{"title":"An exploratory SWATH plasma proteomics analysis of phyllodes tumor- a type of female breast tumor","authors":"M.D. Quasid Akhter , Munish Dwivedi , Shivani Chitkara , Navneet Kaur , Swarnendu Bag","doi":"10.1016/j.jchromb.2025.124508","DOIUrl":null,"url":null,"abstract":"<div><h3>Objective</h3><div>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.</div></div><div><h3>Method</h3><div>Plasma samples from phyllodes tumor cases and controls underwent SWATH-LC-MS/MS based untargeted proteomics analysis. Proteins with 1.5 fold changes & <em>p</em> < 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</div></div><div><h3>Result & conclusion</h3><div>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.</div></div>","PeriodicalId":348,"journal":{"name":"Journal of Chromatography B","volume":"1254 ","pages":"Article 124508"},"PeriodicalIF":2.8000,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chromatography B","FirstCategoryId":"1","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1570023225000601","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
Abstract
Objective
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.
Method
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.
期刊介绍：
The Journal of Chromatography B publishes papers on developments in separation science relevant to biology and biomedical research including both fundamental advances and applications. Analytical techniques which may be considered include the various facets of chromatography, electrophoresis and related methods, affinity and immunoaffinity-based methodologies, hyphenated and other multi-dimensional techniques, and microanalytical approaches. The journal also considers articles reporting developments in sample preparation, detection techniques including mass spectrometry, and data handling and analysis.
Developments related to preparative separations for the isolation and purification of components of biological systems may be published, including chromatographic and electrophoretic methods, affinity separations, field flow fractionation and other preparative approaches.
Applications to the analysis of biological systems and samples will be considered when the analytical science contains a significant element of novelty, e.g. a new approach to the separation of a compound, novel combination of analytical techniques, or significantly improved analytical performance.
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