Gene expression profiling of spheres from primary ovarian cancer cells and from primary fallopian tube epithelial cells

The biological features of ovarian cancer stem cells (OCSC) remain elusive, mainly because 1) most studies so far have focused on cell lines that recapitulate the human disease only to a limited extend; and 2) because the identification of OCSC has relied on markers inferred from different and unrelated tumor types. Our study has harnessed the intrinsic, stemness-related properties of OCSC to identify and isolate this cell subpopulation from primary cultures freshly established from high-grade serous ovarian cancer (HGSOC), the most common and aggressive from of the disease. In addition, OCSC were compared to stem cell-enriched cultures from fallopian tube epithelium, which is the most accredited tissue of origin for HGSOC. The transcriptomes of the two cell types were compared to infer genes differentially regulated in OCSC. We used affymetrix expression microarray to analyze the transcriptional profile of spheres deriving from high-grade serous ovarian cancer or from normal ovarian fimbria. Total RNA was extracted from primary cells derived from either 7 HGSOC ascites samples or 9 normal ovarian fimbriae samples. Samples were pooled together (3-5 samples/pool; Ascites, N=2; Fimbria, N=2) and analyzed using the Affymetrix Human Gene 2.1-st, following manufacturer's standard protocols. Raw affymetrix data were analyzed ausing the Expression Consol suite (Affymetrix) and normalized by RMA_sketch.