An integrated genomics approach for novel biomarker discovery in squamous cell cervical carcinoma

Detection of copy number dependent gene expression profiles in epithelial tumours has lead to the discovery of genes significant in diagnosis, prognosis and of therapeutic value. We sought to apply the technologies of gene expression profiling and copy number aberration detection by high density oligonucleotide microarray analysis to detect genes with expression profiles regulated by copy number. We surveyed copy number aberrations in 27 squamous cell carcinomas tissues and ten cervical carcinoma cell lines by Agilent 244k aCGH, and in a companion study of 77 tissues we obtained transcriptional profiles of a broader ranger of histologies. Briefly, for normal (NAD) and squamous intraepithelial lesions (SILs), DNA and RNA were extracted from approximately 5 - 25 x 5 mm thin sections of fresh frozen cervical tissue, respectively. Epithelial were microdissected, pooled and processed as follows. For RNA extraction, tissue was collected in Trizol (Invitrogen, UK) and subject to homogenization (Polytron), total RNA was recovered following standard processes, and quality assessed by BioAnalyzer (Agilent). DNA was recovered following Proteinase K digestion, phenol chloroform extraction, and ethanol precipitation. Contaminating RNA was removed by RNAse A treatment, and a second round of phenol chloroform extraction and ethanol precipitation. For SCCs, RNA and DNA was extracted from whole tumour (>85%), following similar strategies as previously described. This submission describes the copy number aberrations of 27 cervical SCC tissues and 10 common cervical SCC cell lines