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2. A mouse SWATH-mass spectrometry reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts

Author

Krasny, Lukas, Bland, Philip, Burns, Jessica, Lima, Nadia Carvalho, Harrison, Peter T., Pacini, Laura, Elms, Mark L., Ning, Jian, Martinez, Victor Garcia, Yu, Yi-Ru, Acton, Sophie E., Ho, Ping-Chih, Calvo, Fernando, Swain, Amanda, Howard, Beatrice A., Natrajan, Rachael C., Huang, Paul H., The Institute of Cancer Research (UK), Breast Cancer Research Foundation, Medical Research Council (UK), Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), and European Research Council

Subjects
Male, Proteomics, Proteome, Mouse, DCIS, lcsh:Medicine, Mice, Nude, Mouse Models, Breast Neoplasms, Cell Communication, Mice, SCID, Mice, Breast cancer, Species Specificity, Tandem Mass Spectrometry, Cell Line, Tumor, lcsh:Pathology, Tumor Microenvironment, Animals, Humans, Resource Article, Databases, Protein, Xenografts, Breast Neoplasms/metabolism, Breast Neoplasms/pathology, Carcinoma, Intraductal, Noninfiltrating/metabolism, Carcinoma, Intraductal, Noninfiltrating/pathology, Chromatography, Liquid, Female, Heterografts, Mice, Inbred C57BL, NIH 3T3 Cells, Neoplasm Proteins/metabolism, Neoplasm Transplantation, Stromal Cells/metabolism, Stromal Cells/pathology, Mass spectrometry, SWATH-MS, lcsh:R, Neoplasm Proteins, Carcinoma, Intraductal, Noninfiltrating, Stromal Cells, lcsh:RB1-214
Abstract

© 2020. Published by The Company of Biologists Ltd., SWATH-mass spectrometry (MS) enables accurate and reproducible proteomic profiling in multiple model organisms including the mouse. Here, we present a comprehensive mouse reference spectral library (MouseRefSWATH) that permits quantification of up to 10,597 proteins (62.2% of the mouse proteome) by SWATH-MS. We exploit MouseRefSWATH to develop an analytical pipeline for species-specific deconvolution of proteomic alterations in human tumour xenografts (XenoSWATH). This method overcomes the challenge of high sequence similarity between mouse and human proteins, facilitating the study of host microenvironment-tumour interactions from ‘bulk tumour’ measurements. We apply the XenoSWATH pipeline to characterize an intraductal xenograft model of breast ductal carcinoma in situ and uncover complex regulation consistent with stromal reprogramming, where the modulation of cell migration pathways is not restricted to tumour cells but also operates in the mouse stroma upon progression to invasive disease. MouseRefSWATH and XenoSWATH open new opportunities for in-depth and reproducible proteomic assessment to address wide-ranging biological questions involving this important model organism., P.H.H. is supported by grants from the Institute of Cancer Research, Breast Cancer Now (2013NovPhD185 and 2014NovPR360) and Cancer Research UK (C36478/ A19281). B.A.H. and R.C.N. are supported by Breast Cancer Now programmatic funding. S.E.A. is supported by grants from Cancer Research UK (CRUK/A19763) and the Medical Research Council (MC_U12266B). F.C. is supported by grants from the Institute of Cancer Research, the Ramon y Cajal Research Programme (RYC2016-20352) and Ministerio de Ciencia, Innovación y Universidades/Agencia Estatal de Investigación/European Regional Development Fund (RTI2018-096778- A-I00). P.-C.H. is supported in part by a Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung project grant (31003A_182470) and a European Research Council Starting Grant (802773-MitoGuide).

Published
2020

3. A mouse SWATH-mass spectrometry reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts

Author

The Institute of Cancer Research (UK), Breast Cancer Research Foundation, Medical Research Council (UK), Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Research Council, Krasny, Lukas, Bland, Philip, Burns, Jessica, Carvalho Lima, Nadia, Harrison, Peter T., Pacini, Laura, Elms, Mark L., Ning, Jian, Garcia Martinez, Victor, Yu, Yi-Ru, Acton, Sophie E., Ho, Ping-Chih, Calvo, Fernando, Swain, Amanda, Howard, Beatrice A., Natrajan, Rachael C., Huang, Paul H., The Institute of Cancer Research (UK), Breast Cancer Research Foundation, Medical Research Council (UK), Ministerio de Economía y Competitividad (España), Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), European Research Council, Krasny, Lukas, Bland, Philip, Burns, Jessica, Carvalho Lima, Nadia, Harrison, Peter T., Pacini, Laura, Elms, Mark L., Ning, Jian, Garcia Martinez, Victor, Yu, Yi-Ru, Acton, Sophie E., Ho, Ping-Chih, Calvo, Fernando, Swain, Amanda, Howard, Beatrice A., Natrajan, Rachael C., and Huang, Paul H.

