Researchers have uncovered a genetic variant that drives aggressive head – neck and lung cancers in Asian population


Researchers from the Cancer Science Institute of Singapore (CSI Singapore) at the National University of Singapore (NUS) have uncovered a genetic variant in a gene called MET that is responsible for more aggressive growth of head and neck, and lung cancers.

A further probe into the finding revealed therapeutic strategies that could potentially target this genetic alteration, thereby paving the way for clinicians to develop better and more effective treatments for cancer patients of such profile.

The study, published in prestigious scientific journal Nature Communications on 25 March 2020, was conducted in close collaboration with clinicians from the National University Cancer Institute, as well as researchers from the National Cancer Centre Singapore and the Bioinformatics Institute at the Agency for Science, Technology and Research, Singapore.

The MET gene encodes for a cancer-promoting protein that relays growth, survival and transmission of signals in cancer cells.

In the study led by Professor Goh Boon Cher and Dr. Kong Li Ren from CSI Singapore, the team of researchers identified a form of MET protein, which showed ethnic preference with higher incidence among Asians, and is associated with poorer prognosis in patients diagnosed with head and neck squamous cell carcinoma or lung squamous cell carcinoma.

Even though the MET variant does not seem to predispose an individual to cancer, it leads to more aggressive growth of cancers that have already developed.

Unlike other MET mutants, this genetic variant also does not appear to be inhibited by existing MET-blocking drugs that have been developed and approved in the clinical setting, prompting the researchers to conduct further investigation on the mechanism behind the genetic alteration.

Leveraging the research team’s multi-disciplinary expertise and state-of-the-art molecular modelling, the team found that the single amino-acid change in the MET receptor from the genetic alternation leads to preferential strong binding to another cancer promoting protein, HER2.

Both proteins then work cooperatively to drive cancer aggression and enable cancer cells to survive therapies involving MET-blocking drugs.

“The mechanism of this MET variant is novel and unreported. This finding contributes to the growing evidence of the role of genetic variants in affecting clinical outcome, and underscores the importance of diving deep into our genetic inheritance in cancer research,” said Dr. Kong, Research Fellow at CSI Singapore who initiated the study.

Knowledge of this unique mechanism also facilitated the team in identifying several HER2 inhibitors capable of blocking cancer progression caused by this genetic alteration using laboratory models.

Prof Goh, Deputy Director and Senior Principal Investigator at CSI Singapore, said, “Our study represents a conceptual advancement to cancer research, as we have shown that it is possible to block the activity of a cancer-driving gene by administrating a targeted therapy directed not against the mutant protein in question, but rather, a corresponding protein with which it binds to.

The remarkable anti-tumour responses observed in our experimental models, coupled with the availability of FDA-approved HER2 inhibitors also presents a huge opportunity for clinicians to improve disease outcome of this genetic alteration via precision medicine.”


The oncogenic role of MET has been established in multiple cancers, with gene amplification, somatic mutations, and splicing variants being the driving mechanisms for oncogenic MET function, while rare germline-activating mutations in the tyrosine kinase (TK) domain have been reported in hereditary papillary renal cell carcinoma28.

However, these events are rare in SCC. We describe here an aberrant oncogenic activity of a polymorphic Sema variant of MET, which when present, enhances the aggressiveness of SCC tumors in vitro and in vivo.

Patients with HNSCC and LUSC who carry the METN375S polymorphism have higher risk of disease recurrence, mediated by a novel mechanism of oncogenicity that involves enhanced dimerization to another oncogenic membrane-bound RTK receptor HER2 without HGF ligand activation (Supplementary Fig. 11).

This mechanism of Sema-domain activation due to a single amino acid substitution adds to the other more established molecular mechanisms of oncogenic MET signaling, which mostly revolve around constitutive and persistent kinase activity.

It is interesting to note that Sema proteins have been shown to act as oncogenic ligands in the activation of RTKs that include MET and HER227.

Based on molecular modeling and simulations, we postulate that the asparagine-to-serine substitution could induce significant localized conformational changes (Supplementary Fig. 12A, B), which improve surface interactions between METN375S and HER2 (Supplementary Fig. 12C, D), leading to gain-of-function of the polymorphic variant.

