Pathology-guided enrichment of targetable gene rearrangements in BRAF wild-type papillary thyroid carcinoma

While papillary thyroid carcinoma (PTC) with gene rearrangements is associated with specific pathological features, further validation is needed to determine whether screening based on these specific pathological findings is useful. RNA sequencing was performed on 103 patients with PTC having wild-type BRAF. Group 1 (n = 57) included cases selected by an endocrine pathologist based on distinct pathological features such as multinodular invasive growth, prominent intratumoral stromal fibrosis, mixed growth patterns with varying degrees of nuclear atypia, pale eosinophilic to clear cytoplasm, and/or multiple lymph node (LN) metastases. These cases underwent pan-TRK, ALK and RET IHC and RNA sequencing. Group 2 (n = 46) consisted of randomly selected cases that underwent RNA sequencing. Gene rearrangements were identified in 66 patients (64.1%), with a significantly higher proportion in Group 1 (78.9%) than in Group 2 (45.7%). NTRK was the most frequent gene rearrangement (30.1%), followed by RET (19.4%), ALK (9.7%), and BRAF (2.9%). Patients with gene rearrangements were significantly younger and had smaller primary tumors, although they demonstrated greater extrathyroidal extension and LN metastasis than those without rearrangements. Pan-TRK IHC showed a sensitivity of 52% and a specificity of 94%, whereas RET and ALK IHC demonstrated higher sensitivities (78% and 88%) and specificities (81% and 100%), respectively. This study suggests that pathologic prescreening can enrich for targetable gene rearrangements in BRAF wild-type PTC and serve as a resource-sparing strategy before RNA sequencing. In prescreened cases, ALK IHC performed well, while pan-TRK and RET IHC had limitations.