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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doaj-72bd932c9079468a9baf2be34f40d25f2021-05-30T11:46:33ZengNature Publishing Groupnpj Systems Biology and Applications2056-71892021-05-017112310.1038/s41540-021-00184-8Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasmaYassene Mohammed0Sarah A. Michaud1Helena Pětrošová2Juncong Yang3Milan Ganguly4David Schibli5Ann M. Flenniken6Lauryl M. J. Nutter7Hibret A. Adissu8K. C. Kent Lloyd9Colin McKerlie10Christoph H. Borchers11University of Victoria—Genome BC Proteomics CentreUniversity of Victoria—Genome BC Proteomics CentreUniversity of Victoria—Genome BC Proteomics CentreUniversity of Victoria—Genome BC Proteomics CentreThe Center for PhenogenomicsUniversity of Victoria—Genome BC Proteomics CentreThe Center for PhenogenomicsThe Center for PhenogenomicsCovance Inc.Department of Surgery, School of Medicine, and Mouse Biology Program, University of CaliforniaThe Hospital for Sick ChildrenProteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill UniversityAbstract 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.https://doi.org/10.1038/s41540-021-00184-8 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
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 |
spellingShingle |
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 npj Systems Biology and Applications |
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 Publishing Group |
series |
npj Systems Biology and Applications |
issn |
2056-7189 |
publishDate |
2021-05-01 |
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. |
url |
https://doi.org/10.1038/s41540-021-00184-8 |
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