Activity-dependent neuroprotective protein (ADNP) is a critical regulator of neurodevelopment, and most pathogenic variants reported in Helsmoortel–Van der Aa syndrome (HVDAS) are truncating variants. In contrast, the functional consequences of ADNP missense variants remain largely unclear. We integrated an ADNP variant cohort in China with variants recorded in the NCBI ClinVar database, revealing a major gap in the interpretation of ADNP missense variants. We investigated a rare de novo ADNP missense variant, p.C687R, predicted to disrupt the ninth zinc finger domain. In vitro, p.C687R was overexpressed in HEK293T cells to assess subnuclear localization by immunofluorescence and chromatin binding patterns using CUT Tag, with chromatin interactions inferred from published Hi-C datasets. CRISPR/Cas9-mediated ADNP knockout was performed for comparison. In vivo, wild-type ADNP or p.C687R was introduced into the embryonic mouse cortex at E14.5 via in utero electroporation (IUE) and neuronal development was evaluated at E18.5 and P14. Patient-derived induced pluripotent stem cells (iPSCs) from a de novo p.C687R carrier were differentiated into neural progenitor cells (NPCs) and analyzed by multi-omic profiling (RNA-seq, ChIP-seq, ATAC-seq), with lineage-specific markers examined by immunofluorescence. p.C687R displays altered subnuclear localization and redistributes wild-type ADNP when overexpressed in HEK293T. IUE in the mouse cortical plate revealed impaired neuronal migration and abnormal cortical arborization. Genome-wide profiling in HEK293T demonstrated a p.C687R-specific chromatin occupancy pattern, preferentially targeting histone modification-related genes. Knockout of ADNP led to upregulation of neuronal genes, including GABAergic lineage-associated genes. In patient-derived iPSCs, a distinct set of neurodevelopmental genes, including key regulators of GABAergic differentiation, showed increased bivalent histone marks (H3K4me3/H3K27me3). Although their promoters remained in an open chromatin state, these genes were transcriptionally silent in pluripotent cells but became more activated upon GABAergic differentiation. This study is based on a single patient-derived line in combination with complementary experimental models. In the heterozygous endogenous context, distinguishing increased functional activity from dosage-related effects requires further investigation. Replication in additional patient-derived or engineered lines is required to determine the generalizability. Our results suggest that p.C687R may exert gain-of-function-like effects in experimental systems and underscore chromatin-mediated regulation of GABAergic lineage genes in HVDAS.

DYRK1A syndrome is a neurodevelopmental disorder caused by DYRK1A haploinsufficiency. We generated a human induced pluripotent stem cell (iPSC) line, FDIBSi002-A, from a 4-year-old female patient carrying a de novo heterozygous c.1042G>A (p.G348R) mutation in DYRK1A. Peripheral blood mononuclear cells (PBMCs) were reprogrammed using non-integrating episomal vectors. The established iPSC line exhibited a normal karyotype (46, XX), expressed pluripotency markers, and demonstrated trilineage differentiation potential. This patient-specific cell line provides a valuable model for investigating the pathogenic mechanisms of DYRK1A-related intellectual disability and for drug screening.

CHARGE syndrome is a multisystem neurodevelopmental disorder characterized by coloboma, heart defects, atresia choanae, growth retardation, genital abnormalities, and ear abnormalities. The CHD7 gene is the causal gene. A human iPSC line harboring a de novo heterozygous CHD7 mutation (c.3982C>T) was generated from peripheral blood mononuclear cells of a patient with CHARGE syndrome. This iPSC line exhibited typical human embryonic stem cell-like morphology, pluripotent markers, normal karyotype, and could differentiate into the three germ layers. This iPSC line is valuable for studying disease mechanisms and conducting drug screening in patient with CHARGE syndrome.

