Distinct clinical, molecular and multi-omics biomarkers in early-onset head and neck squamous cell carcinoma

Background Early-onset head and neck squamous cell carcinoma (EOHNSCC) incidence is rising globally, often independent of traditional risk factors such as tobacco and alcohol. Whether EOHNSCC harbors distinct molecular and multi-omics signatures compared to typical-onset HNSCC (TOHNSCC) remains poorly understood. Methods We analyzed The Cancer Genome Atlas (TCGA) Firehose Legacy and AACR GENIE datasets to compare EOHNSCC (18-49 years) and TOHNSCC (>49 years) HNSCC. Features included somatic mutations, copy number alterations (CNAs), structural variants, gene fusions, DNA methylation, mRNA expression, and protein expression. HNSCC onset group differences were assessed for significance using Fisher's exact and Wilcoxon rank sum tests (p < 0.05). Pathway enrichment leveraged GO, KEGG, Reactome, and CORUM databases. Multivariable logistic regression evaluated associations between EOHNSCC and clinical covariates. Results Across both datasets, our study cohort was composed of 2,472 individuals with HNSCC (N AACR GENIE = 1,961; N TCGA =511). In AACR GENIE, EOHNSCC patients were more likely female (aOR = 1.49, 95% CI: 1.09-2.02), non-white (aOR = 1.99, 95% CI: 1.38-2.83), and had lower mutation burden (aOR = 0.44, 95% CI: 0.29-0.64). However, in TCGA, EO-HNSCC patients had lower histological grade tumors (G3 vs G1 aOR = 0.38, 95% CI: 0.14-1.00), more likely to receive neoadjuvant therapy (aOR = 17.02, 95% CI: 3.32-101.65), and had little to no prior smoking history (reformed vs non-smoker: aOR = 0.28, 95% CI: 0.13-0.57). Molecular markers in TCGA for EOHNSCC was characterized by concurrent mutation and mRNA overexpression in GDNF, FRYL, KIAA0586, CADPS, MYF5 , and DCTN1 , enriched in hypoxia-related pathways. Integration of CNAs and expression highlighted ASH2L and SERPIND1 , which are associated with cell cycle regulation signaling. Methylation-driven expression involved motility genes ( SPIPM6, SPAG6, ODAD3, RSPH4A ), enriched in cilium movement and DAP12 signaling. HSPA2 hypomethylation was correlated with HSPA2 CNA and upregulated mRNA expression, linked to cancer invasion and metastasis. Genes with mRNA-protein concordance included NOTCH1, SYK, SERPINE1, IRS1, CHEK2, EIF4E ; associated with translation initiation. In AACR GENIE, EOHNSCC showed higher KCNIP1 mutation, while TOHNSCC was enriched for NOTCH1, FAT1, KMT2D , and PIK3CA . Of note, FAT1 was the only gene mutated in both datasets; consistently in TOHNSCC. Conclusions EOHNSCC exhibits distinct multi-omics signatures involving hypoxia, cell motility, cell cycle regulation, cancer metastasis, and translation initiation. Candidate biomarkers include GDNF, ASH2L, SPAG6, HSPA2, EIF4E and KCNIP1 . Minimal overlap across datasets underscores the need for validation and exploration of prognostic and therapeutic implications.