Brain-Region-Specific Organoids Using Mini-bioreactors for Modeling ZIKV Exposure

Generation, interrogation, and future applications of microglia-containing brain organoids

Brain organoids encompass a large collection of in vitro stem cell-derived 3D culture systems that aim to recapitulate multiple aspects of in vivo brain development and function. First, this review provides a brief introduction to the current state-of-the-art for neuro-ectoderm brain organoid development, emphasizing their biggest advantages in comparison with classical two-dimensional cell cultures and animal models. However, despite their usefulness for developmental studies, a major limitation for most brain organoid models is the absence of contributing cell types from endodermal and mesodermal origin. As such, current research is highly investing towards the incorporation of a functional vasculature and the microglial immune component. In this review, we will specifically focus on the development of immune-competent brain organoids. By summarizing the different approaches applied to incorporate microglia, it is highlighted that immune-competent brain organoids are not only important for studying neuronal network formation, but also offer a clear future as a new tool to study inflammatory responses in vitro in 3D in a brain-like environment. Therefore, our main focus here is to provide a comprehensive overview of assays to measure microglial phenotype and function within brain organoids, with an outlook on how these findings could better understand neuronal network development or restoration, as well as the influence of physical stress on microglia-containing brain organoids. Finally, we would like to stress that even though the development of immune-competent brain organoids has largely evolved over the past decade, their full potential as a pre-clinical tool to study novel therapeutic approaches to halt or reduce inflammation-mediated neurodegeneration still needs to be explored and validated.

An immunocompetent mouse model revealed that congenital Zika virus infection disrupted hippocampal function by activating autophagy

Congenital Zika virus (ZIKV) infection significantly affects neurological development in infants and subsequently induces neurodevelopmental abnormality symptoms; however, the potential mechanism is still unknown. Therefore, in order to effectively intervene in neurodevelopmental abnormalities in infected infants, it is necessary to identify the main brain regions affected by congenital infection. In this study, we constructed a congenital ZIKV-infected murine model using immunocompetent human STAT2 knock-in mice, which presented long-term neurodevelopmental abnormalities with abnormal neurodevelopmental symptoms. We found that the hippocampus, which regulates cognitive behaviour and processes spatial information and navigation, was the main brain region affected by congenital infection and that hippocampal cells were more prone to autophagy during the growth period of these mice at the transcriptional and pathological levels. These findings highlighted that congenital ZIKV infection could interrupt hippocampal function by activating autophagy, thus providing a theoretical basis for the clinical treatment of congenital ZIKV-infected infants.

Cartilage repair: unleashing PRP's potential in organoid models

Platelet-rich plasma (PRP) has emerged as a promising biological therapy in regenerative medicine due to its high concentration of growth factors and cytokines, which promote tissue healing and regeneration. In recent years, its application in cartilage tissue engineering has garnered significant attention. This study explores the synergistic interaction between PRP and cartilage organoids, a novel three-dimensional in vitro culture system that closely mimics the structural and functional properties of native cartilage. Cartilage organoids serve as a physiologically relevant model for studying cartilage development, disease progression, and regeneration. By integrating PRP with cartilage organoids, this review aims to enhance chondrogenesis, extracellular matrix synthesis, and cellular proliferation within the organoids. Emerging evidence suggests that PRP supplementation significantly improves chondrocyte viability, growth, and differentiation in cartilage organoids, thereby accelerating their maturation. This combination holds great potential for advancing cartilage repair strategies, providing a robust platform for preclinical studies, and paving the way for innovative therapeutic approaches for cartilage-related injuries and degenerative diseases. These key aspects-chondrogenesis, matrix synthesis, and cellular proliferation-were specifically selected due to their fundamental roles in cartilage tissue engineering and regeneration. Chondrogenesis is crucial for chondrocyte differentiation and maintenance, matrix synthesis ensures the structural integrity and functional properties of regenerated cartilage, and cellular proliferation supports tissue viability and repair. Addressing these factors is essential, as current cartilage regeneration strategies often suffer from limited long-term efficacy and inadequate extracellular matrix production. By elucidating the synergistic effects of PRP and cartilage organoids in these areas, this study seeks to bridge existing knowledge gaps and provide valuable insights for improving regenerative approaches in clinical applications, particularly for osteoarthritis and cartilage defects.

Self-organization and applications of neural organoids

Organoid technology has become a field that attract many researcher's attention and involvement. "Organoid" is a coined word which means organ like-tissue (Organ+oid), and organoid is determined as stem cell-derived three-dimensional (3D) tissues that recapitulate developmental processes and tissue specific function in vivo. Generally, they are derived from pluripotent stem cells (PSCs) including induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs), or from tissue stem cells. The first report that created human 3D cerebral tissue arose in 2008 which is currently considered as the pioneering work of "neural organoid" (Eiraku et al., 2008, Sasai 2013a, Sasai 2013b). The neural organoids provide living human neural tissues that bring opportunities to study human development, human neuroscience, neurological and psychiatric disorders, and evolutions. The neural organoid can be said as "cut & paste" of developmental biological process into a dish. Thus, understanding the background of neural organoid needs developmental knowledge, but current organoid researches looks to use organoid as a tool to study the aim that the researchers want to focus. This leads the organoid research more methodological, and the improvement or sophistication of organoid methods has still been difficult for most of new coming researchers. For this problem, this review provide insights of how to assemble organoid methods from viewpoints of development especially from morphological/structual changes. In this review, I start from the brief history of how neural organoid research emerged from developmental biology. Then I introduce some interesting aspects of neural organoid generation focusing on self-organization of regions and structures. From the viewpoint of a developer of this field, this review also show how to think and adjust the methods to generate novel regional organoids taking hippocampal organoids as an example. Regarding structural self-organization I will introduce cerebral organoid for an example of layer organization in a dish. By showing background knowledge with scientific achievements and interesting aspects, this review will help researchers who want to create novel neural organoids.

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.

Protein Arginine Methyltransferases from Regulatory Function to Clinical Implication in Central Nervous System

Arginine methylation, catalyzed by protein arginine methyltransferases (PRMTs), is a regulatory key mechanism involved in various cellular processes such as gene expression, RNA processing, DNA damage repair. Increasing evidence highlights the crucial role of PRMTs in human diseases, including cancer, cardiovascular and metabolic diseases. Here, this review focuses on the latest findings regarding PRMTs in the central nervous system (CNS), emphasizing their regulatory roles in neural stem cells, neurons, and glial cells. Additionally, we examine the connection between PRMTs dysregulation and neurological diseases affecting the CNS, including brain tumors, neurodegenerative diseases, and neurodevelopmental disorders. Therefore, this review aims to deepen our understanding of PRMTs-mediated arginine methylation in CNS and open avenues for developing novel therapeutic strategies for neurological diseases.