Dysfunction of striatal medium spiny neurons (MSNs) is implicated in several neurological disorders, including Huntington's disease (HD). Despite progress in characterizing MSN pathology in HD, mechanisms underlying MSN susceptibility remain unknown, driving the need for MSNs derived from human pluripotent stem cells (hPSCs), especially subtypes in research and therapy. Here, we established a scalable 3D-default culture system to produce striatal MSNs efficiently from hPSCs by activation of the endogenous sonic hedgehog (SHH) pathway. These cells expressed canonical markers of striatal progenitors and dopamine D1 (D1) and dopamine D2 (D2) MSNs and presented dynamic specification and transcriptional signatures that closely resemble endogenous MSNs at single-cell resolution, both in vitro and post-transplantation in HD mice with quinolinic acid (QA) lesions. Grafted human cells survived and matured into D1-/D2-like MSNs and projected axons to endogenous targets including globus pallidus externus, globus pallidus internus, and substantia nigra pars reticulata to reconstruct the basal ganglia pathways. Functionally, they displayed spontaneous synaptic currents, received regulation from host cortex and thalamus, and were modulated by dopamine to either enhance or reduce neuronal excitability, similar to the endogenous D1-/D2-MSNs, subsequently improving behavior in QA-lesioned HD mice. Our study presents a method for generating authentic MSNs, providing a reliable cell source for HD cell therapy, mechanistic studies, and drug screening.

The low in vivo yield of midbrain dopaminergic (mDA) neurons and uncertain lineage fates of donor cells following transplantation impede clinical application of human pluripotent stem cell (hPSC)-based cell therapy for Parkinson’s disease (PD). We developed a three-dimensional (3D) differentiation method, SphereDiff, to generate high-purity mDA progenitors (mDAPs), leading to a significant enrichment of mDA neurons post transplantation. Grafted mDA neurons fully restored dopamine levels and corrected motor deficits in PD model mice. Single-cell spatial transcriptomics revealed a patterned distribution of mDA neuron subtypes and glial cells. Using cross-transplantation single-cell split barcoding (TX-SISBAR), we elucidated the clonal lineage fates of donor cells post transplantation, revealing the mDA neuron and astrocyte fates of mDAPs and glutamatergic neuron fates of diencephalic progenitors. Leveraging these lineage insights, we further refined SphereDiff and eliminated off-target lineage cells. Producing high in vivo efficacy, lineage-defined donor cells supports safer and more effective PD cell therapy in regenerative medicine.

Neonatal brain development constitutes a critical period of structural and functional maturation underpinning sensory, motor, and cognitive capacities. The glymphatic system—a cerebral waste clearance network—remains poorly understood in neonates. We investigated non-invasive magnetic resonance imaging (MRI) biomarkers of glymphatic system and their developmental correlates in neonates. In 117 neonates undergoing high-resolution T1-weighted and diffusion MRI, we quantified two glymphatic metrics: (1) diffusion tensor imaging along the perivascular space (DTI-ALPS) index, reflecting perivascular fluid dynamics; (2) choroid plexus (CP) volume, a cerebrospinal fluid (CSF) production marker. Associations with postmenstrual age (PMA) at MRI scan, gestational age (GA), birth weight (BW), and sex were analyzed using covariate-adjusted models. Preterm neonates displayed significantly reduced DTI-ALPS indices versus term neonates (total index: 1.01 vs. 1.05, P = 0.002), with reductions persisting after adjustment (P < 0.05). CP volumes showed right-dominant pre-adjustment differences (preterm: 0.33 vs. term: 0.39, P = 0.039) that attenuated post-adjustment (P = 0.348). DTI-ALPS indices demonstrated transient correlations with PMA/GA/BW in unadjusted analyses (P < 0.05), whereas CP volumes maintained robust PMA associations post-adjustment in all neonates (P = 0.037) and term subgroup (P = 0.013). No significant effects of sex on both metrics were observed. Our findings reveal prematurity-associated delays in glymphatic maturation, rather than biological sex. The persistent PMA-CP volume relationship suggests developmental regulation of CSF production, while attenuated DTI-ALPS correlations highlight covariate-mediated effects. These glymphatic metrics show potential for monitoring neurodevelopmental trajectories, though longitudinal validation is required to establish their clinical utility in neonatal care. Not applicable.

