hospital Duran i Reynals, Avinguda de la Gran Via 199-203, 08908 Hospitalet de Llobregat (Barcelona), Spain
| | - Cristina García-Pastor
- ‡Center of Regenerative Medicine in Barcelona (CMRB), 3rd Floor Hospital Duran i Reynals, Avinguda de la Gran Via 199-203, 08908 Hospitalet de Llobregat (Barcelona), Spain
| | - Ignasi Jorba
- ‖Institute for Bioengineering of Catalonia (IBEC), Barcelona Science Park, Baldiri Reixac 15-21, 08028 Barcelona, Spain; **Unit of Biophysics and Bioengineering, Department of Physiological Sciences I, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; ‡‡Center for Networked Biomedical Research on Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
| | - Daniel Navajas
- ‖Institute for Bioengineering of Catalonia (IBEC), Barcelona Science Park, Baldiri Reixac 15-21, 08028 Barcelona, Spain; **Unit of Biophysics and Bioengineering, Department of Physiological Sciences I, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; ‡‡Center for Networked Biomedical Research on Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
| | - Francesc Canals
- §§Proteomics group, Vall d'Hebron Institut of Oncology (VHIO), Cellex center, Natzaret 115-117, 08035 Barcelona, Spain
| | - Angel Raya
- ‡Center of Regenerative Medicine in Barcelona (CMRB), 3rd Floor Hospital Duran i Reynals, Avinguda de la Gran Via 199-203, 08908 Hospitalet de Llobregat (Barcelona), Spain; §Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 08908 Hospitalet de Llobregat (Barcelona), Spain; ¶¶Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
| |
Collapse
|
13
|
Rosso M, Lapyckyj L, Besso MJ, Monge M, Reventós J, Canals F, Quevedo Cuenca JO, Matos ML, Vazquez-Levin MH. Characterization of the molecular changes associated with the overexpression of a novel epithelial cadherin splice variant mRNA in a breast cancer model using proteomics and bioinformatics approaches: identification of changes in cell metabolism and an increased expression of lactate dehydrogenase B. Cancer Metab 2019; 7:5. [PMID: 31086659 PMCID: PMC6507066 DOI: 10.1186/s40170-019-0196-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 04/04/2019] [Indexed: 12/17/2022] Open
Abstract
Background Breast cancer (BC) is the most common female cancer and the leading cause of cancer death in women worldwide. Alterations in epithelial cadherin (E-cadherin) expression and functions are associated to BC, but the underlying molecular mechanisms have not been fully elucidated. We have previously reported a novel human E-cadherin splice variant (E-cadherin variant) mRNA. Stable transfectants in MCF-7 human BC cells (MCF7Ecadvar) depicted fibroblast-like cell morphology, E-cadherin wild-type downregulation, and other molecular changes characteristic of the epithelial-to-mesenchymal transition process, reduced cell-cell adhesion, and increased cell migration and invasion. In this study, a two-dimensional differential gel electrophoresis (2D-DIGE) combined with mass spectrometry (MS) protein identification and bioinformatics analyses were done to characterize biological processes and canonical pathways affected by E-cadherin variant expression. Results By 2D-DIGE and MS analysis, 50 proteins were found differentially expressed (≥ Δ1.5) in MCF7Ecadvar compared to control cells. Validation of transcript expression was done in the ten most overexpressed and underexpressed proteins. Bioinformatics analyses revealed that 39 of the 50 proteins identified had been previously associated to BC. Moreover, metabolic processes were the most affected, and glycolysis the canonical pathway most altered. The lactate dehydrogenase B (LDHB) was the highest overexpressed protein, and transcript levels were higher in MCF7Ecadvar than in control cells. In agreement with these findings, MCF7Ecadvar conditioned media had lower glucose and higher lactate levels than control cells. MCF7Ecadvar cell treatment with 5 mM of the glycolytic inhibitor 2-deoxy-glucose led to decreased cell viability, and modulation of LDHB expression in MCF7Ecadvar cells with a specific small interfering RNA resulted in decreased cell proliferation. Finally, a positive association between expression levels of the E-cadherin variant and LDHB transcripts was demonstrated in 21 human breast tumor tissues, and breast tumor samples with higher Ki67 expression showed higher LDHB mRNA levels. Conclusions Results from this investigation contributed to further characterize molecular changes associated to the novel E-cadherin splice variant expression in BC cells. They also revealed an association between expression of the novel variant and changes related to BC progression and aggressiveness, in particular those associated to cell metabolism.
Collapse
Affiliation(s)
- Marina Rosso
- Laboratorio de Estudios de Interacción Celular en Reproducción y Cáncer, Instituto de Biología y Medicina Experimental (IBYME; CONICET-FIBYME), Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina
| | - Lara Lapyckyj
- Laboratorio de Estudios de Interacción Celular en Reproducción y Cáncer, Instituto de Biología y Medicina Experimental (IBYME; CONICET-FIBYME), Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina
| | - María José Besso
- Laboratorio de Estudios de Interacción Celular en Reproducción y Cáncer, Instituto de Biología y Medicina Experimental (IBYME; CONICET-FIBYME), Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina
| | - Marta Monge
- 2Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Jaume Reventós
- 3Departament de Ciències Bàsiques, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Francesc Canals
- 2Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Jorge Oswaldo Quevedo Cuenca
- Laboratorio de Estudios de Interacción Celular en Reproducción y Cáncer, Instituto de Biología y Medicina Experimental (IBYME; CONICET-FIBYME), Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina
| | - María Laura Matos
- Laboratorio de Estudios de Interacción Celular en Reproducción y Cáncer, Instituto de Biología y Medicina Experimental (IBYME; CONICET-FIBYME), Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina
| | - Mónica Hebe Vazquez-Levin
- Laboratorio de Estudios de Interacción Celular en Reproducción y Cáncer, Instituto de Biología y Medicina Experimental (IBYME; CONICET-FIBYME), Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina
| |
Collapse
|
14
|
Marcelino I, Colomé-Calls N, Holzmuller P, Lisacek F, Reynaud Y, Canals F, Vachiéry N. Sweet and Sour Ehrlichia: Glycoproteomics and Phosphoproteomics Reveal New Players in Ehrlichia ruminantium Physiology and Pathogenesis. Front Microbiol 2019; 10:450. [PMID: 30930869 PMCID: PMC6429767 DOI: 10.3389/fmicb.2019.00450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/20/2019] [Indexed: 01/31/2023] Open
Abstract
Unraveling which proteins and post-translational modifications (PTMs) affect bacterial pathogenesis and physiology in diverse environments is a tough challenge. Herein, we used mass spectrometry-based assays to study protein phosphorylation and glycosylation in Ehrlichia ruminantium Gardel virulent (ERGvir) and attenuated (ERGatt) variants and, how they can modulate Ehrlichia biological processes. The characterization of the S/T/Y phosphoproteome revealed that both strains share the same set of phosphoproteins (n = 58), 36% being overexpressed in ERGvir. The percentage of tyrosine phosphorylation is high (23%) and 66% of the identified peptides are multi-phosphorylated. Glycoproteomics revealed a high percentage of glycoproteins (67% in ERGvir) with a subset of glycoproteins being specific to ERGvir (n = 64/371) and ERGatt (n = 36/343). These glycoproteins are involved in key biological processes such as protein, amino-acid and purine biosynthesis, translation, virulence, DNA repair, and replication. Label-free quantitative analysis revealed over-expression in 31 proteins in ERGvir and 8 in ERGatt. While further PNGase digestion confidently localized 2 and 5 N-glycoproteins in ERGvir and ERGatt, respectively, western blotting suggests that many glycoproteins are O-GlcNAcylated. Twenty-three proteins were detected in both the phospho- and glycoproteome, for the two variants. This work represents the first comprehensive assessment of PTMs on Ehrlichia biology, rising interesting questions regarding ER–host interactions. Phosphoproteome characterization demonstrates an increased versatility of ER phosphoproteins to participate in different mechanisms. The high number of glycoproteins and the lack of glycosyltransferases-coding genes highlight ER dependence on the host and/or vector cellular machinery for its own protein glycosylation. Moreover, these glycoproteins could be crucial to interact and respond to changes in ER environment. PTMs crosstalk between of O-GlcNAcylation and phosphorylation could be used as a major cellular signaling mechanism in ER. As little is known about the Ehrlichia proteins/proteome and its signaling biology, the results presented herein provide a useful resource for further hypothesis-driven exploration of Ehrlichia protein regulation by phosphorylation and glycosylation events. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD012589.
Collapse
Affiliation(s)
- Isabel Marcelino
- CIRAD, UMR ASTRE, Petit-Bourg, France.,ASTRE, CIRAD, INRA, Université de Montpellier, Montpellier, France.,Unitè TReD-Path (Transmission Rèservoirs et Diversitè des Pathogènes), Institut Pasteur de Guadeloupe, Les Abymes, France
| | - Núria Colomé-Calls
- Proteomics Laboratory, Vall Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Philippe Holzmuller
- ASTRE, CIRAD, INRA, Université de Montpellier, Montpellier, France.,CIRAD, UMR ASTRE, Montpellier, France
| | - Frédérique Lisacek
- Proteome Informatics, Swiss Institute of Bioinformatics, Geneva, Switzerland.,Computer Science Department and Section of Biology, University of Geneva, Geneva, Switzerland
| | - Yann Reynaud
- Unitè TReD-Path (Transmission Rèservoirs et Diversitè des Pathogènes), Institut Pasteur de Guadeloupe, Les Abymes, France
| | - Francesc Canals
- Proteomics Laboratory, Vall Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Nathalie Vachiéry
- ASTRE, CIRAD, INRA, Université de Montpellier, Montpellier, France.,CIRAD, UMR ASTRE, Montpellier, France
| |
Collapse
|
15
|
Marinelli P, Navarro S, Baño-Polo M, Morel B, Graña-Montes R, Sabe A, Canals F, Fernandez MR, Conejero-Lara F, Ventura S. Global Protein Stabilization Does Not Suffice to Prevent Amyloid Fibril Formation. ACS Chem Biol 2018; 13:2094-2105. [PMID: 29966079 DOI: 10.1021/acschembio.8b00607] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mutations or cellular conditions that destabilize the native protein conformation promote the population of partially unfolded conformations, which in many cases assemble into insoluble amyloid fibrils, a process associated with multiple human pathologies. Therefore, stabilization of protein structures is seen as an efficient way to prevent misfolding and subsequent aggregation. This has been suggested to be the underlying reason why proteins living in harsh environments, such as the extracellular space, have evolved disulfide bonds. The effect of protein disulfides on the thermodynamics and kinetics of folding has been extensively studied, but much less is known on its effect on aggregation reactions. Here, we designed a single point mutation that introduces a disulfide bond in the all-α FF domain, a protein that, despite being devoid of preformed β-sheets, forms β-sheet-rich amyloid fibrils. The novel and unique covalent bond in the FF domain dramatically increases its thermodynamic stability and folding speed. Nevertheless, these optimized properties cannot counteract the inherent aggregation propensity of the protein, thus indicating that a high global protein stabilization does not suffice to prevent amyloid formation unless it contributes to hide from exposure the specific regions that nucleate the aggregation reaction.
