Lung- MET Gene Amplification (September 2019): Multidisciplinary Molecular Tumor Board

ASCO University
Sep 17, 2019 10:12 AM

Participant Instructions: Welcome to the Multidisiplinary Molecular Oncology Tumor Board Series! This educational initiative is a collaboration between the American Society of Clinical Oncology (ASCO), College of American Pathologists (CAP), and Association for Molecular Pathology (AMP).

A new case will be presented bi-monthly with discussions led by an expert pathologist and medical oncologist. This month’s topic is led by Drs. Ravi Salgia (Medical Oncologist from City of Hope) and Sanja Dacic (Pathologist from the University of Pittsburgh).

Do you have an interesting case in mind? Submit your hypothetical patient cases for consideration in an upcoming Multidisciplinary Molecular Tumor Board discussion forum.

Participants are encouraged to leave comments and post questions about the case in order to generate a wide discussion among the cancer care community. You can also receive email notifications when new comments are posted by clicking the “Follow this Conversation” option located at the bottom of this page.

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16556

ASCO University
Re: Lung- MET Gene Amplification (September 2019): Multidisciplinary Molecular Tumor Board
Sep 18, 2019 10:49 AM

Patient Case 1

History

Patient is a 59-year-old gentleman who initially presented with a history of low back discomfort, that eventually progressed to upper back pain that was not well managed.

Diagnosis

He consulted an orthopedic surgeon in September 2013 who performed an MRI scan that revealed multiple metastases throughout the lumbar spine, visualized sacrum, and pelvis. Full work-up revealed a right lung mass and a bronchoscopy revealed non-small cell lung cancer consistent with poorly differentiated adenocarcinoma. The right hilar mass was inseparable from the wedge-shaped consolidation/mass extending into the right lower lobe. The mass/consolidation measured approximately 5.6 cm x 5 cm. 

 

Initial Treatment

Oct 2013

  • Received four cycles of carboplatin and docetaxel
  • During chemotherapy tissue was tested for ALK and EGFR and returned positive for EGFR exon 19 deletion.

Jan 2014

  • Started on erlotinib and denosumab with immediate clinical and biochemical response 
  • No severe symptoms and bone pain eventually went away, possibly due to the bones healing from thereapy.
  • By May 2015, the primary right hilar mass had shrunk to 2.1 cm x 1.5 cm on the CT.

Complications

  • May 2016 developed papulopustular lesions, paronychia and xerosis, and Klebsiella folliculitis, which necessitated discontinuation of the sulfamethoxazole and trimethoprim that he had been taking for the acneiform lesions.
  • A brief course of ciprofloxacin led to the resolution of the papulopustular eruption.
  • Other complication included a persistent elevation of carcinoembryonic antigen.

 

Progression

June 2016

  • A CT showed progression consistent with lung adenocarcinoma which was confirmed by a CT guided biopsy.
  • Restarted chemotherapy with carboplatin/pemetrexed for one cycle.
  • Tumor and blood were sent for molecular testing, the liquid biopsy assay showed EGFR exon 19 deletion, T790M, FGFR3 L406R, RHOA E47K, APC D1512N, NTRK1 T360T, PDGFRA 1497I, TP53 R196Q, FGFR2 E767K, BRCA1 E962K.

July 2016

  • He promptly started treatment with osimertinib

August 2016

  • Next-generation sequencing (NGS) showed EGFR exon 19 deletion (but no T790M mutation) and also detected CDK4 amplification, MDM2 amplification, GLI1 amplification, as well as several variants of uncertain significance.
  • Subsequent CT scans showed response and the patient continued on osimertinib

June 2018

  • PET scan showed several FDG avid lytic metastases
  • Osimertinib was held and a spinal surgery was performed
  • Tissue and blood samples were obtained, and a liquid biopsy showed only an EGFR exon 19 deletion. NGS of the tissue sample showed EGFR exon 19 deletion, MET amplification, CDK4 amplification, MDM2 amplification, PTCH1 rearrangement intron 16, and SMAD4 Y260fs*1.
  • Osimertinib was restarted at 80 mg, and the patient started palliative radiation to T-spine, bilateral femurs at 30 Gy.