A10 dopaminergic neurons located in the ventral tegmental area play central roles in reward-related and goal-directed behaviors and are proposed to be target cells for treatment of various psychiatric disorders, including depression. Here, we report an efficient differentiation method to generate A10-like midbrain dopaminergic (mDA) neurons from human pluripotent stem cells (hPSCs) and found that post-mitotic patterning by Notch inhibitor, glial cell line-derived neurotrophic factor (GDNF), and ascorbic acid (AA) induced A10 subtype specification. These hPSC-derived mDA neurons exhibited characteristics of the A10 subtype, including gene expression profiles and electrophysiological properties. Moreover, grafted A10-like mDA neurons specifically project to their endogenous target brain regions and induce the anxiolytic phenotype in normal mice or antidepressant-like phenotypes in depression model mice. These results indicate that grafted A10-like mDA neurons can reconstruct specific circuits and functionally restore impaired circuits, highlighting the promising application of hPSC-derived neuron subtypes in the treatment of neuropsychiatric disorders.

ADNP syndrome is a neurodevelopmental disorder characterized by autism, intellectual disability, and other physical and behavioral health manifestations. Mutations in ADNP gene is responsible for ADNP syndrome. A human iPSC line with a de novo heterozygous ADNP mutation (ADNP c. 2059 T>C) was generated from peripheral blood mononuclear cells of a patient with ADNP syndrome. This iPSC line showed typical human embryonic stem cell-like morphology, normal karyotype, pluripotency, and ability to differentiate into three germ layers. This iPSC line provides a useful resource to study the pathogenesis and drug screening of ADNP syndrome.

Focal cortical dysplasia (FCD) II is a cortical malformation characterized by cortical architectural abnormalities, dysmorphic neurons, with or without balloon cells. Here, we systematically explored the pathophysiological role of the GATOR1 subunit NPRL3 variants including a novel mutation from iPSCs derived from one FCD II patient. Three FCD II children aged 0.5–7 years who underwent cerebral lesion resection in our hospital from March 2019 to October 2019 were included in this study. We generated patient-derived iPSCs and performed whole-exome sequencing to accurately identify somatic cells with mutations. The effect of the newly identified NPRL3 mutation found in one of our FCD II patients was evaluated using the personalized cortical organoid model and the NPRL3 knockout HEK293T cells. Whole-exome sequencing of iPSCs derived from FCD II patients revealed a novel NPRL3 C.767G > C (p.R256P) heterozygous mutation. Cortical organoids generated from iPSCs of FCD II patients were larger than control iPSCs, with increased number of p-S6+ cells and NeuN+ neurons. In NPRL3 knockout HEK293T cells, overexpression of NPRL3 together with NPRL2 protein is necessary to reduce p-S6 level upon amino acid starvation. The reduced binding between NPRL3 Arg256Pro and NPRL2 protein leads to downregulation of the relative total protein amount of both proteins in the cell. Our study describes a novel cortical organoid model generated from iPSCs of the FCD patients to investigate the underlying mechanism of NPRL3-related epilepsy. The mutation of NPRL3 Arg256Pro impaired the function of NPRL3 protein via affecting the binding with NPRL2 protein, which resulted in unstable protein monomer.

