Enrichment of SMARCA4 mutations in lung carcinomas presenting as cancer of unknown primary

OBJECTIVES: Identifying the primary tumor in cancer of unknown primary (CUP) remains a major clinical challenge. While WGS-based tissue-of-origin (TOO) prediction has improved diagnostic precision, its use is constrained by cost and availability. We investigated whether a low-complexity surrogate, combining SMARCA4 mutations and smoking history, can identify a lung cancer origin in CUP (CUP-Lung). METHODS: We retrospectively identified 305 provisional CUP cases from two Dutch CUP referral centers (2022-2025). Integration of whole-genome sequencing (WGS)-based TOO prediction with clinicopathological data identified 58 patients (18.9%) with CUP-Lung. Associations between SMARCA4 mutations, smoking history, and CUP-Lung were assessed using comparative and regression analyses. RESULTS: SMARCA4 mutations were present in 36.2% of CUP-Lung cases, significantly higher than in the overall CUP cohort (10.7%) and TCGA lung cancer datasets (6-8%). CUP-Lung cases had higher tumor mutational burden (median 21.5 vs. 12.6 mut/Mb, p < 0.001) and enriched smoking-related mutational signatures (p < 0.001). Smoking history was reported in 87.9% of cases. Smoking history (OR 4.9, 95% CI 2.2-10.9, p < 0.001) and SMARCA4 mutation (OR 10.3, 95% CI 4.5-23.8, p < 0.001) independently predicted CUP-Lung, together conferring a 76.0% probability of lung origin. No statistical differences were found between cases with and without detectable pulmonary involvement. CONCLUSION: Combined smoking history and SMARCA4 mutations support lung cancer classification even in the absence of detectable pulmonary involvement enabling organ-directed treatment when WGS is unavailable.