Abstract 7150: Elucidating co-mutation landscapes in ALK fusion subtypes: implications for targeted therapy in non-small cell lung cancer (NSCLC)

Abstract Background: EML4-ALK is a prevalent ALK fusion variant with diverse breakpoints and subtypes. Different fusion partners and subtypes exhibit varied responses to ALK tyrosine kinase inhibitors (TKIs) and unique resistance mechanisms. Co-mutated genes influence the efficacy of targeted therapies. This study explores the molecular characteristics and co-mutation profiles of NSCLC with non-EML4-ALK fusions and various EML4-ALK subtypes. Methods: We analyzed 615 NSCLC samples harboring ALK fusions, confirmed by next-generation sequencing (NGS) using a 733-gene panel. Tumor mutational burden (TMB) was defined as the total count of nonsynonymous somatic mutations in coding regions. Results: Of 615 patients with ALK fusions, 543 had EML4-ALK fusions, with V1 as the most common subtype (40.88%, 222 cases), followed by V3 (36.46%, 198) and non-V1V3 subtypes (22.65%, 123). In the 72 non-EML4-ALK cases, intergenic-ALK fusion(ALK-IR)was the most prevalent (44.44%), followed by HIP1-ALK, KIF5B-ALK, and STRN-ALK. Analysis of co-mutations showed similar rates across EML4-ALK subtypes [V1: 85.14% (189/222); V3: 83.3% (165/198); non-V1V3: 87.0% (107/123)], while non-EML4-ALK fusions displayed a lower rate (79.16%, 57/72). In V1 and V3 substitutions were the predominant mutation type, whereas amplifications and substitutions were more common in non-EML4-ALK fusions. TP53 was the most frequently co-mutated gene across all EML4-ALK subtypes [∼30%]. Apart from TP53, the distribution of co-mutated genes varied among subtypes, with CDKN2A and ALK-IR showing relatively high mutation frequencies across multiple subtypes. To explore resistance mechanisms, we analyzed mutations associated with ALK-TKI resistance pathways, including RTKsMET, EGFR, SRC, IGF-1R, HER2, and HER3. The non-V1V3 subtype had the highest rate of resistance-related mutations (14.63%), while V1 and V3 displayed similar rates (10.81% and 10.1%). In V1, MET amplification was the primary resistance mechanism (3.15%), absent in other subtypes. Conversely, EGFR mutations were most common in non-V1V3 (5.69%) and V3 (2.53%) and less frequent in V1 (0.90%). ERBB3 amplification was more prevalent in V3 [V1 (0.45%) vs. V3 (1.01%) vs. non-V1V3 (0.81%)], while KRAS mutations were highest in non-V1V3 [V1 (1.35%) vs. V3 (1.52%) vs. non-V1V3 (3.25%)]. These findings indicate subtype-specific resistance patterns, potentially impacting treatment choices and prognosis. TMB analysis revealed a higher proportion of TMB-H (TMB ≥10) in V3 patients (9.10%) compared to V1 (5.86%) and non-V1V3 (6.21%), suggesting differential responses to immunotherapy among EML4-ALK subtypes. Conclusion: Distinct co-mutation and resistance patterns among EML4-ALK subtypes, providing insights that support personalized treatment strategies and prognostic assessments for NSCLC patients with various EML4-ALK fusion subtypes. Citation Format: Yang Zebo, Yuanyuan Zhang, Songlin Zhang. Elucidating co-mutation landscapes in ALK fusion subtypes: implications for targeted therapy in non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7150.