The 3C (Cell Culture, Computer Simulation, Clinical Trial) Solution for Optimizing the 3R (Replace, Reduction, Refine) Framework during Preclinical Research Involving Laboratory Animals

Preclinical research has traditionally utilized laboratory animals to elucidate the safety, tolerability, pharmacokinetics, and pharmacodynamics of new chemical entities prior to human trials. The use of animal models has been pivotal in advancing scientific knowledge and medical breakthroughs, contributing significantly to our understanding of the complex biological processes and human diseases. However, many promising treatments that have demonstrated efficacy in animal studies have failed to translate to human subjects during clinical trials. Consequently, animal testing faces ethical concerns and criticism regarding its predictive reliability for human responses. This has led to the development of 3R principles (Replacement, Reduction, Refinement), introduced in 1959, advocating for alternative methods and improved animal welfare in research. Furthermore, regulatory frameworks and recent legislation, such as the 2022 FDA Modernisation Act, emphasize modern scientific alternatives to traditional animal testing. Emerging approaches, known as the 3Cs-cell culture, computer simulation, and phase 0 clinical trials-offer promising nonanimal solutions that could accelerate drug development and address ethical concerns, potentially rendering preclinical research more humane and efficient.

Development of a brain-penetrant G9a methylase inhibitor to target Alzheimer's disease-associated proteopathology

Current Aβ-targeting therapeutics for Alzheimer's disease (AD) only slow cognitive decline due to poor understanding of AD pathogenesis. Here we describe a mechanism of AD pathogenesis in which the histone methyltransferase G9a noncanonically regulates translation of hippocampal proteins associated with AD pathology. Correspondingly, we developed a brain-penetrant inhibitor of G9a, MS1262, which restored both age-related learning & memory and noncognitive functions in multiple AD mouse models. Further, comparison of AD pathology-correlated mouse proteomes with those of AD patients found G9a regulates pathological pathways that promote Aβ and neurofibrillary tangles. This mouse-to-human overlap of G9a regulated AD-associated pathologic proteins supports at the molecular level the efficacy of targeting G9a translational mechanism for treating AD patients. Additionally, MS1262 treatment reversed the AD-characteristic expression or phosphorylation of multiple clinically validated biomarkers of AD that have the potential to be used for early-stage AD diagnosis and companion diagnosis of individualized drug effects.

m6A deficiency impairs hypothalamic neurogenesis of feeding-related neurons in mice and human organoids and leads to adult obesity in mice

N6-methyladenosine (m6A), the most prevalent internal modification on mRNAs, plays important roles in the nervous system. Whether neurogenesis in the hypothalamus, a region critical for controlling appetite, is regulated by m6A signaling, especially in humans, remains unclear. Here, we showed that deletion of m6A writer Mettl14 in the mouse embryonic hypothalamus led to adult obesity, with impaired glucose-insulin homeostasis and increased energy intake. Mechanistically, deletion of Mettl14 leads to hypothalamic arcuate nucleus neurogenesis deficits with reduced generation of feeding-related neurons and dysregulation of neurogenesis-related m6A-tagged transcripts. Deletion of m6A writer Mettl3 or m6A reader Ythdc1 shared similar phenotypes. METTL14 or YTHDC1 knockdown also led to reduced generation of feeding-related neurons in human brain subregion-specific arcuate nucleus organoids. Our studies reveal a conserved role of m6A signaling in arcuate nucleus neurogenesis in mice and human organoids and shed light on the developmental basis of epitranscriptomic regulation of food intake and energy homeostasis.

Emerging brain organoids: 3D models to decipher, identify and revolutionize brain

Brain organoids are an emerging in vitro 3D brain model that is integrated from pluripotent stem cells. This model mimics the human brain's developmental process and disease-related phenotypes to a certain extent while advancing the development of human brain-based biological intelligence. However, many limitations of brain organoid culture (e.g., lacking a functional vascular system, etc.) prevent in vitro-cultured organoids from truly replicating the human brain in terms of cell type and structure. To improve brain organoids' scalability, efficiency, and stability, this paper discusses important contributions of material biology and microprocessing technology in solving the related limitations of brain organoids and applying the latest imaging technology to make real-time imaging of brain organoids possible. In addition, the related applications of brain organoids, especially the development of organoid intelligence combined with artificial intelligence, are analyzed, which will help accelerate the rational design and guidance of brain organoids.

A new protocol for the development of organoids based on molecular mechanisms in the developing newborn rat brain: Prospective applications in the study of Alzheimer's disease

BACKGROUND

Brain organoids have emerged as powerful models for studying brain development and neurological disorders COMPARISON WITH EXISTING METHODS: Current models rely on stem cell isolation and differentiation using different growth factors. Thus, their composition varies according to the protocol followed.

NEW METHOD

We developed a simple protocol to generate organoids from newborn rat whole brain. It is a one-step procedure that yields organoids of consistent composition. The whole brains from 3-day old pups were digested enzymatically. All isolated cells were seeded in culture plates using a basement membrane extract (BME) matrix as a scaffold and cultured in the presence of the appropriate medium.

RESULTS

Hematoxylin-eosin staining of 28-day-old cultured domes revealed their structural integrity, while immunohistochemistry confirmed the presence of neurons, astrocytes, microglia, and progenitor stem cells in the structures. To assess whether these organoids can serve as a model to study brain physiopathology, and in particular neurodegenerative diseases such as Alzheimer's disease (AD), we determined how these organoids respond upon their exposure to lipopolysaccharides (LPS), a potent neuroinflammatory factor. LPS-induced amyloid precursor protein (APP), tau protein and glial fibrillary acidic protein (GFAP) expression. Moreover, the intracellular levels of IL-1β and the extracellular levels of amyloid-beta (Aβ) were also elevated.

CONCLUSIONS

Therefore, this simple protocol results in the generation of functional brain organoids with a consistent structure, that requires no use of varying factors that may affect the structure and function of the produced organoids, thus providing a valuable tool for the study of the physiopathology of neurodegenerative disorders.

Modelling human brain development and disease with organoids

Organoids are systems derived from pluripotent stem cells at the interface between traditional monolayer cultures and in vivo animal models. The structural and functional characteristics of organoids enable the modelling of early stages of brain development in a physiologically relevant 3D environment. Moreover, organoids constitute a tool with which to analyse how individual genetic variation contributes to the susceptibility and progression of neurodevelopmental disorders. This Roadmap article describes the features of brain organoids, focusing on the neocortex, and their advantages and limitations - in comparison with other model systems - for the study of brain development, evolution and disease. We highlight avenues for enhancing the physiological relevance of brain organoids by integrating bioengineering techniques and unbiased high-throughput analyses, and discuss future applications. As organoids advance in mimicking human brain functions, we address the ethical and societal implications of this technology.

