Gene expression profiling in women with breast cancer in a Saudi population

To generate consensus gene expression profiles of invasive breast tumors from a small cohort of Saudi females, and to explore the possibility that they may be broadly conserved between Caucasian and Middle Eastern populations. This study was performed at King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia, from January 2005 to January 2007. Gene expression profiles were generated from 38 invasive breast tumors, and 8 tumor adjacent tissues [TATs] using BD Atlas cDNA expression arrays containing 1176 genes. Results were confirmed by reverse transcriptase polymerase chain reaction, and analyzed by 2-dimensional unsupervised hierarchical clustering. The analysis identified 48 differentially expressed genes in tumors from which 25 are already reported by various western studies. Forty-three of these genes were also differentially expressed in TATs. The same data set has been able to distinguish between tumors and the TATs, interestingly by using only 4 of the differentially expressed genes. Moreover, we were able to group the patients according to prognosis to an extent by hierarchical clustering. Our results indicate that expression profiles between Saudi females with breast cancer and the Caucasian population are conserved to some extent, and can be used to classify patients according to prognostic groups. We also suggest 3 differentially-expressed genes [IGHG3, CDK6, and RPS9] in tumors may have a novel role in breast cancer. In addition, the role of TATs is much more essential in breast cancer, and needs to be explored thoroughly

Gene expression profiles of the flbroblasts from breast tumors and normal tissue compared with the tumor expression profiles

The study was designed to examine whether the gene expression profiles of fibroblast cell lines, established from the tumor and the normal tissue from the same breast, exhibit any similarities with the profiles of the original tissues. Fibroblast cell lines were established from invasive ductal carcinoma [IDC] and ductal carcinoma in situ [DCIS] of the breast and the adjacent normal tissues. Isolated total RNA from the cell lines and tissues were used to prepare labeled cDNA which was hybridized to Becton Dickinson Atlas TM microarrays for obtaining profiles of expressed genes. The profiles of tumors and cell lines were compared. This study was carried out at King Faisal specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia, during 2004 and 2005. Alterations of expression of most of the genes in the tissues were not detectable in the cell lines. The expression of a lower number of genes was altered in DCIS compared with that in IDC tumors. Although the fibroblasts discharge important functions, their gene expression profiles do not represent the breast tissue to the extent that any prognostic decisions could be made

Quick gene expression profiling of promyelocytic cell line Hl-60

A number of techniques have been developed to perform gene expression profiling. We report preliminary results from our exploratory study, using sequential analysis of gene expression [SAGE] technique, to profile the undifferentiated and differentiated HL-60 cells in line with our interest to characterize the cancer phenotype. The aim of the study is to evaluate the technique and to understand the molecular bases of these 2 states of cells. HL-60 cells were differentiated after treatment with dimethyl sulfoxide. Tag libraries were prepared from the messenger RNAs of the undifferentiated and differentiated cells according to the SAGE protocol. The search for genes corresponding to the tags was carried out using SAGE software. The tags and the genes from the 2 libraries were compared for their levels of expression. The study was carried out at the King Faisal Specialist Hospital and Research Centre, Riyadh, Kingdom of Saudi Arabia during the year 2001. A comparison of tags from the 2 libraries revealed that 151 tags corresponding to 57 genes expressed differentially: 60 tags were elevated and 59 were repressed in the undifferentiated cells. Thirty- two tags were equally expressed in both types of cells. Of the corresponding genes, 25 were expressed at higher, 17 at lower, while 15 were expressed at comparable levels in both cell types. In the profile of undifferentiated cells, the genes involved in mitochondrial function and protein synthesis were prominent, while in the differentiated cells, the genes coding for proteins associated with cell membranes, signal transduction and for cell specific functions were prominent. The genes, expressed equally in both the cell types, were concerned with the maintenance of the living state. Sequential analysis of gene expression is a useful technique for gene expression profiling. As previously indicated by others, a dedicated team can generate useful data within reasonable time limits