STK11 and KEAP1 Mutations as Prognostic Biomarkers in an Observational Real-World Lung Adenocarcinoma Cohort

Importance Understanding the mechanisms of primary resistance to immune checkpoint blockade therapy is of paramount importance for treatment selection. Somatic mutations in STK11 and KEAP1 , frequently co-mutated in nonsquamous non–small cell lung cancer, have been associated with poor response to immune checkpoint blockade. However, previous reports lack non–immune checkpoint blockade controls needed to properly ascertain the predictive nature of those biomarkers. Objective To evaluate the predictive vs prognostic effect of STK11 or KEAP1 mutations across different treatment classes in nonsquamous non–small cell lung cancer. Design A retrospective, real-world data cohort from the Flatiron Health network linked with genetic testing from Foundation Medicine, from January 1, 2011, through December 31, 2018. Setting Multicenter, including academic and community practices. Participants Patients diagnosed with stage IIIB, IIIC, IVA, or IVB nonsquamous non–small cell lung cancer who initiated first-line treatment within 90 days after diagnosis. Main Outcomes and Measures Real-world, progression-free survival and overall survival calculated from time of initiation of first-line treatment. Results We analyzed clinical and mutational data for 2276 patients with advanced, nonsquamous non–small cell lung cancer (mean age at advanced diagnosis, 66.3 years [SD 10.3], 54.4% female, 80.1% with a history of smoking), including patients treated with anti–programmed death-1/anti–programmed death ligand 1 inhibitors at first line (n = 574). Mutations in STK11 or KEAP1 were associated with poor outcomes across multiple therapeutic classes and were not specifically associated with poor outcomes in immune checkpoint blockade cohorts. There was no observable interaction between STK11 mutations and anti–programmed death-1/anti–programmed death ligand 1 treatment on real-world, progression-free survival (HR, 1.05; 95% CI, 0.76-1.44; P = .785) or overall survival (HR, 1.13; 95% CI, 0.76-1.67; P = .540). Similarly, there was no observable interaction between KEAP1 on real-world, progression-free survival (HR, 0.93; 95% CI, 0.67-1.28; P = .653) or overall survival (HR, 0.98; 95% CI, 0.66-1.45; P = .913). Results were consistent in KRAS -mutated patients. Conclusion and Relevance Our results show that STK11 - KEAP1 mutations are prognostic, not predictive, biomarkers for anti–programmed death-1/anti–programmed death ligand 1 therapy. Question Are loss-of-function somatic mutations in STK11 and KEAP1 predictive of response to immune checkpoint blockade or simply prognostic? Findings In this observational real-world cohort totaling 2276 patients, including 574 treated with immune checkpoint blockade, we find that mutations in STK11 and KEAP1 are associated with poor prognosis across multiple first-line treatment classes. Meaning Mutations in STK11 and KEAP1 are prognostic biomarkers of poor response to both immune checkpoint blockade and chemotherapy. ### Competing Interest Statement All authors are BMS employees and shareholders. PD is a J&J shareholder, RD is a Merck and J&J shareholder. ### Funding Statement This work was funded by Bristol-Myers Squibb ### Author Declarations All relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript. Yes All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Data was licensed from Flatiron Health.