Genomic and clinical characteristics of MET exon14 alterations in a large cohort of Chinese cancer patients revealed distinct features and a novel resistance mechanism for crizotinib

Tianli Cheng; Zhongping Gu; Danni Song; Sisi Liu; Xiaoling Tong; Xue Wu; Zhifeng Lin; Wei Hong

doi:10.7150/jca.49391

Genomic and clinical characteristics of MET exon14 alterations in a large cohort of Chinese cancer patients revealed distinct features and a novel resistance mechanism for crizotinib

J Cancer. 2021 Jan 1;12(3):644-651. doi: 10.7150/jca.49391. eCollection 2021.

Authors

Tianli Cheng¹, Zhongping Gu², Danni Song³, Sisi Liu³, Xiaoling Tong⁴, Xue Wu⁴, Zhifeng Lin⁵, Wei Hong^{6

7}

Affiliations

¹ Thoracic Medicine Department 1, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, Hunan, China.
² Department of Thoracic Surgery, The Second Affiliated Hospital, Air Force Military Medical University, Xi'an, China.
³ Department of Research and Development, Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, China.
⁴ Translational Medicine Research Institute, Geneseeq Technology Inc., Toronto, Ontario, Canada.
⁵ Department of Thoracic Surgery, Shanghai General Hospital, Shanghai, China.
⁶ Department of Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China.
⁷ Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China.

Abstract

Background: Alterations in MET exon 14 (METex14) and its flanking intronic regions have been identified in a variety of cancers. Patients with METex14 alterations often benefit from MET inhibitors such as crizotinib. Given the unique mutation profiles of Chinese lung cancer patients, it is necessary to investigate the prevalence of METex14 alterations in a large cohort of cancer patients. Patients and methods: Cases carrying METex14 alterations were screened from 26,391 Chinese cancer patients by next-generation sequencing (NGS), and the clinicopathologic and molecular characteristics were reviewed. Results: Compared to Western population (~3%), the frequency of METex14 alterations is much lower in Chinese cancer patients (0.7%, n=184) and lung cancer patients (1.1%, n=175). Seventy-eight distinct METex14 alterations, including several novel alteration types were detected. Concurrent MET copy gain and non-exon14 MET mutations were also found. EGFR copy gain (11%) and mutations (8%), KRAS (5%) and PIK3CA (5%), appeared in a mutually exclusive pattern. Female patients contain much less TP53 mutations than male patients (65% vs. 24%, FDR = 0.01). Co-amplification of CDK4 and MDM2, CDK6 and EGFR were identified, which indicated cell cycle dysregulation and EGFR alteration are important co-occurring features in patients with METex 14 alteration. Of 9 tissue specimens having PD-L1 immunohistochemistry (IHC) results, 5 of them (55.5%) were found PD-L1 positive, which is comparable to other types of tumor. In 14 crizotinib-treated patients, the median progression free survival (mPFS) was 7 months. Upon resistance to crizotinib, two patients acquired secondary mutations in MET and one patient acquired BRAF p.K601E that can be a novel resistance mechanism. Conclusion: Chinese cancer patients have a relatively lower frequency of METex14 alterations compared to Western patients. Patients with METex14 alterations showed distinct molecular characteristics and the representative case study showed responses to MET tyrosine kinase inhibitor (TKI).

Keywords: MET exon 14 alterations; crizotinib-resistant mutation; lung cancer; next-generation sequencing.