Can a Comparative Description of the Developing Human and Macaque Prefrontal Cortex Provide Deep Insight?

The development of the human prefrontal cortex, which requires the implementation of tightly regulated spatial and temporal gene expression programs (Herring et al., Sydnor et al., and Molnar et al.), has provided humans with superior cognitive abilities compared to non-human primates (Sousa et al., Baldauf & Desimone, and Gabrieli et al.). Comparative research has defined spatiotemporal transcriptomic profiles in human and macaque brains at prenatal and adult stages (Zhu et al., Bakken et al., Zhong et al., and Nowakowski et al.); however, we still lack a complete understanding of the prefrontal cortex´s postnatal development, which may provide clues regarding how higher cognitive function emerged and how neurodevelopmental disorders develop.

A team of researchers led by Lixin Cai (Peking University), Suijuan Zhong, Xiaoqun Wang, and Qian Wu (Beijing Normal University) sought to create a comparative repository of single-cell gene expression, chromatin accessibility, and spatial transcriptomic data covering human and macaque postnatal prefrontal cortex development to reveal conserved and species-specific features of tissue maturation. Their recent Nature Neuroscience article now provides deep insight into human-specific regulatory programs associated with postnatal cortical maturation and coordinated neuronal and glial development, with broad implications for our understanding of cognition and the development of neurodevelopmental disorders (Zhang et al.).

While this study focused on single-cell transcriptomics and chromatin accessibility to understand regulatory programs, could simultaneous histone modification and transcriptomic profiling in the same single cell have provided more insight into postnatal prefrontal cortex development? ]Paired-Tag](https:/epigenometech.com/products/droplet-paired-tag.html) technology from Epigenome Technologies generates joint epigenetic and transcriptomic profiles at single-cell resolution and detects histone modifications and RNA transcripts in individual nuclei with efficiency comparable to single-nucleus RNA-seq/ChIP-seq assays.

Altered Prefrontal Cortex Development: The Driving Force Behind Cognition and Disease Development in Humans?

The authors first combined single-nucleus RNA-seq, single-nucleus ATAC−seq, and single-cell spatial transcriptomic profiles spanning prenatal and postnatal stages in humans (gestational week to 25 years old) and macaques (embryonic day 90 to 4 years old) to establish single-cell profiles of the developing postnatal prefrontal cortex with cell-type and spatial localization information. While analyzing this dataset revealed the conservation of major cell types, they also noted an extended period of postnatal prefrontal cortex development, which associated with distinctive gene expression profiles and gene regulatory features, in humans compared to macaques. The authors posit that this prolonged period of “plasticity” in humans shapes cortical morphology and supports behaviors such as learning and memory. Of particular interest, the analysis of differentially expressed genes and differentially accessible chromatin regions in each major cell type revealed human-specific differentially expressed genes linked to higher-level cognitive functions and the development of specific neurological disorders. These data also helped define critical windows of postnatal prefrontal cortex maturation in humans, reporting a peak in synapse formation in infancy, synapse pruning and cell death in toddlers and preschoolers, and circuit wiring in preschoolers and children. Furthermore, observed increases and decreases in prefrontal cortex thickness agreed with imaging evidence, which identified a peak of gray matter volume at around 6 years of age (Bethlehem, Seidlitz, and White et al.).

The subsequent systematic examination of neuron diversity and heterogeneity during postnatal prefrontal cortex development in humans and macaques revealed that the human-specific diversification of neuron subtypes, their sublaminar organization, and gene regulatory programs together underpinned the observed protracted period of postnatal development and maturation of the prefrontal cortex and support the associated cognitive functions. Further analysis of human neurons also suggested that human prefrontal cortex development occurred in the context of a prolonged period of synaptogenesis, layer-specific expression of neurotransmitter receptors, and delayed maturation of neural activity, highlighting an extended period of functional refinement of cortical circuits in humans relative to macaques. Of note, the study highlighted more pronounced differences between species in excitatory than in inhibitory neuron subtypes, as measured by transcriptomic similarity.

The authors next sought to explore the world of glial cells, given that i) postnatal prefrontal complex development involves intricate coordination between neurons and glia and that ii) strengthened glia–neuron interactions during the early postnatal years coincide with developmental windows for learning, memory, and language acquisition. Here, they discovered that human prefrontal cortex astrocytes and oligodendrocytes retained their proliferative capacity well into the postnatal period (compared to macaques), thereby facilitating neuronal maturation through distinct ligand–receptor interactions, and identified CD44 and IGFBP5 (Insulin-like growth factor binding protein 5) as critical regulators of human astrocyte progenitor proliferation.

Finally, the authors sought to explore the development of neurological and neuropsychiatric disorders by combining single-nucleus RNA-seq and single-nucleus ATAC−seq data to identify transcription factor families enriched across human and macaque cell types and weighted gene co-expression network analysis; excitingly, this approach revealed that i) human-specific transcriptional regulation by the CUT and Fork transcription factor families functioned to shape postnatal dendritic development, and that ii) the cell-type-specific and window-specific enrichment of disorder-associated genes underlay vulnerabilities to the development of specific neurological and neuropsychiatric disorders.

Could Paired-Tag Provide Yet More Insight into Human Prefrontal Cortex Development?

Overall, this exciting study combined transcriptomic and epigenetic data to elucidate the cellular and molecular features of human prefrontal cortex development and to identify human-specific characteristics that may contribute to the advanced cognitive functions humans are blessed (or cursed?) with, and that may help us understand many neurological and neuropsychiatric disorders. Overall, the data support a model in which a prolonged period of prefrontal cortex maturation is associated with higher levels of cognition but may also increase susceptibility to neurodevelopmental and neuropsychiatric disorders.

The implementation of Paired-Tag technology from Epigenome Technologies, which generates joint epigenetic and transcriptomic profiles at single-cell resolution and detects histone modifications and RNA transcripts in individual nuclei with efficiency comparable to single-nucleus RNA-seq/ChIP-seq assays, has the potential to provide deeper insight into such research aims. What more could the simultaneous single-cell analysis of histone modification and transcriptomic profiles tell us about human prefrontal cortex development?