Bioengineering innovations for neural organoids with enhanced fidelity and function

Neural organoids have been utilized to recapitulate different aspects of the developing nervous system. While hailed as promising experimental tools for studying human neural development and neuropathology, current neural organoids do not fully recapitulate the anatomy or microcircuitry-level functionality of the developing brain, spinal cord, or peripheral nervous system. In this review, we discuss emerging bioengineering approaches that control morphogen signals and biophysical microenvironments, which have improved the efficiency, fidelity, and utility of neural organoids. Furthermore, advancements in bioengineered tools have facilitated more sophisticated analyses of neural organoid functions and applications, including improved neural-bioelectronic interfaces and organoid-based information processing. Emerging bioethical issues associated with advanced neural organoids are also discussed. Future opportunities of neural organoid research lie in enhancing their fidelity, maturity, and complexity and expanding their applications in a scalable manner.

Interferon-dependent R-loop induction by Zika virus contributes to growth attenuation

Zika virus (ZIKV) infection in human neural progenitors triggers DNA damage and activates DNA damage response, leading to cell cycle arrest that can retard brain development. Here, we link the ZIKV-induced S phase arrest to replication fork stalling and R-loop induction. DRIP-seq reveals that ZIKV infection induces R loops at specific loci strongly enriched in the interferon (IFN)-stimulated genes (ISGs). Bromouridine sequencing results further indicate that nascent ISGs transcripts are prone to R-loop induction upon infection. Knockout of IFN receptor eliminated the R loops on ISGs and partially rescued S-phase arrest in infected cells. And overexpression of RNaseH1 reduced ZIKV-mediated DNA damage and cell cycle arrest. We conclude that unscheduled expression of ISGs induced by ZIKV alters R-loop homeostasis and perturbs replication fork progression, leading to fork stalling and eventually DNA damage. IFN-dependent R-loop induction represents a previously unknown, nucleic acid-based mechanism for cell cycle arrest.

The potential of brain organoids in addressing the heterogeneity of synucleinopathies

Synucleinopathies are a group of diseases characterized by neuronal and glial accumulation of α-synuclein (aSyn) linked with different clinical presentations, including Parkinson's disease (PD), Parkinson's disease with dementia (PDD), Dementia with Lewy Bodies (DLB) and Multiple system atrophy (MSA). Interestingly, the structure of the aSyn aggregates can vary across different synucleinopathies. Currently, it is unclear how the aSyn protein can aggregate into diverse structures and affect distinct cell types and various brain regions, leading to different clinical symptoms. Recent advances in induced pluripotent stem cells (iPSCs)-based brain organoids (BOs) technology provide an unprecedented opportunity to define the etiology of synucleinopathies in human brain cells within their three-dimensional (3D) context. In this review, we will summarize current advances in investigating the mechanisms of synucleinopathies using BOs and discuss the scope of this platform to define mechanisms underlining the selective vulnerability of cell types and brain regions in synucleinopathies.

Brain organoids: building higher-order complexity and neural circuitry models

Brain organoids are 3D tissue models of the human brain that are derived from pluripotent stem cells (PSCs). They have enabled studies that were previously stymied by the inaccessibility of human brain tissue or the limitations of mouse models of some brain diseases. Despite their enormous potential, brain organoids have had significant limitations that prevented them from recapitulating the full complexity of the human brain and reduced their utility in disease studies. We describe recent progress in addressing these limitations, especially building complex organoids that recapitulate the interactions between multiple brain regions, and reconstructing in vitro the neural circuitry present in in vivo. These major advances in the human brain organoid technology will remarkably facilitate brain disease modeling and neuroscience research.

From organoids to organoids-on-a-chip: Current applications and challenges in biomedical research

ABSTRACT

The high failure rates in clinical drug development based on animal models highlight the urgent need for more representative human models in biomedical research. In response to this demand, organoids and organ chips were integrated for greater physiological relevance and dynamic, controlled experimental conditions. This innovative platform-the organoids-on-a-chip technology-shows great promise in disease modeling, drug discovery, and personalized medicine, attracting interest from researchers, clinicians, regulatory authorities, and industry stakeholders. This review traces the evolution from organoids to organoids-on-a-chip, driven by the necessity for advanced biological models. We summarize the applications of organoids-on-a-chip in simulating physiological and pathological phenotypes and therapeutic evaluation of this technology. This section highlights how integrating technologies from organ chips, such as microfluidic systems, mechanical stimulation, and sensor integration, optimizes organoid cell types, spatial structure, and physiological functions, thereby expanding their biomedical applications. We conclude by addressing the current challenges in the development of organoids-on-a-chip and offering insights into the prospects. The advancement of organoids-on-a-chip is poised to enhance fidelity, standardization, and scalability. Furthermore, the integration of cutting-edge technologies and interdisciplinary collaborations will be crucial for the progression of organoids-on-a-chip technology.

The promise of cerebral organoids for neonatology

PURPOSE OF REVIEW

Applying discoveries from basic research to patients in the neonatal intensive care unit (NICU) is challenging given the difficulty of modeling this population in animal models, lack of translational relevance from animal models to humans, and scarcity of primary human tissue. Human cell-derived cerebral organoid models are an appealing way to address some of these gaps. In this review, we will touch on previous work to model neonatal conditions in cerebral organoids, some limitations of this approach, and recent strategies that have attempted to address these limitations.

RECENT FINDINGS

While modeling of neurodevelopmental disorders has been an application of cerebral organoids since their initial description, recent studies have dramatically expanded the types of brain regions and disease models available. Additionally, work to increase the complexity of organoid models by including immune and vascular cells, as well as modeling human heterogeneity with mixed donor organoids will provide new opportunities to model neonatal pathologies.

SUMMARY

Organoids are an attractive model to study human neurodevelopmental pathologies relevant to patients in the neonatal ICU. New technologies will broaden the applicability of these models to neonatal research and their usefulness as a drug screening platform.

Modeling forebrain regional development and connectivity by human brain organoids

The forebrain is one of the most important brain structures for modern human existence, which houses the uniquely sophisticated social and cognitive functions that distinguish our species. Therefore, modeling the forebrain development by using human cells is especially critical for our understanding of the intricacies of human development and devising treatments for related diseases. Recent advancements in brain organoid fields have offered unprecedented tools to investigate forebrain development from studies on specific regions to exploring tract formation and connectivity between different regions of the forebrain. In this review, we discuss the developmental biology of the forebrain and diverse methods for modeling its development by using organoids.

