panorama0000ProteomicsCarine SteinerSRM/MRMHomo Sapienshttps://panoramaweb.org/TNBC_FFPE.urlcarine.steiner@roche.comF. Hoffmann-La RochePanoramaPublicThe identification of clinically relevant biomarkers represents an important challenge in oncology. This problem can be addressed with biomarker discovery and verification studies performed directly in tumor samples using formalin-fixed paraffin-embedded (FFPE) tissues. However, reliably measuring proteins in FFPE samples remains challenging. Here, we demonstrate the use of liquid chromatography coupled to multiple reaction monitoring mass spectrometry (LC-MRM/MS) as an effective technique for such applications. An LC-MRM/MS method was developed to simultaneously quantify hundreds of peptides extracted from FFPE samples and was applied to the targeted measurement of 200 proteins in 48 triple-negative, 19 HER2-overexpressing, and 20 luminal A breast tumors. Quantitative information was obtained for 185 proteins, including known markers of breast cancer such as HER2, hormone receptors, Ki-67, or inflammation-related proteins. LC-MRM/MS results for these proteins matched immunohistochemistry or chromogenic in situ hybridization data. In addition, comparison of our results with data from the literature showed that several proteins representing potential biomarkers were identified as differentially expressed in triple-negative breast cancer samples. These results indicate that LC-MRM/MS assays can reliably measure large sets of proteins using the analysis of surrogate peptides extracted from FFPE samples. This approach allows to simultaneously quantify the expression of target proteins from various pathways in tumor samples. LC-MRM/MS is thus a powerful tool for the relative quantification of proteins in FFPE tissues and for biomarker discovery.Relative Quantification of Proteins in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissue Using Multiplexed Mass Spectrometry Assays.Steiner Carine C, Lescuyer Pierre P, Cutler Paul P, Tille Jean-Christophe JC, Ducret Axel Aliquid chromatography tandem mass spectroscopy, Erbb-2, triple-receptor negative breast cancer, malignant tumor of the breast, Biological Markers, Viral Marker, Formol, Surrogate Endpoints, Inflammations, Tandem, determination, Laboratory, Breast Neoplasms, Biochemical, Mbp1, mammary neoplasm, Endpoint, Human Mammary Neoplasms, Serum, Tumor, Mass Spectrometry Mass Spectrometry, TNBC, CD340, triple-negative breast cancer, Polypeptides, Laboratory Markers, Techniques, Kiaa3023, tumor of the breast, peptido, "neoplasm of breast (disorder)" EXACT [SNOMEDCT_2005_07_31:126926005], Biological, Method, Methanal, Parafilm, triple-negative breast carcinoma, cancer of the breast, myd, BC, Mammary Neoplasms, malignant neoplasm of breast, LCMSMS, Luminal A subtype of breast carcinoma, inflammatory response, peptides, Hormone Receptor, Formaldehyd, Tissue, Oxomethane, Human Mammary Carcinomas, Mbp-1, Mass Spectrometry, endocrine, neoplasm of breast, Immune, Markers, Methodological Studies, breast neoplasm, cancer of breast, scientific observation, Viral Markers, mammary cancer, Breast Malignant Neoplasms, Tumors, LC-MS2, Luminal A breast carcinoma, Carcinoma, Viral, "breast neoplasm" EXACT [MTH:120], Surrogate Endpoint, gyltl1b-b, Liquid Chromatography, LC-MS/MS, Biochemical Markers, MLN19, Receptor Agonists, Procedure, Biologic Marker, Ki67, results, Literatures, Marker, MDDGA6, CIS, mKIAA0609, G18, NOS, KIAA0609, fixed, Malignant Neoplasm of Breast, c-neu, tumor of breast, Luminal A, Carcinomas, fg, CIS-1, gyltl1b, tumour of the breast, End Points, MS/MS, NEOPL BREAST, mdc1d, expanded, D630048A14Rik, Immunologic, Methodological, 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Marker, Methylene oxide, Protein Gene Products, plan specification, Gene Proteins, ER Negative PR Negative HER2 Negative Breast Neoplasms, Oxomethylene, Innate Inflammatory Responses, Breast Cancer, Immunogold-Silver Technics, Immunolabeling Techniques, Peptid, Cancer of Breast, assay, Neoplasia, HER2, breast, Immune Markers0falseBiomarker Discovery in FFPE tissues by SRMThe identification of clinically relevant biomarkers represents an important challenge in oncology. This can be addressed with biomarker discovery studies in formalin-fixed paraffin-embedded (FFPE) tissues. However, reliably measuring large sets of proteins in FFPE tissues remains challenging. Here we demonstrate the use of liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) as a promising technique for such applications. An LC-MS/MS method was developed to simultaneously quantify hundreds of peptides extracted from FFPE samples. 200 proteins were measured in 48 triple-negative (TNBC), 19 HER2-overexpressing, and 20 luminal A breast tumors. Quantitative information was obtained for 185 proteins, including known markers such as HER2, hormone receptors, ki-67, or inflammation-related proteins. MS results for these proteins matched IHC or CISH data. In addition, several proteins representing potential biomarkers were identified as differentially expressed in TNBC samples. Comparison of our results with data from the literature showed that MS assays can reliably and simultaneously measure many proteins in FFPE tissues using the analysis of surrogate peptides. Therefore LC-MS/MS is a powerful tool for the relative quantification of proteins in FFPE tissues and for biomarker discovery.Sun Sep 25 00:00:00 BST 2022PXD025135960636152753