Abstract
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.
Highlights
Systematic studies of sets of cell-lines have provided insights on biological processes and their mechanisms, and have proved useful for devising diagnostic and therapeutic approaches
GeneChipH miRNA 1.0 microarrays from AffymetrixH were used to examine the expression of 847 microRNAs in total RNA of 60 cell-lines of the National Cancer Institute (NCI)-60 cancer cell-line panel
RNA used for the expression profiling was obtained from frozen cells, similar to a previous study of microRNA expression in the NCI-60 panel [21]
Summary
Systematic studies of sets of cell-lines have provided insights on biological processes and their mechanisms, and have proved useful for devising diagnostic and therapeutic approaches. Phosphatase and tensin homologue (PTEN)-dependent and independent tumor suppressor mechanisms have been identified using a panel of melanoma cell-lines [1], and genetic markers of sensitivity to the anti-cancer drug, trastuzumab (HerceptinTM) have been delineated using a panel of breast cancer cell-lines [2]. The NCI-60 panel of 60 human tumor cell-lines of diverse histologies and nine different tissues of origin was developed by the National Cancer Institute (NCI) of USA in the late 1980s for the purpose of screening anti-cancer drugs [3]. Analyses of data integrated from multiple studies have yielded significant insights of biological and clinical importance [8]
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