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Reina-Ortiz C, Mozas MP, Ovelleiro D, Gao F, Villalba M, Anel A. Dynamic Changes in miRNA Expression during the Generation of Expanded and Activated NK Cells. Int J Mol Sci 2023; 24:13556. [PMID: 37686362 PMCID: PMC10488243 DOI: 10.3390/ijms241713556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Therapies based on allogenic Natural Killer (NK) cells are becoming increasingly relevant, and our laboratory has produced expanded and activated NK (eNK) cells that are highly cytotoxic against several hematological cancers when used alone or in combination with currently approved therapeutic monoclonal antibodies. In order to produce eNK cells, healthy human donor NK cells undergo a 20-day expansion protocol with IL-2, IL-15 and Epstein-Barr virus (EBV)-transformed lymphoblastoid feeder cells. In order to produce an even more potent eNK-based therapy, we must elucidate the changes our protocol produces within healthy NK cells. To understand the post-transcriptional changes responsible for the increased cytolytic abilities of eNK cells, we performed microRNA (miRNA) expression analysis on purified NK cells from day 0 and day 20 of the protocol using quantitative reverse transcription PCR (RT-qPCR). Of the 384 miRNAs profiled, we observed changes in the expression of 64 miRNAs, with especially significant changes in 7 of them. The up-regulated miRNAs of note were miRs-146a, -124, -34a, and -10a, which are key in the regulation of cell survival through the modulation of pro-apoptotic genes such as PUMA. The down-regulation of miRs-199a, -223, and -340 was also detected and is associated with the promotion of NK cell cytotoxicity. We validated our analysis using immunoblot and flow cytometry studies on specific downstream targets of both up- and down-regulated miRNAs such as PUMA and Granzyme B. These results corroborate the functional importance of the described miRNA expression patterns and show the wide variety of changes that occur in eNK cells at day 20.
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Affiliation(s)
- Chantal Reina-Ortiz
- Apoptosis, Immunity and Cancer Group, Department Biochemistry and Molecular and Cell Biology, Aragón Health Research Institute (IIS-Aragón), University of Zaragoza, 50009 Zaragoza, Spain; (C.R.-O.); (M.P.M.)
| | - Mª Pilar Mozas
- Apoptosis, Immunity and Cancer Group, Department Biochemistry and Molecular and Cell Biology, Aragón Health Research Institute (IIS-Aragón), University of Zaragoza, 50009 Zaragoza, Spain; (C.R.-O.); (M.P.M.)
| | - David Ovelleiro
- Peripheral Nervous System, Vall d’Hebron Institut de Recerca (VHIR), 08035 Barcelona, Spain;
| | - Fei Gao
- Institute of Regenerative Medicine and Biotherapy, University of Montpellier, INSERM, CNRS, University Hospital Center Montpellier, 34000 Montpellier, France; (F.G.); (M.V.)
- Immuno-Oncology Laboratory, School of Basic Medicine, Central South University, Changsha 410017, China
| | - Martín Villalba
- Institute of Regenerative Medicine and Biotherapy, University of Montpellier, INSERM, CNRS, University Hospital Center Montpellier, 34000 Montpellier, France; (F.G.); (M.V.)
| | - Alberto Anel
- Apoptosis, Immunity and Cancer Group, Department Biochemistry and Molecular and Cell Biology, Aragón Health Research Institute (IIS-Aragón), University of Zaragoza, 50009 Zaragoza, Spain; (C.R.-O.); (M.P.M.)