Cross-species immune activation and immunobiotics: a new frontier in vector-borne pathogen control

The persistent global burden of vector-borne diseases (VBDs) needs innovative control strategies, as traditional methods are compromised by acaricides and drug resistance and variable vaccine efficacy. We propose a dual-action strategy using cross-species immune activation: human microbiota triggers the production of natural antibodies that directly target pathogens in the host and modulate vector immunity by interacting with vector microbiota. The human microbiota also modulates cytokine responses, enhancing immune defenses in both host and vector. These mechanisms can be further optimized by identifying immunobiotics - specific gut microbes that stimulate protective immune responses against VBDs. This approach offers a sustainable framework to bridge the gap between host and vector immunity, introducing a novel method to combat VBDs.

Engineering organoids as cerebral disease models

Cerebral organoids pioneered in replicating complex brain tissue architectures in vitro, offering a vast potential for human disease modeling. They enable the in vitro study of human physiological and pathophysiological mechanisms of various neurological diseases and disorders. The trajectory of technological advancements in brain organoid generation and engineering over the past decade indicates that the technology might, in the future, mature into indispensable solutions at the horizon of personalized and regenerative medicine. In this review, we highlight recent advances in the engineering of brain organoids as disease models and discuss some of the challenges and opportunities for future research in this rapidly evolving field.

Development of a Three-Dimensional Pathology-Simulating Model of Neurotrauma Using a Polymer-Encapsulated Neural Cell Network

Penetrating traumatic injuries of the brain have a poor clinical prognosis necessitating development of new therapies to improve neurological outcomes. Laboratory research is hampered by reliance on highly invasive experimental approaches in living animals to simulate penetrating injuries e.g., by cutting/crushing the brain tissue, with a range of associated ethical, technical and logistical challenges. Accordingly, there is a critical need to develop neuromimetic in vitro alternative neural models to reduce harm to animals. However, most in vitro, reductionist simulations of brain injury are too simplistic to simulate the complex environment of the injured nervous system. We recently reported a complex, two-dimensional in vitro mouse model of neurotrauma containing five major brain cell types to replicate neural architecture, grown on a "hard" glass substrate in a brain cell sheet. We now demonstrate the translation of this approach into a three-dimensional tissue injury model, by propagating the entire cellular network in a "soft" compliant collagen hydrogel, similar to native brain tissue stiffness (an important determinant of cell fate). A multicellular network of neural cells was observed to form in the polymer matrix containing all major brain cell populations, including the immune cells (microglia). We demonstrate that it is feasible to create a reproducible, focal traumatic injury in the synthesised neural tissue construct. Importantly, key pathological features of neurological injury, such as astrocyte scarring, immune cell (microglial) activation, impeded axonal outgrowth and stem/progenitor cell migration, can be successfully induced. We also prove that it is feasible to implant a biomaterial into the lesion gap to study neural cell responses for screening applications. The findings support the concept that the model can be used in a versatile manner for advanced neural modelling.

Bioengineering tools for next-generation neural organoids

Human stem cell-derived neural organoids were recently introduced as powerful in vitro 3D experimental model systems that innately undergo critical steps of organogenesis in culture and exhibit molecular, cellular, and structural features similar to the fetal human nervous system. These organoids have yielded new insights into human neurodevelopment and associated disorders. However, neural organoids have some crucial limitations that arise from the loosely controlled conditions for their development, an inability to maintain their spatial orientation in culture and a lack of technologies for taking long-term measurements on their morphology and electrical activity. Here, we review recent progress in using bioengineering methods to improve neural organoid formation and analysis by leveraging microfabrication, biomaterials, 3D printing, and flexible electrodes. We discuss how the applications of each technique can help to address critical limitations with standard neural organoid models. We conclude with a perspective on future applications of bioengineered next-generation neural organoids.

Protocol for generating human assembloids to investigate thalamocortical and corticothalamic synaptic transmission and plasticity

Human induced pluripotent stem cells (hiPSCs) can be used to generate assembloids that recreate thalamocortical circuitry displaying short-term and long-term synaptic plasticity. Here, we describe a protocol for differentiating hiPSCs into thalamic and cortical organoids and then fusing them to generate thalamocortical assembloids. We detail the steps for using whole-cell patch-clamp electrophysiology to investigate the properties of synaptic transmission and synaptic plasticity in this model system. For complete details on the use and execution of this protocol, please refer to Patton et al.1.

Shaping early neural development by timed elevated tissue oxygen tension: Insights from multiomic analysis on human cerebral organoids

Oxygen plays a critical role in early neural development in brains, particularly before establishment of complete vasculature; however, it has seldom been investigated due to technical limitations. This study uses an in vitro human cerebral organoid model with multiomic analysis, integrating advanced microscopies and single-cell RNA sequencing, to monitor tissue oxygen tension during neural development. Results reveal a key period between weeks 4 and 6 with elevated intra-organoid oxygen tension, altered energy homeostasis, and rapid neurogenesis within the organoids. The timed oxygen tension elevation can be suppressed by hypoxia treatment or silencing of neuroglobin gene. This study provides insights into the role of oxygen in early neurogenesis from functional, genotypic, phenotypic, and proteomic aspects. These findings highlight the significance of the timed tissue oxygen tension elevation in neurogenesis and provide insights into the role of neuroglobin in neural development, with potential implications for understanding neurodegenerative diseases and therapeutic strategies.

Organoids-on-a-chip: microfluidic technology enables culture of organoids with enhanced tissue function and potential for disease modeling

Organoids are stem-cell derived tissue structures mimicking specific structural and functional characteristics of human organs. Despite significant advancements in the field over the last decade, challenges like limited long-term functional culture and lack of maturation are hampering the implementation of organoids in biomedical research. Culture of organoids in microfluidic chips is being used to tackle these challenges through dynamic and precise control over the organoid microenvironment. This review highlights the significant breakthroughs that have been made in the innovative field of "organoids-on-chip," demonstrating how these have contributed to advancing organoid models. We focus on the incorporation of organoids representative for various tissues into chips and discuss the latest findings in multi-organoids-on-chip approaches. Additionally, we examine current limitations and challenges of the field towards the development of reproducible organoids-on-chip systems. Finally, we discuss the potential of organoids-on-chip technology for both in vitro and in vivo applications.

