Unraveling the Significance of MET Focal Amplification in Lung Cancer: Integrative NGS, FISH, and IHC Investigation

MET amplification (METamp) represents a promising therapeutic target in non-small cell lung cancer (NSCLC), but no consensus has been established to identify METamp-dependent tumors that could potentially benefit from MET inhibitors. In this study, a comprehensive and thorough analysis of MET amplification/overexpression status was performed in a retrospectively recruited cohort comprising 231 NSCLC patients from Shanghai Chest Hospital (SCH-cohort) using three methods: fluorescence in situ hybridization (FISH), hybrid capture-based next-generation sequencing (NGS), and immunohistochemistry (IHC) for c-MET and phospho-MET. The SCH-cohort included 130 cases known to be METamp positive by FISH and 101 negative controls. The clinical relevance of these approaches in predicting the efficacy of MET inhibitors was evaluated. Additionally, NGS data from another two cohorts including 22,010 lung cancer cases was utilized to examine the biological characteristics of different METamp subtypes. Of the 231 cases, 145 showed MET amplification/overexpression using at least one method, whereas only half of them could be identified by all three methods. METamp can occur as focal amplification or polysomy. Our study revealed that the inconsistency between NGS and FISH primarily occurred in the polysomy subtype. Further investigations indicated that compared to polysomy, focal amplification correlated with fewer co-occurring driver mutations, higher protein expressions of c-MET and phospho-MET, and higher incidence in acquired resistance than de novo setting. Moreover, patients with focal amplification presented a more robust response to MET inhibitors compared to those with polysomy. Notably, a strong correlation was observed between focal amplification and PD-L1 expression, indicating potential therapeutic implications with combined MET inhibitor and immunotherapy for patients with both alterations. Our findings provide insights into the molecular complexity and clinical relevance of METamp in lung cancer, highlighting the role of MET focal amplification as an oncogenic driver and its feasibility as a primary biomarker to further investigate the clinical activity of MET inhibitors in future studies.