Collapse
Affiliation(s)
- Patrizia Marinelli
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Manuel Baño-Polo
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Bertrand Morel
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Ricardo Graña-Montes
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Anna Sabe
- Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron University Hospital, 08135 Barcelona, Spain
| | - Francesc Canals
- Vall d’Hebron Institute of Oncology (VHIO), Vall d’Hebron University Hospital, 08135 Barcelona, Spain
| | - Maria Rosario Fernandez
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Francisco Conejero-Lara
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| |
Collapse
|
16
|
Simats A, García-Berrocoso T, Penalba A, Giralt D, Llovera G, Jiang Y, Ramiro L, Bustamante A, Martinez-Saez E, Canals F, Wang X, Liesz A, Rosell A, Montaner J. CCL23: a new CC chemokine involved in human brain damage. J Intern Med 2018; 283:461-475. [PMID: 29415332 DOI: 10.1111/joim.12738] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND CCL23 role in the inflammatory response after acute brain injuries remains elusive. Here, we evaluated whether CCL23 blood levels associate with acquired cerebral lesions and determined CCL23 predictive capacity for assessing stroke prognosis. We used preclinical models to study the CCL23 homologous chemokines in rodents, CCL9 and CCL6. METHODS Baseline CCL23 blood levels were determined on 245 individuals, including ischaemic strokes (IS), stroke mimics and controls. Temporal profile of circulating CCL23 was explored from baseline to 24 h in 20 of the IS. In an independent cohort of 120 IS with a 3-month follow-up, CCL23 blood levels were included in logistic regression models to predict IS outcome. CCL9/CCL6 cerebral expression was evaluated in rodent models of brain damage. Both chemokines were also profiled in circulation and histologically located on brain following ischaemia. RESULTS Baseline CCL23 blood levels did not discriminate IS, but permitted an accurate discrimination of patients presenting acute brain lesions (P = 0.003). IS exhibited a continuous increase from baseline to 24 h in circulating CCL23 (P < 0.001). Baseline CCL23 blood levels resulted an independent predictor of IS outcome at hospital discharge (ORadj : 19.702 [1.815-213.918], P = 0.014) and mortality after 3 months (ORadj : 21.47 [3.434-134.221], P = 0.001). In preclinics, expression of rodent chemokines in neurons following cerebral lesions was elevated. CCL9 circulating levels decreased early after ischaemia (P < 0.001), whereas CCL6 did not alter within the first 24 h after ischaemia. CONCLUSIONS Although preclinical models do not seem suitable to characterize CCL23, it might be a novel promising biomarker for the early diagnosis of cerebral lesions and might facilitate the prediction of stroke patient outcome.
Collapse
Affiliation(s)
- A Simats
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - T García-Berrocoso
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - A Penalba
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - D Giralt
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - G Llovera
- Institute for Stroke and Dementia Research, Klinikum de Universität München, Munich, Germany
| | - Y Jiang
- Neuroprotection Research Laboratory, Departments of Neurology and Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - L Ramiro
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - A Bustamante
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - E Martinez-Saez
- Neuropathology Unit, Department of Pathology, Vall d'Hebron Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - F Canals
- Proteomics Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - X Wang
- Proteomics Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - A Liesz
- Institute for Stroke and Dementia Research, Klinikum de Universität München, Munich, Germany
| | - A Rosell
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - J Montaner
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| |
Collapse
|
17
|
Fraga H, Pujols J, Gil-Garcia M, Roque A, Bernardo-Seisdedos G, Santambrogio C, Bech-Serra JJ, Canals F, Bernadó P, Grandori R, Millet O, Ventura S. Disulfide driven folding for a conditionally disordered protein. Sci Rep 2017; 7:16994. [PMID: 29208936 PMCID: PMC5717278 DOI: 10.1038/s41598-017-17259-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 05/09/2017] [Accepted: 11/23/2017] [Indexed: 11/09/2022] Open
Abstract
Conditionally disordered proteins are either ordered or disordered depending on the environmental context. The substrates of the mitochondrial intermembrane space (IMS) oxidoreductase Mia40 are synthesized on cytosolic ribosomes and diffuse as intrinsically disordered proteins to the IMS, where they fold into their functional conformations; behaving thus as conditionally disordered proteins. It is not clear how the sequences of these polypeptides encode at the same time for their ability to adopt a folded structure and to remain unfolded. Here we characterize the disorder-to-order transition of a Mia40 substrate, the human small copper chaperone Cox17. Using an integrated real-time approach, including chromatography, fluorescence, CD, FTIR, SAXS, NMR, and MS analysis, we demonstrate that in this mitochondrial protein, the conformational switch between disordered and folded states is controlled by the formation of a single disulfide bond, both in the presence and in the absence of Mia40. We provide molecular details on how the folding of a conditionally disordered protein is tightly regulated in time and space, in such a way that the same sequence is competent for protein translocation and activity.
Collapse
Affiliation(s)
- Hugo Fraga
- Institut de Biotecnologia i Biomedicina. Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departamento de Bioquimica, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Jordi Pujols
- Institut de Biotecnologia i Biomedicina. Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Marcos Gil-Garcia
- Institut de Biotecnologia i Biomedicina. Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Alicia Roque
- Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | | | - Carlo Santambrogio
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | | | - Francesc Canals
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM-U1054, CNRS UMR-5048, Université de Montpellier, 29, rue de Navacelles, 34090, Montpellier, France
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, Italy
| | - Oscar Millet
- Protein Stability and Inherited Diseases Laboratory, CIC bioGUNE, 48160, Derio, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina. Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. .,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| |
Collapse
|
18
|
García-Berrocoso T, Llombart V, Colàs-Campàs L, Hainard A, Licker V, Penalba A, Ramiro L, Simats A, Bustamante A, Martínez-Saez E, Canals F, Sanchez JC, Montaner J. Single Cell Immuno-Laser Microdissection Coupled to Label-Free Proteomics to Reveal the Proteotypes of Human Brain Cells After Ischemia. Mol Cell Proteomics 2017; 17:175-189. [PMID: 29133510 DOI: 10.1074/mcp.ra117.000419] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Indexed: 12/13/2022] Open
Abstract
Cerebral ischemia entails rapid tissue damage in the affected brain area causing devastating neurological dysfunction. How each component of the neurovascular unit contributes or responds to the ischemic insult in the context of the human brain has not been solved yet. Thus, the analysis of the proteome is a straightforward approach to unraveling these cell proteotypes. In this study, post-mortem brain slices from ischemic stroke patients were obtained corresponding to infarcted (IC) and contralateral (CL) areas. By means of laser microdissection, neurons and blood brain barrier structures (BBB) were isolated and analyzed using label-free quantification. MS data are available via ProteomeXchange with identifier PXD003519. Ninety proteins were identified only in neurons, 260 proteins only in the BBB and 261 proteins in both cell types. Bioinformatics analyses revealed that repair processes, mainly related to synaptic plasticity, are outlined in microdissected neurons, with nonexclusive important functions found in the BBB. A total of 30 proteins showing p < 0.05 and fold-change> 2 between IC and CL areas were considered meaningful in this study: 13 in neurons, 14 in the BBB and 3 in both cell types. Twelve of these proteins were selected as candidates and analyzed by immunohistofluorescence in independent brains. The MS findings were completely verified for neuronal SAHH2 and SRSF1 whereas the presence in both cell types of GABT and EAA2 was only validated in neurons. In addition, SAHH2 showed its potential as a prognostic biomarker of neurological improvement when analyzed early in the plasma of ischemic stroke patients. Therefore, the quantitative proteomes of neurons and the BBB (or proteotypes) after human brain ischemia presented here contribute to increasing the knowledge regarding the molecular mechanisms of ischemic stroke pathology and highlight new proteins that might represent putative biomarkers of brain ischemia or therapeutic targets.
Collapse
Affiliation(s)
- Teresa García-Berrocoso
- From the ‡Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Víctor Llombart
- From the ‡Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Colàs-Campàs
- From the ‡Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alexandre Hainard
- §Proteomics Core Facility, Faculty of medicine, University Medical Center, University of Geneva, Geneva, Switzerland
| | - Virginie Licker
- ¶Neuroproteomics Group, Human protein sciences department, University Medical Center, University of Geneva, Geneva, Switzerland
| | - Anna Penalba
- From the ‡Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Ramiro
- From the ‡Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alba Simats
- From the ‡Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Alejandro Bustamante
- From the ‡Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elena Martínez-Saez
- ‖Neuropathology, Pathology department, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Francesc Canals
- **Proteomics Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jean-Charles Sanchez
- ‡‡Translational biomarker group, Human protein sciences department, University Medical Center, University of Geneva, Geneva, Switzerland
| | - Joan Montaner
- From the ‡Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain;
| |
Collapse
|
19
|
Mateo F, Arenas EJ, Aguilar H, Serra-Musach J, de Garibay GR, Boni J, Maicas M, Du S, Iorio F, Herranz-Ors C, Islam A, Prado X, Llorente A, Petit A, Vidal A, Català I, Soler T, Venturas G, Rojo-Sebastian A, Serra H, Cuadras D, Blanco I, Lozano J, Canals F, Sieuwerts AM, de Weerd V, Look MP, Puertas S, García N, Perkins AS, Bonifaci N, Skowron M, Gómez-Baldó L, Hernández V, Martínez-Aranda A, Martínez-Iniesta M, Serrat X, Cerón J, Brunet J, Barretina MP, Gil M, Falo C, Fernández A, Morilla I, Pernas S, Plà MJ, Andreu X, Seguí MA, Ballester R, Castellà E, Nellist M, Morales S, Valls J, Velasco A, Matias-Guiu X, Figueras A, Sánchez-Mut JV, Sánchez-Céspedes M, Cordero A, Gómez-Miragaya J, Palomero L, Gómez A, Gajewski TF, Cohen EEW, Jesiotr M, Bodnar L, Quintela-Fandino M, López-Bigas N, Valdés-Mas R, Puente XS, Viñals F, Casanovas O, Graupera M, Hernández-Losa J, Ramón Y Cajal S, García-Alonso L, Saez-Rodriguez J, Esteller M, Sierra A, Martín-Martín N, Matheu A, Carracedo A, González-Suárez E, Nanjundan M, Cortés J, Lázaro C, Odero MD, Martens JWM, Moreno-Bueno G, Barcellos-Hoff MH, Villanueva A, Gomis RR, Pujana MA. Stem cell-like transcriptional reprogramming mediates metastatic resistance to mTOR inhibition. Oncogene 2016; 36:2737-2749. [PMID: 27991928 PMCID: PMC5442428 DOI: 10.1038/onc.2016.427] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [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: 03/10/2016] [Revised: 08/31/2016] [Accepted: 10/10/2016] [Indexed: 01/16/2023]
Abstract
Inhibitors of the mechanistic target of rapamycin (mTOR) are currently used to treat advanced metastatic breast cancer. However, whether an aggressive phenotype is sustained through adaptation or resistance to mTOR inhibition remains unknown. Here, complementary studies in human tumors, cancer models and cell lines reveal transcriptional reprogramming that supports metastasis in response to mTOR inhibition. This cancer feature is driven by EVI1 and SOX9. EVI1 functionally cooperates with and positively regulates SOX9, and promotes the transcriptional upregulation of key mTOR pathway components (REHB and RAPTOR) and of lung metastasis mediators (FSCN1 and SPARC). The expression of EVI1 and SOX9 is associated with stem cell-like and metastasis signatures, and their depletion impairs the metastatic potential of breast cancer cells. These results establish the mechanistic link between resistance to mTOR inhibition and cancer metastatic potential, thus enhancing our understanding of mTOR targeting failure.
