Single-cell sensor analyses reveal signaling programs enabling Ras-G12C drug resistance

Nat Chem Biol. 2025 Jan;21(1):47-58. doi: 10.1038/s41589-024-01684-4. Epub 2024 Aug 5.

Abstract

Clinical resistance to rat sarcoma virus (Ras)-G12C inhibitors is a challenge. A subpopulation of cancer cells has been shown to undergo genomic and transcriptional alterations to facilitate drug resistance but the immediate adaptive effects on Ras signaling in response to these drugs at the single-cell level is not well understood. Here, we used Ras biosensors to profile the activity and signaling environment of endogenous Ras at the single-cell level. We found that a subpopulation of KRas-G12C cells treated with Ras-G12C-guanosine-diphosphate inhibitors underwent adaptive signaling and metabolic changes driven by wild-type Ras at the Golgi and mutant KRas at the mitochondria, respectively. Our Ras biosensors identified major vault protein as a mediator of Ras activation through its scaffolding of Ras signaling pathway components and metabolite channels. Overall, methods including ours that facilitate direct analysis on the single-cell level can report the adaptations that subpopulations of cells adopt in response to cancer therapies, thus providing insight into drug resistance.

MeSH terms

  • Antineoplastic Agents / pharmacology
  • Biosensing Techniques* / methods
  • Cell Line, Tumor
  • Drug Resistance, Neoplasm* / drug effects
  • Humans
  • Mitochondria / drug effects
  • Mitochondria / metabolism
  • Proto-Oncogene Proteins p21(ras)* / antagonists & inhibitors
  • Proto-Oncogene Proteins p21(ras)* / genetics
  • Proto-Oncogene Proteins p21(ras)* / metabolism
  • Signal Transduction* / drug effects
  • Single-Cell Analysis* / methods
  • Vault Ribonucleoprotein Particles / genetics
  • Vault Ribonucleoprotein Particles / metabolism

Substances

  • Proto-Oncogene Proteins p21(ras)
  • KRAS protein, human
  • Vault Ribonucleoprotein Particles
  • major vault protein
  • Antineoplastic Agents