Screening of differential expression genes between primary breast cancer and its lymph node metastasis using single primer amplification of cDNA for microarray

Objective To screen genes related to breast cancer metastasis by comparing difference of expression profile between primary breast cancer and its lymph node metastasis.Methods The cell total RNA was extracted from 10 breast cancer specimens, including the primary cancer and metastatic cancer tissues of axillary lymph nodes resected during operation. Single primer amplification (SPA) was used to prepare fluorescence labeled targets and then Oligo microarray concluding 21 000 human functional genes was used to screen out 1 5 fold or more differential expression genes in at least 5 pairs of samples. The screened out genes were identified by real time PCR. Results Preparing targets by using SPA reduced the initial RNA to 0 25 μg, with 57 genes screened out, the expression of 19 of which were up regulated and the expression of 38 of which were down regulated in the metastatic tissues. Eight differentially expressed genes were related to cell migration and adhesion, 14 to signal transduction, and 14 to cell growth or metabolism. Real time PCR showed that the fibronection (FN) mRNA expression in the lymph node metastasis was only 1/3 6 of that in the matched primary breast cancer in 30 cases ( t= -3 188, P =0 003). Conclusion SPA is a sensitive method for preparing targets. Genes related to cell migration and adhesion, signal transduction, and ell growth or metabolism, which are associated with the biology process of metastasis have been screened out. FN as a potent marker may contribute to diagnosis of metastasis and prognosis for breast cancer patients.