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      Alteration of ribosome function upon 5-fluorouracil treatment favors cancer cell drug-tolerance

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      Nature Communications
      Nature Publishing Group UK
      Cancer therapeutic resistance, RNA modification, Translation, Ribosome

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          Abstract

          Mechanisms of drug-tolerance remain poorly understood and have been linked to genomic but also to non-genomic processes. 5-fluorouracil (5-FU), the most widely used chemotherapy in oncology is associated with resistance. While prescribed as an inhibitor of DNA replication, 5-FU alters all RNA pathways. Here, we show that 5-FU treatment leads to the production of fluorinated ribosomes exhibiting altered translational activities. 5-FU is incorporated into ribosomal RNAs of mature ribosomes in cancer cell lines, colorectal xenografts, and human tumors. Fluorinated ribosomes appear to be functional, yet, they display a selective translational activity towards mRNAs depending on the nature of their 5′-untranslated region. As a result, we find that sustained translation of IGF-1R mRNA, which encodes one of the most potent cell survival effectors, promotes the survival of 5-FU-treated colorectal cancer cells. Altogether, our results demonstrate that “man-made” fluorinated ribosomes favor the drug-tolerant cellular phenotype by promoting translation of survival genes.

          Abstract

          Different mechanisms have been reported to explain resistance to chemotherapy in cancer. Here, the authors show that the chemotherapeutic drug 5-fluorouracil alters the function of ribosomes to promote pro-survival gene translation leading to chemotherapy resistance.

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          Most cited references59

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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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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              Cutadapt removes adapter sequences from high-throughput sequencing reads

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                Author and article information

                Contributors
                frederic.catez@lyon.unicancer.fr
                jean-jacques.diaz@lyon.unicancer.fr
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                10 January 2022
                10 January 2022
                2022
                : 13
                : 173
                Affiliations
                [1 ]GRID grid.462282.8, ISNI 0000 0004 0384 0005, Inserm U1052, CNRS UMR5286 Centre de Recherche en Cancérologie de Lyon, ; F-69000 Lyon, France
                [2 ]GRID grid.418116.b, ISNI 0000 0001 0200 3174, Centre Léon Bérard, ; F-69008 Lyon, France
                [3 ]GRID grid.7849.2, ISNI 0000 0001 2150 7757, Université de Lyon 1, ; F-69000 Lyon, France
                [4 ]GRID grid.15140.31, ISNI 0000 0001 2175 9188, CIRI-Inserm U1111, Ecole Normale Supérieure de Lyon, ; Lyon, F-693643 France
                [5 ]GRID grid.463879.7, ISNI 0000 0004 0383 1432, Laboratoire de chimie analytique, Faculté de pharmacie de Lyon, ; 8 avenue Rockefeller, F-69373 Lyon, France
                [6 ]Laboratoire de biochimie et de pharmaco-toxicologie, Centre hospitalier Lyon-Sud – HCL, F-69495 Pierre Bénite, France
                [7 ]GRID grid.464638.b, ISNI 0000 0004 0599 0488, LIRMM, UMR 5506, University of Montpellier, CNRS, ; Montpellier, France
                [8 ]GRID grid.461890.2, ISNI 0000 0004 0383 2080, IGF, Univ. Montpellier, CNRS, INSERM, ; Montpellier, France
                [9 ]GRID grid.411165.6, ISNI 0000 0004 0593 8241, Department of Digestive Surgery, CHU Nimes, Univ Montpellier, ; Nimes, France
                [10 ]GRID grid.121334.6, ISNI 0000 0001 2097 0141, IRMB-PPC, Univ Montpellier, INSERM, CHU Montpellier, CNRS, ; Montpellier, France
                [11 ]GRID grid.412180.e, ISNI 0000 0001 2198 4166, Department of Endoscopy and Gastroenterology, Pavillon L, Edouard Herriot Hospital, ; Lyon, France
                [12 ]GRID grid.15140.31, ISNI 0000 0001 2175 9188, Ecole Normale Supérieure de Lyon, ; Lyon, France
                [13 ]GRID grid.510302.5, Institut Français de Bioinformatique, ; CNRS UMS 3601 Évry, France
                [14 ]GRID grid.25697.3f, ISNI 0000 0001 2172 4233, Laboratoire de toxicologie, Faculté de pharmacie de Lyon, , Université de Lyon, ; 8 avenue Rockefeller, F-69373 Lyon, France
                [15 ]Institut Convergence PLAsCAN, F-69373 Lyon, France
                [16 ]GRID grid.503348.9, ISNI 0000 0004 0620 5541, Present Address: Inserm U1060, CARMEN, ; F-69310 Pierre Bénite, France
                [17 ]GRID grid.418116.b, ISNI 0000 0001 0200 3174, Present Address: Department of Translational Research and Innovation, Centre Léon Bérard, ; 69373 Lyon, France
                Author information
                http://orcid.org/0000-0001-9430-4061
                http://orcid.org/0000-0002-4494-8034
                http://orcid.org/0000-0003-4616-7685
                http://orcid.org/0000-0002-4539-589X
                http://orcid.org/0000-0002-0924-5691
                http://orcid.org/0000-0002-9557-8221
                http://orcid.org/0000-0003-3374-5298
                http://orcid.org/0000-0002-5958-6662
                http://orcid.org/0000-0003-3365-1339
                http://orcid.org/0000-0003-4524-2233
                http://orcid.org/0000-0003-3791-3973
                http://orcid.org/0000-0001-6180-5708
                http://orcid.org/0000-0002-4553-3535
                http://orcid.org/0000-0001-8255-9091
                http://orcid.org/0000-0002-7914-4319
                Article
                27847
                10.1038/s41467-021-27847-8
                8748862
                35013311
                125aebf3-8c5d-42c9-a3df-8c9fa1519bc4
                © The Author(s) 2022

                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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 25 May 2020
                : 10 December 2021
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100004099, Ligue Contre le Cancer;
                Award ID: Thèse
                Award ID: Thèse GT
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100001665, Agence Nationale de la Recherche (French National Research Agency);
                Award ID: ANR-13-BSV8-0012
                Award ID: PC201507
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100006364, Institut National Du Cancer (French National Cancer Institute);
                Award ID: ARC_INCa_LNCC_7625
                Award Recipient :
                Categories
                Article
                Custom metadata
                © The Author(s) 2022

                Uncategorized
                cancer therapeutic resistance,rna modification,translation,ribosome
                Uncategorized
                cancer therapeutic resistance, rna modification, translation, ribosome

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