Development and Arealization of the Cerebral Cortex

Generation of Neural Organoids and Their Application in Disease Modeling and Regenerative Medicine

The complexity and precision of the human nervous system have posed significant challenges for researchers seeking suitable models to elucidate refractory neural disorders. Traditional approaches, including monolayer cell cultures and animal models, often fail to replicate the intricacies of human neural tissue. The advent of organoid technology derived from stem cells has addressed many of these limitations, providing highly representative platforms for studying the structure and function of the human embryonic brain and spinal cord. Researchers have induced neural organoids with regional characteristics by mimicking morphogen gradients in neural development. Recent advancements have demonstrated the utility of neural organoids in disease modeling, offering insights into the pathophysiology of various neural disorders, as well as in the field of neural regeneration. Developmental defects in neural organoids due to the lack of microglia or vascular systems are addressed. In addition to induction methods, microfluidics is used to simulate the dynamic physiological environment; bio-manufacturing technologies are employed to regulate physical signaling and shape the structure of complex organs. These technologies further expand the construction strategies and application scope of neural organoids. With the emergence of new material paradigms and advances in AI, new possibilities in the realm of neural organoids are witnessed.

The patient-specific mouse model with Foxg1 frameshift mutation provides insights into the pathophysiology of FOXG1 syndrome

Single allelic mutations in the FOXG1 gene lead to FOXG1 syndrome (FS). To understand the pathophysiology of FS, which vary depending on FOXG1 mutation types, patient-specific animal models are critical. Here, we report a patient-specific Q84Pfs heterozygous (Q84Pfs-Het) mouse model, which recapitulates various FS phenotypes across cellular, brain structural, and behavioral levels. Q84Pfs-Het cortex shows dysregulations of genes controlling cell proliferation, neuronal projection and migration, synaptic assembly, and synaptic vesicle transport. The Q84Pfs allele produces the N-terminal fragment of FOXG1 (Q84Pfs protein) in Q84Pfs-Het mouse brains, which forms intracellular speckles, interacts with FOXG1 full-length protein, and triggers the sequestration of FOXG1 to distinct subcellular domains. Q84Pfs protein promotes the radial glial cell identity and suppresses neuronal migration in the cortex. Our study uncovers the role of the FOXG1 fragment from FS-causing FOXG1 variants and identifies the genes involved in FS-like cellular and behavioral phenotypes, providing insights into the pathophysiology of FS.

Spatial transcriptomics reveals human cortical layer and area specification

The human cerebral cortex is composed of six layers and dozens of areas that are molecularly and structurally distinct1-4. Although single-cell transcriptomic studies have advanced the molecular characterization of human cortical development, a substantial gap exists owing to the loss of spatial context during cell dissociation5-8. Here we used multiplexed error-robust fluorescence in situ hybridization (MERFISH)9, augmented with deep-learning-based nucleus segmentation, to examine the molecular, cellular and cytoarchitectural development of the human fetal cortex with spatially resolved single-cell resolution. Our extensive spatial atlas, encompassing more than 18 million single cells, spans eight cortical areas across seven developmental time points. We uncovered the early establishment of the six-layer structure, identifiable by the laminar distribution of excitatory neuron subtypes, 3 months before the emergence of cytoarchitectural layers. Notably, we discovered two distinct modes of cortical areal specification during mid-gestation: (1) a continuous, gradual transition observed across most cortical areas along the anterior-posterior axis and (2) a discrete, abrupt boundary specifically identified between the primary (V1) and secondary (V2) visual cortices as early as gestational week 20. This sharp binary transition in V1-V2 neuronal subtypes challenges the notion that mid-gestation cortical arealization involves only gradient-like transitions6,10. Furthermore, integrating single-nucleus RNA sequencing with MERFISH revealed an early upregulation of synaptogenesis in V1-specific layer 4 neurons. Collectively, our findings underscore the crucial role of spatial relationships in determining the molecular specification of cortical layers and areas. This study establishes a spatially resolved single-cell analysis paradigm and paves the way for the construction of a comprehensive developmental atlas of the human brain.

Tracking single-cell evolution using clock-like chromatin accessibility loci

Single-cell chromatin accessibility sequencing (scATAC-seq) reconstructs developmental trajectory by phenotypic similarity. However, inferring the exact developmental trajectory is challenging. Previous studies showed age-associated DNA methylation (DNAm) changes in specific genomic regions, termed clock-like differential methylation loci (ClockDML). Age-associated DNAm could either result from or result in chromatin accessibility changes at ClockDML. As cells undergo mitosis, the heterogeneity of chromatin accessibility on clock-like loci is reduced, providing a measure of mitotic age. In this study, we developed a method, called EpiTrace, that counts the fraction of opened clock-like loci from scATAC-seq data to determine cell age and perform lineage tracing in various cell lineages and animal species. It shows concordance with known developmental hierarchies, correlates well with DNAm-based clocks and is complementary with mutation-based lineage tracing, RNA velocity and stemness predictions. Applying EpiTrace to scATAC-seq data reveals biological insights with clinically relevant implications, ranging from hematopoiesis, organ development, tumor biology and immunity to cortical gyrification.

Predicting progression from MCI to dementia using cortical disarray measurement from diffusion MRI

BACKGROUND

This study evaluates the capability of cortical microstructural measures from diffusion magnetic resonance imaging (MRI) to predict progression from mild cognitive impairment (MCI) to dementia, compared to commonly used macrostructural measures. Identification of high-risk individuals can support both clinical practice and trials.

METHODS

Structural and diffusion MRI scans of 826 participants from the National Alzheimer's Coordinating Center (NACC) were analyzed to extract macrostructural measures and three minicolumn-related diffusivity metrics: AngleR, PerpPD+, and ParlPD. Kaplan-Meier survival analysis was used to investigate time to progression to dementia, with participants stratified by biomarker metrics.

RESULTS

Cortical diffusivity (PerpPD+ in medial-temporal and connected regions) outperformed hippocampal volume, cortical volume, and cortical thickness in Kaplan-Meier survival analysis, predicting faster conversion to dementia.

DISCUSSION

Cortical microstructural measures from diffusion MRI provide powerful biomarkers for predicting progression from MCI to dementia, offering enhanced prognostic capabilities that could support earlier intervention strategies in clinical practice and improve the power of clinical trials.

HIGHLIGHTS

Cortical minicolumn-related diffusivity metrics measure neurodegeneration. We compare the predictive value of magnetic resonance imaging (MRI) measures for mild cognitive impairment to dementia progression. Microstructural cortical disarray outperforms macrostructural markers. These results support using diffusion MRI biomarkers to identify and monitor at-risk patients.

The generalizability of cortical area parcellations across early childhood

The cerebral cortex consists of distinct areas that develop through intrinsic embryonic patterning and postnatal experiences. Accurate parcellation of these areas in neuroimaging studies improves statistical power and cross-study comparability. Given significant brain changes in volume, microstructure, and connectivity during early life, we hypothesized that cortical areas in 1- to 3-year-olds would differ markedly from neonates and increasingly resemble adult patterns as development progresses. Here, we parcellated the cerebral cortex into putative areas using local functional connectivity (FC) gradients in 92 toddlers at 2 years old. We demonstrate high reproducibility of these cortical areas across 1- to 3-year-olds in two independent datasets. The area boundaries in 1- to 3-year-olds were more similar to those in adults than those in neonates. While the age-specific group area parcellation better fits the underlying FC in individuals during the first 3 years, adult area parcellations still have utility in developmental studies, especially in children older than 6 years. Additionally, we provide connectivity-based community assignments of the area parcels, showing fragmented anterior and posterior components based on the strongest connectivity, yet alignment with adult systems when weaker connectivity was included.

