Global microRNA Analysis of the NCI-60 Cancer Cell Panel

Abstract

MicroRNAs (miRNA) are a group of short noncoding RNAs that regulate gene expression at the posttranscriptional level. They are involved in many biological processes, including development, differentiation, apoptosis, and carcinogenesis. Because miRNAs may play a role in the initiation and progression of cancer, they comprise a novel class of promising diagnostic and prognostic molecular markers and potential drug targets. By applying an LNA-enhanced microarray platform, we studied the expression profiles of 955 miRNAs in the NCI-60 cancer cell lines and identified tissue-and cell-type-specific miRNA patterns by unsupervised hierarchical clustering and statistical analysis. A comparison of our data to three previously published miRNA expression studies on the NCI-60 panel showed a remarkably high correlation between the different technical platforms. In addition, the current work contributes expression data for 369 miRNAs that have not previously been profiled. Finally, by matching drug sensitivity data for the NCI-60 cells to their miRNA expression profiles, we found numerous drug-miRNAs pairs, for which the miRNA expression and drug sensitivity profiles were highly correlated and thus represent potential candidates for further investigation of drug resistance and sensitivity mechanisms. Mol Cancer Ther; 10(3); 375-84. Ó2011 AACR.

Diagnostic microRNA profiling in cutaneous T-cell lymphoma (CTCL)

“…At present, it is unclear why miR-155 was not identified as differentially expressed in our microarray analysis. Because the LNA-based microarray platform used here has been used previously to identify miR-155 as differentially expressed in the NCI-60 cell line panel, 39 it is unlikely that the difference is because of platform related issues. We therefore speculate that cross-hybridization or presence of pre-miR-155 might have masked the signal of the mature miR-155 because the hybridization probes do not discriminate between mature and pre-miRNAs in the microarray platform.…”

Mapping posttranscriptional regulation of the human glycome uncovers microRNA defining the glycocode

“…We analyzed the NCI-60, a cancer cell line panel containing 59 cell lines from nine tissue types, using our lectin microarray technology. This cell panel is a model for integrated analysis across multiple data types because of the availability of chemosensitivity profiles for these cells (21)(22)(23). The miRNA and mRNA profiles of the NCI-60 show the most coherent signatures for four tissue types: colon, leukemia, melanoma, and renal (22,23).…”

“…This cell panel is a model for integrated analysis across multiple data types because of the availability of chemosensitivity profiles for these cells (21)(22)(23). The miRNA and mRNA profiles of the NCI-60 show the most coherent signatures for four tissue types: colon, leukemia, melanoma, and renal (22,23). We first profiled the glycome of cells from these four tissue types for integration with miRNA datasets and observed clear segregation by tissue of origin (SI Appendix, Fig.…”

Dielectrophoresis has broad applicability to marker-free isolation of tumor cells from blood by microfluidic systems

“…In this article, we address these questions by showing that the cell types in the widely representative NCI-60 panel of cancers [23][24][25][26] are amenable to isolation from blood by DEP. Recently, we modified this DEP-FFF approach to allow continuous-flow sorting of cells to achieve throughputs >10 6 nucleated cells/min, allowing 10 ml blood specimens to be processed in under an hour, 27,28 a method now being developed commercially.…”