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2
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Bullich G, Matalonga L, Pujadas M, Papakonstantinou A, Piscia D, Tonda R, Artuch R, Gallano P, Garrabou G, González JR, Grinberg D, Guitart M, Laurie S, Lázaro C, Luengo C, Martí R, Milà M, Ovelleiro D, Parra G, Pujol A, Tizzano E, Macaya A, Palau F, Ribes A, Pérez-Jurado LA, Beltran S. Systematic Collaborative Reanalysis of Genomic Data Improves Diagnostic Yield in Neurologic Rare Diseases. J Mol Diagn 2022; 24:529-542. [PMID: 35569879 DOI: 10.1016/j.jmoldx.2022.02.003] [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: 06/22/2021] [Revised: 12/16/2021] [Accepted: 02/03/2022] [Indexed: 11/26/2022] Open
Abstract
Many patients experiencing a rare disease remain undiagnosed even after genomic testing. Reanalysis of existing genomic data has shown to increase diagnostic yield, although there are few systematic and comprehensive reanalysis efforts that enable collaborative interpretation and future reinterpretation. The Undiagnosed Rare Disease Program of Catalonia project collated previously inconclusive good quality genomic data (panels, exomes, and genomes) and standardized phenotypic profiles from 323 families (543 individuals) with a neurologic rare disease. The data were reanalyzed systematically to identify relatedness, runs of homozygosity, consanguinity, single-nucleotide variants, insertions and deletions, and copy number variants. Data were shared and collaboratively interpreted within the consortium through a customized Genome-Phenome Analysis Platform, which also enables future data reinterpretation. Reanalysis of existing genomic data provided a diagnosis for 20.7% of the patients, including 1.8% diagnosed after the generation of additional genomic data to identify a second pathogenic heterozygous variant. Diagnostic rate was significantly higher for family-based exome/genome reanalysis compared with singleton panels. Most new diagnoses were attributable to recent gene-disease associations (50.8%), additional or improved bioinformatic analysis (19.7%), and standardized phenotyping data integrated within the Undiagnosed Rare Disease Program of Catalonia Genome-Phenome Analysis Platform functionalities (18%).
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Affiliation(s)
- Gemma Bullich
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Leslie Matalonga
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Montserrat Pujadas
- Genetics Unit, University Pompeu Fabra, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain
| | - Anastasios Papakonstantinou
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Davide Piscia
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Raúl Tonda
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rafael Artuch
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu (IRSJD), Barcelona, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Pia Gallano
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Genetics Department, Institut d'Investigacions Biomèdiques (IIB) Sant Pau, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Glòria Garrabou
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Muscle Research and Mitochondrial Function Laboratory, CELLEX-Institut d'Investigació Biomèdica August Pi i Sunyer (IDIBAPS), Internal Medicine Department, Hospital Clinic of Barcelona, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Juan R González
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; Centro de Investigaciones Biomédicas en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Daniel Grinberg
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Institute of Biomedicine of the University of Barcelona (IBUB), Institut de Recerca Sant Joan de Déu (IRSJD), Barcelona, Spain
| | - Míriam Guitart
- Genetics Laboratory, Paediatric Unit, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Steven Laurie
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Conxi Lázaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Catalan Institute of Oncology, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Cristina Luengo
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ramon Martí
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Research Group on Neuromuscular and Mitochondrial Diseases, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Montserrat Milà
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, Institut d'Investigació Biomèdica August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - David Ovelleiro
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Genís Parra
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Aurora Pujol
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Neurometabolic Diseases Laboratory, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL)-Hospital Duran i Reynals, Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Eduardo Tizzano
- Department of Clinical and Molecular Genetics, Medicine Genetics Group Vall d'Hebron Institut de Recerca (VHIR), European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Universitat Autònoma de Barcelona, Hospital Vall d´Hebron, Barcelona, Spain
| | - Alfons Macaya
- Pediatric Neurology Research Group, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Francesc Palau
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Department of Genetic and Molecular Medicine, Pediatric Institute of Rare Diseases (IPER), Hospital Sant Joan de Déu, Clinic Institute of Medicine and Dermatology, Hospital Clínic de Barcelona and Division of Pediatrics, Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Antònia Ribes
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Secció d'Errors Congènits del Metabolisme-Institute of Clinical Biochemistry (IBC), Servei de Bioquímica i Genètìca Molecular, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Luis A Pérez-Jurado
- Genetics Unit, University Pompeu Fabra, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona, Spain; Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Women's and Children's Hospital, South Australian Health and Medical Research Institute and The University of Adelaide, Adelaide, South Australia, Australia
| | - Sergi Beltran
- Centro Nacional Análisis Genómico (CNAG)-Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain; Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.
