Facilitating Organoid Production for Biopharmaceutical Applications

Facilitating Organoid Production for Biopharmaceutical Applications


Organoids, tiny yet powerful replicas of organs derived from stem cells, are revolutionizing diagnostics, drug discovery, and precision medicine. Researchers are making progress in creating more complex organoids that closely mimic the structure and function of real organs. As these advancements continue, the potential for using organoids in regenerative medicine to repair or replace damaged tissues becomes increasingly promising. Despite the exciting progress, manufacturing challenges still stand in the way of organoid-based therapies becoming widespread. The Celligent platform from Cell X Technologies offers an innovative, automated, and customizable solution for producing high-quality, GMP-compliant 3D cell cultures, including organoids, paving the way for future breakthroughs.

Understanding Organoids: A Journey in Biopharma

Organoids, despite their roots stretching back to the 1970s, have only recently captured the biopharma spotlight. In the past decade, the conversation around organoids has ebbed and flowed, and now, they’re here again — and for good reason. These tiny, lab-grown organ replicas are revolutionizing therapeutics, yet they remain under-discussed. It's high time we bring their versatility and potential to the forefront.

Think of organoids as miniature, meticulously crafted models of human organs. They mimic the structure and function of their full-sized counterparts, offering a unique window into human biology. Unlike the simpler spheroids—3D cell aggregates lacking the intricate architecture of specific organs—organoids are complex, containing multiple cell types that self-organize into structures that intend to mimic real organs. This distinction, though often blurred, is crucial.

Derived from various sources like induced pluripotent stem cells or tissue-based stem cells,1 organoids can be tailored to model both healthy and diseased tissues, including infectious diseases, genetic disorders, and cancers. This versatility extends to their origin: they can be created from allogeneic stem cells to represent a general model or from autologous cells to reflect a patient's unique biology.

The breadth of organoids' applications is astounding. They've been generated from brain, lung, intestinal, stomach, kidney, liver, cardiac, skeletal, bone, retinal tissues, and even various tumors.2,3 Each organoid serves as a powerful tool, offering insights that could lead to groundbreaking treatments and personalized medicine.

Let’s explore some the compelling uses of organoids the research and development of biopharmaceuticals.

Applications for Organoids Across the Industry

Regenerative Medicine

The buzz around organoids in regenerative medicine is growing. Researchers have long pursued the dream of building human organs in a dish to create accurate models of human diseases and replace worn-out or diseased organs. In regenerative medicine, the potential of organoids to repair and replace damaged tissues is markedly valuable. Imagine replacing diseased or damaged tissues with precisely engineered, functional tissues derived from organoids. This isn't just a future possibility; it's a rapidly approaching reality. For instance, liver and pancreatic organoids have shown great potential for restoring function in patients with organ failure. Studies have demonstrated that liver organoids can aid in liver regeneration and repair by mimicking the organ's natural architecture and function.4 Similarly, pancreatic organoids have been explored for their ability to generate insulin-producing cells, offering a potential therapeutic approach for diabetes treatment.5 An additional example, intestinal organoids have demonstrated much promise for treating gastrointestinal diseases.6 These advancements highlighting the potential of organoids to develop into complex tissues open up new avenues for autologous and allogeneic cell therapies, promising to restore normal function to affected areas and change countless lives for the better. See Case Study below.

Drug Discovery and Development

In the field of drug discovery, organoids are truly transformative. These miniature organs could provide a more accurate model of human responses than traditional animal models, transforming how we identify drug targets and test potential therapies. By offering insights into efficacy and safety, organoids streamline the drug discovery process, potentially slashing costs and reducing time-to-market. Organoids from tissues like liver, kidney, and brain are pivotal for high-throughput screening, helping us select the most promising drug candidates and identify critical biomarkers. Their ability to mimic human organs surpasses traditional 2D cultures and animal models, giving us a front-row seat to disease progression and drug toxicity. The integration of engineering and computational sciences has only enhanced this technology, making organoids more scalable for widespread drug development applications. Moreover, for drug discovery and development, the promise of organoids as preclinical alternatives is immense. They can reduce costs and improve the relevance of preclinical data. Traditional preclinical models, such as mice, often fail to capture the complexities of human biology, leading to failed clinical trials due to lack of relevance and, subsequently, wasted resources. Organoids, on the other hand, can provide a better representation of human physiology, offering a path to more successful preclinical research. The FDA's push for non-animal and in silico testing, highlighted in the Modernization Act 2.0, underscores the significance of this shift. Organoids are poised to play a critical role in this transformation, bridging the gap between preclinical promise and clinical success. 

