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.

PURPOSE

This study aimed to conduct functional proteomics across breast cancer subtypes with bioinformatics analyses.

METHODS

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).

RESULTS

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 , , , and 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 (, , , ), and gene expression signature (log-rank test, P = 0.06).

CONCLUSION

Functional proteomics suggested that collagen proteins, thrombospondin 1 and lumican are differentially expressed across breast cancer subtypes.