Outside canonical BRAF p.V600E Box: 7 novel BRAF gene fusions in BRAF p.V600E WT papillary thyroid carcinoma

BRAF, when mutated at V600E, is a well-known potent early oncogenic driver in papillary thyroid carcinoma (PTC), with potential prognostic and therapeutic implications. Non-V600E mutations are less common and without clear functional or therapeutic significance. One class of non-V600E mutations is BRAF gene fusions, which typically involve the C-terminal kinase domain of BRAF joined to a wide repertoire of potential N-terminal fusion partners. The aim of this study was to employ a sequential algorithmic approach to identify patients with BRAF fusions based on an integrated analysis of histologic, immunohistochemistry (IHC), and molecular (NGS) features of BRAF-rearranged PTCs. Nine patients with PTC previously scrutinized as BRAF V600E negative by IHC were analyzed by NGS. The studied 9 cases showed conventional PTC growth; 2 cases displayed a minor high-grade component (tall cell and hobnailing, < 20%), 1 case qualified as high-grade differentiated thyroid carcinoma (presence of necrosis and mitotic activity > 5 MF/ 2 mm²; adjacent conventional PTC was present), and 1 case represented neck (lymph node) recurrence after 10 years. BRAF fusions were detected in all cases (10 different fusion partners: NRF1, MKRN1, MACF1, MTDH1, ARHGAP26, STRBF, FCHSDH2, POM121C, UBAP2L, SND1). To our knowledge, 7 of these fusions have not been reported so far in PTC (NRF1::BRAF, MTDH1::BRAF, ARHGAP26::BRAF, BRAF::STRBF, FCHSDH2::BRAF, BRAF::POM121C, UBAP2L::BRAF). In 3 PTCs, BRAF fusions were sole genomic events. Concurrent TERT (c.-124C > T) mutations were detected in 3 PTCs; pathogenic IGF2 amplification was present in another PTC, in addition to BRAF fusion. Two simultaneous fusions BRAF::STRBF and FCHSDH2::BRAF were found in one case of PTC; two BRAF fusions (BRAF::POM121C; UBAP2L::BRAF) co-existed with 2 FOXO1 fusions (FOXO1::TES, YWHAG::FOXO1) in one PTC. In summary, we report 7 new BRAF fusions in PTC BRAF V600E-WT. Additional clinical research is needed to elucidate the behavior of BRAF fusion-driven thyroid carcinomas and the therapeutic utility of MAPK pathway inhibitors.