Insulative Compression of Neuronal Tissues on Microelectrode Arrays by Perfluorodecalin Enhances Electrophysiological Measurements

Microelectrode array (MEA) techniques provide a powerful method for exploration of neural network dynamics. A critical challenge is to interface 3D neural tissues including neural organoids with the flat MEAs surface, as it is essential to place neurons near to the electrodes for recording weak extracellular signals of neurons. To enhance performance of MEAs, most research have focused on improving their surface treatment, while little attention has been given to improve the tissue-MEA interactions from the medium side. Here, a strategy is introduced to augment MEA measurements by overlaying perfluorodecalin (PFD), a biocompatible fluorinated solvent, over neural tissues. Laying PFD over cerebral organoids insulates and compresses the tissues on MEA, which significantly enhances electrophysiological recordings. Even subtle signals such as the propagation of action potentials in bundled axons of motor nerve organoids can be detected with the technique. Moreover, PFD stabilizes tissues in acute recordings and its transparency allows optogenetic manipulations. This research highlights the potential of PFD as a tool for refining electrophysiological measurements of in vitro neuronal cultures. This can open new avenues to leverage precision of neuroscientific investigations and expanding the toolkit for in vitro studies of neural function and connectivity.

Phosphorylated-tau associates with HSV-1 chromatin and correlates with nuclear speckles decondensation in low-density host chromatin regions

Abnormal tau phosphorylation is a key mechanism in neurodegenerative diseases. Evidence implicates infectious agents, such as Herpes Simplex Virus 1 (HSV-1), as co-factors in the onset or the progression of neurodegenerative diseases, including Alzheimer's disease. This has led to divergence in the field regarding the contribution of viruses in the etiology of neurodegenerative diseases. Research indicates that viruses may function as risk factors driving neurodegenerative disease rather than playing a causative role. Investigating HSV-1 in abnormal tau phosphorylation is important for understanding the role of infectious agents in neurodegeneration. We generated cellular models of HSV-1 acute, latent infection, and viral reactivation from latency in cortical brain organoids and investigated the interplay between tau phosphorylation and HSV-1 infection by employing human induced pluripotent stem cell (iPSC)-derived monolayer neuronal cultures and brain organoids. Acute infection with HSV-1 strains 17syn+ and KOS caused nuclear accumulation of phosphorylated tau (p-tau) in neurons and neural precursor cells. Antivirals prevented nuclear accumulation of p-tau. Viral reactivation was accompanied by the nuclear translocation of p-tau. Chromatin immunoprecipitation analysis indicated an interaction of p-tau with the viral chromatin. A reduction in abundance of component of nuclear speckles and their loss of organized morphology in low-denisty host chromatin regions was observed, with strain-specific differences. HSV-1 infection was followed by an increase in the abundance of BRSKs and TAOKs, kinases known to phosphorylate tau. These findings show interaction between p-tau and HSV-1 chromatin and demonstrate the ability of HSV-1 to activate mechanisms that are observed in Alzheimer's disease.

The Application of Biomaterial-Based Spinal Cord Tissue Engineering

Advancements in biomaterial-based spinal cord tissue engineering technology have profoundly influenced regenerative medicine, providing innovative solutions for both spinal cord organoid development and engineered spinal cord injury (SCI) repair. In spinal cord organoids, biomaterials offer a supportive microenvironment that mimics the natural extracellular matrix, facilitating cell differentiation and organization and advancing the understanding of spinal cord development and pathophysiology. Furthermore, biomaterials are essential in constructing engineered spinal cords for SCI repair. The incorporation of biomaterials with growth factors, fabrication of ordered scaffold structures, and artificial spinal cord assemblies are critical insights for SCI to ensure structural integrity, enhance cell viability, and promote neural regeneration in transplantation. In summary, this review summarizes the contribution of biomaterials to the spinal cord organoids progression and discusses strategies for biomaterial-based spinal cord engineering in SCI therapy. These achievements underscore the transformative potential of biomaterials to improve treatment options for SCI and accelerate future clinical applications.

Toxicity assessment using neural organoids: innovative approaches and challenges

Assessment of toxicity and efficacy in the nervous system is essential to ensure the safety of compounds and the efficacy of neurotherapeutics. Recently, technologies using neural organoids to mimic the structural and functional properties of human brain tissue have been developed to improve our understanding of human-specific brain development and to model neurodevelopmental disorders. This approach offers the potential for standardized toxicity testing and large-scale drug screening at the organ level. Here, we review recent advances in neural organoids and explore the possibility of establishing more accurate and efficient systems for toxicological screening applications. Our review provides insights into toxicity and efficacy assessment research using neural organoids.

Magnetically reshapable 3D multi-electrode arrays of liquid metals for electrophysiological analysis of brain organoids

To comprehend the volumetric neural connectivity of a brain organoid, it is crucial to monitor the spatiotemporal electrophysiological signals within the organoid, known as intra-organoid signals. However, previous methods risked damaging the three-dimensional (3D) cytoarchitecture of organoids, either through sectioning or inserting rigid needle-like electrodes. Also, the limited numbers of electrodes in fixed positions with non-adjustable electrode shapes were insufficient for examining the complex neural activity throughout the organoid. Herein, we present a magnetically reshapable 3D multi-electrode array (MEA) using direct printing of liquid metals for electrophysiological analysis of brain organoids. The adaptable distribution and the softness of these printed electrodes facilitate the spatiotemporal recording of intra-organoid signals. Furthermore, the unique capability to reshape these soft electrodes within the organoid using magnetic fields allows a single electrode in the MEA to record from multiple points, effectively increasing the recording site density without the need for additional electrodes.

Identification of antiviral RNAi regulators, ILF3/DHX9, recruit at ZIKV stem loop B to protect against ZIKV induced microcephaly

Zika virus (ZIKV) is a member of the Flaviviridae family and causes congenital microcephaly and Guillain-Barré syndrome. Currently, there is a lack of approved vaccines or therapies against ZIKV infection. In this study, we profile vRNA‒host protein interactomes at ZIKV stem‒loop B (SLB) and reveal that interleukin enhancer binding factor 3 (ILF3) and DEAH-box helicase 9 (DHX9) form positive regulators of antiviral RNA inference in undifferentiated human neuroblastoma cells and induced pluripotent stem cell-derived human neural stem cells (iPSC-NSCs). Functionally, ablation of ILF3 in brain organoids and Nestin-Cre ILF3 cKO foetal mice significantly enhance ZIKV replication and aggravated ZIKV-induced microcephalic phenotypes. Mechanistically, ILF3/DHX9 enhance DICER processing of ZIKV vRNA-derived siRNAs (vsiR-1 and vsiR-2) to exert anti-flavivirus activity. VsiR-1 strongly inhibits ZIKV NS5 polymerase activity and RNA translation. Treatment with the vsiR-1 mimic inhibits ZIKV replication in vitro and in vivo and protected mice from ZIKV-induced microcephaly. Overall, we propose a novel therapeutic strategy to combat flavivirus infection.