Fate plasticity of interneuron specification

Neuronal subtype generation in the mammalian central nervous system is governed by competing genetic programs. The medial ganglionic eminence (MGE) produces two major cortical interneuron (IN) populations, somatostatin (Sst) and parvalbumin (Pvalb), which develop on different timelines. The extent to which external signals influence these identities remains unclear. Pvalb-positive INs are crucial for cortical circuit regulation but challenging to model in vitro. We grafted mouse MGE progenitors into diverse 2D and 3D co-culture systems, including mouse and human cortical, MGE, and thalamic models. Strikingly, only 3D human corticogenesis models promoted efficient, non-autonomous Pvalb differentiation, characterized by upregulation of Pvalb maturation markers, downregulation of Sst-specific markers, and the formation of perineuronal nets. Additionally, lineage-traced postmitotic Sst-positive INs upregulated Pvalb when grafted onto human cortical models. These findings reveal unexpected fate plasticity in MGE-derived INs, suggesting that their identities can be dynamically shaped by the environment.

Early Development and Co-Evolution of Microstructural and Functional Brain Connectomes: A Multi-Modal MRI Study in Preterm and Full-Term Infants

Functional networks characterized by coherent neural activity across distributed brain regions have been observed to emerge early in neurodevelopment. Synchronized maturation across regions that relate to functional connectivity (FC) could be partially reflected in the developmental changes in underlying microstructure. Nevertheless, covariation of regional microstructural properties, termed "microstructural connectivity" (MC), and its relationship to the emergence of functional specialization during the early neurodevelopmental period remain poorly understood. We investigated the evolution of MC and FC postnatally across a set of cortical and subcortical regions, focusing on 45 preterm infants scanned longitudinally, and compared to 45 matched full-term neonates as part of the developing Human Connectome Project (dHCP) using direct comparisons of grey-matter connectivity strengths as well as network-based analyses. Our findings revealed a global strengthening of both MC and FC with age, with connection-specific variability influenced by the connection maturational stage. Prematurity at term-equivalent age was associated with significant connectivity disruptions, particularly in FC. During the preterm period, direct comparisons of MC and FC strength showed a positive linear relationship, which seemed to weaken with development. On the other hand, overlaps between MC- and FC-derived networks (estimated with Mutual Information) increased with age, suggesting a potential convergence towards a shared underlying network structure that may support the co-evolution of microstructural and functional systems. Our study offers novel insights into the dynamic interplay between microstructural and functional brain development and highlights the potential of MC as a complementary descriptor for characterizing brain network development and alterations due to perinatal insults such as premature birth.

Cell2fate infers RNA velocity modules to improve cell fate prediction

RNA velocity exploits the temporal information contained in spliced and unspliced RNA counts to infer transcriptional dynamics. Existing velocity models often rely on coarse biophysical simplifications or numerical approximations to solve the underlying ordinary differential equations (ODEs), which can compromise accuracy in challenging settings, such as complex or weak transcription rate changes across cellular trajectories. Here we present cell2fate, a formulation of RNA velocity based on a linearization of the velocity ODE, which allows solving a biophysically more accurate model in a fully Bayesian fashion. As a result, cell2fate decomposes the RNA velocity solutions into modules, providing a biophysical connection between RNA velocity and statistical dimensionality reduction. We comprehensively benchmark cell2fate in real-world settings, demonstrating enhanced interpretability and power to reconstruct complex dynamics and weak dynamical signals in rare and mature cell types. Finally, we apply cell2fate to the developing human brain, where we spatially map RNA velocity modules onto the tissue architecture, connecting the spatial organization of tissues with temporal dynamics of transcription.

Spontaneous mesoscale calcium dynamics reflect the development of the modular functional architecture of the mouse cerebral cortex

The mature cerebral cortex operates through the segregation and integration of specialized functions to generate complex cognitive states. In the mouse, the anatomical and functional correlates of this organization arise during the perinatal period and are critically shaped by neural activity. Understanding how early activity patterns distribute, interact, and generate large-scale cortical dynamics is essential to elucidate the proper development of the cortex. Here, we investigate spontaneous mesoscale cortical dynamics during the first two postnatal weeks by performing wide-field calcium imaging in GCaMP6s transgenic mice. Our results demonstrate a marked change in the spatiotemporal features of spontaneous cortical activity across fine stages of postnatal development. Already after birth, the cortical hemisphere presents a primordial macroscopic organization, which undergoes a steady refinement based on the parcellation of the cortex. As calcium activity transitions from large, widespread events to swift waves between the first and second postnatal week, significant topographic differences emerge across different cortical regions. Functional connectivity profiles of the cortex gradually segregate into main subnetworks and give rise to a highly modular network topology at the end of the second postnatal week. Overall, spontaneous mesoscale activity reflects the maturation of cortical networks, and reveals critical breakpoints in the development of the functional architecture of the cortex.

Development of the rodent prefrontal cortex: circuit formation, plasticity, and impacts of early life stress

The prefrontal cortex (PFC), located at the anterior region of the cerebral cortex, is a multimodal association cortex essential for higher-order brain functions, including decision-making, attentional control, memory processing, and regulation of social behavior. Structural, circuit-level, and functional abnormalities in the PFC are often associated with neurodevelopmental disorders. Here, we review recent findings on the postnatal development of the PFC, with a particular emphasis on rodent studies, to elucidate how its structural and circuit properties are established during critical developmental windows and how these processes influence adult behaviors. Recent evidence also highlights the lasting effects of early life stress on the PFC structure, connectivity, and function. We explore potential mechanisms underlying these stress-induced alterations, with a focus on epigenetic regulation and its implications for PFC maturation and neurodevelopmental disorders. By integrating these insights, this review provides an overview of the developmental processes shaping the PFC and their implications for brain health and disease.

Single-cell spatial transcriptomic atlas of the whole mouse brain

A comprehensive atlas of genes, cell types, and their spatial distribution across a whole mammalian brain is fundamental for understanding the function of the brain. Here, using single-nucleus RNA sequencing (snRNA-seq) and Stereo-seq techniques, we generated a mouse brain atlas with spatial information for 308 cell clusters at single-cell resolution, involving over 4 million cells, as well as for 29,655 genes. We have identified cell clusters exhibiting preference for cortical subregions and explored their associations with brain-related diseases. Additionally, we pinpointed 155 genes with distinct regional expression patterns within the brainstem and unveiled 513 long non-coding RNAs showing region-enriched expression in the adult brain. Parcellation of brain regions based on spatial transcriptomic information revealed fine structure for several brain areas. Furthermore, we have uncovered 411 transcription factor regulons showing distinct spatiotemporal dynamics during neurodevelopment. Thus, we have constructed a single-cell-resolution spatial transcriptomic atlas of the mouse brain with genome-wide coverage.

Interneuron migration impairment and brain region-specific DNA damage response following irradiation during early neurogenesis in mice

Embryonic DNA damage resulting from DNA repair deficiencies or exposure to ionizing radiation during early neurogenesis can lead to neurodevelopmental disorders, including microcephaly. This has been linked to an excessive DNA damage response in dorsal neural progenitor cells (NPCs), resulting in p53-dependent apoptosis and premature neuronal differentiation which culminates in depletion of the NPC pool. However, the effect of DNA damage on ventral forebrain NPCs, the origin of interneurons, remains unclear. In this study, we investigated the sequelae of irradiation of mouse fetuses at an early timepoint of forebrain neurogenesis. We focused on the neocortex (NCX) and medial ganglionic eminence (MGE), key regions for developing dorsal and ventral NPCs, respectively. Although both regions showed a typical p53-mediated DNA damage response consisting of cell cycle arrest, DNA repair and apoptosis, NCX cells displayed prolonged cell cycle arrest, while MGE cells exhibited more sustained apoptosis. Moreover, irradiation reduced the migration speed of interneurons in acute living brain slices and MGE explants, the latter indicating a cell-intrinsic component in the defect. RNA sequencing and protein analyses revealed disruptions in actin and microtubule cytoskeletal-related cellular machinery, particularly in MGE cells. Despite massive acute apoptosis and an obvious interneuron migration defect, prenatally irradiated animals did not show increased sensitivity to pentylenetetrazole-induced seizures, nor was there a reduction in cortical interneurons in young adult mice. This suggests a high plasticity of the developing brain to acute insults during early neurogenesis. Overall, our findings indicate that embryonic DNA damage induces region-specific responses, potentially linked to neurodevelopmental disorders.

