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How human-derived brain organoids are built differently from brain organoids derived from genetically-close relatives: a multi-scale hypothesis.
How genes influence tissue-scale organization remains a longstanding biological puzzle. While experimental efforts quantify gene expression, chromatin, cellular, and tissue structure, computational models lag behind. To help accelerate multiscale modeling, we demonstrate how a tissue-scale, cellular-based model can be merged with a cell nuclear model incorporating a deformable lamina shell and chromatin to test hypotheses linking chromatin and tissue scales. Specifically, we propose a hypothesis to explain structural differences between human, chimpanzee, and gorilla-derived brain organoids. Recent experiments reveal that a cell fate transition from neuroepithelial to radial glial cells includes a new intermediate state that is delayed in human-derived organoids, leading to significantly narrowed and lengthened apical cells. Additional experiments also demonstrated that ZEB2, a transcription factor, plays a major role in the onset of the novel intermediate state. We hypothesize that this delay stems from chromatin reorganization triggered by mechanical strain as the respective brain organoids develop, with a higher critical threshold in human-derived cells. Here, we computationally test the feasibility of such a hypothesis by exploring how slightly different initial configurations of chromatin, as modeled by different numbers of chromatin crosslinkers, organize in response to mechanical strain with increasingly different initial configurations representing less genetically-close relatives. We find that even small differences in the number of chromatin crosslinkers (>0.01%) yield distinguishable chromatin displacement on average beyond 35% mechanical strain. At higher strains, we observe a new type of nonlinear chromatin scaling law with an exponent of 3.24(5). Finally, we show how differences in chromatin strain maps and more conventional contact maps can reveal structural distinctions between genetically-close species.
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Generating LGE/CGE Organoids from Human Pluripotent Stem Cell-derived Brain Organoids Without External Signal Induction.
Human pluripotent stem cell (hPSC)-derived GABAergic neurons offer potential for treating neurological disorders by restoring disrupted inhibitory circuits, yet current differentiation methods show limited efficiency, purity, and subtype specificity. We present an approach for generating lateral/caudal ganglionic eminence (LGE/CGE) organoids (LCOs) from hPSC-derived brain organoids (BOs) without external signal induction. LCOs bud from the BO surface and are predominantly composed of LGE/CGE-type GABAergic neurons that mature into functional inhibitory neurons. LCOs and BOs exhibit distinct subtype compositions: LCOs contain both LGE-type neurons, with the capacity to form striatal medium spiny neurons, and abundant CGE-type neurons, whereas BOs contain fewer CGE-type neurons. Single-cell transcriptomic analysis reveals that LCOs closely resemble human embryonic LGE/CGE neurons at gestational weeks 12-13. We also developed a method to selectively enrich CXCR4+ CGE-type neurons from LCOs. This platform enables efficient generation of human LGE/CGE-type GABAergic neurons for disease modeling and cell therapy development.
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CRISPR-based genetic screens in human pluripotent stem cells derived neurons and brain organoids.
Recent large-scale genome-wide association and single-cell RNA sequencing (scRNA-seq) studies have uncovered disease-associated genetic risk factors and cell type-specific genetic alterations. However, our understanding of how these genetic variants cause diseases and the underlying mechanisms remains largely unknown. Functional genomics screens using CRISPR-based technologies offer an effective tool for studying genes relevant to disease phenotypes. Here, we summarize recent CRISPR-based functional genomics screen approaches applied to human pluripotent stem cell (hPSC)-derived neurons and brain organoids. These screens have identified genes crucial for neurogenesis, neuronal survival, morphological development, and migration. Combining CRISPR-based genetic screens with scRNA-seq, researchers have revealed downstream genes and cellular pathways impacted by these genetic variants in human neural cells, providing new insights into the pathogenesis of neurodevelopmental disorders, such as microcephaly and autism spectrum disorders. Finally, we discuss current challenges and future directions for using CRISPR-based screens in furthering our understanding of neurological diseases and developing potential therapeutic strategies. Despite challenges, CRISPR-based screens have enormous potential for advancing the therapeutic development of many diseases.
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Nanotherapeutic Modulation of Human Neural Cells and Glioblastoma in Organoids and Monocultures.
Inflammatory processes in the brain are orchestrated by microglia and astrocytes in response to activators such as pathogen-associated molecular patterns, danger-associated molecular patterns and some nanostructures. Microglia are the primary immune responders in the brain and initiate responses amplified by astrocytes through intercellular signaling. Intercellular communication between neural cells can be studied in cerebral organoids, co-cultures or in vivo. We used human cerebral organoids and glioblastoma co-cultures to study glia modulation by dendritic polyglycerol sulfate (dPGS). dPGS is an extensively studied nanostructure with inherent anti-inflammatory properties. Under inflammatory conditions, lipocalin-2 levels in astrocytes are markedly increased and indirectly enhanced by soluble factors released from hyperactive microglia. dPGS is an effective anti-inflammatory modulator of these markers. Our results show that dPGS can enter neural cells in cerebral organoids and glial cells in monocultures in a time-dependent manner. dPGS markedly reduces lipocalin-2 abundance in the neural cells. Glioblastoma tumoroids of astrocytic origin respond to activated microglia with enhanced invasiveness, whereas conditioned media from dPGS-treated microglia reduce tumoroid invasiveness. Considering that many nanostructures have only been tested in cancer cells and rodent models, experiments in human 3D cerebral organoids and co-cultures are complementary in vitro models to evaluate nanotherapeutics in the pre-clinical setting. Thoroughly characterized organoids and standardized procedures for their preparation are prerequisites to gain information of translational value in nanomedicine. This study provides data for a well-characterized dendrimer (dPGS) that modulates the activation state of human microglia implicated in brain tumor invasiveness.