Process Development

When it comes to cell therapy process development, even the simpler relatives of organoids, spheroids, are game-changers. The biopharmaceutical industry increasingly relies on 3D scale-down models, which are essential for process development, optimization, and validation. Given the complexity of biological products, their manufacturing processes must be thoroughly understood, characterized, and controlled. Typically, as development progresses, the process is refined and tested through benchtop bioreactors, pilot-scale bioreactors, and ultimately commercial-scale production. Scale-down models play a crucial role throughout this journey, enabling process specialists to acquire process knowledge and translate it into optimal operating conditions in a cost-effective and timely manner. For instance, these models are applied across a wide range of process development activities, such as cell line selection and high-throughput growth medium optimization. Multivariable experimental studies conducted in scale-down models allow for extensive testing of process parameters, which would be impractical or too costly to perform at commercial scale. paving the way for smoother, faster development cycles.

Personalized Medicine

Creating organoids from a patient's cells allows us to study that individual's unique condition in unprecedented detail, predicting how they will respond to various treatments. This ability is particularly important in rare diseases and when patient variability plays a huge role in the therapeutic decision, such as in cancer treatments. In rare diseases, research is significantly hindered by the small number of individuals available for participation in studies. Additionally, many rare diseases lack suitable animal models, making it difficult for scientists to conduct early testing of new treatments. One such example is the use of organoids to develop therapeutics for Timothy syndrome, a rare disease where 80% of children with this syndrome will die within 2.5 years after birth. Researchers developed an antisense oligonucleotide (ASO) therapeutic and successfully demonstrated correction of function in organoids derived from individuals with Timothy syndrome. Additionally, human-derived organoids were transplanted into newborn rat brains, where they integrated well, and ASO treatment reduced abnormal function.7 This study not only highlights a potential treatment for Timothy syndrome but also offers a promising approach for other rare genetic disorders. In cancer treatment, the ability to recapitulate the heterogeneity of a patient-specific tumor could potentially be the difference between recurrence and remission. Since cancer cells change over time, patient-specific organoids can be analyzed for responses to combinatorial treatments at various stages of disease progression. Indeed, research has shown that the timing and duration of drug exposure can significantly affect results, and since tumor organoids can be grown indefinitely, we can experiment with different drug doses and schedules in the lab until the best match for a specific patient.  In addition, patient-derived tumor organoids can also be used to select individual patients for novel targeted therapies.8 Altogether, these functional data help tailor therapies to individual needs, ensuring patients receive the most effective treatments for their specific conditions.

Overcoming Production Challenges: A Personal Journey into Organoids

The path to producing organoids is fraught with challenges. It demands immense time and effort, where each step often relies on the meticulous hands of skilled operators. This manual nature, while rooted in expertise, inevitably opens the door to errors, inconsistencies, and soaring production costs. The heart of the problem lies in the delicate art of culturing stem cells — the very foundation of organoids.9 

Each organoid’s creation is a unique endeavor, where its specific type and function will be shaped by many factors. Factors such as the choice of starting cells, matrix material (whether biologically derived like laminins or synthetic like hydrogels), growth factors, cytokines, proteins, and physical cues like shaking or stirring, all play pivotal roles. The complexity of these variables means that producing high-quality organoids is no small feat.

