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Single-cell transcriptomic maps of the human fetal subpallium a, Cell clustering of human fetal subpallial samples at gestational weeks (GW) 9 to 12 integrated using harmony and depicted using t-SNE. b, The distribution of each subclusters in the subpallium at four developing stages. Colors indicate cell clusters as shown in a. c, Clustering of all cells from four developing stages after batch correction visualized using t-SNE. d, Heatmap illustrating differentially expressed genes (DEGs) in five major clusters and 17 subclusters. e, Assessment of 71 genes from 2,922 DEGs using Random Forest Classifier from scikit-learn of the remaining 16 subclusters after removing excitatory lineages. ‘True label’ indicates the manual annotation based on the 71 genes.
Source publication
Precise generation of excitatory neurons and inhibitory interneurons is crucial for proper formation and function of neural circuits in the mammalian brain. Because of the size and complexity of the human brain, it is a challenge to reveal the rich diversity of interneurons. To decipher origin and diversity of interneurons in the human fetal subpal...
Citations
... On the other hand, the impaired development, migration, or dysfunction of cortical GABAergic interneurons, referred to as interneuronopathy, further exacerbates the dysregulation of GABAergic network formation and related signaling and contribute to the large variety of epilepsies and cooccurring neurodevelopmental disorders (NDDs) [27,39,50]. GABAergic signaling is mediated by a variety of different interneuron subpopulations [60,66]. The neuronal diversity in the cortex is associated with the specific transient germinal zones, named the medial and caudal ganglionic eminences (MGE and CGE, respectively) [38,42]. ...
GABAergic interneurons play a critical role in maintaining neural circuit balance, excitation–inhibition regulation, and cognitive function modulation. In tuberous sclerosis complex (TSC), GABAergic neuron dysfunction contributes to disrupted network activity and associated neurological symptoms, assumingly in a cell type-specific manner. This GABAergic centric study focuses on identifying specific interneuron subpopulations within TSC, emphasizing the unique characteristics of medial ganglionic eminence (MGE)- and caudal ganglionic eminence (CGE)-derived interneurons. Using single-nuclei RNA sequencing in TSC patient material, we identify somatostatin-expressing (SST+) interneurons as a unique and immature subpopulation in TSC. The disrupted maturation of SST+ interneurons may undergo an incomplete switch from excitatory to inhibitory GABAergic signaling during development, resulting in reduced inhibitory properties. Notably, this study reveals markers of immaturity specifically in SST+ interneurons, including an abnormal NKCC1/KCC2 ratio, indicating an imbalance in chloride homeostasis crucial for the postsynaptic consequences of GABAergic signaling as well as the downregulation of GABAA receptor subunits, GABRA1, and upregulation of GABRA2. Further exploration of SST+ interneurons revealed altered localization patterns of SST+ interneurons in TSC brain tissue, concentrated in deeper cortical layers, possibly linked to cortical dyslamination. In the epilepsy context, our research underscores the diverse cell type-specific roles of GABAergic interneurons in shaping seizures, advocating for precise therapeutic considerations. Moreover, this study illuminates the potential contribution of SST+ interneurons to TSC pathophysiology, offering insights for targeted therapeutic interventions.
... After arriving in the cortex, early interneurons migrate horizontally in cortical plates and then more interneurons are produced, migrating through the intermediate zone. At a later time of cortical formation (E14-15), three migratory routes (also known as tangential migration flows) can be observed in the cortex, from the marginal area, basal area and lower middle and subventricular area [10]. ...
A variety of neurological and psychiatric disorders have recently been shown to be highly associated with the abnormal development and function of oligodendrocytes (OLs) and interneurons. OLs are the myelin-forming cells in the central nervous system (CNS), while interneurons are important neural types gating the function of excitatory neurons. These two types of cells are of great significance for the establishment and function of neural circuits, and they share similar developmental origins and transcriptional architectures, and interact with each other in multiple ways during development. In this review, we compare the similarities and differences in these two cell types, providing an important reference and further revealing the pathogenesis of related brain disorders.