Abstract

SWATH-mass spectrometry (MS) enables accurate and reproducible proteomic profiling in multiple model organisms including the mouse. Here, we present a comprehensive mouse reference spectral library (MouseRefSWATH) that permits quantification of up to 10,597 proteins (62.2% of the mouse proteome) by SWATH-MS. We exploit MouseRefSWATH to develop an analytical pipeline for species-specific deconvolution of proteomic alterations in human tumour xenografts (XenoSWATH). This method overcomes the challenge of high sequence similarity between mouse and human proteins, facilitating the study of host microenvironment-tumour interactions from ‘bulk tumour’ measurements. We apply the XenoSWATH pipeline to characterize an intraductal xenograft model of breast ductal carcinoma in situ and uncover complex regulation consistent with stromal reprogramming, where the modulation of cell migration pathways is not restricted to tumour cells but also operates in the mouse stroma upon progression to invasive disease. MouseRefSWATH and XenoSWATH open new opportunities for in-depth and reproducible proteomic assessment to address wide-ranging biological questions involving this important model organism.

Published
2020

4. A mouse SWATH-MS reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts

Author

Krasny, Lukas, primary, Bland, Philip, additional, Burns, Jessica, additional, Lima, Nadia Carvalho, additional, Harrison, Peter T., additional, Pacini, Laura, additional, Elms, Mark L., additional, Ning, Jian, additional, Garcia Martinez, Victor, additional, Yu, Yi-Ru, additional, Acton, Sophie E., additional, Ho, Ping-Chih, additional, Calvo, Fernando, additional, Swain, Amanda, additional, Howard, Beatrice A., additional, Natrajan, Rachael C., additional, and Huang, Paul H., additional

Published
2020
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6. A mouse SWATH-mass spectrometry reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts.

Author

Krasny L, Bland P, Burns J, Lima NC, Harrison PT, Pacini L, Elms ML, Ning J, Martinez VG, Yu YR, Acton SE, Ho PC, Calvo F, Swain A, Howard BA, Natrajan RC, and Huang PH

Subjects
Animals, Breast Neoplasms pathology, Carcinoma, Intraductal, Noninfiltrating pathology, Cell Communication, Cell Line, Tumor, Chromatography, Liquid, Databases, Protein, Female, Heterografts, Humans, Male, Mice, Mice, Inbred C57BL, Mice, Nude, Mice, SCID, NIH 3T3 Cells, Neoplasm Transplantation, Species Specificity, Stromal Cells pathology, Tumor Microenvironment, Breast Neoplasms metabolism, Carcinoma, Intraductal, Noninfiltrating metabolism, Neoplasm Proteins metabolism, Proteome, Proteomics, Stromal Cells metabolism, Tandem Mass Spectrometry
Abstract

SWATH-mass spectrometry (MS) enables accurate and reproducible proteomic profiling in multiple model organisms including the mouse. Here, we present a comprehensive mouse reference spectral library (MouseRefSWATH) that permits quantification of up to 10,597 proteins (62.2% of the mouse proteome) by SWATH-MS. We exploit MouseRefSWATH to develop an analytical pipeline for species-specific deconvolution of proteomic alterations in human tumour xenografts (XenoSWATH). This method overcomes the challenge of high sequence similarity between mouse and human proteins, facilitating the study of host microenvironment-tumour interactions from 'bulk tumour' measurements. We apply the XenoSWATH pipeline to characterize an intraductal xenograft model of breast ductal carcinoma in situ and uncover complex regulation consistent with stromal reprogramming, where the modulation of cell migration pathways is not restricted to tumour cells but also operates in the mouse stroma upon progression to invasive disease. MouseRefSWATH and XenoSWATH open new opportunities for in-depth and reproducible proteomic assessment to address wide-ranging biological questions involving this important model organism., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2020. Published by The Company of Biologists Ltd.)

Published
2020
Full Text
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