KEAP1/NFE2L2 mutations to predict local recurrence after radiotherapy but not surgery in localized non-small cell lung cancer.

Abstract

9012 Background: Tumor genotyping in localized non-small cell lung cancer (NSCLC) is not broadly performed due to lack of actionable associations of mutations with treatment or outcome. We sought to identify recurrent mutations in localized NSCLC that are associated with local recurrence (LR) after radiotherapy (RT) or surgery. Methods: We identified consecutive patients with NSCLC treated with chemoradiotherapy (CRT), stereotactic ablative radiotherapy (SABR) or surgery from 2009-2018 at our institution with stage IA1-IIIC NSCLC who had genotyping performed on tumor tissue using a targeted gene panel. Our primary objective was to identify somatic tumor mutations that predicted LR after RT but not surgery. We also performed functional screening assays by expressing open reading frame constructs harboring patient-derived mutations in knock-out cell lines generated by CRISPR-Cas9 and evaluating effects on in vitro radioresistance. Results: We identified 232 consecutive patients with localized NSCLC (87.1% adenocarcinoma, 10.3% squamous, 2.3% other) who received tumor biopsy or resection specimen and underwent tumor genotyping. 47 patients with locally advanced NSCLC received CRT, 50 patients with early stage NSCLC received SABR, and 135 patients with early stage NSCLC underwent surgical resection. Of all recurrent mutations ( > 5% mutation frequency), only mutations in Kelch-like ECH-associated protein 1 ( KEAP1) or Nuclear Factor Erythroid 2-Related Factor 2 ( NFE2L2) genes (K/NMUT) were significantly associated with LR after CRT or SABR, with 2-year LR in the combined RT cohort of 42.4% for K/NMUT versus 12.5% for wildtype (P = 0.005). Furthermore, K/NMUT were present in nearly half of all LR events. Strikingly, there was no significant difference in LR for K/NMUT tumors following CRT versus SABR (P = 0.47). Local recurrence was rare for patients who received surgery (n = 2) and was not associated with K/N mutation status (P = 0.60). Functional evaluation by expression of K/N mutations in knock-out cell lines revealed that LR only occurred in patients with mutations that induced radioresistance (i.e. pathogenic) but not passenger mutations (P = 0.04). In contrast to genotyping, NFE2L2 target gene expression analysis via RNA-seq did not predict LR (P = 0.93). Conclusions: Our findings suggest that KEAP1/NFE2L2 mutations are a predictive biomarker of clinical radioresistance and a dominant cause of LR after RT. Genotyping for KEAP1/NFE2L2 mutations could therefore facilitate treatment personalization in localized NSCLC.