Comparison of the genomic background of MET-altered carcinomas of the lung: biological differences and analogies

Abstract

Although non-small-cell lung cancer is a leading cause of cancer-related deaths, the molecular characterization and classification of its genetic alterations has drastically changed treatment options and overall survival within the last few decades. In particular, tyrosine kinase inhibitors targeting specific molecular alterations, among other MET, have greatly improved the prognosis of non-small-cell lung cancer patients. Here, we compare the genomic background of a subset of non-small-cell lung cancer cases harboring either a MET high-level amplification (n = 24) or a MET exon 14 skipping mutation (n = 26), using next-generatison sequencing, fluorescence in situ hybridization, immunohistochemistry, and Nanostring nCounter^® technology. We demonstrate that the MET-amplified cohort shows a higher genetic instability, compared with the mutant cohort (p < 0.001). Furthermore, MET mutations occur at high allele frequency and in the presence of co-occurring TP53 mutations (n = 7), as well as MDM2 (n = 7), CDK4 (n = 6), and HMGA2 (n = 5) co-amplifications. No other potential driver mutation has been detected. Conversely, in the MET-amplified group, we identify co-occurring pathogenic NRAS and KRAS mutations (n = 5) and a significantly higher number of TP53 mutations, compared with the MET-mutant cohort (p = 0.048). Of note, MET amplifications occur more frequently as subclonal events. Interestingly, despite the significantly (p = 0.00103) older age at diagnosis of stage IIIb/IV of MET-mutant patients (median 77 years), compared with MET high-level amplified patients (median 69 years), MET-mutant patients with advanced-stage tumors showed a significantly better prognosis at 12 months (p = 0.04). In conclusion, the two groups of MET genetic alterations differ, both clinically and genetically: our data strongly suggest that MET exon 14 skipping mutations represent an early driver mutation. In opposition, MET amplifications occur usually in the background of other strong genetic events and therefore MET amplifications should be interpreted in the context of each tumor's genetic background, rather than as an isolated driver event, especially when considering MET-specific treatment options.

Fig. 1

Histology and immunohistochemical analyses. a Adenocarcinoma of the lung. b Large cell carcinoma of the lung. c-f MET immunohistochemistry, score 0 + (c), score 1 + (d), score 2 + (e) score 3+. (f) Pictures taken at 20x magnification power

Fig. 2

Clinic and genetic features of patients. Overview of the cohort of MET-altered lung cancer. Heatmap illustrating the clinical and immunohistochemical features, sequencing results of KRAS and TP53, copy number variation analysis. Cases are represented in columns; parameters are depicted in rows and color-coded according to the key. ctrl gene copy number control, n.a. not available, wt wild type

Fig. 3

FISH analysis. a High-level amplified case showing high intratumoral heterogeneity of MET in the FISH analysis. Tumor cell nuclei with big clusters of the MET gene alternating with tumor cell nuclei with regular gene copy numbers of MET. b MDM2 amplification. c MYC amplification. d CDK4 amplification. Pictures taken at 63x magnification power

Fig. 4

Comparison of MET FISH and immunohistochemistry in MET-mutant and -amplified carcinomas. a–c Immunohistochemical analyses of MET. a Example of  MET high-level amplified case, score 3+. b Example of MET-mutant case with negative immunohistochemistry staining, score 1+. c Example of MET-mutant case with positive immunohistochemistry staining, score 3+. Pictures taken at 20x magnification power. d–f Paired FISH of MET. d Ratio MET/CEP17 7.36. e Ratio MET/CEP17 0,66. f Ratio MET/CEP17 1,18. Pictures taken at 63x magnification power

Fig. 5

Survival curve at 12 months after diagnosis of stage IIIb/IV for the whole cohort (n = 50) of MET-altered lung cancer. Amplified: non-small cell lung cancer harboring MET high-level amplification. Mutant: non-small cell lung cancer harboring MET exon 14 skipping mutations