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Complex activity and short-term plasticity of human cerebral organoids reciprocally connected with axons.
An inter-regional cortical tract is one of the most fundamental architectural motifs that integrates neural circuits to orchestrate and generate complex functions of the human brain. To understand the mechanistic significance of inter-regional projections on development of neural circuits, we investigated an in vitro neural tissue model for inter-regional connections, in which two cerebral organoids are connected with a bundle of reciprocally extended axons. The connected organoids produced more complex and intense oscillatory activity than conventional or directly fused cerebral organoids, suggesting the inter-organoid axonal connections enhance and support the complex network activity. In addition, optogenetic stimulation of the inter-organoid axon bundles could entrain the activity of the organoids and induce robust short-term plasticity of the macroscopic circuit. These results demonstrated that the projection axons could serve as a structural hub that boosts functionality of the organoid-circuits. This model could contribute to further investigation on development and functions of macroscopic neuronal circuits in vitro.
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Cerebral organoids with chromosome 21 trisomy secrete Alzheimer's disease-related soluble aggregates detectable by single-molecule-fluorescence and super-resolution microscopy.
Understanding the role of small, soluble aggregates of beta-amyloid (Aβ) and tau in Alzheimer's disease (AD) is of great importance for the rational design of preventative therapies. Here we report a set of methods for the detection, quantification, and characterisation of soluble aggregates in conditioned media of cerebral organoids derived from human iPSCs with trisomy 21, thus containing an extra copy of the amyloid precursor protein (APP) gene. We detected soluble beta-amyloid (Aβ) and tau aggregates secreted by cerebral organoids from both control and the isogenic trisomy 21 (T21) genotype. We developed a novel method to normalise measurements to the number of live neurons within organoid-conditioned media based on glucose consumption. Thus normalised, T21 organoids produced 2.5-fold more Aβ aggregates with a higher proportion of larger (300-2000 nm2) and more fibrillary-shaped aggregates than controls, along with 1.3-fold more soluble phosphorylated tau (pTau) aggregates, increased inflammasome ASC-specks, and a higher level of oxidative stress inducing thioredoxin-interacting protein (TXNIP). Importantly, all this was detectable prior to the appearance of histological amyloid plaques or intraneuronal tau-pathology in organoid slices, demonstrating the feasibility to model the initial pathogenic mechanisms for AD in-vitro using cells from live genetically pre-disposed donors before the onset of clinical disease. Then, using different iPSC clones generated from the same donor at different times in two independent experiments, we tested the reproducibility of findings in organoids. While there were differences in rates of disease progression between the experiments, the disease mechanisms were conserved. Overall, our results show that it is possible to non-invasively follow the development of pathology in organoid models of AD over time, by monitoring changes in the aggregates and proteins in the conditioned media, and open possibilities to study the time-course of the key pathogenic processes taking place.
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Engineering human cerebral organoids to explore mechanisms of arsenic-induced developmental neurotoxicity.
Modeling brain development and function is challenging due to complexity of the organ. Human pluripotent stem cell (PSC)-derived brain-like organoids provide new tools to study the human brain. Compared with traditional in vivo toxicological studies, these 3D models, together with 2D cellular assays, enhance our understanding of the mechanisms of developmental neurotoxicity (DNT) during the early stages of neurogenesis and offer numerous advantages including a rapid, cost-effective approach for understanding compound mechanisms and assessing chemical safety. Arsenic (As) exposure is associated with DNT, although the mechanisms involved are not well-defined. Here, we used 3D PSC-derived embryoid bodies (EBs) to recapitulate events involved in embryogenesis and neurogenesis before neural induction, and EB-derived cerebral organoids to mimic neural development in vivo. As (0.5 μM; 35 ppb) increased ectoderm differentiation within the EBs by upregulating genes (PAX6, SOX1) critical for embryonic development. Histological staining of EBs showed As disrupted neural rosette structures. qPCR and RNA-seq showed As inhibited expression of markers of mature neural cells (MAP2+/vGLUT2+) and astrocytes (GFAP+). In organoids, Ingenuity Pathway Analysis was used to identify the top 5 pathways affected by As exposure, and Gene Ontology enrichment analysis found several key signaling pathways to be inhibited by As exposure. These data provide insights into pathways contributing to As-induced inhibition of neurite outgrowth and disrupted neural rosette structures in the 2D neurite outgrowth assay and in organoids, respectively. Results herein show this multipronged 2D/3D approach can provide valuable insights into cellular events and molecular mechanisms of As-induced DNT.
