Distinct ALK Expression Patterns Are Associated with Canonical and Noncanonical STRN::ALK Transcript Architectures in Oncocytic Thyroid Neoplasms

Oncocytic thyroid carcinomas are characterized by a unique chromosomal landscape and frequent resistance to radioactive iodine therapy, underscoring the need for improved molecular characterization. Although ALK rearrangements, particularly STRN::ALK fusions, have been described in thyroid carcinomas, their biological and clinical significance in oncocytic thyroid neoplasms remains unclear. This study investigated STRN exon 3-ALK exon 20-derived transcripts in 56 oncocytic thyroid neoplasms using RT-PCR, followed by cloning and Sanger sequencing of positive cases. Transcript-positive cases were further evaluated by fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and in silico structural modeling. STRN::ALK-derived transcripts were detected in 9 of 56 tumors; however, their frequency reflected the combined detection of distinct transcript architectures. Only 2 of 56 tumors (3.6%) harbored canonical in-frame STRN::ALK fusions, whereas 7 of 56 tumors (12.5%) contained noncanonical out-of-frame variants. Although ALK rearrangement by FISH was confirmed in all transcript-positive tumors irrespective of transcript architecture, detectable ALK protein expression by IHC was observed only in tumors harboring canonical in-frame fusions, whereas all noncanonical variants lacked detectable ALK protein expression. Structural modeling was concordant with these observations, suggesting preservation of kinase-domain features in canonical fusions and predicted disruption in noncanonical variants. Overall, STRN::ALK transcripts in oncocytic thyroid neoplasms exhibit marked architectural heterogeneity with distinct ALK protein expression patterns. ALK FISH-positive/IHC-negative cases should be interpreted cautiously, as they may not represent biologically equivalent ALK-driven neoplasia, with uncertain therapeutic relevance. Integrated molecular and protein-level assessment may support interpretation of ALK alterations in oncocytic thyroid neoplasms.