Patient-derived organoids enable researchers to study disease processes in cells obtained directly from individual patients. By observing how these miniature tissues develop, respond to drugs, and undergo genetic changes, it becomes possible to predict patient-specific treatment responses and move closer to practical precision medicine.

Traditionally, most work with human cells has been carried out in flat, two-dimensional (2D) cultures. These systems are relatively inexpensive, easy to maintain, and compatible with many experimental tools. However, they cannot reproduce the three-dimensional (3D), multicellular architecture of real organs or the complex interactions between different cell types and the surrounding matrix. To overcome these limitations and better mimic what happens inside the body, organoid cultures have emerged as a more physiologically relevant option.

What are organoids?

What are organoids?

Organoids are 3D clusters of cells that self-organize into structures resembling miniature organs. They are usually derived from pluripotent stem cells (embryonic stem cells or induced pluripotent stem cells) or adult stem cells and are grown under specific conditions so that they form organized tissues that resemble the brain, liver, gut, kidney, and other organs.

In culture, these cell aggregates develop internal organization, distinct cell layers, and functional properties that resemble their organ of origin. Because of this, organoids are increasingly used to study organ development, model human diseases, test drugs, and explore potential regenerative therapies.

The ability to generate organoids from embryonic, induced pluripotent, or adult stem cells has significantly changed experimental approaches in developmental biology, disease modeling, and drug discovery. Organoids enable analysis of organ formation and disease mechanisms in greater detail and evaluation of candidate therapies in systems more closely aligned with human physiology.

Organoids are particularly notable for their capacity to self-organize. Under appropriate conditions, they recapitulate features of tissue architecture and intercellular communication that are difficult to reproduce in standard cultures. In some cases, their composition and behavior are so similar to those of native tissue that they can be difficult to distinguish histologically from the corresponding organ. For example, one study showed that colon epithelium organoids grown from Lgr5+ stem cells closely matched the structure and cell composition of the original tissue¹.

Forebrain-specific organoids have also been created that reproduce several important aspects of human cortical tissue, including gene expression patterns, neurogenesis, the presence of an outer radial glia layer that is characteristic of human brains, and organized progenitor zones. Lung organoids containing both type I and type II alveolar epithelial cells have been generated as well, and these cells can reproduce many of the functional properties of the alveolar epithelium^2,3,4,5.

Organoids compared with traditional 2D cell cultures

Conventional 2D cell cultures are useful for basic experiments, rapid proliferation, and straightforward imaging. However, they are usually simple monolayers composed of a single cell type, although co-culture systems are now more common. This simplicity makes it difficult to model the interactions between different cell types or to reproduce the gradients of nutrients, oxygen, and signaling molecules that exist in living tissues.

As a result, 2D cultures do not capture many of the cell–cell and cell–matrix interactions that are essential for organ function. Organoids, in contrast, typically comprise multiple cell types and exhibit a degree of spatial organization that is much closer to that observed in vivo. They reproduce aspects of tissue architecture, transcellular signaling, gene-expression profiles, and cellular behavior in a manner that more closely reflects human physiology and disease processes.

2D cultures also lack a proper extracellular matrix (ECM) environment and do not normally form complex structures such as lumens, crypts, or villi. Organoids, grown in a supportive 3D matrix, generate these structures more readily and can even develop rudimentary vasculature-like networks or be combined with endothelial cells to approximate vascularization in some systems.

A defining feature of organoids is their self-organizing behavior, which is guided by intrinsic genetic programs, external signaling factors, and ECM properties. This combination enables organoids to model tissue-specific functions and disease mechanisms with a fidelity that conventional 2D cultures generally cannot reach.

Types of organoids

Organoids can be categorized in several ways, most commonly by their cell source or intended application.

Tissue-derived organoids are generated directly from adult or fetal tissues. These cultures preserve many characteristics of the original organ, such as regional identity and differentiated cell types. They have been established for organs such as the liver, intestine, and pancreas.

Pluripotent stem cell-derived organoids are produced from embryonic stem cells or induced pluripotent stem cells. These systems are frequently used to study organ development and lineage differentiation because they can model the steps of organogenesis under controlled conditions.