A Comprehensive Review on Utilizing Human Brain Organoids to Study Neuroinflammation in Neurological Disorders

Most current information about neurological disorders and diseases is derived from direct patient and animal studies. However, patient studies in many cases do not allow replication of the early stages of the disease and, therefore, offer limited opportunities to understand disease progression. On the other hand, although the use of animal models allows us to study the mechanisms of the disease, they present significant limitations in developing drugs for humans. Recently, 3D-cultured in vitro models derived from human pluripotent stem cells have surfaced as a promising system. They offer the potential to connect findings from patient studies with those from animal models. In this comprehensive review, we discuss their application in modeling neurodevelopmental conditions such as Down Syndrome or Autism, neurodegenerative diseases such as Alzheimer's or Parkinson's, and viral diseases like Zika virus or HIV. Furthermore, we will discuss the different models used to study prenatal exposure to drugs of abuse, as well as the limitations and challenges that must be met to transform the landscape of research on human brain disorders.

Organoid Models to Study Human Infectious Diseases

Infectious diseases have become significant events that threaten global public health and economic development. Since the 20th century, multiple outbreaks of infectious diseases have gradually deepened humanity's understanding of viral infections, prevention and treatment. Organoids possess a high degree of similarity to human physiological states and have strong self-organising capabilities. Research on infectious diseases based on organoids offers significant advantages in terms of availability, editability and diversity. In this perspective, we briefly introduce the development of organoids, focusing on historically significant infectious diseases that have caused fatal harm to human health, such as HIV, ZIKV, SARS-CoV-2 and MPXV. We further summarise relevant research on the pathogenic mechanisms of these viruses based on organoid models, host reactivity, and therapeutic strategies. Finally, we list the latest research techniques combined with organoid models, discuss the challenges faced in the development of organoids and look forward to the future prospects of organoids in vaccine and drug development.

Characterization of Native Extracellular Matrix of Patient-Derived Glioblastoma Multiforme Organoids

Model systems play a crucial role in biological and biomedical research, especially in the search for new treatments for challenging diseases such as glioblastoma multiforme (GBM). Organoids are 3D in vitro multicellular "middle-ground" model systems that recapitulate highly organized and heterogeneous in vivo organ-like systems, often through stem cell differentiation. Incorporating Matrigel™ or other exogenous extracellular matrices (ECMs) that do not naturally occur in the human body is common practice for organoid generation, ignoring the role of dynamic reciprocity between the cells and the ECM in tissue development. In this study, we describe a method to develop GBM organoids (GBOs) from cells without the need for exogenous ECM encapsulation and without cell culture media changes to produce stable tissue-like organoids that reach a 4 mm diameter in as little as 6 weeks. We observed a transition from homogenous cell populations to tissue-like structures when GBOs were larger than 1 mm in diameter. Transcriptomic analysis revealed that the greatest gene expression changes occurred when GBOs were 2 mm in diameter, with collagen VI as the most upregulated ECM-related gene. Quantitative and histochemical assessments further supported native ECM synthesis with significantly higher levels of glycosaminoglycans and collagen in GBOs compared with spheroids. To our knowledge, this study presents the first reproducibly large GBOs with natively produced ECMs. Organoids with natively synthesized ECMs promise to eliminate artifacts and variability from aged, homogeneic, or xenogeneic scaffolds and to provide insights for ECM-targeted drug development.

Advances and Challenges in Modeling Autosomal Dominant Polycystic Kidney Disease: A Focus on Kidney Organoids

Autosomal dominant polycystic kidney disease (ADPKD) is a prevalent hereditary disorder characterized by distinct phenotypic variability that has posed challenges for advancing in-depth research. Recent advancements in kidney organoid construction technologies have enabled researchers to simulate kidney development and create simplified in vitro experimental environments, allowing for more direct observation of how genetic mutations drive pathological phenotypes and disrupt physiological functions. Emerging technologies, such as microfluidic bioreactor culture systems and single-cell transcriptomics, have further supported the development of complex ADPKD organoids, offering robust models for exploring disease mechanisms and facilitating drug discovery. Nevertheless, significant challenges remain in constructing more accurate ADPKD disease models. This review will summarize recent advances in ADPKD organoid construction, focusing on the limitations of the current techniques and the critical issues that need to be addressed for future breakthroughs. New and Noteworthy: This review presents recent advancements in ADPKD organoid construction, particularly iPSC-derived models, offering new insights into disease mechanisms and drug discovery. It focuses on challenges such as limited vascularization and maturity, proposing potential solutions through emerging technologies. The ongoing optimization of ADPKD organoid models is expected to enhance understanding of the disease and drive breakthroughs in disease mechanisms and targeted therapy development.

Structural Analysis of Cerebral Organoids Using Confocal Microscopy and Transmission/Scanning Electron Microscopy

Cerebral organoid cultures from human-induced pluripotent stem cells are widely used to study complex human brain development; however, there is still limited ultrastructural information regarding the development. In this study, we examined the structural details of cerebral organoids using various microscopy techniques. Two protocols were chosen as representative methods for the development of brain organoids: the classic whole-cerebral organoid (Whole-CO) culture technique, and the air-liquid interface-cerebral organoid (ALI-CO) culture technique. Immunostained confocal laser scanning microscopy (CLSM) revealed the formation of the CTIP2- and TBR1-positive cortical deep layer on days 90 and 150, depending on the developmental progress of both methods. Furthermore, the presence of astrocytes and oligodendrocytes was verified through immunostained CLSM utilizing two-dimensional and three-dimensional reconstruction images after a 150-day period. Transmission electron microscopy analysis revealed nanometer-resolution details of the cellular organelles and neuron-specific structures including synapses and myelin. Large-area scanning electron microscopy confirmed the well-developed neuronal connectivity from each culture method on day 150. Using those microscopy techniques, we clearly showed significant details within two representative culture protocols, the Whole-CO and ALI-CO culture methods. These multi-level images provide ultrastructural insight into the features of cerebral organoids depending on the developmental stage.

Opportunities and challenges for patient-derived models of brain tumors in functional precision medicine

Here, we review a growing paradigm shift from genomics-based precision medicine toward functional precision medicine, which evaluates therapeutic efficacy by directly treating living patient tumors ex vivo to better predict patient-specific responses to treatment. We discuss several classes of patient-derived models of central nervous system tumors, highlighting unique features of each. Each class of models holds promise to improve treatment selection, prolong survival, and enhance patient outcomes.

