Cerebral organoids recapitulate in vivo phenotypes and physiological functions of the brain and have great potential in studying brain development, modeling diseases, and conducting neural network research. It is essential to obtain whole-mount three-dimensional (3D) images of cerebral organoids at cellular levels to explore their characteristics and applications. Existing histological strategies sacrifice inherent spatial characteristics of organoids, and the strategy for volume imaging and 3D analysis of entire organoids is urgently needed. Here, we proposed a high-resolution imaging pipeline based on fluorescent labeling by viral transduction and 3D immunostaining with fluorescence micro-optical sectioning tomography (fMOST). We were able to image intact organoids using our pipeline, revealing cytoarchitecture information of organoids and the spatial localization of neurons and glial fibrillary acidic protein positive cells (GFAP⁺ cells). We performed single-cell reconstruction to analyze the morphology of neurons and GFAP⁺ cells. Localization and quantitative analysis of cortical layer markers revealed heterogeneity of organoids. This pipeline enabled acquisition of high-resolution spatial information of millimeter-scale organoids for analyzing their cell composition and morphology.

Organoids can recapitulate human-specific phenotypes and functions in vivo and have great potential for research in development, disease modeling, and drug screening. Due to the inherent variability among organoids, experiments often require a large sample size. Embedding, staining, and imaging each organoid individually require a lot of reagents and time. Hence, there is an urgent need for fast and efficient methods for analyzing the phenotypic changes in organoids in batches. Here, we provide a comprehensive strategy for array embedding, staining, and imaging of cerebral organoids in both agarose sections and in 3D to analyze the spatial distribution of biomarkers in organoids in situ. We constructed several disease models, particularly an aging model, as examples to demonstrate our strategy for the investigation of the phenotypic analysis of organoids. We fabricated an array mold to produce agarose support with microwells, which hold organoids in place for live/dead imaging. We performed staining and imaging of sectioned organoids embedded in agarose and 3D imaging to examine phenotypic changes in organoids using fluorescence micro-optical sectioning tomography (fMOST) and whole-mount immunostaining. Parallel studies of organoids in arrays using the same staining and imaging parameters enabled easy and reliable comparison among different groups. We were able to track all the data points obtained from every organoid in an embedded array. This strategy could help us study the phenotypic changes in organoids in disease models and drug screening.

The basal forebrain (BF)-hippocampus (HPC) circuit is indispensable for learning and memory, and in vitro models are essential for dissecting its age-related decline. Nonetheless, current culture methods endure brief survival or confine cells to two dimensions, leaving the circuit’s progressive degeneration refractory to long-term investigation. Here, we developed a simple, three-dimensional (3D) compartmentalized co-culture model that mimics the anatomical organization of BF and HPC neurons. Results demonstrate that basal forebrain cholinergic neurons (BFCNs) co-cultured with primary HPC neurons remain viable for more than two months without exogenous growth factors, significantly promoting BFCNs growth, polarity development, and functional maturation. In this system, BFCNs somata were confined within the hydrogel, whereas cholinergic axons extended toward adjacent hippocampal area, reaching 1681.9 ± 351.8 μm by week 5—significantly longer than in BFCNs monocultures. This model can successfully recapitulate age-dependent progressive neuronal degeneration during long-term culture, validating this long-term co-culture as a platform for studying circuit aging and degeneration. Therefore, this low-cost and highly physiological platform provides a new avenue for in-depth investigations into the mechanisms of neurodegenerative diseases.

Neuronal senescence-like states are increasingly implicated in age-related neurodegeneration, yet the neuron-intrinsic regulators that drive these phenotypes remain poorly defined. Guided by prior transcriptomic analysis of aged basal forebrain cholinergic neurons, we investigated Srebf2 and Zmiz1 using primary basal forebrain neuronal cultures with adeno-associated virus-mediated gain- and loss-of-function, quantitative immunocytochemistry, and low-input transcriptomic profiling of fluorescence-activated cell sorting-isolated neurons. Both perturbation strategies produced the expected directional changes in target transcripts. Overexpression of either gene increased the other, whereas knockdown did not elicit reciprocal suppression, indicating asymmetric regulatory coupling. Phenotypically, Srebf2 showed a bidirectional association with senescence-like changes, as both overexpression and knockdown increased p16 and p21, whereas Zmiz1 acted more directionally, with overexpression increasing and knockdown reducing these markers. Transcriptomic profiling revealed broad direction-dependent remodeling, including a set of 55 genes that changed concordantly across perturbation directions. Pathway analysis further showed specialization, with Zmiz1 preferentially associated with an Alzheimer’s disease-related signature and Srebf2 more strongly linked to cholinergic synapse programs. Together, these findings identify Srebf2 and Zmiz1 as coupled but non-equivalent regulators of a neuronal senescence-like program.

There was an error in the original publication