Tumor organoids are created from cancer biopsies or surgical specimens. They retain key genetic and phenotypic features of the original tumor and are used to study tumor biology, drug sensitivity, and resistance mechanisms.

Assembloids are more complex constructs in which different types of organoids are combined or integrated with additional technologies. For example, organoids-on-chips couple organoid cultures with microfluidic platforms to better mimic the physical and biochemical conditions found in vivo.

Examples and functions of major organoid types

Brain organoids

The human brain is difficult to study directly, partly because of its complexity and partly because commonly used models, such as post-mortem samples or animal systems, do not capture all aspects of human neural development and gene regulation. Brain organoids, derived from human induced pluripotent stem cells (iPSCs), address some of these limitations.

These organoids form structures that resemble developing brain regions and generate a variety of neural cell types. They often rely on growth factors such as FGF2 and EGF to maintain neural progenitor proliferation. Retinoic acid helps specify regional identities, including forebrain regions, while neurotrophic factors such as brain-derived neurotrophic factor (BDNF) and neurotrophin 3 (NT3) support neuronal maturation⁶.

Brain organoids reproduce key aspects of early human brain development, including the emergence of distinct neural lineages, regional patterning, and early circuit formation. This enables the study of human-specific processes and disease mechanisms that are difficult to model in animals.

In addition to developmental research, brain organoids have been interfaced with electronic systems, including silicon chips, to explore their potential in advanced computation, data processing, and neuromorphic applications. They are also being used to study neurological disorders such as brain tumors, autism spectrum disorders, Alzheimer’s disease, and Parkinson’s disease, helping to explore network changes and possible treatment strategies.

Studies using brain organoids have shown, for example, that Zika virus infection can provoke pathological changes reminiscent of those seen in neurodegenerative diseases such as Alzheimer’s disease⁷. These findings are particularly relevant because traditional models struggle to capture the interplay between viral infection and neurodegeneration. A platform known as neoplastic cerebral organoid (neoCOR) has been developed to identify tumor-associated mutations in brain tissue, including glioblastoma-like and central nervous system primitive neuroectodermal tumor (CNS-PNET)-like neoplasms⁸.

Another notable result is that neuronal organoids, when co-cultured with endothelial cells, can recapitulate several properties of the blood–brain barrier, thereby enabling researchers to screen compounds targeting the central nervous system⁹.

Liver organoids

Liver organoids, derived from pluripotent stem cells or adult tissue, reproduce important aspects of liver structure and function. Because there are relatively few good models for human liver biology, these organoids are especially valuable for studying hepatocyte development, metabolic function, and disease.

Liver organoids often require factors such as hepatocyte growth factor and FGF10 for differentiation into hepatic lineages and progenitor cells. Oncostatin M and dexamethasone promote hepatocyte maturation and metabolic activity. Wnt3a and R-spondin support hepatic stem cell proliferation and long-term maintenance of organoid cultures¹⁰.

Traditional models, such as primary human hepatocytes, can be informative but tend to lose replicative capacity and undergo functional decline over time. Immortalized cell lines are easier to maintain but may not faithfully replicate normal hepatocyte behavior due to genetic alterations. Human precision-cut liver slices have limited viability and metabolic lifespan. Liver organoids help address these problems by enabling longer-term culture, repeated experimentation, and more physiologically relevant responses.

For example, screening organoids derived from primary liver cancer helped identify an ERK inhibitor, SCH772984, as a promising drug candidate¹¹. Human liver organoids have also been used to study the life cycle of the hepatitis B virus (HBV) and to examine how chronic infection contributes to liver cancer development^12,13.

Cholangiocyte organoids derived from human iPSCs can express primary cilia and high levels of CFTR, key features of biliary epithelium. In one study, cholangiocytes from cystic fibrosis (CF) patients cultured in 96-well plates exhibited distinct responses to combinations of CF drugs, providing a functional readout of patient-specific drug sensitivity¹⁴. Another screening study found a strong correlation between the drug responses of more than 25 anticancer compounds and the mutational profiles of primary liver cancer organoids¹⁵.

When genomic, transcriptomic, and functional data from primary liver cancer organoids are integrated, they can reveal potential prognostic biomarkers and therapeutic targets and demonstrate how organoids can be integrated with multi-omics data to guide personalized treatment strategies.

