Oncogene amplification of CCND1 via extrachromosomal DNA impacts overall survival in head and neck squamous cell carcinoma

Extrachromosomal DNA (ecDNA) drives oncogene amplification and transcriptional rewiring in many cancers. For head‑and‑neck squamous cell carcinoma (HNSCC), the prevalence of ecDNA has been reported on the top across various cancer types. However, the clinical significance of ecDNA remain incompletely defined. This study aimed to (1) systematically evaluate ecDNA frequency and architecture in HNSCC, (2) examine its associations with clinical characteristics, and (3) identify driver oncogenes amplified by ecDNA, if any, that might impact patient prognosis.

We analyzed primary tumor data from 153 HNSCC cases in TCGA. ecDNAs were detected using the AmpliconArchitect pipeline on TCGA whole-genome sequencing. HPV status was retrieved from the TCGA HNSC landmark study. Differences in the frequency of ecDNA based on anatomical subsite and sex were assessed using chi-square tests. Patient age was compared using independent samples t-test. We compiled a panel of 38 candidate oncogenes from TCGA HNSC landmark paper and published ecDNA studies, then evaluated how often these genes were amplified on ecDNA in our cohort. The association of each ecDNA-amplified gene with overall survival (OS) was estimated using Kaplan-Meier curves, and differences in survival were analyzed using the log-rank test.

ecDNA was present in 68.0% (104/153) of tumors. The most common ecDNA structures were linear (47.7%), followed by break‑fusion‑break (BFB, 30.1%), heavily rearranged (26.1%), and circular (25.5%). No significant differences were observed by anatomical site or sex. Patients with ecDNA were younger (median 57.7 vs. 62.0 years, p = 0.038). Among the 38 oncogenes examined, amplification of a cluster of 11q13 genes including FADD, CTTN, and CCND1 via ecDNA occurred most frequently, followed by EGFR, BIRC2, WHSC1L1 and YAP1. Overall, ecDNA status alone did not significantly affect OS (log‑rank p = 0.442). However, patients harboring CCND1‑ecDNA had markedly poorer OS (log‑rank p = 1.5 × 10⁻⁴), underscoring the adverse prognostic impact of CCND1 amplification through ecDNA. Notably, CCND1 ecDNA events are mutually exclusive with HPV-positive tumors, suggesting a distinct oncogenic pathway in HPV-negative HNSCC.

ecDNA is common in HNSCC and is associated with a younger age of onset. Although ecDNA presence itself does not independently predict overall survival, ecDNA‑mediated amplification of CCND1 is strongly linked to worse outcomes. These findings highlight the amplification of CCND1 and other 11q13 genes via ecDNA as a key oncogenic mechanism in HNSCC and suggest that it could serve as a prognostic biomarker and potential therapeutic target.