|Year : 2019 | Volume
| Issue : 4 | Page : 909-913
Prevalence of MET exon 14 skipping mutation in pulmonary sarcomatoid carcinoma patients without common targetable mutations: A single-institute study
Yongfeng Yu1, Qing Zhang2, Jie Zhang2, Shun Lu1
1 Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
2 Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
|Date of Web Publication||14-Aug-2019|
Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Xuhui District, Shanghai 200030
Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Xuhui District, Shanghai 200030
Source of Support: None, Conflict of Interest: None
Background: Pulmonary sarcomatoid carcinoma (PSC) is a rare histologic subtype of nonsmall cell lung cancer with limited targeted treatment options. In this study, we aimed to investigate the prevalence of MET ex14 skipping mutation in PSC patients without common targetable mutations in EGFR, KRAS, ALK, ROS1, and RET.
Materials and Methods: In total, 46 resected specimens of PSC without these mutations were assessed for MET ex14 skipping mutation by next-generation sequencing (NGS) based on the Oncomine Focus Assay libraries.
Results: Among 52 cancer-relevant genes included in the targeted NGS panel, the MET ex14 skipping mutation was the only mutation identified in our cohort, which was present in 4 (9%) of 46 patients. For patients with METex14 skipping mutation, the median overall survival (OS) was 35 months (1050 days) compared with a median OS of 27 months (807 days) for those without METex14 skipping mutation (hazard ratio [HR] = 0.59, P = 0.488). The median disease-free survival (DFS) in METex14 skipping mutation-positive patients was 18 months (540 days) compared with a median DFS of 13.6 months (408 days) for negative patients (HR = 0.76, P = 0.680).
Conclusions: These findings reflect the prevalence of MET ex14 skipping mutation as up to 9% in Chinese patients with PSC negative for other common targetable mutations, allowing provision of appropriate genetic counseling and treatment in these patients. A larger population-based study is warranted to determine the clinicopathological and prognostic implications of MET ex14 skipping mutation in PSC.
Keywords: METex14 skipping, next-generation sequencing, pulmonary sarcomatoid carcinoma
|How to cite this article:|
Yu Y, Zhang Q, Zhang J, Lu S. Prevalence of MET exon 14 skipping mutation in pulmonary sarcomatoid carcinoma patients without common targetable mutations: A single-institute study. J Can Res Ther 2019;15:909-13
|How to cite this URL:|
Yu Y, Zhang Q, Zhang J, Lu S. Prevalence of MET exon 14 skipping mutation in pulmonary sarcomatoid carcinoma patients without common targetable mutations: A single-institute study. J Can Res Ther [serial online] 2019 [cited 2019 Nov 16];15:909-13. Available from: http://www.cancerjournal.net/text.asp?2019/15/4/909/264294
| > Introduction|| |
Pulmonary sarcomatoid carcinoma (PSC) is a rare but aggressive lung malignancy, accounting for 0.3%–3% of all nonsmall cell lung carcinomas, with an overall 5-year survival rate of approximately 20%.,,, Conventional chemotherapy has produced unsatisfactory results. Further studies are needed to explore tumor mutational profiles and identify novel therapeutic targets.
MET is located on chromosome 7 and encodes a tyrosine kinase receptor for hepatocyte growth factor. Alterations in MET, such as gene amplification, protein overexpression, and gain of function mutations, are found in many human cancers., MET ex14 skipping is a novel MET alteration that drives the oncogenic event in multiple cancers., MET exon 14 skipping is emerging as a clinically relevant biomarker to predict treatment response to MET inhibitors., However, such alterations show diverse sequence composition, ranging from single-nucleotide mutations to large insertion/deletions. Hence, detecting MET exon 14 skipping mutations using DNA-based next-generation sequencing (NGS) methods is challenging for diagnostic testing, whereas RNA-based testing can circumvent the complexity of DNA-based changes.
