MicroRNA expression profiling predicts clinical outcome in patients with locally advanced larynx and hypopharynx cancer treated with chemoradiotherapy

Background For patients with locally advanced larynx and hypopharynx cancer, organ preservation chemoradiotherapy (CRT) protocols are frequently applied. However, some tumors are resistant to CRT or will recur within a short time frame. For these patients upfront surgical resection may result in an improved cure rate. Currently, there are no molecular markers that can predict CRT response. In this study, tumor microRNA (miRNA) profiling was performed to predict clinical outcome in patients with locally advanced larynx or hypopharynx cancer treated with CRT. Methods First, matched fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) tumor biopsies from 12 patients were profiled by Next Generation Sequencing (NGS) to ensure valid miRNA results from FFPE. Next, miRNA profiles of FFPE tumor biopsies from 37 patients with larynx or hypopharynx cancer, treated with primary CRT, were determined. Clinicopathological data, including response to CRT, tumor stage and nodal stage, was collected of all patients. Differential expression analysis was performed to compare patients with poor clinical outcome, i.e residual tumor after treatment or progression free survival (PFS) 2 years. The median follow up of this cohort was 60 months (range 6 - 118). The Cancer Genome Atlas (TCGA) head and neck miRNA expression data of larynx and hypopharynx tumors and normal squamous cell tissues were used to select tumor specific miRNAs. By group-regularized penalized logistic ridge regression analysis, a model to predict clinical outcome was generated using tumor specific miRNAs combined with clinical covariates. Results In total, 324 novel candidate and 2,262 mature miRNAs were detected. A comparative analysis of miRNA profiles generated using matched FF and FFPE tumor biopsies showed a high correlation (mean r2=0.75). Using only FFPE samples, 13 miRNAs were significantly differentially expressed between patients with good versus poor clinical outcome (p Conclusion NGS miRNA profiling using FFPE tumor biopsies from patients with head and neck cancer is technically feasible, resulting in high quality miRNA expression data comparable to fresh frozen tissue. Based on miRNA expression profiling, candidate miRNAs were identified predictive for clinical outcome following treatment with CRT. A validation study is ongoing. Citation Format: Dennis Poel, Francois Rustenburg, Daoud Sie, Hendrik F. van Essen, Paul P. Eijk, Elisabeth Bloemena, Teresita E. Benites, Bauke Ylstra, Brakenhoff H. Ruud, Rene C. Leemans, Tineke E. Buffart, Henk M. Verheul, Jens Voortman. MicroRNA expression profiling predicts clinical outcome in patients with locally advanced larynx and hypopharynx cancer treated with chemoradiotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1801.