A distinct expression profile in the cerebellum and striatum for genes under selection within introgression deserts

Analyses of ancient DNA from extinct hominins have provided unique insights into the complex evolutionary history of Homo sapiens, intricately related to that of the Neanderthals and the Denisovans as revealed by several instances of admixture events. These analyses have also allowed the identification of introgression deserts: genomic regions in our species that are depleted of `archaic' haplotypes. The presence of genes like FOXP2 in these deserts has been taken to be suggestive of brain-related functional differences between Homo species. Here, we seek a deeper characterization of these regions, taking into account signals of positive selection in our lineage. Analyzing publicly available transcriptomic data from the human brain at different developmental stages, we found that structures outside the cerebral neocortex, and especially the cerebellum and the striatum at prenatal stages, show the most divergent transcriptomic profiles when considering genes under positive selection within introgression deserts.

Introduction

An introduction is provided to neurons; computation by biologically plausible networks of neurons; the representation of information in the brain; the functions of different brain areas; and the structure and connectivity of the cerebral neocortex.

Comprehensive characterization of migration profiles of murine cerebral cortical neurons during development using FlashTag labeling

SummaryIn mammalian cerebral neocortex, different regions have different cytoarchitecture, neuronal birthdates and functions. In most regions, neuronal migratory profiles have been speculated similar to each other based on observations using thymidine analogues. Few reports investigated regional migratory differences from mitosis at the ventricular surface. Here, in mice, we applied FlashTag technology, in which dyes are injected intraventricularly, to describe migratory profiles. We revealed a mediolateral regional difference in migratory profiles of neurons that is dependent on the developmental stages, e.g., neurons labeled at E12.5-15.5 reached their destination earlier dorsomedially than dorsolaterally even where there were underlying ventricular surfaces, reflecting sojourning below the subplate. This difference was hardly recapitulated by thymidine analogues, which visualize neurogenic gradient, suggesting biological significance different from neurogenic gradient. These observations advance understanding of cortical development, portraying strength of FlashTag in studying migration, and are thus a resource for studies of normal and abnormal neurodevelopment.

Hominini-Specific Regulation of CBLN2 Increases Prefrontal Synaptogenesis

The similarities and differences between nervous systems of various species result from developmental constraints and specific adaptations 1-4. Comparative analyses of the prefrontal cortex (PFC), a region of the cerebral cortex involved in higher-order cognition and complex social behaviors, have identified confirmed and putative human-specific structural and molecular changes 4-8. For example, one crucial specialization involves the anterior-posterior gradient in synaptic density, with a disproportionately higher number of dendritic spines specifically in the human PFC compared to other analyzed primates 5. These changes are likely mediated by divergence in spatio-temporal patterns of gene expression 9-17, which are prominent in the mid-fetal human cerebral neocortex 15,18-20. Analyzing developmental human and macaque brain transcriptomic data 15,20, we identified a transient PFC- and laminar-specific upregulation of the gene encoding cerebellin 2 (CBLN2), a neurexin (NRXN) and glutamate receptor delta (GRID/GluD)-associated synaptic organizer 21-27, in human mid-fetal development coinciding with the initiation of synaptogenesis. Moreover, we show that this difference in expression level and laminar distribution of CBLN2, is due to Hominini-specific deletions affecting SOX5 binding sites within a retinoic acid-responsive CBLN2 enhancer. In situ genetic humanization of the mouse Cbln2 enhancer drives increased and ectopic laminar Cbln2 expression and promotes glutamatergic and GABAergic synaptogenesis specifically in the PFC. These findings identify a putative genetic and molecular basis for the disproportionately increased connectivity in the Hominini PFC and suggest a developmental mechanism linking dysfunction of the NRXN-GRID-CBLN2 complex, to the pathogenesis of neuropsychiatric disorders.

Sex-Dependent Effects of Bmal1-Deficiency on Mouse Cerebral Cortex Infarction in Response to Photothrombotic Stroke

Stroke is a leading cause of disability and death worldwide. There is increasing evidence that occurrence of ischemic stroke is affected by circadian system and sex. However, little is known about the effect of these factors on structural recovery after ischemic stroke. Therefore, we studied infarction in cerebral neocortex of male and female mice with deletion of the clock gene Bmal1 (Bmal1−/−) after focal ischemia induced by photothrombosis (PT). The infarct core size was significantly smaller 14 days (d) as compared to seven days after PT, consistent with structural recovery during the sub-acute phase. However, when sexes were analyzed separately 14 days after PT, infarct core was significantly larger in wild-type (Bmal1+/+) female as compared to male Bmal1+/+ mice, and in female Bmal1+/+, as compared to female Bmal1−/− mice. Volumes of reactive astrogliosis and densely packed microglia closely mirrored the size of infarct core in respective groups. Estradiol levels were significantly higher in female Bmal1−/− as compared to Bmal1+/+ mice. Our data suggests a sex-dependent effect and an interaction between sex and genotype on infarct size, the recruitment of astrocytes and microglia, and a relationship of these cells with structural recovery probably due to positive effects of estradiol during the subacute phase.

Mathematical modelling of cortical neurogenesis reveals that the founder population does not necessarily scale with neuronal output

The mammalian cerebral neocortex has a unique structure, composed of layers of different neuron types, interconnected in a stereotyped fashion. While the overall developmental program seems to be conserved, there are divergent developmental factors generating cortical diversity amongst mammalian species. In terms of cortical neuronal numbers some of the determining factors are the size of the founder population, the duration of cortical neurogenesis, the proportion of different progenitor types, and the fine-tuned balance between self-renewing and differentiative divisions. We develop a mathematical model of neurogenesis that, accounting for these factors, aims at explaining the high diversity in neuronal numbers found across mammalian species. By framing our hypotheses in rigorous mathematical terms, we are able to identify paths of neurogenesis that match experimentally observed patterns in mouse, macaque and human. Additionally, we use our model to identify key parameters that would particularly benefit from accurate experimental investigation. We find that the timing of a switch in favor of symmetric neurogenic divisions produces the highest variation in cortical neuronal numbers. Surprisingly, in our model the increase in cortical neuronal numbers does not necessarily reflect a larger size of founder population, a prediction that identified a specific need for experimental quantifications.