Metabolic Atlas of Early Human Cortex Identifies Regulators of Cell Fate Transitions

Characterization of cell type emergence during human cortical development, which enables unique human cognition, has focused primarily on anatomical and transcriptional characterizations. Metabolic processes in the human brain that allow for rapid expansion, but contribute to vulnerability to neurodevelopmental disorders, remain largely unexplored. We performed a variety of metabolic assays in primary tissue and stem cell derived cortical organoids and observed dynamic changes in core metabolic functions, including an unexpected increase in glycolysis during late neurogenesis. By depleting glucose levels in cortical organoids, we increased outer radial glia, astrocytes, and inhibitory neurons. We found the pentose phosphate pathway (PPP) was impacted in these experiments and leveraged pharmacological and genetic manipulations to recapitulate these radial glia cell fate changes. These data identify a new role for the PPP in modulating radial glia cell fate specification and generate a resource for future exploration of additional metabolic pathways in human cortical development.

Genetic overlap between schizophrenia and constipation: insights from a genome-wide association study in a European population

BACKGROUND

Patients with schizophrenia (SCZ) experience constipation at significantly higher rates compared with the general population. This relationship suggests a potential genetic overlap between these two conditions.

METHODS

We analyzed genome-wide association study (GWAS) data for both SCZ and constipation using a five-part approach. The first and second parts assessed the overall and local genetic correlations using methods such as linkage disequilibrium score regression (LDSC) and heritability estimation from summary statistics (HESS). The third part investigated the causal association between the two traits using Mendelian randomization (MR). The fourth part employed conditional/conjunctional false discovery rate (cond/conjFDR) to analyze the genetic overlap with different traits based on the statistical theory. Finally, an LDSC-specifically expressed gene (LDSC-SEG) analysis was conducted to explore the tissue-level associations.

RESULTS

Our analyses revealed both overall and specific genetic correlations between SCZ and constipation at the genomic level. The MR analysis suggests a positive causal relationship between SCZ and constipation. The ConjFDR analysis confirms the genetic overlap between the two conditions and identifies two genetic risk loci (rs7583622 and rs842766) and seven mapped genes (GPR75-ASB3, ASB3, CHAC2, ERLEC1, GPR75, PSME4, and ACYP2). Further investigation into the functions of these genes could provide valuable insights. Interestingly, disease-related tissue analysis revealed associations between SCZ and constipation in eight brain regions (substantia nigra, anterior cingulate cortex, hypothalamus, cortex, hippocampus, cortex, amygdala, and spinal cord).

CONCLUSION

This study provides the first genetic evidence for the comorbidity of SCZ and constipation, enhancing our understanding of the pathophysiology of both conditions.

Causal association of sarcopenia-related traits with brain cortical structure: a bidirectional Mendelian randomization study

BACKGROUND

Patients with sarcopenia often experience cognitive decline, affecting cortical structures, but the causal link remains unclear. We used bidirectional Mendelian randomization (MR) to explore the relationship between sarcopenia-related traits and cortical structure.

METHODS

We selected genetic variables from genome-wide association study data. Three different MR methods were used: inverse-variance weighted analysis, MR-Egger regression, and the weighted median test. For significant estimates, we further conducted Cochran's Q test, MR-Egger intercept test, leave-one-out analyses, and MR-PRESSO to assess heterogeneity.

RESULTS

In forward MR analysis, appendicular lean mass (ALM) decreased the thickness (TH) of lateral occipital gyrus and increased the TH of pars opercularis gyrus (β = -0.0079 mm, 95% CI: -0.0117 mm to -0.0041 mm, P < 0.0001; β = 0.0080 mm, 95% CI: 0.0042 mm to 0.0117 mm, P < 0.0001). In reverse MR analysis, a significant negative correlation was found between the TH of bankssts and ALM, while positive correlations were observed between the TH of frontal pole, rostral anterior cingulate, temporal pole, and ALM. The TH of temporal pole was positively correlated with right hand grip strength (HGS-R) (β = 0.1596 mm, 95% CI: 0.1349 mm to 0.1843 mm, P < 0.0001), and the TH of pars triangularis was positively correlated with left-hand grip strength (HGS-L) (β = 0.3251 mm, 95% CI: 0.2339 mm to 0.4163 mm, P < 0.0001).

CONCLUSIONS

Sarcopenia-related traits and cortical structure have bidirectional effects, supporting the muscle-brain axis theory. This links sarcopenia to neurocognitive diseases and provides new strategies for the prevention and intervention of both sarcopenia and cognitive decline.

The Generalizability of Cortical Area Parcellations Across Early Childhood

The cerebral cortex consists of distinct areas that develop through intrinsic embryonic patterning and postnatal experiences. Accurate parcellation of these areas in neuroimaging studies improves statistical power and cross-study comparability. Given significant brain changes in volume, microstructure, and connectivity during early life, we hypothesized that cortical areas in 1- to 3-year-olds would differ markedly from neonates and increasingly resemble adult patterns as development progresses. Here, we parcellated the cerebral cortex into putative areas using local functional connectivity gradients in 92 toddlers at 2 years old. We demonstrate high reproducibility of these cortical regions across 1- to 3-year-olds in two independent datasets. The area boundaries in 1- to 3-year-olds were more similar to those in adults than those in neonates. While the age-specific group area parcellation better fit the underlying functional connectivity in individuals during the first 3 years, adult area parcellations might still have some utility in developmental studies, especially in children older than 6 years. Additionally, we provide connectivity-based community assignments of the parcels, showing fragmented anterior and posterior components based on the strongest connectivity, yet alignment with adult systems when weaker connectivity was included.

Activity-dependent regulation of microglia numbers by pyramidal cells during development shape cortical functions

Beyond their role as immune sentinels, microglia are actively involved in establishing and maintaining cortical circuits. Alteration in microglial numbers has been associated with abnormal behaviors akin to those observed in neurodevelopmental disorders. Consequently, establishing the appropriate microglial numbers during development is crucial for ensuring normal cortical function. Here, we uncovered a dynamic relationship between pyramidal cells and microglia that tunes microglial numbers and development through distinct phases of mouse postnatal development. Changes in pyramidal cell activity during development induce differential release of activity-dependent proteins such as Activin A, which, in turn, adjusts microglial numbers accordingly. Decoupling of this relationship not only changes microglial numbers but has a long-term consequence on their role as synaptic organizers, which ultimately affects cortical function. Our findings reveal that microglia adapt their numbers to changes in pyramidal cell activity during a critical time window in development, consequently adjusting their numbers and function to the demands of the developing local circuits.

Comparative molecular landscapes of immature neurons in the mammalian dentate gyrus across species reveal special features in humans

Immature dentate granule cells (imGCs) arising from adult hippocampal neurogenesis contribute to plasticity, learning and memory, but their evolutionary changes across species and specialized features in humans remain poorly understood. Here we performed machine learning-augmented analysis of published single-cell RNA-sequencing datasets and identified macaque imGCs with transcriptome-wide immature neuronal characteristics. Our cross-species comparisons among humans, monkeys, pigs, and mice showed few shared (such as DPYSL5), but mostly species-specific gene expression in imGCs that converged onto common biological processes regulating neuronal development. We further identified human-specific transcriptomic features of imGCs and demonstrated functional roles of human imGC-enriched expression of a family of proton-transporting vacuolar-type ATPase subtypes in development of imGCs derived from human pluripotent stem cells. Our study reveals divergent gene expression patterns but convergent biological processes in the molecular characteristics of imGCs across species, highlighting the importance of conducting independent molecular and functional analyses for adult neurogenesis in different species.

