Transcription factor‐based subtype assignment in pulmonary large cell neuroendocrine carcinoma

Aims Pulmonary large cell neuroendocrine carcinoma (LCNEC) can be difficult to diagnose due to histological overlap with small cell lung carcinoma (SCLC). SCLC comprises multiple transcription factor‐based subtypes. We aimed to evaluate the clinicopathological significance of transcription factor‐based subtyping in pulmonary LCNEC. Methods and results We identified a consecutive series of 117 patients in 2010–2024 with samples diagnosed as pulmonary LCNEC ( n = 70) or high‐grade neuroendocrine carcinoma with combined or intermediate morphology ( n = 47). Cytomorphological score was assessed as a weighted average from two areas. Immunohistochemistry (IHC) for ASCL1, NeuroD1, POU2F3, YAP1, and HNF4A was evaluated using H ‐scores, with subtype assignment based on the highest H ‐score. Next‐generation sequencing (NGS) was performed in selected cases. IHC subtyping identified 73 (62%) ASCL1‐dominant, 20 (17%) YAP1‐dominant, 9 (8%) NeuroD1‐dominant, 7 (6%) POU2F3‐dominant, 2 (2%) HNF4A‐dominant, and 6 (5%) quintuple‐negative samples. While YAP1 was often co‐expressed with other subtypes and HNF4A was frequently co‐expressed with ASCL1, POU2F3 was mutually exclusive from ASCL1/NeuroD1/HNF4A. Unlike ASCL1/NeuroD1/POU2F3, YAP1 and HNF4A H ‐scores each correlated with large‐cell morphology—both across the entire cohort and in the lung resection subgroup. NeuroD1 dominance was more common in tumours with combined/intermediate morphology than LCNEC. Some of the tumours with intermediate morphology straddling between prototypical LCNEC and SCLC harboured POU2F3 dominance, or EGFR or other non‐ KRAS driver mutations. In 19 patients with multiple samples (including nine with paired pre‐ and post‐treatment samples), all showed concordant subtypes after accounting for codominance. Conclusion YAP1 and HNF4A expression correlated significantly with large‐cell morphology.