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Suzuki, I. K.

Publications and source records attributed to Suzuki, I. K..

6 recordsLinked to original sources

Human-specific NOTCH2NL promotes astrogenesis by expanding proliferative glial progenitor states

The human cerebral cortex contains an unusually large number of glial cells, particularly astrocytes, yet the developmental and genetic mechanisms underlying their expansion remain poorly understood. While human-specific genes have been shown to promote neuronal production during cortical development, whether such genes also regulate gliogenesis has remained unclear. Here, we identify a previously unrecognized role for the human-specific gene family NOTCH2NL in promoting astrocyte-lineage expansion. Reanalysis of human fetal single-cell transcriptomic datasets revealed that NOTCH2NL is robustly expressed along the gliogenic trajectory, from glial intermediate progenitor cells to astrocytes. Functional perturbations in a human astrocyte culture system demonstrated that NOTCH2NL is both required and sufficient for astrocyte proliferation. In vivo overexpression of NOTCH2NLB in the developing mouse cortex shifted progenitor output toward the astrocyte lineage, increasing the astrocyte-to-neuron ratio from the early postnatal period through adulthood. This phenotype was associated with an expansion of proliferative glial progenitors around birth. Single-nucleus transcriptomic profiling further showed that NOTCH2NLB suppresses neuronal gene programs while activating transcriptional modules related to cell proliferation and cellular homeostasis during gliogenesis. Together, these findings indicate that human-specific NOTCH2NL acts at a conserved developmental decision point to amplify astrocyte production. Our study extends the function of NOTCH2NL beyond neurogenesis and suggests that human lineage-specific gene duplications can modulate gliogenesis, providing a developmental mechanism that may have contributed to the coordinated expansion of neuronal and glial populations in the human cortex.

developmental biology↗

Orthogonal Modes of Gene Expression Evolution Shape Human Neocortical Development and Disease Vulnerability

The neocortex is responsible for higher-order cognitive abilities such as language, abstract reasoning, and executive function--capacities that are particularly advanced in humans. To elucidate the molecular foundations of neocortical evolution in the human lineage, it is essential to examine how conserved gene repertoires have undergone expression changes relative to other mammals. The expression changes in conserved genes are widely regarded as key drivers of the phenotypic evolution of human-specific traits. In this study, we performed a comprehensive comparative single-cell transcriptomic analysis of fetal neocortical development across four mammalian species: human, macaque, mouse, and ferret. To validate human-specific expression changes, we further analyzed brain organoids derived from both human and chimpanzee stem cells. Genes exhibiting human-specific expression shifts were systematically classified along three orthogonal dimensions: overall expression level (Human Level Distinctive; HLD), temporal expression trend (Human Trend Distinctive; HTD), and differentiation lineage specificity (Human Differentiation trajectory Distinctive; HDD). HLD genes were frequently enriched for long introns and located near Human Accelerated Regions (HARs), and showed pronounced upregulation in humans. These genes were strongly associated with neurodevelopmental disorders such as autism spectrum disorder and developmental delay, as well as with megalencephaly and glioblastoma. HTD genes, in contrast, exhibited a unique pattern in humans, peaking early in development and subsequently declining--opposite to the steadily increasing trends observed in other species. These genes were significantly enriched for oxidative phosphorylation and ribosomal functions, pointing to a temporally restricted elevation in biosynthetic activity in early human corticogenesis. HDD genes displayed a marked shift in lineage-specific expression: cilia-related genes that are typically expressed in apical progenitors in non-human species were instead highly expressed in outer radial glia (oRGs) in humans. This spatial reorganization of ciliary gene activity suggests an oRG-specific adaptation in signaling architecture. Together, these results highlight the diversity of regulatory changes that have shaped human cortical development. Distinct classes of gene expression evolution--mediated in part by HARs--appear to have contributed not only to the expansion and increased complexity of the human neocortex, but also to its heightened vulnerability to neurodevelopmental and oncogenic pathologies. The identified human distinctive genes will be the target of future experimental verification to elucidate the precise molecular mechanisms regulating human-specific aspects of cortical development.

