GABA/Glutamate neuron differentiation imbalance and increased AKT/mTOR signalling in CNTNAP2 ^-/- cerebral organoids

We developed a human cerebral organoid model derived from induced pluripotent stem cells (iPSCs) with targeted genome editing to abolish protein expression of the Contactin Associated Protein-like 2 ( CNTNAP2) autism spectrum disorder (ASD) risk gene, mimicking loss-of-function mutations seen in patients. CNTNAP2 ^-/- cerebral organoids displayed accelerated cell cycle, ventricular zone disorganisation and increased cortical folding. Proteomic analysis revealed disruptions in Glutamatergic/GABAergic synaptic pathways and neurodevelopment, highlighting increased protein expression of corticogenesis and neurodevelopment-related genes such as Forkhead box protein G1 (FOXG1) and Paired box 6 (PAX6). Transcriptomic analysis revealed differentially expressed genes (DEG) belonging to inhibitory neuron-related gene networks. Interestingly, there was a weak correlation between the transcriptomic and proteomic data, suggesting nuanced translational control mechanisms. Along these lines we found upregulated Protein Kinase B (Akt)/mechanistic target of rapamycin (mTOR) signalling in CNTNAP2 ^-/- organoids. Spatial transcriptomics analysis of CNTNAP2 ^-/- ventricular-like zones demonstrated pervasive changes in gene expression, particularly in PAX6 ^- cells, implicating upregulation of cell cycle regulation pathways, synaptic and Glutamatergic/GABAergic pathways. We noted a significant overlap of all D30 cerebral organoids ‘omics datasets with an idiopathic ASD (macrocephaly) iPSC-derived telencephalic organoids DEG dataset, where FOXG1 was upregulated. Moreover, we detected increased Glutamate decarboxylase 1 (GAD1) and decreased T-Box Brain Transcription Factor 1 (TBR1) expressing cells, suggesting altered GABAergic/Glutamatergic neuron development. These findings potentially highlight a shared mechanism in the early cortical development of various forms of ASD, further elucidate the role of CNTNAP2 in ASD pathophysiology and cortical development and pave the way for targeted therapies using cerebral organoids as preclinical models.