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Peinado MÁ, Ovelleiro D, del Moral ML, Hernández R, Martínez-Lara E, Siles E, Pedrajas JR, García-Martín ML, Caro C, Peralta S, Morales ME, Ruiz MA, Blanco S. Biological Implications of a Stroke Therapy Based in Neuroglobin Hyaluronate Nanoparticles. Neuroprotective Role and Molecular Bases. Int J Mol Sci 2021; 23:247. [PMID: 35008673 PMCID: PMC8745106 DOI: 10.3390/ijms23010247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 12/11/2022] Open
Abstract
Exogenous neuroprotective protein neuroglobin (Ngb) cannot cross the blood-brain barrier. To overcome this difficulty, we synthesized hyaluronate nanoparticles (NPs), able to deliver Ngb into the brain in an animal model of stroke (MCAO). These NPs effectively reached neurons, and were microscopically identified after 24 h of reperfusion. Compared to MCAO non-treated animals, those treated with Ngb-NPs showed survival rates up to 50% higher, and better neurological scores. Tissue damage improved with the treatment, but no changes in the infarct volume or in the oxidative/nitrosative values were detected. A proteomics approach (p-value < 0.02; fold change = 0.05) in the infarcted areas showed a total of 219 proteins that significantly changed their expression after stroke and treatment with Ngb-NPs. Of special interest, are proteins such as FBXO7 and NTRK2, which were downexpressed in stroke, but overexpressed after treatment with Ngb-NPs; and ATX2L, which was overexpressed only under the effect of Ngb. Interestingly, the proteins affected by the treatment with Ngb were involved in mitochondrial function and cell death, endocytosis, protein metabolism, cytoskeletal remodeling, or synaptic function, and in regenerative processes, such as dendritogenesis, neuritogenesis, or sinaptogenesis. Consequently, our pharmaceutical preparation may open new therapeutic scopes for stroke and possibly for other neurodegenerative pathologies.
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Affiliation(s)
- María Ángeles Peinado
- Department of Experimental Biology, Campus de Las Lagunillas s/n, University of Jaén, Building B3, 23071 Jaen, Spain; (D.O.); (M.L.d.M.); (R.H.); (E.M.-L.); (E.S.); (J.R.P.)
| | - David Ovelleiro
- Department of Experimental Biology, Campus de Las Lagunillas s/n, University of Jaén, Building B3, 23071 Jaen, Spain; (D.O.); (M.L.d.M.); (R.H.); (E.M.-L.); (E.S.); (J.R.P.)
| | - María Luisa del Moral
- Department of Experimental Biology, Campus de Las Lagunillas s/n, University of Jaén, Building B3, 23071 Jaen, Spain; (D.O.); (M.L.d.M.); (R.H.); (E.M.-L.); (E.S.); (J.R.P.)
| | - Raquel Hernández
- Department of Experimental Biology, Campus de Las Lagunillas s/n, University of Jaén, Building B3, 23071 Jaen, Spain; (D.O.); (M.L.d.M.); (R.H.); (E.M.-L.); (E.S.); (J.R.P.)
| | - Esther Martínez-Lara
- Department of Experimental Biology, Campus de Las Lagunillas s/n, University of Jaén, Building B3, 23071 Jaen, Spain; (D.O.); (M.L.d.M.); (R.H.); (E.M.-L.); (E.S.); (J.R.P.)
| | - Eva Siles
- Department of Experimental Biology, Campus de Las Lagunillas s/n, University of Jaén, Building B3, 23071 Jaen, Spain; (D.O.); (M.L.d.M.); (R.H.); (E.M.-L.); (E.S.); (J.R.P.)
| | - José Rafael Pedrajas
- Department of Experimental Biology, Campus de Las Lagunillas s/n, University of Jaén, Building B3, 23071 Jaen, Spain; (D.O.); (M.L.d.M.); (R.H.); (E.M.-L.); (E.S.); (J.R.P.)
| | - María Luisa García-Martín
- BIONAND-Centro Andaluz de Nanomedicina y Biotecnología, Junta de Andalucía, Universidad de Málaga, Parque Tecnológico de Andalucía, 29590 Malaga, Spain; (M.L.G.-M.); (C.C.)
