Based on its relatively high sensitivity to drug-induced ROS generation and apoptosis, NB4 was chosen as a prototype cell line for cellular and molecular assessments prior to detailed transcriptome analysis.
Three NCI prototype cancer cell lines, PC3 prostate cancer, MCF-7 breast cancer and NCI-H460 NSCL, were used in our initial screen.
In cell culture experiments, the treatment with α-naphthoflavone (αNF), a prototype SAhRM, exerted cell line-specific effects: in ERα-negative human UACC-3199 sporadic breast cancer cell line, it rescued BRCA-1 and ERα expression, while inducing CYP1A1; in ERα-positive MCF-7 breast cancer cells, αNF antagonized E2-dependent stimulation of BRCA-1 without affecting ERα expression.
A prototype compound 12b showed an anti-inflammatory effect in LPS-stimulated RAW 264.7 cell lines and in a zebrafish model.
Verapamil, the prototype calcium channel blocker, reversibly inhibits cell proliferation in many normal and tumour cell lines (Schmidt et al., Cancer Res., 48, 3617, 1988).
Reproducibility of the PAM50 assay was determined using 3 cell lines (MCF7, ME16C and SKBR3) and a pool of Luminal A prototype samples that were each run 12 times (3 runs across 4 batches of PAM50 plates) over 30 days.
In addition, the expression of St2 was assessed in the following cell lines, namely L929, 3T3, MC38, Hepa 1.6, P815 and H5V as prototypes of dermal fibroblasts, embryonic fibroblasts, colonocytes, hepatocytes, mast cells and colonic endothelial cells respectively.
Since the results were similar in all the cell lines tested (data not shown), we have selected SH-SY-5Y cells as the prototype of MYCN-non-amplified cells, and SK-N-BE-2C as the model of MYCN-amplified cells.
Moreover, GOBO offers the possibility of investigation of gene expression levels in breast cancer subgroups and breast cancer cell lines for gene sets, as well as creation of potential metagenes based on iterative correlation analysis to a prototype gene.