September 2018

  • Started on crizotinib 250 mg twice per day, based on the MET amplification, alongside the 80 mg osimertinib.
  • Due to increasing liver function abnormalities, crizotinib had to be held for a week and crizotinib was restarted at a reduced dose of 200 mg per day.

January 2019

  • A CT revealed disease progression
  • Started carboplatin, pemetrexed, pembrolizumab for three cycles

April 2019

  • CT showed disease progression and increased right-sided epidural tumor at T3
  • Received radiation to T3 at 20 Gy,
  • Liquid biopsy showed EGFR exon 19 deletion, CDK6 amplification, TP53 C176Y, TP53 V216M, SMAD4 Y260fs
  • After radiation he started docetaxel and ramucirumab.

June 2019

  • Leptomeningeal disease diagnosed and whole brain radiation started at 30 Gy
  • Patient continues on cycle 5 of docetaxel/ramucirumab.  

 

16566

ASCO University
Re: Lung- MET Gene Amplification (September 2019): Multidisciplinary Molecular Tumor Board
Sep 18, 2019 2:01 PM

Discussion Questions

  • What are the biomarkers for MET alterations in lung cancer?
  • What are some of the diagnostic tools for detection? 

16571

ASCO University
Re: Lung- MET Gene Amplification (September 2019): Multidisciplinary Molecular Tumor Board
Sep 18, 2019 2:07 PM

 

Course Faculty Response on behalf of Sanja Dacic

  • MET amplification and MET exon 14 skipping alterations are clinically most relevant alterations of the MET gene. Several national and international guidelines for molecular testing in advanced non-small cell lung carcinoma (NSCLC) recommend testing for MET alterations, but no particular assay is recommended. MET testing in lung cancer has gone through several phases based on the understanding of the mechanism of activation and clinical scenarios.

 

  • MET amplification is reported as a mechanism of secondary resistance in 5% to 22% of EGFR TKI resistance. Targeted gene amplification assay, such as FISH was the most commonly used early approach, although there were no guidelines for MET FISH positivity interpretation. Several positivity criteria have been reported, such as five or more MET signals per cell, a MET/CEP7 ratio ≥2 (PathVysion kit) and adopted HER2 criteria for breast cancer. MET amplification was also classified by using MET:CEP7 ratio as low (≥1.8 to ≤2.2), intermediate (≥2.2 to <5), and high (≥5).

 

  • MET amplification can occur synchronously with other oncogenic mutations such as KRAS, EGFR or BRAF in 41% to 63% of the lung carcinomas. Furthermore, about 20% of lung adenocarcinomas with MET exon 14 mutations also have high-level MET amplification. In contrast to MET amplification, MET exon 14 mutations are mutually exclusive with oncogenic driver mutations and gene fusions characteristic of lung adenocarcinomas. MET exon 14 splicing alterations were strongly coincident with amplification of MDM2 and CDK4, while amplifications of MET were not significantly coincident with those two alterations.

 

  • Altogether, these findings illustrate the complexity of a genomic profile of NSCLC and provide a strong support for NGS as a preferred method for routine clinical testing. Two basic types of NGS assays commonly used in clinical laboratories include amplicon-based and hybrid capture-based.

 

  • Amplicon-based assays use multiple PCR primers to directly amplify genomic regions of interest. These assays are typically small panels that cover hot spots or highly selected regions of clinical interest, and are suitable for small samples. Most amplicon-based assays cannot reliably detect fusions or copy number alterations.

 

  •  Hybrid capture-based panels use hybridization to capture larger genomic regions and can be designed to assess mutations, copy number alterations, and gene rearrangements. Both approaches have been used in clinical academic and commercial laboratories, and include various not always perfect designs for assessment of MET alterations.