| | - Carlos Caro
- BIONAND-Centro Andaluz de Nanomedicina y Biotecnología, Junta de Andalucía, Universidad de Málaga, Parque Tecnológico de Andalucía, 29590 Malaga, Spain; (M.L.G.-M.); (C.C.)
| | - Sebastián Peralta
- Department of Pharmacy and Pharmaceutical Technology, Campus de Cartuja s/n, School of Pharmacy, University of Granada, 18071 Granada, Spain; (S.P.); (M.E.M.); (M.A.R.)
| | - María Encarnación Morales
- Department of Pharmacy and Pharmaceutical Technology, Campus de Cartuja s/n, School of Pharmacy, University of Granada, 18071 Granada, Spain; (S.P.); (M.E.M.); (M.A.R.)
| | - María Adolfina Ruiz
- Department of Pharmacy and Pharmaceutical Technology, Campus de Cartuja s/n, School of Pharmacy, University of Granada, 18071 Granada, Spain; (S.P.); (M.E.M.); (M.A.R.)
| | - Santos Blanco
- Department of Experimental Biology, Campus de Las Lagunillas s/n, University of Jaén, Building B3, 23071 Jaen, Spain; (D.O.); (M.L.d.M.); (R.H.); (E.M.-L.); (E.S.); (J.R.P.)
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Romero-Ruiz A, Pineda B, Ovelleiro D, Perdices-Lopez C, Torres E, Vazquez MJ, Guler I, Jiménez Á, Pineda R, Persano M, Romero-Baldonado C, Arjona JE, Lorente J, Muñoz C, Paz E, Garcia-Maceira FI, Arjona-Sánchez Á, Tena-Sempere M. Molecular diagnosis of polycystic ovary syndrome in obese and non-obese women by targeted plasma miRNA profiling. Eur J Endocrinol 2021; 185:637-652. [PMID: 34403358 DOI: 10.1530/eje-21-0552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Received: 05/24/2021] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Polycystic ovary syndrome (PCOS) is diagnosed based on the clinical signs, but its presentation is heterogeneous and potentially confounded by concurrent conditions, such as obesity and insulin resistance. miRNA have recently emerged as putative pathophysiological and diagnostic factors in PCOS. However, no reliable miRNA-based method for molecular diagnosis of PCOS has been reported. The aim of this study was to develop a tool for accurate diagnosis of PCOS by targeted miRNA profiling of plasma samples, defined on the basis of unbiased biomarker-finding analyses and biostatistical tools. METHODS A case-control PCOS cohort was cross-sectionally studied, including 170 women classified into four groups: non-PCOS/lean, non-PCOS/obese, PCOS/lean, and PCOS/obese women. High-throughput miRNA analyses were performed in plasma, using NanoString technology and a 800 human miRNA panel, followed by targeted quantitative real-timePCR validation. Statistics were applied to define optimal normalization methods, identify deregulated biomarker miRNAs, and build classification algorithms, considering PCOS and obesity as major categories. RESULTS The geometric mean of circulating hsa-miR-103a-3p, hsa-miR-125a-5p, and hsa-miR-1976, selected among 125 unchanged miRNAs, was defined as optimal reference for internal normalization (named mR3-method). Ten miRNAs were identified and validated after mR3-normalization as differentially expressed across the groups. Multinomial least absolute shrinkage and selection operator regression and decision-tree models were built to reliably discriminate PCOS vs non-PCOS, either in obese or non-obese women, using subsets of these miRNAs as performers. CONCLUSIONS We define herein a robust method for molecular classification of PCOS based on unbiased identification of miRNA biomarkers and decision-tree protocols. This method allows not only reliable diagnosis of non-obese women with PCOS but also discrimination between PCOS and obesity. CAPSULE We define a novel protocol, based on plasma miRNA profiling, for molecular diagnosis of PCOS. This tool not only allows proper discrimination of the condition in non-obese women but also permits distinction between PCOS and obesity, which often display overlapping clinical presentations.
