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ARID1B controls transcriptional programs of axon projection in an organoid model of the human corpus callosum.
Mutations in ARID1B, a member of the mSWI/SNF complex, cause severe neurodevelopmental phenotypes with elusive mechanisms in humans. The most common structural abnormality in the brain of ARID1B patients is agenesis of the corpus callosum (ACC), characterized by the absence of an interhemispheric white matter tract that connects distant cortical regions. Here, we find that neurons expressing SATB2, a determinant of callosal projection neuron (CPN) identity, show impaired maturation in ARID1B+/- neural organoids. Molecularly, a reduction in chromatin accessibility of genomic regions targeted by TCF-like, NFI-like, and ARID-like transcription factors drives the differential expression of genes required for corpus callosum (CC) development. Through an in vitro model of the CC tract, we demonstrate that this transcriptional dysregulation impairs the formation of long-range axonal projections, causing structural underconnectivity. Our study uncovers new functions of the mSWI/SNF during human corticogenesis, identifying cell-autonomous axonogenesis defects in SATB2+ neurons as a cause of ACC in ARID1B patients.
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MEA-NAP: A flexible network analysis pipeline for neuronal 2D and 3D organoid multielectrode recordings.
Microelectrode array (MEA) recordings are commonly used to compare firing and burst rates in neuronal cultures. MEA recordings can also reveal microscale functional connectivity, topology, and network dynamics-patterns seen in brain networks across spatial scales. Network topology is frequently characterized in neuroimaging with graph theoretical metrics. However, few computational tools exist for analyzing microscale functional brain networks from MEA recordings. Here, we present a MATLAB MEA network analysis pipeline (MEA-NAP) for raw voltage time series acquired from single- or multi-well MEAs. Applications to 3D human cerebral organoids or 2D human-derived or murine cultures reveal differences in network development, including topology, node cartography, and dimensionality. MEA-NAP incorporates multi-unit template-based spike detection, probabilistic thresholding for determining significant functional connections, and normalization techniques for comparing networks. MEA-NAP can identify network-level effects of pharmacologic perturbation and/or disease-causing mutations and thus can provide a translational platform for revealing mechanistic insights and screening new therapeutic approaches. VIDEO ABSTRACT.
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Microelectrode Arrays Technology for Brain-on-a-Chip Applications.
Brain-on-a-chip (BOC) refers to a miniaturized in vitro platform that integrates living neuronal networks on a micro-engineered chip, enabling the simulation of brain functions, neural activities and physiological responses. BOC technology is an advanced evolution of microphysiological systems (MPS) and Lab-on-a-Chip platforms, providing novel paradigms for in vitro modeling and exploring early-stage biocomputing by interfacing living neural networks with engineered electronics. Microelectrode arrays (MEAs) serve as the critical physical interface for bidirectional communication in these systems. In this review, we systematically examine the technological landscape and engineering requirements of MEAs tailored for BOC applications, evaluating them across electrical characteristics, structural properties, and biocompatibility. Two primary classes of current MEA technologies, including planar arrays for 2D neural cultures and 3D flexible arrays for brain organoids, are discussed in detail. We highlight the transition from passive planar electrodes to high-density active CMOS and TFT-based arrays, and detail how 3D flexible MEAs utilize endogenous integration and exogenous wrapping strategies to overcome tissue-mechanics mismatches. Furthermore, the integration of MEAs with microfluidics, optoelectronics, and electrochemical sensors to enable multimodal monitoring is explored. With the advantages of the various MEAs, the application of MEAs for BOC, particularly in biological computing and network plasticity research, is discussed. Finally, future technological developments in scalability bottlenecks, chronic stability, and the incorporation of artificial intelligence for MEAs of BOC are prospected.
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KMT2D deficiency leads to cellular developmental disorders and enhancer dysregulation in neural-crest-containing brain organoids.