To relevantly mimic the behavior and function of real organs, organoids need the right type of interactions with the right types of cells in the right places. Achieving this requires more than just careful planning — it demands the organoid produce differentiated cells, secrete crucial signaling compounds, and respond to external stimuli accurately. Yet, even under the same conditions, we often end up with a wide variety of shapes, sizes, and cell compositions. This intricate dance of biology often takes months, if not years, of painstaking experimentation and optimization.

Another hurdle is the characterization of these organoids. With such variability, aligning on standardized criteria for what makes a "good" organoid and defining and achieving critical quality attributes (CQAs) can feel like navigating a maze in the dark. This variability underscores the importance of optimizing and standardizing the workflow to minimize inconsistencies between batches.

To address these challenges, researchers are turning to innovative techniques. For instance, micropatterning in 2D cultures can create a more reproducible starting condition, which then evolves into the desired 3D structures. Controlling matrix properties and applying physical forces like stretching can direct specific tissue morphogenesis. 

As with other processes where automation provides the key to consistency and reproducibility to achieve the desired results, organoids can benefit from automated, reliable production processes. Imagine a robotic cell-culture platform where one technician oversees the simultaneous production of multiple cell lines. Imagine, furthermore, a scenario where different cell types are consistently placed in exact coordinates, ensuring the relevant spatial interactions. Furthermore, picture organoids in development undergoing automatic inspection, allowing only those that meet stringent criteria to progress, ultimately resulting in the most homogenous population of organoids possible. This would significantly accelerate the quality control process, ensuring consistency and reliability at an unprecedented level, all while boosting production rates.

Embracing Automation for Organoid Production

At Cell X Technologies, we're passionate about tackling the hurdles in the cell therapy field, knowing that our efforts can profoundly impact the therapeutic industry. Consistent organoid production is one of those hurdles. Our solution? The Celligent™ robotic platform, designed to take the labor-intensive, error-prone steps of generating organoids and transform them into a seamless, automated process. By simplifying and standardizing the generation of organoids, Celligent ensures consistency and precision that manual methods struggle to achieve, especially at scale and under GMP conditions.

The beauty of the Celligent platform lies in its ability to automate critical tasks. Imagine having a system that handles imaging and tracking cells, changing cell culture media, selecting colonies of induced pluripotent stem cells (iPSCs), and eliminating unwanted cells. These tasks are often highly variable and operator dependent, poorly documented, and error-prone when done manually. These become effortlessly consistent, reliable, and rigorously documented when automated using the Celligent platform.

Celligent addresses two key challenges in organoid generation:

  1. Consistency: By automating the preparation of initial starting materials (iPSCs) and the differentiation process (when multiple cell types are involved), Celligent ensures a uniform and high-quality foundation for organoid development.

  2. Optimization: The platform tracks and fine-tunes the organoid generation process to produce organoids with most relevant attributes for specific applications, making them more effective and reliable.

Operating within a cGMP-compliant Biospherix Xvivo system, the Celligent platform maintains aseptic conditions during operations and uses disposable components, further reducing the risk of contamination. Advanced algorithms within Celligent integrate external data with real-time information generated during cell culture, identifying CQAs and crucial process parameters. Every action is documented in a GMP-compliant database, ensuring traceability.

At Cell X Technologies, we’re more than just automating processes; we're dedicated to thoughtfully bridging gaps in cell therapy to drive down costs and improve patient access. We’ve envisioned a new era in organoid production—one where consistency, efficiency, and innovation lead to real breakthroughs in biopharma.

Case Study: Revolutionizing Clinical-Grade iPSCs with the Celligent Platform10

In an inspiring real-world application, the Celligent precision robotic platform generated high-quality, clinical-grade patient iPSCs that successfully formed organoids rich with transplantable retinal progenitor and photoreceptor precursor cells. 

The journey began with dermal fibroblasts isolated from skin biopsies of patients suffering from inherited retinal degenerative blindness. These cells were reprogrammed and, the subsequent clones of the reprogrammed iPSCs were “picked” using automated methods and  expanded. In today’s version, the Celligent platform automates the entire culture process — growth, picking, and clonal expansion of the iPSCs. Clonal populations were compared and selected based on proliferation, morphology, and differentiation attributes. Selected clones were used to generate high-quality neural organoids rich in photoreceptor cells with quality equal to traditional manual methods. 