Collapse
Affiliation(s)
- F Mateo
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - E J Arenas
- Oncology Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - H Aguilar
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - J Serra-Musach
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - G Ruiz de Garibay
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - J Boni
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - M Maicas
- Centre for Applied Medical Research (CIMA) and Department of Biochemistry and Genetics, University of Navarra, Pamplona, Spain
| | - S Du
- Department of Radiation Oncology, New York University School of Medicine, New York, NY, USA
| | - F Iorio
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK.,Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - C Herranz-Ors
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - A Islam
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - X Prado
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - A Llorente
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - A Petit
- Department of Pathology, University Hospital of Bellvitge, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - A Vidal
- Department of Pathology, University Hospital of Bellvitge, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - I Català
- Department of Pathology, University Hospital of Bellvitge, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - T Soler
- Department of Pathology, University Hospital of Bellvitge, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - G Venturas
- Department of Pathology, University Hospital of Bellvitge, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - A Rojo-Sebastian
- Department of Pathology, MD Anderson Cancer Center, Madrid, Spain
| | - H Serra
- Angiogenesis Research Group, ProCURE, ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - D Cuadras
- Statistics Unit, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - I Blanco
- Hereditary Cancer Programme, ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - J Lozano
- Department of Molecular Biology and Biochemistry, Málaga University, and Molecular Oncology Laboratory, Mediterranean Institute for the Advance of Biotechnology and Health Research (IBIMA), University Hospital Virgen de la Victoria, Málaga, Spain
| | - F Canals
- ProteoRed-Instituto de Salud Carlos III, Proteomic Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - A M Sieuwerts
- Department of Medical Oncology, Erasmus University Medical Center, Daniel den Hoed Cancer Center, Cancer Genomics Centre, Rotterdam, The Netherlands
| | - V de Weerd
- Department of Medical Oncology, Erasmus University Medical Center, Daniel den Hoed Cancer Center, Cancer Genomics Centre, Rotterdam, The Netherlands
| | - M P Look
- Department of Medical Oncology, Erasmus University Medical Center, Daniel den Hoed Cancer Center, Cancer Genomics Centre, Rotterdam, The Netherlands
| | - S Puertas
- Chemoresistance and Predictive Factors Laboratory, ProCURE, ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - N García
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - A S Perkins
- University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, NY, USA
| | - N Bonifaci
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - M Skowron
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - L Gómez-Baldó
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - V Hernández
- Biological Clues of the Invasive and Metastatic Phenotype Laboratory, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - A Martínez-Aranda
- Biological Clues of the Invasive and Metastatic Phenotype Laboratory, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - M Martínez-Iniesta
- Chemoresistance and Predictive Factors Laboratory, ProCURE, ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - X Serrat
- Cancer and Human Molecular Genetics, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - J Cerón
- Cancer and Human Molecular Genetics, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - J Brunet
- Hereditary Cancer Programme, ICO, Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - M P Barretina
- Department of Medical Oncology, ICO, IDIBGI, Girona, Spain
| | - M Gil
- Department of Medical Oncology, ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - C Falo
- Department of Medical Oncology, ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - A Fernández
- Department of Medical Oncology, ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - I Morilla
- Department of Medical Oncology, ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - S Pernas
- Department of Medical Oncology, ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - M J Plà
- Department of Gynecology, University Hospital of Bellvitge, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - X Andreu
- Department of Pathology, Parc Taulí Hospital Consortium, Sabadell, Barcelona, Spain
| | - M A Seguí
- Medical Oncology Service, Parc Taulí Hospital Consortium, Sabadell, Barcelona, Spain
| | - R Ballester
- Department of Radiation Oncology, University Hospital Germans Trias i Pujol, ICO, Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona, Spain
| | - E Castellà
- Department of Pathology, University Hospital Germans Trias i Pujol, ICO, IGTP, Badalona, Barcelona, Spain
| | - M Nellist
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - S Morales
- Hospital Arnau de Vilanova, University of Lleida, Biomedical Research Institute of Lleida (IRB Lleida), Lleida, Spain
| | - J Valls
- Hospital Arnau de Vilanova, University of Lleida, Biomedical Research Institute of Lleida (IRB Lleida), Lleida, Spain
| | - A Velasco
- Hospital Arnau de Vilanova, University of Lleida, Biomedical Research Institute of Lleida (IRB Lleida), Lleida, Spain
| | - X Matias-Guiu
- Hospital Arnau de Vilanova, University of Lleida, Biomedical Research Institute of Lleida (IRB Lleida), Lleida, Spain
| | - A Figueras
- Angiogenesis Research Group, ProCURE, ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - J V Sánchez-Mut
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - M Sánchez-Céspedes
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - A Cordero
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - J Gómez-Miragaya
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - L Palomero
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - A Gómez
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - T F Gajewski
- Departments of Pathology and Medicine, University of Chicago, Chicago, IL, USA
| | - E E W Cohen
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - M Jesiotr
- Department of Pathology, Military Institute of Medicine, Warsaw, Poland
| | - L Bodnar
- Department of Oncology, Military Institute of Medicine, Warsaw, Poland
| | - M Quintela-Fandino
- Breast Cancer Clinical Research Unit, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - N López-Bigas
- Department of Experimental and Health Sciences, Barcelona Biomedical Research Park, Pompeu Fabra University (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - R Valdés-Mas
- Department of Biochemistry and Molecular Biology, University Institute of Oncology of Asturias, University of Oviedo, Oviedo, Spain
| | - X S Puente
- Department of Biochemistry and Molecular Biology, University Institute of Oncology of Asturias, University of Oviedo, Oviedo, Spain
| | - F Viñals
- Angiogenesis Research Group, ProCURE, ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - O Casanovas
- Angiogenesis Research Group, ProCURE, ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - M Graupera
- Angiogenesis Research Group, ProCURE, ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - J Hernández-Losa
- Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - S Ramón Y Cajal
- Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - L García-Alonso
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - J Saez-Rodriguez
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - M Esteller
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain
| | - A Sierra
- Molecular and Translational Oncology Laboratory, Biomedical Research Center CELLEX-CRBC, Biomedical Research Institute 'August Pi i Sunyer' (IDIBAPS), and Systems Biology Department, Faculty of Science and Technology, University of Vic, Central University of Catalonia, Barcelona, Spain
| | - N Martín-Martín
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain
| | - A Matheu
- Neuro-Oncology Section, Oncology Department, Biodonostia Research Institute, San Sebastian, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - A Carracedo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Derio, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao, Spain.,Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - E González-Suárez
- Cancer Epigenetics and Biology Program (PEBC), IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - M Nanjundan
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, FL, USA
| | - J Cortés
- Department of Medical Oncology, VHIO, Vall d'Hebron University Hospital, Barcelona, Spain
| | - C Lázaro
- Hereditary Cancer Programme, ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - M D Odero
- Centre for Applied Medical Research (CIMA) and Department of Biochemistry and Genetics, University of Navarra, Pamplona, Spain
| | - J W M Martens
- Department of Medical Oncology, Erasmus University Medical Center, Daniel den Hoed Cancer Center, Cancer Genomics Centre, Rotterdam, The Netherlands
| | - G Moreno-Bueno
- Department of Biochemistry, Autonomous University of Madrid (UAM), Biomedical Research Institute 'Alberto Sols' (Spanish National Research Council (CSIC)-UAM), Translational Research Laboratory, Hospital La Paz Institute for Health Research (IdiPAZ), and MD Anderson International Foundation, Madrid, Spain
| | - M H Barcellos-Hoff
- Department of Radiation Oncology, New York University School of Medicine, New York, NY, USA
| | - A Villanueva
- Chemoresistance and Predictive Factors Laboratory, ProCURE, ICO, IDIBELL, L'Hospitalet del Llobregat, Barcelona, Spain
| | - R R Gomis
- Oncology Program, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - M A Pujana
- Breast Cancer and Systems Biology Laboratory, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| |
Collapse
|
20
|
Vialas V, Colomé-Calls N, Abian J, Aloria K, Alvarez-Llamas G, Antúnez O, Arizmendi JM, Azkargorta M, Barceló-Batllori S, Barderas MG, Blanco F, Casal JI, Casas V, de la Torre C, Chicano-Gálvez E, Elortza F, Espadas G, Estanyol JM, Fernandez-Irigoyen J, Fernandez-Puente P, Fidalgo MJ, Fuentes M, Gay M, Gil C, Hainard A, Hernaez ML, Ibarrola N, Kopylov AT, Lario A, Lopez JA, López-Lucendo M, Marcilla M, Marina-Ramírez A, Marko-Varga G, Martín L, Mora MI, Morato-López E, Muñoz J, Odena MA, de Oliveira E, Orera I, Ortea I, Pasquarello C, Ray KB, Rezeli M, Ruppen I, Sabidó E, Del Pino MMS, Sancho J, Santamaría E, Vazquez J, Vilaseca M, Vivanco F, Walters JJ, Zgoda VG, Corrales FJ, Canals F, Paradela A. A multicentric study to evaluate the use of relative retention times in targeted proteomics. J Proteomics 2016; 152:138-149. [PMID: 27989941 DOI: 10.1016/j.jprot.2016.10.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/27/2016] [Accepted: 10/24/2016] [Indexed: 12/19/2022]
Abstract
Despite the maturity reached by targeted proteomic strategies, reliable and standardized protocols are urgently needed to enhance reproducibility among different laboratories and analytical platforms, facilitating a more widespread use in biomedical research. To achieve this goal, the use of dimensionless relative retention times (iRT), defined on the basis of peptide standard retention times (RT), has lately emerged as a powerful tool. The robustness, reproducibility and utility of this strategy were examined for the first time in a multicentric setting, involving 28 laboratories that included 24 of the Spanish network of proteomics laboratories (ProteoRed-ISCIII). According to the results obtained in this study, dimensionless retention time values (iRTs) demonstrated to be a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups both intra- and inter-laboratories. iRT values also showed very low variability over long time periods. Furthermore, parallel quantitative analyses showed a high reproducibility despite the variety of experimental strategies used, either MRM (multiple reaction monitoring) or pseudoMRM, and the diversity of analytical platforms employed. BIOLOGICAL SIGNIFICANCE From the very beginning of proteomics as an analytical science there has been a growing interest in developing standardized methods and experimental procedures in order to ensure the highest quality and reproducibility of the results. In this regard, the recent (2012) introduction of the dimensionless retention time concept has been a significant advance. In our multicentric (28 laboratories) study we explore the usefulness of this concept in the context of a targeted proteomics experiment, demonstrating that dimensionless retention time values is a useful tool for transferring and sharing peptide retention times across different chromatographic set-ups.
Collapse
Affiliation(s)
- Vital Vialas
- ProteoRed-ISCIII, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Núria Colomé-Calls
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | - Joaquín Abian
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, Barcelona 08036, Spain
| | - Kerman Aloria
- Department of Biochemistry and Molecular Biology, University of the Basque Country-UPV/EHU, Leioa 48940, Spain
| | | | - Oreto Antúnez
- ProteoRed-ISCIII, SCSIE Universitat de Valencia, Burjassot 46100, Spain
| | - Jesus M Arizmendi
- ProteoRed-ISCIII, University of the Basque Country-UPV/EHU, Leioa 48940, Spain
| | - Mikel Azkargorta
- ProteoRed-ISCIII, CIC bioGUNE, Science and Technology Park of Bizkaia, Derio, Spain
| | | | - María G Barderas
- ProteoRed-ISCIII, Hospital Nacional de Parapléjicos-SESCAM, Toledo, Spain
| | | | - J Ignacio Casal
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Vanessa Casas
- ProteoRed-ISCIII, Instituto de Investigaciones Biomédicas de Barcelona, IIBB-CSIC/IDIBAPS, Barcelona 08036, Spain
| | - Carolina de la Torre
- ProteoRed-ISCIII, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain
| | - Eduardo Chicano-Gálvez
- ProteoRed-ISCIII, Maimonides Institute for Biomedical Research and Universidad de Córdoba, Córdoba 14004, Spain
| | - Felix Elortza
- ProteoRed-ISCIII, CIC bioGUNE, Science and Technology Park of Bizkaia, Derio, Spain
| | - Guadalupe Espadas
- ProteoRed-ISCIII, Centre de Regulació Genòmica, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Josep M Estanyol
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, Barcelona 08036, Spain
| | | | | | - María José Fidalgo
- ProteoRed-ISCIII, Scientific and Technological Centers (CCiTUB), University of Barcelona, Barcelona 08036, Spain
| | - Manuel Fuentes
- ProteoRed-ISCIII, Cancer Research Center, University of Salamanca-CSIC, IBSAL, Salamanca 37007, Spain
| | - Marina Gay
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain
| | - Concha Gil
- ProteoRed-ISCIII, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Alexandre Hainard
- Proteomics Core Facility CMU, University of Geneva, Geneva, Switzerland
| | | | - Nieves Ibarrola
- ProteoRed-ISCIII, Cancer Research Center, University of Salamanca-CSIC, IBSAL, Salamanca 37007, Spain
| | - Arthur T Kopylov
- Orekhovich Institute of Biomedical Chemistry RAMS, Moscow 119121, Russian Federation
| | - Antonio Lario
- ProteoRed-ISCIII, IPBLN (CSIC), Armilla, Granada, Spain
| | - Juan Antonio Lopez
- ProteoRed-ISCIII, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - María López-Lucendo
- ProteoRed-ISCIII, Centro de Investigaciones Biológicas-CSIC, Madrid 28040, Spain
| | - Miguel Marcilla
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), Madrid 28049, Spain
| | | | - Gyorgy Marko-Varga
- Centre of Excellence in Biological and Medical Mass spectrometry, Lund University, Lund, Sweden
| | - Luna Martín
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain
| | - Maria I Mora
- ProteoRed-ISCIII, CIMA, University of Navarra, Pamplona 31008, Spain
| | | | - Javier Muñoz
- ProteoRed-ISCIII, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | | | | | - Irene Orera
- ProteoRed-ISCIII, Instituto Aragonés de Ciencias de la Salud, Zaragoza 50009, Spain
| | - Ignacio Ortea
- ProteoRed-ISCIII, Maimonides Institute for Biomedical Research and Universidad de Córdoba, Córdoba 14004, Spain
| | - Carla Pasquarello
- Proteomics Core Facility CMU, University of Geneva, Geneva, Switzerland
| | | | - Melinda Rezeli
- Centre of Excellence in Biological and Medical Mass spectrometry, Lund University, Lund, Sweden
| | - Isabel Ruppen
- ProteoRed-ISCIII, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Eduard Sabidó
- ProteoRed-ISCIII, Centre de Regulació Genòmica, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | | | - Jaime Sancho
- ProteoRed-ISCIII, IPBLN (CSIC), Armilla, Granada, Spain
| | - Enrique Santamaría
- ProteoRed-ISCIII, Navarrabiomed Biomedical Research Center-IdiSNa, Pamplona, Spain
| | - Jesus Vazquez
- ProteoRed-ISCIII, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid 28029, Spain
| | - Marta Vilaseca
- ProteoRed-ISCIII, Institute for Research in Biomedicine (IRB Barcelona), Barcelona 08028, Spain
| | | | | | - Victor G Zgoda
- Orekhovich Institute of Biomedical Chemistry RAMS, Moscow 119121, Russian Federation
| | | | - Francesc Canals
- ProteoRed-ISCIII, Vall d'Hebron Institute of Oncology (VHIO), Barcelona 08035, Spain.