... Several factors regulate initial interneuron fate decisions within the MGE, including gradients of diffusible cues, spatial location of progenitors, temporal birthdates and the mode of neurogenesis (Flames et al., 2007;Glickstein et al., 2007;Wonders et al., 2008;Inan et al., 2012;Petros et al., 2015;Bandler et al., 2017Bandler et al., , 2021Mi et al., 2018;Allaway et al., 2021). The advent of single cell sequencing technologies over the last decade has generated a transcriptional and epigenetic 'ground truth' in the ganglionic eminences in mice (Mayer et al., 2018;Mi et al., 2018;Allaway et al., 2021;Bandler et al., 2021;Lee et al., 2022a;Rhodes et al., 2022), and more recently, in primates and humans (Nowakowski et al., 2017;Eze et al., 2021;Shi et al., 2021;Yu et al., 2021;Braun et al., 2022;Schmitz et al., 2022;Velmeshev et al., 2022;Zhao et al., 2022). With this baseline in place, researchers can better characterize how genetic and epigenetic perturbations affect the fate and maturation of GABAergic interneurons. ...
... One gene displayed decreased relative H3K27me3 levels and decreased gene expression in the cKO MGE (Zeb2). ZEB2 is co-expressed with MAF+ cells in the human MGE (Yu et al., 2021), so decreased of Zeb2 expression in the cKO MGE is another predictor of decreased PV+ cells. Three genes displayed increased relative H3K27me3 levels and decreased gene expression in the cKO MGE (Kirrel3, Meis1 and Zfhx3), which represents a logical correlation between H3K27me3 levels and gene expression. ...
Introduction
Enhancer of zeste homolog 2 (Ezh2) is responsible for trimethylation of histone 3 at lysine 27 (H3K27me3), resulting in repression of gene expression. Here, we explore the role of Ezh2 in forebrain GABAergic interneuron development.
Methods
We removed Ezh2 in the MGE by generating Nkx2-1Cre;Ezh2 conditional knockout mice. We then characterized changes in MGE-derived interneuron fate and electrophysiological properties in juvenile mice, as well as alterations in gene expression, chromatin accessibility and histone modifications in the MGE.
Results
Loss of Ezh2 increases somatostatin-expressing (SST+) and decreases parvalbumin-expressing (PV+) interneurons in the forebrain. We observe fewer MGE-derived interneurons in the first postnatal week, indicating reduced interneuron production. Intrinsic electrophysiological properties in SST+ and PV+ interneurons are normal, but PV+ interneurons display increased axonal complexity in Ezh2 mutant mice. Single nuclei multiome analysis revealed differential gene expression patterns in the embryonic MGE that are predictive of these cell fate changes. Lastly, CUT&Tag analysis revealed that some genomic loci are particularly resistant or susceptible to shifts in H3K27me3 levels in the absence of Ezh2, indicating differential selectivity to epigenetic perturbation.
Discussion
Thus, loss of Ezh2 in the MGE alters interneuron fate, morphology, and gene expression and regulation. These findings have important implications for both normal development and potentially in disease etiologies.
... Notably, the advent of single-cell and single-nucleus mRNA sequencing (scRNA-seq and snRNA-seq) technologies has signi cantly advanced the investigation of interneuron transcriptomic types (t-types). These types can mostly be mapped to interneurons with established morphology and electrophysiology properties, underlining the utility of t-type in de ning diverse interneuron cell types [15][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] . ...
... We assumed the expressed canonical gene markers could represent the existence of cgeInNs, and consequently found that NR2F2, NR2F1, PROX1 expressed in MGE and LGE in addition to CGE (Supplementary Fig. 5c). Much more than that, the re-analysis of external in-situ sequencing data of GW12 human brain revealed the sparse distribution of NR2F2 in MGE and LGE ( Supplementary Fig. 5e) 21 . Lastly, pairwise transcriptomic correlation analysis replicated the regional transcriptomic similarity patterns observed in mgeInNs (Fig. 3b), suggesting the same principle could be applied to the molecular programs governing the cortical and ganglionic migration of cgeInNs (Fig. 4b, Supplementary Fig. 7a-b). ...
... However, the debate about whether LGE contributes to the neocortical population of interneurons continues. Notably, LGE has been shown to give rise to 30% of PV and SST cortical interneurons in the human fetal brain 21 . In developing macaques, a recent study reported interneurons probably derived from dorsal LGE showed remarkable enrichment in dorsomedial cortical frontal lobe, and their further investigation found these cells more concentrated in deep white matter and might be contributed by the Arc and Arc-ACC migratory streams 18 . ...
