MET-dependent solid tumours - molecular diagnosis and targeted therapy

Abstract

Attempts to develop MET-targeted therapies have historically focused on MET-expressing cancers, with limited success. Thus, MET expression in the absence of a genomic marker of MET dependence is a poor predictor of benefit from MET-targeted therapy. However, owing to the development of more sensitive methods of detecting genomic alterations, high-level MET amplification and activating MET mutations or fusions are all now known to be drivers of oncogenesis. MET mutations include those affecting the kinase or extracellular domains and those that result in exon 14 skipping. The activity of MET tyrosine kinase inhibitors varies by MET alteration category. The likelihood of benefit from MET-targeted therapies increases with increasing levels of MET amplification, although no consensus exists on the optimal diagnostic cut-off point for MET copy number gains identified using fluorescence in situ hybridization and, in particular, next-generation sequencing. Several agents targeting exon 14 skipping alterations are currently in clinical development, with promising data available from early-phase trials. By contrast, the therapeutic implications of MET fusions remain underexplored. Here we summarize and evaluate the utility of various diagnostic techniques and the roles of different classes of MET-targeted therapies in cancers with MET amplification, mutation and fusion, and MET overexpression.

Figure 1. MET amplification diagnosis.

(A) The identification of MET gene copy number by FISH only requires a single colored probe (yellow) against MET that is counted to determine the number of copies of the gene. This strategy cannot differentiate polysomy from true focal amplification as the absolute number of chromosomes that contain MET cannot be determined. In contrast, the use of an additional probe targeting centromere 7 (CEP7, blue) allows this determination. The MET/CEP7 ratio thus helps differentiate whole genome duplication/polysomy (low MET/CEP7 ratio) from focal amplification (high MET/CEP7 ratio). (B) Using next-generation sequencing, focal MET amplification can be distinguished from broad chromosomal gains that include MET. In the latter, adjacent genes such as LINC01510 and CAPZA2 are concurrently amplified. Focal MET amplification is associated with a higher likelihood of MET-dependence for oncogenesis.

Figure 2.. Targeted therapy for MET amplification.

In six prospective phase I/II clinical trials, patients with cancers possessing higher levels of MET amplification or gene copy number derived increased benefit from MET-directed targeted therapy. Trials included patients with non-small cell lung cancer (NSCLC), papillary renal cell cancer (PRCC), and other solid tumors. While cutoffs for MET amplification/gene copy number varied, the cutoff of a MET/CEP7 ratio or MET gene copy number of 4 was chosen for consistency for trials that used FISH; patient-level data were reviewed to calculate response rates. For the only trial which employed next-generation sequencing (NGS), the trial cutoff of MET gene copy number ≥6 was used. The objective response rate is depicted by cancers that fall below these cutoffs (light red circles) and cancers that met or exceeded these cutoffs (red circles). The size of each circle represents the size of the subpopulation within each trial (with the smallest circle representing an n of 2), and each row represents a single trial. ^§MET amplification was determined by FISH. ^ǂMET amplification was determined by NGS.

Figure 3.. MET mutations.

The MET protein consists of the extracellular semaphorin (SEMA) domain in red, a plexin-semaphorin-integrin (PSI) domain in purple, four immunoglobulin-plexin-transcription (IPT) repeats in yellow, a juxtamembrane domain (encoded by exon 14) in blue, and a kinase domain in green. A) MET exon 14 splice site alterations result in exon 14 exclusion. This results in the absence of the ubiquitin binding site of the juxtamembrane domain, impaired MET degradation, and increased MET signaling. B) Missense mutations in the juxtamembrane domain prevent spliceosome binding or modify the Y1003 ubiquitination site. These ultimately recapitulate the biology of MET exon 14 splice site alterations. C) Mutations in the kinase domain lead to the increased activation of the MET kinase and can be associated with conformational changes that favor the xDFG-out state. D) Other mutations can occur in the semaphorin domain where hepatocyte growth factor, the ligand for MET, binds. The impact of these mutations on MET function are unclear.

Figure 4.. MET Fusion.

A wide variety of MET fusions have been identified. These fusions can result in constitutive MET activation in different ways. The 5’ upstream partners CLIP2, TFG, KIF5B, BAIAP2L1, C8orf34, TPR have coiled-coil domains that promote chimeric oncoprotein dimerization. Other domains (e.g. the MENTAL domain of STARD3NL) can mediate alternate methods of homodimerization. The 3’ MET gene typically includes the kinase domain, however, fusions that include the juxtamembrane domain, or larger regions of the gene have been identified. Interestingly, certain fusions such as TPR-MET result in the exclusion of exon 14. The biology of this fusion is thus thought to be similar to that of MET exon 14-altered cancers. The exons at which the breakpoints for MET can occur are noted in the diagram.