Proteome of Breast Cancer 233 MOLECULAR BIOTECHNOLOGY Volume 29, 2005 RESEARCH PROTOCOL 233 Molecular Biotechnology © 2005 Humana Press Inc. All rights of any nature whatsoever reserved. 1073–6085/2005/29:3/233–244/$30.00 Abstract *Author to whom all correspondence and reprint requests should be addressed. * ,1 National Laboratory of Medical Molecular Biology, Insti- tute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China. E-mail: zhengdx@tom.com or zhengdx@pumc.edu.cn. 2 Proteomics Research Center of Chinese Academy of Medical Sci- ences, Beijing 100176, China. 3 Novo Nordisk R & D Center China, Beijing 100176, China. 4 Peking Union Medical College Hospital, Beijing 100730, China. Comparative Proteome Analysis of Breast Cancer and Normal Breast Yuanming Luo, 1, 2 Jindan Zhang, 1 Yanxin Liu, 1 Allan Christian Shaw, 3 Xiaorong Wang, 2 Shuzhen Wu, 2 Xuan Zeng, 4 Jie Chen, 4 Youhe Gao, 2 and Dexian Zheng 1, 2,* Breast cancer is a leading cause of death for women. The underlying molecular mechanism is still not well understood. In this study, two-dimensional gel electrophoresis combined with mass spectrometry was used to analyze changes in the proteome of infiltrating ductal carcinoma compared to normal breast tissue. Ten sets of two-dimensional gels per experimental condition were analyzed and more than 500 spots each were detected. This revealed 39 spots for which expression in breast cancer cells were reproducibly altered more than twofold compared to normal controls (p < 0.01). These spots represented 25 different proteins after identification using the database search after mass spectrometry, comprising cell defense proteins, enzymes involved in glycolytic energy metabolism and homeostasis, protein folding and structural proteins, proteins involved in cytoskeleton and cell motility, and proteins involved in other functions. In addition, 28 nondifferentially expressed proteins with different functions were also mapped and identified, which might help to establish a two-dimensional gel electrophoresis reference map of human breast cancer. Our study shows that proteomics offers a powerful methodology to detect the proteins that show different expression patterns in breast cancer tissue and may provide an accurate molecular classification. The differentially expressed proteins may be used as potential candidate markers for diagnostic purposes or for determination of tumor sensitivity to therapy. The functional implications of the identified proteins are discussed. Index Entries: Proteome; breast cancer; two-dimensional gel electrophoresis; mass spectrometry. 1. Introduction Breast cancer continues to be a leading cause of death for women (1). Uprooting the threat of breast cancer against women is one of the most arduous tasks that medical workers are facing. Although breast cancer has been studied exten- sively during the past several decades, the under- lying molecular basis is still not fully understood. It is well known that normal cells become pro- gressively transformed to malignancy by mul- tiple sequential events. The evolution to malignant phenotype involves mutation or misexpression of a variety of genes controlling cell proliferation, differentiation, and death. Thus, both cell trans- formation and progression toward malignancy are extremely complex at molecular levels (2). Differ- ent proteins may be upregulated or downregulated simultaneously and conduct distinct cell functions. Consequently, the analysis of single molecular species or even single cell individuals is far from the prediction of the clinical outcome. For this rea- son, molecular characterization of cancer requires approaches able to face the complexity of the dis- ease (i.e., capable of analyzing the expression of a variety of genes in a relatively easy and reproductive way). The newly developed proteomic approaches