BackgroundHypoxic-ischemic encephalopathy (HIE) is a major cause of neonatal disability and mortality. Although intensive studies and therapeutic approaches, there are limited restorative treatments till now. Human embryonic stem cell (hESCs)-derived cortical neural progenitors have shown great potentials in ischemic stroke in adult brain. However, it is unclear whether they are feasible for cortical reconstruction in immature brain with hypoxic-ischemic encephalopathy.MethodsBy using embryonic body (EB) neural differentiation method combined with DAPT pre-treatment and quantitative cell transplantation, human cortical neuroblasts were obtained and transplanted into the cortex of hypoxic-ischemic injured brain with different dosages 2 weeks after surgery. Then, immunostaining, whole-cell patch clamp recordings and behavioral testing were applied to explore the graft survival and proliferation, fate commitment of cortical neuroblasts in vitro, neural circuit reconstruction and the therapeutic effects of cortical neuroblasts in HIE brain.ResultsTransplantation of human cortical neural progenitor cells (hCNPs) in HIE-injured cortex exhibited long-term graft overgrowth. DAPT pre-treatment successfully synchronized hCNPs from different developmental stages (day 17, day 21, day 28) to deep layer cortical neuroblasts which survived well in HIE injured brain and greatly prevented graft overgrowth after transplantation. Importantly, the cortical neuroblasts primarily differentiated into deep-layer cortical neurons and extended long axons to their projection targets, such as the cortex, striatum, thalamus, and internal capsule in both ipsilateral and contralateral HIE-injured brain. The transplanted cortical neurons established synapses with host cortical neurons and exhibited spontaneous excitatory or inhibitory post-synaptic currents (sEPSCs or sIPSCs) five months post-transplantation. Rotarod and open field tests showed greatly improved animal behavior by intra-cortex transplantation of deep layer cortical neuroblasts in HIE injured brain.ConclusionsTransplanted hESCs derived cortical neuroblasts survive, project to endogenous targets, and integrate into host cortical neural circuits to rescue animal behavior in the HIE-injured brain without graft overgrowth, providing a novel and safe cell replacement strategy for the future treatment of HIE.

DYRK1A haploinsufficiency causes a neurodevelopmental syndrome termed DYRK1A-related intellectual disability syndrome which is associated with a range of symptoms including microcephaly, epileptic seizures, and autism spectrum disorder. Here, we generated an induced Pluripotent Stem Cell (iPSC) line with a de novo missense mutation (DYRKIA c.1024G > T) from the peripheral blood mononuclear cells of a patient with DYRK1A-related intellectual disability syndrome. This iPSC line showed normal karyotype, exhibited pluripotency, and has three embryonic germ layers differentiation capacity. This iPSC line will be of great use in investigating the disease mechanisms and drug screening for patients with DYRK1A-related intellectual disability syndrome.

The cell lineages across developmental stages remain to be elucidated. Here, we developed single-cell split barcoding (SISBAR) that allows clonal tracking of single-cell transcriptomes across stages in an in vitro model of human ventral midbrain-hindbrain differentiation. We developed "potential-spective"and "origin-spective"analyses to investigate the cross-stage lineage relationships and mapped a multi-level clonal lineage landscape depicting the whole differentiation process. We uncovered many previously unchar-acterized converging and diverging trajectories. Furthermore, we demonstrate that a transcriptome-defined cell type can arise from distinct lineages that leave molecular imprints on their progenies, and the multilineage fates of a progenitor cell-type represent the collective results of distinct rather than similar clonal fates of individual progenitors, each with distinct molecular signatures. Specifically, we uncovered a ventral midbrain progenitor cluster as the common clonal origin of midbrain dopaminergic (mDA) neurons, midbrain glutama-tergic neurons, and vascular and leptomeningeal cells and identified a surface marker that can improve graft outcomes.

Abstract Perinatal hypoxic–ischaemic encephalopathy is the leading cause of neonatal death and permanent neurological deficits, while the basal ganglia is one of the major nuclei that is selectively and greatly affected in the brains of hypoxic–ischaemic encephalopathy patients, especially in severe cases. Human embryonic stem cell-derived neurons have shown great potential in different types of brain disorders in adults. However, it remains unknown whether and how grafted human embryonic stem cell-derived neurons can repair immature brains with hypoxic–ischaemic encephalopathy. Here, by administrating genetically labelled human embryonic stem cell-derived striatal neural progenitors into the ipsilateral striatum of hypoxic–ischaemic encephalopathy-injured mice, we found that the grafted cells gradually matured into GABA spiny projection neurons morphologically and electrophysiologically, and significantly rescued the area loss of hypoxic–ischaemic encephalopathy-injured brains. Intriguingly, using immunohistochemical staining combined with enhanced ascorbate peroxidase-based immunoelectron microscopy and rabies virus-mediated trans-synaptic tracing, we show that the grafts start to extend axonal projections to the endogenous target areas (globus pallidus externa, globus pallidus internus, substantia nigra), form synapses with host striatal, globus pallidus and nigra neurons, and receive extensive and stable synaptic inputs as early as 2 months post-transplantation. Importantly, we further demonstrated functional neural circuits re-established between the grafted neurons and host cortical, striatal and substantial nigra neurons at 3–6 months post-transplantation in the hypoxic–ischaemic encephalopathy-injured brain by optogenetics combined with electrophysiological recording. Finally, the transplanted striatal spiny projection neurons but not spinal GABA neurons restored the motor defects of hypoxic–ischaemic encephalopathy, which were reversed by clozapine-N-oxide-based inhibition of graft function. These findings demonstrate anatomical and functional reconstruction of the basal ganglia neural circuit including multiple loops by striatal spiny projection neurons in hypoxic–ischaemic encephalopathy-injured immature brains, which raises the possibility of such a cell replacement therapeutic strategy for hypoxic–ischaemic encephalopathy in neonates.

