Genomic predictive biomarkers of anti-EGFR resistance in EGFR-mutated non-small-cell lung cancer: Impact of classical mutations, comutations and secondary CNVs.

Abstract

e20670 Background: Non-small-cell lung cancer (NSCLC) with EGFR mutations, particularly in exons 19 and 21, has shown variable responses to Osimertinib. Objective: characterize genomic and molecular biomarkers of resistance to Osimertinib in patients (pts) with EGFR -mutated NSCLC. Methods: A total of 477 tumor samples from pts with NSCLC were analyzed using next-generation sequencing (NGS) between October 2022 and November 2024. Out of 477 samples, a total of 52 (11%) exhibited mutations in EGFR . However, only 30 cases (6.3%) showed mutations in exons 19 (Ex19del; n=19) and 21 (L858R; n=11) both of which were associated with sensitivity to Osimertinib treatment. DNA and RNA analysis: The mixture containing nucleic acids and sequencing reagents was loaded onto the Ion Torrent Genexus Integrated Sequencer. The Oncomine Precision Assay (OPA) panel was utilized to detect hotspot mutations, copy number variations (CNVs), and gene fusions across 50 cancer-associated genes using the Ion Torrent GX5 chip. Data analysis was performed automatically using the Oncomine Reporter software, and results were filtered using the Oncomine Extended 5.16. Survival and correlation analysis was performed using Kaplan-Meier (Log-rank test) and Chi-squared test. Statistical significance was p<0.05 (SPSSv28 software). Results: In the present study we analyzed a total of 30 pts (females 53.3% / males 46.7%) with NSCLC treated with Osimertinib. Median age was 71 years [50-86]. The most frequent treatment was Osimertinib in monotherapy (25 cases, 83.3%) followed by Osimertinib-chemotherapy (5 pts; 16.7%), all in advanced stages. NSCLC pts with Ex19del treated with Osimertinib exhibited a more favorable prognosis compared to those with L858R mutations (p=0.039), which had a higher incidence of deaths (p=0.02). CNVs were more frequently observed in L858R group (8/11; 72.7%) versus Ex19del group (7/19; 36.8%). The most frequent CNVs in L858R group were in the MET (27.3%), FGFR1 (18.2%), EGFR (18.2%) and KRAS (9.1%) genes. In contrast, the most frequent CNVs in pts with Ex19del were observed in EGFR (31.6%) and CDKN2A (5.3%) genes. Osimertinib resistances were associated with the presence of CNVs (p=0.009). Notably, 26.3% of the Ex19del group progressing to Osimertinib at data cut-off compared to 45.5% in the L858R group. The most robust genomic biomarker associated with a worse overall survival in both groups was TP53 (p=0.024). Conclusions: Our findings highlight the importance of secondary CNVs in NSCLC EGFR -mutated L858R. Tumors with Ex19del show a better prognosis in likely relation to a lower presence of CNVs, being tumors with less clonal heterogeneity. These results are essential in the selection of pts for the different standard therapies (Osimertinib, Osimertinib-chemotherapy or Amivantamab-Lazertinib) and the future clinical trials.