The quest to understand and treat neurodegenerative diseases such as Alzheimer’s disease (AD) and Parkinson’s disease (PD) has entered a new era with the rise of 3D brain organoids. Derived from human-induced pluripotent stem cells (hiPSCs), brain organoids recreate the complex architecture, function, and cellular interactions of the human brain far more effectively than traditional 2D cultures or animal models. The protocols to generate and maintain these 3D cultures can be challenging, but now, reliable, validated 3D organoids are commercially available, generated using scalable platform technologies. This innovation is opening entirely new avenues to study the mechanisms of neurodegenerative diseases and to test candidate therapies with greater fidelity, precision, and scalability.

Modeling the human brain in 3D

Unlike flat 2D cultures that tend to oversimplify cellular behavior or animal models that often fail to translate to humans, 3D brain organoids better replicate the intricate environment of the human brain (Figure 1). These miniature, self-organizing brain tissues can form structures reminiscent of different brain regions—such as the forebrain or midbrain—and support the maturation of a variety of cell types, including neurons, astrocytes, and glial cells.^1–6

Figure 1. Brain organoid. Credit: Molecular Devices

The initial method for generating cerebral organoids from human pluripotent stem cells (hPSCs) was developed by Madeline Lancaster and colleagues.⁵ This protocol has been widely used for modeling human brain development and diseases. Another popular protocol introduces a directed differentiation of induced pluripotent cells into region-specific cortical spheroids.⁶ Those methods take over 60 days and result in the formation of structured organoids with mature neurons and astrocytes. Imaging methods allow for the characterization of cell content and structure of organoids, while functional activities can be captured by various techniques, including electrophysiology, microelectrode arrays (MEA), or by recording calcium oscillation activities.

Another approach utilizes pre-differentiated induced pluripotent stem cells (iPSC)-derived neurons and astrocytes mixed together to form compact brain microtissues. Within a few weeks, those neurospheroids are able to present consistent spontaneous oscillation activities that can be recorded by MEA or by calcium oscillations recorded by imaging or fast kinetic recording instruments such as FLIPR Penta System or FDSS/μCell (Figure 2). 3D neuronal models were successfully used for evaluation of responses to neuro-active compounds or for evaluation of neurotoxicity effects.^7,8

Figure 2. Calcium oscillations. Credit: Molecular Devices

Various multidimensional models offer researchers a valuable tool to examine how diseases like AD and PD unfold at the cellular level. Organoids simulate in vivo tissue complexity by preserving essential features such as cell–cell interactions, diffusion gradients, and tissue morphology. In brain organoids, researchers can observe hallmark features of AD, such as amyloid-beta plaque formation and tau pathology, while PD-related traits, including dopaminergic neuron degeneration, can also be modeled.^9,10 These models not only mirror disease characteristics, but do so in human-derived tissues, enhancing their clinical relevance.

Characterizing brain cells and their functions

A key strength of brain organoids is their ability to host a network of neural cell types.^1–6 Confocal imaging and differential staining techniques allow researchers to visualize and characterize the organization of neurons and supporting cells within the tissue. Astrocytes and glial cells can be identified and studied alongside neurons to understand their roles in neurodegeneration.

Functional maturity is assessed through calcium imaging, a powerful technique that reveals synchronized calcium oscillations—an indicator of neural activity and network functionality. iPSC-derived brain organoids start showing functional activity that can be captured by Microelectrode Array technologies, or by visualizing calcium oscillations using imaging techniques.^8,10,11 In disease modeling, specific mutations related to disease can be introduced, or organoids can be generated from patient iPSC samples that carry known or unknown disease-related genes.

Disease modeling

In vitro systems hold great promise to model neural diseases, like Alzheimer’s or Parkinson’s, when cells are derived from iPSC lines that carry specific mutations related to the disease. Mutations can be introduced by genetic modification of iPSCs or derived from a person who has a relevant mutation. Interestingly, 3D neurospheroids created from iPSC-derived neurons carrying a disease-relevant mutation of the ApoE 4/4 gene showed altered profiles of functional calcium oscillations.^2,7 Moreover, some drugs that are used to treat Alzheimer’s (e.g., memantine) “corrected” the altered calcium oscillation patterns and rescued the phenotype back to normal. Such a model can therefore be used as an assay enabling researchers to identify compounds capable of correcting altered disease-related activity phenotypes.

The adoption of 3D biology represents a major paradigm shift in how drugs are discovered and screened. Traditional drug development often relies on 2D systems or animal models that poorly predict human outcomes, leading to high failure rates in clinical trials. Organoids, by contrast, offer human-derived models that better reflect patient responses.

Paradigm shift in drug discovery

One of the most transformative applications of brain organoids is drug discovery and drug development. Organoids provide a highly controlled, human-relevant setting to evaluate drug safety, efficacy, and toxicity. In a series of experiments using microBrain 3D neurospheroids, researchers exposed organoids to known neuroactive substances and environmental toxins. Using high-throughput imaging and kinetic fluorescence analysis, they detected compound-induced changes in calcium oscillation patterns—a proxy for neural activity disruption or restoration.^8,12

For example, compounds that modified oscillation patterns in Rett syndrome-derived neurospheroids were flagged as potential therapeutic agents.^12,13 This approach allows early identification of promising drug candidates and rejection of those likely to cause neurotoxicity—saving time, cost, and potential harm in clinical development.¹¹ Modification of activation patterns also indicates potential neurotoxicity or neurodevelopmental effect and can be used for screening drugs or other chemicals for potential neurotoxic effects. Peak analysis software used to detect patterns in oscillation waveforms offers over 20 descriptors that can be used to describe the impact.^8,12

The convergence of automation, AI-driven decision-making, and high-throughput screening is accelerating this shift. Researchers are now able to test automated workflows for culturing and screening brain organoids at scale, enhancing reproducibility and reducing manual labor.14 Standardized protocols enable the creation of validated, assay-ready organoids using platform technologies, allowing for high-throughput compound testing.^15,16

The prospects of industrialized organoid technology

Bioprocessing technology overcomes the persistent problem of scalability in organoid research to enable the production of large batches of uniform, assay-ready organoids. Standardized models increase consistency and enable their use in industrial drug screening pipelines. Advanced systems can now culture dorsal forebrain organoids from iPSCs following an optimized, semi-automated protocol. This includes critical steps like neural induction, differentiation, and maturation, all supported by automated media exchanges, imaging, and monitoring.¹⁷

Brain organoids are transforming neuroscience research and drug discovery. By replicating human brain structure and function in three dimensions, they provide more representative models of diseases like Alzheimer’s and Parkinson’s. These models enable researchers to investigate disease mechanisms, characterize brain cell behavior, and evaluate candidate therapies with unmatched precision. When combined with high-content imaging, automation, and AI-powered analysis, brain organoids offer a scalable, predictive platform for early-phase drug discovery. This emerging technology is rapidly becoming a cornerstone of next-generation biomedical research—promising to accelerate the journey of novel therapeutics from bench to clinic for patients affected by neurodegenerative diseases.

References

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