| | - Alberto Paradela
- ProteoRed-ISCIII, Centro Nacional de Biotecnologia (CSIC), Madrid 28049, Spain.
| |
Collapse
|
21
|
Novoa-Herran S, Umaña-Perez A, Canals F, Sanchez-Gomez M. Serum depletion induces changes in protein expression in the trophoblast-derived cell line HTR-8/SVneo. Cell Mol Biol Lett 2016; 21:22. [PMID: 28536624 PMCID: PMC5415790 DOI: 10.1186/s11658-016-0018-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/05/2016] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND How nutrition and growth factor restriction due to serum depletion affect trophoblast function remains poorly understood. We performed a proteomic differential study of the effects of serum depletion on a first trimester human immortalized trophoblast cell line. METHODS The viability of HTR-8/SVneo trophoblast cells in culture with 0, 0.5 and 10 % fetal bovine serum (FBS) were assayed via MTT at 24, 48 and 64 h. A comparative proteomic analysis of the cells grown with those FBS levels for 24 h was performed using two-dimensional electrophoresis (2DE), followed by mass spectrometry for protein spot identification, and a database search and bioinformatics analysis of the expressed proteins. Differential spots were identified using the Kolmogorov-Smirnov test (n = 3, significance level 0.10, D > 0.642) and/or ANOVA (n = 3, p < 0.05). RESULTS The results showed that low serum doses or serum depletion differentially affect cell growth and protein expression. Differential expression was seen in 25 % of the protein spots grown with 0.5 % FBS and in 84 % of those grown with 0 % FBS, using 10 % serum as the physiological control. In 0.5 % FBS, this difference was related with biological processes typically affected by the serum, such as cell cycle, regulation of apoptosis and proliferation. In addition to these changes, in the serum-depleted proteome we observed downregulation of keratin 8, and upregulation of vimentin, the glycolytic enzymes enolase and pyruvate kinase (PKM2) and tumor progression-related inosine-5'-monophosphate dehydrogenase 2 (IMPDH2) enzyme. The proteins regulated by total serum depletion, but not affected by growth in 0.5 % serum, are members of the glycolytic and nucleotide metabolic pathways and the epithelial-to-mesenchymal transition (EMT), suggesting an adaptive switch characteristic of malignant cells. CONCLUSIONS This comparative proteomic analysis and the identified proteins are the first evidence of a protein expression response to serum depletion in a trophoblast cell model. Our results show that serum depletion induces specific changes in protein expression concordant with main cell metabolic adaptations and EMT, resembling the progression to a malignant phenotype.
Collapse
Affiliation(s)
- Susana Novoa-Herran
- Departamento de Química, Grupo de Investigación en Hormonas (Hormone Research Laboratory), Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Cra 30 45-03 Ed 451 Of 464, AA 111321 Bogotá, Colombia
| | - Adriana Umaña-Perez
- Departamento de Química, Grupo de Investigación en Hormonas (Hormone Research Laboratory), Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Cra 30 45-03 Ed 451 Of 464, AA 111321 Bogotá, Colombia
| | - Francesc Canals
- Laboratory of Proteomics, Vall d'Hebron Institute of Oncology (VHIO), Centre Cellex, C Natzaret 115-117, 08035 Barcelona, Spain
| | - Myriam Sanchez-Gomez
- Departamento de Química, Grupo de Investigación en Hormonas (Hormone Research Laboratory), Universidad Nacional de Colombia, Sede Bogotá, Facultad de Ciencias, Cra 30 45-03 Ed 451 Of 464, AA 111321 Bogotá, Colombia
| |
Collapse
|
22
|
Scholz E, Mestre-Ferrer A, Daura X, García-Medel N, Carrascal M, James EA, Kwok WW, Canals F, Álvarez I. A Comparative Analysis of the Peptide Repertoires of HLA-DR Molecules Differentially Associated With Rheumatoid Arthritis. Arthritis Rheumatol 2016; 68:2412-21. [PMID: 27158783 DOI: 10.1002/art.39736] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/26/2016] [Indexed: 02/04/2023]
Abstract
OBJECTIVE To evaluate similarity of the peptide repertoires bound to HLA-DR molecules that are differentially associated with rheumatoid arthritis (RA), and to define structural features of the shared peptides. METHODS Peptide pools bound to HLA-DRB1*01:01, HLA-DRB1*04:01, and HLA-DRB1*10:01 (RA associated) and those bound to HLA-DRB1*15:01 (non-RA-associated) were purified and analyzed by liquid chromatography (LC) matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MS) and LC-ion-trap MS. Peptide pools from each allotype were compared in terms of size, protein origin, composition, and affinity (both theoretical and experimental with some peptides). Finally, 1 peptide sequenced from DR1, DR4, and DR10, but not from DR15, was modeled in complex with all 4 HLA-DRB1 molecules and HLA-DRB5*01:01. RESULTS A total of 6,309 masses and 962 unique peptide sequences were compared. DR10 shared 29 peptides with DR1, 9 with DR4, and 1 with DR15; DR1 shared 6 peptides with DR4 and 9 with DR15; and DR4 and DR15 shared 4 peptides. The direct identification of peptide ligands indicated that DR1 and DR10 were the most similar molecules regarding the peptides that they could share. The peptides common to these molecules contained a high proportion of Leu at P4 and basic residues at P8 binding core positions. CONCLUSION The degree of overlap between peptide repertoires associated with different HLA-DR molecules is low. The repertoires associated with DR1 and DR10 have the highest similarity among the molecules analyzed (∼10% overlap). Among the peptides shared between DR1 and DR10, a high proportion contained Leu(4) and basic residues at the P8 position of the binding core.
Collapse
Affiliation(s)
- Erika Scholz
- Institut de Biotecnologia i de Biomedicina and Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Anna Mestre-Ferrer
- Institut de Biotecnologia i de Biomedicina and Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Xavier Daura
- Institut de Biotecnologia i de Biomedicina and Universitat Autònoma de Barcelona, Bellaterra, Spain, and Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | | | - Montserrat Carrascal
- CSIC/UAB Proteomics Laboratory, IIBB-CSIC/Institut d'Investigacions Biomèdiques August Pi i Sunyer, Bellaterra, Spain
| | - Eddie A James
- Benaroya Research Institute at Virginia Mason, Seattle, Washington
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, Washington
| | - Francesc Canals
- Vall d'Hebron University Hospital Research Institute Proteomics Laboratory, Barcelona, Spain
| | - Iñaki Álvarez
- Institut de Biotecnologia i de Biomedicina and Universitat Autònoma de Barcelona, Bellaterra, Spain.
| |
Collapse
|
23
|
Canals F, Elortza F, Paradela A, Corthals G, Camenzuli M, Muñoz A, Schiltz O, Gonzalez de Peredo A, Sickman A, Borchers C, Corrales FJ. The EuPA Standardization Initiative. EuPA Open Proteomics 2016. [DOI: 10.1016/j.euprot.2016.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
24
|
Aguilera Ó, González-Sancho JM, Zazo S, Rincón R, Fernández AF, Tapia O, Canals F, Morte B, Calvanese V, Orgaz JL, Niell N, Aguilar S, Freije JM, Graña O, Pisano DG, Borrero A, Martínez-Useros J, Jiménez B, Fraga MF, García-Foncillas J, López-Otín C, Lafarga M, Rojo F, Muñoz A. Nuclear DICKKOPF-1 as a biomarker of chemoresistance and poor clinical outcome in colorectal cancer. Oncotarget 2016; 6:5903-17. [PMID: 25788273 PMCID: PMC4467410 DOI: 10.18632/oncotarget.3464] [Citation(s) in RCA: 26] [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: 10/29/2014] [Accepted: 01/22/2015] [Indexed: 12/25/2022] Open
Abstract
Sporadic colorectal cancer (CRC) insurgence and progression depend on the activation of Wnt/β-catenin signaling. Dickkopf (DKK)-1 is an extracellular inhibitor of Wnt/β-catenin signaling that also has undefined β-catenin-independent actions. Here we report for the first time that a proportion of DKK-1 locates within the nucleus of healthy small intestine and colon mucosa, and of CRC cells at specific chromatin sites of active transcription. Moreover, we show that DKK-1 regulates several cancer-related genes including the cancer stem cell marker aldehyde dehydrogenase 1A1 (ALDH1A1) and Ral-binding protein 1-associated Eps domain-containing 2 (REPS2), which are involved in detoxification of chemotherapeutic agents. Nuclear DKK-1 expression is lost along CRC progression; however, it remains high in a subset (15%) of CRC patients (n = 699) and associates with decreased progression-free survival (PFS) after chemotherapy administration and overall survival (OS) [adjusted HR, 1.65; 95% confidence interval (CI), 1.23-2.21; P = 0.002)]. Overexpression of ALDH1A1 and REPS2 associates with nuclear DKK-1 expression in tumors and correlates with decreased OS (P = 0.001 and 0.014) and PFS. In summary, our findings demonstrate a novel location of DKK-1 within the cell nucleus and support a role of nuclear DKK-1 as a predictive biomarker of chemoresistance in colorectal cancer.
Collapse
Affiliation(s)
- Óscar Aguilera
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, Madrid, Spain.,Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, Madrid, Spain
| | - José Manuel González-Sancho
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, Madrid, Spain
| | - Sandra Zazo
- Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, Madrid, Spain
| | - Raúl Rincón
- Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, Madrid, Spain
| | - Agustín F Fernández
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, Oviedo, Spain
| | - Olga Tapia
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria-IFIMAV, Santander, Spain.,Present address: The Scripps Research Institute, La Jolla, CA, USA
| | - Francesc Canals
- Proteomics Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain
| | - Beatriz Morte
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Vincenzo Calvanese
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, Oviedo, Spain.,Present address: Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, CA, USA
| | - José L Orgaz
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, Madrid, Spain.,Present address: Randall Division of Cell and Molecular Biophysics, King's College London, United Kingdom
| | - Núria Niell
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, Madrid, Spain
| | - Susana Aguilar
- Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - José M Freije
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Osvaldo Graña
- Bioinformatics Unit and Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - David G Pisano
- Bioinformatics Unit and Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Aurea Borrero
- Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, Madrid, Spain
| | | | - Benilde Jiménez
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, Madrid, Spain
| | - Mario F Fraga
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, Oviedo, Spain.,Department of Immunology and Oncology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain
| | | | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Miguel Lafarga
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria-IFIMAV, Santander, Spain
| | - Federico Rojo
- Instituto de Investigación Sanitaria-Fundación Jiménez Díaz, Madrid, Spain
| | - Alberto Muñoz
- Instituto de Investigaciones Biomédicas "Alberto Sols", Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid, Madrid, Spain
| |
Collapse
|
25
|
Llombart V, García-Berrocoso T, Bech-Serra JJ, Simats A, Bustamante A, Giralt D, Reverter-Branchat G, Canals F, Hernández-Guillamon M, Montaner J. Characterization of secretomes from a human blood brain barrier endothelial cells in-vitro model after ischemia by stable isotope labeling with aminoacids in cell culture (SILAC). J Proteomics 2015; 133:100-112. [PMID: 26718731 DOI: 10.1016/j.jprot.2015.12.011] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 12/04/2015] [Accepted: 12/17/2015] [Indexed: 10/22/2022]
Abstract
UNLABELLED The human immortalized brain endothelial cell line hCMEC/D3 is considered a simple in-vitro model of the blood-brain-barrier. Our aim was to characterize changes in the secretome of hCMEC/D3 subjected to oxygen and glucose deprivation (OGD) to identify new proteins altered after ischemia and that might trigger blood-brain-barrier disruption and test their potential as blood biomarkers for ischemic stroke. Using a quantitative proteomic approach based on SILAC, 19 proteins were found differentially secreted between OGD and normoxia/normoglycemia conditions. Among the OGD-secreted proteins, protein folding was the main molecular function identified and for the main canonical pathways there was an enrichment in epithelial adherens junctions and aldosterone signaling. Western blot was used to verify the MS results in a set of 9 differentially secreted proteins and 5 of these were analyzed in serum samples of 38 ischemic stroke patients, 18 stroke-mimicking conditions and 18 healthy controls. SIGNIFICANCE "We characterized changes in the secretome of hCMEC/D3 cells after an ischemic insult by SILAC and identified proteins associated with ischemia that might be involved in the disruption of the blood-brain barrier. Besides we analyzed the putative potential of the candidate proteins to become biomarkers for the diagnosis of ischemic stroke.