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Reduced mechanical shear is associated with early cortical differentiation and GDNF-GFRA1/RET signalling in human brain organoids.
Early cortical differentiation in human brain organoids is a critical step of corticogenesis, but remains poorly coordinated under conventional culture conditions. In a standard orbital shaker system, mechanical shear and variability in extracellular matrix support, can disrupt neuroepithelial organisation, leading to inconsistent early cortical differentiation. Here, we investigated how ClinoStar-associated low-shear culture conditions affect early corticogenic marker expression in brain organoids and examined GFRA1/RET-related signaling as a candidate pathway associated with these culture-related effects. Using a low-shear ClinoStar bioreactor, we observed improved neuroepithelial-like expansion, enhanced tissue organisation, and promoted early cortical differentiation during the neuroepithelial expansion stage. Compared with conventional conditions, low-mechanical shear in ClinoStar was associated with increased proliferation capacity and supported the number of TBR2+ intermediate progenitors and TBR1+ early cortical neurons. Transcriptomic analysis revealed enrichment of neuronal differentiation and neuroactive ligand-receptor interaction pathways, with increased upregulation of GDNF signalling components under reduced mechanical shear. Functional experiments showed that GDNF supplementation increased TBR2+ intermediate progenitor-associated and TBR1+ early neuronal marker-related populations in brain organoids, suggesting a positive effect on early corticogenic marker expression. Consistent with this, GFRA1/RET levels were elevated in organoids in the ClinoStar culture with low-mechanical shear stress, and manipulation of GFRA1 affected early cortical differentiation outcomes. These findings suggest that ClinoStar low-shear culture promoted early corticogenic marker expression, potentially associated with GDNF-GFRA1/RET signalling. Collectively, this study provides a refined culture framework for improving the reproducibility and structural organisation of human brain organoid models of early cortical differentiation.
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Organoid and pluripotent stem cells in Parkinson's disease modeling: an expert view on their value to drug discovery.
Introduction: Parkinson's disease is a devastating neurodegenerative disorder preferentially involving loss of dopaminergic neurons in the substantia nigra, leading to typical motor symptoms. While there are still no therapeutics to modify disease course, recent work using induced pluripotent stem cell (iPSC) and 3D brain organoid models have provided further insight into Parkinson's disease pathogenesis and potential therapeutic targets.Areas covered: This review highlights the generation of iPSC neurons and neural organoids as models for studying Parkinson's disease. It further discusses the recent work using patient-derived neurons from both familial and sporadic forms of Parkinson's to study disease pathogenic phenotypes and pathways. It additionally provides an evaluation of iPSC neurons and organoid models for therapeutic development in Parkinson's.Expert opinion: The use of Parkinson's disease patient-derived neurons and organoids provides us with the exciting opportunity to directly investigate pathogenic mechanisms and test drug compounds in human neurons. Future studies will involve generating more sophisticated models of brain organoids, studying neuronal pathways using larger patient cohorts, and routinely assessing therapeutics in these models.
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Approaches to investigating metabolism in human neurodevelopment using organoids: insights from intestinal and cancer studies.
Interrogating the impact of metabolism during development is important for understanding cellular and tissue formation, organ and systemic homeostasis, and dysregulation in disease states. To evaluate the vital functions metabolism coordinates during human brain development and disease, pluripotent stem cell-derived models, such as organoids, provide tractable access to neurodevelopmental processes. Despite many strengths of neural organoid models, the extent of their replication of endogenous metabolic programs is currently unclear and requires direct investigation. Studies in intestinal and cancer organoids that functionally evaluate dynamic bioenergetic changes provide a framework that can be adapted for the study of neural metabolism. Validation of in vitro models remains a significant challenge; investigation using in vivo models and primary tissue samples is required to improve our in vitro model systems and, concomitantly, improve our understanding of human development.
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Cannabidiol in Developmental Epilepsy: Organoid-Guided Precision Medicine Across Critical Neurodevelopmental Windows.
