Personalized phosphoproteomics identifies functional signaling

Protein phosphorylation dynamically integrates environmental and cellular information to control biological processes. Identifying functional phosphorylation amongst the thousands of phosphosites regulated by a perturbation at a global scale is a major challenge. Here we introduce ‘personalized phos...

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Published inNature biotechnology Vol. 40; no. 4; pp. 576 - 584
Main Authors Needham, Elise J., Hingst, Janne R., Parker, Benjamin L., Morrison, Kaitlin R., Yang, Guang, Onslev, Johan, Kristensen, Jonas M., Højlund, Kurt, Ling, Naomi X. Y., Oakhill, Jonathan S., Richter, Erik A., Kiens, Bente, Petersen, Janni, Pehmøller, Christian, James, David E., Wojtaszewski, Jørgen F. P., Humphrey, Sean J.
Format Journal Article
LanguageEnglish
Published New York Nature Publishing Group US 01.04.2022
Nature Publishing Group
Subjects
631/114/2391
631/45/475
631/61/475
Agriculture
Bioinformatics
Biological activity
Biological Phenomena
Biomedical and Life Sciences
Biomedical Engineering/Biotechnology
Biomedicine
Biotechnology
Computer applications
Customization
Glucose metabolism
Information processing
Insulin
Kinases
Life Sciences
Muscles
Perturbation
Phenotypes
Phenotypic variations
Phosphoproteins - genetics
Phosphorylation
Proteins
Proteomics - methods
Signal transduction
Signal Transduction - physiology
Signaling
Skeletal muscle
TOR protein
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Abstract Protein phosphorylation dynamically integrates environmental and cellular information to control biological processes. Identifying functional phosphorylation amongst the thousands of phosphosites regulated by a perturbation at a global scale is a major challenge. Here we introduce ‘personalized phosphoproteomics’, a combination of experimental and computational analyses to link signaling with biological function by utilizing human phenotypic variance. We measure individual subject phosphoproteome responses to interventions with corresponding phenotypes measured in parallel. Applying this approach to investigate how exercise potentiates insulin signaling in human skeletal muscle, we identify both known and previously unidentified phosphosites on proteins involved in glucose metabolism. This includes a cooperative relationship between mTOR and AMPK whereby the former directly phosphorylates the latter on S377, for which we find a role in metabolic regulation. These results establish personalized phosphoproteomics as a general approach for investigating the signal transduction underlying complex biology. Functionally relevant phosphorylation sites are detected by integrating phosphoproteomic and phenotypic data.
AbstractList Protein phosphorylation dynamically integrates environmental and cellular information to control biological processes. Identifying functional phosphorylation amongst the thousands of phosphosites regulated by a perturbation at a global scale is a major challenge. Here we introduce 'personalized phosphoproteomics', a combination of experimental and computational analyses to link signaling with biological function by utilizing human phenotypic variance. We measure individual subject phosphoproteome responses to interventions with corresponding phenotypes measured in parallel. Applying this approach to investigate how exercise potentiates insulin signaling in human skeletal muscle, we identify both known and previously unidentified phosphosites on proteins involved in glucose metabolism. This includes a cooperative relationship between mTOR and AMPK whereby the former directly phosphorylates the latter on S377, for which we find a role in metabolic regulation. These results establish personalized phosphoproteomics as a general approach for investigating the signal transduction underlying complex biology.Protein phosphorylation dynamically integrates environmental and cellular information to control biological processes. Identifying functional phosphorylation amongst the thousands of phosphosites regulated by a perturbation at a global scale is a major challenge. Here we introduce 'personalized phosphoproteomics', a combination of experimental and computational analyses to link signaling with biological function by utilizing human phenotypic variance. We measure individual subject phosphoproteome responses to interventions with corresponding phenotypes measured in parallel. Applying this approach to investigate how exercise potentiates insulin signaling in human skeletal muscle, we identify both known and previously unidentified phosphosites on proteins involved in glucose metabolism. This includes a cooperative relationship between mTOR and AMPK whereby the former directly phosphorylates the latter on S377, for which we find a role in metabolic regulation. These results establish personalized phosphoproteomics as a general approach for investigating the signal transduction underlying complex biology.
