Cell surface thermal proteome profiling tracks perturbations and drug targets on the plasma membrane

Nat Methods. 2021 Jan;18(1):84-91. doi: 10.1038/s41592-020-01022-1. Epub 2021 Jan 4.

Abstract

Numerous drugs and endogenous ligands bind to cell surface receptors leading to modulation of downstream signaling cascades and frequently to adaptation of the plasma membrane proteome. In-depth analysis of dynamic processes at the cell surface is challenging due to biochemical properties and low abundances of plasma membrane proteins. Here we introduce cell surface thermal proteome profiling for the comprehensive characterization of ligand-induced changes in protein abundances and thermal stabilities at the plasma membrane. We demonstrate drug binding to extracellular receptors and transporters, discover stimulation-dependent remodeling of T cell receptor complexes and describe a competition-based approach to measure target engagement of G-protein-coupled receptor antagonists. Remodeling of the plasma membrane proteome in response to treatment with the TGFB receptor inhibitor SB431542 leads to partial internalization of the monocarboxylate transporters MCT1/3 explaining the antimetastatic effects of the drug.

MeSH terms

  • Benzamides / pharmacology*
  • Cell Membrane / drug effects
  • Cell Membrane / metabolism*
  • Dioxoles / pharmacology*
  • Humans
  • K562 Cells
  • Ligands
  • Membrane Proteins / analysis
  • Membrane Proteins / drug effects
  • Membrane Proteins / metabolism*
  • Protein Binding
  • Proteome / analysis
  • Proteome / drug effects
  • Proteome / metabolism*
  • Proteomics / methods*
  • Receptors, Antigen, T-Cell / metabolism*
  • Receptors, Transforming Growth Factor beta / antagonists & inhibitors
  • Temperature
  • U937 Cells

Substances

  • 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide
  • Benzamides
  • Dioxoles
  • Ligands
  • Membrane Proteins
  • Proteome
  • Receptors, Antigen, T-Cell
  • Receptors, Transforming Growth Factor beta