We aimed to evaluate the prevalence of METex14 skipping mutation in Chinese patients with PSC negative for common targetable mutated genes including EGFR, KRAS, ALK, ROS1, and RET. We screened a cohort of 46 PSC cases from formalin-fixed and paraffin-embedded (FFPE) tissues at our institution.
| > Materials and Methods|| |
Subjects and ethical aspects
Study patients were recruited in the city of Shanghai, at Shanghai Chest Hospital from February 2012 to 2016. Histological type was determined according to the 2015 WHO classification. Disease staging was based on the eighth edition of the TNM classification of nonsmall cell lung cancer. All participants were unrelated. The family history of each participant, spanning at least three generations, was recorded. Clinical data are listed in [Table 1]. All participants provided written consent for MET mutation testing, and the Ethics Committee of the Shanghai Chest Hospital approved the project (No. KS1672). In total, 46 patients without EGFR, KRAS, ALK, ROS1, and RET mutations were selected for assessing the existence of other possible therapeutic targets, including MET inhibitors.
|Table 1: Clinical and pathologic characteristics of pulmonary sarcomatoid carcinoma cases|
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MET mutation analysis using next-generation sequencing
Hematoxylin and eosin (H and E)-stained slides of resected tumors were reviewed. FFPE blocks were cut, deparaffinized, and subjected to RNA extraction using the RecoverAll Total Nucleic Acid Isolation Kit (Ambion; Thermo Fisher, Carlsbad, CA, USA). The Oncomine Focus Assay libraries were prepared using the Ion AmpliSeq targeted sequencing technology (Thermo Fisher Scientific). Briefly, 10 ng of RNA was reverse transcribed to complementary DNA (cDNA) using the SuperScript VILO cDNA Synthesis kit (Invitrogen; Thermo Fisher, Carlsbad, CA, USA), and targets were amplified using a multiplex primer pool. Barcode adapters were ligated and normalized to 100 pmol/L. Eight equimolar RNA libraries were pooled before template preparation and enrichment using the Ion OneTouch2 and enrichment system (Thermo Fisher Scientific). Sequencing of 200 base pairs was performed on the Ion PGM 318BC chip (Thermo Fisher).
Next-generation sequencing analysis pipeline and quality control
Sequencing data were first processed with the Ion Torrent Suite software version 5.2.0 (Thermo Fisher Scientific, Carlsbad, CA, USA) for reference mapping and base calling, during which time, validation-defined quality control (QC) specifications were used as acceptance criteria. Quality filters were used at the amplicon level to remove counts below the threshold for detection and at the base pair level for low-quality variant calls. Ion Reporter Software (Thermo Fisher Scientific) was used to detect the fusion with QC metrics.
Quantitative real-time polymerase chain reaction for the detection of MET ex14 skipping mutation
RNA extracted from FFPE samples as described above was reverse transcribed into cDNA using the SuperScript VILO cDNA Synthesis kit (Invitrogen; Thermo Fisher, CA, USA). The products were screened for MET ex14 mutation using an ABI 7500 platform (Applied Biosystems, Foster City, CA) with the following conditions: 95°C for 10 min, 95°C for 15 s, and 60°C for 1 min for 40 cycles.
Statistical significance was determined by the unpaired Student's t-test to compare the age of diagnosis. Fisher's exact test was used to assess the association of MET ex14 skipping mutation status with clinical variables. Hazard ratios and 95% confidence intervals (CIs) were calculated using Cox proportional hazards models, and significant differences for survival analysis were compared using log-rank test. P < 0.05 was considered statistically significant.
| > Results|| |
Clinical features of the cohort
The clinical and pathologic parameters of all 46 patients with PSC are summarized in [Table 1] and detailed in [Supplementary Table 1]. The median age at disease onset was 46 years (range, 45–80 years), 9 (20%) patients were women, and 26 (57%) were never smokers. A majority (74%) of patients reported no family history of cancer. Frequent lymph node invasion (50%) was evident, which is a typical feature of PSC biologic behavior. During this study, nine patients were lost to follow-up. In total, 22 patients died during the follow-up period. The overall median survival time for patients was 26.9 months (range, 7–77 months) [Supplementary Figure 1].
Prevalence of MET ex14 skipping mutation in Chinese pulmonary sarcomatoid carcinoma patients
The 46 PSC patients included in the study were free of targetable mutations such as alterations in EGFR, KRAS, ALK, ROS1, and RET (data not shown). Among the 52 cancer-relevant genes included in the targeted NGS panel, MET ex14 skipping mutation was the only mutation identified. An example of sequence alignments in a patient with MET ex14 skipping mutation is shown in [Figure 1]. Of the 46 PSC patients free of mutations in EGFR, KRAS, ALK, ROS1, and RET, 4 (9%) patients exhibited the MET ex14 skipping mutation. The MET ex14 skipping mutation in these four patients was also confirmed by quantitative real-time polymerase chain reaction [Figure 2]. H and E staining of cancer samples from these four patients showed sarcoma-like structure, characterized by pleomorphic or spindle cells [Supplementary Figure 2].
