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3D Cell Culture Tools and Applications

3D Cell Culture Workflow Tools

Fluorescence image of human colon organoids stained for mucin-1, F-actin, and DAPI

Figure 1. Characterization of human colon organoids using immunocytochemical stains for Mucin-1, F-actin, and DAPI.

What is 3D Cell Culture?

Cells in their natural environment have constant interactions with their extracellular matrix (ECM) and other cells, regulated by complex biological functions. Three-dimensional (3D) cell culture systems allow cells to grow and interact with their surroundings in all three dimensions.

By utilizing 3D cell culture models, researchers can simulate the in vivo physiological microenvironment. These models also provide better predictive in vitro cell models for applications including cancer research, drug discovery, and regenerative medicine. Transitioning to 3D cell culture can bring together the biological relevance of animal models with the accessibility of traditional 2D models.

3D Culture Models 

We offer an extensive portfolio of tools, protocols, and technologies to support 3D cell culture applications such as drug permeability, ADME/toxicity assays, cancer, and autoimmune disorders. 

Explore our Knowledge Center below and discover answers to questions about organoids, hydrogels, and organotypic cultures. Request more information here.


: Apical-out Human Colon Organoids Generation.

Figure 2. Apical-out Human Colon Organoids Generation. The epithelial cell polarity was reversed using the apical-out organoid culture protocol and 3dGRO™ Human Colon Intestinal Organoids. Polarity reversion was determined using DAPI (blue) and ZO-1 (MABT339, Green) immunocytochemical staining.

Organoids are mini-organs derived from stem cells and grown in near-native culture conditions that allow for the development of functional 3D structures preserving key physiological function of the original tissue. They can be derived from patient tissues (patient-derived organoids; PDOs) or induced pluripotent stem cells (iPSCs).

Organoids have been used to study organ-specific disorders and diseases including related cancers, inflammatory bowel disease, and cystic fibrosis. They are also used to study viral respiratory disease, drug transport, drug permeability, ADME/Tox, and organogenesis. Our portfolio includes organoids derived from patient tissues and induced pluripotent stem cells; we also provide expert answers to frequently asked questions about organoid culture

We have now expanded our organoid portfolio to include HUB Organoids. The founder of adult stem cell-derived organoid technology, HUB Organoids specializes in the application of Organoid Technology to preclinical testing, drug discovery, and therapeutic development. Our healthy and diseased patient-derived organoid biobanks include gastrointestinal, lung cancer, and pancreatic ductal adenocarcinoma organoids, and are subjected to rigorous quality control protocols. The biobanks are stable for long-term culture and cryopreservation.

We have also rounded out our portfolio to include access to HUB Organoid screening services. Accelerate the discovery of therapeutic treatments, such as for infectious diseases, oncology, and toxicology investigations, and closely mimic human biology with this novel platform.  


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Moving from 2D to 3D

3D cell culture is an in vitro method for researchers who want to more closely model physiological conditions. It is often more relevant than using traditional 2D methods. 3D cell culture methods promote interactions with other cells and with the physical environment. These interactions can regulate multiple cellular functions, including transcription regulation and apoptosis.

Scaffold-free technologies

One method of 3D cell culture is the scaffold-free model. Scaffold-free 3D cell culture techniques allow cells to self-assemble and form non-adherent cell aggregates, clusters, spheroids, or tumorspheres.

Scaffold-based technologies

In scaffold-based 3D cell culture methods, 3D scaffolds provide structural support for cell attachment and tissue development. This recapitulates elements of the native extracellular matrix (ECM) or cellular environment.

For researchers studying drug safety and efficacy, ADME/toxicity, and biotherapeutics development, 3D cell culture models can reduce the time spent in setting up and performing assays. 

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