Intestinal organoids

Intestinal organoids are 3D structures derived from intestinal stem cells that recapitulate many features of the gut, including crypt–villus architecture, cell diversity, and barrier function. They are used to study intestinal development, nutrient absorption, host–microbe interactions, and disease.

To generate and maintain intestinal organoids, growth conditions typically include Noggin for epithelial formation, Wnt3a and R-spondin for stem cell maintenance, and EGF for proliferation. BMP inhibitors help prevent premature differentiation. Metabolites such as lactate and fatty acids can be added to better mimic the intestinal environment and improve physiological relevance¹⁶.

One difficulty with animal models, such as mice, is that developmental timing and cell differentiation patterns differ from those in humans. For instance, Paneth cells appear in mice about 14 days after birth, while in humans they develop during the first trimester. Intestinal organoids have been used to reproduce budding crypts with progenitor cell populations and villi domains containing differentiated enterocytes, goblet cells, and Paneth cells¹⁷.

These organoids serve as powerful models for diseases such as inflammatory bowel disease and colorectal cancer. An induced human ulcerative colitis-derived organoid (iHUCO) model, for example, has been used to replicate disease-specific mechanisms and functions. Screening in this model identified repertaxin as a compound that can inhibit a specific pathway and reduce features associated with colitis.

Pancreatic organoids

Pancreatic organoids are 3D cultures that model the cellular organization and function of the pancreas. They can be derived from several sources and used to study both healthy and diseased tissue.

Typical protocols rely on activin A to generate definitive endoderm, followed by FGF10 and retinoic acid to form pancreatic progenitors. EGF and Noggin promote differentiation into endocrine and exocrine cell types¹⁸. Insulin and glucagon contribute to endocrine cell maturation, reflecting key steps in pancreatic development.

By recapitulating interactions among endocrine and exocrine compartments and other cell types, pancreatic organoids enable researchers to examine how these relationships change during disease. Patient-derived pancreatic tumor organoids can preserve specific molecular profiles, including genetic mutations and altered signaling pathways, and therefore model conditions such as pancreatic ductal adenocarcinoma and support the design of tailored therapies¹⁹.

In one line of work, researchers developed pancreatic organoids that resemble the normal fetal pancreas and contain acinar, ductal, and endocrine cell types. The same group identified a stem cell population capable of giving rise to all three major lineages, with implications for understanding development and potential regenerative strategies. They also showed that human fetal pancreatic stem cells can differentiate into all pancreatic cell types, expand for extended periods, and survive longer than comparable cells in mice, providing an informative system for studying environmental and genetic influences on pancreatic disease²⁰.

Kidney organoids

Kidney organoids are produced from adult stem cells or pluripotent stem cells and serve as tractable models of nephron development and kidney function. This is important because chronic kidney disease is common, and current treatments such as dialysis and transplantation present major clinical challenges.

Protocols for kidney organoids often include Activin A for mesoderm induction, BMP7 for nephron progenitor differentiation, FGF9 for nephrogenesis, and Wnt3a to promote mesenchymal-to-epithelial transition. Retinoic acid helps guide cells toward kidney-specific lineages^21,22.

These organoids can reproduce essential kidney functions, such as aspects of glomerular filtration and tubular transport, and can self-organize into structures that mimic nephrons in a 3D arrangement. By introducing patient-derived stem cells with defined genetic variants, researchers can model disease states in a personalized way.

Kidney progenitors derived from human iPSCs have been shown to give rise to mesangial cells, podocytes, and perfused glomeruli after transplantation into mice, indicating the potential for in vivo integration. Kidney organoids have been used for drug screening, particularly for compounds with potential nephrotoxic effects, and for modeling genetically driven diseases such as autosomal dominant polycystic kidney disease (ADPKD) and Wilms tumor. In miniature kidney organoids consisting of one or two nephron-like structures, the compound QNZ, a quinazoline derivative, was identified as an inhibitor of cyst growth, including after cyst formation had already begun²³.

