Human colon cancer cell lines - LC-MSMS

Despite the advent of mutant-selective KRAS inhibitors, colorectal cancer (CRC) responses remain limited, with frequent stable disease and rapid recurrence. The mechanisms underlying CRC tolerance to KRAS inhibition and eventual resistance are poorly understood. Here, we explored early transcriptional and proteomic changes following KRAS silencing in 3D CRC spheroid models to identify pathways linked to sensitivity or resistance. Based on growth, cell cycle, and apoptosis responses, cell lines were classified as KRAS silencing-sensitive (HCT116, SW480) or -resistant (LS174T, SW837). Sensitive cells showed upregulation of the unfolded protein response (UPR) and WNT/β-catenin signaling, while these pathways were downregulated in resistant cells. Proteomic analysis confirmed UPR deregulation, with reduced translation-related proteins in sensitive cells. Functional assays revealed that KRAS knockdown in HCT116 reduced protein aggregation and translational capacity, consistent with UPR activation. However, inhibiting IRE1α-mediated UPR signaling did not reverse KRAS silencing-induced arrest or apoptosis. These findings suggest UPR activation as an early adaptive response in KRAS-dependent CRC cells.