MET alterations detected in blood-derived circulating tumor DNA correlate with bone metastases and poor prognosis

MET, also called c-MET or hepatocyte growth factor (HGF) receptor, is a receptor tyrosine kinase discovered as an oncogene in the 1980s [1, 2]. Independent research found that HGF or scatter factor (SF) was a ligand for MET [3]. Upon binding of HGF to MET, the kinase domain phosphorylates growth factor receptor-bound protein 2 (GRB2) and GRB2-associated binding protein 1 (GAB1) and activates diverse downstream signaling pathways important in cancer, including the ERK/MAPK, PI3K-Akt/PKB, Crk-Rap, and Rac-Pak pathways [4]. These pathways form distinct branches that interact to regulate cell proliferation, invasion, migration, angiogenesis, development, organ regeneration, and tumorigenesis [4].

Activating MET mutations are found in diverse human cancer [5]. For instance, activating mutations in the kinase domain are a feature of both hereditary and some non-hereditary forms of papillary renal cell carcinoma [6]. MET amplification is seen in 5 to 20% of non-small cell lung cancer (NSCLC) and gastric cancer [7]. MET overexpression correlates with poor treatment outcome in some malignancies [8].

Drugs that target MET include inhibitors of the HGF/-MET pathway, MET antibodies, and MET kinase inhibitors [8]. Cabozantinib and crizotinib are both Food and Drug Administration (FDA)-approved multikinase inhibitors that are also potent suppressors of MET [9, 10]. Crizotinib induced responses in some patients with highly MET-amplified lung cancer [11]. Studies with the multi-target MET inhibitor cabozantinib have shown significant activity against a variety of solid tumors including melanoma, as well as renal and non-small cell lung, liver, medullary thyroid, breast, and ovarian cancer, but this activity is likely due to other targets of cabozantinib, such as VEGFR or RET [9]. In the phase I setting, patients with MET amplification did not respond to MET inhibitors (but the number of treated patients was small) [5].

Because of their non-invasive nature, liquid biopsies are increasingly used in the clinical setting. Indeed, numerous studies showed a relatively good correlation with tissue sequencing and the potential to detect actionable alterations [12‐16]. In this study, we analyzed MET alterations in the plasma-derived circulating tumor DNA (ctDNA) of 438 patients with diverse malignancies and explored the relationship between MET alterations, demographics, as well as other molecular alterations and clinical outcomes.

This is the largest study interrogating the feasibility and utility of MET alteration detection through blood-derived ctDNA. Liquid biopsy is a non-invasive method to find genomic aberrations and is increasingly utilized in the clinical setting as reflected by the non-small cell lung cancer National Comprehensive Cancer Network (NCCN) guidelines [18, 19]. Our study demonstrated that MET ctDNA alterations were detected in 7.1% of patients with solid tumors. This detection rate is higher compared to previous tissue studies [5, 20, 21]. For instance, a study of MET tissue amplification determined by fluorescent in situ hybridization (FISH) demonstrated that 2.6% of 1115 solid tumor specimens were positive [5]. Furthermore, the MSKCC-IMPACT study showed that 3% of patients had MET tissue alterations [20, 21]. The differences in rate of MET alterations between our study and the other studies could be due to following reasons: (i) our technology detected both single nucleotide substitutions and amplifications, while the previous investigation by Jardim et al. at MD Anderson Cancer Center [5] discerned only amplifications (though the MSKCC study would have discerned both single nucleotide substitutions and amplifications [21]); (ii) our study used blood-derived ctDNA, which could capture shed tumor DNA from multiple sites, while the previous reports used tissue-based testing, which would only detect aberrations in the piece of tissue biopsied. Consistent with the above observations, our tissue NGS testing also showed significantly lower rates of MET alterations than the ctDNA NGS: 3 of 263 patients (1.1%) (who also had ctDNA tests) were positive for MET alterations in tissue versus 31 of 438 ctDNA-tested patients (7%) being positive for MET alterations (P = 0.0002). Further, of 18 patients positive for MET ctDNA alterations who also had tissue NGS, only 2 (11.1%) were also positive for a MET alteration by tissue NGS. The biologic underpinnings of discordance between ctDNA and tissue NGS results have been previously documented and include spatial (intra-tumor and inter-tumor) and temporal heterogeneity in genomic anomalies in cancers along with the fact that ctDNA is comprised of DNA that has leaked into the circulation from diverse metastatic sites while tissue NGS reflects only the tissue specimen analyzed [14].

