Loss of YAP1 C‐terminus expression as an ancillary marker for metaplastic thymoma: a potential pitfall in detecting YAP1::MAML2 gene rearrangement

Aims Metaplastic thymoma is a rare thymic tumour characterized by Yes Associated Protein 1 ( YAP1 ) and Mastermind Like Transcriptional Coactivator 2 ( MAML2 ) gene fusions resulting from an intrachromosomal inversion of chromosome 11. Immunohistochemistry with an antibody directed against the C‐terminus of YAP1 has shown loss of expression in YAP1 ‐rearranged vascular neoplasms, poromas, and porocarcinomas. This study aimed to validate an anti‐YAP1 C‐terminal antibody as an ancillary immunohistochemical marker for the diagnosis of metaplastic thymoma. Materials and methods Ten metaplastic thymomas were selected for the current study. Fluorescence in situ hybridization (FISH), next‐generation sequencing (NGS), and reverse transcription‐polymerase chain reaction (RT‐PCR) analyses were performed to detect YAP1::MAML2 fusions. We then performed immunohistochemistry to detect YAP1 C‐terminus expression in 10 metaplastic thymomas, 50 conventional thymomas (10 each of type A thymoma, type AB thymoma, type B1 thymoma, type B2 thymoma, and type B3 thymoma) and seven thymic carcinomas. Results All 10 cases showed narrow split signals with a distance of nearly two signal diameters and sometimes had false‐negative results in YAP1 and MAML2 break‐apart FISH (BA‐FISH). Abnormal colocalized signals of the YAP1::MAML2 fusion were observed in all 10 cases using fusion FISH (F‐FISH) assays. Eight of 10 cases with adequate nucleic acids were successfully sequenced and all showed YAP1::MAML2 fusions; in two cases the fusions were detected by both DNA and RNA sequencing and in six cases by RNA sequencing only. YAP1::MAML2 fusion transcripts were identified in four cases by RT‐PCR. Metaplastic thymoma showed loss of YAP1 C‐terminus expression in all 10 (100%) cases. All other thymic neoplasms showed retained YAP1 C‐terminus expression. Conclusion YAP1 C‐terminus immunohistochemistry is a highly sensitive and specific ancillary marker that distinguishes metaplastic thymoma from its mimics. BA‐FISH assays could not effectively detect YAP1::MAML2 fusions due to the proximity of the two genes. Loss of YAP1 C‐terminus expression is a reliable surrogate for the detection of YAP1::MAML2 fusions in metaplastic thymoma.