Background and Objective: Evolutionarily speaking, cilia are conserved organelles protruding from the surface of most cells, found in various cellular organisms. For a long period, primary cilia were considered as vestigial or useless organelles in the body. However, with the in-depth study of ultrastructure over recent years, researchers have discovered that abnormal primary cilia involved in corticogenesis could impose severe cilia-related cortical developmental defects or diseases. Till now, the specific mechanisms as well as pathogenesis remain unclear. Further studies are needed to explore the pathogenesis and treatment of ciliopathies associated with neurodevelopmental disorders. Methods: We searched PubMed for English literatures from 1957 to 2021 associated with the ciliary systems and recent advances on their multiple roles in the developing cerebral cortex, using the search terms “cortical development”, “developing cortex”, “primary cilia”, “primary cilium”, and “ciliopathies”. Key Content and Findings: Primary cilia are constituted of basal body, transition zone, axoneme, and ciliary membrane. Its structural and functional abnormalities may lead to cilia-related cortical diseases. Primary cilia present on neural progenitor cells and differentiated neurons with extension into the lateral ventricles. The crucial roles of primary cilia in the proliferation and differentiation of neural progenitor cells, and the migration of newborn neurons, as well as the transduction of signaling have been discovered by studying a multitude of genes/proteins associated with cilia. Conclusions: Primary cilia are essential for normal brain development, which deserve further studies. In the future, we can use brain organoids and mouse models to learn more about the roles of primary cilia to promote the diagnosis and treatment of ciliopathies.

A fundamental interest in developmental neuroscience lies in the ability to map the complete single-cell lineages within the brain. To this end, we developed a CRISPR editing-based lineage-specific tracing (CREST) method for clonal tracing in Cre mice. We then used two complementary strategies based on CREST to map single-cell lineages in developing mouse ventral midbrain (vMB). By applying snapshotting CREST (snapCREST), we constructed a spatiotemporal lineage landscape of developing vMB and identified six progenitor archetypes that could represent the principal clonal fates of individual vMB progenitors and three distinct clonal lineages in the floor plate that specified glutamatergic, dopaminergic or both neurons. We further created pandaCREST (progenitor and derivative associating CREST) to associate the transcriptomes of progenitor cells in vivo with their differentiation potentials. We identified multiple origins of dopaminergic neurons and demonstrated that a transcriptome-defined progenitor type comprises heterogeneous progenitors, each with distinct clonal fates and molecular signatures. Therefore, the CREST method and strategies allow comprehensive single-cell lineage analysis that could offer new insights into the molecular programs underlying neural specification.

CHARGE syndrome (OMIM 214800) is an autosomal dominant disease with coloboma, heart defects, atresia of choanae and retardation of growth and/or development, etc. CHD7 mutation is the major known pathogenic cause in patients with CHARGE syndrome. A human iPSC line with a novel heterozygous mutation (CHD7 c.2939 T > C) was constructed from peripheral blood mononuclear cells of a patient with CHARGE syndrome. The iPSC line showed normal karyotype, highly expressed pluripotency markers, and had differentiation potential of three germ layers. This iPSC line provides a useful model to study the underlying mechanisms and drug screening of CHARGE syndrome.