KMT2D, a H3K4me1 methyltransferase primarily regulating enhancers, is a leading cause of KABUKI syndrome. This multisystem disorder leads to craniofacial and cognitive abnormalities, possibly through neural crest and neuronal lineages. However, the impacted cell-of-origin and molecular mechanism of KMT2D during the development of KABUKI disease remains unknown. Here we have optimized a brain organoid model to investigate neural crest and neuronal differentiation. To pinpoint KMT2D's enhancer target, we developed a genome-wide cis-regulatory element explorer (GREE) based on single-cell multiomic integration. Single cell RNA-seq revealed that KMT2D-knockout (KO) and patient-derived organoids exhibited neural crest deformities and GABAergic overproduction. Mechanistically, GREE identified that KMT2D targets a roof-plate-like niche cell and activates the niche cell-specific WNT3A enhancer, providing the microenvironment for neural crest and neuronal development. Interestingly, KMT2D-mutated mice displayed decreased WNT3A expression in the diencephalon roof plate, indicating impaired niche cell function. Deleting the WNT3A enhancer in the organoids presented phenotypic similarities to KMT2D-depletion, emphasizing the WNT3A enhancer as the predominant target of KMT2D. Conversely, reactivating WNT signaling in KMT2D-KO rescued the lineage defects by restoring the microenvironment. Overall, our discovery of KMT2D's primary target provides insights for reconciling complex phenotypes of KABUKI syndrome and establishes a new paradigm for dissecting the mechanisms of genetic disorders from genotype to phenotype.
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Mispatterning and interneuron deficit in Tourette Syndrome basal ganglia organoids.
Tourette Syndrome (TS) is a neuropsychiatric disorder thought to involve a reduction of basal ganglia (BG) interneurons and malfunctioning of the BG circuitry. However, whether interneurons fail to develop or are lost postnatally remains unknown. To investigate the pathophysiology of early development in TS, induced pluripotent stem cell (iPSC)-derived BG organoids from TS patients and healthy controls were compared on multiple levels of measurement and analysis. BG organoids from TS individuals manifested an impaired medial ganglionic eminence fate and a decreased differentiation of cholinergic and GABAergic interneurons. Transcriptome analyses revealed organoid mispatterning in TS, with a preference for dorsolateral at the expense of ventromedial fates. Our results point to altered expression of GLI transcription factors downstream of the Sonic Hedgehog signaling pathway with cilia disruption at the earliest stages of BG organoid differentiation as a potential mechanism for the BG mispatterning in TS. This study uncovers early neurodevelopmental underpinnings of TS neuropathological deficits using organoids as a model system.
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N-methyl-d-aspartate Receptor-mediated Preconditioning Mitigates Excitotoxicity in Human Induced Pluripotent Stem Cell-derived Brain Organoids.
Studies in rodent models of acute and chronic neurodegenerative disorders have uncovered that glutamate-induced excitotoxic cell death is mediated primarily by extrasynaptic N-methyl-d-aspartate receptors (NMDARs). Rodent neurons can also build up in an activity-dependent manner a protective shield against excitotoxicity. This form of acquired neuroprotection is induced by preconditioning with low doses of NMDA or by activation of synaptic NMDARs triggered by bursts of action potentials. Whether NMDARs in human neurons have similar dichotomous actions in cell death and survival is unknown. To investigate this, we established an induced pluripotent stem cell (iPSC)-derived forebrain organoid model for excitotoxic cell death and explored conditions of NMDAR activation that promote neuronal survival when applied prior to a toxic insult. We found that glutamate-induced excitotoxicity in human iPSC-derived neurons is mediated by NMDARs. Treatment of organoids with high concentrations of glutamate or NMDA caused the typical excitotoxicity pathology, comprising structural disintegration, neurite blebbing, shut-off of the transcription factor CRE binding protein (CREB), and cell death. In contrast, bath-applied low doses of NMDA elicited synaptic activity, a robust and sustained increase in CREB phosphorylation as well as function, and upregulation of immediate-early genes, including neuroprotective genes. Moreover, we found that conditions of enhanced synaptic activity increased survival of human iPSC-derived neurons if applied as pre-treatment before toxic NMDA application. These results revealed that both toxic and protective actions of NMDARs are preserved in human neurons. The experimental platform described in this study may prove useful for the validation of neuroprotective gene products and drugs in human neurons.
