Phosphoproteomic Profiling of Early-Stage Non-Small Cell Lung Cancer Provides Preliminary Evidence of Phosphorylation-Regulated Rho GTPase Signaling Driving Cytoskeletal Remodeling, Angiogenesis, and Cell Cycle Progression

Abstract

Non-small cell lung cancer (NSCLC) is the primary cause of cancer-related deaths worldwide. This can be attributed to the difficulty in early detection and the limited efficacy of available treatments, partly due to an incomplete understanding of the disease biology. Identification of key proteins involved in early-stage progression and understanding the underlying mechanisms can greatly contribute to the development of diagnostic and treatment strategies for NSCLC. Quantitative phosphoproteomic analysis was done on paired tumor tissues and adjacent normal lung tissues from early-stage NSCLC adenocarcinoma (LUAD) patients to allow for the identification of proteins with differential phosphorylation and their associated pathways. A total of 6483 phosphoproteins were identified, with 1229 proteins having significantly higher phosphorylation and 701 proteins having significantly lower phosphorylation in the tumor tissues. All MS data were deposited in ProteomeXchange with the identifier PXD071583. Function enrichment analysis showed that the differentially phosphorylated proteins and phosphosites were primarily involved in Rho GTPase signaling and cytoskeleton remodeling. Analysis of protein interaction networks suggests that the predicted kinase activity likely drives malignant transformation in NSCLC LUAD, presumably through Rho GTPase-mediated angiogenesis and cell cycle progression. More importantly, this study identified several protein phosphosites with differential phosphorylation and inferred kinase-phosphosite activities that have not previously been reported in NSCLC LUAD.