Characterization of MET exon 14 skipping alterations (METex14) in non–small cell lung cancer (NSCLC) using whole transcriptome sequencing (WTS).

Authors

null

So Yeon Kim

Montefiore Medical Center, Bronx, NY

So Yeon Kim , Stephen Bohlman , Jun Yin , Haiying Cheng , Phillip Walker , Sanja Dacic , Chul Kim , Hina Khan , Stephen V. Liu , Patrick C. Ma , Misako Nagasaka , Karen L. Reckamp , Jim Abraham , Dipesh Uprety , Balazs Halmos

Organizations

Montefiore Medical Center, Bronx, NY, Caris Life Sciences, Phoenix, AZ, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, NY, University of Pittsburgh, Pittsburgh, PA, Room 417 (Pod B, Second Floor), Washington, DC, Albert Einstein College of Medicine, Bronx, NY, Georgetown University, Department of Hematology and Oncology, School of Medicine, Washington, DC, Penn State Hershey Medical Center, Hershey, PA, University of California Irvine School of Medicine and Chao Family Comprehensive Cancer Center, Orange, CA, Cedars-Sinai Medical Center, Los Angeles, CA, Karmanos cancer institute, Detroit, MI

Research Funding

No funding received

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.

Summary of clinico-genomic features.

METex14 (N)WT (N)q-valueAlteration%mRNA expression relative to WT
Male1928673<0.05
Female2488553Donor splice site point mutation51.53.5
Age, median7769<0.0001Donor splice site deletion17.34
Adenocarcinoma27310203<0.001Polypyrimidine site deletion16.54
Squamous493878Acceptor splice site deletion7.54
Adenosquamous10147Acceptor splice site point mutation2.11
Sarcomatoid11104METex14 + MET Amp0.0724.4
Large cell145MET Amp0.8914.1
others962831METex142.453.3

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Abstract Details

Meeting

2022 ASCO Annual Meeting

Session Type

Poster Session

Session Title

Lung Cancer—Non-Small Cell Metastatic

Track

Lung Cancer

Sub Track

Metastatic Non–Small Cell Lung Cancer

Citation

J Clin Oncol 40, 2022 (suppl 16; abstr 9122)

DOI

10.1200/JCO.2022.40.16_suppl.9122

Abstract #

9122

Poster Bd #

108

Abstract Disclosures

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