Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma

Abstract We proteotyped blood plasma from 30 mouse knockout strains and corresponding wild-type mice from the International Mouse Phenotyping Consortium. We used targeted proteomics with internal standards to quantify 375 proteins in 218 samples. Our results provide insights into the manifested effe...

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Autores principales:	Yassene Mohammed, Sarah A. Michaud, Helena Pětrošová, Juncong Yang, Milan Ganguly, David Schibli, Ann M. Flenniken, Lauryl M. J. Nutter, Hibret A. Adissu, K. C. Kent Lloyd, Colin McKerlie, Christoph H. Borchers
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/72bd932c9079468a9baf2be34f40d25f
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spelling	oai:doaj.org-article:72bd932c9079468a9baf2be34f40d25f2021-12-02T15:49:54ZProteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma10.1038/s41540-021-00184-82056-7189https://doaj.org/article/72bd932c9079468a9baf2be34f40d25f2021-05-01T00:00:00Zhttps://doi.org/10.1038/s41540-021-00184-8https://doaj.org/toc/2056-7189Abstract We proteotyped blood plasma from 30 mouse knockout strains and corresponding wild-type mice from the International Mouse Phenotyping Consortium. We used targeted proteomics with internal standards to quantify 375 proteins in 218 samples. Our results provide insights into the manifested effects of each gene knockout at the plasma proteome level. We first investigated possible contamination by erythrocytes during sample preparation and labeled, in one case, up to 11 differential proteins as erythrocyte originated. Second, we showed that differences in baseline protein abundance between female and male mice were evident in all mice, emphasizing the necessity to include both sexes in basic research, target discovery, and preclinical effect and safety studies. Next, we identified the protein signature of each gene knockout and performed functional analyses for all knockout strains. Further, to demonstrate how proteome analysis identifies the effect of gene deficiency beyond traditional phenotyping tests, we provide in-depth analysis of two strains, C8a −/− and Npc2 +/− . The proteins encoded by these genes are well-characterized providing good validation of our method in homozygous and heterozygous knockout mice. Ig alpha chain C region, a poorly characterized protein, was among the differentiating proteins in C8a −/− . In Npc2 +/− mice, where histopathology and traditional tests failed to differentiate heterozygous from wild-type mice, our data showed significant difference in various lysosomal storage disease-related proteins. Our results demonstrate how to combine absolute quantitative proteomics with mouse gene knockout strategies to systematically study the effect of protein absence. The approach used here for blood plasma is applicable to all tissue protein extracts.Yassene MohammedSarah A. MichaudHelena PětrošováJuncong YangMilan GangulyDavid SchibliAnn M. FlennikenLauryl M. J. NutterHibret A. AdissuK. C. Kent LloydColin McKerlieChristoph H. BorchersNature PortfolioarticleBiology (General)QH301-705.5ENnpj Systems Biology and Applications, Vol 7, Iss 1, Pp 1-23 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Yassene Mohammed Sarah A. Michaud Helena Pětrošová Juncong Yang Milan Ganguly David Schibli Ann M. Flenniken Lauryl M. J. Nutter Hibret A. Adissu K. C. Kent Lloyd Colin McKerlie Christoph H. Borchers Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma
description	Abstract We proteotyped blood plasma from 30 mouse knockout strains and corresponding wild-type mice from the International Mouse Phenotyping Consortium. We used targeted proteomics with internal standards to quantify 375 proteins in 218 samples. Our results provide insights into the manifested effects of each gene knockout at the plasma proteome level. We first investigated possible contamination by erythrocytes during sample preparation and labeled, in one case, up to 11 differential proteins as erythrocyte originated. Second, we showed that differences in baseline protein abundance between female and male mice were evident in all mice, emphasizing the necessity to include both sexes in basic research, target discovery, and preclinical effect and safety studies. Next, we identified the protein signature of each gene knockout and performed functional analyses for all knockout strains. Further, to demonstrate how proteome analysis identifies the effect of gene deficiency beyond traditional phenotyping tests, we provide in-depth analysis of two strains, C8a −/− and Npc2 +/− . The proteins encoded by these genes are well-characterized providing good validation of our method in homozygous and heterozygous knockout mice. Ig alpha chain C region, a poorly characterized protein, was among the differentiating proteins in C8a −/− . In Npc2 +/− mice, where histopathology and traditional tests failed to differentiate heterozygous from wild-type mice, our data showed significant difference in various lysosomal storage disease-related proteins. Our results demonstrate how to combine absolute quantitative proteomics with mouse gene knockout strategies to systematically study the effect of protein absence. The approach used here for blood plasma is applicable to all tissue protein extracts.
format	article
author	Yassene Mohammed Sarah A. Michaud Helena Pětrošová Juncong Yang Milan Ganguly David Schibli Ann M. Flenniken Lauryl M. J. Nutter Hibret A. Adissu K. C. Kent Lloyd Colin McKerlie Christoph H. Borchers
author_facet	Yassene Mohammed Sarah A. Michaud Helena Pětrošová Juncong Yang Milan Ganguly David Schibli Ann M. Flenniken Lauryl M. J. Nutter Hibret A. Adissu K. C. Kent Lloyd Colin McKerlie Christoph H. Borchers
author_sort	Yassene Mohammed
title	Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma
title_short	Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma
title_full	Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma
title_fullStr	Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma
title_full_unstemmed	Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma
title_sort	proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/72bd932c9079468a9baf2be34f40d25f
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Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma

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