The 16p11.2 gene QPRT, encoding a key enzyme of the kynurenine pathway, has been linked to neurodevelopmental disorders including autism spectrum disorder (ASD). To investigate its role in early human brain development, we inhibited QPRT in stem cell-derived cerebral organoids. QPRT inhibition resulted in reduced organoid size, driven by premature neural differentiation resulting in depleted progenitor populations. Single-cell transcriptomics revealed an excitation/inhibition imbalance, with reduced excitatory and increased inhibitory neuron populations. We observed metabolic stress signatures, including pseudo-hypoxia, oxidative stress, and mitochondrial dysfunction, likely linked to NAD⁺ depletion and QUIN accumulation following QPRT inhibition. Notably, downregulation of LHX2 and PRDX1 may underlie impaired neural patterning and excitotoxic vulnerability. In addition, we report astrocytic and radial glia dysfunctions, indicating broad effects across multiple cell types. Disease gene enrichment analyses showed significant overlap with ASD-associated genes, especially during early differentiation. These findings suggest the loss or reduction of QPRT to shift neural development and neuronal homeostasis towards an imbalance in excitatory and inhibitory neuronal populations, a mechanism previously associated with neurodevelopmental disorders.

Prepublication of the main manuscript is available at bioRxiv
https://doi.org/10.1101/2025.09.08.673916

Human embryonic stem cells (H9) were differentiated towards cerebral organoids
From d3 on, cells were treated with pH-matched media containing 5mM Phthalic acid and compared to cells not treated with Phthalic acid (0mM)

Single Cell Sequencing was performed at d112
Datasets:

230719005_auto_matrix_10X.tar contains 10X barcode, gene and matrix for sample 0mM_PA_d112
230719006_auto_matrix_10X.tar contains 10X barcode, gene and matrix for sample 5mM_PA_d112
scRNA_Haslinger_PA_Seurat.rds is the respective Seurat object (v5)

Bulk Sequencing was performed at d5, d10, d17, d40, d80
Datasets:

Bulk_PA_timeseries_all_SampleAllocation.txt contains the Sample IDand the corresponding RNASeq Lane ID
Bulkdata_Countmatrix.rds is the R dataframe with all counts per genes (entrez ID)