 

  • “Liquid biopsies,” primarily plasma-based circulating tumor DNA (ctDNA) assays, have become extremely popular in oncology practice, particularly in cases with insufficient tumor tissue for molecular testing and in patients with acquired resistance to TKI. Commercially available “liquid biopsies” include assessment of MET alterations, and oncologists have to make a decision when to use “blood first” approach.

 

  • Finally, MET immunohistochemistry has been suggested as a potential surrogate assay for MET amplification or MET exon 14 mutations in lung cancer. However, studies showed that MET immunohistochemistry largely failed as a screening test for MET alterations and therefore the tissue should be prioritized for NGS.

16576

ASCO University
Re: Lung- MET Gene Amplification (September 2019): Multidisciplinary Molecular Tumor Board
Sep 18, 2019 3:03 PM

Course Faculty Response on behalf of Ravi Salgia

We have been working on the MET receptor tyrosine kinase and its ligand hepatocyte growth factor since the early 2000s. MET plays an important role in oncogenesis, cell proliferation, motility, scattering, angiogenesis, EMT, as well as invasion and metastasis. There are various mechanisms for MET to be activated: amplification, mutation, overexpression, inability to be degraded. The biomarkers had been challenging and the most useful ones have been MET exon 14 splice variants, and MET amplification. The expression profile of MET still needs to be investigated much further, as well the degradation of MET by CBL.

Next generation sequencing has been very helpful in detecting the exon 14 splice variant, as well as MET amplification. If needed, amplification can be detected by FISH.

16581

ASCO University
Re: Lung- MET Gene Amplification (September 2019): Multidisciplinary Molecular Tumor Board
Sep 18, 2019 3:08 PM

Patient Case 2

History

Patient is a 79-year-old gentleman who initially presented with a history of prostate cancer that was diagnosed in 2016. In June 2018, he experienced chest pain, dyspnea and fatigue. His family took him to the ER and a computed tomography angiography (CTA) revealed a 3-cm right lower lobe mass abutting the major fissure.

Diagnosis

A CT-guided biopsy in August 2018 revealed well-differentiated adenocarcinoma. The cancer was initially thought to be a Stage Ib (T2aN0) but further work-up revealed Stage IV (T2aN0M1b), with a right pleural based mass, as well as a hypermetabolic mass involving the right chest wall, T6, T8, and L2 were identified by PET.

Treatment

  • He immediately started radiation therapy to right chest wall and t7-T12 spine for 30 Gy each.
  • Genomic testing by NGS was performed on tissue and blood. Advanced sequencing technology revealed MET exon 14 deletion, MET c.2942-22_2942-3del, CDK4 amplification, KRAS amplification, MDM2 amplification, and PD-L1 2%.
  • A liquid biopsy revealed EGFR amplification, CDK4 amplification, KRAS amplification, and MET exon skip mutation.
  • Patient was screened for a MET exon 14 trial, but did not qualify, therefore he started on crizotinib in early July 2019.  

16586

ASCO University
Re: Lung- MET Gene Amplification (September 2019): Multidisciplinary Molecular Tumor Board
Sep 18, 2019 3:10 PM

Discussion Questions

  • How does one detect MET exon 14 splice variants?
  • What are the therapies available for this disease?
  • How do you follow up with patients? 

16591

ASCO University
Re: Lung- MET Gene Amplification (September 2019): Multidisciplinary Molecular Tumor Board
Sep 18, 2019 3:12 PM

Course Faculty Response on behalf of Sanja Dacic

MET exon 14 alterations have been shown to occur in approximately 3% of lung adenocarcinomas, and up to 22% of sarcomatoid carcinomas. MET exon 14 alterations are diverse and include mutations altering the splice acceptor site and/or the splice branch site, mutations altering the splice donor site and/or Tyr1003 codon (DS/Y1003) and large deletions (>150 base pairs). Some mutations occur deeper within intron 13 and do not overlap with the splice acceptor site. All these possibilities have to be kept in mind when designing the diagnostic test for detection of MET exon 14 alterations.