The question that arises is whether or not biological explanations can specifically account for the higher rate of MET alterations in ctDNA. Of interest in this regard, our study showed that bone metastases were independently correlated with MET alterations (Additional file 1: Table S2 and Table S4). Indeed, 14 of 31 patients (45%) positive for MET ctDNA alterations had bone metastases (Additional file 1: Table S4). Of possible relevance in this regard, MET inhibitors are known to show efficacy in bone lesions [22, 23]. In the COMET-1 trial, 682 patients with castrate-resistant prostate cancer who progressed after docetaxel and androgen modulators (abiraterone and/or enzalutamide) were randomly assigned to either cabozantinib (MET inhibitor) or prednisone. Although there was no difference in overall survival, 42% of cabozantinib-treated patients showed bone scan response compared to 3% of prednisone-treated patients (P < 0.001), albeit without prostate surface antigen (PSA) response [24]. In the METEOR trial, 658 patients with advanced renal cell carcinoma who progressed with at least one VEGFR small molecule inhibitor were randomized to the MET inhibitor cabozantinib or the mTOR inhibitor everolimus [25]. In a sub-group analysis, patients randomized to cabozantinib arm with bone metastasis were associated with better overall survival (OS) (hazard ratio (HR) 0.54, 95% confidence interval (CI) 0.34–0.84) compared with non-bone metastasis (HR 0.71, 95% CI 0.55–0.91) [25]. These data together with our results raise the possibility that cancer clones with MET alterations preferentially localize to bone and may therefore explain bone responses after MET inhibitor therapy. Tissue biopsies are rarely performed on bones (none of our 18 patients with MET alterations in ctDNA who also had tissue NGS had a bone biopsy). Of interest in this regard, MET is prominently expressed (as determined by immunohistochemistry) at the site of bone metastases in renal cell cancer [26]. It is therefore conceivable that the high rates of ctDNA positivity for MET alterations, which strongly and independently correlated with bone metastases in our study, reflect shed MET alteration-bearing DNA from bone lesions (Additional file 1: Table S2 and Table S4).

Our study also found that MET ctDNA alterations are associated with poor prognosis, including decreased survival and shorter time to recurrence/metastasis (Tables 4 and 5, Fig. 1b). These results are consistent with those found by correlating MET alterations found in tissue NGS with outcome in specific malignancies, such as astrocytomas [27], breast cancers [28], genitourinary malignancies [29], and ovarian [30] or gastric/esophageal cancers [31]. Specific genes that were co-altered with MET in multivariate analysis of our study participants include PTEN and TP53 (Table 2); previously, another study has also shown the association between MET and PTEN abnormalities [5]. Overall, MET alterations significantly correlated with a higher number of alterations, which may explain—at least in part—the relatively limited efficacy of MET inhibitors as single agents for the treatment of MET-altered advanced malignancies observed in prior studies [5, 29‐31]. Indeed, if patients with MET alterations generally have multiple genomic abnormalities, it is likely that combination therapy, rather than monotherapy with a MET inhibitor, may be necessary to achieve salutary effects.

Our study has several limitations. First, only 60% of our patients (N = 263) with ctDNA analyses also had tissue sequencing and the median time between the two tests in the patients with MET-altered ctDNA was about 6 months. Second, our patients did not have bone biopsies done, which would be of interest to determine if MET alterations are found in such biopsies, since ctDNA MET alterations correlate independently with the presence of bone metastases. Third, though our study with 438 patients is the largest to date, the rarity of MET alterations suggests that investigations of even greater numbers of patients may be worthwhile in order to best understand the biology and correlations of MET alterations.

In summary, our study demonstrated that assessment of MET genomic aberrations by liquid biopsy is feasible. We found that MET ctDNA anomalies were associated with bone metastases, multiple genomic alterations, and a poorer prognosis, including poorer overall survival and a shorter time to recurrence/metastases. Further studies are needed to better understand the biologic relationship between MET alterations and bone lesions, and next-generation trials with MET inhibitors may require combinations of drugs that address the genes such as PTEN that are frequently co-altered in these patients.