Skin organoids

Skin organoids are 3D models that recreate many aspects of human skin, including multiple cell types and appendages. They offer new tools for regenerative medicine and dermatology, including the potential to generate skin substitutes for wound healing.

These organoids can contain hair follicles, adipocytes, muscle-like cells, nerves, Merkel cells, sebaceous glands, and melanocytes. This complex composition allows detailed study of how different skin components communicate and respond to external stimuli.

Skin organoids are typically derived from human pluripotent, fetal, or adult stem cells. Their culture requires coordinated exposure to growth factors such as EGF, members of the FGF and BMP families (modulated by Noggin), VEGF, IGF-1, retinoic acid, and Wnt3a. These signals promote proliferation, differentiation, vascularization, and the formation of specialized structures.

Three-dimensional skin models are particularly important for testing the toxicity and irritation potential of cosmetic and pharmaceutical compounds and can reduce reliance on animal experiments. Due to regulatory restrictions and the limited availability of human skin samples, reconstructed epidermis or full-thickness skin grown on polymer matrices has become more widely used. Such models help assess toxicity, irritation, and the impact of different formulations.

Although reconstructed skin often expresses fewer xenobiotic metabolizing enzymes than native skin, it still performs better than immortalized keratinocyte lines. Validated reconstructed skin models used in cosmetic testing are being refined further, for example, by adding immune cells, to better reproduce human skin responses²⁴.

Methods and technologies in 3D organoid culture

Organoid culture usually begins with isolating stem or progenitor cells from tissues or by differentiating pluripotent stem cells. These cells are then embedded in an ECM-like scaffold that provides mechanical support and biochemical cues.

Matrigel is commonly used because its composition resembles the basement membrane ECM. However, it is not specific to any one organ and can show batch variability. Other scaffolds include naturally derived materials, such as proteins and polysaccharides, as well as synthetic polymers, including poly(lactic-co-glycolic acid) (PLGA), polyethylene glycol (PEG), and poly-L-lactide (PLLA). The choice of scaffold depends on the organ being modeled and the desired mechanical and biochemical properties²⁵.

Decellularized tissue matrices taken from the target organ can also be used. These retain the architecture and many ECM components of the original organ and can provide an environment particularly well suited to organ-specific organoid growth.

Organoid cultures require media enriched with growth factors and signaling molecules that emulate in vivo molecular cues. Conditioned media, which contain factors such as FGF and EGF, have been widely used²⁶. Different organoid systems have specific requirements. For example, intestinal organoids typically require EGF, Noggin, R-spondin-1, nicotinamide, MAPK inhibitors, and ALK inhibitors²⁷. Kidney organoids can be derived from patient-derived kidney cells using FGF10, Wnt agonists, EGF, ALK4/5/7 inhibitors, and Rho kinase inhibitors²⁸. Liver organoid protocols often include FGFs, activin A, dexamethasone, and BMPs²⁹.

Scaffold-based methods use hydrogels or synthetic biomaterials that mimic aspects of the ECM, while scaffold-free approaches, such as suspension cultures, allow cells to aggregate into spheroids that can then organize into organoid-like structures. Culture systems can be further optimized using microfluidic devices and bioreactors, which enhance nutrient and oxygen delivery, waste removal, and mechanical stimulation, and support scaling up of organoid production.

Our alginate hydrogel kit for 3D cell culture (ab241011) delivers a standardized solution for creating 3D cell culture matrices and spheroid formations to support early-stage pharmacological research.

Factors influencing growth and differentiation

Several main variables determine how well organoids grow and how faithfully they reproduce the target tissue:

• The composition of the culture medium is critical. Growth factors such as R-spondins and BMP inhibitors, including Noggin and Gremlin 1, promote stem cell proliferation and prevent premature differentiation, which is essential for sustained expansion.
• The nature of the ECM or scaffold influences structural organization and signal transduction. Synthetic hydrogels and other engineered matrices can be tailored to mimic the stiffness and biochemical composition of specific tissues.
• The source of cells matters. Organoids generated from pluripotent stem cells, adult stem cells, or primary tissues can differ in their developmental potential, stability, and similarity to native tissue.
• Environmental conditions, including oxygen tension, pH, temperature, and nutrient supply, must be carefully controlled to ensure reproducible growth and differentiation.
• The quality and activity of growth factors, such as recombinant R-spondin 1 and Gremlin 1, influence variability between experiments. High-purity reagents help reduce batch-to-batch differences.
• Passaging procedures must preserve viability and differentiation potential across multiple generations. Excessive mechanical stress or inappropriate splitting can reduce organoid quality.
• Advances in synthetic matrices and defined culture systems are helping to reduce reliance on animal-derived ECMs, thereby improving reproducibility and standardization.

