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      Cardiovascular-related proteomic changes in ECFCs exposed to the serum of COVID-19 patients

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          Abstract

          Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection significantly affects the cardiovascular system, causing vascular damage and thromboembolic events in critical patients. Endothelial dysfunction represents one of the first steps in response to COVID-19 that might lead to cardiovascular complications and long-term sequelae. However, despite the enormous efforts in the last two years, the molecular mechanisms involved in such processes remain poorly understood. Herein, we analyzed the protein changes taking place in endothelial colony forming cells (ECFCs) after the incubation with the serum from individuals infected with COVID-19, whether asymptomatic or critical patients, by application of a label free-quantitative proteomics approach. Specifically, ECFCs from healthy individuals were incubated ex-vivo with the serum of either COVID-19 negative donors (PCR-/IgG-, n:8), COVID-19 asymptomatic donors at different infective stages (PCR+/ IgG-, n:8and PCR-/IgG+, n:8), or hospitalized critical COVID-19 patients (n:8), followed by proteomics analysis. In total, 590 proteins were differentially expressed in ECFCs in response to all infected serums. Predictive analysis highlighted several proteins like CAPN5, SURF4, LAMP2 or MT-ND1, as highly discriminating features between the groups compared. Protein changes correlated with viral infection, RNA metabolism or autophagy, among others. Remarkably, the angiogenic potential of ECFCs in response to the infected serums was impaired, and many of the protein alterations in response to the serum of critical patients were associated with cardiovascular-related pathologies.

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          Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

          A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets. Successful analysis requires the integration of a broad set of current biological databases and the application of a robust analytical pipeline to produce readily interpretable results. Metascape is a web-based portal designed to provide a comprehensive gene list annotation and analysis resource for experimental biologists. In terms of design features, Metascape combines functional enrichment, interactome analysis, gene annotation, and membership search to leverage over 40 independent knowledgebases within one integrated portal. Additionally, it facilitates comparative analyses of datasets across multiple independent and orthogonal experiments. Metascape provides a significantly simplified user experience through a one-click Express Analysis interface to generate interpretable outputs. Taken together, Metascape is an effective and efficient tool for experimental biologists to comprehensively analyze and interpret OMICs-based studies in the big data era.
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            The PRIDE database and related tools and resources in 2019: improving support for quantification data

            Abstract The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world’s largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3 years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas.
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              The Perseus computational platform for comprehensive analysis of (prote)omics data.

              A main bottleneck in proteomics is the downstream biological analysis of highly multivariate quantitative protein abundance data generated using mass-spectrometry-based analysis. We developed the Perseus software platform (http://www.perseus-framework.org) to support biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization, pattern recognition, time-series analysis, cross-omics comparisons and multiple-hypothesis testing. A machine learning module supports the classification and validation of patient groups for diagnosis and prognosis, and it also detects predictive protein signatures. Central to Perseus is a user-friendly, interactive workflow environment that provides complete documentation of computational methods used in a publication. All activities in Perseus are realized as plugins, and users can extend the software by programming their own, which can be shared through a plugin store. We anticipate that Perseus's arsenal of algorithms and its intuitive usability will empower interdisciplinary analysis of complex large data sets.
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                Author and article information

                Journal
                Int J Biol Sci
                Int J Biol Sci
                ijbs
                International Journal of Biological Sciences
                Ivyspring International Publisher (Sydney )
                1449-2288
                2023
                5 March 2023
                : 19
                : 6
                : 1664-1680
                Affiliations
                [1 ]Biomedicine, Biotechnology and Public Health Department, University of Cadiz, 11002 Cadiz, Spain
                [2 ]Biomedical Research and Innovation Institute of Cadiz (INiBICA), 11002 Cadiz, Spain
                [3 ]Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
                [4 ]Automation Engineering, Electronics and Computer Architecture and Networks Department, University of Cadiz, 11009 Cadiz, Spain
                [5 ]Department of Nursing, National Paraplegic Hospital, Toledo, Spain
                [6 ]Occupational Health Service, National Paraplegic Hospital, SESCAM, 45071, Toledo, Spain
                [7 ]Internal Medicine Department, University Hospital Virgen del Rocío, Seville, Spain
                [8 ]UGC Microbiología, University Hospital Puerta del Mar, Avda. Ana de Viya 21, 11009, Cádiz, Spain
                [9 ]Cell Biology, Physiology and Immunology Department, Agrifood Campus of International Excellence (ceiA3), University of Cordoba, 14014, Córdoba, Spain
                [10 ]Maimonides Biomedical Research Institute of Cordoba (IMIBIC), UGC Nephrology, Hospital Universitario Reina Sofia, 14004, Cordoba, Spain
                [11 ]Psychology Department, University of Cádiz, 11510, Puerto Real, Spain
                [12 ]Biomedical Research Networking Center for Mental Health Network (CIBERSAM), Institute of Health Carlos III, 28029, Madrid, Spain
                [13 ]Laboratory of Neuroinflammation, National Paraplegic Hospital, 45071 Toledo, Spain
                [14 ]Redes de investigación cooperativa orientadas a resultados en salud, Enfermedades vasculares cerebrales, RICORS-ICTUS, SESCAM
                Author notes
                ✉ Corresponding authors: Rafael Moreno-Luna, PhD; rmluna@ 123456sescam.jccm.es ; Laboratorio de Neuroinflamación, i2-06, Hospital Nacional de Parapléjicos-SESCAM. CP 45071, Toledo, Spain; Mª Carmen Durán-Ruiz, PhD; maricarmen.duran@ 123456gm.uca.es ; Biomedicine, Biotechnology and Public Health Department, Science Faculty, Cádiz University. Torre Sur. Avda. República Saharaui S/N, Polígono Río San Pedro, Puerto Real, 11519 Cádiz, Spain.

                *Both authors have equally contributed to this work.

                Competing Interests: The authors have declared that no competing interest exists.

                Article
                ijbsv19p1664
                10.7150/ijbs.78864
                10092762
                37063416
                d66d3fe5-c83c-49f4-942f-31f818b7541e
                © The author(s)

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/). See http://ivyspring.com/terms for full terms and conditions.

                History
                : 12 September 2022
                : 2 February 2023
                Categories
                Research Paper

                Life sciences
                covid-19,ecfcs,viral infection,rna metabolism,cardiovascular diseases,endothelial dysfunction,autophagy,proteomics,mass spectrometry

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