Collapse
Affiliation(s)
- Victor Llombart
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Teresa García-Berrocoso
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Joan Josep Bech-Serra
- Proteomics Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Alba Simats
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Alejandro Bustamante
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Dolors Giralt
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Gemma Reverter-Branchat
- Proteomics Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Francesc Canals
- Proteomics Laboratory, Vall d'Hebron Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Mar Hernández-Guillamon
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Joan Montaner
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.
| |
Collapse
|
26
|
Ferrer-Mayorga G, Alvarez-Díaz S, Valle N, De Las Rivas J, Mendes M, Barderas R, Canals F, Tapia O, Casal JI, Lafarga M, Muñoz A. Cystatin D locates in the nucleus at sites of active transcription and modulates gene and protein expression. J Biol Chem 2015; 290:26533-48. [PMID: 26364852 DOI: 10.1074/jbc.m115.660175] [Citation(s) in RCA: 21] [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: 04/21/2015] [Indexed: 01/07/2023] Open
Abstract
Cystatin D is an inhibitor of lysosomal and secreted cysteine proteases. Strikingly, cystatin D has been found to inhibit proliferation, migration, and invasion of colon carcinoma cells indicating tumor suppressor activity that is unrelated to protease inhibition. Here, we demonstrate that a proportion of cystatin D locates within the cell nucleus at specific transcriptionally active chromatin sites. Consistently, transcriptomic analysis show that cystatin D alters gene expression, including that of genes encoding transcription factors such as RUNX1, RUNX2, and MEF2C in HCT116 cells. In concordance with transcriptomic data, quantitative proteomic analysis identified 292 proteins differentially expressed in cystatin D-expressing cells involved in cell adhesion, cytoskeleton, and RNA synthesis and processing. Furthermore, using cytokine arrays we found that cystatin D reduces the secretion of several protumor cytokines such as fibroblast growth factor-4, CX3CL1/fractalkine, neurotrophin 4 oncostatin-M, pulmonary and activation-regulated chemokine/CCL18, and transforming growth factor B3. These results support an unanticipated role of cystatin D in the cell nucleus, controlling the transcription of specific genes involved in crucial cellular functions, which may mediate its protective action in colon cancer.
Collapse
Affiliation(s)
- Gemma Ferrer-Mayorga
- From the Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, E-28029 Madrid
| | - Silvia Alvarez-Díaz
- From the Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, E-28029 Madrid
| | - Noelia Valle
- From the Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, E-28029 Madrid
| | - Javier De Las Rivas
- the Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas-Universidad de Salamanca, E-37007 Salamanca
| | - Marta Mendes
- the Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, E-28040 Madrid
| | - Rodrigo Barderas
- the Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, E-28040 Madrid
| | - Francesc Canals
- the Proteomics Laboratory, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, E-08035, and
| | - Olga Tapia
- the Departamento de Anatomía y Biología Celular, Facultad de Medicina, Universidad de Cantabria-Instituto de Investigación Valdecilla, E-39011 Santander, Spain
| | - J Ignacio Casal
- the Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, E-28040 Madrid
| | - Miguel Lafarga
- the Departamento de Anatomía y Biología Celular, Facultad de Medicina, Universidad de Cantabria-Instituto de Investigación Valdecilla, E-39011 Santander, Spain
| | - Alberto Muñoz
- From the Instituto de Investigaciones Biomédicas "Alberto Sols," Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, E-28029 Madrid,
| |
Collapse
|
27
|
Hidalgo-Galiana A, Monge M, Biron DG, Canals F, Ribera I, Cieslak A. Protein expression parallels thermal tolerance and ecologic changes in the diversification of a diving beetle species complex. Heredity (Edinb) 2015; 116:114-23. [PMID: 26328758 DOI: 10.1038/hdy.2015.80] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/26/2015] [Accepted: 07/29/2015] [Indexed: 11/09/2022] Open
Abstract
Physiological changes associated with evolutionary and ecological processes such as diversification, range expansion or speciation are still incompletely understood, especially for non-model species. Here we study differences in protein expression in response to temperature in a western Mediterranean diving beetle species complex, using two-dimensional differential gel electrophoresis with one Moroccan and one Iberian population each of Agabus ramblae and Agabus brunneus. We identified proteins with significant expression differences after thermal treatments comparing them with a reference EST library generated from one of the species of the complex (A. ramblae). The colonisation during the Middle Pleistocene of the Iberian peninsula by A. ramblae, where maximum temperatures and seasonality are lower than in the ancestral north African range, was associated with changes in the response to 27 °C in proteins related to energy metabolism. The subsequent speciation of A. brunneus from within populations of Iberian A. ramblae was associated with changes in the expression of several stress-related proteins (mostly chaperons) when exposed to 4 °C. These changes are in agreement with the known tolerance to lower temperatures of A. brunneus, which occupies a larger geographical area with a wider range of climatic conditions. In both cases, protein expression changes paralleled the evolution of thermal tolerance and the climatic conditions experienced by the species. However, although the colonisation of the Iberian peninsula did not result in morphological change, the speciation process of A. brunneus within Iberia involved genetic isolation and substantial differences in male genitalia and body size and shape.
Collapse
Affiliation(s)
- A Hidalgo-Galiana
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - M Monge
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - D G Biron
- Laboratoire 'Microorganismes: Génome et Environnement', UMR CNRS 6023, Equipe Interactions hôtes-parasites, Université Blaise Pascal, Aubière Cedex, France
| | - F Canals
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - I Ribera
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - A Cieslak
- Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| |
Collapse
|
28
|
Percy AJ, Tamura-Wells J, Albar JP, Aloria K, Amirkhani A, Araujo GD, Arizmendi JM, Blanco FJ, Canals F, Cho JY, Colomé-Calls N, Corrales FJ, Domont G, Espadas G, Fernandez-Puente P, Gil C, Haynes PA, Hernáez ML, Kim JY, Kopylov A, Marcilla M, McKay MJ, Mirzaei M, Molloy MP, Ohlund LB, Paik YK, Paradela A, Raftery M, Sabidó E, Sleno L, Wilffert D, Wolters JC, Yoo JS, Zgoda V, Parker CE, Borchers CH. Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment. EuPA Open Proteomics 2015. [DOI: 10.1016/j.euprot.2015.06.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
29
|
Rosa M, Bech-Serra JJ, Canals F, Zajac JM, Talmont F, Arsequell G, Valencia G. Optimized Proteomic Mass Spectrometry Characterization of Recombinant Human μ-Opioid Receptor Functionally Expressed in Pichia pastoris Cell Lines. J Proteome Res 2015; 14:3162-73. [PMID: 26090583 DOI: 10.1021/acs.jproteome.5b00104] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human μ-opioid receptor (hMOR) is a class-A G-protein-coupled receptor (GPCR), a prime therapeutic target for the management of moderate and severe pain. A chimeric form of the receptor has been cocrystallized with an opioid antagonist and resolved by X-ray diffraction; however, further direct structural analysis is still required to identify the active form of the receptor to facilitate the rational design of hMOR-selective agonist and antagonists with therapeutic potential. Toward this goal and in spite of the intrinsic difficulties posed by the highly hydrophobic transmembrane motives of hMOR, we have comprehensively characterized by mass spectrometry (MS) analysis the primary sequence of the functional hMOR. Recombinant hMOR was overexpressed as a C-terminal c-myc and 6-his tagged protein using an optimized expression procedure in Pichia pastoris cells. After membrane solubilization and metal-affinity chromatography purification, a procedure was devised to enhance the concentration of the receptor. Subsequent combinations of in-solution and in-gel digestions using either trypsin, chymotrypsin, or proteinase K, followed by matrix-assisted laser desorption ionization time-of-flight MS or nanoliquid chromatography coupled with tandem MS analyses afforded an overall sequence coverage of up to >80%, a level of description first attained for an opioid receptor and one of the six such high-coverage MS-based analyses of any GPCR.
Collapse
Affiliation(s)
- Mònica Rosa
- †Unit of Glycoconjugate Chemistry, Department of Biomedicinal Chemistry, Institute of Advanced Chemistry of Catalonia, Spanish National Research Council (IQAC-CSIC), 08034 Barcelona, Spain
| | - Joan Josep Bech-Serra
- ‡Proteomics Laboratory, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, ProteoRed ISCIII, 08035 Barcelona, Spain
| | - Francesc Canals
- ‡Proteomics Laboratory, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, ProteoRed ISCIII, 08035 Barcelona, Spain
| | - Jean Marie Zajac
- §Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Université Paul Sabatier, 31077 Toulouse, France
| | - Franck Talmont
- §Institut de Pharmacologie et de Biologie Structurale, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Université Paul Sabatier, 31077 Toulouse, France
| | - Gemma Arsequell
- †Unit of Glycoconjugate Chemistry, Department of Biomedicinal Chemistry, Institute of Advanced Chemistry of Catalonia, Spanish National Research Council (IQAC-CSIC), 08034 Barcelona, Spain
| | - Gregorio Valencia
- †Unit of Glycoconjugate Chemistry, Department of Biomedicinal Chemistry, Institute of Advanced Chemistry of Catalonia, Spanish National Research Council (IQAC-CSIC), 08034 Barcelona, Spain
| |
Collapse
|
30
|
Tababat-Khani P, de la Torre C, Canals F, Bennet H, Simo R, Hernandez C, Fex M, Agardh CD, Hansson O, Agardh E. Photocoagulation of human retinal pigment epithelium in vitro: unravelling the effects on ARPE-19 by transcriptomics and proteomics. Acta Ophthalmol 2015; 93:348-54. [PMID: 25604382 DOI: 10.1111/aos.12649] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 11/24/2014] [Indexed: 02/06/2023]
Abstract
PURPOSE Despite the extensive use of retinal photocoagulation for ischaemia and vascular leakage in retinal vascular disease, the molecular mechanisms behind its clinical beneficial effects are still poorly understood. One important target of laser irradiation is the retinal pigment epithelium (RPE). In this study, we aimed at identifying the isolated effects of photocoagulation of RPE at both the mRNA and protein expression levels. METHODS Human ARPE-19 cells were exposed to photocoagulation. Gene expression and protein expression were compared to untreated cells using microarray and liquid chromatography-mass spectrometry analysis. Genes and proteins queried by microarray and mass spectrometry were subjected to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database pathway analyses. RESULTS Laser irradiation resulted in an induction of the cytoprotective heat-shock protein subfamily Hsp70 as well as in a suppression of the vascular permeability factor carbonic anhydrase 9 (CA9). These expression patterns were evident at both the mRNA and protein levels. KEGG pathway analyses revealed genes and proteins involved in cellular turnover, repair and inflammation. CONCLUSIONS By characterizing the transcriptional and translational effects of laser coagulation on the RPE cells in culture, we have revealed responses, which might contribute to some of the beneficial effects obtained by photocoagulation for ischaemia and vascular leakage in retinal vascular disease.