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Affiliation(s)
- Antonio Romero-Ruiz
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
- Department of Cell Biology, Physiology and Immunology, University of Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofia, Córdoba, Spain
| | - Beatriz Pineda
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
- Hospital Universitario Reina Sofia, Córdoba, Spain
| | - David Ovelleiro
- Area of Cellular Biology, Department of Experimental Biology, University of Jaen, Jaen, Spain
| | - Cecilia Perdices-Lopez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
- Department of Cell Biology, Physiology and Immunology, University of Córdoba, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Córdoba, Spain
| | - Encarnación Torres
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
- Department of Cell Biology, Physiology and Immunology, University of Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofia, Córdoba, Spain
| | - María J Vazquez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
- Department of Cell Biology, Physiology and Immunology, University of Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofia, Córdoba, Spain
| | - Ipek Guler
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
| | - Álvaro Jiménez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
| | - Rafael Pineda
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
- Department of Cell Biology, Physiology and Immunology, University of Córdoba, Córdoba, Spain
| | - Mariasara Persano
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
- Hospital Universitario Reina Sofia, Córdoba, Spain
| | | | | | - Juan Lorente
- Hospital Universitario Reina Sofia, Córdoba, Spain
| | - Concepción Muñoz
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
- Hospital Universitario Reina Sofia, Córdoba, Spain
| | | | | | - Álvaro Arjona-Sánchez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
- Hospital Universitario Reina Sofia, Córdoba, Spain
| | - Manuel Tena-Sempere
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
- Department of Cell Biology, Physiology and Immunology, University of Córdoba, Córdoba, Spain
- Hospital Universitario Reina Sofia, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Córdoba, Spain
- Institute of Biomedicine, University of Turku, Turku, Finland
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Ovelleiro D, Blanco S, Hernández R, Peinado MÁ. Comparative proteomic study of early hypoxic response in the cerebral cortex of rats submitted to two different hypoxic models. Proteomics Clin Appl 2017; 11. [PMID: 28697276 DOI: 10.1002/prca.201700058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 04/07/2017] [Revised: 06/21/2017] [Accepted: 06/30/2017] [Indexed: 11/07/2022]
Abstract
PURPOSE The present study analyses and compares the cortical brain proteomic profiles of two different models of cerebral hypoxic insult in rats (HH: hypobaric hypoxia and HHI: ischemia followed by hypobaric hypoxia) in an attempt to describe the alterations of the early molecular hypoxic adaptive response underlying each one. EXPERIMENTAL DESIGN A quantitative proteomic profile of left-brain cortices of rats under HH, HHI, and control conditions was determined using isobaric labeling (Tandem Mass Tag™) on the protein extracts from pools of five individuals. Data are available via ProteomeXchange with identifier PXD004091. RESULTS Altogether, 339 proteins were confidently quantified, 99 of them showing significant variations in the hypoxic conditions with respect to the control. The HHI model presents a global effect of protein downregulation while HH produces an overall increase of the protein levels. While HH mainly affecting oxidative and energetic metabolism, HHI also interferes with synaptic transmission, neurotransmitter secretion, substantia nigra development, and triggers apoptosis through mitochondrial pathway. CONCLUSIONS AND CLINICAL RELEVANCE The findings obtained show an overview of protein alterations under two hypoxic models of different aetiology and provide a basis for more detailed studies in order to unravel new specific mechanisms and therapies for hypoxic pathologies.
