Gene Expression profiles from FFPE samples with improved RNA decrosslinking technology A case study: Molecular profiling of breast cancer from formalin-fixed, archival material

Abstract
We have developed a novel demodifaction/decrosslinking protocol for RNA recovery from archival (FFPE) material. The resulting FFPE RNA quality is superior to RNA obtained with other commercial FFPE RNA isolation kits: larger RNAs can be recovered, and RT-qPCR data demonstrate less variability and lower Cq values. This FFPE RNA is suitable for differential gene expression measurement by qPCR, high concordance with parallel RNA samples from fresh-frozen tissues was observed.
Prognosis of breast cancer is determined by clinicopathological and molecular factors. We developed and validated molecular scores reflecting the hormone status (ER, PGR, HER2 scores) and the proliferation status (PRO score) of breast cancer cells. The scores can be combined to an overall RISK score. Molecular scores are independent prognostic parameters, they were validated in postmenopausal patients with estrogen receptor positive breast cancer. Multivariate analysis revealed that PRO and RISK scores outperform conventional parameters (histological grading and Ki-67 labeling index). Molecular scores are based on routine pathological material, testing can be implemented easily into routine diagnosis.