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      Proteomic analysis of machine perfusion solution from brain dead donor kidneys reveals that elevated complement, cytoskeleton and lipid metabolism proteins are associated with 1‐year outcome

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          SUMMARY

          Assessment of donor kidney quality is based on clinical scores or requires biopsies for histological assessment. Noninvasive strategies to identify and predict graft outcome at an early stage are, therefore, needed. We evaluated the perfusate of donation after brain death (DBD) kidneys during nonoxygenated hypothermic machine perfusion (HMP). In particular, we compared perfusate protein profiles of good outcome (GO) and suboptimal outcome (SO) 1‐year post‐transplantation. Samples taken 15 min after the start HMP (T1) and before the termination of HMP (T2) were analysed using quantitative liquid chromatography–tandem mass spectrometry (LC‐MS/MS). Hierarchical clustering of the 100 most abundant proteins showed discrimination between grafts with a GO and SO at T1. Elevated levels of proteins involved in classical complement cascades at both T1 and T2 and a reduced abundance of lipid metabolism at T1 and of cytoskeletal proteins at T2 in GO versus SO was observed. ATP‐citrate synthase and fatty acid‐binding protein 5 (T1) and immunoglobulin heavy variable 2‐26 and desmoplakin (T2) showed 91% and 86% predictive values, respectively, for transplant outcome. Taken together, DBD kidney HMP perfusate profiles can distinguish between outcome 1‐year post‐transplantation. Furthermore, it provides insights into mechanisms that could play a role in post‐transplant outcomes.

          Abstract

          Experimental design, workflow and results. Elevated complement, cytoskeleton and lipid metabolism proteins were identified.

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          Most cited references63

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          Cytoscape: a software environment for integrated models of biomolecular interaction networks.

          Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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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

                Contributors
                l.l.van.leeuwen@umcg.nl
                Journal
                Transpl Int
                Transpl Int
                10.1111/(ISSN)1432-2277
                TRI
                Transplant International
                John Wiley and Sons Inc. (Hoboken )
                0934-0874
                1432-2277
                26 August 2021
                September 2021
                : 34
                : 9 ( doiID: 10.1111/tri.v34.9 )
                : 1618-1629
                Affiliations
                [ 1 ] Department of Surgery University of Groningen University Medical Centre Groningen Groningen The Netherlands
                [ 2 ] Nuffield Department of Medicine Target Discovery Institute Centre for Medicines Discovery University of Oxford Oxford UK
                [ 3 ] Department of Anaesthesiology University of Groningen University Medical Centre Groningen Groningen The Netherlands
                [ 4 ] Nuffield Department of Surgical Sciences University of Oxford BRC Oxford and NHS Blood and Transplant Oxford UK
                [ 5 ] Department of Nephrology and Hypertension University Medical Centre Utrecht Utrecht The Netherlands
                Author notes
                [*] [* ] Correspondence

                L. Leonie van Leeuwen MSc, Department of Surgery, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands.

                Tel: +31 624762959

                e‐mail: l.l.van.leeuwen@ 123456umcg.nl

                [*]

                Authors contributed equally

                Author information
                https://orcid.org/0000-0003-4666-2993
                https://orcid.org/0000-0001-8614-589X
                https://orcid.org/0000-0003-1997-0982
                https://orcid.org/0000-0002-9762-843X
                https://orcid.org/0000-0001-5550-2364
                https://orcid.org/0000-0002-9161-634X
                https://orcid.org/0000-0002-3204-2059
                https://orcid.org/0000-0001-7801-665X
                https://orcid.org/0000-0002-8160-2446
                https://orcid.org/0000-0001-5036-2999
                Article
                TRI13984
                10.1111/tri.13984
                9292651
                34448265
                ea2f0cde-492a-4a0e-b65f-73f147480e51
                © 2021 The Authors. Transplant International published by John Wiley & Sons Ltd on behalf of Steunstichting ESOT

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 14 July 2021
                : 25 June 2021
                : 15 July 2021
                Page count
                Figures: 5, Tables: 1, Pages: 12, Words: 6980
                Funding
                Funded by: Biomedical Research Centre (NIHR)
                Funded by: Tekke Huizinga Foundation
                Categories
                Original Article
                Original Articles
                Custom metadata
                2.0
                September 2021
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.1.7 mode:remove_FC converted:18.07.2022

                Transplantation
                biomarker discovery,complement activation,donation after brain death,hypothermic machine perfusion,kidney preservation,proteomics

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