Topographic Axes of Wiring Space Converge to Genetic Topography in Shaping the Human Cortical Layout

Genetic information is involved in the gradual emergence of cortical areas since the neural tube begins to form, shaping the heterogeneous functions of neural circuits in the human brain. Informed by invasive tract-tracing measurements, the cortex exhibits marked interareal variation in connectivity profiles, revealing the heterogeneity across cortical areas. However, it remains unclear about the organizing principles possibly shared by genetics and cortical wiring to manifest the spatial heterogeneity across the cortex. Instead of considering a complex one-to-one mapping between genetic coding and interareal connectivity, we hypothesized the existence of a more efficient way that the organizing principles are embedded in genetic profiles to underpin the cortical wiring space. Leveraging vertex-wise tractography in diffusion-weighted MRI, we derived the global connectopies (GCs) in both female and male to reliably index the organizing principles of interareal connectivity variation in a low-dimensional space, which captured three dominant topographic patterns along the dorsoventral, rostrocaudal, and mediolateral axes of the cortex. More importantly, we demonstrated that the GCs converge with the gradients of a vertex-by-vertex genetic correlation matrix on the phenotype of cortical morphology and the cortex-wide spatiomolecular gradients. By diving into the genetic profiles, we found that the critical role of genes scaffolding the GCs was related to brain morphogenesis and enriched in radial glial cells before birth and excitatory neurons after birth. Taken together, our findings demonstrated the existence of a genetically determined space that encodes the interareal connectivity variation, which may give new insights into the links between cortical connections and arealization.

Differential neurogenic patterns underlie the formation of primary and secondary areas in the developing somatosensory cortex

The cerebral cortex consists of hierarchically organized areas interconnected by reciprocal axonal projections. However, the coordination of neurogenesis to optimize neuronal production and wiring between distinct cortical areas remains largely unexplored. The somatosensory cortex plays a crucial role in processing tactile information, with inputs from peripheral sensory receptors relayed through the thalamus to the primary and secondary somatosensory areas. To investigate the dynamics of neurogenesis in cortical circuit formation, we employed temporal genetic fate mapping of glutamatergic neuron cohorts across the somatosensory cortices. Our analysis revealed that neuronal production in the secondary somatosensory cortex (S2) precedes that of the primary somatosensory cortex (S1) from the deep-layer neuron production period and terminates earlier. We further revealed a progressive decline in upper-layer neuron output in S2, attributed to the attenuation of the apical ventricular surface, resulting in a reduced number of upper-layer neurons within S2. These findings support the existence of a protomap mechanism governing the area-specific assembly of primary and secondary areas in the developing neocortex.

Developmental maturation of millimeter-scale functional networks across brain areas

Processing sensory information, generating perceptions, and shaping behavior engages neural networks in brain areas with highly varied representations, ranging from unimodal sensory cortices to higher-order association areas. In early development, these areas share a common distributed and modular functional organization, but it is not known whether this undergoes a common developmental trajectory, or whether such organization persists only in some brain areas. Here, we examine the development of network organization across diverse cortical regions in ferrets using in vivo wide field calcium imaging of spontaneous activity. In both primary sensory (visual, auditory, and somatosensory) and higher order association (prefrontal and posterior parietal) areas, spontaneous activity remained significantly modular with pronounced millimeter-scale correlations over a 3-wk period spanning eye opening and the transition to externally-driven sensory activity. Over this period, cortical areas exhibited a roughly similar set of developmental changes, along with area-specific differences. Modularity and long-range correlation strength generally decreased with age, along with increases in the dimensionality of activity, although these effects were not uniform across all brain areas. These results indicate an interplay of area-specific factors with a conserved developmental program that maintains modular functional networks, suggesting modular organization may be involved in functional representations in diverse brain areas.

Geometric influences on the regional organization of the mammalian brain

The mammalian brain is comprised of anatomically and functionally distinct regions. Substantial work over the past century has pursued the generation of ever-more accurate maps of regional boundaries, using either expert judgement or data-driven clustering of functional, connectional, and/or architectonic properties. However, these approaches are often purely descriptive, have limited generalizability, and do not elucidate the underlying generative mechanisms that shape the regional organization of the brain. Here, we develop a novel approach that leverages a simple, hierarchical principle for generating a multiscale parcellation of any brain structure in any mammalian species using only its geometry. We show that this approach yields regions at any resolution scale that are more homogeneous than those defined in nearly all existing benchmark brain parcellations in use today across hundreds of anatomical, functional, cellular, and molecular brain properties measured in humans, macaques, marmosets, and mice. We additionally show how our method can be generalized to previously unstudied mammalian species for which no parcellations exist. Finally, we demonstrate how our approach captures the essence of a simple, hierarchical reaction-diffusion mechanism, in which the geometry of a brain structure shapes the spatial expression of putative patterning molecules linked to the formation of distinct regions through development. Our findings point to a highly conserved and universal influence of geometry on the regional organization of the mammalian brain.

Prenatal Valproic Acid Exposure Impairs Offspring Cognition Through Disturbing Interneuron Development

AIMS

Valproic acid (VPA) exposure during the gestational period has been found to impair the cognition of the offspring. The study aimed to investigate whether VPA leads to offspring cognitive impairment through disturbing interneuron development.

METHODS

Pregnant mice were injected with VPA peritoneally to establish the prenatal VPA exposure model. Cortical interneurons were labeled with Rosa26-EYFP/- reporter mice activated by Nkx2.1-Cre. Interneuron subtypes both in the cortex and the hippocampus were detected by immunofluorescence. A battery of behavioral tests was conducted on postnatal Day 28 to assess the cognition and anxiety of the offspring. RNA-Seq analysis was performed to investigate the underlying molecular mechanisms.

RESULTS

We found that after the exposure to VPA, all the groups of the male offspring exerted anxiety. When VPA injection was performed on gestational Day 12.5, the memory of the offspring was impaired. Mechanistically, the distribution of cortical interneurons was disrupted. The distribution of interneuron subtypes was abnormal both in the cortex and hippocampus after the VPA exposure, which affected the somatostatin-positive neurons but not the parvalbumin-positive neurons, indicating the effects of VPA were subtype specific. Biological processes related to ion homeostasis were greatly changed after VPA exposure.

CONCLUSION

Prenatal VPA exposure during the neurogenic period impaired the cognition of the offspring by disrupting interneuron migration and differentiation. The study provides a novel perspective on the influence of VPA over neurodevelopment.

Prospects of induced pluripotent stem cells in treating advancing Alzheimer's disease: A review

The World Health Organization has identified Alzheimer's disease (AD), the leading cause of dementia globally, as a public health priority. However, the complex multifactorial pathology of AD means that its etiology remains incompletely understood. Despite being recognized a century ago, incomplete knowledge has hindered the development of effective treatments for AD. Recent scientific advancements, particularly in induced pluripotent stem cell (iPSC) technology, show great promise in elucidating the fundamental mechanisms of AD. iPSCs play a dual role in regenerating damaged cells for therapeutic purposes and creating disease models to understand AD pathology and aid in drug screening. Nevertheless, as an emerging field, iPSC technology requires further technological advancement to develop effective AD treatments in the future. Thus, this review summarizes recent advances in stem cell therapies, specifically iPSCs, aimed at understanding AD pathology and developing treatments.

