A single-cell multiomic analysis identifies molecular and gene-regulatory mechanisms dysregulated in developing Down syndrome neocortex.

Down syndrome (DS) is the most common genetic cause of intellectual disability, yet the cellular and molecular mechanisms driving this developmental disorder remain unclear. In this study, we profiled human mid-gestation neocortex with snMultiomics across 26 donors. We observed a reduction in neural progenitors and corticothalamic neurons and an increase of intratelencephalic neurons, accompanied by accelerated neuronal specification. We uncovered widespread changes in gene expression, chromatin accessibility, and cell interaction networks affecting neurogenesis, specification, and maturation; and in gene-regulatory networks directing these processes, including those downstream of human chromosome 21 (HSA21)-encoded genes. We identified cell-specific molecular pathways shared with other neurodevelopmental disorders and enrichment of genome-wide association study signals in DS-altered chromatin. Together, our data revealed a cascade of molecular dysregulation outlining the earliest steps in DS, providing a foundation for future therapeutic targets.