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Analysis of functional network in metastatic early breast cancer using SWATH proteomics

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Year of publication 2016
Type Conference abstract
Description A novel panel of proteins associated with lymph node metastasis of low-grade luminal A breast cancer was recently identified using proteomics, transcriptomics and immunohistochemistry in the set of well characterized 96 breast tumours. Of these, carboxypeptidase B1 (CBP1) is a secreted protease, PDZ and LIM domain protein 2 (PDLIM2), RING finger protein 25 (RNF25) and TRAF3 Interacting Protein 2 (TRAF3IP2) are NF-?B associated proteins and stathmin (STMN1) is an oncoprotein involved in mitosis regulation. Our subsequent research has focused on understanding their molecular function in metastasis at the level of biological network. We overexpressed CPB1, PDLIM2, RNF25 and TRAF3IP2 in MCF7 breast cancer cells using plasmids carrying the encoding genes, silenced STMN1 expression in MDA-MB-231 cells using siRNA and quantitatively analyzed the whole proteome at 24/48/72, or 48/72/96 hrs after the transfection, or gene expression silencing, respectively. Moreover, pull-down-MS experiments were performed to identify CPB1 interacting partners in cells and in secretome. The digested protein extracts were analyzed in SWATH mode on TripleTOF 5600+ LC-MS system, quantitative data were extracted using Spectronaut 9 and statistically evaluated using mapDIA. The analysis of the network has revealed new potential functional relationships to NF-?B, p53, cytoskeleton, tumour progression, cell proliferation, and cell adhesion that may contribute to the metastatic phenotype of low grade breast tumours. This work was supported by Czech Science Foundation (project No. 14-19250S), by the project MEYS – NPS I – LO1413 and by MH CZ - DRO (MMCI, 00209805)
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