Detecting Rare ALK Gene Fusions in Unclassified Spindle Cell Lung Tumors Using Anchored Multiplex PCR/Targeted RNA Next-Generation Sequencing.

Pulmonary spindle cell tumors are aggressive neoplasms with limited systemic treatment options, although a subset may harbor actionable genomic alterations. Because conventional fusion assays may miss rearrangements involving atypical or previously uncharacterized partners, we systematically investigated oncogenic fusions in pulmonary spindle cell tumors using anchored multiplex PCR-based targeted RNA sequencing. Formalin-fixed, paraffin-embedded tumor samples from 11 surgically resected pulmonary spindle cell tumors, excluding metastatic sarcomas, were analyzed using the FusionPlex Sarcoma panel supplemented with custom primers for RET, NTRK1, NTRK2, and NRG1. Two tumors (18.2%) harbored ALK fusions, identified as PPFIBP1::ALK and SYCL3::ALK. Both tumors showed positive ALK immunohistochemical staining. Histologically, the PPFIBP1::ALK-positive tumor was composed of spindle-shaped cells with a layered architecture, whereas the SYCL3::ALK-positive tumor showed relatively round cells arranged in clusters with collagenous stroma, highlighting the morphologic heterogeneity of ALK-rearranged pulmonary spindle cell tumors. These findings expand the molecular spectrum of pulmonary spindle cell tumors and identify rare ALK fusion partners in this setting. Our results support the incorporation of ALK immunohistochemistry as a screening tool and demonstrate the utility of anchored multiplex PCR-based RNA sequencing for the detection of therapeutically relevant fusions, particularly those with uncommon partners. This integrated approach may refine the diagnosis and support consideration of ALK-directed therapy in these rare tumors.