KAT6A mutations drive transcriptional dysregulation of cell cycle and Autism risk genes in an Arboleda-Tham Syndrome cerebral organoid model

Arboleda-Tham Syndrome (ARTHS, OMIM#616268) is a rare neurodevelopmental disorder caused by de novo mutations in KAT6A. Individuals with ARTHS typically exhibit varying degrees of intellectual disability, speech and language deficits and clinical manifestations across multiple systems that lead to abnormal: vision, craniofacial features, cardiac morphology, and gastrointestinal function. To gain insight into the potential neuropathological mechanisms underlying ARTHS, we investigate how KAT6A mutations disrupt in vitro brain development using induced pluripotent stem cells (iPSCs) and cerebral organoids (COs) derived from ARTHS patients harboring KAT6A nonsense mutations. In this study, we conducted comprehensive transcriptomic profiling by performing time-course experiments and generating short-read and long-read RNA sequencing (RNA-seq) data from undifferentiated iPSCs and COs at 15 and 25 days of neural differentiation. Our analysis revealed abnormal expression of 235 genes in ARTHS across all three timepoints examined. Notably, we observed persistent dysregulation of genes such as CTSF, ZNF229, PCDHB12, and PAK3. Additionally, we found a consistent enrichment of PTBP1-target genes among the upregulated genes in ARTHS at all three stages assessed by RNA-seq. During neural differentiation, we identified 980 genes that consistently display aberrant transcription in ARTHS at both CO stages. These genes are enriched for genes involved in cell fate determination through modulation of cell-cycle dynamics (e.g. E2F family) and cell-adhesion molecules (e.g. PCDH genes). Our findings indicate that ARTHS COs exhibit slower downregulation of pluripotency and cell cycle genes compared to controls and that this delay led to an overrepresentation of cycling human neural progenitor markers during neural differentiation in ARTHS. Finally, matching the variable neurodevelopment phenotypes in ARTHS, we discovered that the aberrantly expressed genes in ARTHS are enriched for genes associated with Autism Spectrum Disorder and Epilepsy, with a subset showing isoform-specific dysregulation. Strikingly, the same PTBP1-target genes were enriched amongst the genes that display differential isoform usage in ARTHS. For the first time, we demonstrate that KAT6A mutations lead to a delay in repressing pluripotency and cell cycle genes during neural differentiation, suggesting that prolonged activation of these gene networks disrupts the temporal dynamics of human brain development in ARTHS.