Multiomic dissection of KRAS signaling reveals targetable metabolic and DNA repair vulnerabilities in colorectal cancer

Background: KRAS is among the most common oncogenic drivers in colorectal cancer and is historically “undruggable”; yet direct KRAS inhibitors are now entering clinical trials. The systems-level effects of KRAS modulation remain poorly characterized, limiting therapeutic insights. We applied integrated multiomic profiling to reveal mechanistic vulnerabilities that could enhance translational strategies. Methods: Isogenic HCT-116 colorectal carcinoma cells (homozygous KRAS^G13D mutation vs. partial KRAS loss) were analyzed in biological replicates (n = 3-5) across transcriptomics (15,432 genes), proteomics (6,654 proteins), phosphoproteomics (10,034 phosphopeptides), and metabolomics (3,015 metabolites). Multi-layer data (>30,000 analytes) were integrated via pathway enrichment, correlation networks, and dimensionality reduction to identify core molecular modules downstream of KRAS. Results: KRAS deletion produced broad molecular reprogramming: 640 transcripts, 74 proteins, 744 phosphopeptides, and 519 metabolites showed significant changes (q<0.05). Metabolomics was most perturbed (>17%), revealing increased mitochondrial respiration and branched-chain amino acid catabolism, alongside suppressed glycolysis. Downregulated signaling included collagen biosynthesis, EGFR, IGF transport, and IL-4/IL-13 pathways. Network integration distilled >30,000 features into <100 molecular modules, highlighting metabolic shifts in plasmalogen-associated lipid remodeling and altered phosphorylation of nuclear pore, ribosomal, and DNA repair proteins (ATRX, DAXX). These findings indicate vulnerabilities in oxidative metabolism, lipid metabolism, ribosome biogenesis, and genome stability. Conclusions: This comprehensive multiomic analysis reveals that KRAS-driven colorectal cancer depends on coordinated control of metabolism, extracellular matrix signaling, and DNA repair pathways. KRAS attenuation shifts cells to oxidative metabolism while exposing vulnerabilities in lipid metabolism and DNA repair machinery. These findings suggest combinatorial therapeutic strategies integrating KRAS inhibition with metabolic or DNA damage-targeted therapies.