Multi-omics analysis identifies drivers of protein phosphorylation
Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The abundance of a phosphorylated peptide (phosphopeptide) is determined by the abundance of its parent protein and the proportion of target sites that are p...
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Published in | Genome Biology Vol. 24; no. 1; p. 52 |
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Main Authors | , , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
England
BioMed Central
21.03.2023
BMC |
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Abstract | Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The abundance of a phosphorylated peptide (phosphopeptide) is determined by the abundance of its parent protein and the proportion of target sites that are phosphorylated.
We quantified phosphopeptides, proteins, and transcripts in heart, liver, and kidney tissue samples of mice from 58 strains of the Collaborative Cross strain panel. We mapped ~700 phosphorylation quantitative trait loci (phQTL) across the three tissues and applied genetic mediation analysis to identify causal drivers of phosphorylation. We identified kinases, phosphatases, cytokines, and other factors, including both known and potentially novel interactions between target proteins and genes that regulate site-specific phosphorylation. Our analysis highlights multiple targets of pyruvate dehydrogenase kinase 1 (PDK1), a regulator of mitochondrial function that shows reduced activity in the NZO/HILtJ mouse, a polygenic model of obesity and type 2 diabetes.
Together, this integrative multi-omics analysis in genetically diverse CC strains provides a powerful tool to identify regulators of protein phosphorylation. The data generated in this study provides a resource for further exploration. |
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AbstractList | BackgroundPhosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The abundance of a phosphorylated peptide (phosphopeptide) is determined by the abundance of its parent protein and the proportion of target sites that are phosphorylated.ResultsWe quantified phosphopeptides, proteins, and transcripts in heart, liver, and kidney tissue samples of mice from 58 strains of the Collaborative Cross strain panel. We mapped ~700 phosphorylation quantitative trait loci (phQTL) across the three tissues and applied genetic mediation analysis to identify causal drivers of phosphorylation. We identified kinases, phosphatases, cytokines, and other factors, including both known and potentially novel interactions between target proteins and genes that regulate site-specific phosphorylation. Our analysis highlights multiple targets of pyruvate dehydrogenase kinase 1 (PDK1), a regulator of mitochondrial function that shows reduced activity in the NZO/HILtJ mouse, a polygenic model of obesity and type 2 diabetes.ConclusionsTogether, this integrative multi-omics analysis in genetically diverse CC strains provides a powerful tool to identify regulators of protein phosphorylation. The data generated in this study provides a resource for further exploration. Abstract Background Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The abundance of a phosphorylated peptide (phosphopeptide) is determined by the abundance of its parent protein and the proportion of target sites that are phosphorylated. Results We quantified phosphopeptides, proteins, and transcripts in heart, liver, and kidney tissue samples of mice from 58 strains of the Collaborative Cross strain panel. We mapped ~700 phosphorylation quantitative trait loci (phQTL) across the three tissues and applied genetic mediation analysis to identify causal drivers of phosphorylation. We identified kinases, phosphatases, cytokines, and other factors, including both known and potentially novel interactions between target proteins and genes that regulate site-specific phosphorylation. Our analysis highlights multiple targets of pyruvate dehydrogenase kinase 1 (PDK1), a regulator of mitochondrial function that shows reduced activity in the NZO/HILtJ mouse, a polygenic model of obesity and type 2 diabetes. Conclusions Together, this integrative multi-omics analysis in genetically diverse CC strains provides a powerful tool to identify regulators of protein phosphorylation. The data generated in this study provides a resource for further exploration. Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The abundance of a phosphorylated peptide (phosphopeptide) is determined by the abundance of its parent protein and the proportion of target sites that are phosphorylated. We quantified phosphopeptides, proteins, and transcripts in heart, liver, and kidney tissue samples of mice from 58 strains of the Collaborative Cross strain panel. We mapped ~700 phosphorylation quantitative trait loci (phQTL) across the three tissues and applied genetic mediation analysis to identify causal drivers of phosphorylation. We identified kinases, phosphatases, cytokines, and other factors, including both known and potentially novel interactions between target proteins and genes that regulate site-specific phosphorylation. Our analysis highlights multiple targets of pyruvate dehydrogenase kinase 1 (PDK1), a regulator of mitochondrial function that shows reduced activity in the NZO/HILtJ mouse, a polygenic model of obesity and type 2 diabetes. Together, this integrative multi-omics analysis in genetically diverse CC strains provides a powerful tool to identify regulators of protein phosphorylation. The data generated in this study provides a resource for further exploration. Abstract Background Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The abundance of a phosphorylated peptide (phosphopeptide) is determined by the abundance of its parent protein and the proportion of target sites that are phosphorylated. Results We quantified phosphopeptides, proteins, and transcripts in heart, liver, and kidney tissue samples of mice from 58 strains of the Collaborative Cross strain panel. We mapped ~700 phosphorylation quantitative trait loci (phQTL) across the three tissues and applied genetic mediation analysis to identify causal drivers of phosphorylation. We identified kinases, phosphatases, cytokines, and other factors, including both known and potentially novel interactions between target proteins and genes that regulate site-specific phosphorylation. Our analysis highlights multiple targets of pyruvate dehydrogenase kinase 1 (PDK1), a regulator of mitochondrial function that shows reduced activity in the NZO/HILtJ mouse, a polygenic model of obesity and type 2 diabetes. Conclusions Together, this integrative multi-omics analysis in genetically diverse CC strains provides a powerful tool to identify regulators of protein phosphorylation. The data generated in this study provides a resource for further exploration. |
ArticleNumber | 52 |
Author | Munger, Steven C Gyuricza, Isabela Gerdes Bell, Timothy A de Villena, Fernando Pardo-Manuel Ferris, Martin T Churchill, Gary A Shaw, Ginger D Vincent, Matthew Zhang, Tian Hock, Pablo Keele, Gregory R Gygi, Steven P Paulo, Joao A Brunton, Catherine |
Author_xml | – sequence: 1 givenname: Tian surname: Zhang fullname: Zhang, Tian organization: Harvard Medical School, Boston, MA, 02115, USA – sequence: 2 givenname: Gregory R surname: Keele fullname: Keele, Gregory R organization: The Jackson Laboratory, Bar Harbor, ME, 04609, USA – sequence: 3 givenname: Isabela Gerdes surname: Gyuricza fullname: Gyuricza, Isabela Gerdes organization: The Jackson Laboratory, Bar Harbor, ME, 04609, USA – sequence: 4 givenname: Matthew surname: Vincent fullname: Vincent, Matthew organization: The Jackson Laboratory, Bar Harbor, ME, 04609, USA – sequence: 5 givenname: Catherine surname: Brunton fullname: Brunton, Catherine organization: The Jackson Laboratory, Bar Harbor, ME, 04609, USA – sequence: 6 givenname: Timothy A surname: Bell fullname: Bell, Timothy A organization: Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA – sequence: 7 givenname: Pablo surname: Hock fullname: Hock, Pablo organization: Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA – sequence: 8 givenname: Ginger D surname: Shaw fullname: Shaw, Ginger D organization: Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA – sequence: 9 givenname: Steven C surname: Munger fullname: Munger, Steven C organization: The Jackson Laboratory, Bar Harbor, ME, 04609, USA – sequence: 10 givenname: Fernando Pardo-Manuel surname: de Villena fullname: de Villena, Fernando Pardo-Manuel organization: Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA – sequence: 11 givenname: Martin T surname: Ferris fullname: Ferris, Martin T organization: Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA – sequence: 12 givenname: Joao A surname: Paulo fullname: Paulo, Joao A organization: Harvard Medical School, Boston, MA, 02115, USA – sequence: 13 givenname: Steven P surname: Gygi fullname: Gygi, Steven P email: steven_gygi@hms.harvard.edu organization: Harvard Medical School, Boston, MA, 02115, USA. steven_gygi@hms.harvard.edu – sequence: 14 givenname: Gary A orcidid: 0000-0001-9190-9284 surname: Churchill fullname: Churchill, Gary A email: gary.churchill@jax.org organization: The Jackson Laboratory, Bar Harbor, ME, 04609, USA. gary.churchill@jax.org |
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Keywords | Phosphorylation Quantitative trait loci (QTL) Collaborative Cross Medation analysis Multi-omics Phosphorylation regulation |
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Snippet | Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The abundance of... Abstract Background Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling... BackgroundPhosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The... BACKGROUNDPhosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling cascades. The... Abstract Background Phosphorylation of proteins is a key step in the regulation of many cellular processes including activation of enzymes and signaling... |
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Title | Multi-omics analysis identifies drivers of protein phosphorylation |
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