Illuminating oncogenic KRAS signaling by multi-dimensional chemical proteomics

Mutated KRAS is among the most frequent activating genetic alterations in cancer. Drug discovery efforts have led to inhibitors that block mutant KRAS activity. To better understand the molecular basis of their cytostatic rather than cytotoxic effects, we performed comprehensive dose-dependent proteome-wide target deconvolution, pathway engagement, and protein expression characterization in response to KRAS, MEK, ERK, SHP2, and SOS1 inhibitors in pancreatic (KRAS G12C, G12D) and lung cancer (KRAS G12C) cell lines. Analysis of the dose-response curves available online revealed common and cell line-specific signaling networks dominated by KRAS activity. Time-dose experiments separated early ERK-driven effects from those that result from cell cycle arrest. The transition occurred without substantial proteome re-modelling but extensive changes in phosphorylation and ubiquitinylation. Our resource highlights the complexity of KRAS signaling in cancer and places a large number of new proteins and their modifications into this functional context for further exploration.

We provide all dose-response curve data processed using internal pipelines or CurveCurator v0.5.0 (https://github.com/kusterlab/curve_curator). A README file is included with details about each file and a Meta table describing the experimental conditions. Each CurveCurator folder contains both the input data (including the TOML parameter file used for curve generation) and the output, which includes interactive dashboards (dashboard.html) and processed curve data (curves.txt).

Phospho-proteome, whole proteome, ubiquitinome, Kinobead pulldown, and cysteine profiling data are provided in separate ZIP folders. Additionally, we include all aggregated supplementary tables and analysis output tables used for figure generation in the manuscript.