An exploratory SWATH plasma proteomics analysis of phyllodes tumor- a type of female breast tumor

Phyllodes tumors (PT) are rare fibroepithelial breast tumors with poorly understood molecular pathology. This study intent to identify the potential plasma markers of phyllodes tumors compared to controls using Sequential window acquisition of all theoretical fragment ion spectra-mass spectrometry (SWATH-LC-MS) based proteomics approach.

Plasma samples from phyllodes tumor cases and controls underwent SWATH-LC-MS/MS based untargeted proteomics analysis. Proteins with 1.5 fold changes & p < 0.05 in PT cases compared to control were considered for further analysis. Statistical analysis was done by using R 4.3.1 software and proteomics analysis was performed by using Spectronaut Software RESULT & CONCLUSION: Three hundred and nineteen proteins were identified. Amongst them 30 proteins were significantly altered in PT case compared to control. 26 were upregulated and 4 were downregulated. Again Protein-Protein network analysis revealed that 21 proteins were matched with STRING data base and out of 21 proteins 19 were highly connected in the interaction analysis. As per our knowledge, this is the first exploratory study on LC-MS/MS-SWATH based phyllodes tumor proteomics. Different proteins like APMAP, HGFAC,TTR, PNO3 etc., and associated pathways like FCGR3A-mediated IL10 synthesis, arylesterase activity, EMT related Wnt/β-catenin Pathway etc. were significantly altered in Phyllodes tumor cases. Hence. this study will help to find the plausible theranostic markers and druggable targets for the phyllodes tumors in future.