After 10 passages, the iPSC lines underwent rigorous karyotyping and scorecard analysis to confirm their genetic integrity and potency. The subsequent retinal differentiation process yielded organoids that, by days 120 and 160, expressed key photoreceptor markers and displayed morphology and gene expression profiles akin to those generated via manual methods.

This case study illustrates the power of the Celligent platform to transform a very manual process into a series to automated, linked protocols. By automating complex and labor-intensive processes, the production of high-quality, consistent organoids suitable for clinical applications can be achieved. This streamlines workflows and  opens up new possibilities in regenerative medicine, providing hope and tangible progress in the fight against blindness and other debilitating conditions.

Cell X Technologies: Our Mission

At Cell X, our mission is to customize our manufacturing solutions to perfectly align with our customers' unique processes and goals. We collaborate closely to design Celligent protocols tailored to customer’s specific needs. This personalized approach ensures that the operations of the Celligent system we create is suited to the unique processes and targeted iPSC- (or other stem cell) based products, including organoids.

We understand that every process is unique. As such, we have designed the Celligent platform to be programmable by a bench scientist and to adapt to the input of subject matter experts by refining cell selection and weeding algorithms as the process moves forward. We understand that time is the greatest limiting factor, and by automating cell and organoid processing steps, scientists are freed up to move to other priorities. 

We are putting a unique focus on creating documented, transferrable processes that are appropriate for GMP production. We understand that a process successful with a research-only cell line might not translate seamlessly to a GMP line. The key is to use the power of automation to establish GMP-ready cell lines earlier in the process, alleviating the necessity to have re-define process parameters when time is most critical.

By using the Celligent platform throughout the process development phase of cell therapy or organoid  development, we provide a traceable, trackable, and mineable data structure that is amenable to developing artificial intelligence approaches.

Looking to the future, Cell X is dedicated to continuously innovating and refining our solutions, remaining committed to supporting our customers in achieving their goals, and advancing the field of regenerative medicine.


  1. Zhao, Z., Chen, X., Dowbaj, A.M. et al.Organoids.” Nat Rev Methods Primers. 2: 94 (2022). 

  2. Zieba, Jennifer.What Are Organoids and How Are They Made?” The Scientist. 11 Aug. 2022. 

  3. Chakraborty, Debomita.An Introduction to Organoids, Organoid Creation, Culture and Applications.” Technology Networks. 17 Jan. 2023. 

  4. Lam, D.T.U.H., Y.Y. Dan, Y.S. Chan, et al.Emerging liver organoid platforms and technologies.” Cell Regen. 10: 27 (2021). 

  5. Jin , Chen, Lu Jin , Wang Shu-Na , AND Miao Chao-Yu.Application and challenge of pancreatic organoids in therapeutic research.” Frontiers in Pharmacology. 15 (2024). 

  6. Sato, T., and H. Clevers.Growing self-organizing mini-guts from a single intestinal stem cell: mechanism and applications.” Science. 340: 1190–1194 (2013).  

  7. Chen X, et al.Antisense oligonucleotide therapeutic approach for Timothy syndrome.” Nature. 628: 818–825 (2024). 

  8. Weeber, Fleur, Salo N. Ooft, Krijn K. Dijkstra, and Emile E. Voest.Tumor Organoids as a Pre-clinical Cancer Model for Drug Discovery.” Cell Chemical Biology. 9: 1092–1100 (2017). 

  9. Weisinger, Karen.Intelligent Cell Processing Enables Consistent, Reproducible, and Scalable GMP-Compliant Processes.” Pharma’s Almanac. 30 May 2024.

  10. Bohrer, LR, et al.Automating iPSC generation to enable autologous photoreceptor cell replacement therapy.” J. Transl. Med. 21: 161 (2023).

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