NGS tissue-based testing is the most commonly used approach, with advances in sequencing technologies that resulted in better detection of MET exon 14 mutations. Poirot et al. analyzed in silico the ability of eight different amplicon-based NGS panels to detect MET exon 14 alterations.   None of the panels would have been able to detect more than 63% of the reported cases of MET exon 14 mutations, and most of them would have detected less than 24% of the expected cases. However, recent amplicon based and hybrid-capture NGS platforms have been optimized for detection of MET exon 14 alterations. It has been shown that RNA-based NGS detects a higher proportion of MET exon 14 mutations than DNA-based amplicon mediated NGS.

In addition to NGS platforms, single-gene testing approaches have been used. RT-PCR and qRT-PCR assays can be appropriate for screening as a single-gene. Mostly clinically obsolete, Sanger sequencing can detect MET exon 14 mutation, but has a low sensitivity for detection of large deletions or low allele frequency mutations. The availability of a noninvasive plasma-based assay provides an alternate approach to tissue-based assays.

The main concern with liquid biopsy assay is how its results compare with those of tissue samples.  Recently completed multicenter prospective Noninvasive versus Invasive Lung Evaluation (NILE)  trial compared the performance of plasma NGS test to tissue-based genotyping  in advanced  NSCLC at the time of. The results showed that testing of plasma with 73-gene NGS at baseline was not inferior to tissue-based genotyping. The main limitation of the study was that circulating free DNA (cfDNA) testing utilized a single platform, while tissue testing was not standardized, and included various assays (NGS, PCR hot spot, FISH and/or IHC, Sanger) that have variable sensitivities and specificities for detection of different genomic alterations. Overall, NGS tissue-based assessment of MET exon 14 alterations remains the main approach in the current clinical practice.

16596

ASCO University
Re: Lung- MET Gene Amplification (September 2019): Multidisciplinary Molecular Tumor Board
Sep 18, 2019 3:13 PM

Course Faculty Response on behalf of Ravi Salgia

Crizotinib has an FDA breakthrough therapy designation for the treatment of patients with MET exon 14 alterations with disease progression on or after platinum-based chemotherapy.

16601

ASCO University
Re: Lung- MET Gene Amplification (September 2019): Multidisciplinary Molecular Tumor Board
Sep 18, 2019 3:15 PM

Key Takeaways on behalf of Sanja Dacic

  • MET amplification and MET exon 14 mutations have been recognized by current clinical practice guidelines as genetic alterations to be tested as part of a standard molecular panel for lung adenocarcinomas
  • NGS assays (amplicon-based or hybrid-capture) are preferred method of testing for MET alterations
  • Not all types of alterations are detected by all commercially available NGS platforms, and it is important for treating physicians and pathologists to be familiar with each assay characteristics
  • FISH can be used for detection of MET amplification
  • MET IHC should not be used as a screening test for MET alterations
  • “Liquid biopsies” show good concordance with tissue-based genotyping for detection of MET alterations and may be considered as an alternative testing approach 

16606

ASCO University
Re: Lung- MET Gene Amplification (September 2019): Multidisciplinary Molecular Tumor Board
Sep 18, 2019 3:17 PM

Key Takeaways on behalf of Ravi Salgia

  • There can be several biomarkers that are relevant to MET biology and therapeutics
  • MET therapeutics have come to clinical fruition, with predictive biomarkers (amplification, exon 14 skipping, CBL alteration, etc.)
  • MET therapeutics in synergy with other novel therapeutics would be useful to investigate (most recently we have shown that this pathway can affect the mitochondrial dynamics)
  • It is not clear how MET and its family member RON are important in immune-modulation
  • It would be useful to determine the relationship between MET inhibition and standard therapies, as well as in combination with targeted approaches/mitochondrial therapeutics/immune therapeutics

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