bioinformatics↗

Adaptive Evolution of Gene Regulatory Networks in Mammalian Neocortical Neurons

Mammals have evolved a plethora of adaptations that have enabled them to thrive in diverse environments. Among the most significant is the emergence of a more complex brain, exemplified by the dramatic transformation of the dorsal cortex from a single layer of excitatory projection neurons (ExNs) in ancestors to a multilayered cerebral neocortex enriched with diverse intratelencephalic (IT) and extratelencephalic (ET) ExN subtypes. These ExNs established specialized projection systems, such as the corticospinal tract and corpus callosum, enhancing brain connectivity and functionality. However, the evolutionary mechanisms underlying these mammalian-specific adaptations remain elusive. By comparing the landscape of gene expression and cis-regulatory elements (CREs) in mouse ExN subtypes and by cross-species examination of mammalian and non-mammalian CREs, we identified mammalian-specific CREs and expression patterns. The mammalian-specific CREs include a subset bound by ZBTB18 that are associated with genes defining IT and ET subtypes and connectivity. Both ZBTB18 and these target genes have previously been implicated in intellectual disability and autism. Deletion of Zbtb18 in mouse ExNs dysregulated target gene expression, reduced molecular diversity, diminished corticospinal and callosal projections, and increased intrahemispheric cortico-cortical association projections to the prefrontal cortex, resembling features of non-mammalian dorsal pallium. Interestingly, ZBTB18 binding motifs are highly enriched in callosally projecting IT-biased CREs, where they show higher conservation specifically in mammals. This study uncovers critical components and mammalian-specific evolutionary adaptations within a regulatory node essential for neocortical ExN identity and connectivity, with implications for neurodevelopmental and neuropsychiatric disorders.

neuroscience↗

Non-uniform temporal scaling of neurogenesis for species-specific dosing of cortical excitatory subtypes

Mammals share a laminar cerebral cortex, with excitatory neuron subtypes organized in distinct layers. Although this framework is conserved, subtype balance varies markedly between species due to unknown mechanisms. This study shows that species-specific neuronal composition arises from non-uniform scaling of the temporal dynamics of neurogenesis. Comparative histology of eight mammalian species revealed a significant, rat-specific expansion of the cortical deeper layer (DL). This species difference results from a specific extension of the early neurogenetic phase for DL neuron production before transitioning to the upper layer (UL) in rats, as confirmed by birthdating and single-cell transcriptomics. The duration of DL neuron production is regulated by a genetic program controlling progenitor aging, including canonical Wnt signaling. Comparative single-cell transcriptomics revealed that cortical progenitors in rats exhibit significantly elevated Wnt ligand expression. Thus, while sequential cortical neurogenesis is conserved, its progression is non-uniformly scaled in each species. Such precise heterochronic fine-tuning allows evolutionary refinement of cellular configuration without drastic remodeling of the conserved corticogenesis program. TeaserDifferential temporal progression of neural progenitor program contributes to species-specific cellular composition of mammalian cerebral cortex

developmental biology↗

Long-read sequencing identifies GGC repeat expansion in human-specific NOTCH2NLC associated with neuronal intranuclear inclusion disease

Neuronal intranuclear inclusion disease (NIID) is a progressive neurodegenerative disease characterized by eosinophilic hyaline intranuclear inclusions in neuronal and somatic cells. The wide range of clinical manifestations in NIID makes ante-mortem diagnosis difficult 1-8, but skin biopsy realized its ante-mortem diagnosis 9,10 and many NIID cases have been diagnosed by skin biopsy11,12. Most cases of NIID are sporadic, but several familial cases are known. Using a large NIID family, we conducted linkage mapping, found a 58.1-Mb linked-region at 1p22.1-q21.3 with a maximum logarithm of odds (LOD) score of 4.21, and successfully identified a GGC repeat expansion in the 5 portion of NOTCH2NLC in all affected members by long-read sequencing, but not in unaffected members. We further found the similar expansions in additional 8 unrelated families with NIID as well as 39 sporadic NIID patients. Repeat-primed PCR consistently detected the GGC repeat expansion in all the familial and sporadic patients diagnosed by skin biopsy, but never in unaffected family members nor 200 controls. This shows that pathogenic changes in a human-specific gene evolutionarily generated by segmental duplication indeed causes a human disease.

genetics↗

Hominin-specific NOTCH2 paralogs expand human cortical neurogenesis through regulation of Delta/Notch interactions.

The human cerebral cortex has undergone rapid expansion and increased complexity during recent evolution. Hominid-specific gene duplications represent a major driving force of evolution, but their impact on human brain evolution remains unclear. Using tailored RNA sequencing (RNAseq), we profiled the spatial and temporal expression of Hominid-specific duplicated (HS) genes in the human fetal cortex, leading to the identification of a repertoire of 36 HS genes displaying robust and dynamic patterns during cortical neurogenesis. Among these we focused on NOTCH2NL, previously uncharacterized HS paralogs of NOTCH2. NOTCH2NL promote the clonal expansion of human cortical progenitors by increasing self-renewal, ultimately leading to higher neuronal output. NOTCH2NL function by activating the Notch pathway, through inhibition of Delta/Notch interactions. Our study uncovers a large repertoire of recently evolved genes linking genomic evolution to human brain development, and reveals how hominin-specific NOTCH paralogs may have contributed to the expansion of the human cortex.

developmental biology↗