Cortical interneurons generated from ganglionic eminence via a long-distance journey of tangential migration display evident cellular and molecular differences across brain regions, which seeds the heterogeneous cortical circuitry in primates. However, whether such regional specifications in interneurons are intrinsically encoded or gained through interactions with the local milieu remains elusive. Here, we recruit over 700,000 interneurons from cerebral cortex and subcortex including ganglionic eminence within the developing human and macaque species. Our integrative and comparative analyses reveal that less transcriptomic alteration is accompanied by interneuron migration within the ganglionic eminence subdivisions, in contrast to the dramatic changes observed in cortical tangentialmigration, which mostly characterize the transcriptomic specification for different destinations and for species divergence. Moreover, the in-depth survey of temporal regulation illustrates species differences in the developmental dynamics of cell types, e.g., the employment of CRH in primate interneurons during late-fetal stage distinguishes from their postnatal emergence in mice, and our entropy quantifications manifest the interneuron diversities gradually increase along the developmental ages in human and macaque cerebral cortices. Overall, our analyses depict the spatiotemporal features appended to cortical interneurons, providing a new proxy for understanding the relationship between cellular diversity and functional progression.
... In situ sequencing was achieved using an improved assay that exploits a novel probing and barcoding approach 44 for highly multiplexed in situ gene expression profiling compared with earlier methods. 45,46 This approach improves not only signal intensity but also the specificity of in situ gene expression. Mice that underwent 4WMI displayed a nearly 6-fold increase of Piezo1 + cells in the TDRG relative to 4Wsham mice ( Figure 1F and 1G). ...
BACKGROUND
Heart failure is associated with a high rate of mortality and morbidity, and ventricular remodeling invariably precedes heart failure. Ventricular remodeling is fundamentally driven by mechanotransduction that is regulated by both the nervous system and the immune system. However, it remains unknown which key molecular factors govern the neuro/immune/cardio axis that underlies mechanotransduction during ventricular remodeling. Here, we investigated whether the mechanosensitive Piezo cation channel–mediated neurogenic inflammatory cascade underlies ventricular remodeling–related mechanotransduction.
METHODS
By ligating the left coronary artery of rats to establish an in vivo model of chronic myocardial infarction (MI), lentivirus-mediated thoracic dorsal root ganglion (TDRG)–specific Piezo1 knockdown rats and adeno-associated virus–PHP.S—mediated TDRG neuron–specific Piezo1 knockout mice were used to investigate whether Piezo1 in the TDRG plays a functional role during ventricular remodeling Subsequently, neutralizing antibody–mediated TDRG IL-6 (interleukin-6) inhibition rats and adeno-associated virus–PHP.S—mediated TDRG neuron–specific IL-6 knockdown mice were used to determine the mechanism underlying neurogenic inflammation. Primary TDRG neurons were used to evaluate Piezo1 function in vitro.
RESULTS
Expression of Piezo1 and IL-6 was increased, and these factors were functionally activated in TDRG neurons at 4 weeks after MI. Both knockdown of TDRG-specific Piezo1 and deletion of TDRG neuron–specific Piezo1 lessened the severity of ventricular remodeling at 4 weeks after MI and decreased the level of IL-6 in the TDRG or heart. Furthermore, inhibition of TDRG IL-6 or knockdown of TDRG neuron–specific IL-6 also ameliorated ventricular remodeling and suppressed the IL-6 cascade in the heart, whereas the Piezo1 level in the TDRG was not affected. In addition, enhanced Piezo1 function, as reflected by abundant calcium influx induced by Yoda1 (a selective agonist of Piezo1), led to increased release of IL-6 from TDRG neurons in mice 4 weeks after MI.
CONCLUSIONS
Our findings point to a critical role for Piezo1 in ventricular remodeling at 4 weeks after MI and reveal a neurogenic inflammatory cascade as a previously unknown facet of the neuronal immune signaling axis underlying mechanotransduction.
... Although recent studies have demonstrated relatively good conservation of some gene expression between rodent and human brains, large differences in the expression of many genes have also been observed 8,23,26,30,42,51,53,77,[80][81][82] . Importantly, many common drug targets in psychiatric research show considerably different expression patterns between rodents and human neuronal and glial cell types across brain regions (Fig. 3). ...
In spite of major efforts and investment in development of psychiatric drugs, many clinical trials have failed in recent decades, and clinicians still prescribe drugs that were discovered many years ago. Although multiple reasons have been discussed for the drug development deadlock, we focus here on one of the major possible biological reasons: differences between the characteristics of drug targets in preclinical models and the corresponding targets in patients. Importantly, based on technological advances in single-cell analysis, we propose here a framework for the use of available and newly emerging knowledge from single-cell and spatial omics studies to evaluate and potentially improve the translational predictivity of preclinical models before commencing preclinical and, in particular, clinical studies. We believe that these recommendations will improve preclinical models and the ability to assess drugs in clinical trials, reducing failure rates in expensive late-stage trials and ultimately benefitting psychiatric drug discovery and development.