Our guides on cell culture and cell culture and maintenance offer valuable insights to help overcome common challenges, such as maintaining aseptic conditions, optimizing growth media for specific cell types, and ensuring genetic and functional stability through regular monitoring during prolonged culture or passage.

Applications of organoids in drug discovery, screening, and toxicology testing

Organoids provide substantial advantages for drug discovery and toxicology studies. Because they more closely resemble human tissues, they can offer more predictive data on drug efficacy and toxicity than conventional 2D cultures or many animal models.

High-throughput screening systems based on organoids enable testing of large numbers of compounds. For example, human liver organoids derived from pluripotent stem cells have been used to build a screening platform for drug-induced liver injury (DILI)³⁰. In one study, 238 marketed drugs, including 206 known to cause DILI, were evaluated, and the organoid system showed good sensitivity.

These liver organoids have also been used to correlate specific genotypes with drug-induced toxicity. An association was observed between bosentan-induced cholestasis and a specific HLO genotype, CYP2C9*2, illustrating how organoid systems can reveal genotype–phenotype relationships. Organoid models also avoid many of the limitations of animal studies, such as interspecies genetic differences and high cost.

In colorectal cancer research, organoid-based screening has identified dozens of compounds with antitumor activity from larger molecular libraries³¹.

Organoids frequently express key drug-metabolizing enzymes, such as members of the cytochrome P450 family, thereby making them physiologically relevant platforms for studying drug metabolism and environmental toxicant effects. Experiments have examined the impact of substances such as lead, mercury, thallium, and glyphosate on liver and heart organoids³². Brain organoids are used to evaluate the neurotoxicity of compounds, including methylmercury, herbicides, and drugs, and have become useful models for developmental neurotoxicity³³. Intestinal organoids enable testing of gastrointestinal toxicity caused by drugs such as nonsteroidal anti-inflammatory drugs (eg, diclofenac) and chemotherapeutic agents such as irinotecan³⁴.

Kidney organoids derived from ADPKD patients are used to study disease progression and to test drugs such as tolvaptan, which targets cyst growth and expansion³⁵. Pancreatic organoids are used to investigate diabetes and pancreatic cancer and to identify therapeutic targets, including approaches that modulate KRAS signaling in pancreatic ductal adenocarcinoma³⁶.

Lung organoids have been instrumental in studying infections such as SARS-CoV-2 and in testing potential treatments, including remdesivir and camostat mesylate, which have been reported to limit viral replication. They are also used to assess the toxicity of inhaled substances, such as e-cigarette emissions and environmental pollutants³⁷.

Regenerative medicine and tissue engineering

Organoids are central to new strategies in regenerative medicine because they reproduce key aspects of tissue architecture and function in vitro. They can be used to model tissue damage, test regenerative drugs, and, in some cases, serve as starting material for transplantation.

Transplantation studies using human organoids have shown that these constructs can integrate with host tissue in animal models. For example, protocols have been developed for transplanting human brain organoids into adult mouse brains, where they can survive, extend processes, integrate into neuronal networks, and become vascularized³⁸.

In another example, human islet-like organoids transplanted into diabetic mice restored glucose regulation, demonstrating functional insulin production. Liver organoids derived from stem cells are being explored as potential sources for tissue replacement in liver disease and as test systems for compounds that promote liver regeneration³⁹.

Intestinal organoids are used to study mucosal repair in conditions such as inflammatory bowel disease and short-bowel syndrome. They model gut injury and recovery, thereby informing strategies for restoring intestinal function⁴⁰. Brain organoids are being used to investigate neurodegenerative diseases and test experimental therapies aimed at promoting neuronal survival and synaptic integration, with potential implications for stroke and Alzheimer’s disease⁴¹. Pancreatic organoids are being studied as a source of insulin-producing beta cells for type 1 diabetes and as a platform to explore broader pancreatic regeneration⁴². Skin organoids, with their complex architecture, are promising for the development of full-thickness skin grafts for burns and chronic wounds, as well as for broader regenerative treatments for skin damage⁴⁰.

