Automating Brain Organoids To Boost Neurodegenerative Research

Neurodegenerative disease research faces a fundamental challenge: There are no good model systems for these conditions available. While these diseases have existed for a long time, researchers previously only had animal models or 2D cellular systems at their disposal. The advent of brain organoids – first developed in 2014 by Lancaster et al. – represents a new field that makes this research more accessible.

However, even with the development of brain organoids, significant obstacles remain. Culturing these organoids manually while achieving consistent and reproducible quality is extremely difficult, and researchers face scalability limitations – a human’s manual capacity is finite, as are the number of hours in a day, so additional tools are essential for making lab work more efficient.

The field also lacks standardization. Every lab operates with different protocols and every postdoc or PhD student develops their own variation of existing methods. To achieve high-quality organoids, researchers must adhere to very strict feeding schedules, but laboratory schedules often conflict with personal ones. Weekend plans, vacations or simply arriving late to work can shift cell culture conditions and impact quality.

This creates a storm of challenges: inadequate traditional models, labor-intensive manual processes, lack of standardization and the impossibility of maintaining required schedules over the 100+ day culture periods that brain organoids require.

The human brain is the most complicated and highly organized structure in the known universe and no animal has a brain close to that of a human. When studying human brain diseases using only animal models, researchers face critical problems: The tissue isn't complex enough to capture human brain complexity and animals' short lifespans makes it difficult to replicate late-onset neurodegenerative conditions. Additionally, animals are not humans, and so results obtained from animal studies are unfortunately not always translatable to patients.

Brain organoids offer a transformative approach to studying neurological diseases by overcoming the limitations of traditional in vitro models. First, they are generated from human stem cells that differentiate into distinct brain regions, allowing them to more accurately replicate the complexity of human brain tissue. Second, by using cells from both healthy and diseased individuals, researchers can investigate the genetic and molecular mechanisms underlying various neurological conditions, making organoids a powerful tool for disease modeling and therapeutic discovery. In addition, the integration of organoid technologies with CRISPR tools is a powerful combination, which, for example, allowed researchers to generate the first organoid model system for Alzheimer's disease that showed plaque formation – similar to what is seen in patients. 

There are three key advantages of using automated systems for brain organoid cultivation. First, they can achieve the reproducibility required for consistency at scale. Second, they have the monitoring capabilities by light microscopy, essential for quality control. Third, they can achieve the scalability needed for meaningful research. This gives researchers more time to do what they do best –  develop evidence-based answers to complex research questions.

Manually maintaining just 10 brain organoid plates requires nearly 30 hours of hands-on time each week, but automation reduces this to just a few hours. Automated systems can process many more plates than humans while adhering to strict feeding and passaging schedules. For monitoring purposes, images can frequently be acquired over the entire culture duration and provide important information about the culture quality. The scale of this challenge becomes clear when considering that brain organoids need to be cultured for – on average – 100 days. With 60 plates in a system requiring daily feeding and imaging, researchers suddenly face more work than a single person can manage, in addition to a huge amount of data that's nearly impossible to acquire manually. Not to mention, these datasets are very challenging to handle in terms of storage, organization and analysis.  

The new rocking incubator in the CellXpress.ai® Automated Cell Culture System is crucial for automating the successful generation of brain organoids because it allows the brain organoids to be kept in motion. These organoids are incredibly hungry, need a constant flow of nutrients and oxygen and produce significant amounts of waste products. Diffusion over larger scales is very slow, but the rocking incubator, which automatically and gently rocks plates within the incubator, ensures proper media mixing inside each well, providing optimal conditions throughout the experiment.

Without constant agitation, organoids sink to the bottom of wells, cells may migrate out or organoids clump together. To maintain optimal culture conditions over long periods, it's essential to agitate the media and keep organoids floating.

The update also includes modules that natively integrate external components with the CellXpress.ai cell culture system, such as centrifuges, high-content imaging systems or high-throughput kinetic screening systems for endpoint assays and quality control during cultivation.

To tackle drug discovery for these diseases effectively, researchers need to test numerous compounds and conditions, which requires many organoids of similar quality. However, several missing pieces currently prevent the scalability of proper organoid production.

The CellXpress.ai cell culture system addresses current key bottlenecks, such as protocol standardization and variability of culture conditions over time (especially when multiple people are involved).

The system tackles these challenges by providing standardized protocols that can be exported and imported across many labs to achieve reliable and consistent generation across different geographic locations.

The rocking incubator accommodates up to six rocking racks, each holding up to 10 plates, providing substantial scale-up capacity. Mixing and matching rocking and non-rocking racks allows researchers to cultivate stem cells and brain organoids in the same incubator.

The system includes AI-driven software to analyze large, complex datasets and can seamlessly integrate with peripheral devices if needed. This delivers a comprehensive end-to-end solution spanning stem cell cultivation, organoid differentiation and maturation, endpoint assays and data analysis – addressing key pain points that have historically limited progress in neurodegenerative disease research.