Signaling and transcriptional dynamics underlying early adaptation to oncogenic BRAF inhibition

Area of Science:

• Molecular Biology
• Cancer Research
• Pharmacology

Background:

• Drug-induced cellular adaptation, involving signaling and gene regulatory network remodeling, leads to drug-tolerant phenotypes and reduced sensitivity to anti-cancer kinase inhibitors.
• Understanding the temporal dynamics of subcellular events following kinase inhibition is crucial for overcoming adaptive therapy resistance.

Purpose of the Study:

• To resolve the scale and kinetics of subcellular events after oncogenic kinase inhibition and before cell cycle re-entry.
• To investigate the adaptive signaling network remodeling in response to BRAF kinase inhibitor therapy in BRAF-mutant melanoma.
• To identify potential therapeutic strategies to overcome adaptive resistance.

Main Methods:

• Utilized mass spectrometry-based phosphoproteomics and RNA sequencing to capture molecular snapshots at early time points (minutes, hours, days) after BRAF kinase inhibitor exposure.
• Enriched specific phospho-motifs to monitor dynamics of protein phosphorylation events related to growth and survival.
• Employed statistical inference of kinetically-defined signaling and transcriptional modules.

Main Results:

• Observed early and sustained inhibition of the BRAF-ERK signaling axis and gradual downregulation of cell cycle signals.
• Identified three distinct, reversible phase transitions toward quiescence.
• Revealed a dominant compensatory induction of SRC family kinase (SFK) signaling, partly driven by reactive oxygen species accumulation due to impaired redox homeostasis.

Conclusions:

• Early temporal dynamics of signaling and transcriptional networks reveal adaptive resistance mechanisms in melanoma.
• Compensatory SFK signaling is a key adaptive response to BRAF inhibition.
• Co-treatment with an SFK inhibitor demonstrates translational potential for overcoming adaptive resistance in melanoma models.