Oligodendrocyte spheroids (OL-spheroids) containing oligodendrocytes and neurons provide an accessible system to dissect demyelinating diseases and test therapeutic treatment. However, generation of human OL-spheroids is still technically challenging and time-consuming until now. Here, we presented evidence that overexpression of SOX10 and OLIG2 (SO) in human embryonic stem cells (hESCs)-derived ventral forebrain neural progenitors is sufficient to produce forebrain pre-oligodendrocytes (pre-OLs) and mature oligodendrocytes (OLs) within 20-40 days. More importantly, optimizing this procedure by overexpression of SO in ventral forebrain spheroids, we successfully generated OL-spheroids with pre-OLs, mature OLs, and neurons 40 days after OL-induction. We further demonstrated oligodendrocyte-neuron interactions and obvious axon myelination in OL-spheroids. Finally, over 30% cells developed into mature oligodendrocytes with forebrain identity and myelinate axons in mouse brain 3 months after transplantation. This study provides a strategy to generate forebrain OL-spheroids rapidly and efficiently which would facilitate development of new therapeutics for demyelinating disorders.

Human pluripotent stem cell–based (hPSC-based) replacement therapy holds great promise for the treatment of Parkinson's disease (PD). However, the heterogeneity of hPSC-derived donor cells and the low yield of midbrain dopaminergic (mDA) neurons after transplantation hinder its broad clinical application. Here, we have characterized the single-cell molecular landscape during mDA neuron differentiation. We found that this process recapitulated the development of multiple but adjacent fetal brain regions including the ventral midbrain, the isthmus, and the ventral hindbrain, resulting in a heterogenous donor cell population. We reconstructed the differentiation trajectory of the mDA lineage and identified calsyntenin 2 (CLSTN2) and protein tyrosine phosphatase receptor type O (PTPRO) as specific surface markers of mDA progenitors, which were predictive of mDA neuron differentiation and could facilitate high enrichment of mDA neurons (up to 80%) following progenitor cell sorting and transplantation. Marker-sorted progenitors exhibited higher therapeutic potency in correcting motor deficits of PD mice. Different marker-sorted grafts had a strikingly consistent cellular composition, in which mDA neurons were enriched, while off-target neuron types were mostly depleted, suggesting stable graft outcomes. Our study provides a better understanding of cellular heterogeneity during mDA neuron differentiation and establishes a strategy to generate highly purified donor cells to achieve stable and predictable therapeutic outcomes, raising the prospect of hPSC-based PD cell replacement therapies.

Background and Objective During embryonic development, the dysregulation of the proliferation and differentiation of neuronal progenitors triggers congenital brain malformations. These malformations are common causes of morbidity and mortality in patients younger than 2 years old. Animal models have provided considerable insights into the etiology of diseases that cause congenital brain malformations. However, the interspecies differences in brain structure limit the ability to transfer these insights directly to studies of humans. In recent years, brain organoids generated from human embryonic stem cells (hESCs) or human induced pluripotent stem cells (hiPSCs) using a 3-dimensional (3D) culture system have been used to resemble the structure and function of a developing human brain. Therefore, we aimed to summarize the different congenital brain malformations that have been modeled by organoids and discuss the ability of this model to reveal the cellular and molecular mechanisms of congenital brain malformations. Methods A comprehensive search was performed using PubMed and Web of Science’s Core Collection for literature published from July 1, 2000 to July 1, 2022. Keywords included terms related to brain organoids and congenital brain malformations, as well as names of individual malformations. Key Content and Findings The self-assembled 3D aggregates have been used to recapitulate structural malformations of human brains, such as microcephaly, macrocephaly, lissencephaly (LIS), and periventricular nodular heterotopia (PH). The use of disease-specific brain organoids has revealed unprecedented details of mechanisms that cause congenital brain malformations. Conclusions This review summarizes the establishment and development of brain organoid technologies and provides an overview of their applications in modeling congenital brain malformations. Although several hurdles still need to be overcome, using brain organoids has greatly expanded our ability to reveal the pathogenesis of congenital brain malformations. Compared with existing methods, the combination with cutting-edge technologies enables a more accurate diagnosis and development of increasingly personalized targeted therapy for patients with congenital brain diseases.