ZMYND11 Functions in Bimodal Regulation of Latent Genes and Brain-like Splicing to Safeguard Corticogenesis [RNA-seq]

While the identification of pathogenic variants linked to neurodevelopmental (NDD) and autism spectrum disorders (ASD) has advanced rapidly, the mechanisms underlying these genetic risks remain unclear. Here, we leveraged a human pluripotent stem cell model to uncover the neurodevelopmental consequences of mutations in ZMYND11, a newly implicated risk gene. ZMYND11, known for its tumor suppressor function, encodes a histone-reader that recognizes sites of transcriptional elongation and acts as a co-repressor. Our findings reveal that ZMYND11 deficient cortical neural stem cells exhibit upregulation expression of latent developmental pathways, leading to impaired production of secondary neural progenitors and neurons. In addition to its chromatin-related functions, we found ZMYND11 orchestrates a brain specific isoform switch that affects migration and proliferation of cortical neural stem cells. We further demonstrated that brain specificity is likely to involve the activity of the splicing regulator RBFOX2. Finally, we extended our findings to 10 additional lines with different chromatin-related NDD/ASD risk factors and identified a subset displaying similar activation of developmental pathways and splicing dysregulation, which could partially be rescued by leveraging the transcriptional repression and splicing coordination of ZMYND11. Collectively, our work highlights the critical role of ZMYND11 in regulating developmental signals and alternative splicing, offering novel insights into the molecular pathology of ZMYND11-associated NDDs. Moreover, these findings suggest broader convergence with other genetic risk factors for NDD/ASD, presenting potential therapeutic avenues for intervention. To investigate the role of ZMYND11 in corticogenesis, we performed RNA-seq on WT and ZMYND11 mutant human embryonic stem cells and d18 cortical neural stem cells, WT d18 cortical neural stem cells that overexpressed FLAG-ZMYND11 or not for 3 days, and d18 cortical neural stem cells differentiated from a subset of Autistic mutants (termed "Class I") and isogenic controls (UMOD edited).