Saliva vs Plasma in Liquid Biopsy Sampling for Head and Neck Cancer: A Comparative Study

Head and neck squamous cell carcinoma (HNSCC) presents significant diagnostic and therapeutic challenges due to its rising incidence and poor prognosis. Liquid biopsy, utilizing biofluids such as blood and saliva, offers a noninvasive approach to detect circulating tumor DNA (ctDNA), circulating tumor RNA (ctRNA), and small extracellular vesicles (sEVs) containing DNA (sEV-DNA) and RNA (sEV-RNA), which reflect tumor biology. However, comprehensive comparisons of these liquid biopsy markers are limited.

Paired plasma and saliva samples were collected from HNSCC patients and healthy controls. We analyzed ctDNA and sEV-DNA from both plasma and saliva for tumor fraction (TF), copy number variations (CNVs), and methylation patterns. Additionally, we profiled small RNAs from saliva-derived ctRNA and sEV-RNA to explore their potential as biomarkers for disease monitoring.

Saliva sEV-DNA exhibited significantly higher TF compared to plasma sEV-DNA in HNSCC patients (mean, 0.0744 vs 0.0253, P < 0.001), suggesting superior tumor DNA capture in saliva. CNV analysis revealed shared and distinct genomic alterations across different sample types. Aberrant methylation patterns were observed more frequently in sEV-DNA than in ctDNA across both saliva and plasma samples. Small RNA profiling demonstrated broader coverage of differentially expressed genes in saliva sEV-RNA, enhancing its biomarker potential.

Our findings suggest that saliva-derived sEVs hold promise as noninvasive biomarkers for HNSCC. Saliva-based liquid biopsies, particularly sEV-DNA and sEV-RNA, provide a comprehensive molecular portrait of HNSCC that may facilitate the development of personalized medicine strategies.