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Affiliation(s)
- David Ovelleiro
- Area of Bioinformatics, Instituto Maimónides de Investigación Biomédica de Córdoba, Jaén, Spain
| | - Santos Blanco
- Area of Cellular Biology, Department of Experimental Biology, University of Jaén, Jaén, Spain
| | - Raquel Hernández
- Area of Cellular Biology, Department of Experimental Biology, University of Jaén, Jaén, Spain
| | - María Ángeles Peinado
- Area of Cellular Biology, Department of Experimental Biology, University of Jaén, Jaén, Spain
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Gallardo Ó, Ovelleiro D, Gay M, Carrascal M, Abian J. A collection of open source applications for mass spectrometry data mining. Proteomics 2014; 14:2275-9. [DOI: 10.1002/pmic.201400124] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/03/2014] [Accepted: 07/21/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Óscar Gallardo
- CSIC/UAB Proteomics Laboratory; Instituto de Investigaciones Biomédicas de Barcelona-Consejo Superior de Investigaciones Científicas; IDIBAPS; Barcelona Spain
| | - David Ovelleiro
- CSIC/UAB Proteomics Laboratory; Instituto de Investigaciones Biomédicas de Barcelona-Consejo Superior de Investigaciones Científicas; IDIBAPS; Barcelona Spain
| | - Marina Gay
- CSIC/UAB Proteomics Laboratory; Instituto de Investigaciones Biomédicas de Barcelona-Consejo Superior de Investigaciones Científicas; IDIBAPS; Barcelona Spain
| | - Montserrat Carrascal
- CSIC/UAB Proteomics Laboratory; Instituto de Investigaciones Biomédicas de Barcelona-Consejo Superior de Investigaciones Científicas; IDIBAPS; Barcelona Spain
| | - Joaquin Abian
- CSIC/UAB Proteomics Laboratory; Instituto de Investigaciones Biomédicas de Barcelona-Consejo Superior de Investigaciones Científicas; IDIBAPS; Barcelona Spain
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Peinado MÁ, Hernández R, Peragón J, Ovelleiro D, Pedrosa JÁ, Blanco S. Proteomic characterization of nitrated cell targets after hypobaric hypoxia and reoxygenation in rat brain. J Proteomics 2014; 109:309-21. [DOI: 10.1016/j.jprot.2014.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 06/16/2014] [Accepted: 07/08/2014] [Indexed: 12/17/2022]
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Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaíno JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M. The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database (Oxford) 2013; 2013:bat009. [PMID: 23482073 PMCID: PMC3594986 DOI: 10.1093/database/bat009] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Controlled vocabularies (CVs), i.e. a collection of predefined terms describing a modeling domain, used for the semantic annotation of data, and ontologies are used in structured data formats and databases to avoid inconsistencies in annotation, to have a unique (and preferably short) accession number and to give researchers and computer algorithms the possibility for more expressive semantic annotation of data. The Human Proteome Organization (HUPO)–Proteomics Standards Initiative (PSI) makes extensive use of ontologies/CVs in their data formats. The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS–related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics. The CV contains terms required for a complete description of an MS analysis pipeline used in proteomics, including sample labeling, digestion enzymes, instrumentation parts and parameters, software used for identification and quantification of peptides/proteins and the parameters and scores used to determine their significance. Owing to the range of topics covered by the CV, collaborative development across several PSI working groups, including proteomics research groups, instrument manufacturers and software vendors, was necessary. In this article, we describe the overall structure of the CV, the process by which it has been developed and is maintained and the dependencies on other ontologies. Database URL: http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo
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Affiliation(s)
- Gerhard Mayer
- Medizinisches Proteom Center (MPC), Ruhr-Universität Bochum, D-44801 Bochum, Germany
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Vizcaíno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Pérez-Riverol Y, Reisinger F, Ríos D, Wang R, Hermjakob H. The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res 2012. [PMID: 23203882 PMCID: PMC3531176 DOI: 10.1093/nar/gks1262] [Citation(s) in RCA: 1579] [Impact Index Per Article: 131.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.
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Affiliation(s)
- Juan Antonio Vizcaíno
- EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HWP, van Breukelen B, Heck AJR, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, Hermjakob H, Vizcaíno JA. The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium. Mol Cell Proteomics 2012; 11:1682-9. [PMID: 22949509 PMCID: PMC3518121 DOI: 10.1074/mcp.o112.021543] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [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: 11/30/2022] Open
Abstract
The original PRIDE Converter tool greatly simplified the process of submitting mass spectrometry (MS)-based proteomics data to the PRIDE database. However, after much user feedback, it was noted that the tool had some limitations and could not handle several user requirements that were now becoming commonplace. This prompted us to design and implement a whole new suite of tools that would build on the successes of the original PRIDE Converter and allow users to generate submission-ready, well-annotated PRIDE XML files. The PRIDE Converter 2 tool suite allows users to convert search result files into PRIDE XML (the format needed for performing submissions to the PRIDE database), generate mzTab skeleton files that can be used as a basis to submit quantitative and gel-based MS data, and post-process PRIDE XML files by filtering out contaminants and empty spectra, or by merging several PRIDE XML files together. All the tools have both a graphical user interface that provides a dialog-based, user-friendly way to convert and prepare files for submission, as well as a command-line interface that can be used to integrate the tools into existing or novel pipelines, for batch processing and power users. The PRIDE Converter 2 tool suite will thus become a cornerstone in the submission process to PRIDE and, by extension, to the ProteomeXchange consortium of MS-proteomics data repositories.
