Assessment of tumor mutation burden based on whole-exome sequencing of extracellular vesicle-derived DNA from bronchoalveolar lavage fluid in advanced non-small cell lung cancer treated with pembrolizumab: a prospective, multicenter, observational study

Background: Obtaining sufficient tumor tissue for molecular testing remains challenging in advanced non-small cell lung cancer (NSCLC). We evaluated tumor mutation burden (TMB) using extracellular vesicle (EV)-derived DNA from bronchoalveolar lavage fluid (BALF) and assessed the correlation between BALF and tissue TMB.

Methods: In this prospective, multicenter, observational study, we enrolled patients with pathologically confirmed stage IV NSCLC who received pembrolizumab at three academic institutions in South Korea. TMB was quantified by whole-exome sequencing (WES) of EV-derived DNA isolated from BALF and from matched tumor tissue obtained prior to treatment. The concordance of TMB between BALF EV-derived DNA and matched tumor tissue was assessed using Spearman’s rank correlation coefficient. Associations between BALF EV-TMB and clinical outcomes—including overall survival (OS), progression-free survival (PFS), and objective response rate—were evaluated over a median follow-up of 17.0 months (range, 1–63 months).

Results: Out of 64 patients, 46 (71.9%) had evaluable tissue TMB, and 53 (82.8%) had evaluable BALF TMB. There were no significant differences between BALF and tissue regarding DNA amounts, estimated library size, mean depth, and uniformity. The median tissue TMB and BALF TMB were 4.738 and 1.82 mut/Mb, respectively. A modest positive correlation was observed between tissue TMB and BALF TMB (r=0.61, P<0.001). Neither tissue TMB nor BALF TMB showed significant differences in PFS. However, higher TMB is associated with a more favorable OS outcome in patients with advanced NSCLC.

Conclusions: These findings demonstrate the feasibility of WES-based TMB quantification from BALF EV-derived DNA and suggest its potential as a complementary prognostic measure in pembrolizumab-treated NSCLC. Validation in larger, prospective cohorts is warranted before clinical implementation.