NRP1 is identified as one of the cell surface receptor that interacts with Sema 3A

moval of DNA. RNA was eluted and the concentration measured using a GeneQuant machine. RNA integrity was assessed by microanalysis and amplified using the WT-OvationTM Pico RNA Amplification System following the manufacturers protocol which employs SPITM amplification to amplify the RNA about 15,000fold. Results Activation of Wnt Signalling in Orange Yellow S web breast Cancer Cell Lines Comprehensive analysis of WNT pathway mRNA expression across a large panel of breast cell lines was performed, which revealed cell type specific gene expression within the cell lines tested. Well established downstream targets, AXIN2 and LEF1 showed higher expression in breast cancer cell lines suggesting activation of canonical WNT signalling. Consistent with its gene 27216982 expression level, LEF1 protein was higher in five breast cancer cell lines compared to two normal cell lines, providing further evidence that WNT signalling is active in breast cancer cell lines. Interestingly, we observed high levels of LEF1 in the HER2 expressing cell line BT474. HER2 is known to activate b-catenin activity which may account for this increase in the downstream target LEF1. A WNT receptor and a WNT ligand were also dysregulated in breast cancer cell lines, FZD4 showed higher expression in breast cancer cell lines whilst WNT10A expression was decreased. The expression pattern of WNT pathway genes largely clustered the cell lines by estrogen receptor-a status; ER+ve cell lines predominately expressed the downstream target LEF1 whilst ER-ve cell lines express another downstream gene AXIN2. As reported by others, WNT5A, LBH, WISP1 and TCF4 were expressed at lower levels in ER+ cell lines compared to ER-ve cancer but also compared to immortalised normal breast cell lines, perhaps reflecting their ER-ve status. Independent of ER status, overall WNT pathway signalling assessed by the canonical downstream target genes AXIN2 and LEF1 is higher in breast cancer cell lines compared to normal breast cell lines. Custom Gene Expression Microarray Analysis of Monolayer and AR Breast Cells Custom microarray chips were designed using Agilent technology. cDNA was fluorescently labelled using the FL-OvationTM cDNA Fluorescent Module kit with a single tag which incorporates into the cDNA. The fluorescently tagged cDNA was loaded onto a microarray slides and the Agilent microarray chips attached. Slides were incubated at 65uC for 40 hours in a hybridisation oven to allow hybridisation to occur. The chips were then washed and scanned using an Agilent scanner. Primary Breast Cancer Microarray Affymetrix gene expression data representing a total of 1107 primary breast tumors from six previously published microarray studies were integrated as described previously using ComBat to remove batch effects. Centroid prediction was used to assign the tumors from each dataset to the five Norway/Stanford subtypes, ER-ve and ER+ve breast cancer cell lines. A) mRNA expression was normalised to 11078888 house keeper genes. Cluster analysis was performed and data displayed in a heatmap: decreased or increased expression compared to the mean mRNA expression. qq Indicates significant increased expression q indicates a trend towards increased expression. QQ Indicates significant increased expression Q indicated a trend towards increased expression. B) Protein expression of Lef 1 and B-actin in normal breast cell lines, ER-ve and ER+ve breast cancer cell lines. doi:10.1371/journal.pone.0067811.g001 across the subgroups. Confirming the result