In vitro modeling for inherited neurological diseases using induced pluripotent stem cells: from 2D to organoid

Phase-amplitude coupling detection and analysis of human 2-dimensional neural cultures in multi-well microelectrode array in vitro

BACKGROUND

Human induced pluripotent stem cell (hiPSC)- derived neurons offer the possibility of studying human-specific neuronal behaviors in physiologic and pathologic states in vitro. It is unclear whether cultured neurons can achieve the fundamental network behaviors required to process information in the brain. Investigating neuronal oscillations and their interactions, as occurs in cross-frequency coupling (CFC), addresses this question.

NEW METHODS

We examined whether networks of two-dimensional (2D) cultured hiPSC-derived cortical neurons grown with hiPSC-derived astrocytes on microelectrode array plates recapitulate the CFC that is present in vivo. We employed the modulation index method for detecting phase-amplitude coupling (PAC) and used offline spike sorting to analyze the contribution of single neuron spiking to network behavior.

RESULTS

We found that PAC is present, the degree of PAC is specific to network structure, and it is modulated by external stimulation with bicuculline administration. Modulation of PAC is not driven by single neurons, but by network-level interactions.

COMPARISON WITH EXISTING METHODS

PAC has been demonstrated in multiple regions of the human cortex as well as in organoids. This is the first report of analysis demonstrating the presence of coupling in 2D cultures.

CONCLUSION

CFC in the form of PAC analysis explores communication and integration between groups of neurons and dynamical changes across networks. In vitro PAC analysis has the potential to elucidate the underlying mechanisms as well as capture the effects of chemical, electrical, or ultrasound stimulation; providing insight into modulation of neural networks to treat nervous system disorders in vivo.

Retinal organoids from human-induced pluripotent stem cells: From studying retinal dystrophies to early diagnosis of Alzheimer's and Parkinson's disease

Human-induced pluripotent stem cells (hiPSCs) have provided new methods to study neurodegenerative diseases. In addition to their wide application in neuronal disorders, hiPSCs technology can also encompass specific conditions, such as inherited retinal dystrophies. The possibility of evaluating alterations related to retinal disorders in 3D organoids increases the truthfulness of in vitro models. Moreover, both Alzheimer's (AD) and Parkinson's disease (PD) have been described as causing early retinal alterations, generating beta-amyloid protein accumulation, or affecting dopaminergic amacrine cells. This review addresses recent advances and future perspectives obtained from in vitro modeling of retinal diseases, focusing on retinitis pigmentosa (RP). Additionally, we depicted the possibility of evaluating changes related to AD and PD in retinal organoids obtained from potential patients long before the onset of the disease, constituting a valuable tool in early diagnosis. With this, we pointed out prospects in the study of retinal dystrophies and early diagnosis of AD and PD.

Advances in the knowledge and therapeutics of schizophrenia, major depression disorder, and bipolar disorder from human brain organoid research

Tridimensional cultures of human induced pluripotent cells (iPSCs) experimentally directed to neural differentiation, termed "brain organoids" are now employed as an in vitro assay that recapitulates early developmental stages of nervous tissue differentiation. Technical progress in culture methodology enabled the generation of regionally specialized organoids with structural and neurochemical characters of distinct encephalic regions. The technical process of organoid elaboration is undergoing progressively implementation, but current robustness of the assay has attracted the attention of psychiatric research to substitute/complement animal experimentation for analyzing the pathophysiology of psychiatric disorders. Numerous morphological, structural, molecular and functional insights of psychiatric disorders have been uncovered by comparing brain organoids made with iPSCs obtained from control healthy subjects and psychiatric patients. Brain organoids were also employed for analyzing the response to conventional treatments, to search for new drugs, and to anticipate the therapeutic response of individual patients in a personalized manner. In this review, we gather data obtained by studying cerebral organoids made from iPSCs of patients of the three most frequent serious psychiatric disorders: schizophrenia, major depression disorder, and bipolar disorder. Among the data obtained in these studies, we emphasize: (i) that the origin of these pathologies takes place in the stages of embryonic development; (ii) the existence of shared molecular pathogenic aspects among patients of the three distinct disorders; (iii) the occurrence of molecular differences between patients bearing the same disorder, and (iv) that functional alterations can be activated or aggravated by environmental signals in patients bearing genetic risk for these disorders.