Advantages of organoids over animal models

Animal models have contributed greatly to biomedical research; however, several challenges, including ethical considerations and species-specific differences in genetics and physiology, limit translation to humans. Creating and genetically modifying animal models can also be time-consuming. For example, generating a mouse line with specific genetic changes can take several months, whereas organoid models can often be established and modified within weeks⁴³.

Organoids lend themselves to high-throughput experimentation. Large numbers of organoids can be prepared in parallel, enabling systematic genetic manipulation, drug screening, or mechanistic studies across many conditions. This scale is difficult to achieve in whole-animal experiments.

Certain diseases are particularly hard to reproduce in animals. Complex eye diseases, such as glaucoma, or detailed aspects of brain development and brain disorders, are not fully captured in animal models, and studies can be slow and costly. Organoids that reproduce relevant human cellular and tissue features offer a promising alternative⁴⁴.

Human-specific biology and personalized medicine applications

Because organoids can be derived from a patient’s own cells, they are well suited for personalized medicine. They can reproduce many aspects of an individual’s disease physiology and can be used to test candidate therapies on a patient-specific model before treatment.

Tumor organoids derived from patients with cancers of the rectum, breast, pancreas, lung, gallbladder, and other tissues retain many of the genetic and histopathological features of the original tumors. Gallbladder cancer organoids, for example, have been shown to preserve tumor characteristics and remain stable in culture over several months⁴⁵. Screening these models can identify compounds such as CUDC-907 that inhibit growth across multiple organoids, indicating potential broad activity in genetically diverse tumors.

Functional readouts from organoids can be correlated with patient outcomes. In rectal organoids from cystic fibrosis patients, forskolin-induced swelling has been linked to clinical measures such as sweat chloride concentration and lung function⁴⁶. Collections of patient-derived organoids can serve as biobanks that support the systematic evaluation of therapies in large, genetically defined cohorts and provide a basis for individualized treatment strategies.

Complex tissue modeling and insights into cellular interactions

One of the strengths of organoids is their ability to model complex tissue structures and interactions between different cell types. Within these 3D systems, cells communicate through direct contact, secreted factors, and ECM-mediated signaling, as they do in the body.

Organoids can be used to study interactions between epithelial cells and immune cells, tumor cells and their microenvironment, or host cells and microbes. These higher-order interactions are difficult to reproduce in simpler models. In cases where direct experimentation in humans or large animals is not feasible, organoids provide an alternative. For example, testicular organoids have been developed to investigate spermatogenesis and to screen for compounds that affect germ cells^47,48.

The gut is a prime example in which organoids are used to study host–microbiota interactions. Human intestinal enteroids have been used to investigate how specific probiotic strains, such as Lactobacillus rhamnosus GG (LGG), influence intestinal barrier function and symptoms associated with conditions such as irritable bowel syndrome⁴⁹.

Recent advancements in organoid research

Improvements in culture methods and organoid complexity

Recent work has focused on enhancing the physiologic realism of organoids. One approach is decellularization, in which immunogenic components are removed from tissues, leaving an ECM scaffold that retains organ-specific structure and protein composition⁵⁰. These scaffolds can provide a more biomimetic microenvironment for organoid growth.

Microfluidic technologies that control fluid flow at small scales have been introduced into organoid culture. These systems enable precise regulation and monitoring of variables such as pH, metabolite levels, and oxygen, and support the controlled delivery of nutrients and signaling molecules. For example, cerebral organoids grown in dynamic microfluidic environments have shown improved cortical layer formation and electrophysiological activity compared with static cultures⁵¹.

