METODO PER EFFETTUARE PROGNOSI DEL CANCRO DELLA MAMMELLA, KIT ED USO DI QUESTI

Based on clinical and molecular parameters, breast cancer is differentiated in different subtypes: luminal type, erb-B2 type, basal type. Luminal carcinomas, 65% of breast cancers, have a heterogeneous behavior, with recurrence occurring in about 40-50% and 5-years mortality in two thirds of recurrent patients, despite apparent low aggressiveness at the initial pathological examination. The study aimed to identify biomolecular parameters for luminal carcinomas in order to obtain a reliable assessment of recurrence risk and to implement a personalized surgical and adjuvant therapy for each individual patient. The study provided for the sequencing of the total transcriptome (RNA) of the specimen of 40 patients operated in the two-year period 1994/1995. Twenty of them died within 4 years from diagnosis, while 20 were alive and disease free at December 31, 2013, thus aiming at identifying a group of genes distinctly expressed between the two study arms (patients with good prognosis and patients with poor prognosis). Sample characteristics: patients with infiltrating carcinoma, 1st tumor, age <75 years, T <5 cm. The stages of analysis were the total RNA extraction from formalin-fixed and paraffin-embedded samples (FFPE), the preparation of a Library for RNA-Seq with validation of the extraction method suitable for the Library preparation, the Illumina HiSeq 1500 sequencing - 2 x 100 PE modality and the bioinformatic analysis. From the gene expression profile, additional information are derived that specifically correlates the expression of some genes to the response to specific therapies. The study highlighted 28 hyper-expressed genes (23 in luminal and 5 in non-luminal) two of which always present in a specific group: CXCL13 gene in living group and IFITM10 gene in dead patients. The bioinformatics analysis calculated the differential expression of Luminal samples (1994-2005) in the tumor/healthy (TH) and alive/dead (AD) comparison and was always conducted with DESeq2 and edgeR in the R / Bioconductor ambience with the following settings: DESeq2, Pvalue < 0,05, P adjusted value < 0,1, edgeR, Pvalue < 0.05, false Discovery rate < 0,1. From the gene expression profile, additional information can be obtained that specifically correlate the expression of some genes to specific treatments response. For example, in HER2 positive patients, the high expression of IGF1R and of CCNE1 correlates with the resistance to Herceptin, while ER + patients with high PDGFRA expression are resistant to tamoxifen treatment.