The COMPARE program of the NCI Developmental Therapeutics Program was used to examine the correlation between the LMR-12 staining results and sensitivity for compounds tested, and with basal patterns of gene expression in the 55 cell lines measured by cDNA microarray.
Olopade and Grushko [ 42] suggest that tumors with BRCA1 mutations may be consistent with a basal-like pattern of gene expression because six out of seven tumors from patients with BRCA1 mutations stained positive for basal keratins and none showed ERBB2 overexpression.
Overall, the pattern of gene expression changes suggests a cellular response to oxidative stress, coherent with the observed increase in the basal rate of oxidative phosphorylation.
We noted a basal expression pattern of both genes in the young root tip, including the susceptible zone and did not observe a discernible change in expression pattern of neither MtCCD7 nor MtCCD8 following LCO treatment (Additional file 4).
Interestingly, while the basal cell signature overlaps that of basal-like cells of other organs, the human airway basal cell signature has features not previously associated with this cell type, including a unique pattern of genes encoding extracellular matrix components, G protein-coupled receptors, neuroactive ligands and receptors, and ion channels.
Gene set enrichment analysis (GSEA) revealed exclusive enrichment patterns of gene signatures related to basal (mammary basal cell signature and p63 pathway, Fig.1d) and luminal (mammary luminal cell signature and AR pathway, Fig. 1e) epithelial phenotypes, respectively.
