Lung Squamous Cell Carcinoma Harbouring a Novel PAX8::PPARγ Fusion and a FGFR2 Exon 7 Missense Mutation

Comprehensive molecular profiling is now routinely performed in newly diagnosed non-small cell lung carcinomas (NSCLCs) to identify actionable genomic alterations. Although numerous molecular abnormalities have been described in lung carcinomas, rare and unexpected gene fusions may create significant diagnostic challenges, particularly when they are characteristically associated with tumours of different lineages. To our knowledge, this is the first reported case of a primary lung squamous cell carcinoma harbouring an in-frame PAX8::PPARγ fusion with a concurrent FGFR2 exon 7 missense mutation (p.W290C). An 80-year-old man with a smoking history exceeding 50 years presented with a rapidly enlarging PET-avid right upper lobe pulmonary mass. Bronchial brushing cytology demonstrated a hypercellular malignant neoplasm composed of pleomorphic squamoid cells with hyperchromatic nuclei, dense cytoplasm and extensive necrosis. Cell block material showed squamous morphology and diffuse p40 positivity, supporting squamous differentiation. Reflex next-generation sequencing identified an FGFR2 exon 7 missense mutation (p.W290C; c.870G>C) and targeted RNA fusion analysis demonstrated an in-frame PAX8::PPARγ fusion resulting from a t(2;3)(q13;p25.2) translocation. Because PAX8::PPARγ rearrangements are strongly associated with follicular thyroid neoplasms, extensive clinicoradiologic and immunohistochemical correlation was performed to exclude metastatic thyroid carcinoma. Imaging studies showed no thyroid lesion or residual thyroid tissue, and tumour cells were negative for thyroglobulin, TTF-1 and PAX8. Correlation of the clinical history, radiologic findings, cytomorphology, immunophenotype and molecular profile supported the diagnosis of primary lung squamous cell carcinoma. This case expands the molecular spectrum of lung squamous cell carcinoma and highlights the importance of integrated cytopathologic, immunohistochemical, molecular and radiologic evaluation when unexpected gene fusions are identified in cytology specimens.