Collapse
Affiliation(s)
- Poya Tababat-Khani
- Unit on Vascular Diabetic Complications; Department of Clinical Sciences; Lund University Diabetes Center; Malmö Sweden
| | - Carolina de la Torre
- Proteomics Laboratory; Vall d'Hebron Institute of Oncology (VHIO); Vall d'Hebron University Hospital; Universitat Autònoma de Barcelona; Barcelona Spain
| | - Francesc Canals
- Proteomics Laboratory; Vall d'Hebron Institute of Oncology (VHIO); Vall d'Hebron University Hospital; Universitat Autònoma de Barcelona; Barcelona Spain
| | - Hedvig Bennet
- Unit on Diabetes and Celiac Disease; Department of Clinical Sciences; Lund University Diabetes Center; Malmö Sweden
| | - Rafael Simo
- Diabetes and Metabolism Research Unit and CIBERDEM; Vall d'Hebron Research Institute; Universitat Autònoma de Barcelona; Barcelona Spain
| | - Cristina Hernandez
- Diabetes and Metabolism Research Unit and CIBERDEM; Vall d'Hebron Research Institute; Universitat Autònoma de Barcelona; Barcelona Spain
| | - Malin Fex
- Unit on Diabetes and Celiac Disease; Department of Clinical Sciences; Lund University Diabetes Center; Malmö Sweden
| | - Carl-David Agardh
- Unit on Vascular Diabetic Complications; Department of Clinical Sciences; Lund University Diabetes Center; Malmö Sweden
| | - Ola Hansson
- Unit on Diabetes & Endocrinology; Department of Clinical Sciences; Lund University Diabetes Center; Malmö Sweden
| | - Elisabet Agardh
- Unit on Vascular Diabetic Complications; Department of Clinical Sciences; Lund University Diabetes Center; Malmö Sweden
| |
Collapse
|
31
|
Campos A, Díaz R, Martínez-Bartolomé S, Sierra J, Gallardo O, Sabidó E, López-Lucendo M, Ignacio Casal J, Pasquarello C, Scherl A, Chiva C, Borras E, Odena A, Elortza F, Azkargorta M, Ibarrola N, Canals F, Albar JP, Oliveira E. Multicenter experiment for quality control of peptide-centric LC-MS/MS analysis - A longitudinal performance assessment with nLC coupled to orbitrap MS analyzers. J Proteomics 2015; 127:264-74. [PMID: 25982386 DOI: 10.1016/j.jprot.2015.05.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 05/07/2015] [Accepted: 05/11/2015] [Indexed: 11/19/2022]
Abstract
Proteomic technologies based on mass spectrometry (MS) have greatly evolved in the past years, and nowadays it is possible to routinely identify thousands of peptides from complex biological samples in a single LC-MS/MS experiment. Despite the advancements in proteomic technologies, the scientific community still faces important challenges in terms of depth and reproducibility of proteomics analyses. Here, we present a multicenter study designed to evaluate long-term performance of LC-MS/MS platforms within the Spanish Proteomics Facilities Network (ProteoRed-ISCIII). The study was performed under well-established standard operating procedures, and demonstrated that it is possible to attain qualitative and quantitative reproducibility over time. Our study highlights the importance of deploying quality assessment metrics routinely in individual laboratories and in multi-laboratory studies. The mass spectrometry data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000205.This article is part of a Special Issue entitled: HUPO 2014.
Collapse
Affiliation(s)
- Alex Campos
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, Barcelona, Spain; Integromics, Madrid, Spain.
| | - Ramón Díaz
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, Barcelona, Spain
| | | | | | - Oscar Gallardo
- ProteoRed-ISCIII, CSIC/UAB Proteomics Laboratory, Instituto de Investigaciones Biomédicas de Barcelona, Spanish National Research Council, Barcelona, Spain
| | - Eduard Sabidó
- ProteoRed-ISCIII, Proteomics Unit, Universitat Pompeu Fabra (UPF) and Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Maria López-Lucendo
- ProteoRed-ISCIII, Proteomics Facility and Functional Proteomics Laboratory, Centro de Investigaciones, Biológicas, Madrid, Spain
| | - J Ignacio Casal
- ProteoRed-ISCIII, Proteomics Facility and Functional Proteomics Laboratory, Centro de Investigaciones, Biológicas, Madrid, Spain
| | | | - Alexander Scherl
- Department of Human Protein Sciences, CMU, University of Geneva, Switzerland
| | - Cristina Chiva
- ProteoRed-ISCIII, Proteomics Unit, Universitat Pompeu Fabra (UPF) and Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Eva Borras
- ProteoRed-ISCIII, Proteomics Unit, Universitat Pompeu Fabra (UPF) and Centre de Regulació Genòmica (CRG), Barcelona, Spain
| | - Antonia Odena
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, Barcelona, Spain
| | - Félix Elortza
- ProteoRed-ISCIII, Proteomics Platform, CIC bioGUNE, CIBERehd, Technology Park of Bizkaia, Derio, Spain
| | - Mikel Azkargorta
- ProteoRed-ISCIII, Proteomics Platform, CIC bioGUNE, CIBERehd, Technology Park of Bizkaia, Derio, Spain
| | - Nieves Ibarrola
- ProteoRed-ISCIII, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Salamanca, Spain
| | - Francesc Canals
- ProteoRed-ISCIII, Proteomic Laboratory, Vall d'Hebron Institute of Oncology-VHIO, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Juan P Albar
- ProteoRed-ISCIII, Proteomics Facility, Centro Nacional de Biotecnología - CSIC, Madrid, Spain
| | - Eliandre Oliveira
- ProteoRed-ISCIII, Proteomics Platform, Barcelona Science Park, Barcelona, Spain
| |
Collapse
|
32
|
Martino-Echarri E, Fernández-Rodríguez R, Bech-Serra JJ, Plaza-Calonge MDC, Vidal N, Casal C, Colomé N, Seoane J, Canals F, Rodríguez-Manzaneque JC. Relevance of IGFBP2 proteolysis in glioma and contribution of the extracellular protease ADAMTS1. Oncotarget 2015; 5:4295-304. [PMID: 24962328 PMCID: PMC4147324 DOI: 10.18632/oncotarget.2009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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] [Indexed: 01/09/2023] Open
Abstract
Expression of IGFBP2 (Insulin-like Growth Factor Binding Protein 2) has been positively correlated with glioma progression. Although the proteolysis of IGFBP2 has been widely recognized, with consequences as a major modulator of IGFII signaling, the relevance of this post-translational modification has not been well studied in tumors. Using an in vivo proteomic approach by Isotope-Coded Protein Label (ICPL), we identified IGFBP2 as a target of the extracellular protease ADAMTS1 (A Disintegrin And Metalloproteinase with ThromboSpondin motifs 1). Notably, the proteolytic pattern of IGFBP2 was also detected in human glioma culture cells and, more importantly, in all glioma samples evaluated. In addition, high expression of ADAMTS1 correlates with higher levels of cleaved IGFBP2 in glioblastoma multiforme cases. Using gene expression public databases, we confirmed that IGFBP2 is a poor prognosis marker for gliomas, and we also observed an important contribution of ADAMTS1.Finally, we showed the impact of ADAMTS1 on IGFII-mediated IGF1R phosphorylation and cellular migration. Our results support a functional interaction between IGFBP2 and ADAMTS1 and suggest the need to evaluate post-translational modifications of IGFBP2 in glioma, in order to approach new therapies.
Collapse
Affiliation(s)
- Estefanía Martino-Echarri
- GENYO. Centre for Genomics and Oncological Research: Pfizer/Universidad de Granada/Junta de Andalucía, Granada, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Vilà-Rico M, Contesse S, Barcena Llona JE, Rojas-García R, Valle F, Planas A, Canals F, Campistol JM. Mass spectrometry analysis of transthyretin (TTR) post-translational modifications (PTMs) in hereditary ATTR: a case-control Spanish experience. Orphanet J Rare Dis 2015. [PMCID: PMC4642106 DOI: 10.1186/1750-1172-10-s1-p53] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
|
34
|
Esteve-Puig R, Gil R, González-Sánchez E, Bech-Serra JJ, Grueso J, Hernández-Losa J, Moliné T, Canals F, Ferrer B, Cortés J, Bastian B, Ramón y Cajal S, Martín-Caballero J, Flores JM, Vivancos A, García-Patos V, Recio JÁ. A mouse model uncovers LKB1 as an UVB-induced DNA damage sensor mediating CDKN1A (p21WAF1/CIP1) degradation. PLoS Genet 2014; 10:e1004721. [PMID: 25329316 PMCID: PMC4199501 DOI: 10.1371/journal.pgen.1004721] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 08/30/2014] [Indexed: 11/29/2022] Open
Abstract
Exposure to ultraviolet (UV) radiation from sunlight accounts for 90% of the symptoms of premature skin aging and skin cancer. The tumor suppressor serine-threonine kinase LKB1 is mutated in Peutz-Jeghers syndrome and in a spectrum of epithelial cancers whose etiology suggests a cooperation with environmental insults. Here we analyzed the role of LKB1 in a UV-dependent mouse skin cancer model and show that LKB1 haploinsufficiency is enough to impede UVB-induced DNA damage repair, contributing to tumor development driven by aberrant growth factor signaling. We demonstrate that LKB1 and its downstream kinase NUAK1 bind to CDKN1A. In response to UVB irradiation, LKB1 together with NUAK1 phosphorylates CDKN1A regulating the DNA damage response. Upon UVB treatment, LKB1 or NUAK1 deficiency results in CDKN1A accumulation, impaired DNA repair and resistance to apoptosis. Importantly, analysis of human tumor samples suggests that LKB1 mutational status could be a prognostic risk factor for UV-induced skin cancer. Altogether, our results identify LKB1 as a DNA damage sensor protein regulating skin UV-induced DNA damage response. Environmental insults are directly involved in cancer development. In particular, Ultraviolet (UV) radiation has been associated to the acquisition of different types skin cancer and premature skin aging. UV radiation causes modifications in the genetic material of cells (DNA) that if not repaired properly will lead to a mutated DNA (mutated genes) which might trigger the development of cancer. Understanding the molecular basis of the UV-induced DNA damage response is important to elucidate the mechanisms of skin homeostasis and tumorigenesis. Here we provide a UVB-induced skin cancer animal model showing that LKB1 tumor suppressor is also a DNA damage sensor. Importantly, the data suggest that reduced amounts of LKB1 protein in skin could be a risk factor for UV-induced skin carcinogenesis in humans.
Collapse
Affiliation(s)
- Rosaura Esteve-Puig
- Animal Models and Cancer Laboratory, Vall d'Hebron Research Institute (VHIR), Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Rosa Gil
- Animal Models and Cancer Laboratory, Vall d'Hebron Research Institute (VHIR), Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Elena González-Sánchez
- Animal Models and Cancer Laboratory, Vall d'Hebron Research Institute (VHIR), Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Joan Josep Bech-Serra
- Proteomic Laboratory Medical Oncology Research Program, Vall d'Hebron Institute of Oncology - VHIO, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Judit Grueso
- Animal Models and Cancer Laboratory, Vall d'Hebron Research Institute (VHIR), Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | | | - Teresa Moliné
- Pathology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Francesc Canals
- Proteomic Laboratory Medical Oncology Research Program, Vall d'Hebron Institute of Oncology - VHIO, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Berta Ferrer
- Pathology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Javier Cortés
- Clinical Oncology Program, Vall d'Hebron Institute of Oncology - VHIO, Barcelona, Spain
| | - Boris Bastian
- Department of Dermatology, University of California San Francisco, San Francisco, California, United States of America
| | | | | | - Juana Maria Flores
- Surgery and Medicine Department, Veterinary School, Universidad Complutense de Madrid, Madrid, Spain
| | - Ana Vivancos
- Cancer Genomics Group Translational Research Program, Vall d'Hebron Institute of Oncology - VHIO, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Vicenç García-Patos
- Dermatology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Juan Ángel Recio
- Animal Models and Cancer Laboratory, Vall d'Hebron Research Institute (VHIR), Hospital Universitari Vall d'Hebron, Barcelona, Spain
- * E-mail:
| |
Collapse
|
35
|
Hidalgo-Galiana A, Monge M, Biron DG, Canals F, Ribera I, Cieslak A. Reproducibility and consistency of proteomic experiments on natural populations of a non-model aquatic insect. PLoS One 2014; 9:e104734. [PMID: 25133588 PMCID: PMC4136769 DOI: 10.1371/journal.pone.0104734] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 07/15/2014] [Indexed: 01/13/2023] Open
Abstract
Population proteomics has a great potential to address evolutionary and ecological questions, but its use in wild populations of non-model organisms is hampered by uncontrolled sources of variation. Here we compare the response to temperature extremes of two geographically distant populations of a diving beetle species (Agabus ramblae) using 2-D DIGE. After one week of acclimation in the laboratory under standard conditions, a third of the specimens of each population were placed at either 4 or 27°C for 12 h, with another third left as a control. We then compared the protein expression level of three replicated samples of 2-3 specimens for each treatment. Within each population, variation between replicated samples of the same treatment was always lower than variation between treatments, except for some control samples that retained a wider range of expression levels. The two populations had a similar response, without significant differences in the number of protein spots over- or under-expressed in the pairwise comparisons between treatments. We identified exemplary proteins among those differently expressed between treatments, which proved to be proteins known to be related to thermal response or stress. Overall, our results indicate that specimens collected in the wild are suitable for proteomic analyses, as the additional sources of variation were not enough to mask the consistency and reproducibility of the response to the temperature treatments.