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Affiliation(s)
- Richard G Côté
- Proteomics Services Team, EMBL Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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11
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Deutsch EW, Chambers M, Neumann S, Levander F, Binz PA, Shofstahl J, Campbell DS, Mendoza L, Ovelleiro D, Helsens K, Martens L, Aebersold R, Moritz RL, Brusniak MY. TraML--a standard format for exchange of selected reaction monitoring transition lists. Mol Cell Proteomics 2012; 11:R111.015040. [PMID: 22159873 PMCID: PMC3322582 DOI: 10.1074/mcp.r111.015040] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 12/02/2011] [Indexed: 11/06/2022] Open
Abstract
Targeted proteomics via selected reaction monitoring is a powerful mass spectrometric technique affording higher dynamic range, increased specificity and lower limits of detection than other shotgun mass spectrometry methods when applied to proteome analyses. However, it involves selective measurement of predetermined analytes, which requires more preparation in the form of selecting appropriate signatures for the proteins and peptides that are to be targeted. There is a growing number of software programs and resources for selecting optimal transitions and the instrument settings used for the detection and quantification of the targeted peptides, but the exchange of this information is hindered by a lack of a standard format. We have developed a new standardized format, called TraML, for encoding transition lists and associated metadata. In addition to introducing the TraML format, we demonstrate several implementations across the community, and provide semantic validators, extensive documentation, and multiple example instances to demonstrate correctly written documents. Widespread use of TraML will facilitate the exchange of transitions, reduce time spent handling incompatible list formats, increase the reusability of previously optimized transitions, and thus accelerate the widespread adoption of targeted proteomics via selected reaction monitoring.
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Affiliation(s)
- Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, USA.
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Csordas A, Ovelleiro D, Wang R, Foster JM, Ríos D, Vizcaíno JA, Hermjakob H. PRIDE: quality control in a proteomics data repository. Database (Oxford) 2012; 2012:bas004. [PMID: 22434838 PMCID: PMC3308160 DOI: 10.1093/database/bas004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The PRoteomics IDEntifications (PRIDE) database is a large public proteomics data repository, containing over 270 million mass spectra (by November 2011). PRIDE is an archival database, providing the proteomics data supporting specific scientific publications in a computationally accessible manner. While PRIDE faces rapid increases in data deposition size as well as number of depositions, the major challenge is to ensure a high quality of data depositions in the context of highly diverse proteomics work flows and data representations. Here, we describe the PRIDE curation pipeline and its practical application in quality control of complex data depositions. Database URL:http://www.ebi.ac.uk/pride/.
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Affiliation(s)
- Attila Csordas
- EMBL Outstation, European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.
