Gen expression and epigenetic analysis of 34 genes in invasive breast cancer

Quantitative Real Time PCR gene expression data of 34 genes (including 6 reference genes) from 64 breast tumor and 51 tumor neighboring tissues with 4 normal breast tissues obtained from breast reduction surgeries were analyzed to look for an opportunity of improving the period of diagnosis and determination of treatment modality by considering a molecular tumor classification. All PCR were performed on fresh tissue samples. Also epigenetic changes of CDH1 and P16 were examined by methylation specific PCR and their relation with histological and clinical data was studied. CDH1 methylation was observed as %32 in lobular, 10.5% in ductal and 24% in mixed tumors when sorted on the histologic types. Methylated states of P16 were significantly high at stage 0, while of CDH1 were found to be high at advanced grades. More than ninety percent of the histological grades could be estimated by levels of BRCA2, P16, P53, P73, CDH1, THBS1, PAX5, STK11, BCL2, CASP8, ESR, RARb and MLH3 when 73.6% of the stages by: BRCA1, BRCA2, CDH1, P16, P15, P73, CDK6, GSTP1, TIMP3, CDH13, ATM, CASP8, ESR, HER2, MLH3; 42.2% of the nuclear grade by: BRCA1, BCL2, CASP8, ESR, MSH6, MLH3; 52.9% of the invasive grade by: P53, CDK6, TIMP3, RASSF1, PAX5, STK11, BCL2, RARb; 52.8% of the differentiation by P53, CDK6, TIMP3, PAX5, STK11, BCL2, CASP8, RARb; %56.9 of lymph node positivity by: BRCA1, BRCA2, CDH1, P16, P15, CDK6, ATM, ESR and 55.5% of the metastasis by: CDH1, P73, P53, TIMP3, CDH13, ATM, CASP8, HER2 and MSH6. CDH1 and TIMP3 gene expression changes could predict 51,4% of histologic typing in breast cancer when ESR, HER2, GSTP1 ve CDH13 expression changes predicts 85.5% of the sorting on hormone receptor status (ER+HER2+, ER+HER-, ER-HER+,ER-HER2-). We suppose that these results could help in better classification of the breast cancer patients for their treatment decisions.