Human Transcriptome Array 2.0 (HTA) in matched colorectal cancer and normal colonic mucosa and in widely used cancer cell lines

We analyzed, by HTA 2.0, colorectal adenocarcinoma samples and matched normal colonic tissues in order to determine the whole transcriptome expression levels. Three widely used colorectal cancer cell lines (Caco-2, HT-29,HCT-116), one human breast adenocarcinoma cell line (MCF-7) and one human prostate adenocarcinoma cell line (PC3) were also analyzed. Results provided insights into the regulation, at transcript level, of genes involved in copper homeostasis. 37 tumoral bioptic samples, deriving from 27 patients, were collected directly after surgical resection. The mean age was 66.61 years (SD 16.31) for 18 male patients and 68.67 (SD 15.63) for 9 female patients. In 9 patients, two samples were taken at arbitrary positions in the tumor area, separated by at least 1 cm (double-sampling pairs, indicated as tumoral sample 1 or 2). In one patient a sample from a synchronous colorectal adenocarcinoma was also collected (tumoral sample 3). In 19 cases biopsies of adjacent normal mucosa (at distance of 3-6 cm from the tumor) were also collected (matched tumor/mucosa pairs). 18 tumoral samples and 12 normal colonic mucosa samples were analyzed in duplicate arrays (indicated as array 1 or 2).