Collagen proteins, thrombospondin 1 and lumican are differentially expressed across breast cancer subtypes by functional proteomics from core needle biopsy samples of Taiwanese breast cancer.

This study aimed to conduct functional proteomics across breast cancer subtypes with bioinformatics analyses. Candidate proteins were identified using nanoscale liquid chromatography with tandem mass spectrometry (NanoLC-MS/MS) from core needle biopsy samples of early stage (0-III) breast cancers, followed by external validation with public domain gene-expression datasets (TCGA TARGET GTEx and TCGA BRCA). Seventeen proteins demonstrated significantly differential expression and protein-protein interaction (PPI) found the strong networks including COL2A1, COL11A1, COL6A1, COL6A2, THBS1 and LUM. Public domain databases also showed that COL2A1, COL11A1, COL6A1, COL6A2 and LUM were higher in primary/metastatic tumor than in normal tissue (one-way ANOVA, all P-values less than 0.001), and all six genes were differentially expressed across four molecular subtypes based on hormone receptor (HR) status and human epidermal growth factor receptor II (HER2) status (one-way ANOVA, all P-values less than 0.001). Disease-specific survival discrepancy was observed comparing breast cancer patients of the upper and lower quartile of the collagen family (COL2A1, COL11A1, COL6A1, COL6A2), THBS1 and LUM gene expression signature (log-rank test, P = 0.06). Functional proteomics suggested that collagen proteins, thrombospondin 1 and lumican are differentially expressed across breast cancer subtypes.