The patient-specific mouse model with Foxg1 frameshift mutation provides insights into the pathophysiology of FOXG1 syndrome

Single allelic mutations in the forebrain-specific transcription factor gene FOXG1 lead to FOXG1 syndrome (FS). To decipher the disease mechanisms of FS, which vary depending on FOXG1 mutation types, patient-specific animal models are critical. Here, we report the first patient-specific FS mouse model, Q84Pfs heterozygous (Q84Pfs-Het) mice, which emulates one of the most predominant FS variants. Remarkably, Q84Pfs-Het mice recapitulate various human FS phenotypes across cellular, brain structural, and behavioral levels, such as microcephaly, corpus callosum agenesis, movement disorders, repetitive behaviors, and anxiety. Q84Pfs-Het cortex showed dysregulations of genes controlling cell proliferation, neuronal projection and migration, synaptic assembly, and synaptic vesicle transport. Interestingly, the FS-causing Q84Pfs allele produced the N-terminal fragment of FOXG1, denoted as Q84Pfs protein, in Q84Pfs-Het mouse brains. Q84Pfs fragment forms intracellular speckles, interacts with FOXG1 full-length protein, and triggers the sequestration of FOXG1 to distinct subcellular domains. Q84Pfs protein also promotes the radial glial cell identity and suppresses neuronal migration in the cortex. Together, our study uncovered the role of the FOXG1 fragment derived from FS-causing FOXG1 variants and identified the genes involved in FS-like cellular and behavioral phenotypes, providing essential insights into the pathophysiology of FS.

Molecular and cellular dynamics of the developing human neocortex

The development of the human neocortex is highly dynamic, involving complex cellular trajectories controlled by gene regulation1. Here we collected paired single-nucleus chromatin accessibility and transcriptome data from 38 human neocortical samples encompassing both the prefrontal cortex and the primary visual cortex. These samples span five main developmental stages, ranging from the first trimester to adolescence. In parallel, we performed spatial transcriptomic analysis on a subset of the samples to illustrate spatial organization and intercellular communication. This atlas enables us to catalogue cell-type-specific, age-specific and area-specific gene regulatory networks underlying neural differentiation. Moreover, combining single-cell profiling, progenitor purification and lineage-tracing experiments, we have untangled the complex lineage relationships among progenitor subtypes during the neurogenesis-to-gliogenesis transition. We identified a tripotential intermediate progenitor subtype-tripotential intermediate progenitor cells (Tri-IPCs)-that is responsible for the local production of GABAergic neurons, oligodendrocyte precursor cells and astrocytes. Notably, most glioblastoma cells resemble Tri-IPCs at the transcriptomic level, suggesting that cancer cells hijack developmental processes to enhance growth and heterogeneity. Furthermore, by integrating our atlas data with large-scale genome-wide association study data, we created a disease-risk map highlighting enriched risk associated with autism spectrum disorder in second-trimester intratelencephalic neurons. Our study sheds light on the molecular and cellular dynamics of the developing human neocortex.

Deciphering the physiopathology of neurodevelopmental disorders using brain organoids

Neurodevelopmental disorders (NDD) encompass a range of conditions marked by abnormal brain development in conjunction with impaired cognitive, emotional and behavioural functions. Transgenic animal models, mainly rodents, traditionally served as key tools for deciphering the molecular mechanisms driving NDD physiopathology and significantly contributed to the development of pharmacological interventions aimed at treating these disorders. However, the efficacy of these treatments in humans has proven to be limited, due in part to the intrinsic constraint of animal models to recapitulate the complex development and structure of the human brain but also to the phenotypic heterogeneity found between affected individuals. Significant advancements in the field of induced pluripotent stem cells (iPSCs) offer a promising avenue for overcoming these challenges. Indeed, the development of advanced differentiation protocols for generating iPSC-derived brain organoids gives an unprecedented opportunity to explore human neurodevelopment. This review provides an overview of how 3D brain organoids have been used to investigate various NDD (i.e. Fragile X syndrome, Rett syndrome, Angelman syndrome, microlissencephaly, Prader-Willi syndrome, Timothy syndrome, tuberous sclerosis syndrome) and elucidate their pathophysiology. We also discuss the benefits and limitations of employing such innovative 3D models compared to animal models and 2D cell culture systems in the realm of personalized medicine.

Antiamnesic and Neurotrophic Effects of Parkia biglobosa (Jacq.) R. Br (Fabaceae) Aqueous Extract on In Vivo and In Vitro Models of Excitotoxicity

Amnesia is a memory disorder marked by the inability to recall or acquire information. Hence, drugs that also target the neurogenesis process constitute a hope to discover a cure against memory disorders. This study is aimed at evaluating the antiamnesic and neurotrophic effects of the aqueous extract of Parkia biglobosa (P. biglobosa) on in vivo and in vitro models of excitotoxicity. For the in vivo study, 42 adult male rats were divided into six groups of seven rats each and treated daily for 30 days as follows: normal control group (distilled water, 10 mL/kg, po), negative control group (distilled water, 10 mL/kg, po), positive control group (piracetam, 200 mg/kg, po), and 03 test groups (extract, 44, 88, and 176 mg/kg, po). Scopolamine (0.5 mg/kg, ip) was administered once daily, 45 min after these treatments, for 14 days, except in the normal control group. The animals were then subjected to short-term memory (new object recognition and T-maze) and long-term memory (radial arm maze) tests for 15 following days. Animals were then euthanized, and biochemical analyses (neurotransmitters, oxidative status, and neuroinflammation) were performed in the prefrontal cortex, hippocampus, and serum. Histological analysis of these organs was also carried out. In the in vitro study, the effect of the extract (5, 10, 19, 40, 77, 153, 306, 615, 1225, and 2450 μg/mL) was assessed on the viability of primary cortical neurons exposed to L-glutamate (0.1 mg/mL). Scopolamine induced memory impairment and increased oxidative stress, neuroinflammation, and neuronal loss. P. biglobosa extract (44 mg/kg) reduced (p < 0.001) short- and long-term memory deficit. It also increased (p < 0.01) the concentration of acetylcholine, reduced (p < 0.001) that of malondialdehyde, and limited (p < 0.001) neuroinflammation and neuronal loss (p < 0.001). In addition, the extract (2450 μg/mL) increased (p < 0.001) the percentage of viable cells. These results suggest that the extract has effects on amnesia and neurogenesis. These effects seem to be mediated by antioxidant and anti-inflammatory modulations.

Evolutionary convergence of sensory circuits in the pallium of amniotes

The amniote pallium contains sensory circuits that are structurally and functionally equivalent, yet their evolutionary relationship remains unresolved. We used birthdating analysis, single-cell RNA and spatial transcriptomics, and mathematical modeling to compare the development and evolution of known pallial circuits across birds (chick), lizards (gecko), and mammals (mouse). We reveal that neurons within these circuits' stations are generated at varying developmental times and brain regions across species and found an early developmental divergence in the transcriptomic progression of glutamatergic neurons. Our research highlights developmental distinctions and functional similarities in the sensory circuit between birds and mammals, suggesting the convergence of high-order sensory processing across amniote lineages.

Structural MRI of brain similarity networks

Recent advances in structural MRI analytics now allow the network organization of individual brains to be comprehensively mapped through the use of the biologically principled metric of anatomical similarity. In this Review, we offer an overview of the measurement and meaning of structural MRI similarity, especially in relation to two key assumptions that often underlie its interpretation: (i) that MRI similarity can be representative of architectonic similarity between cortical areas and (ii) that similar areas are more likely to be axonally connected, as predicted by the homophily principle. We first introduce the historical roots and technical foundations of MRI similarity analysis and compare it with the distinct MRI techniques of structural covariance and tractography analysis. We contextualize this empirical work with two generative models of homophilic networks: an economic model of cost-constrained connectional homophily and a heterochronic model of ontogenetically phased cortical maturation. We then review (i) studies of the genetic and transcriptional architecture of MRI similarity in population-averaged and disorder-specific contexts and (ii) developmental studies of normative cohorts and clinical studies of neurodevelopmental and neurodegenerative disorders. Finally, we prioritize knowledge gaps that must be addressed to consolidate structural MRI similarity as an accessible, valid marker of the architecture and connectivity of an individual brain network.