... The colors label the cell type identities in the graphs. (q) Schematic representation of embryonic brain regions as the in vivo counterpart of the diverse neural cell fates found within COs. aRG: apical radial glial, bRG: basal radial glial, AST: astrocyte, OPC: oligodendrocyte progenitor cell, PCP: primary cortical plate, DL1,2: Deep layer cortical neuron 1,2, UL1,2: Upper layer cortical neuron 1,2, CGEIN: caudal ganglionic eminences interneuron, LGEIN: lateral ganglionic eminences interneuron, CRIN: Cajal-Retzius interneuron, OBIN: olfactory bulb interneuron, NPs: neural progenitor cells, IPC: intermediate progenitor cell, ExNs: excitatory neurons, INs: inhibitory neurons, MGE: medial ganglionic eminences) TSHZ1 for olfactory bulb interneurons (OBINs) (Figure 4m and S4m and S5m), SCGN, DLX, CALB2 expression for both lateral and caudal ganglionic eminences (LGE, CGE), and higher expression of PROX1 and NR2F2 (COUP-TFII) for caudal ganglionic eminence (Figure 4b,n and S4b,n and S5b,n) (Schmitz et al., 2022;Yu et al., 2021). This indicated presence of cells from only the most dorsal parts of the subpallium structure (LGE, CGE) and absence of ventrally located medial ganglionic eminence (MGE) cells, which is consistent with the previously mentioned lack of NKX2.1 expression. ...
Human cerebral organoids (COs) are self-organizing three-dimensional (3D) neural structures that provide a human-specific platform to study the cellular and molecular processes that underlie different neurological events. The first step of CO generation from human pluripotent stem cells (hPSCs) is neural induction, which is an in vitro simulation of neural ectoderm development. Several signaling pathways cooperate during neural ectoderm development and in vitro differentiation of hPSCs toward neural cell lineages is also affected by them. In this study, we considered some of the known sources of these variable signaling cues arising from cell culture media components and sought to modulate their effects by applying a comprehensive combination of small molecules and growth factors for CO generation. Histological analysis demonstrated that these COs recapitulate the neural progenitor zone and early cortical layer organization, containing different types of neuronal and glial cells which was in accordance with single-nucleus transcriptome profiling results. Moreover, patch clamp and intracellular Ca²⁺ dynamic studies demonstrated that the COs behave as a functional neural network. Thus, this method serves as a facile protocol for generating hPSC-derived COs that faithfully mimic the features of their in vivo counterparts in the developing human brain.
See also Figure 1(Fig. 1).
... We initially analyzed the subpallium in the human fetal brain. We captured 278 cells associated with the oligodendrocyte lineage according to known oligodendrocyte markers, and analyzed 271 cells in detail after processing quality control (see methods; Supplementary Table 3; GSE165388) [22]. We grouped these 271 cells into 5 clusters, characterized as 3 oligodendrocyte progenitor cell clusters, OPC1subpallium (OPC1-Sub), OPC2-Sub, and OPC3-Sub, and oligodendrocyte 1 and 2 (OL1-Sub and OL2-Sub) using principal component dimensionality reduction and Uniform Manifold Approximation and Projection (UMAP) dimensionality reduction of Seurat ( Fig. 1A and B). ...
Oligodendrocytes form myelin sheaths and wrap axons of neurons to facilitate various crucial neurological functions. Oligodendrocyte progenitor cells (OPCs) persist in the embryonic, postnatal, and adult central nervous system (CNS). OPCs and mature oligodendrocytes are involved in a variety of biological processes such as memory, learning, and diseases. How oligodendrocytes are specified in different regions in the CNS, in particular in humans, remains obscure. We here explored oligodendrocyte development in three CNS regions, subpallium, brainstem, and spinal cord, in human fetuses from gestational week 8 (GW8) to GW12 using single-cell RNA sequencing. We detected multiple lineages of OPCs and illustrated distinct developmental trajectories of oligodendrocyte differentiation in three CNS regions. We also identified major genes, particularly transcription factors, which maintain status of OPC proliferation and promote generation of mature oligodendrocytes. Moreover, we discovered new marker genes that might be crucial for oligodendrocyte specification in humans, and detected common and distinct genes expressed in oligodendrocyte lineages in three CNS regions. Our study has demonstrated molecular heterogeneity of oligodendrocyte lineages in different CNS regions and provided references for further investigation of roles of important genes in oligodendrocyte development in humans.