Bioreactors have been developed to address limitations of traditional static cultures. In static systems, nutrient and oxygen gradients, as well as waste accumulation, can reduce viability and limit size. Bioreactors introduce controlled mixing and flow to better reproduce in vivo conditions. Common systems include stirred bioreactors, microfluidic bioreactors, rotating-wall vessels, and electrically stimulated bioreactors⁵². Stirred bioreactors are relatively simple and provide good mixing, but are less flexible for fine control. Microfluidic and rotating systems allow more precise flow regulation, and electrically stimulating bioreactors add controlled electrical inputs.

These dynamic culture systems can be combined with air–liquid interface (ALI) methods. In ALI cultures, organoids are grown with one side facing the medium and the other exposed to air⁵⁴. This setup is particularly relevant for tissues that naturally contact both air and fluid, such as the respiratory epithelium. ALI culture tends to promote maturation and differentiation more effectively than fully submerged systems, thereby improving the functional accuracy of organoid models.

Development of multi-organ systems for more holistic studies

Multi-organ systems, often in the form of linked organoids or organoids integrated into organ-on-chip platforms, have been created to study systemic responses to drugs and disease. By combining organoids representing different tissues, researchers can examine how a compound is metabolized in one organ and how its metabolites affect others.

These integrated systems can capture inter-organ interactions that are absent in isolated cultures and may provide more realistic predictions of efficacy and toxicity in humans.

Organoids on a chip

Organoids-on-chips combine the 3D self-organization of organoids with the precise environmental control of microfluidic organ-on-chip devices. In these systems, organoids are placed in channels or chambers where fluid flow, oxygen gradients, mechanical forces, and 3D structure can be carefully controlled.

Such platforms have been used to study developmental processes, for example, with placenta-on-a-chip models, and to model diseases of the pancreas, liver, gut, brain, heart, and retina⁵⁵. A retina-on-a-chip model, for instance, reproduced critical interactions between retinal pigment epithelium and photoreceptor segments and allowed analysis of calcium signaling. It also revealed retinopathic effects of compounds such as chloroquine and gentamicin, underscoring the potential of organoids-on-chips as drug-testing platforms^56,57.

By combining biological realism with engineering control, organoids-on-chips bridge the gap between traditional culture systems and in vivo studies and may play an important role in translational research and precision therapy.

Patient-derived stem cells and personalized organoid models

Organoids generated from patient-derived stem cells reproduce structural and functional aspects of individual organs and contain patient-specific genetic variants. These models allow researchers to study disease mechanisms, test candidate drugs, and explore gene–environment interactions in a personalized context.

Despite this promise, several obstacles remain. Maintaining genetic stability over long-term culture is challenging, scalability can be limited, and moving from experimental models to clinical applications will require further optimization. Cost is another important factor, particularly for therapies in regenerative medicine, as manufacturing and quality control for patient-specific products can be expensive.

Challenges and limitations of organoid research

Organoid systems, although powerful, are not without drawbacks. Culture conditions are not yet fully standardized, and protocols often require adaptation for each laboratory and application. Achieving reproducible, scalable production of organoids, particularly those with functional vasculature, remains an active area of research.

Heterogeneity is a significant issue. Organoids generated using the same protocols can vary in size, shape, cellular composition, and gene expression⁵⁸. This variability complicates comparisons between experiments and across laboratories and underscores the need for improved quality control and standardized methods.

Organoids sometimes express stress-related genes at higher levels than native tissues, likely because culture conditions do not perfectly reflect the in vivo environment. Prolonged culture can lead to necrotic cores, structural deterioration, and loss of specific differentiation states. Differences in the behavior of iPSC lines, even when derived from the same donor, introduce additional variability.

The cost is higher than that of many traditional models. Specialized matrices, growth factors, and technical expertise are required, and some researchers have highlighted the need to make organoid culture more cost-effective⁵⁸.

The immune microenvironment presents another challenge. Simply mixing organoid cells with immune cells does not recreate the organized immune niches found in tissues. More research is needed to develop organoid systems that incorporate immune components in a structured and physiologically meaningful way⁵⁹.

Scaffolds used for organoid growth each have specific advantages and limitations, and an ideal matrix that satisfies all requirements has not yet been identified⁵⁹. In addition, our understanding of organ development at the single-cell level is incomplete, which limits the ability to fully direct organoid maturation⁶⁰. Organoids often resemble fetal or early postnatal tissue rather than adult organs, which constrains their utility for studying late-onset or degenerative conditions. In some systems, organoid-derived cells exhibit incomplete or altered gene expression relative to native cells, particularly in neural models.