Inflammatory responses revealed through HIV infection of microglia-containing cerebral organoids

Cerebral organoids (COs) are valuable tools for studying the intricate interplay between glial cells and neurons in brain development and disease, including HIV-associated neuroinflammation. We developed a novel approach to generate microglia containing COs (CO-iMs) by co-culturing hematopoietic progenitors and inducing pluripotent stem cells. This approach allowed for the differentiation of microglia within the organoids concomitantly with the neuronal progenitors. Compared with conventional COs, CO-iMs were more efficient at generating CD45+/CD11b+/Iba-1+ microglia and presented a physiologically relevant proportion of microglia (~ 7%). CO-iMs presented substantially increased expression of microglial homeostatic and sensome markers as well as markers for the complement cascade. CO-iMs are susceptible to HIV infection, resulting in a significant increase in several pro-inflammatory cytokines/chemokines, which are abrogated by the addition of antiretrovirals. Thus, CO-iM is a robust model for deciphering neuropathogenesis, neuroinflammation, and viral infections of brain cells in a 3D culture system.

Early cell cycle genes in cortical organoid progenitors predict interindividual variability in infant brain growth trajectories

Human induced pluripotent stem cell (iPSC) derived cortical organoids (hCOs) model neurogenesis on an individual's genetic background. The degree to which hCO phenotypes recapitulate the brain growth of the participants from which they were derived is not well established. We generated up to 3 iPSC clones from each of 18 participants in the Infant Brain Imaging Study, who have undergone longitudinal brain imaging during infancy. We identified consistent hCO morphology and cortical cell types across clones from the same participant. hCO cross-sectional area and production of cortical hem cells were associated with in vivo cortical growth rates. Cell cycle associated genes expression in early progenitors at the crux of fate decision trajectories were correlated with cortical growth rate from 6-12 months of age, and were enriched in microcephaly and neurodevelopmental disorder genes. Our data suggest the hCOs capture inter-individual variation in cortical cell types influencing infant cortical surface area expansion.

Non-Invasive Quality Control of Organoid Cultures Using Mesofluidic CSTR Bioreactors and High-Content Imaging

Human brain organoids produce anatomically relevant cellular structures and recapitulate key aspects of in vivo brain function, which holds great potential to model neurological diseases and screen therapeutics. However, the long growth time of 3D systems complicates the culturing of brain organoids and results in heterogeneity across samples hampering their applications. We developed an integrated platform to enable robust and long-term culturing of 3D brain organoids. We designed a mesofluidic bioreactor device based on a reaction-diffusion scaling theory, which achieves robust media exchange for sufficient nutrient delivery in long-term culture. We integrated this device with longitudinal tracking and machine learning-based classification tools to enable non-invasive quality control of live organoids. This integrated platform allows for sample pre-selection for downstream molecular analysis. Transcriptome analyses of organoids revealed that our mesofluidic bioreactor promoted organoid development while reducing cell death. Our platform thus offers a generalizable tool to establish reproducible culture standards for 3D cellular systems for a variety of applications beyond brain organoids.

Human brain organoids for understanding substance use disorders

Substance use disorders (SUDs) are complex mental health conditions involving a problematic pattern of substance use. Challenges remain in understanding its neural mechanisms, which are likely to lead to improved SUD treatments. Human brain organoids, brain-like 3D in vitro cultures derived from human stem cells, show unique potential in recapitulating the response of a developing human brain to substances. Here, we review the recent progress in understanding SUD using human brain organoid models focusing on neurodevelopmental perspectives. We first summarize the background of SUD in humans. Moreover, we introduce the development of various human brain organoid models and then discuss current progress and findings underlying the abuse of substances like nicotine, alcohol, and other addictive drugs using organoid models. Furthermore, we review efforts to develop organ chips and microphysiological systems to engineer better human brain organoids for advancing SUD studies. Lastly, we conclude by elaborating on the current challenges and future directions of SUD studies using human brain organoids.

A Study on the Inflammatory Response of the Brain in Neurosyphilis

Neurosyphilis (NS) is a clinical condition caused by infection of the central nervous system (CNS) by Treponema pallidum (Tp) that can lead to asymptomatic meningitis and more serious neurological diseases, such as dementia and blindness. However, current studies on the pathogenesis of NS are limited. Here, through the integration analysis of proteomics and single-cell transcriptomics, Toll-like/NF-κB signaling is identified as the key pathway involved in CNS damage caused by Tp. Moreover, monocyte-derived macrophages are key cells involved in the inflammatory response to Tp in the CNS of NS patients. In addition, it is found that inflammatory cells in peripheral blood may cause neurological damage through disruption of the blood‒brain barrier (BBB) in individuals with NS. Notably, activation of the Toll-like/NF-κB signaling pathway, as well as dysregulation of neural function, is likewise validated in an in vitro NS brain organoid model. In conclusion, the results revealed the mechanisms of inflammation-mediated brain injury in Tp-induced NS and provided new ideas for the clinical treatment of Tp infection.

Biomaterial-assisted organoid technology for disease modeling and drug screening

Developing disease models and screening for effective drugs are key areas of modern medical research. Traditional methodologies frequently fall short in precisely replicating the intricate architecture of bodily tissues and organs. Nevertheless, recent advancements in biomaterial-assisted organoid technology have ushered in a paradigm shift in biomedical research. This innovative approach enables the cultivation of three-dimensional cellular structures in vitro that closely emulate the structural and functional attributes of organs, offering physiologically superior models compared to conventional techniques. The evolution of biomaterials plays a pivotal role in supporting the culture and development of organ tissues, thereby facilitating more accurate disease state modeling and the rigorous evaluation of drug efficacy and safety profiles. In this review, we will explore the roles that various biomaterials play in organoid development, examine the fundamental principles and advantages of utilizing these technologies in constructing disease models, and highlight recent advances and practical applications in drug screening using disease-specific organoid models. Additionally, the challenges and future directions of organoid technology are discussed. Through continued research and innovation, we aim to make remarkable strides in disease treatment and drug development, ultimately enhancing patient quality of life.

Human Brain Organoids Model Abnormal Prenatal Neural Development Induced by Thermal Stimulation

The developing human foetal brain is sensitive to thermal stimulation during pregnancy. However, the mechanisms by which heat exposure affects human foetal brain development remain unclear, largely due to the lack of appropriate research models for studying thermal stimulation. To address this, we have developed a periodic heating model based on brain organoids derived from human pluripotent stem cells. The model recapitulated neurodevelopmental disruptions under prenatal heat exposure at the early stages, providing a paradigm for studying the altered neurodevelopment under environmental stimulation. Our study found that periodic heat exposure led to decreased size and impaired neural tube development in the brain organoids. Bulk RNA-seq analysis revealed that the abnormal WNT signalling pathway and the reduction of G2/M progenitor cells might be involved in heat stimulation. Further investigation revealed increased neural differentiation and decreased proliferation under heat stimulation, indicating that periodic heat exposure might lead to abnormal brain development by altering key developmental processes. Hence, our model of periodically heating brain organoids provides a platform for modelling the effects of maternal fever on foetal brain development and could be extended to applications in neurodevelopmental disorders intervention.