Phase-Amplitude Coupling Detection and Analysis of Human 2-Dimensional Neural Cultures in Multi-well Microelectrode Array in Vitro

Human induced pluripotent stem cell (hiPSC) - derived neurons offer the possibility of studying human-specific neuronal behaviors in physiologic and pathologic states in vitro . However, it is unclear whether these cultured neurons can achieve the fundamental network behaviors that are required to process information in the human brain. Investigating neuronal oscillations and their interactions, as occurs in cross-frequency coupling (CFC), is potentially a relevant approach. Microelectrode array culture plates provide a controlled framework to study populations of hiPSC-derived cortical neurons (hiPSC-CNs) and their electrical activity. Here, we examined whether networks of two-dimensional cultured hiPSC-CNs recapitulate the CFC that is present in networks in vivo . We analyzed the electrical activity recorded from hiPSC-CNs grown in culture with hiPSC-derived astrocytes. We employed the modulation index method for detecting phase-amplitude coupling (PAC) and used an offline spike sorting method to analyze the contribution of a single neuron's spiking activities to network behavior. Our analysis demonstrates that the degree of PAC is specific to network structure and is modulated by external stimulation, such as bicuculine administration. Additionally, the shift in PAC is not driven by a single neuron's properties but by network-level interactions. CFC analysis in the form of PAC explores communication and integration between groups of nearby neurons and dynamical changes across the entire network. In vitro , it has the potential to capture the effects of chemical agents and electrical or ultrasound stimulation on these interactions and may provide valuable information for the modulation of neural networks to treat nervous system disorders in vivo .

Significance

Phase amplitude coupling (PAC) analysis demonstrates that the complex interactions that occur between neurons and network oscillations in the human brain, in vivo , are present in 2-dimensional human cultures. This coupling is implicated in normal cognitive function as well as disease states. Its presence in vitro suggests that PAC is a fundamental property of neural networks. These findings offer the possibility of a model to understand the mechanisms and of PAC more completely and ultimately allow us to understand how it can be modulated in vivo to treat neurologic disease.

Merits and challenges of iPSC-derived organoids for clinical applications

Induced pluripotent stem cells (iPSCs) have entered an unprecedented state of development since they were first generated. They have played a critical role in disease modeling, drug discovery, and cell replacement therapy, and have contributed to the evolution of disciplines such as cell biology, pathophysiology of diseases, and regenerative medicine. Organoids, the stem cell-derived 3D culture systems that mimic the structure and function of organs in vitro, have been widely used in developmental research, disease modeling, and drug screening. Recent advances in combining iPSCs with 3D organoids are facilitating further applications of iPSCs in disease research. Organoids derived from embryonic stem cells, iPSCs, and multi-tissue stem/progenitor cells can replicate the processes of developmental differentiation, homeostatic self-renewal, and regeneration due to tissue damage, offering the potential to unravel the regulatory mechanisms of development and regeneration, and elucidate the pathophysiological processes involved in disease mechanisms. Herein, we have summarized the latest research on the production scheme of organ-specific iPSC-derived organoids, the contribution of these organoids in the treatment of various organ-related diseases, in particular their contribution to COVID-19 treatment, and have discussed the unresolved challenges and shortcomings of these models.

Advancements in Ocular Regenerative Therapies

The use of stem cells (SCs) has emerged as a promising avenue in ophthalmology, offering potential therapeutic solutions for various vision impairments and degenerative eye diseases. SCs possess the unique ability to self-renew and differentiate into specialised cell types, making them valuable tools for repairing damaged tissues and restoring visual function. Stem cell-based therapies hold significant potential for addressing conditions such as age-related macular degeneration (AMD), retinitis pigmentosa (RP), corneal disorders, and optic nerve damage. Therefore, researchers have explored different sources of stem cells, including embryonic stem cells (ESC), induced pluripotent stem cells (iPSCs), and adult stem cells, for ocular tissue regeneration. Preclinical studies and early-phase clinical trials have demonstrated promising outcomes, with some patients experiencing improved vision following stem cell-based interventions. However, several challenges remain, including optimising the differentiation protocols, ensuring transplanted cells' safety and long-term viability, and developing effective delivery methods. The field of stem cell research in ophthalmology witnesses a constant influx of new reports and discoveries. To effectively navigate these tons of information, it becomes crucial to summarise and systematise these findings periodically. In light of recent discoveries, this paper demonstrates the potential applications of stem cells in ophthalmology, focusing on their use in various eye tissues, including the cornea, retina, conjunctiva, iris, trabecular meshwork, lens, ciliary body, sclera, and orbital fat.