Spatiotemporal modeling of molecular holograms

Quantifying spatiotemporal dynamics during embryogenesis is crucial for understanding congenital diseases. We developed Spateo (https://github.com/aristoteleo/spateo-release), a 3D spatiotemporal modeling framework, and applied it to a 3D mouse embryogenesis atlas at E9.5 and E11.5, capturing eight million cells. Spateo enables scalable, partial, non-rigid alignment, multi-slice refinement, and mesh correction to create molecular holograms of whole embryos. It introduces digitization methods to uncover multi-level biology from subcellular to whole organ, identifying expression gradients along orthogonal axes of emergent 3D structures, e.g., secondary organizers such as midbrain-hindbrain boundary (MHB). Spateo further jointly models intercellular and intracellular interaction to dissect signaling landscapes in 3D structures, including the zona limitans intrathalamica (ZLI). Lastly, Spateo introduces "morphometric vector fields" of cell migration and integrates spatial differential geometry to unveil molecular programs underlying asymmetrical murine heart organogenesis and others, bridging macroscopic changes with molecular dynamics. Thus, Spateo enables the study of organ ecology at a molecular level in 3D space over time.

Initial regional cytoarchitectonic differences in dorsal and orbitobasal human developing frontal cortex revealed by spatial transcriptomics

Early development of the human fetal cerebral cortex involves a set of precisely coordinated molecular processes that remains rather underexplored. Previous studies indicate that the laminar identity and the molecular specification of cortical neurons driven by genetic programming, as well as associated histogenetic events begin during early fetal development. Our recent study discovered unique regional cytoarchitectonic features in the developing human frontal lobe, including migratory waves of postmitotic neurons in the dorsal frontal cortex and the "double plate" feature in orbitobasal cortex (Kopić et al. in Cells 12:231, 2023). Notably, neurons of these two cytoarchitectonic features typically express deep projection neuron (DPN) markers (TBR1, TLE4, SOX5). This paper aims to conduct an in-depth investigation of these cytoarchitectonic features at the transcriptomic level, whilst preserving spatial information. Here, we employed NanoString GeoMx™ Digital Spatial Profiler (DSP) technology to examine gene expression differences in the transient cortical compartments of the dorsal and ventral regions of the developing frontal lobe, focusing specifically on 15 post-conceptional weeks (PCW), that is a critical period for subplate formation. We identified multiple differentially expressed genes between the transient cellular compartments of the dorsal and orbitobasal regions of the developing human frontal cortex. These new findings additionally confirm that regional patterning and specification of the prospective higher-order association prefrontal cortex emerges early in fetal development, contributing to the highly organized cortical architecture of the human brain.

The neuronal Golgi in neural circuit formation and reorganization

The Golgi apparatus is a central hub in the intracellular secretory pathway. By positioning in the specific intracellular region and transporting materials to spatially restricted compartments, the Golgi apparatus contributes to the cell polarity establishment and morphological specification in diverse cell types. In neurons, the Golgi apparatus mediates several essential steps of initial neural circuit formation during early brain development, such as axon-dendrite polarization, neuronal migration, primary dendrite specification, and dendritic arbor elaboration. Moreover, neuronal activity-dependent remodeling of the Golgi structure enables morphological changes in neurons, which provides the cellular basis of circuit reorganization during postnatal critical period. In this review, I summarize recent findings illustrating the unique Golgi positioning and its developmental dynamics in various types of neurons. I also discuss the upstream regulators for the Golgi positioning in neurons, and functional roles of the Golgi in neural circuit formation and reorganization. Elucidating how Golgi apparatus sculpts neuronal connectivity would deepen our understanding of the cellular/molecular basis of neural circuit development and plasticity.

Development of the basic architecture of neocortical circuitry in the human fetus as revealed by the coupling spatiotemporal pattern of synaptogenesis along with microstructure and macroscale in vivo MR imaging

In humans, a quantifiable number of cortical synapses appears early in fetal life. In this paper, we present a bridge across different scales of resolution and the distribution of synapses across the transient cytoarchitectonic compartments: marginal zone (MZ), cortical plate (CP), subplate (SP), and in vivo MR images. The tissue of somatosensory cortex (7-26 postconceptional weeks (PCW)) was prepared for electron microscopy, and classified synapses with a determined subpial depth were used for creating histograms matched to the histological sections immunoreacted for synaptic markers and aligned to in vivo MR images (1.5 T) of corresponding fetal ages (maternal indication). Two time periods and laminar patterns of synaptogenesis were identified: an early and midfetal two-compartmental distribution (MZ and SP) and a late fetal three-compartmental distribution (CP synaptogenesis). During both periods, a voluminous, synapse-rich SP was visualized on the in vivo MR. Another novel finding concerns the phase of secondary expansion of the SP (13 PCW), where a quantifiable number of synapses appears in the upper SP. This lamina shows a T2 intermediate signal intensity below the low signal CP. In conclusion, the early fetal appearance of synapses shows early differentiation of putative genetic mechanisms underlying the synthesis, transport and assembly of synaptic proteins. "Pioneering" synapses are likely to play a morphogenetic role in constructing of fundamental circuitry architecture due to interaction between neurons. They underlie spontaneous, evoked, and resting state activity prior to ex utero experience. Synapses can also mediate genetic and environmental triggers, adversely altering the development of cortical circuitry and leading to neurodevelopmental disorders.

Molecular Lineages and Spatial Distributions of Subplate Neurons in the Human Fetal Cerebral Cortex

The expansion of neural progenitors and production of distinct neurons are crucial for architectural assembly and formation of connectivity in human brains. Subplate neurons (SPNs) are among the firstborn neurons in the human fetal cerebral cortex, and play a critical role in establishing intra- and extracortical connections. However, little is known about SPN origin and developmental lineages. In this study, spatial landscapes and molecular trajectories of SPNs in the human fetal cortices from gestational weeks (GW) 10 to 25 are created by performing spatial transcriptomics and single-cell RNA sequencing. Genes known to be evolutionarily human-specific and genes associated with extracellular matrices (ECMs) are found to maintain stable proportions of subplate neurons among other neuronal types. Enriched ECM gene expression in SPNs varies in distinct cortical regions, with the highest level in the frontal lobe of human fetal brains. This study reveals molecular origin and lineage specification of subplate neurons in the human fetal cerebral cortices, and highlights underpinnings of SPNs to cortical neurogenesis and early structural folding.

Molecular signatures of cortical expansion in the human foetal brain

The third trimester of human gestation is characterised by rapid increases in brain volume and cortical surface area. Recent studies have revealed a remarkable molecular diversity across the prenatal cortex but little is known about how this diversity translates into the differential rates of cortical expansion observed during gestation. We present a digital resource, μBrain, to facilitate knowledge translation between molecular and anatomical descriptions of the prenatal brain. Using μBrain, we evaluate the molecular signatures of preferentially-expanded cortical regions, quantified in utero using magnetic resonance imaging. Our findings demonstrate a spatial coupling between areal differences in the timing of neurogenesis and rates of neocortical expansion during gestation. We identify genes, upregulated from mid-gestation, that are highly expressed in rapidly expanding neocortex and implicated in genetic disorders with cognitive sequelae. The μBrain atlas provides a tool to comprehensively map early brain development across domains, model systems and resolution scales.

