A zebrafish model of NEXMIF-related encephalopathy identified drivers of hyperlocomotion and provides a scalable platform for drug discovery

ABSTRACT: X-linked Intellectual Disability type 98 (XLID-98) is a neurodevelopmental disorder (NDD) with a broad phenotypic spectrum caused by pathogenic variants in the Neurite Extension and Migration Factor (NEXMIF) gene, formerly known as KIAA2022, KIDLIA or XPN (OMIM 300524). To investigate the pathogenic mechanisms of XLID-98, a double knock-out zebrafish model (nexmifa/b-/-) was generated using CRISPR/Cas9 technology. Mutant larvae displayed notable morphological differences, most prominently an increase in total body length. They also exhibited significant hyperlocomotion in the visual-startle OFF assay—a behavioral phenotype reversed by treatment with sodium valproate (VPA) and topiramate (TPM), thereby supporting the pharmacological validity of the model. Transcriptomic analysis of larval head at 7 dpf revealed 414 differentially expressed genes (DEGs), enriched in microtubule-associated protein kinase (MAPK) signaling, cell adhesion and sodium transport pathways. Functional analyses demonstrated that the upregulated genes entpd3 (Ectonucleoside Triphosphate Diphosphohydrolase 3) and ddx43 (DEAD-Box Helicase 43) act synergistically to attenuate neuronal excitability, while downregulation of kbtbd7 (Kelch repeat and BTB domain-containing protein 7) contributes directly to the hyperactive phenotype. A targeted screen of 87 natural compounds identified kahweol acetate, veratridine and rauwolscine as potent inducers of entpd3. However, despite robust transcriptional activation, rauwolscine failed to improve behavioral outcomes, suggesting that modulation of a single target may be insufficient for phenotypic rescue. Collectively, these findings establish the first zebrafish model of NEXMIF-related encephalopathy, identify entpd3, ddx43 and kbtbd7 as key modulators of neuronal excitability, and provide a scalable platform for targeted therapeutic discovery in XLID-98.

ORGANISM(S): Danio rerio

PROVIDER: GSE334219 | GEO | 2026/08/19

REPOSITORIES: GEO