Assessing in-vitro models for microglial development and fetal programming: a critical review

This review evaluates in-vitro models for studying how maternal influences during pregnancy impact the development of offspring microglia, the immune cells of the central nervous system. The models examined include primary microglia cultures, microglia cell lines, iPSC-derived microglia, PBMC-induced microglia-like cells, 3D brain organoids derived from iPSCs, and Hofbauer cells. Each model is assessed for its ability to replicate the in-vivo environment of the developing brain, with a focus on their strengths, limitations, and practical challenges. Key factors such as scalability, genetic and epigenetic fidelity, and physiological relevance are highlighted. Microglia cell lines are highly scalable but lack genetic and epigenetic fidelity. iPSC-derived microglia provide moderate physiological relevance and patient-specific genetic insights but face operational and epigenetic challenges inherent to reprogramming. 3D brain organoids, derived from iPSCs, offer an advanced platform for studying complex neurodevelopmental processes but require extensive resources and technical expertise. Hofbauer cells, which are fetal macrophages located in the placenta and share a common developmental origin with microglia, are uniquely exposed to prenatal maternal factors and, depending on fetal barrier maturation, exhibit variable epigenetic fidelity. This makes them particularly useful for exploring the impact of maternal influences on fetal programming of microglial development. The review concludes that no single model comprehensively captures all aspects of maternal influences on microglial development, but it offers guidance on selecting the most appropriate model based on specific research objectives and experimental constraints.

Emerging approaches to enhance human brain organoid physiology

Brain organoids are important 3D models for studying human brain development, disease, and evolution. To overcome some of the existing limitations that affect organoid quality, reproducibility, characteristics, and in vivo resemblance, current efforts are directed to improve their physiological relevance by exploring different, yet interconnected, routes. In this review, these approaches and their latest developments are discussed, including stem cell optimization, refining morphogen administration strategies, altering the extracellular matrix (ECM) niche, and manipulating tissue architecture to mimic in vivo brain morphogenesis. Additionally, strategies to increase cell diversity and enhance organoid maturation, such as establishing co-cultures, assembloids, and organoid in vivo xenotransplantation, are reviewed. We explore how these various factors can be tuned and intermingled and speculate on future avenues towards even more physiologically-advanced brain organoids.

Examining the NEUROG2 lineage and associated gene expression in human cortical organoids

Proneural genes are conserved drivers of neurogenesis across the animal kingdom. How their functions have adapted to guide human-specific neurodevelopmental features is poorly understood. Here, we mined transcriptomic data from human fetal cortices and generated from human embryonic stem cell-derived cortical organoids (COs) to show that NEUROG1 and NEUROG2 are most highly expressed in basal neural progenitor cells, with pseudotime trajectory analyses indicating that NEUROG1-derived lineages predominate early and NEUROG2 lineages later. Using ChIP-qPCR, gene silencing and overexpression studies in COs, we show that NEUROG2 is necessary and sufficient to directly transactivate known target genes (NEUROD1, EOMES, RND2). To identify new targets, we engineered NEUROG2-mCherry knock-in human embryonic stem cells for CO generation. The mCherry-high CO cell transcriptome is enriched in extracellular matrix-associated genes, and two genes associated with human-accelerated regions: PPP1R17 and FZD8. We show that NEUROG2 binds COL1A1, COL3A1 and PPP1R17 regulatory elements, and induces their ectopic expression in COs, although NEUROG2 is not required for this expression. Neurog2 similarly induces Col3a1 and Ppp1r17 in murine P19 cells. These data are consistent with a conservation of NEUROG2 function across mammalian species.

Using cortical organoids to understand the pathogenesis of malformations of cortical development

Malformations of cortical development encompass a broad range of disorders associated with abnormalities in corticogenesis. Widespread abnormalities in neuronal formation or migration can lead to small head size or microcephaly with disorganized placement of cell types. Specific, localized malformations are termed focal cortical dysplasias (FCD). Neurodevelopmental disorders are common in all types of malformations of cortical development with the most prominent being refractory epilepsy, behavioral disorders such as autism spectrum disorder (ASD), and learning disorders. Several genetic pathways have been associated with these disorders from control of cell cycle and cytoskeletal dynamics in global malformations to variants in growth factor signaling pathways, especially those interacting with the mechanistic target of rapamycin (mTOR), in FCDs. Despite advances in understanding these disorders, the underlying developmental pathways that lead to lesion formation and mechanisms through which defects in cortical development cause specific neurological symptoms often remains unclear. One limitation is the difficulty in modeling these disorders, as animal models frequently do not faithfully mirror the human phenotype. To circumvent this obstacle, many investigators have turned to three-dimensional human stem cell models of the brain, known as organoids, because they recapitulate early neurodevelopmental processes. High throughput analysis of these organoids presents a promising opportunity to model pathophysiological processes across the breadth of malformations of cortical development. In this review, we highlight advances in understanding the pathophysiology of brain malformations using organoid models.

Two- and Three-Dimensional In Vitro Models of Parkinson's and Alzheimer's Diseases: State-of-the-Art and Applications

In vitro models play a pivotal role in advancing our understanding of neurodegenerative diseases (NDs) such as Parkinson's and Alzheimer's disease (PD and AD). Traditionally, 2D cell cultures have been instrumental in elucidating the cellular mechanisms underlying these diseases. Cultured cells derived from patients or animal models provide valuable insights into the pathological processes at the cellular level. However, they often lack the native tissue environment complexity, limiting their ability to fully recapitulate their features. In contrast, 3D models offer a more physiologically relevant platform by mimicking the 3D brain tissue architecture. These models can incorporate multiple cell types, including neurons, astrocytes, and microglia, creating a microenvironment that closely resembles the brain's complexity. Bioengineering approaches allow researchers to better replicate cell-cell interactions, neuronal connectivity, and disease-related phenotypes. Both 2D and 3D models have their advantages and limitations. While 2D cultures provide simplicity and scalability for high-throughput screening and basic processes, 3D models offer enhanced physiological relevance and better replicate disease phenotypes. Integrating findings from both model systems can provide a better understanding of NDs, ultimately aiding in the development of novel therapeutic strategies. Here, we review existing 2D and 3D in vitro models for the study of PD and AD.