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Epigenetics and cerebral organoids: promising directions in autism spectrum disorders.
Autism spectrum disorders (ASD) affect 1 in 68 children in the US according to the Centers for Disease Control and Prevention (CDC). It is characterized by impairments in social interactions and communication, restrictive and repetitive patterns of behaviors, and interests. Owing to disease complexity, only a limited number of treatment options are available mainly for children that alleviate but do not cure the debilitating symptoms. Studies confirm a genetic link, but environmental factors, such as medications, toxins, and maternal infection during pregnancy, as well as birth complications also play a role. Some studies indicate a set of candidate genes with different DNA methylation profiles in ASD compared to healthy individuals. Thus epigenetic alterations could help bridging the gene-environment gap in deciphering the underlying neurobiology of autism. However, epigenome-wide association studies (EWAS) have mainly included a very limited number of postmortem brain samples. Hence, cellular models mimicking brain development in vitro will be of great importance to study the critical epigenetic alterations and when they might happen. This review will give an overview of the state of the art concerning knowledge on epigenetic changes in autism and how new, cutting edge expertise based on three-dimensional (3D) stem cell technology models (brain organoids) can contribute in elucidating the multiple aspects of disease mechanisms.
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Modeling Alzheimer's Disease Using Human Brain Organoids.
Alzheimer's disease (AD) is the primary cause of dementia, to date. The urgent need to understand the biological and biochemical processes related to this condition, as well as the demand for reliable in vitro models for drug screening, has led to the development of novel techniques, among which stem cell methods are of utmost relevance for AD research, particularly the development of human brain organoids. Brain organoids are three-dimensional cellular aggregates derived from induced pluripotent stem cells (iPSCs) that recreate different neural cell interactions and tissue characteristics in culture. Here, we describe the protocol for the generation of brain organoids derived from AD patients and for the analysis of AD-derived pathology. AD organoids can recapitulate beta-amyloid and tau pathological features, making them a promising model for studying the molecular mechanisms underlying disease and for in vitro drug testing.
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Organoids: the third dimension of human brain development and disease.
Stem cell technologies have opened up new avenues in the study of human biology and disease. In particular, the advent of human embryonic stem cells followed by reprograming technologies for generation of induced pluripotent stem cells have instigated studies into modeling human brain development and disease by providing a means to simulate a human tissue otherwise completely or largely inaccessible to researchers. Brain development is a complex process achieved in a remarkably controlled spatial and temporal manner through coordinated cellular and molecular events. In vitro models aim to mimic these processes and recapitulate brain organogenesis. Initially, two-dimensional neural cultures presented an innovative landmark for investigating human neuronal and, more recently, glial biology, as well as for modeling brain neurodevelopmental and neurodegenerative diseases. The establishment of three-dimensional cultures in the form of brain organoids was an equally important milestone in the field. Brain organoids mimic more closely the in vivo tissue composition and architecture and are more physiologically relevant than monolayer cultures. They therefore represent a more realistic cellular environment for modeling the cell biology and pathology of the nervous system. Here we highlight the journey towards recapitulating human brain development and disease in a dish, progressing from two-dimensional in vitro systems to the third dimension provided by brain organoids. We discuss the potential of these approaches for modeling human brain development and evolution, and their promising contribution towards understanding and treating brain disease.
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Brain organoids: A promising model to assess oxidative stress-induced central nervous system damage.
Oxidative stress (OS) is one of the most significant propagators of systemic damage with implications for widespread pathologies such as vascular disease, accelerated aging, degenerative disease, inflammation, and traumatic injury. OS can be induced by numerous factors such as environmental conditions, lifestyle choices, disease states, and genetic susceptibility. It is tied to the accumulation of free radicals, mitochondrial dysfunction, and insufficient antioxidant protection, which leads to cell aging and tissue degeneration over time. Unregulated systemic increase in reactive species, which contain harmful free radicals, can lead to diverse tissue-specific OS responses and disease. Studies of OS in the brain, for example, have demonstrated how this state contributes to neurodegeneration and altered neural plasticity. As the worldwide life expectancy has increased over the last few decades, the prevalence of OS-related diseases resulting from age-associated progressive tissue degeneration. Unfortunately, vital translational research studies designed to identify and target disease biomarkers in human patients have been impeded by many factors (e.g., limited access to human brain tissue for research purposes and poor translation of experimental models). In recent years, stem cell-derived three-dimensional tissue cultures known as "brain organoids" have taken the spotlight as a novel model for studying central nervous system (CNS) diseases. In this review, we discuss the potential of brain organoids to model the responses of human neural cells to OS, noting current and prospective limitations. Overall, brain organoids show promise as an innovative translational model to study CNS susceptibility to OS and elucidate the pathophysiology of the aging brain.
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Anesthetic-induced neurodevelopmental changes with region-specific responses to propofol in forebrain organoids.
Propofol, a common anesthetic, has unclear effects on fetal brain development. While previous studies in animal models and 2D culture systems have reported neurotoxic effects, few have addressed the region-specific vulnerability of the developing human brain. This study investigated the distinct effects of propofol on human dorsal (hCS) and ventral (hSS) forebrain organoids, uncovering region-specific differences in neuronal differentiation and maturation. Detailed electrophysiological analysis revealed that propofol enhanced neuronal activity-increased action potential frequency and amplitude-in hCS organoids. Transcriptomic analysis further indicated a metabolic shift away from hypoxic stress toward efficient aerobic pathways. These findings provide a deeper understanding of how anesthesia affects brain development, particularly in early stages, and highlight the importance of considering regional differences and long-term effects in future research.
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Brain organoids get vascularized.