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

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.

Mapping the GALNT1 substrate landscape with versatile proteomics tools

“…Obviously, substrates not demonstrating a shift in solubility will be missed in SIESTA-PISA 38 . There are estimates that the solubility of only a small fraction of substrates changes significantly upon post-translational modification 38,51,61,73 ; however, the substrates undergoing larger solubility changes should be of higher biological importance. Another complication is that some acceptor Thr and Ser residues on substrates might be occupied by other common modifications, such as phosphorylation.…”

System-wide profiling by proteome integral solubility alteration assay of drug residence times for target characterization

“…In addition, the cell experiment did not require extensive filtering that may result in protein loss. On the other hand, the cell experiment required normalization of each PISA dataset by separately measured protein abundance, as in PISA-Express 25 , and thus demands multiplexing of a larger number of samples. In order to meet this increased demand, we metabolically labeled proteins in cells with light and heavy Stable Isotope Labeling by Amino acids in Cell culture (SILAC) 31 reagents and additionally used TMT16-plex labeling of tryptic peptides.…”

“…Some time ago we have introduced Proteome Integral Solubility Alteration (PISA) assay as a high-throughput analogue of TPP 23 . PISA analysis was used for deconvoluting the action mechanism of redox modulating anti-cancer compounds 24 and profiling stem cell transitions 25 . Here we hypothesize that the ∆Sm solubility shift in PISA will reflect the degree of target engagement by a drug in a cell lysate or intact cell at certain time past drug removal by filtration (for lysate) or washing (for cells).…”

Ion-Based Proteome-Integrated Solubility Alteration Assays for Systemwide Profiling of Protein–Molecule Interactions

“…Therefore, TPP is now widely used in diverse applications, such as the study of protein–protein interactions, 12 metabolite–protein interactions, 13 , 14 determination of the enzyme substrates, 15 and studying cellular mechanisms. 16 − 20 …”