Integrative proteomic and phosphoproteomic profiling of invasive micropapillary breast carcinoma

Invasive micropapillary carcinoma (IMPC) is a rare subtype of breast cancer with an aggressive phenotype and a poor prognosis. The mechanism of tumorigenesis of IMPC in breast remains unknown. Integrative analysis of the proteome and phosphoproteome may shed light on the mechanism of IMPC carcinogenesis. In our study, primary IMPC and paired normal breast tissue were collected from six patients and subjected to label free LC-MS/MS for quantitative proteomic and phosphoproteomic analysis. Kinase-substrate enrichment analysis (KSEA) was conducted to identify hyperactivated/inhibited kinases. Proteomic and phosphoproteomic data was combined to investigate cancer specific activated pathways. A total of 1331 differentially expressed proteins were identified. The proteomic analysis revealed a dysregulation of protein homeostasis in IMPC. Phosphoproteomic profiling identified 856 differentially phosphorylated phosphosites in 655 proteins. KSEA found that cyclin dependent kinases (CDKs) and the p90 ribosomal S6 kinases (RSKs) were highly activated, while protein kinase A (PKA) and protein kinase C (PKC) families were significantly inhibited in IMPC. Finally, cancer-specific activation of mTORC1/S6K2 signaling was also discerned in our integrative analysis. Overall, this study provides a comprehensive landscape of the proteome and phosphoproteome of IMPC, which will contribute to a further understanding of IMPC tumorigenesis and treatment. SIGNIFICANCE: This is the first study to provide the integrative proteomic and phosphoproteomic landscape of IMPC. Our study demonstrated that protein homeostasis dysregulation is one of the most prominent characteristics in IMPC. We also identifying several kinases which might have the potential to be novel targets in clinical practice. Cancer-specific activation of mTORC1/S6K2 signaling was discerned by integrative proteomic and phosphoproteomic analysis. The present study might contribute to a further understanding of IMPC tumorigenesis and treatment.