Protein phosphorylation dynamically integrates environmental and cellular information to control biological processes. Identifying functional phosphorylation amongst the thousands of phosphosites regulated by a perturbation at a global scale is a major challenge. Here we introduce 'personalized phosphoproteomics', a combination of experimental and computational analyses to link signaling with biological function by utilizing human phenotypic variance. We measure individual subject phosphoproteome responses to interventions with corresponding phenotypes measured in parallel. Applying this approach to investigate how exercise potentiates insulin signaling in human skeletal muscle, we identify both known and previously unidentified phosphosites on proteins involved in glucose metabolism. This includes a cooperative relationship between mTOR and AMPK whereby the former directly phosphorylates the latter on S377, for which we find a role in metabolic regulation. These results establish personalized phosphoproteomics as a general approach for investigating the signal transduction underlying complex biology.
Protein phosphorylation dynamically integrates environmental and cellular information to control biological processes. Identifying functional phosphorylation amongst the thousands of phosphosites regulated by a perturbation at a global scale is a major challenge. Here we introduce ‘personalized phosphoproteomics’, a combination of experimental and computational analyses to link signaling with biological function by utilizing human phenotypic variance. We measure individual subject phosphoproteome responses to interventions with corresponding phenotypes measured in parallel. Applying this approach to investigate how exercise potentiates insulin signaling in human skeletal muscle, we identify both known and previously unidentified phosphosites on proteins involved in glucose metabolism. This includes a cooperative relationship between mTOR and AMPK whereby the former directly phosphorylates the latter on S377, for which we find a role in metabolic regulation. These results establish personalized phosphoproteomics as a general approach for investigating the signal transduction underlying complex biology.Functionally relevant phosphorylation sites are detected by integrating phosphoproteomic and phenotypic data.
Protein phosphorylation dynamically integrates environmental and cellular information to control biological processes. Identifying functional phosphorylation amongst the thousands of phosphosites regulated by a perturbation at a global scale is a major challenge. Here we introduce ‘personalized phosphoproteomics’, a combination of experimental and computational analyses to link signaling with biological function by utilizing human phenotypic variance. We measure individual subject phosphoproteome responses to interventions with corresponding phenotypes measured in parallel. Applying this approach to investigate how exercise potentiates insulin signaling in human skeletal muscle, we identify both known and previously unidentified phosphosites on proteins involved in glucose metabolism. This includes a cooperative relationship between mTOR and AMPK whereby the former directly phosphorylates the latter on S377, for which we find a role in metabolic regulation. These results establish personalized phosphoproteomics as a general approach for investigating the signal transduction underlying complex biology. Functionally relevant phosphorylation sites are detected by integrating phosphoproteomic and phenotypic data.
Author Morrison, Kaitlin R.
Wojtaszewski, Jørgen F. P.
Petersen, Janni
Pehmøller, Christian
Onslev, Johan
Ling, Naomi X. Y.
Højlund, Kurt
James, David E.
Hingst, Janne R.
Yang, Guang
Needham, Elise J.
Kristensen, Jonas M.
Oakhill, Jonathan S.
Richter, Erik A.
Parker, Benjamin L.
Kiens, Bente
Humphrey, Sean J.
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BackLink https://www.ncbi.nlm.nih.gov/pubmed/34857927$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
Copyright The Author(s), under exclusive licence to Springer Nature America, Inc. 2021
2021. The Author(s), under exclusive licence to Springer Nature America, Inc.
The Author(s), under exclusive licence to Springer Nature America, Inc. 2021.
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Snippet Protein phosphorylation dynamically integrates environmental and cellular information to control biological processes. Identifying functional phosphorylation...
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SubjectTerms 631/114/2391
631/45/475
631/61/475
Agriculture
Bioinformatics
Biological activity
Biological Phenomena
Biomedical and Life Sciences
Biomedical Engineering/Biotechnology
Biomedicine
Biotechnology
Computer applications
Customization
Glucose metabolism
Information processing
Insulin
Kinases
Life Sciences
Muscles
Perturbation
Phenotypes
Phenotypic variations
Phosphoproteins - genetics
Phosphorylation
Proteins
Proteomics - methods
Signal transduction
Signal Transduction - physiology
Signaling
Skeletal muscle
TOR protein
Title Personalized phosphoproteomics identifies functional signaling
URI https://link.springer.com/article/10.1038/s41587-021-01099-9
https://www.ncbi.nlm.nih.gov/pubmed/34857927
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