Clinicopathological and molecular genetic characteristics of Epstein–Barr virus‐positive small cell neuroendocrine carcinoma of the nasopharynx

BACKGROUND: Epstein-Barr virus (EBV)-positive small cell neuroendocrine carcinoma of the nasopharynx (SCNEC-nasopharynx) is exceptionally rare and aggressive, with poorly characterized molecular features. METHODS: Clinicopathological, immunohistochemical (synaptophysin, INSM1, chromogranin A, CK-pan, EGFR, NUT, INI1), and molecular profiles of 15 EBV-positive SCNEC-nasopharynx cases (2012-2025) were analysed. EBV status was confirmed by EBER-ISH. Exploratory next-generation sequencing compared nine SCNEC with five EBV-positive nasopharyngeal non-keratinizing carcinomas (NKUC). RESULTS: Patients (median age 51; male:female = 2:1) presented with advanced-stage disease and cervical lymphadenopathy. Histology showed solid nests of small cells with high-grade features. All tumours were diffusely positive for synaptophysin and EBER, showed perinuclear dot-like CK-pan staining, and were negative for squamous markers and EGFR. NUT was negative and INI1 retained. Comparative genomics revealed greater mutational burden and unique alterations enriched in cell cycle/DNA damage pathways in SCNEC versus NKUC. After multimodal therapy, median overall survival was 33 months. CONCLUSION: This largest integrated study defines the distinct clinicopathological and molecular profile of EBV-positive SCNEC-nasopharynx. The identified diagnostic immunophenotype and potential oncogenic pathways provide a foundation for precise diagnosis and future targeted therapy development.