Abstract 5101: Comparative genomic analysis reveals distinctive immune profiles in MET exon 14 mutated and MET amplified lung cancer
Authors: Javeri Saahil , Minne Rachel , Ramesh Shrey , Baschnagel Andrew , Kimple Randy , Lamb Laura , Tomlins Scott , Johnson Bryan , Khazanov Nickolay 
Published: March 2024

Background: In non-small cell lung cancer (NSCLC), the MET tyrosine kinase receptor can be mutated or amplified resulting in dysregulation of receptor function leading to tumor proliferation. MET exon 14 (METEx14) mutated and MET amplified NSCLC tumors have shown varied response to immunotherapy. Therefore, we sought to compare the genomic and immune landscape of MET-altered NSCLC.

Methods: The genomic profiles of 3,821 NSCLC tumors sequenced using the Strata Select assay on the Strata Oncology Platform were analyzed. Tumors were sorted based on METex14 mutations, MET amplification (METamp) defined as copy number gain (CNG) ≥6 and MET wild-type (METwt). The RNA expression of 19 immune regulatory genes, tumor mutation burden (TMB), Strata Immunotherapy Response Signature (IRS) score and the frequency of gene co-alterations were compared across groups. Statistical comparisons of medians were done with Kruskal-Wallis testing and categorical comparisons with Chi square using R Studio version 4.3.2.

Results: 122 (3.2%) METex14, 70 (1.8%) METamp, and 3,629 (95.0%) METwt were identified. Patients with METex14 were older and more frequently female. MET gene expression was found to be higher in METamp (median 14.4) compared to METex14 (median 12.3) (P&lt;0.01). TMB was lowest in METex14 (median 2.7) group compared to METamp (median 7.1) and METwt (median 5.1) (P&lt;0.001). High PD-L1 expression occurred in 71.4% of METamp, 68.0% of METex14 and 41.3% of METwt (P&lt;0.001). Overall, METamp tumors had a greater proportion of high IRS scores (52.9%) compared to METex14 (35.2%) and METwt (45.4%) (P&lt;0.01). mRNA expression of immune checkpoints CTLA4, PD-1, LAG3, IDO1, TIGIT and HAVCR2 were all higher in METex14 compared to METamp and METwt (P&lt;0.001 for all). METex14 tumors also exhibited higher gene expression of CD4, CD8A and FOXP3 compared to METamp and METwt (p&lt;0.001). METex14 had higher prevalence of MDM2 amplification (34% vs 3% vs 4%) and lower prevalence of alterations in EGFR (0.8% vs 22% vs 21%), KRAS (0.8% vs 10% vs 26%), CDKN2A (17% vs 29% v 28%) and TP53 (34% vs 87% vs 64%) compared with METamp and METwt tumors, respectively (p&lt;0.05).

Conclusion: METex14 and METamp tumors harbor distinct immune-gene expression profiles and co-occurring gene alterations that distinguish themselves from each other and METwt tumors. Further analysis must be conducted to determine how these variations impact immunotherapy in MET-altered NSCLC.

Citation Format: Saahil Javeri, Rachel Minne, Shrey Ramesh, Andrew Baschnagel, Randy Kimple, Laura Lamb, Scott Tomlins, Bryan Johnson, Nickolay Khazanov. Comparative genomic analysis reveals distinctive immune profiles in MET exon 14 mutated and MET amplified lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5101.