Neuronal fate resulting from indirect neurogenesis in the mouse neocortex

Excitatory cortical neurons originate from cortical radial glial cells (RGCs). Initially, these neurons were thought to derive directly from RGCs (direct neurogenesis) and be distributed in an inside-out fashion. However, the discovery of indirect neurogenesis, whereby intermediate neuronal progenitors (INPs) generate neurons, challenged this view. To investigate the integration of neurons via these two modes, we developed a method to identify INP progeny and analyze their fate using transgenic mice expressing tamoxifen-inducible Cre recombinase under the neurogenin-2 promoter, alongside thymidine analog incorporation. Their fate was further analyzed using mosaic analysis with double markers in mice. Indirect neurogenesis was prominent during early neurogenesis, generating neuron types that would emerge slightly later than those produced via direct neurogenesis. Despite the timing difference, both neurogenic modes produced fundamentally similar neuron types, as evidenced by marker expression and cortical-depth location. Furthermore, INPs generated pairs of similar phenotype neurons. These findings suggest that indirect neurogenesis, like direct neurogenesis, generates neuron types in a temporally ordered sequence and increases the number of similar neuron types, particularly in deep layers. Thus, both neurogenic modes cooperatively generate a diverse array of neuron types in a similar order, and their progeny populate together to form a coherent cortical structure.

Molecular Signatures of Resilience to Alzheimer's Disease in Neocortical Layer 4 Neurons

Single-cell omics is advancing our understanding of selective neuronal vulnerability in Alzheimer's disease (AD), revealing specific subtypes that are either susceptible or resilient to neurodegeneration. Using single-nucleus and spatial transcriptomics to compare neocortical regions affected early (prefrontal cortex and precuneus) or late (primary visual cortex) in AD, we identified a resilient excitatory population in layer 4 of the primary visual cortex expressing RORB, CUX2, and EYA4. Layer 4 neurons in association neocortex also remained relatively preserved as AD progressed and shared overlapping molecular signatures of resilience. Early in the disease, resilient neurons upregulated genes associated with synapse maintenance, synaptic plasticity, calcium homeostasis, and neuroprotective factors, including GRIN2A, RORA, NRXN1, NLGN1, NCAM2, FGF14, NRG3, NEGR1, and CSMD1. We also identified KCNIP4, which encodes a voltage-gated potassium (Kv) channel-interacting protein that interacts with Kv4.2 channels and presenilins, as a key factor linked to resilience. KCNIP4 was consistently upregulated in the early stages of pathology. Furthermore, AAV-mediated overexpression of Kcnip4 in a humanized AD mouse model reduced the expression of the activity-dependent genes Arc and c-Fos, suggesting compensatory mechanisms against neuronal hyperexcitability. Our dataset provides a valuable resource for investigating mechanisms underlying resilience to neurodegeneration.

Generation of Mammalian Astrocyte Functional Heterogeneity

Mammalian astrocytes have regional roles within the brain parenchyma. Indeed, the notion that astrocytes are molecularly heterogeneous could help explain how the central nervous system (CNS) retains embryonic positional information through development into specialized regions into adulthood. A growing body of evidence supports the concept of morphological and molecular differences between astrocytes in different brain regions, which might relate to their derivation from regionally patterned radial glia and/or local neuron inductive cues. Here, we review evidence for regionally encoded functions of astrocytes to provide an integrated concept on lineage origins and heterogeneity to understand regional brain organization, as well as emerging technologies to identify and further investigate novel roles for astrocytes.

A polarized FGF8 source specifies frontotemporal signatures in spatially oriented cell populations of cortical assembloids

Organoids generating major cortical cell types in distinct compartments are used to study cortical development, evolution and disorders. However, the lack of morphogen gradients imparting cortical positional information and topography in current systems hinders the investigation of complex phenotypes. Here, we engineer human cortical assembloids by fusing an organizer-like structure expressing fibroblast growth factor 8 (FGF8) with an elongated organoid to enable the controlled modulation of FGF8 signaling along the longitudinal organoid axis. These polarized cortical assembloids mount a position-dependent transcriptional program that in part matches the in vivo rostrocaudal gene expression patterns and that is lost upon mutation in the FGFR3 gene associated with temporal lobe malformations and intellectual disability. By producing spatially oriented cell populations with signatures related to frontal and temporal area identity within individual assembloids, this model recapitulates in part the early transcriptional divergence embedded in the protomap and enables the study of cortical area-relevant alterations underlying human disorders.

FGF8-mediated gene regulation affects regional identity in human cerebral organoids

The morphogen FGF8 establishes graded positional cues imparting regional cellular responses via modulation of early target genes. The roles of FGF signaling and its effector genes remain poorly characterized in human experimental models mimicking early fetal telencephalic development. We used hiPSC-derived cerebral organoids as an in vitro platform to investigate the effect of FGF8 signaling on neural identity and differentiation. We found that FGF8 treatment increases cellular heterogeneity, leading to distinct telencephalic and mesencephalic-like domains that co-develop in multi-regional organoids. Within telencephalic regions, FGF8 affects the anteroposterior and dorsoventral identity of neural progenitors and the balance between GABAergic and glutamatergic neurons, thus impacting spontaneous neuronal network activity. Moreover, FGF8 efficiently modulates key regulators responsible for several human neurodevelopmental disorders. Overall, our results show that FGF8 signaling is directly involved in both regional patterning and cellular diversity in human cerebral organoids and in modulating genes associated with normal and pathological neural development.

Consequences of trisomy 21 for brain development in Down syndrome

The appearance of cognitive deficits and altered brain morphology in newborns with Down syndrome (DS) suggests that these features are driven by disruptions at the earliest stages of brain development. Despite its high prevalence and extensively characterized cognitive phenotypes, relatively little is known about the cellular and molecular mechanisms that drive the changes seen in DS. Recent technical advances, such as single-cell omics and the development of induced pluripotent stem cell (iPSC) models of DS, now enable in-depth analyses of the biochemical and molecular drivers of altered brain development in DS. Here, we review the current state of knowledge on brain development in DS, focusing primarily on data from human post-mortem brain tissue. We explore the biological mechanisms that have been proposed to lead to intellectual disability in DS, assess the extent to which data from studies using iPSC models supports these hypotheses, and identify current gaps in the field.

Temporally distinct 3D multi-omic dynamics in the developing human brain

The human hippocampus and prefrontal cortex play critical roles in learning and cognition1,2, yet the dynamic molecular characteristics of their development remain enigmatic. Here we investigated the epigenomic and three-dimensional chromatin conformational reorganization during the development of the hippocampus and prefrontal cortex, using more than 53,000 joint single-nucleus profiles of chromatin conformation and DNA methylation generated by single-nucleus methyl-3C sequencing (snm3C-seq3)3. The remodelling of DNA methylation is temporally separated from chromatin conformation dynamics. Using single-cell profiling and multimodal single-molecule imaging approaches, we have found that short-range chromatin interactions are enriched in neurons, whereas long-range interactions are enriched in glial cells and non-brain tissues. We reconstructed the regulatory programs of cell-type development and differentiation, finding putatively causal common variants for schizophrenia strongly overlapping with chromatin loop-connected, cell-type-specific regulatory regions. Our data provide multimodal resources for studying gene regulatory dynamics in brain development and demonstrate that single-cell three-dimensional multi-omics is a powerful approach for dissecting neuropsychiatric risk loci.

Stage-specific expression patterns and co-targeting relationships among miRNAs in the developing mouse cerebral cortex

microRNAs are crucial regulators of brain development, however, miRNA regulatory networks are not sufficiently well characterized. By performing small RNA-seq of the mouse embryonic cortex at E14, E17, and P0 as well as in neural progenitor cells and neurons, here we detected clusters of miRNAs that were co-regulated at distinct developmental stages. miRNAs such as miR-92a/b acted as hubs during early, and miR-124 and miR-137 during late neurogenesis. Notably, validated targets of P0 hub miRNAs were enriched for downregulated genes related to stem cell proliferation, negative regulation of neuronal differentiation and RNA splicing, among others, suggesting that miRNAs are particularly important for modulating transcriptional programs of crucial factors that guide the switch to neuronal differentiation. As most genes contain binding sites for more than one miRNA, we furthermore constructed a co-targeting network where numerous miRNAs shared more targets than expected by chance. Using luciferase reporter assays, we demonstrated that simultaneous binding of miRNA pairs to neurodevelopmentally relevant genes exerted an enhanced transcriptional silencing effect compared to single miRNAs. Taken together, we provide a comprehensive resource of miRNA longitudinal expression changes during murine corticogenesis. Furthermore, we highlight several potential mechanisms through which miRNA regulatory networks can shape embryonic brain development.

