Gene expression profile of FFPE samples collected with translational purposes from the MITO16/MaNGO-OV2 clinical trial

MITO16/MaNGO-OV2 (NCT01706120) is a multicenter, phase IV, single arm trial for advanced stage IIIB-IV or recurrent, previously untreated, ovarian cancer patients receiving carboplatin, paclitaxel plus bevacizumab for six 3-weekly cycles followed by bevacizumab single agent until progression or unacceptable toxicity up to a maximum of 22 total cycles. The trial that was specifically designed with a translational primary endpoint to explore if selected clinical and biological factors could identify ovarian cancer patients with better prognosis in terms of progression free survival and overall survival after combined first-line treatment with chemotherapy plus Bevacizumab. The translational study, designed together with the clinical trial, the translational study implicated the collection of patients’ tissue (formalin-fixed paraffin-embedded – FFPE) and blood samples. Gene expression profile was among the molecular analyses proposed on FFPE samples. After pathological revision, two 1 mm-cores of FFPE tissues cores were selected to represent at least a percentage >70% of tumor cells, no significant signs of necrosis and to avoid excessive presence of stromal tissue for RNA extraction. RNA from 195 patients of MITO16/MaNGO-OV2 trial was isolated using Qiagen RNeasy FFPE kit (Qiagen, Hilden, Germany) and quality checked. RNA concentration was assessed by the Nanodrop 2000 UV-Vis Spectrophotometer. Sample purity was assessed by 260/280 and 260/230 ratios and the recorded values ranged from 1.9-2.2. Gene expression profiling was performed using the GeneChip WT Pico kit (Affymetrix, Thermo Fisher Scientific) following the guidelines for FFPE material. EGFR status: M0,negative; MM,100%membrane expression; M,≤ 30%.