Ethical considerations in organoid research

• Ethical questions in organoid research focus on how tissue is obtained and used, how donor privacy is protected, and how commercial interests intersect with altruistic donation. Informed consent must cover potential future uses of donated tissue, including genetic analysis and organoid derivation. Because organoids can be generated from stem cells, including embryonic stem cells and iPSCs, ethical issues associated with these cells also apply.Work with embryonic stem cells involves the destruction of embryos and raises questions about the moral status and control of pluripotent cells in host environments. iPSC-based models carry a risk of teratoma formation if undifferentiated cells remain in grafts. Commercialization of organoids, especially those derived from donor tissues, can raise concerns about profit sharing and ownership of biological materials⁶¹.As organoids become more complex, additional issues arise. Brain organoids, in particular, have prompted discussion about whether advanced forms might exhibit rudimentary forms of consciousness or sentience and what ethical status they might then have. Human–animal chimeras created by integrating human organoids into animal hosts introduce questions about animal welfare, identity, and the appropriate limits of such experiments⁶¹.

Future directions in organoid research

Ongoing innovations aim to address current limitations and expand the applications of organoids. Approaches such as co-culturing organoid cells with endothelial cells or transplanting organoids into animal hosts are being used to improve vascularization and reduce hypoxia in larger organoids. New scaffolding materials, including artificial oxygen carriers like perfluorocarbons, are being explored to enhance oxygen delivery and structural stability.

Combining organoids with organ-on-chip technology can model multi-organ interactions and improve predictions of systemic drug effects. Efforts to standardize matrices and protocols should reduce variability and increase reproducibility.

In regenerative medicine, organoids generated from patient cells can be engineered to match human leukocyte antigen (HLA) profiles, reducing the risk of rejection. Studies have demonstrated that intestinal organoids transplanted into mouse models of colonic injury can contribute to tissue repair, while liver organoids from iPSCs have restored liver function in acute failure models. Progress in vascularization has brought kidney organoids with perfused glomeruli closer to potential therapeutic use.

Cancer organoids derived from gastric, colorectal, liver, and prostate tumors preserve patient-specific mutations and microarchitectural features. They can be used to test targeted therapies, combination regimens, and responses to androgen receptor inhibitors in prostate cancer, and to identify treatments for chemotherapy-resistant tumors.

Beyond regenerative medicine and oncology, organoids are increasingly used to study infectious diseases and genetic disorders. Examples include modeling Helicobacter pylori infection in gastric organoids, investigating Zika virus-induced neurodegeneration in cerebral organoids, and exploring hepatitis C virus entry in hepatocyte-like organoids. Organoids have contributed to understanding SARS-CoV-2 tropism, mechanisms of host cell entry, and organ-specific pathology.

Organoid models have aided research on genetic diseases such as cystic fibrosis, where they have been used to screen for therapeutic compounds and to test genome editing approaches such as CRISPR/Cas9. They also provide powerful tools to study fundamental developmental processes, including intestinal and neural organogenesis.

FAQs

Can organoids be used to develop new treatments for diseases?

Yes, organoids can be used to develop new treatments for diseases as they closely mimic human tissue structures and functions, enabling precise modeling of diseases, drug testing, and personalized therapy development. Their ability to replicate complex biological systems makes them invaluable for advancing regenerative medicine, cancer treatment, and genetic disease research.

How are organoids used in personalized medicine?

Organoids are used in personalized medicine by serving as patient-derived models that mimic an individual’s disease physiology and drug response, enabling the prediction of effective therapies tailored to the patient’s unique genetic and phenotypic profile. These models are particularly valuable in testing treatments for cancers, genetic disorders, and rare diseases.

What are the technical challenges in culturing organoids?

Culturing organoids presents technical challenges such as maintaining stringent growth conditions with precise growth factor mixes, ensuring genetic and functional stability through successive passages, and requiring specialized training and expensive reagents for consistent and reproducible results. These complexities demand adherence to standardized protocols and resource availability to achieve successful and scalable organoid cultures.

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