krahmer2018pcp: Subcellular Reorganization in Diet-Induced Hepatic Steatosis

In lgatto/pRolocdata: Data accompanying the pRoloc package

Subcellular Reorganization in Diet-Induced Hepatic Steatosis

Description

Data from 'Organellar Proteomics and Phospho-Proteomics Reveal Subcellular Reorganization in Diet-Induced Hepatic Steatosis' Developmental cell.

Lipid metabolism is highly compartmentalized between cellular organelles that dynamically adapt their compositions and interactions in response to metabolic challenges. Here, we investigate how diet-induced hepatic lipid accumulation, observed in non-alcoholic fatty liver disease (NAFLD), affects protein localization, organelle organization, and protein phosphorylation in vivo. We develop a mass spectrometric workflow for protein and phosphopeptide correlation profiling to monitor levels and cellular distributions of 6,000 liver proteins and 16,000 phosphopeptides during development of steatosis. Several organelle contact site proteins are targeted to lipid droplets (LDs) in steatotic liver, tethering organelles orchestrating lipid metabolism. Proteins of the secretory pathway dramatically redistribute, including the mis-localization of the COPI complex and sequestration of the Golgi apparatus at LDs. This correlates with reduced hepatic protein secretion. Our systematic in vivo analysis of subcellular rearrangements and organelle-specific phosphorylation reveals how nutrient overload leads to organellar reorganization and cellular dysfunction.

Usage

  data("krahmer2018pcp")
  data("krahmer2018phosphopcp")

Format

The data is an instance of class MSnSet from package MSnbase.

References

Organellar proteomics and phospho-proteomics reveal subcellular reorganization in diet-induced hepatic steatosis. Krahmer N, Najafi B, Schueder F, Quagliarini F, Steger M, Seitz S, Kasper R, Salinas F, Cox J, Uhlenhaut NH, Walther TC. Developmental Cell. 2018 Oct 22;47(2):205-21. https://doi.org/10.1016/j.devcel.2018.09.017

Examples

data(krahmer2018pcp)
krahmer2018pcp
pData(krahmer2018pcp)
exprs(krahmer2018pcp)[1:3,1:3]

library("pRoloc")
plot2D(krahmer2018pcp, fcol = "Organelle" , main = "Krahmer 2018")

data(krahmer2018phosphopcp)
krahmer2018phosphopcp
exprs(krahmer2018phosphopcp)[1:3,1:3]
  
plot2D(krahmer2018phosphopcp, main = "Krahmer 2018")

lgatto/pRolocdata documentation built on Nov. 27, 2024, 12:12 a.m.