|Figure 1: Representative image of read alignments indicative of METex14 skipping mutation by next-generation sequencing. Red arrow indicates the METex14 skipping mutation detected by next-generation sequencing analysis|
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|Figure 2: Amplification curves of quantitative real-time polymerase chain reaction showing METex14 skipping mutation-positive samples (red arrow) and a METex14 skipping mutation-negative sample|
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Clinicopathological implications of METex14 skipping mutation in pulmonary sarcomatoid carcinoma
The four PSC patients with MET ex14 skipping mutation are listed in [Table 1]. We compared the clinicopathological characteristics of the cohort of patients with MET ex14 skipping mutation with those of patients without the MET ex14 skipping mutation. We found no significant relationships between MET ex14 skipping mutation and clinicopathological features including gender, age at diagnosis, smocking status, family history of cancer, recurrence rate, T stage, lymph node invasion status, and survival status, most likely due to the limited cohort size. For patients with MET ex14 skipping mutation, the median OS was 37.2 months (1117 days) compared with a median OS of 27 months (810 days) for patients without the MET ex14 skipping mutation (hazard ratio [HR] = 0.49, 95% CI = 0.11–2.19; P = 0.488) [Table 1]. The median disease-free survival (DFS) in MET ex14 skipping positive patients was 35 months (1050 days) compared with a median DFS of 13.7 months (412 days) in negative patients (HR = 0.74, 95% CI = 0.24–2.67; P = 0.680) [Table 1].
| > Discussion|| |
Data on the prevalence and clinicopathological implications of MET ex14 skipping in PSC are limited because the disease is rare. Here, we present a single-institution cohort of Chinese patients with PSC negative for EGFR, KRAS, ALK, ROS1, and RET mutations. The prevalence of MET ex14 skipping mutation in our cohort (9%) was different from that described in previous studies, probably due to different inclusion and exclusion criteria for participation.,,,, Given the original attempt to screen for PSC patients without other targeted treatment options, only PSC cases without common driver mutations including EGFR, KRAS, ALK, ROS1, and RET were included in this study. In addition, intratumoral heterogeneity (e.g., percentage of sarcomatoid component) might also have an impact on the estimation of mutation prevalence. The differences in the frequency of MET ex14 skipping mutation could also be due to the patient's ethnicity or the different sensitivity of the sequencing assay.
Molecular characterization of targetable genetic alterations in PSC has increased our understanding of patient groups likely to benefit from targeted treatments. Using three different genetic testing methods, we reported a frequency of 9% (4/46) for MET ex14 skipping mutation in PSC patients in whom common targeted treatments are not suitable due to lack of targets including EGFR, KRAS, ALK, ROS1, and RET. Importantly, this type of alteration is emerging as a clinically relevant biomarker to predict response to treatment with MET inhibitors, as illustrated by several clinical trials with the MET inhibitors crizotinib and cabozantinib in lung adenocarcinoma patients harboring the MET ex14 skipping mutation., Considering that MET ex14 skipping mutation has been reported to promote MET activation in multiple tumor types and confer sensitivity to MET inhibitors,,,, our results provide a rationale for the potential use of MET inhibitors in PSC patients with MET ex14 skipping mutation. Indeed, a recent case report of rapid dramatic clinical improvement with crizotinib in a 74-year-old female with PSC harboring a MET ex14 skipping mutation further corroborates the clinical relevance of our findings.
| > Conclusions|| |
This study demonstrated that MET ex14 skipping mutation was detected in 9% (4/46) of Chinese PSC patients without other common targetable mutations in EGFR, KRAS, ALK, ROS1, and RET. A larger population-based study is needed to explore the clinicopathological and prognostic implications of the MET ex14 skipping mutation in PSC. Our findings suggest the need for additional efforts to test the MET ex14 skipping mutation in PSC patients and to evaluate their responsiveness to MET inhibitors in large-scale clinical trials.
Financial support and sponsorship
This work was supported by the National Key R&D Program in China (2016YFC1303300), the National Natural Science Foundation in China (81672272), the Key Project of Shanghai Health and Family Planning (201540365), and the Shanghai Municipal Science Technology Commission Research Project (17431906103 to S. Lu and 16431903200 to Y. Yu).
Conflicts of interest
There are no conflicts of interest.
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