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

Abstract

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.