Collapse
Affiliation(s)
- Amparo Hidalgo-Galiana
- Animal Biodiversity and Evolution program, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Marta Monge
- Vall d'Hebron Institute of Oncology (VHIO) Edifici Collserola, Barcelona, Spain
| | - David G. Biron
- Laboratoire “Microorganismes: Génome et Environnement”, UMR CNRS 6023, Equipe Interactions hôtes-parasites, Université Blaise Pascal, Aubière, France
| | - Francesc Canals
- Vall d'Hebron Institute of Oncology (VHIO) Edifici Collserola, Barcelona, Spain
| | - Ignacio Ribera
- Animal Biodiversity and Evolution program, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Alexandra Cieslak
- Animal Biodiversity and Evolution program, Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| |
Collapse
|
36
|
Beaulieu M, Whitfield J, Jauset T, Massó-Vallés D, Serrano E, Canals F, Lavigne P, Montagne M, Maltais L, Soucek L. 773: A novel pharmacological approach to inhibit Myc in cancer. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)50678-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
37
|
Campos-Martorell M, Salvador N, Monge M, Canals F, García-Bonilla L, Hernández-Guillamon M, Ayuso MI, Chacón P, Rosell A, Alcazar A, Montaner J. Brain proteomics identifies potential simvastatin targets in acute phase of stroke in a rat embolic model. J Neurochem 2014; 130:301-12. [PMID: 24661059 DOI: 10.1111/jnc.12719] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [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: 12/15/2013] [Revised: 03/12/2014] [Accepted: 03/18/2014] [Indexed: 12/19/2022]
Abstract
Finding an efficient neuroprotectant is of urgent need in the field of stroke research. The goal of this study was to test the effect of acute simvastatin administration after stroke in a rat embolic model and to explore its mechanism of action through brain proteomics. To that end, male Wistar rats were subjected to a Middle Cerebral Arteria Occlusion and simvastatin (20 mg/kg s.c) (n = 11) or vehicle (n = 9) were administered 15 min after. To evaluate the neuroprotective mechanisms of simvastatin, brain homogenates after 48 h were analyzed by two-dimensional fluorescence Difference in Gel Electrophoresis (DIGE) technology. We confirmed that simvastatin reduced the infarct volume and improved neurological impairment at 48 h after the stroke in this model. Considering our proteomics analysis, 66 spots, which revealed significant differences between groups, were analyzed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry allowing the identification of 27 proteins. From these results, we suggest that simvastatin protective effect can be partly explained by the attenuation of the oxidative and stress response at blood-brain barrier level after cerebral ischemia. Interestingly, analyzing one of the proteins (HSP75) in plasma from stroke patients who had received simvastatin during the acute phase, we confirmed the results found in the pre-clinical model. Our aim was to study statins benefits when administered during the acute phase of stroke and to explore its mechanisms of action through brain proteomics assay. Using an embolic model, simvastatin-treated rats showed significant infarct volume reduction and neurological improvement compared to vehicle-treated group. Analyzing their homogenated brains by two-dimensional fluorescence Difference in Gel Electrophoresis (DIGE) technology, we concluded that the protective effect of simvastatin can be attributable to oxidative stress response attenuation and blood-brain barrier protection after cerebral ischemia.
Collapse
Affiliation(s)
- Mireia Campos-Martorell
- Neurovascular Research Laboratory, Institut de Recerca Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Fraga H, Bech-Serra JJ, Canals F, Ortega G, Millet O, Ventura S. The mitochondrial intermembrane space oxireductase Mia40 funnels the oxidative folding pathway of the cytochrome c oxidase assembly protein Cox19. J Biol Chem 2014; 289:9852-64. [PMID: 24569988 DOI: 10.1074/jbc.m114.553479] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mia40-catalyzed disulfide formation drives the import of many proteins into the mitochondria. Here we characterize the oxidative folding of Cox19, a twin CX9C Mia40 substrate. Cox19 oxidation is extremely slow, explaining the persistence of import-competent reduced species in the cytosol. Mia40 accelerates Cox19 folding through the specific recognition of the third Cys in the second helical CX9C motif and the subsequent oxidation of the inner disulfide bond. This renders a native-like intermediate that oxidizes in a slow uncatalyzed reaction into native Cox19. The same intermediate dominates the pathway in the absence of Mia40, and chemical induction of an α-helical structure by trifluoroethanol suffices to accelerate productive folding and mimic the Mia40 folding template mechanism. The Mia40 role is to funnel a rough folding landscape, skipping the accumulation of kinetic traps, providing a rationale for the promiscuity of Mia40.
Collapse
Affiliation(s)
- Hugo Fraga
- From the Institut de Biotecnologia i Biomedicina and
| | | | | | | | | | | |
Collapse
|
39
|
García-Berrocoso T, Penalba A, Boada C, Giralt D, Cuadrado E, Colomé N, Dayon L, Canals F, Sanchez JC, Rosell A, Montaner J. From brain to blood: New biomarkers for ischemic stroke prognosis. J Proteomics 2013; 94:138-48. [DOI: 10.1016/j.jprot.2013.09.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 09/02/2013] [Accepted: 09/14/2013] [Indexed: 11/26/2022]
|
40
|
|
41
|
Segura V, Medina-Aunon JA, Mora MI, Martínez-Bartolomé S, Abian J, Aloria K, Antúnez O, Arizmendi JM, Azkargorta M, Barceló-Batllori S, Beaskoetxea J, Bech-Serra JJ, Blanco F, Monteiro MB, Cáceres D, Canals F, Carrascal M, Casal JI, Clemente F, Colomé N, Dasilva N, Díaz P, Elortza F, Fernández-Puente P, Fuentes M, Gallardo O, Gharbi SI, Gil C, González-Tejedo C, Hernáez ML, Lombardía M, Lopez-Lucendo M, Marcilla M, Mato JM, Mendes M, Oliveira E, Orera I, Pascual-Montano A, Prieto G, Ruiz-Romero C, Sánchez del Pino MM, Tabas-Madrid D, Valero ML, Vialas V, Villanueva J, Albar JP, Corrales FJ. Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome. J Proteome Res 2013; 13:158-72. [PMID: 24138474 DOI: 10.1021/pr400721r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The Spanish team of the Human Proteome Project (SpHPP) marked the annotation of Chr16 and data analysis as one of its priorities. Precise annotation of Chromosome 16 proteins according to C-HPP criteria is presented. Moreover, Human Body Map 2.0 RNA-Seq and Encyclopedia of DNA Elements (ENCODE) data sets were used to obtain further information relative to cell/tissue specific chromosome 16 coding gene expression patterns and to infer the presence of missing proteins. Twenty-four shotgun 2D-LC-MS/MS and gel/LC-MS/MS MIAPE compliant experiments, representing 41% coverage of chromosome 16 proteins, were performed. Furthermore, mapping of large-scale multicenter mass spectrometry data sets from CCD18, MCF7, Jurkat, and Ramos cell lines into RNA-Seq data allowed further insights relative to correlation of chromosome 16 transcripts and proteins. Detection and quantification of chromosome 16 proteins in biological matrices by SRM procedures are also primary goals of the SpHPP. Two strategies were undertaken: one focused on known proteins, taking advantage of MS data already available, and the second, aimed at the detection of the missing proteins, is based on the expression of recombinant proteins to gather MS information and optimize SRM methods that will be used in real biological samples. SRM methods for 49 known proteins and for recombinant forms of 24 missing proteins are reported in this study.
Collapse
Affiliation(s)
- Víctor Segura
- ProteoRed-ISCIII, Center for Applied Medical Research (CIMA), University of Navarra , Pío XII, 55; Ed. CIMA, 31008 Pamplona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Espinosa G, Collado JA, Scholz E, Mestre-Ferrer A, Kuse N, Takiguchi M, Carrascal M, Canals F, Pujol-Borrell R, Jaraquemada D, Alvarez I. Peptides presented by HLA class I molecules in the human thymus. J Proteomics 2013; 94:23-36. [PMID: 24029068 DOI: 10.1016/j.jprot.2013.08.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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: 06/11/2013] [Revised: 08/26/2013] [Accepted: 08/28/2013] [Indexed: 12/31/2022]
Abstract
UNLABELLED The thymus is the organ in which T lymphocytes mature. Thymocytes undergo exhaustive selection processes that require interactions between the TCRs and peptide-HLA complexes on thymus antigen-presenting cells. The thymic peptide repertoire associated with HLA molecules must mirror the peptidome that mature T cells will encounter at the periphery, including peptides that arise from tissue-restricted antigens. The transcriptome of specific thymus cell populations has been widely studied, but there are no data on the HLA-I peptidome of the human thymus. Here, we describe the HLA-I-bound peptide repertoire from thymus samples, showing that it is mostly composed of high-affinity ligands from cytosolic and nuclear proteins. Several proteins generated more than one peptide, and some redundant peptides were found in different samples, suggesting the existence of antigen immunodominance during the processes that lead to central tolerance. Three HLA-I ligands were found to be derived from proteins expressed by stromal cells, including one from the protein TBATA (or SPATIAL), which is present in the thymus, brain and testis. The expression of TBATA in medullary thymic epithelial cells has been reported to be AIRE dependent. Thus, this report describes the first identification of a thymus HLA-I natural ligand derived from an AIRE-dependent protein with restricted tissue expression. BIOLOGICAL SIGNIFICANCE We present the first description of the HLA-I-bound peptide repertoire from ex vivo thymus samples. This repertoire is composed of standard ligands from cytosolic and nuclear proteins. Some peptides seem to be dominantly presented to thymocytes in the thymus. Most importantly, some HLA-I associated ligands derived from proteins expressed by stromal cells, including one peptide, restricted by HLA-A*31:01, arising from an AIRE-dependent protein with restricted tissue expression.
Collapse
Affiliation(s)
- Gabriel Espinosa
- Immunology Unit, Department of Cell Biology, Physiology and Immunology and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Hernández C, García-Ramírez M, Colomé N, Corraliza L, García-Pascual L, Casado J, Canals F, Simó R. Identification of new pathogenic candidates for diabetic macular edema using fluorescence-based difference gel electrophoresis analysis. Diabetes Metab Res Rev 2013; 29:499-506. [PMID: 23568601 DOI: 10.1002/dmrr.2419] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [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: 10/22/2012] [Revised: 03/20/2013] [Accepted: 03/30/2013] [Indexed: 11/08/2022]
Abstract
BACKGROUND Diabetic macular edema is the main cause of visual impairment in diabetic patients. The aim of the present study was to explore the differential proteomic pattern of the vitreous fluid from diabetic macular edema patients by means of fluorescence-based difference gel electrophoresis (DIGE). METHODS Samples of vitreous from eight type 2 diabetic patients [four with diabetic macular edema without proliferative diabetic retinopathy and four with proliferative diabetic retinopathy without diabetic macular edema), and eight from non-diabetic subjects with idiopathic macular hole (control group) were selected from our vitreous bank for proteomic analysis. To further confirm the potential candidates identified by DIGE, 18 additional samples (six proliferative diabetic retinopathy, six diabetic macular edema and six macular hole, matched by age) were analysed by enzyme-linked immuno sorbent assay (ELISA). RESULTS Selecting an abundance ratio of 1.5-fold, p < 0.05, as the threshold for the study, four proteins were specifically associated with diabetic macular edema. Hemopexin was significantly higher in the vitreous fluid of patients with diabetic macular edema in comparison with both control subjects and proliferative diabetic retinopathy patients. By contrast, clusterin, transthyretin and crystallin S were significantly decreased in the vitreous of patients with diabetic macular edema. The differential production of hemopexin, clusterin and transthyretin was further confirmed by ELISA. CONCLUSIONS Proteomic analysis by DIGE was useful in identifying new potential candidates involved in the pathogenesis of diabetic macular edema. These results could open up new strategies in the treatment of diabetic macular edema.
