Tumor Mutation Burden as a Biomarker in Resected Non-Small-Cell Lung Cancer

Abstract

Purpose: The survival benefit with adjuvant chemotherapy for patients with resected stage II-III non-small-cell lung cancer (NSCLC) is modest. Efforts to develop prognostic or predictive biomarkers in these patients have not yielded clinically useful tests. We report findings from the Lung Adjuvant Cisplatin Evaluation (LACE)-Bio-II study, in which we analyzed next-generation sequencing and long-term outcomes data from > 900 patients with early-stage NSCLC treated prospectively in adjuvant landmark clinical trials. We used a targeted gene panel to assess the prognostic and predictive effect of mutations in individual genes, DNA repair pathways, and tumor mutation burden (TMB).

Methods: A total of 908 unmatched, formalin-fixed, paraffin-embedded, resected lung cancer tumor specimens were sequenced using a targeted panel of 1,538 genes. Stringent filtering criteria were applied to exclude germline variants and artifacts related to formalin fixation. Disease-free survival, overall survival, and lung cancer-specific survival (LCSS) were assessed in Cox models stratified by trial and adjusted for treatment, age, sex, performance score, histology, type of surgery, and stage.

Results: Nonsynonymous mutations were identified in 1,515 genes in 908 tumor samples. High nonsynonymous TMB (> 8 mutations/Mb) was prognostic for favorable outcomes (ie, overall survival, disease-free survival, and LCSS) in patients with resected NSCLC. LCSS benefit with adjuvant chemotherapy was more pronounced in patients with low nonsynonymous TMBs (≤ 4 mutations/Mb). Presence of mutations in DNA repair pathways, tumor-infiltrating lymphocytes, TP53 alteration subtype, and intratumor heterogeneity was neither prognostic nor predictive. Statistically significant effect of mutations in individual genes was difficult to determine due to high false-discovery rates.

Conclusion: High nonsynonymous TMB was associated with a better prognosis in patients with resected NSCLC. In addition, the benefit of adjuvant chemotherapy on LCSS was more pronounced in patients with low nonsynonymous TMBs. Studies are warranted to confirm these findings.

Fig 1.

Waterfall plots showing the frequency and types of mutations in genes mutated at a statistically significant level in The Cancer Genome Atlas cohort, across (A) LUAD (n = 375) and (B) LUSC (n = 414) samples from the LACE-Bio II cohort. LUAD, lung adenocarcinoma; LUSC, squamous cell carcinoma of the lung.

Fig 2.

(A) Approximately 70% of LUAD samples had at least one mutation in RTK/RAS/RAF pathway genes. (B) Distribution and type of mutation affecting these genes across all LUAD samples in the LACE-Bio II cohort. Percentages of samples with mutations listed for each gene are overlapping (and do not add up to 100%). LUAD, lung adenocarcinoma.

Fig 3.

Kaplan-Meier plots showing prognostic effect of nonsynonymous TMB on (A) overall survival, (B) disease-free survival, and (C) lung cancer–specific survival (LCSS) across all tumor samples. (D) Effect of mutational burden on hazard ratio for LCSS benefit with adjuvant chemotherapy when a flexible “spline” model is used. (E–G) Predictive effect of nonsynonymous TMB on LCSS at different levels of TMB (P = .357). TMB, tumor mutation burden.