Brain metastases are a devastating consequence of
cancer and currently there are no specific
biomarkers or therapeutic targets for risk prediction, diagnosis, and treatment. Here the
proteome of the brain metastatic
breast cancer cell line 231-BR has been compared with that of the parental cell line MDA-MB-231, which is also metastatic but has no organ selectivity. Using SILAC and nanoLC-MS/MS, 1957
proteins were identified in reciprocal labeling experiments and 1584 were quantified in the two cell lines. A total of 152
proteins were confidently determined to be up- or down-regulated by more than twofold in 231-BR. Of note, 112/152
proteins were decreased as compared with only 40/152 that were increased, suggesting that down-regulation of specific
proteins is an important part of the mechanism underlying the ability of
breast cancer cells to metastasize to the brain. When matched against transcriptomic data, 43% of individual
protein changes were associated with corresponding changes in
mRNA, indicating that the transcript level is a limited predictor of
protein level. In addition, differential
miRNA analyses showed that most
miRNA changes in 231-BR were up- (36/45) as compared with down-regulations (9/45). Pathway analysis revealed that
proteome changes were mostly related to cell signaling and cell cycle, metabolism and extracellular matrix remodeling. The major
protein changes in 231-BR were confirmed by parallel reaction monitoring mass spectrometry and consisted in increases (by more than fivefold) in the
matrix metalloproteinase-1,
ephrin-B1, stomatin, myc target-1, and decreases (by more than 10-fold) in transglutaminase-2, the
S100 calcium-binding protein A4, and
l-plastin. The clinicopathological significance of these major proteomic changes to predict the occurrence of
brain metastases, and their potential value as therapeutic targets, warrants further investigation.