KAT6Amutations drive transcriptional dysregulation of cell cycle and Autism risk genes in an Arboleda-Tham Syndrome cerebral organoid model

Abstract

AbstractArboleda-Tham Syndrome (ARTHS, OMIM#616268) is a rare neurodevelopmental disorder caused byde novomutations inKAT6A. 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 howKAT6Amutations disruptin vitrobrain development using induced pluripotent stem cells (iPSCs) and cerebral organoids (COs) derived from ARTHS patients harboringKAT6Anonsense 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 asCTSF,ZNF229,PCDHB12, andPAK3. Additionally, we found a consistent enrichment ofPTBP1-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.E2Ffamily) and cell-adhesion molecules (e.g.PCDHgenes). 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 samePTBP1-target genes were enriched amongst the genes that display differential isoform usage in ARTHS. For the first time, we demonstrate thatKAT6Amutations 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.