Silver nanoparticles exposure induces developmental neurotoxicity in hiPSC-derived cerebral organoids

Silver nanoparticles (AgNPs) are used in various research fields. Although the neurotoxicity of AgNPs has been explored in animal models and 2D cell-culture models, including human stem cells, these models cannot accurately mimic the development of the human brain. Therefore, the potential mechanisms of AgNPs-induced developmental neurotoxicity in humans are still largely unclear. In this study, cerebral organoids derived from induced pluripotent stem cells were treated with 0.1 μg/mL or 0.5 μg/mL AgNPs for 7 days. At the low concentration (0.1 μg/mL), AgNPs increased the cell proliferation and inhibited the neural apoptosis in the organoids, but impaired the cilium assembly and elongation, which may perturb the cell cycle and induce abnormal cerebral-organoid growth. Conversely, at the high concentration (0.5 μg/mL), AgNPs significantly inhibited cell proliferation and induced apoptosis in cerebral organoids. High-concentration AgNPs reduced the expression and co-localization of the cytoskeleton proteins F-actin, myosin, and tubulin, thereby perturbing neurite growth. In conclusion, AgNPs exposure induces developmental neurotoxic effects in cerebral organoids and is thus a potential congenital risk factor.

A Simple Method for Generating Cerebral Organoids from Human Pluripotent Stem Cells

Background and Objectives

In recent years, brain organoid technologies have been the most innovative advance in neural differentiation research. In line with this, we optimized a method to establish cerebral organoids from feeder-free cultured human pluripotent stem cells. In this study, we focused on the consistent and robust production of cerebral organoids comprising neural progenitor cells and neurons. We propose an optimal protocol for cerebral organoid generation that is applicable to both human embryonic stem cells and human induced pluripotent stem cells.

Methods and Results

We investigated formation of neuroepithelium, neural tube, and neural folding by observing the morphology of embryoid bodies at each stage during the cerebral organoid differentiation process. Furthermore, we characterized the cerebral organoids via immunocytochemical staining of sectioned organoid samples, which were prepared using a Cryostat and Vibratome. Finally, we established a routine method to generate early cerebral organoids comprising a cortical layer and a neural progenitor zone.

Conclusions

We developed an optimized methodology for the generation of cerebral organoids using hESCs and hiPSCs. Using this protocol, consistent and efficient cerebral organoids could be obtained from hiPSCs as well as hESCs. Further, the morphology of brain organoids could be analyzed through 2D monitoring via immunostaining and tissue sectioning, or through 3D monitoring by whole tissue staining after clarification.

Human Trisomic iPSCs from Down Syndrome Fibroblasts Manifest Mitochondrial Alterations Early during Neuronal Differentiation

BACKGROUND

The presence of mitochondrial alterations in Down syndrome suggests that it might affect neuronal differentiation. We established a model of trisomic iPSCs, differentiating into neural precursor cells (NPCs) to monitor the occurrence of differentiation defects and mitochondrial dysfunction.

METHODS

Isogenic trisomic and euploid iPSCs were differentiated into NPCs in monolayer cultures using the dual-SMAD inhibition protocol. Expression of pluripotency and neural differentiation genes was assessed by qRT-PCR and immunofluorescence. Meta-analysis of expression data was performed on iPSCs. Mitochondrial Ca²⁺, reactive oxygen species (ROS) and ATP production were investigated using fluorescent probes. Oxygen consumption rate (OCR) was determined by Seahorse Analyzer.

RESULTS

NPCs at day 7 of induction uniformly expressed the differentiation markers PAX6, SOX2 and NESTIN but not the stemness marker OCT4. At day 21, trisomic NPCs expressed higher levels of typical glial differentiation genes. Expression profiles indicated that mitochondrial genes were dysregulated in trisomic iPSCs. Trisomic NPCs showed altered mitochondrial Ca²⁺, reduced OCR and ATP synthesis, and elevated ROS production.

