An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation

Pierre Sabatier,Magnus Nordenskjöld,Alexander Kel,J Carlos Villaescusa,Massimiliano Gaetani,Vincent Millischer,Amir Ata Saei ,Christian M Beusch,Per‐Olof Berggren ,Niels Leijten,Sandeep Kadekar,Karl‐Henrik Grinnemo ,Noah Moruzzi,Sergey Rodin,Oscar E Simonson ,Rikard Holmdahl,Alexander G Tonevitsky,Kamilya Altynbekova,Ana Lúcia Coelho ,D V Maltseva ,Patrick Micke,Mike Aoun,Roman A Zubarev

doi:10.1038/s41467-021-26879-4

Abstract

Detailed characterization of cell type transitions is essential for cell biology in general and particularly for the development of stem cell-based therapies in regenerative medicine. To systematically study such transitions, we introduce a method that simultaneously measures protein expression and thermal stability changes in cells and provide the web-based visualization tool ProteoTracker. We apply our method to study differences between human pluripotent stem cells and several cell types including their parental cell line and differentiated progeny. We detect alterations of protein properties in numerous cellular pathways and components including ribosome biogenesis and demonstrate that modulation of ribosome maturation through SBDS protein can be helpful for manipulating cell stemness in vitro. Using our integrative proteomics approach and the web-based tool, we uncover a molecular basis for the uncoupling of robust transcription from parsimonious translation in stem cells and propose a method for maintaining pluripotency in vitro.

Highlights

1234567890():,; Detailed characterization of cell type transitions is essential for cell biology in general and for the development of stem cell-based therapies in regenerative medicine
The use of five cell lineages allowed us to fit the full replicate of the proteome-wide integral solubility alteration (PISA)-Express analysis within a single proteomics experiment by multiplexing ten tandem mass tags (TMT10)
We studied the proteome conversion from iPSC to hFF via EB as an evolution of two trajectories (Tn), Fig. 2 Charting protein trajectories during cell-type transitions using combined protein stability and expression analysis. a principal component analysis (PCA) plot of protein stability (Sm) in hi[12] iPSC, H9 ESC, EB, hFF, and RKO cells. b PCA plot of protein expression (Exp) in each cell type. c Violin plots showing the distribution of Sm and Exp fold changes (FCs) of each cell line against iPSC and number of proteins with a log[2] fold change (FC) in stability and expression exceeding three standard deviations in each cell line compared to iPSC

Summary

Introduction

1234567890():,; Detailed characterization of cell type transitions is essential for cell biology in general and for the development of stem cell-based therapies in regenerative medicine To systematically study such transitions, we introduce a method that simultaneously measures protein expression and thermal stability changes in cells and provide the web-based visualization tool ProteoTracker. By analyzing the Sankey diagrams, we detect alterations in protein properties after transition between PSCs and other cell types and map the altered proteins to various pathways and compartments, such as chromatin remodeling, DNA replication, cytoskeleton, cell adhesion, glucose metabolism, and ribosomes This combined analysis provides a more detailed view of protein behavior that is difficult to obtain from transcriptomic, expression proteomic or TPP analysis only. We show that SBDS protein, which is involved in ribosome biogenesis, plays a role in stem cell maintenance and differentiation, and could be targeted to modulate pluripotency in vitro

Methods

Results

Conclusion