Epilepsy is a progressive network disorder in which recurrent seizures drive maladaptive neurodevelopmental remodeling, cognitive decline, and pharmacoresistance, particularly in developmental epileptic encephalopathies. Cannabidiol (CBD) has emerged as an evidence-based adjunctive therapy for selected childhood-onset epilepsies; however, its broader clinical utility remains limited by heterogeneous responsiveness, restricted indications, and an incomplete understanding of developmental stage-specific efficacy and safety. Here, we synthesize molecular, preclinical and clinical evidence supporting the pleiotropic antiseizure and neuroprotective actions of CBD, including modulation of endocannabinoid-related G protein-coupled receptors, adenosine signaling, transient receptor potential channels, GABAergic maturation, and neuroinflammatory cascades. We highlight critical neurodevelopmental windows during which timely CBD intervention may exert disease-modifying effects by preventing pathological consolidation of hyperexcitable networks. Furthermore, we position human brain organoids as transformative translational platforms that recapitulate early human cortical development and epileptic network dynamics, enabling functional stratification of CBD-responsive phenotypes, developmental safety profiling, and precision therapeutic discovery within human-relevant neural circuits. Collectively, organoid-guided frameworks provide a mechanistic foundation for personalized, developmentally informed CBD therapy and advance precision medicine strategies aimed at modifying epileptogenic trajectories rather than solely suppressing seizures.
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Parkinson's Disease Modeling Using Directly Converted 3D Induced Dopaminergic Neuron Organoids and Assembloids.
Parkinson's disease (PD) is characterized by the progressive loss of dopaminergic neurons and the accumulation of α-synuclein aggregates, yet current models inadequately mimic the complex human brain environment. Recent advances in brain organoid models offer a more physiologically relevant platform for studying PD, however, iPSC-derived brain organoids require long maturation times and may not accurately represent the aged brain's epigenetics and cellular contexts, limiting their applicability for modeling late-onset diseases like PD. In this study, a novel approach for generating 3D-induced dopaminergic (iDA) neuron organoids directly from human fibroblasts is presented. It is confirmed that these 3D iDA organoids more closely resemble the aged human brain and accurately replicate PD pathologies. Furthermore, this model is extended by incorporating astrocytes to create 3D iDA neuron-astrocyte assembloids, recognizing the critical role of glial cells in neurodegenerative processes. It is identified that PD assembloids incorporating control astrocytes with A53T mutant iDAs demonstrated the neuroprotective effects of healthy astrocytes. In contrast, A53T mutant astrocytes progressively contributed to neuronal degeneration and synucleinopathy in 3D-iDA assembloids. These findings suggest that directly converted 3D-iDA organoids and assembloids provide a robust and physiologically relevant model for studying PD pathogenesis and evaluating therapeutic interventions.
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Protocol for comparative gene expression data analysis between brains and organoids using a cloud-based web app.
Here, we present a protocol for using Brain and Organoid Manifold Alignment (BOMA), a cloud-based web app for comparative gene expression data analysis between brains and organoids. We describe steps for performing a global alignment of developmental gene expression data from both brains and organoids. We then detail procedures for investigating both shared and distinctive developmental pathways across brains and organoids by refining alignment locally using manifold learning. This protocol is applicable for working with single-cell and bulk RNA sequencing data. For complete details on the use and execution of this protocol, please refer to He et al.1.
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Human Forebrain Organoids from Induced Pluripotent Stem Cells: A Novel Approach to Model Repair of Ionizing Radiation-Induced DNA Damage in Human Neurons.
Human induced pluripotent stem cells (iPSCs) can generate virtually any cell type and therefore are applied to studies of organ development, disease modeling, drug screening and cell replacement therapy. Under proper culture conditions in vitro induced pluripotent stem cells (iPSCs) can be differentiated to form organ-like tissues, also known as "organoids", which resemble organs more closely than cells, in vivo. We hypothesized that human brain organoids can be used as an experimental model to study mechanisms underlying DNA repair in human neurons and their progenitors after radiation-induced DNA double-strand breaks (DSBs), the most severe form of DNA damage. To this end, we customized a protocol for brain organoid generation that is time efficient. These organoids recapitulate key features of human cortical neuron development, including a subventricular zone containing neural progenitors that mature to postmitotic cortical neurons. Using immunofluorescence to measure DNA DSB markers, such as γ-H2AX and 53BP1, we quantified the kinetics of DSB repair in neural progenitors within the subventricular zone for up to 24 h after a single 2 Gy dose of ionizing radiation. Our data on DNA repair in progenitor versus mature neurons indicate a similar timeline: both repair DNA DSBs which is mostly resolved by 18 h postirradiation. However, repair kinetics are more acute in progenitors than mature neurons in the mature organoid. Overall, this study supports the use of 3D organoid culture technology as a novel platform to study DNA damage responses in developing or mature neurons, which has been previously difficult to study.