Integrated multiomic profiling of SCN2A loss-of-function reveals widespread molecular remodeling in patient hiPSC-derived neurons

SCN2A-related neurodevelopmental disorders comprise a genetically and mechanistically diverse group of early-onset brain conditions. Loss-of-function (LoF) variants in SCN2A represent one of the strongest genetic risk factors for autism spectrum disorder and intellectual disability, yet the molecular cascade linking reduced NaV1.2 dosage to neuronal dysfunction remains poorly understood. Here, we combine deep isoform-resolved transcriptomics, high-content imaging, and high-content cellular phenotyping in human hiPSC-derived neurons from three unrelated individuals carrying pathogenic SCN2A LoF variants and three independent healthy donor lines to delineate the multi-layered consequences of NaV1.2 insufficiency. We show that SCN2A LoF activates the nonsense-mediated decay (NMD) mechanism, selectively depleting canonical SCN2A isoforms and modifying the cells RNA processing. These molecular deficits translate into robust structural phenotypes, including axon initial segment shortening, reduced sodium channel density, and simplified dendritic arborization. Transcriptomic analysis converged on remodeling of synaptic and axonal pathways. RNA-seq identified coordinated alterations in gene programs linked to synaptic signaling, ion channel activity, and neuronal projection development, consistent with the structural and functional phenotypes observed. Transcript-level analysis further uncovered extensive perturbation of long non-coding RNA (lncRNA) networks, including lncRNAs strongly correlated with SYN1 and ANK3 isoforms. Together, these findings reveal that SCN2A haploinsufficiency induces a phenotype spanning NMD activation, isoform-specific dysregulation, axon initial segment destabilization and lncRNA-dependent regulatory shifts. This multiscale framework clarifies how reduced NaV1.2 disrupts neuronal development and highlights isoform-level restoration and modulation of post-transcriptional control as promising therapeutic avenues for SCN2A-related neurodevelopmental disorders.