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Our in-vivo protein turnover work published in Cell

We are thrilled to announce that our latest study, "Turnover Atlas of Proteome and Phosphoproteome Across Mouse Tissues and Brain Regions," is published in Cell.



Key Highlights:

  • Tissue proteomes are shaped by both protein abundance and lifetime. Using advanced quantitative proteomics (DIA and TMT) and stable isotope labeling, we mapped the abundance and turnover of 11,000 proteins and 40,000 phosphosites across 16 mouse tissues and brain regions.

  • Protein half-life is a key determinant of tissue function. We developed the Heat-Circle (HC) plot, an innovative visualization integrating protein abundance and lifetime across tissues, revealing cellular proteomic energy expenditure at multiple levels.

  • Distinct turnover rates for proteasome, lysosome, and E3 ligases across tissues. Our data show that K48-linked ubiquitin (UPS-targeted) turns over more slowly than K63-linked ubiquitin (lysosomal degradation), indicating distinct ubiquitin recycling strategies in different tissues.

  • Protein-protein interaction (PPI) networks exhibit highly coordinated turnover across tissues. We discovered that protein lifetime is constrained by tissue-specific PPI networks, and remarkably, protein lifetime across tissues can predict PPIs with high accuracy.

  • Tissue-specific turnover diversity in peroxisomal proteins. Peroxisome proteins are shorter-lived in fast-turnover tissues and longer-lived in slow-turnover tissues, likely adapting to metabolic and cellular demands.

  • Site-specific phosphorylations alter protein lifetime in vivo. We identified key phosphorylation sites on neurodegeneration-related proteins, including Tau and α-synuclein, that stabilize or destabilize these proteins, with potential implications for disease pathology.


Explore our dataset through Turnover-PPT: https://yslproteomics.shinyapps.io/tissuePPT/


This work would not have been possible without our incredible collaborators: Junmin Peng Lab and Eugenio Fornasiero Lab!



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