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      Age-related long-term response in rat thyroid tissue and plasma after internal low dose exposure to 131I

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          Abstract

          131I is used clinically for therapy, and may be released during nuclear accidents. After the Chernobyl accident papillary thyroid carcinoma incidence increased in children, but not adults. The aims of this study were to compare 131I irradiation-dependent differences in RNA and protein expression in the thyroid and plasma of young and adult rats, and identify potential age-dependent biomarkers for 131I exposure. Twelve young (5 weeks) and twelve adult Sprague Dawley rats (17 weeks) were i.v. injected with 50 kBq 131I (absorbed dose to thyroid = 0.1 Gy), and sixteen unexposed age-matched rats were used as controls. The rats were killed 3–9 months after administration. Microarray analysis was performed using RNA from thyroid samples, while LC–MS/MS analysis was performed on proteins extracted from thyroid tissue and plasma. Canonical pathways, biological functions and upstream regulators were analysed for the identified transcripts and proteins. Distinct age-dependent differences in gene and protein expression were observed. Novel biomarkers for thyroid 131I exposure were identified: (PTH), age-dependent dose response (CA1, FTL1, PVALB (youngsters) and HSPB6 (adults)), thyroid function ( Vegfb (adults)). Further validation using clinical samples are needed to explore the role of the identified biomarkers.

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          The PRIDE database and related tools and resources in 2019: improving support for quantification data

          Yasset Perez-Riverol, Attila Csordas, Jingwen Bai … (2018)
          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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            Gene Expression Omnibus: NCBI gene expression and hybridization array data repository.

            R. Edgar (2002)
            The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data. GEO provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-throughput gene expression and genomic hybridization experiments. GEO is not intended to replace in house gene expression databases that benefit from coherent data sets, and which are constructed to facilitate a particular analytic method, but rather complement these by acting as a tertiary, central data distribution hub. The three central data entities of GEO are platforms, samples and series, and were designed with gene expression and genomic hybridization experiments in mind. A platform is, essentially, a list of probes that define what set of molecules may be detected. A sample describes the set of molecules that are being probed and references a single platform used to generate its molecular abundance data. A series organizes samples into the meaningful data sets which make up an experiment. The GEO repository is publicly accessible through the World Wide Web at http://www.ncbi.nlm.nih.gov/geo.
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              The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses.

              Gil Stelzer, Naomi Rosen, Inbar Plaschkes … (2016)
              GeneCards, the human gene compendium, enables researchers to effectively navigate and inter-relate the wide universe of human genes, diseases, variants, proteins, cells, and biological pathways. Our recently launched Version 4 has a revamped infrastructure facilitating faster data updates, better-targeted data queries, and friendlier user experience. It also provides a stronger foundation for the GeneCards suite of companion databases and analysis tools. Improved data unification includes gene-disease links via MalaCards and merged biological pathways via PathCards, as well as drug information and proteome expression. VarElect, another suite member, is a phenotype prioritizer for next-generation sequencing, leveraging the GeneCards and MalaCards knowledgebase. It automatically infers direct and indirect scored associations between hundreds or even thousands of variant-containing genes and disease phenotype terms. VarElect's capabilities, either independently or within TGex, our comprehensive variant analysis pipeline, help prepare for the challenge of clinical projects that involve thousands of exome/genome NGS analyses. © 2016 by John Wiley & Sons, Inc.
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                Author and article information

                Contributors
                Malin Larsson: malin.larsson@gu.se
                Journal
                Journal ID (nlm-ta): Sci Rep
                Journal ID (iso-abbrev): Sci Rep
                Title: Scientific Reports
                Publisher: Nature Publishing Group UK (London )
                ISSN (Electronic): 2045-2322
                Publication date (Electronic): 8 February 2022
                Publication date PMC-release: 8 February 2022
                Publication date Collection: 2022
                Volume: 12
                Electronic Location Identifier: 2107
                Affiliations
                [1 ]GRID grid.8761.8, ISNI 0000 0000 9919 9582, Department of Medical Radiation Sciences, Institute of Clinical Sciences, Sahlgrenska Center for Cancer Research, Sahlgrenska Academy, , University of Gothenburg, ; 413 45 Gothenburg, Sweden
                [2 ]GRID grid.240145.6, ISNI 0000 0001 2291 4776, Department of Thoracic/Head and Neck Medical Oncology, , University of Texas MD Anderson, ; Houston, TX 77030 USA
                [3 ]GRID grid.240145.6, ISNI 0000 0001 2291 4776, Department of Immunology, , University of Texas MD Anderson, ; Houston, TX 77030 USA
                [4 ]GRID grid.38142.3c, ISNI 000000041936754X, John B. Little Center for Radiation Sciences, , Harvard T. H. Chan School of Public Health, ; Boston, MA 02115 USA
                [5 ]GRID grid.8761.8, ISNI 0000 0000 9919 9582, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Center for Cancer Research, Sahlgrenska Academy, , University of Gothenburg, ; 413 45 Gothenburg, Sweden
                [6 ]GRID grid.267313.2, ISNI 0000 0000 9482 7121, UT Department of Radiation Oncology, Division of Molecular Radiation Biology, , UT Southwestern Medical Center, ; 2201 Inwood Rd., Dallas, TX 75390 USA
                [7 ]GRID grid.1649.a, ISNI 000000009445082X, Department of Medical Physics and Biomedical Engineering, , Sahlgrenska University Hospital, ; 413 45 Gothenburg, Sweden
                Article
                Publisher ID: 6071
                DOI: 10.1038/s41598-022-06071-4
                PMC ID: 8825795
                PubMed ID: 35136135
                SO-VID: 93d13095-83da-45ce-b452-cc7e70a59c32
                Copyright © © The Author(s) 2022
                License:

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                Date received : 4 March 2021
                Date accepted : 18 January 2022
                Funding
                Funded by: the Sahlgrenska University Hospital Research Funds, the Assar Gabrielsson Cancer Research Foundation, the Adlerbertska Research Foundation, the Knut and Alice Wallenberg Foundation, the Royal Society of Arts and Sciences in Gothenburg (KVVS), and the Wilhelm and Martina Lundgren Research Foundation
                Funded by: the Swedish Cancer Society
                Funded by: the Swedish Research Council
                Funded by: the Swedish state under the agreement between the Swedish government and the county councils – the ALF-agreement
                Funded by: the King Gustav V Jubilee Clinic Cancer Research Foundation
                Funded by: Swedish Radiation Safety Authority (SSM)
                Funded by: BioCARE – a National Strategic Research Program at the University of Gothenburg, the Swedish Cancer Society
                Funded by: University of Gothenburg
                Open Access :

                Open access funding provided by University of Gothenburg.

                Categories
                Subject: Article
                Custom metadata
                issue-copyright-statement © The Author(s) 2022

                ScienceOpen disciplines: Uncategorized
                Keywords: biological techniques,cancer,cell biology,biomarkers,physics
                Data availability:
                ScienceOpen disciplines: Uncategorized
                Keywords: biological techniques, cancer, cell biology, biomarkers, physics

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