Systematic analysis of proteome turnover in an organoid model of pancreatic cancer by dSILO

The role of protein turnover in pancreatic ductal adenocarcinoma (PDA) metastasis has not been previously investigated. We introduce dynamic stable-isotope labeling of organoids (dSILO): a dynamic SILAC derivative that combines a pulse of isotopically labeled amino acids with isobaric tandem mass-ta...

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Bibliographic Details
Published in:Cell reports methods 2024-05, Vol.4 (5), p.100760-100760, Article 100760
Main Authors: Ross, Alison B., Gorhe, Darvesh, Kim, Jenny Kim, Hodapp, Stefanie, DeVine, Lela, Chan, Karina M., Chio, Iok In Christine, Jovanovic, Marko, Ayres Pereira, Marina
Format: Article
Language:English
Subjects:
Carcinoma, Pancreatic Ductal - metabolism
Carcinoma, Pancreatic Ductal - pathology
dSILO
Humans
Isotope Labeling
metastases
Organoids - metabolism
Organoids - pathology
Pancreatic Neoplasms - metabolism
Pancreatic Neoplasms - pathology
PDA
protein half-life
protein turnover
Proteome - metabolism
Proteomics - methods
respirasome
SILAC
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Summary:The role of protein turnover in pancreatic ductal adenocarcinoma (PDA) metastasis has not been previously investigated. We introduce dynamic stable-isotope labeling of organoids (dSILO): a dynamic SILAC derivative that combines a pulse of isotopically labeled amino acids with isobaric tandem mass-tag (TMT) labeling to measure proteome-wide protein turnover rates in organoids. We applied it to a PDA model and discovered that metastatic organoids exhibit an accelerated global proteome turnover compared to primary tumor organoids. Globally, most turnover changes are not reflected at the level of protein abundance. Interestingly, the group of proteins that show the highest turnover increase in metastatic PDA compared to tumor is involved in mitochondrial respiration. This indicates that metastatic PDA may adopt alternative respiratory chain functionality that is controlled by the rate at which proteins are turned over. Collectively, our analysis of proteome turnover in PDA organoids offers insights into the mechanisms underlying PDA metastasis. [Display omitted] •dSILO is a method to measure proteome-wide protein turnover rates in an organoid system•Turnover rates are overall higher in PDA metastatic organoids than in tumor organoids•Mitochondrial proteins have the highest turnover increase•Turnover changes are not generally correlated with changes in protein abundance We sought to profile protein abundance and turnover rate in organoids derived from a pancreatic cancer mouse model using dynamic SILAC labeling. By doing so in paired primary and metastatic tumor organoids derived from an autochthonous PDA mouse model, we aim to gain deeper, unbiased insights into potential mechanisms driving PDA metastasis. Ross et al. present dynamic Stable-Isotope Labeling of Organoids (dSILO), a dynamic SILAC approach to measure proteome-wide protein turnover rates in organoids. They apply the method in a pancreatic ductal adenocarcinoma mouse model and discover that the metastatic organoids display accelerated proteome turnover compared to primary tumor organoids.
ISSN:2667-2375
2667-2375
DOI:10.1016/j.crmeth.2024.100760