Quantitative Proteome and Phosphoproteome Profiling across Three Cell Lines Revealed Potential Proteins Relevant to Nasopharyngeal Carcinoma Metastasis

Abstract

Despite the substantial reduction in the mortality rates of nasopharyngeal carcinoma (NPC), metastasis remains the primary cause of death in NPC cases. To explore metastasis-related proteins, we conducted proteomic and phosphoproteomic analyses of three NPC cell lines: SUNE1 and its subclones, 5–8F (high metastatic potential) and 6–10B (low metastatic potential). Using TMT-based quantification, we identified 1231, 1524, and 166 differentially regulated proteins (DRPs), as well as 177, 270, and 20 differentially regulated phosphoproteins (DRpPs) in 5–8F/SUNE1, 6–10B/SUNE1 and 5–8F/6–10B, respectively. These were enriched in cancer metastasis-related pathways, including cell migration and PPAR and PI3K pathways. Notably, 5–8F and 6–10B showed greater proteomic and phosphoproteomic similarity. To identify key proteins involved in NPC metastasis, we focused on the top 10 DRPs in 5–8F/6–10B. Knockdown experiments revealed that eight of these proteins, CRABP2, DNAJC15, NACAD, MYL9, DPYSL3, MAOA, MCAM, and S100A2, significantly influenced cell migration or invasion, with CRABP2, NACAD, and DPYSL3 dramatically enhancing these processes. Notably, DNAJC15 and NACAD are identified for the first time as novel metastasis-related proteins. Our findings demonstrate the effectiveness of this approach in identifying NPC metastasis biomarker candidates and offer new insights into underlying metastasis mechanisms, thus laying the groundwork for future research endeavors.