... These expressed genes associated with ventral telencephalic 142 identity, including DLX2/5/6, and GAD1/2 and lacked expression of dorsal telencephalic 143 marker EMX1 (Fig 2B) (Supp table). Integration with published scRNAseq data from fetal 144 human ventral telencephalon (Yu et al., 2021) showed that IN1 and 2 cells are most similar to 145 interneuron precursors in the lateral and medial ganglionic eminences (LGE and MGE 146 respectively) (Supp Fig 2B,C). (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. ...
The transcription factor PAX6 is a crucial regulator of multiple aspects of embryonic forebrain development. Its well-known roles in mice include regulating differentiation of excitatory and inhibitory neurons in the embryonic cortex. PAX6’s roles during human forebrain development are less well understood. Using human cerebral organoids, we investigated PAX6’s roles in human neurodevelopment. Homozygous PAX6 mutant ( PAX6 -/- ) organoids were larger than controls and contained inhibitory cell types not found in PAX6 +/+ controls. These inhibitory cells exhibited clear transcriptomic similarities and comparable distribution to analogous inhibitory cells previously described in Pax6 -/- mice. Differentiation trajectory inferencing showed that the inhibitory cells were generated from both radial glia and neuroectodermal progenitor populations. Inferring cell-cell communication using CellChat showed that loss of PAX6 in cerebral organoids increased the probability of cells engaging with inappropriate signalling pathways. Our findings indicate that while PAX6’s role in controlling excitatory versus inhibitory neural differentiation is conserved, there are alterations in the activities of intercellular signalling pathways in human PAX6 -/- cortical progenitors that have not been described in mice, indicating potential species-specific mechanistic differences.
Summary Statement
To identify likely roles of PAX6 during human embryonic development, we generated and analysed human PAX6 mutant cerebral organoids, revealing strong similarities and some differences to Pax6’s well-known roles in rodents.
... We generated vCOs from an isogenic control (CTRL) and the E370K iPSC line and characterized both at different stages of development. In particular, we analyzed the expression of typical markers of MGE (NKX2-1), CGE (PAX6), and LGE (MEIS2) (7,24,25) in vCOs at day 30 (D30), D45, and D60 of culture (Fig. 1, A to F, and fig. S1, C to N). ...
... The mammalian neocortex is mainly populated by glutamatergic excitatory neurons, while GABAergic inhibitory neurons [here, "interneurons" (INs)] are present in smaller proportions (3). In rodents, approximately 15 to 20% of neocortical neurons are INs (4), while primates, including humans, have higher proportions (circa 24%) (5)(6)(7). ...
... For this reason, we decided to dissect the transcriptional signatures of vMOs-E370K, performing scRNA-seq analysis on vMCOs (Fig. 5A). The 4898 identified cells were clustered into five main clusters (Fig. 5, B and C), including progenitors expressing TOP2A; IP expressing NKX2-1, ASCL1, and PAX6; and neurons expressing DLX5 and MAP2 (Fig. 5D) (7,11). ...
Disruption in neurogenesis and neuronal migration can influence the assembly of cortical circuits, affecting the excitatory-inhibitory balance and resulting in neurodevelopmental and neuropsychiatric disorders. Using ventral cerebral organoids and dorsoventral cerebral assembloids with mutations in the extracellular matrix gene LGALS3BP, we show that extracellular vesicles released into the extracellular environment regulate the molecular differentiation of neurons, resulting in alterations in migratory dynamics. To investigate how extracellular vesicles affect neuronal specification and migration dynamics, we collected extracellular vesicles from ventral cerebral organoids carrying a mutation in LGALS3BP, previously identified in individuals with cortical malformations and neuropsychiatric disorders. These results revealed differences in protein composition and changes in dorsoventral patterning. Proteins associated with cell fate decision, neuronal migration, and extracellular matrix composition were altered in mutant extracellular vesicles. Moreover, we show that treatment with extracellular vesicles changes the transcriptomic profile in neural progenitor cells. Our results indicate that neuronal molecular differentiation can be influenced by extracellular vesicles.