Collapse
Affiliation(s)
- Cristina Hernández
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Instituto de Salud Carlos III, Barcelona, Spain; Diabetes and Metabolism Research Unit, Vall Hebron Institut de Recerca, Barcelona, Spain
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Collado JA, Alvarez I, Ciudad MT, Espinosa G, Canals F, Pujol-Borrell R, Carrascal M, Abian J, Jaraquemada D. Composition of the HLA-DR-associated human thymus peptidome. Eur J Immunol 2013; 43:2273-82. [PMID: 23719902 DOI: 10.1002/eji.201243280] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [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: 12/20/2012] [Revised: 04/17/2013] [Accepted: 05/27/2013] [Indexed: 11/05/2022]
Abstract
Major histocompatibility complex class II (MHC-II) molecules bind to and display antigenic peptides on the surface of antigen-presenting cells (APCs). In the absence of infection, MHC-II molecules on APCs present self-peptides and interact with CD4(+) T cells to maintain tolerance and homeostasis. In the thymus, self-peptides bind to MHC-II molecules expressed by defined populations of APCs specialised for the different steps of T-cell selection. Cortical epithelial cells present peptides for positive selection, whereas medullary epithelial cells and dendritic cells are responsible for peptide presentation for negative selection. However, few data are available on the peptides presented by MHC molecules in the thymus. Here, we apply mass spectrometry to analyse and identify MHC-II-associated peptides from five fresh human thymus samples. The data show a diverse self-peptide repertoire, mostly consisting of predicted MHC-II high binders. Despite technical limitations preventing single cell population analyses of peptides, these data constitute the first direct assessment of the HLA-II-bound peptidome and provide insight into how this peptidome is generated and how it drives T-cell repertoire formation.
Collapse
Affiliation(s)
- Javier A Collado
- Immunology Unit, Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Barcelona, Spain; Departament de Biologia Cel·lular, Fisiologia i Immunologia (BCFI), Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Martínez-Bartolomé S, Deutsch EW, Binz PA, Jones AR, Eisenacher M, Mayer G, Campos A, Canals F, Bech-Serra JJ, Carrascal M, Gay M, Paradela A, Navajas R, Marcilla M, Hernáez ML, Gutiérrez-Blázquez MD, Velarde LFC, Aloria K, Beaskoetxea J, Medina-Aunon JA, Albar JP. Guidelines for reporting quantitative mass spectrometry based experiments in proteomics. J Proteomics 2013; 95:84-8. [PMID: 23500130 DOI: 10.1016/j.jprot.2013.02.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Revised: 02/25/2013] [Accepted: 02/27/2013] [Indexed: 10/27/2022]
Abstract
UNLABELLED Mass spectrometry is already a well-established protein identification tool and recent methodological and technological developments have also made possible the extraction of quantitative data of protein abundance in large-scale studies. Several strategies for absolute and relative quantitative proteomics and the statistical assessment of quantifications are possible, each having specific measurements and therefore, different data analysis workflows. The guidelines for Mass Spectrometry Quantification allow the description of a wide range of quantitative approaches, including labeled and label-free techniques and also targeted approaches such as Selected Reaction Monitoring (SRM). BIOLOGICAL SIGNIFICANCE The HUPO Proteomics Standards Initiative (HUPO-PSI) has invested considerable efforts to improve the standardization of proteomics data handling, representation and sharing through the development of data standards, reporting guidelines, controlled vocabularies and tooling. In this manuscript, we describe a key output from the HUPO-PSI-namely the MIAPE Quant guidelines, which have developed in parallel with the corresponding data exchange format mzQuantML [1]. The MIAPE Quant guidelines describe the HUPO-PSI proposal concerning the minimum information to be reported when a quantitative data set, derived from mass spectrometry (MS), is submitted to a database or as supplementary information to a journal. The guidelines have been developed with input from a broad spectrum of stakeholders in the proteomics field to represent a true consensus view of the most important data types and metadata, required for a quantitative experiment to be analyzed critically or a data analysis pipeline to be reproduced. It is anticipated that they will influence or be directly adopted as part of journal guidelines for publication and by public proteomics databases and thus may have an impact on proteomics laboratories across the world. This article is part of a Special Issue entitled: Standardization and Quality Control.
Collapse
Affiliation(s)
- Salvador Martínez-Bartolomé
- Proteomics Facility, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), ProteoRed ISCIII, Madrid, Spain.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Angelini PD, Zacarias Fluck MF, Pedersen K, Parra-Palau JL, Guiu M, Bernadó Morales C, Vicario R, Luque-García A, Navalpotro NP, Giralt J, Canals F, Gomis RR, Tabernero J, Baselga J, Villanueva J, Arribas J. Constitutive HER2 signaling promotes breast cancer metastasis through cellular senescence. Cancer Res 2013; 73:450-8. [PMID: 23288917 DOI: 10.1158/0008-5472.can-12-2301] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [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
Senescence, a terminal cell proliferation arrest, can be triggered by oncogenes. Oncogene-induced senescence is classically considered a tumor defense barrier. However, several findings show that, under certain circumstances, senescent cells may favor tumor progression because of their secretory phenotype. Here, we show that the expression in different breast epithelial cell lines of p95HER2, a constitutively active fragment of the tyrosine kinase receptor HER2, results in either increased proliferation or senescence. In senescent cells, p95HER2 elicits a secretome enriched in proteases, cytokines, and growth factors. This secretory phenotype is not a mere consequence of the senescence status and requires continuous HER2 signaling to be maintained. Underscoring the functional relevance of the p95HER2-induced senescence secretome, we show that p95HER2-induced senescent cells promote metastasis in vivo in a non-cell-autonomous manner.
Collapse
Affiliation(s)
- Pier Davide Angelini
- Preclinical Research, Vall d'Hebron Institute of Oncology (VHIO, Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Segura V, Medina-Aunon JA, Guruceaga E, Gharbi SI, González-Tejedo C, Sánchez del Pino MM, Canals F, Fuentes M, Casal JI, Martínez-Bartolomé S, Elortza F, Mato JM, Arizmendi JM, Abian J, Oliveira E, Gil C, Vivanco F, Blanco F, Albar JP, Corrales FJ. Spanish human proteome project: dissection of chromosome 16. J Proteome Res 2012; 12:112-22. [PMID: 23234512 DOI: 10.1021/pr300898u] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The Chromosome 16 Consortium forms part of the Human Proteome Project that aims to develop an entire map of the proteins encoded by the human genome following a chromosome-centric strategy (C-HPP) to make progress in the understanding of human biology in health and disease (B/D-HPP). A Spanish consortium of 16 laboratories was organized into five working groups: Protein/Antibody microarrays, protein expression and Peptide Standard, S/MRM, Protein Sequencing, Bioinformatics and Clinical healthcare, and Biobanking. The project is conceived on a multicenter configuration, assuming the standards and integration procedures already available in ProteoRed-ISCIII, which is encompassed within HUPO initiatives. The products of the 870 protein coding genes in chromosome 16 were analyzed in Jurkat T lymphocyte cells, MCF-7 epithelial cells, and the CCD18 fibroblast cell line as it is theoretically expected that most chromosome 16 protein coding genes are expressed in at least one of these. The transcriptome and proteome of these cell lines was studied using gene expression microarray and shotgun proteomics approaches, indicating an ample coverage of chromosome 16. With regard to the B/D section, the main research areas have been adopted and a biobanking initiative has been designed to optimize methods for sample collection, management, and storage under normalized conditions and to define QC standards. The general strategy of the Chr-16 HPP and the current state of the different initiatives are discussed.
Collapse
Affiliation(s)
- V Segura
- ProteoRed-ISCIII, Center for Applied Medical Research, CIMA, University of Navarra, Pamplona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Koziol A, Gonzalo P, Mota A, Pollán Á, Lorenzo C, Colomé N, Montaner D, Dopazo J, Arribas J, Canals F, Arroyo AG. The protease MT1-MMP drives a combinatorial proteolytic program in activated endothelial cells. FASEB J 2012; 26:4481-94. [PMID: 22859368 DOI: 10.1096/fj.12-205906] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The mechanism by which proteolytic events translate into biological responses is not well understood. To explore the link of pericellular proteolysis to events relevant to capillary sprouting within the inflammatory context, we aimed at the identification of the collection of substrates of the protease MT1-MMP in endothelial tip cells induced by inflammatory stimuli. We applied quantitative proteomics to endothelial cells (ECs) derived from wild-type and MT1-MMP-null mice to identify the substrate repertoire of this protease in TNF-α-activated ECs. Bioinformatics analysis revealed a combinatorial MT1-MMP proteolytic program, in which combined rather than single substrate processing would determine biological decisions by activated ECs, including chemotaxis, cell motility and adhesion, and vasculature development. MT1-MMP-deficient ECs inefficiently processed several of these substrates (TSP1, CYR61, NID1, and SEM3C), validating the model. This novel concept of MT1-MMP-driven combinatorial proteolysis in angiogenesis might be extendable to proteolytic actions in other cellular contexts.
Collapse
Affiliation(s)
- Agnieszka Koziol
- Vascular Biology Department, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Lecube A, Poca MA, Colomé N, Bech-Serra JJ, Hernández C, García-Ramírez M, Gándara D, Canals F, Simó R. Proteomic analysis of cerebrospinal fluid from obese women with idiopathic intracranial hypertension: a new approach for identifying new candidates in the pathogenesis of obesity. J Neuroendocrinol 2012; 24:944-52. [PMID: 22296024 DOI: 10.1111/j.1365-2826.2012.02288.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Body weight control is tightly regulated in the hypothalamus. The inaccessibility of human brain tissue can be partially solved by using cerebrospinal fluid (CSF) as a tool for assessing the central nervous system's production of orexigen and anorexigen factors. Using proteomic analysis, the present study investigated the differentially displayed proteins in human CSF from obese and non-obese subjects. We designed a case-control study conducted in a reference hospital where eight obese (cases) and eight non-obese (controls) women with idiopathic intracranial hypertension were included. Intracranial hypertension was normalised through the placement of a ventriculo- or lumboperitoneal shunt in the 12 months before their inclusion in the study. Isotope-coded protein label (for proteins > 10 kDa) and label-free liquid chromatography (for proteins < 10 kDa) associated with mass spectrometry analysis were used. Eighteen differentially expressed proteins were identified. Many of them fall into three main groups: inflammation (osteopontin, fibrinogen γ and β chain, α1 acid glycoprotein 2 and haptoglobin), neuroendocrine mediators (neurosecretory protein VGF, neuroendocrine protein 7B2, chromogranin-A and chromogranin B), and brain plasticity (testican-1, isoform 10 of fibronectin, galectin-3 binding protein and metalloproteinase inhibitor type 2). The differential production of osteopontin, neurosecretory protein VGF, chromogranin-A and fibrinogen γ chain was further confirmed by either enzyme-linked immunosorbent assay or western blotting. In conclusion, we have identified potential candidates that could be involved in the pathogenesis of obesity. Further studies aiming to investigating the precise role of these proteins in the pathogenesis of obesity and their potential therapeutic implications are needed.
Collapse
Affiliation(s)
- A Lecube
- Department of Endocrinology, CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III (ISCIII), Diabetes and Metabolism Research Unit, Institut de Recerca i Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Abstract
Mycoplasma genitalium is a human pathogen associated with several sexually transmitted diseases. Proteomic technologies, along with other methods for global gene expression analysis, play a key role in understanding the mechanisms of bacterial pathogenesis and physiology. The proteome of M. genitalium, model of a minimal cell, has been extended using a combination of different proteomic approaches and technologies. The total proteome of this microorganism has been analyzed using gel-based and gel-free approaches, achieving the identification of 85.3% of the predicted ORFs. In addition, a comprehensive analysis of membrane subproteome has been performed. For this purpose, the TX-114 soluble fraction has been analyzed as well as the surface proteins, using cell-surface protein labeling with CyDye. Finally, the serological response of M. genitalium-infected patients and healthy donors has been analyzed to identify proteins that trigger immunological response. Here, we present the most extensive M. genitalium proteome analysis (85.3% of predicted ORFs), a comprehensive M. genitalium membrane analysis, and a study of the human serological response to M. genitalium.
Collapse
Affiliation(s)
- Noemí Párraga-Niño
- Institut de Biotecnologia i de Biomedicina (IBB) and Dpt Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona (UAB), E-08193 Cerdanyola del Vallès (Barcelona), Spain
| | | | | | | | | |
Collapse
|