Integrative proteomic characterization of human lung adenocarcinoma with KRAS G12 mutations reveals molecular pathogenesis

Integrated proteogenomic studies of lung adenocarcinoma (LUAD) have provided unique insights with potential clinical effects. Comprehensive proteomic analyses are needed to better understand the molecular landscape of LUAD with KRAS G12 mutations. This study aims to characterize the proteogenomic profile of LUAD with KRAS G12 mutation variants. We performed next-generation sequencing (NGS) on 9,479 solid tumors, including 3,523 lung cancers. Proteomic profiling was conducted on 96 LUAD patients with KRAS G12 mutations or wild-type status using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The LUAD tumor immune microenvironment (TIME) was characterized by multiplex immunohistochemistry (mIHC), and protein-protein interactions (PPIs) in KRAS G12-mutant lung cancer cells were mapped using biotin-based proximity labeling. Genomic analysis revealed heterogeneous KRAS-informed mutational profiles across pan-cancer and lung cancer, with allele-specific resolution for KRAS G12 mutations. Proteomic profiling of KRAS G12-mutant LUAD delineated distinct molecular features and tumor progression hallmarks. Unsupervised clustering identified three molecular subtypes, with the immune modulation subtype (S2) characterized by KRAS G12C enrichment, aggressive clinical features, and the greatest potential benefit from immunotherapy. The immune landscape of LUAD showed increased immune cell infiltration in KRAS G12C-mutant tumors. Additionally, proximal proteomics mapped a landscape of gain-of-interactions driven by KRAS G12 mutations, with ion transporter SLC4A7 emerged as a potential effector in immune modulation in the G12C variant. This comprehensive proteogenomic study provides insights into the molecular features of LUAD harboring KRAS G12 mutations, which may inform patient stratification and potential therapeutic approaches, pending further clinical validation.