Transcription factor 4 expression in the developing non-human primate brain: a comparative analysis with the mouse brain

Transcription factor 4 (TCF4) has been implicated in a range of neuropsychiatric disorders, including major depressive disorder, bipolar disorder, and schizophrenia. Mutations or deletions in TCF4 cause Pitt-Hopkins syndrome (PTHS), a rare neurodevelopmental disorder. A detailed understanding of its spatial expression across the developing brain is necessary for comprehending TCF4 biology and, by extension, to develop effective treatments for TCF4-associated disorders. However, most current knowledge is derived from mouse models, which are invaluable for preclinical studies but may not fully capture the complexities of human neuropsychiatric phenotypes. This study compared TCF4 expression in the developing mouse brain to its regional and cellular expression patterns in normal prenatal, neonatal, and young adult rhesus macaque brains, a species more relevant to human neurodevelopment. While the general developmental expression of TCF4 is largely conserved between macaques and mice, we saw several interspecies differences. Most notably, a distinct layered pattern of TCF4 expression was clear in the developing macaque neocortex but largely absent in the mouse brain. High TCF4 expression was seen in the inner dentate gyrus of adult mice but not in macaques. Conversely, TCF4 expression was higher in the adult macaque striatum compared to the mouse striatum. Further research is needed to show the significance of these interspecies differences. Still, they underscore the importance of integrating rodent and primate studies to comprehensively understand TCF4 function and its implications for human disorders. Moreover, the primate-specific expression patterns of TCF4 will inform genetic and other therapeutic strategies to treat TCF4-associated disorders.

Gelatin Methacrylic Acid Hydrogel-Based Nerve Growth Factors Enhances Neural Stem Cell Growth and Differentiation to Promote Repair of Spinal Cord Injury

Background

The challenge in treating irreversible nerve tissue damage has resulted in suboptimal outcomes for spinal cord injuries (SCI), underscoring the critical need for innovative treatment strategies to offer hope to patients.

Methods

In this study, gelatin methacrylic acid hydrogel scaffolds loaded with nerve growth factors (GMNF) were prepared and used to verify the performance of SCI. The physicochemical and biological properties of the GMNF were tested. The effect of GMNF on activity of neuronal progenitor cells (NPCs) was investigated in vitro. Histological staining and motor ability was carried out to assess the ability of SCI repair in SCI animal models.

Results

Achieving nerve growth factors sustained release, GMNF had good biocompatibility and could effectively penetrate into the cells with good targeting permeability. GMNF could better enhance the activity of NPCs and promote their directional differentiation into mature neuronal cells in vitro, which could exert a good neural repair function. In vivo, SCI mice treated with GMNF recovered their motor abilities more effectively and showed better wound healing by macroscopic observation of the coronal surface of their SCI area. Meanwhile, the immunohistochemistry demonstrated that the GMNF scaffolds effectively promoted SCI repair by better promoting the colonization and proliferation of neural stem cells (NSCs) in the SCI region and targeted differentiation into mature neurons.

Conclusion

The application of GMNF composite scaffolds shows great potential in SCI treatment, which are anticipated to be a potential therapeutic bioactive material for clinical application in repairing SCI in the future.

Individualized cortical gyrification in neonates with congenital heart disease

Congenital heart disease is associated with impaired early brain development and adverse neurodevelopmental outcomes. This study investigated how individualized measures of preoperative cortical gyrification index differ in 142 infants with congenital heart disease, using a normative modelling approach with reference data from 320 typically developing infants. Gyrification index Z-scores for the whole brain and six major cortical areas were generated using two different normative models: one accounting for post-menstrual age at scan, post-natal age at scan and sex, and another additionally accounting for supratentorial brain volume. These Z-scores were compared between congenital heart disease and control groups to test the hypothesis that cortical folding in infants with congenital heart disease deviates from the normal developmental trajectory. The relationships between whole-brain gyrification index Z-scores from the two normative models and both cerebral oxygen delivery and neurodevelopmental outcomes were also investigated. Global and regional brain gyrification was significantly reduced in neonates with congenital heart disease, but not when supratentorial brain volume was accounted for. This finding suggests that whilst cortical folding is reduced in congenital heart disease, it is primarily driven by a reduction in brain size. There was a significant positive correlation between cerebral oxygen delivery and whole-brain gyrification index Z-scores in congenital heart disease, but not when supratentorial brain volume was accounted for. Cerebral oxygen delivery is therefore likely to play a more important role in the biological processes underlying volumetric brain growth than cortical folding. No significant associations between whole-brain gyrification index Z-scores and motor/cognitive outcomes or autism traits were identified in the 70 infants with congenital heart disease who underwent neurodevelopmental assessment at 22-months. Our results suggest that chronic in utero and early post-natal hypoxia in congenital heart disease is associated with reductions in cortical folding that are proportional to reductions in supratentorial brain volume.

Continuous cell type diversification throughout the embryonic and postnatal mouse visual cortex development

The mammalian cortex is composed of a highly diverse set of cell types and develops through a series of temporally regulated events that build out the cell type and circuit foundation for cortical function. The mechanisms underlying the development of different cell types remain elusive. Single-cell transcriptomics provides the capacity to systematically study cell types across the entire temporal range of cortical development. Here, we present a comprehensive and high-resolution transcriptomic and epigenomic cell type atlas of the developing mouse visual cortex. The atlas was built from a single-cell RNA-sequencing dataset of 568,674 high-quality single-cell transcriptomes and a single-nucleus Multiome dataset of 194,545 high-quality nuclei providing both transcriptomic and chromatin accessibility profiles, densely sampled throughout the embryonic and postnatal developmental stages from E11.5 to P56. We computationally reconstructed a transcriptomic developmental trajectory map of all excitatory, inhibitory, and non-neuronal cell types in the visual cortex, identifying branching points marking the emergence of new cell types at specific developmental ages and defining molecular signatures of cellular diversification. In addition to neurogenesis, gliogenesis and early postmitotic maturation in the embryonic stage which gives rise to all the cell classes and nearly all subclasses, we find that increasingly refined cell types emerge throughout the postnatal differentiation process, including the late emergence of many cell types during the eye-opening stage (P11-P14) and the onset of critical period (P21), suggesting continuous cell type diversification at different stages of cortical development. Throughout development, we find cooperative dynamic changes in gene expression and chromatin accessibility in specific cell types, identifying both chromatin peaks potentially regulating the expression of specific genes and transcription factors potentially regulating specific peaks. Furthermore, a single gene can be regulated by multiple peaks associated with different cell types and/or different developmental stages. Collectively, our study provides the most detailed dynamic molecular map directly associated with individual cell types and specific developmental events that reveals the molecular logic underlying the continuous refinement of cell type identities in the developing visual cortex.

SynBot is an open-source image analysis software for automated quantification of synapses

The formation of precise numbers of neuronal connections, known as synapses, is crucial for brain function. Therefore, synaptogenesis mechanisms have been one of the main focuses of neuroscience. Immunohistochemistry is a common tool for visualizing synapses. Thus, quantifying the numbers of synapses from light microscopy images enables screening the impacts of experimental manipulations on synapse development. Despite its utility, this approach is paired with low-throughput analysis methods that are challenging to learn, and the results are variable between experimenters, especially when analyzing noisy images of brain tissue. We developed an open-source ImageJ-based software, SynBot, to address these technical bottlenecks by automating the analysis. SynBot incorporates the advanced algorithms ilastik and SynQuant for accurate thresholding for synaptic puncta identification, and the code can easily be modified by users. The use of this software will allow for rapid and reproducible screening of synaptic phenotypes in healthy and diseased nervous systems.