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. Editor's summary: Down syndrome (DS) is characterized by intellectual disabilities and delays in brain development. In a pair of manuscripts, cortical development in DS has been unveiled at the molecular level using single-nucleus multiomic sequencing. Analyzing the neocortex at midgestation, Vuong et al. identified alterations in the speed of development of specific populations of neurons, including commissural/callosal and deep layer projection neurons. The neurons produced also showed abnormal specification. Risgaard et al. profiled the prefrontal cortex of DS juvenile brains and reported widespread dysregulation of chromatin accessibility and gene expression in pathways involved in synapse development, metabolism, and neuroinflammation, among others. Combined, the results of these studies provide valuable insights into alterations in brain development in DS (see the Perspective by Haydar and Li). —Mattia Maroso INTRODUCTION: Down syndrome (DS), caused by triplication of human chromosome 21 (Ts21), is the most common genetic cause of intellectual disability. Individuals with DS show deficits in learning, memory, and attention; delayed language and motor development; and atypical sensory processing. The early emergence of structural abnormalities in the neocortex and of cognitive defects suggests that corticogenesis is disrupted in DS. Yet the molecular and cellular mechanisms leading to changes in the developing DS brain remain to be elucidated. RATIONALE: Precise temporal and molecular processes driving cell type–specific gene expression programs govern the development of the human brain, a process not yet completely captured by either in vitro or animal models of DS. To address this, we leveraged single-nucleus multiomics (gene expression plus chromatin accessibility) in developing control (Ctrl) and Ts21 neocortex during the period of peak neurogenesis to characterize the cellular and molecular processes and the gene-regulatory mechanisms underpinning DS. RESULTS: We profiled neocortex from a cohort of 26 Ctrl and Ts21 donors from gestation weeks (GW) 13 to 23 using paired single-nucleus multiomics to capture gene expression and regions of open chromatin across 113,000 nuclei. We uncovered altered cell composition in the Ts21 neocortex, including a reduction in progenitors and misspecification of excitatory neurons. The neurogenic timeline was accelerated in Ts21, with increased commitment of newborn neurons to the upper layer intratelencephalic (IT) neuron fate at the expense of deep layer corticothalamic (CT) neurons. We then systematically assessed gene expression and coexpression networks altered in Ts21 to identify molecular pathways underlying these cellular changes. This revealed widespread gene dysregulation encompassing proliferative and metabolic pathways involved in maintaining the progenitor pool, as well as aberrant expression of pro-IT gene programs in newborn and deep layer neurons. Altered cell composition, timing of neurogenesis, and molecular programs were recapitulated by using primary human neural progenitor cells derived from Ctrl and Ts21 donors. We used gene expression to examine intercellular interactions, finding proneurogenic changes in the neurovascular niche and early evidence of microglial activation. We then combined paired gene expression and chromatin accessibility to identify gene-regulatory networks and the transcription factors controlling gene programs altered in Ts21. Among these we identified a human chromosome 21 (HSA21)–encoded TF, BACH1, as an activator of pro-IT programs. We leveraged new knowledge of these gene expression and regulatory changes to understand the molecular mechanisms shared between DS and other neurodevelopmental and psychiatric disorders with cognitive impairment, identifying deep layer neurons and specification programs as a point of shared vulnerability. CONCLUSION: Our study reveals the neurodevelopmental changes occurring in the Ts21 neocortex and defines the gene-regulatory mechanisms driving them. Our findings offer new insight into the earliest steps leading to DS and provide a foundation for future therapeutic targets. Defining molecular mechanisms regulating altered neurogenesis and specification in the developing Ts21 neocortex.: We uncovered an accelerated neurogenic timeline and altered excitatory neuron specification leading to increased intratelencephalic (IT) neurons at the expense of corticothalamic (CT) neurons in the developing Ts21 neocortex (top). We used systematic analyses of paired gene expression and chromatin accessibility to define changes in differentiation trajectory, gene expression programs, and regulatory networks driving neurodevelopmental changes and identified genetic mechanisms shared among neurodevelopmental disorders (NDDs) (bottom). ASD, autism spectrum disorder; OxPhos, oxidative phosphorylation; RG-vasc., radial glia–vasculature signaling. [ABSTRACT FROM AUTHOR]