Validation of a Machine Learning Model to Predict Immunotherapy Response in Head and Neck Squamous Cell Carcinoma

Simple Summary Recurrent and/or metastatic head and neck squamous-cell carcinoma (R/M HNSCC) is a clinically challenging disease with a poor prognosis. Despite advances in survival through the use of immune-checkpoint blockade, only a minority of patients experience benefit from such treatments, and it is difficult to identify the patients most likely to benefit. Machine learning approaches integrating clinical and genomic data can predict response to immune-checkpoint blockade across all cancers; however, the performance of this model in HNSCC has not been examined. Here, we validate this previously described immune-checkpoint blockade response prediction model in R/M HNSCC patients. This model was able to predict response as well as overall survival following immune-checkpoint blockade in patients with R/M HNSCC. Further investigation will be needed to further delineate the importance of HNSCC-specific features.Abstract Head and neck squamous-cell carcinoma (HNSCC) is a disease with a generally poor prognosis; half of treated patients eventually develop recurrent and/or metastatic (R/M) disease. Patients with R/M HNSCC generally have incurable disease with a median survival of 10 to 15 months. Although immune-checkpoint blockade (ICB) has improved outcomes in patients with R/M HNSCC, identifying patients who are likely to benefit from ICB remains a challenge. Biomarkers in current clinical use include tumor mutational burden and immunohistochemistry for programmed death-ligand 1, both of which have only modest predictive power. Machine learning (ML) has the potential to aid in clinical decision-making as an approach to estimate a tumor's likelihood of response or a patient's likelihood of experiencing clinical benefit from therapies such as ICB. Previously, we described a random forest ML model that had value in predicting ICB response using 11 or 16 clinical, laboratory, and genomic features in a pan-cancer development cohort. However, its applicability to certain cancer types, such as HNSCC, has been unknown, due to a lack of cancer-type-specific validation. Here, we present the first validation of a random forest ML tool to predict the likelihood of ICB response in patients with R/M HNSCC. The tool had adequate predictive power for tumor response (area under the receiver operating characteristic curve = 0.65) and was able to stratify patients by overall (HR = 0.53 [95% CI 0.29-0.99], p = 0.045) and progression-free (HR = 0.49 [95% CI 0.27-0.87], p = 0.016) survival. The overall accuracy was 0.72. Our study validates an ML predictor in HNSCC, demonstrating promising performance in a novel cohort of patients. Further studies are needed to validate the generalizability of this algorithm in larger patient samples from additional multi-institutional contexts.