Comparative profiling of breast cancer tissue membrane proteome by use of SDS-PAGE based cICAT method

Breast cancer is the most common cancer among women worldwide. There is an emerging interest in protein expression profiling with the aim of identifying novel diagnostic markers and therapeutic targets in breast cancer. We analyzed breast cancer tissues by using the cICAT (cleavable isotope-coded affinity tag) labeling approach and tandem mass spectrometry. Breast cancer and matched normal tissues were fractionated by ultracentrifugation to enrich membrane proteins, and cICAT labeled proteins were separated by SDS-PAGE. A total of 364 proteins were identified and quantified. Among the proteins that showed >1.5 fold difference between normal and cancer (36.6%), five (RPN1, ERp29, Trop2, PrP and PIGR) were selected for confirmation. Western blot on 10 pairs of normal and cancer tissues revealed that the expression of RPN1 and ERp29 were increased in breast cancer tissue, while Trop2, PrP and PIGR were decreased. Those Western blot results were highly consistent with cICAT results. Higher level of RPN1 and ERp29 and lower level of Trop2 in breast cancer cell lines compared to normal breast cell lines were observed. The result supports reliability of our SDS-PAGE based ICAT method in quantifying cancer tissue proteome.