Uncovering urinary proteogenomic signatures associated with head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a major clinical challenge due to its aggressive nature and poor prognosis in advanced stages. Late detection, often due to a delayed diagnosis, limits treatment success. With the aim of improving the early diagnosis of HNSCC, we analysed urine samples from 19 male HNSCC patients and 10 healthy male subjects and identified 1427 proteins by mass spectrometry (MS)-based proteomics. Of these, 351 proteins were consistently detected in all subjects and selected for quantitative comparisons, which highlighted potential prognostic markers such as RNASE1, LRG1, and CD44. Proteogenomic cross-referencing of MS-identified peptides with cancer variant databases suggested the presence of HNSCC-associated protein variants [e.g. GAA p.(Trp746Cys) and SIAE p.(Pro210Leu)] as potential indicators of advanced disease. Functional analyses linked the identified proteins to important tumour-related processes, including the epithelial-mesenchymal transition and neutrophil degranulation. These results support urine as a valuable body fluid for proteogenomic profiling, as it can be collected non-invasively, is available in large volumes, and enables the longitudinal monitoring of molecular changes over time, providing a convenient window into systemic and tumour-associated processes. This study provides a proof of concept that tumour-related protein variants originating from HNSCC can be detected in urine, supporting its potential as a source of biomarkers for early detection. However, given the small, male-only cohort, these findings should be regarded as preliminary and will require validation in larger, sex-balanced cohorts, including patients with benign or inflammatory head and neck conditions, to confirm disease specificity. Altogether, our data underscore the translational promise of urinary proteogenomics in HNSCC management.