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      Modulating the unfolded protein response with ONC201 to impact on radiation response in prostate cancer cells

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          Abstract

          Prostate cancer (PCa) is the most common non-cutaneous cancer in men and a notable cause of cancer mortality when it metastasises. The unfolded protein response (UPR) can be cytoprotective but when acutely activated can lead to cell death. In this study, we sought to enhance the acute activation of the UPR using radiation and ONC201, an UPR activator. Treating PCa cells with ONC201 quickly increased the expression of all the key regulators of the UPR and reduced the oxidative phosphorylation, with cell death occurring 72 h later. We exploited this time lag to sensitize prostate cancer cells to radiation through short-term treatment with ONC201. To understand how priming occurred, we performed RNA-Seq analysis and found that ONC201 suppressed the expression of cell cycle and DNA repair factors. In conclusion, we have shown that ONC201 can prime enhanced radiation response.

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          Most cited references63

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            STAR: ultrafast universal RNA-seq aligner.

            Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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              KEGG: kyoto encyclopedia of genes and genomes.

              M Kanehisa (2000)
              KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information. The genomic information is stored in the GENES database, which is a collection of gene catalogs for all the completely sequenced genomes and some partial genomes with up-to-date annotation of gene functions. The higher order functional information is stored in the PATHWAY database, which contains graphical representations of cellular processes, such as metabolism, membrane transport, signal transduction and cell cycle. The PATHWAY database is supplemented by a set of ortholog group tables for the information about conserved subpathways (pathway motifs), which are often encoded by positionally coupled genes on the chromosome and which are especially useful in predicting gene functions. A third database in KEGG is LIGAND for the information about chemical compounds, enzyme molecules and enzymatic reactions. KEGG provides Java graphics tools for browsing genome maps, comparing two genome maps and manipulating expression maps, as well as computational tools for sequence comparison, graph comparison and path computation. The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/).
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                Author and article information

                Contributors
                f.amoroso@qub.ac.uk
                ian.mills@nds.ox.ac.uk
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                19 February 2021
                19 February 2021
                2021
                : 11
                : 4252
                Affiliations
                [1 ]GRID grid.4777.3, ISNI 0000 0004 0374 7521, Patrick G Johnston Centre for Cancer Research, , Queen’s University Belfast, ; Belfast, BT9 7AE UK
                [2 ]GRID grid.10772.33, ISNI 0000000121511713, Faculdade de Ciências e Tecnologia, , Universidade Nova de Lisboa, ; 2825-516 Lisbon, Portugal
                [3 ]GRID grid.18886.3f, ISNI 0000 0001 1271 4623, Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, ; London, SW3 6JB UK
                [4 ]GRID grid.430063.2, Research and Development, Oncoceutics Inc., ; Philadelphia, PA 19104 USA
                [5 ]GRID grid.412914.b, ISNI 0000 0001 0571 3462, The Northern Ireland Cancer Centre, , Belfast City Hospital, ; Belfast, BT9 7AB UK
                [6 ]GRID grid.1024.7, ISNI 0000000089150953, Queensland University of Technology, ; Brisbane City, QLD 4000 Australia
                [7 ]Nuffield Department of Surgical Sciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU UK
                [8 ]GRID grid.7914.b, ISNI 0000 0004 1936 7443, Centre for Cancer Biomarkers, , University of Bergen, ; 5021 Bergen, Norway
                [9 ]GRID grid.7914.b, ISNI 0000 0004 1936 7443, Department of Clinical Science, , University of Bergen, ; 5021 Bergen, Norway
                Article
                83215
                10.1038/s41598-021-83215-y
                7896060
                33608585
                a6cb16ab-5306-411c-adc0-021bf400915f
                © The Author(s) 2021

                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
                : 27 May 2020
                : 1 February 2021
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100000771, Prostate Cancer UK;
                Award ID: CEO13_2-004
                Funded by: FundRef http://dx.doi.org/10.13039/501100005416, Norges Forskningsråd;
                Award ID: 230559
                Award Recipient :
                Categories
                Article
                Custom metadata
                © The Author(s) 2021

                Uncategorized
                oncology,cancer,urological cancer,prostate cancer
                Uncategorized
                oncology, cancer, urological cancer, prostate cancer

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