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Mouse induced pluripotent stem cells-derived Alzheimer's disease cerebral organoid culture and neural differentiation disorders.
Alzheimer's disease (AD) is a progressive neurodegenerative disease, characterized by cognitive impairment. However, the pathogenesis of AD are very complicated, and the theories of Aβ and neurofibrillary tangles cannot explain all pathological alterations and clinical symptoms. Here, we used three-dimensional (3D) neural organoids culture derived from mouse induced pluripotent stem cells (iPSCs) to investigate the pathological mechanisms of AD. In this study, AD cerebral organoids were generated by overexpressing familial AD mutations (APP and PS1 genes) in mouse induced pluripotent stem cells, so that the early pathogenesis of AD could be investigated well with protein and cellular phenotype analyses. The results showed that AD cerebral organoids appeared some AD pathological alterations, and high levels of Aβ and p-Tau were induced as well. Furthermore, the number of GFAP-positive astrocytes and glutamatergic excitatory neurons increased significantly, but the number of GABAergic interneurons decreased. In conclusion, we suggest that cerebral organoids are a suitable AD model for scientific study, and that will provide us a novel insight into the understanding of the pathogenesis of AD.
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Human Oligodendrocytes and Myelin In Vitro to Evaluate Developmental Neurotoxicity.
Neurodevelopment is uniquely sensitive to toxic insults and there are concerns that environmental chemicals are contributing to widespread subclinical developmental neurotoxicity (DNT). Increased DNT evaluation is needed due to the lack of such information for most chemicals in common use, but in vivo studies recommended in regulatory guidelines are not practical for the large-scale screening of potential DNT chemicals. It is widely acknowledged that developmental neurotoxicity is a consequence of disruptions to basic processes in neurodevelopment and that testing strategies using human cell-based in vitro systems that mimic these processes could aid in prioritizing chemicals with DNT potential. Myelination is a fundamental process in neurodevelopment that should be included in a DNT testing strategy, but there are very few in vitro models of myelination. Thus, there is a need to establish an in vitro myelination assay for DNT. Here, we summarize the routes of myelin toxicity and the known models to study this particular endpoint.
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The need for a global effort to attend to human neural organoid and assembloid research.
A continuing international process is needed to monitor and advise this rapidly progressing field.
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REST deficiency and neurogenic-to-gliogenic shift in down syndrome human cerebral organoids.
Down syndrome (DS) features impaired cortical neurogenesis and excess gliogenesis, yet the temporal regulatory events driving this imbalance remain unclear. Here, we combine multi-timepoint transcriptomic analyses from publicly available datasets, network modelling, and machine-learning prioritization, with validation in isogenic human iPSC-derived cerebral organoids, to identify a discrete pathogenic window at 90 days in vitro (DIV 90). Across five developmental stages, REST target genes were preferentially dysregulated in DS organoids. WGCNA revealed a DS-associated module at DIV-90 that strongly overlapped with REST targets, and two orthogonal machine-learning approaches converged on six REST-regulated hub genes-CSTB, MCM3AP, PFKL, POFUT2, PRMT2, and RWDD2B. In trisomic organoids, REST mRNA and nuclear protein were markedly reduced at DIV-90, accompanied by diminished DCX expression and activation of NFIA and STAT3, suggesting a neurogenic-to-gliogenic fate transition. These findings suggest REST dysfunction as a potential temporal regulator of lineage imbalance in DS and highlight REST-linked networks as potential targets for early developmental intervention.