ALK^ATI Drives Nuclear Anaplastic Lymphoma Kinase (ALK) Expression in Histiocytic Neoplasms Without ALK Fusions

Anaplastic lymphoma kinase (ALK)-positive histiocytosis is a rare histiocytic neoplasm defined by oncogenic ALK fusions. The disease frequently involves the nervous system and is responsive to ALK inhibition. A distinct subset of histiocytoses expresses ALK in the absence of detectable ALK fusions. We aimed to determine the frequency and molecular characteristics of these ALK protein-positive, fusion-negative neoplasms. RNA was extracted from histiocytosis-affected tissue samples of 398 patients with diverse histiocytoses, converted to cDNA, and subjected to targeted sequencing using a custom gene panel. ALK fusions and gene expression levels were assessed; the presence of ALK isoforms was investigated using targeted digital PCR. In a subset of cases, ALK protein expression was evaluated using immunohistochemistry (clone 1A4). Of 398 cases, 303 (76%) passed quality control and were included in the analysis. Among these, 64 (21.5%) had substantial ALK gene expression, while not harboring ALK fusions. Immunohistochemistry revealed consistent nuclear and cytoplasmic ALK expression in these cases, whereas ALK expression in fusion-positive cases was restricted to the cytoplasm. Analysis of ALK intron 19 expression by targeted PCR revealed the presence of a novel ALK isoform (ALK^ATI), which was linked to nuclear ALK expression. No specific clinical or molecular features distinguished histiocytic neoplasms with ALK^ATI from those without. In conclusion, many histiocytic neoplasms express ALK but are not ALK-positive histiocytosis. Most cases can be identified by nuclear ALK expression, which is linked to alternative transcription initiation-a known mechanism of ALK activation independent of genetic aberrations. Future studies should elucidate whether these neoplasms respond to ALK inhibition.