CONCLUSIONS

Human trisomic iPSCs can be rapidly and efficiently differentiated into NPC monolayers. The trisomic NPCs obtained exhibit greater glial-like differentiation potential than their euploid counterparts and manifest mitochondrial dysfunction as early as day 7 of neuronal differentiation.

Exploiting hiPSCs in Leber's Hereditary Optic Neuropathy (LHON): Present Achievements and Future Perspectives

More than 30 years after discovering Leber's hereditary optic neuropathy (LHON) as the first maternally inherited disease associated with homoplasmic mtDNA mutations, we still struggle to achieve effective therapies. LHON is characterized by selective degeneration of retinal ganglion cells (RGCs) and is the most frequent mitochondrial disease, which leads young people to blindness, in particular males. Despite that causative mutations are present in all tissues, only a specific cell type is affected. Our deep understanding of the pathogenic mechanisms in LHON is hampered by the lack of appropriate models since investigations have been traditionally performed in non-neuronal cells. Effective in-vitro models of LHON are now emerging, casting promise to speed our understanding of pathophysiology and test therapeutic strategies to accelerate translation into clinic. We here review the potentials of these new models and their impact on the future of LHON patients.

Patient-Derived Induced Pluripotent Stem Cells (iPSCs) and Cerebral Organoids for Drug Screening and Development in Autism Spectrum Disorder: Opportunities and Challenges

Autism spectrum disorder (ASD) represents a group of neurodevelopmental diseases characterized by persistent deficits in social communication, interaction, and repetitive patterns of behaviors, interests, and activities. The etiopathogenesis is multifactorial with complex interactions between genetic and environmental factors. The clinical heterogeneity and complex etiology of this pediatric disorder have limited the development of pharmacological therapies. The major limit to ASD research remains a lack of relevant human disease models which can faithfully recapitulate key features of the human pathology and represent its genetic heterogeneity. Recent advances in induced pluripotent stem cells (iPSCs), reprogrammed from somatic cells of patients into all types of patient-specific neural cells, have provided a promising cellular tool for disease modeling and development of novel drug treatments. The iPSCs technology allowed not only a better investigation of the disease etiopathogenesis but also opened up the potential for personalized therapies and offered new opportunities for drug discovery, pharmacological screening, and toxicity assessment. Moreover, iPSCs can be differentiated and organized into three-dimensional (3D) organoids, providing a model which mimics the complexity of the brain’s architecture and more accurately recapitulates tissue- and organ-level disease pathophysiology. The aims of this review were to describe the current state of the art of the use of human patient-derived iPSCs and brain organoids in modeling ASD and developing novel therapeutic strategies and to discuss the opportunities and major challenges in this rapidly moving field.

Role of DNA Methyl-CpG-Binding Protein MeCP2 in Rett Syndrome Pathobiology and Mechanism of Disease

Rett Syndrome (RTT) is a severe, rare, and progressive developmental disorder with patients displaying neurological regression and autism spectrum features. The affected individuals are primarily young females, and more than 95% of patients carry de novo mutation(s) in the Methyl-CpG-Binding Protein 2 (MECP2) gene. While the majority of RTT patients have MECP2 mutations (classical RTT), a small fraction of the patients (atypical RTT) may carry genetic mutations in other genes such as the cyclin-dependent kinase-like 5 (CDKL5) and FOXG1. Due to the neurological basis of RTT symptoms, MeCP2 function was originally studied in nerve cells (neurons). However, later research highlighted its importance in other cell types of the brain including glia. In this regard, scientists benefitted from modeling the disease using many different cellular systems and transgenic mice with loss- or gain-of-function mutations. Additionally, limited research in human postmortem brain tissues provided invaluable findings in RTT pathobiology and disease mechanism. MeCP2 expression in the brain is tightly regulated, and its altered expression leads to abnormal brain function, implicating MeCP2 in some cases of autism spectrum disorders. In certain disease conditions, MeCP2 homeostasis control is impaired, the regulation of which in rodents involves a regulatory microRNA (miR132) and brain-derived neurotrophic factor (BDNF). Here, we will provide an overview of recent advances in understanding the underlying mechanism of disease in RTT and the associated genetic mutations in the MECP2 gene along with the pathobiology of the disease, the role of the two most studied protein variants (MeCP2E1 and MeCP2E2 isoforms), and the regulatory mechanisms that control MeCP2 homeostasis network in the brain, including BDNF and miR132.