Taken together with the imaging and biochemical characterization, our data collectively implicate that the N375S modification may reconfigure the Sema domain for MET interaction with HER2. The resulting METN375S phosphorylation is necessary for HER2 activation, as rSemaN375S proteins lacking the tyrosine kinase domain could inhibit HER2 phosphorylation.

HER2 is rarely amplified or mutated in HNSCC/LUSC31, but this activation through polymorphic MET may lead to constitutive HER2 signaling and drive these cancers. Our data further demonstrates that the heterodimeric signal between METN375S and HER2 is specifically dependent on an intact subdomain IV on HER2, which is the binding site of trastuzumab, explaining the enhanced sensitivity of METN375S tumors to trastuzumab relative to HER2 TKIs.

While MET has been previously demonstrated to be a heterodimeric partner of HER232, our work on SCC shows a strong addiction of METN375S tumors to HER2 signaling.

The HER2 receptor lacks a ligand-binding domain, and its activation relies heavily on heterodimerization with other ligand activated receptors, particularly HER330,33. Notwithstanding, HER2 mediates potent downstream signaling when activated through its highly catalytic TK domain34, and is a strong inducer of cell motility and metastasis35.

Our findings strongly indicate that phosphorylated METN375S leads to constitutively active HER2 that mediates signaling regardless of MET inhibition. This insensitivity to MET inhibition is surprising and remains unexplained; possible reasons could include involvement of other HER2 activating mechanisms. Conversely, HER2 inhibitors effectively suppress oncogenic METN375S signaling in SCC tumors, as evidenced by their strong anti-proliferative activity both in vitro and in vivo.

This adds on to the growing recognition that HER2 inhibition could be effective in TKI-relapsed MET-driven tumors36, and METN375S exemplifies emerging evidence that germline polymorphisms can drive malignancy and represent bona fide biomarkers to select therapeutic agents clinically.

Although HER2-amplified H2170 was primarily used in the study which may influence sensitivity to HER2 inhibitors, we recapitulated the experimental findings in non-HER2 overexpressing cells like Calu-1 and patient-derived NPC7 cells.

The treatment of SCC is often challenging due to the lack of common actionable driver oncogenes. Cetuximab plus platinum-based chemotherapy has been established as first-line treatment in recurrent or metastatic HNSCC as EGFR is often hyperexpressed in this disease37,38, whereas standard-of-care regimens comprise of platinum-based doublet in combination with vinorelbine, gemcitabine or taxane for LUSC, and has remained largely unchanged over the past decades39.

To address this substantial unmet therapeutic need, we are currently conducting a clinical trial to treat patients with metastatic HNSCC and LUSC who screened positive for the METN375S polymorphism with HER2 blockade (NCT03938012).

However, it is unclear at this point which anti-HER2 therapy would be optimal clinically; based on our in vivo models, trastuzumab appears to be the most promising.

Currently, the oncogenic role of the N375S variant in other cancers remains unclear. Theoretically, tumors overexpressing MET should be subjected to the similar aggressive influences of the polymorphic receptor, notwithstanding, our data demonstrated the ineffectiveness of HER2 inhibition in METN375S-positive HCC, suggesting that this strategy is tumor-context dependent, and is effective particularly in tumors with activated METN375S.

Our data do not suggest that the METN375S polymorphism increases cancer susceptibility; however, whether the risks are elevated in the homozygous state needs further clarification, as the majority of the individuals in our study were heterozygotes.

In the clinical context, HER2 amplification is common in a variety of cancers— such as breast and hepatocellular carcinoma—and how this potentially cooperates with METN375S to promote malignancy is unclear, though our experimental models have shown that HER2 amplification is not essential for the oncogenic phenotype conferred by the MET variant.

Nonetheless, the lack of efficacy of HER2 inhibitors in METN375S HCC tumors with low p-HER2 expression suggest that other mechanisms are more dominant in HCC, and that HER2 activation is necessary for therapeutic impact.

Our current work contributes to the emerging notion that germline genetic events could impact the selection of oncotherapeutic agents, and in this case, specifically in SCC. While the MET (N375S) polymorphism may be more prevalent among Asians, the findings should be broadly applicable to all patients selected on the basis of this biomarker.

More information: Li Ren Kong et al. A common MET polymorphism harnesses HER2 signaling to drive aggressive squamous cell carcinoma, Nature Communications (2020). DOI: 10.1038/s41467-020-15318-5


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