Expression profiling of vulvar carcinoma: clues for deranged extracellular matrix remodeling and effects on multiple signaling pathways combined with discrete patient subsets

The molecular mechanisms of vulvar squamous cell carcinoma (VSCC) remain obscure. To this end, we investigated systematically for the first time the expression profile of VSCC using the microarray technology, in a total of 11 snap-frozen samples, from five VSCC patients covering early and advanced stages of VSCC undergoing radical surgery and from six matched healthy controls. All experiments were performed using Affymetrix Human Genome U133A 2.0 oligonucleotide arrays, covering 22,277 probe sets. Genes were filtered and analyzed using analysis of variance, t test, fold-change calculations, and unsupervised hierarchical cluster analysis. Further processing included functional analysis and overrepresentation calculations based on Gene Ontology, Database for Annotation, Visualization, and Integrated Discovery, and Ingenuity Pathway Analysis. The molecular phenotypes of VSCC patients exhibited significant and discrete transcriptional differences from the healthy controls, whereas principal component analysis documented that this separation is mediated by a consistent set of gene expression differences. We detected 1077 genes (306 upregulated and 771 downregulated) that were differentially expressed between VSCC patients and healthy controls by at least twofold (P < .01), whereas a novel subset of patients was revealed displaying a distinct pattern of 125 upregulated genes involved in multiple cellular processes. Functional analysis of the 1077 genes documented their involvement in more than 50 signaling pathways, such as PTEN, oncostatin M, and extracellular signal-regulated kinase signaling, affecting extracellular matrix remodeling and invasion. Comparison of our data set with those of the single VIN study revealed that the two entities share a limited number of genes and display unique features.