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13
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Wang R, Fabregat A, Ríos D, Ovelleiro D, Foster JM, Côté RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, Vizcaíno JA. PRIDE Inspector: a tool to visualize and validate MS proteomics data. Nat Biotechnol 2012; 30:135-7. [PMID: 22318026 PMCID: PMC3277942 DOI: 10.1038/nbt.2112] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Ndegwa N, Côté RG, Ovelleiro D, D'Eustachio P, Hermjakob H, Vizcaíno JA, Croft D. Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations. Database (Oxford) 2011; 2011:bar047. [PMID: 22025670 PMCID: PMC3199918 DOI: 10.1093/database/bar047] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reversible phosphorylation of serine, threonine and tyrosine hydroxyl groups is an especially prominent form of post-translational modification (PTM) of proteins. It plays critical roles in the regulation of diverse processes, and mutations that directly or indirectly affect these phosphorylation events have been associated with many cancers and other pathologies. Here, we describe the development of a new BioMart tool that gathers data from three different biological resources to provide the user with an integrated view of phosphorylation events associated with a human protein of interest, the complexes of which the protein (modified or not) is a part, the reactions in which the protein and its complexes participate and the somatic mutations that might be expected to perturb those functions. The three resources used are the Reactome, PRIDE and COSMIC databases. The Reactome knowledgebase contains annotations of phosphorylated human proteins linked to the reactions in which they are phosphorylated and dephosphorylated, to the complexes of which they are parts and to the reactions in which the phosphorylated proteins participate as substrates, catalysts and regulators. The PRIDE database holds extensive mass spectrometry data from which protein phosphorylation patterns can be inferred, and the COSMIC database holds records of somatic mutations found in human cancer cells. This tool supports both flexible, user-specified queries and standard (‘canned’) queries to retrieve frequently used combinations of data for user-specified proteins and reactions. We demonstrate using the Wnt signaling pathway and the human c-SRC protein how the tool can be used to place somatic mutation data into a functional perspective by changing critical residues involved in pathway modulation, and where available, check for mass spectrometry evidence in PRIDE supporting identification of the critical residue. Database URL:http://www.reactome.org/cgi-bin/mart
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Affiliation(s)
- Nelson Ndegwa
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Carrascal M, Gay M, Ovelleiro D, Casas V, Gelpí E, Abian J. Characterization of the human plasma phosphoproteome using linear ion trap mass spectrometry and multiple search engines. J Proteome Res 2010; 9:876-84. [PMID: 19941383 DOI: 10.1021/pr900780s] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Major plasma protein families play different roles in blood physiology and hemostasis and in immunodefense. Other proteins in plasma can be involved in signaling as chemical messengers or constitute biological markers of the status of distant tissues. In this respect, the plasma phosphoproteome holds potentially relevant information on the mechanisms modulating these processes through the regulation of protein activity. In this work we describe for the first time a collection of phosphopeptides identified in human plasma using immunoaffinity separation of the seven major serum protein families from other plasma proteins, SCX fractionation, and TiO(2) purification prior to LC-MS/MS analysis. One-hundred and twenty-seven phosphosites in 138 phosphopeptides mapping 70 phosphoproteins were identified with FDR < 1%. A high-confidence collection of phosphosites was obtained using a combined search with the OMSSA, SEQUEST, and Phenyx search engines.
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Affiliation(s)
- Montserrat Carrascal
- LP-CSIC/UAB, IIBB-CSIC, IDIBAPS, Rosellón 161, 7a Planta, 08036 Barcelona, Spain
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Carrascal M, Ovelleiro D, Casas V, Gay M, Abian J. Phosphorylation Analysis of Primary Human T Lymphocytes Using Sequential IMAC and Titanium Oxide Enrichment. J Proteome Res 2008; 7:5167-76. [DOI: 10.1021/pr800500r] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [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)
- Montserrat Carrascal
- CSIC/UAB Proteomics Laboratory, IIBB-CSIC, IDIBAPS, Facultad de Medicina, Campus UAB, 08193 Bellaterra, Spain
| | - David Ovelleiro
- CSIC/UAB Proteomics Laboratory, IIBB-CSIC, IDIBAPS, Facultad de Medicina, Campus UAB, 08193 Bellaterra, Spain
| | - Vanessa Casas
- CSIC/UAB Proteomics Laboratory, IIBB-CSIC, IDIBAPS, Facultad de Medicina, Campus UAB, 08193 Bellaterra, Spain
| | - Marina Gay
- CSIC/UAB Proteomics Laboratory, IIBB-CSIC, IDIBAPS, Facultad de Medicina, Campus UAB, 08193 Bellaterra, Spain
| | - Joaquin Abian
- CSIC/UAB Proteomics Laboratory, IIBB-CSIC, IDIBAPS, Facultad de Medicina, Campus UAB, 08193 Bellaterra, Spain
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