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Kim SY, Yin J, Bohlman S, Walker P, Dacic S, Kim C, Khan H, Liu SV, Ma PC, Nagasaka M, Reckamp KL, Abraham J, Uprety D, Wang F, Xiu J, Zhang J, Cheng H, Halmos B. Characterization of MET Exon 14 Skipping Alterations (in NSCLC) and Identification of Potential Therapeutic Targets Using Whole Transcriptome Sequencing. JTO Clin Res Rep 2022; 3:100381. [PMID: 36082279 PMCID: PMC9445394 DOI: 10.1016/j.jtocrr.2022.100381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 11/26/2022] Open
Abstract
Introduction Genomic alterations in the juxtamembrane exon 14 splice sites in NSCLC lead to increased MET stability and oncogenesis. We present the largest cohort study of MET Exon 14 (METex14) using whole transcriptome sequencing. Methods A total of 21,582 NSCLC tumor samples underwent complete genomic profiling with next-generation sequencing of DNA (592 Gene Panel, NextSeq, whole exome sequencing, NovaSeq) and RNA (NovaSeq, whole transcriptome sequencing). Clinicopathologic information including programmed death-ligand 1 and tumor mutational burden were collected and RNA expression for mutation subtypes and MET amplification were quantified. Immunogenic signatures and potential pathways of invasion were characterized using single-sample gene set enrichment analysis and mRNA gene signatures. Results A total of 533tumors (2.47%) with METex14 were identified. The most common alterations were point mutations (49.5%) at donor splice sites. Most alterations translated to increased MET expression, with MET co-amplification resulting in synergistic increase in expression (q < 0.05). Common coalterations were amplifications of MDM2 (19.0% versus 1.8% wild-type [WT]), HMGA2 (13.2% versus 0.98% WT), and CDK4 (10.0% versus 1.5% WT) (q < 0.05). High programmed death-ligand 1 > 50% (52.5% versus 27.3% WT, q < 0.0001) and lower proportion of high tumor mutational burden (>10 mutations per megabase, 8.3% versus 36.7% WT, p < 0.0001) were associated with METex14, which were also enriched in both immunogenic signatures and immunosuppressive checkpoints. Pathways associated with METex14 included angiogenesis and apical junction pathways (q < 0.05). Conclusions METex14 splicing alterations and MET co-amplification translated to higher and synergistic MET expression at the transcriptomic level. High frequencies of MDM2 and CDK4 co-amplifications and association with multiple immunosuppressive checkpoints and angiogenic pathways provide insight into potential actionable targets for combination strategies in METex14 NSCLC.
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Affiliation(s)
- So Yeon Kim
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, New York
- Yale School of Medicine, New Haven, Connecticut
| | - Jun Yin
- Caris Life Sciences, Phoenix, Arizona
| | - Stephen Bohlman
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, New York
| | | | - Sanja Dacic
- Yale School of Medicine, New Haven, Connecticut
| | - Chul Kim
- Georgetown Lombardi Comprehensive Cancer Center, Washington, District of Columbia
| | - Hina Khan
- Warren Alpert Medical School of Brown University, Providence, Rhode Island
| | - Stephen V. Liu
- Georgetown Lombardi Comprehensive Cancer Center, Washington, District of Columbia
| | | | | | | | | | | | - Feng Wang
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, New York
| | | | | | - Haiying Cheng
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, New York
| | - Balazs Halmos
- Department of Medical Oncology, Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, New York
- Corresponding author. Address for correspondence: Balazs Halmos, MD, Montefiore Medical Center, Albert Einstein Cancer Center, Bronx, New York.
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Kim SY, Bohlman S, Yin J, Cheng H, Walker P, Dacic S, Kim C, Khan H, Liu SV, Ma PC, Nagasaka M, Reckamp KL, Abraham J, Uprety D, Halmos B. Characterization of MET exon 14 skipping alterations ( METex14) in non–small cell lung cancer (NSCLC) using whole transcriptome sequencing (WTS). J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.9122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
9122 Background: Multiple DNA alterations in exon 14 splice sites have been identified in NSCLC and result in skipping of the juxtamembrane domain Cbl-E3 ubiquitin ligase binding region, leading to increased MET stability and oncogenesis. The effects of these alterations on transcriptome-level have not been fully characterized. We present the largest cohort study of METex14 using WTS and identify key cellular pathways associated with invasion and metastases in METex14. Methods: 17,666 NSCLC tumor samples underwent genomic profiling at Caris Life Sciences. Analyses included next generation sequencing of DNA (592 Gene Panel, NextSeq, whole exome sequencing, NovaSeq) and RNA (NovaSeq, WTS). METex14 was captured via WTS. ssGSEA analysis was used to evaluate pathway enrichment. Wilcoxon, Fisher’s exact were used for statistical significance (p without and q values with multiple comparison correction). Results: 440 patients (2.5%) with METex14 were identified. METex14 patients were of older age, female gender, and enriched in sarcomatoid histology (Table 1). The most common alterations were point mutations (51.5%) and deletions (17.3%) at donor splice sites. Splice site alterations except point mutations at splice acceptor site translated to increased mRNA expression compared to wild-type MET (WT). MET amplification translated to higher mRNA expression compared to METex14 and WT with synergistic expression when co-altered with METex14 (q<0.05). The most common co-alterations were amplifications of MDM2 (18.5% vs. 1.8% WT), HMGA2 (13.7% vs 0.9% WT), and CDK4 (10.4% vs 1.4% WT) (q < 0.05). METex14 were mutually exclusive to mutations in KRAS and EGFR. High PD-L1 (22c3) > 50% (53% vs. 27.6% WT, q<0.001) and lower TMB (4 mut/Mb vs. 7 mut/Mb WT, p<0.001) were observed with METex14 and pathways associated with skipping variants included IFNγ signaling, angiogenesis, and apical junction pathways on univariate analysis (q<0.05). Conclusions: We present the largest WTS analysis of METex14. Splicing alterations and MET co-amplification translated to higher and synergistic MET expression at transcriptome level, respectively. Association with upregulated angiogenic and apical junction pathways support preclinical observation of vascular and cytoskeletal remodeling as potential mechanisms of invasion and metastases in MET ex14 NSCLC.[Table: see text]
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Affiliation(s)
| | | | - Jun Yin
- Caris Life Sciences, Phoenix, AZ
| | - Haiying Cheng
- Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY
| | | | | | - Chul Kim
- Room 417 (Pod B, Second Floor), Washington, DC
| | - Hina Khan
- Albert Einstein College of Medicine, Bronx, NY
| | - Stephen V. Liu
- Georgetown University, Department of Hematology and Oncology, School of Medicine, Washington, DC
| | | | - Misako Nagasaka
- University of California Irvine School of Medicine and Chao Family Comprehensive Cancer Center, Orange, CA
| | | | | | | | - Balazs Halmos
- Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY
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Abstract
In this issue of Cancer Cell, Gu et al. characterize small molecules that inhibit the interaction of Mdm2 with the mRNA that encodes the anti-apoptotic XIAP, simultaneously decreasing expression of both proteins. This represents a novel approach that has relevance in tumor cells independent of p53 status.
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Affiliation(s)
- Stephen Bohlman
- Department of Oncological Sciences and The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - James J Manfredi
- Department of Oncological Sciences and The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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