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Expression of MicroRNAs in the NCI-60 Cancer Cell-Lines
The NCI-60 panel of 60 human cancer cell-lines of nine different tissues of origin has been extensively characterized in biological, molecular and pharmacological studies. Analyses of data from such studies have provided valuable information for understanding cellular processes and developing strate...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509128/ https://www.ncbi.nlm.nih.gov/pubmed/23209617 http://dx.doi.org/10.1371/journal.pone.0049918 |
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author | Patnaik, Santosh K. Dahlgaard, Jesper Mazin, Wiktor Kannisto, Eric Jensen, Thomas Knudsen, Steen Yendamuri, Sai |
author_facet | Patnaik, Santosh K. Dahlgaard, Jesper Mazin, Wiktor Kannisto, Eric Jensen, Thomas Knudsen, Steen Yendamuri, Sai |
author_sort | Patnaik, Santosh K. |
collection | PubMed |
description | The NCI-60 panel of 60 human cancer cell-lines of nine different tissues of origin has been extensively characterized in biological, molecular and pharmacological studies. Analyses of data from such studies have provided valuable information for understanding cellular processes and developing strategies for the diagnosis and treatment of cancer. Here, Affymetrix® GeneChip™ miRNA version 1 oligonucleotide microarrays were used to quantify 847 microRNAs to generate an expression dataset of 495 (58.4%) microRNAs that were identified as expressed in at least one cell-line of the NCI-60 panel. Accuracy of the microRNA measurements was partly confirmed by reverse transcription and polymerase chain reaction assays. Similar to that seen among the four existing NCI-60 microRNA datasets, the concordance of the new expression dataset with the other four was modest, with mean Pearson correlation coefficients of 0.37–0.54. In spite of this, comparable results with different datasets were noted in clustering of the cell-lines by their microRNA expression, differential expression of microRNAs by the lines’ tissue of origin, and correlation of specific microRNAs with the doubling-time of cells or their radiation sensitivity. Mutation status of the cell-lines for the TP53, PTEN and BRAF but not CDKN2A or KRAS cancer-related genes was found to be associated with changes in expression of specific microRNAs. The microRNA dataset generated here should be valuable to those working in the field of microRNAs as well as in integromic studies of the NCI-60 panel. |
format | Online Article Text |
id | pubmed-3509128 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-35091282012-12-03 Expression of MicroRNAs in the NCI-60 Cancer Cell-Lines Patnaik, Santosh K. Dahlgaard, Jesper Mazin, Wiktor Kannisto, Eric Jensen, Thomas Knudsen, Steen Yendamuri, Sai PLoS One Research Article The NCI-60 panel of 60 human cancer cell-lines of nine different tissues of origin has been extensively characterized in biological, molecular and pharmacological studies. Analyses of data from such studies have provided valuable information for understanding cellular processes and developing strategies for the diagnosis and treatment of cancer. Here, Affymetrix® GeneChip™ miRNA version 1 oligonucleotide microarrays were used to quantify 847 microRNAs to generate an expression dataset of 495 (58.4%) microRNAs that were identified as expressed in at least one cell-line of the NCI-60 panel. Accuracy of the microRNA measurements was partly confirmed by reverse transcription and polymerase chain reaction assays. Similar to that seen among the four existing NCI-60 microRNA datasets, the concordance of the new expression dataset with the other four was modest, with mean Pearson correlation coefficients of 0.37–0.54. In spite of this, comparable results with different datasets were noted in clustering of the cell-lines by their microRNA expression, differential expression of microRNAs by the lines’ tissue of origin, and correlation of specific microRNAs with the doubling-time of cells or their radiation sensitivity. Mutation status of the cell-lines for the TP53, PTEN and BRAF but not CDKN2A or KRAS cancer-related genes was found to be associated with changes in expression of specific microRNAs. The microRNA dataset generated here should be valuable to those working in the field of microRNAs as well as in integromic studies of the NCI-60 panel. Public Library of Science 2012-11-28 /pmc/articles/PMC3509128/ /pubmed/23209617 http://dx.doi.org/10.1371/journal.pone.0049918 Text en © 2012 Patnaik et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Patnaik, Santosh K. Dahlgaard, Jesper Mazin, Wiktor Kannisto, Eric Jensen, Thomas Knudsen, Steen Yendamuri, Sai Expression of MicroRNAs in the NCI-60 Cancer Cell-Lines |
title | Expression of MicroRNAs in the NCI-60 Cancer Cell-Lines |
title_full | Expression of MicroRNAs in the NCI-60 Cancer Cell-Lines |
title_fullStr | Expression of MicroRNAs in the NCI-60 Cancer Cell-Lines |
title_full_unstemmed | Expression of MicroRNAs in the NCI-60 Cancer Cell-Lines |
title_short | Expression of MicroRNAs in the NCI-60 Cancer Cell-Lines |
title_sort | expression of micrornas in the nci-60 cancer cell-lines |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509128/ https://www.ncbi.nlm.nih.gov/pubmed/23209617 http://dx.doi.org/10.1371/journal.pone.0049918 |
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