3D Cell Culture 101: An Overview of Advanced Tools and Techniques

2D vs 3D cell culture techniques

Cell culture techniques are ubiquitous in areas of developmental biology, drug discovery, regenerative medicine and protein production. Since the introduction of cell culture techniques, cells have been cultured in two-dimensions, attached to tissue culture plasticware or ECM attachment proteins. Cells in the physiological environment have constant interaction with the extracellular matrix, regulating complex biological functions like cellular migration, apoptosis, transcriptional regulation, and receptor expression1. In-vitro experimental data cannot be translated into clinical trials completely2 when cells are grown in 2D conditions since complicated cellular signals between cells and its matrix cannot be reproduced3. Three-dimensional cell cultures address this challenge and serve as a better model representing in vivo physiological conditions closely. Table 1 indicates the difference between 2D and 3D cell culture systems.

Key Characteristics  2D-Cell Culture 3D-Cell Culture References
Cell Shape Flat and stretched Natural shape (ellipsoid/polarized) is retained 257683383
Cell interface to medium All cells are equally exposed to media components As in physiological conditions, there is gradient availability of media components. Upper layer of cells are highly exposed over the lower layer (Heterogeneous exposure) 159758244, 235011055
Cell junction Cell junctions are less prevalent and does not resemble physiological conditions Cell junctions are prevalent and enable cell to cell communication. 226622786
Cell Differentiation Moderately and poorly differentiated Well differentiated 230223967
Drug metabolism Drug metabolism not well observed Enhanced drug metabolism with increased expression of CYP enzymes 237285278, 167716489
Drug Sensitivity Cells are sensitive and drugs show high efficacy Cells often show resistance and drugs show low potency 1771142310
Cell Proliferation Higher proliferation rate than in natural environment Proliferation rate may be high or low, it is based on cell type and 3D-cell culture technique. 920151111, 1557619212
Response to stimuli Poor response to mechanical stimuli of cells well-established responses to mechanical stimuli of cells 2688769813
Viability Sensitive to cytotoxin Greater viability and less susceptible to external factor 1771142310
Apoptosis Highly susceptible to drug-induced apoptosis Enhanced resistance to drug-induced apoptotic stimuli 1902072914

Table 1: Cell behavior: 2D vs 3D cell culture conditions

Moreover, several studies have reported a difference in gene and protein expression profiles of the cells grown in 3D environment when compared to its 2D counterpart. Also, expression profiles in 3D culture conditions are thought to be more physiologically relevant than 2D cell culture conditions.

Advantages of 3D cell culture

Cellular events in 3D culture resemble physiological conditions closely and have the following distinct advantages over the 2D culture conditions

  • Stem cells grown in 3D exhibit significantly higher differentiation potential15.
  • Drug safety and efficacy studies are efficient and relatively easier to perform in 3D cultures reducing the time spent in drug discovery by pharmaceutical companies16. Drug-induced hepatotoxicity can be efficiently studied in 3D cell models16.
  • 3D cultures provide better data in the prediction of drug resistance. Alkylating agents demonstrated resistance in a 3D culture that was comparative with in-vivo tumors17.
  • Viral pathogenesis including viral growth, infection and pathogen-host interactions can be studied with reduced hazard levels using 3D models18.

Overview of 3D cell culture techniques

The choice of 3D cell culture technique should depend on several parameters, including the nature of the cells themselves (cell line, primary cell, tissue origin), or the final aim of the study. It’s crucial to evaluate these parameters before choosing the most relevant 3D cell culture technique.

Broadly, 3D cell culture techniques are classified as Scaffold-based or non-scaffold-based techniques.

Scaffold based techniques

In scaffold based techniques cells are grown in presence of a support. 2 major types of support can be used:

  1. Hydrogel-based support: hydrogels are by definition polymer networks extensively swollen with water. Cells can be embedded in these hydrogels or simply coated at the surface. Depending on the nature of the polymer, hydrogels can be classified in to different categories (ECM protein-based hydrogels, natural hydrogels and synthetic hydrogels) with distinct properties.
  2. Polymeric hard material based support: cells are cultivated in presence of fibers or sponge-like structures: cell recover a more physiological shape because they are not plated on a flat surface. Materials used for these supports can be polystyrene (adapted for imaging studies because of its transparency) but also biodegradable tools like polycaprolactone.

    Attributes related to these scaffolds are summarized in the following table:
ECM-based Scaffolds  Natural Hydrogels Synthetic Hydrogels  Polymeric Hard Scaffolds 
Product Description (Laminin, Collagen,
ECM gel
(Hystem®) (TrueGel3D™, Hydromatrix™) (3D Biotek Inserts, Cellusponge, Gelatin Scaffolds)
Biological relevance +++   +++  +/-  +/-
Consistency/Reproducibility  -  ++  +++  +++
Risk of contamination  -  ++  +++  +++
Modularity/customization - + ++ -
Cell retrieval +/-   +  ++ +++ 
Downstream analysis (Imaging, molecular analysis)  +  ++  ++ ++ 
HTS/HCS analysis +/-  +/-   +

Suitability: +++ = High; ++ = Medium; + = Low; - = Unsuitable; +/- = varies with scaffold components

Table 2:  Scaffold-based 3D techniques overview with attributes

Scaffold free techniques

Scaffold-free techniques allow the cells to self-assemble to form non-adherent cell aggregates called spheroids. Spheroids mimic the solid tissues by secreting their own extracellular matrix and displaying differential nutrient availability. Spheroids grown via non-scaffold based techniques are consistent in size and shape and are better in-vitro cellular models for high-throughput screening.

Application Note: Cancer Stem Cell Proliferation in Human Prostate and Breast Cancer Cell Lines Utilizing a New Defined Serum-Free 3D Spheroid Media.

Protocol Guide: Cancer Stem Cell Tumorsphere Formation Protocol.

Different platforms, from specialized plate to more integrated systems, can be used to generate spheroids: attributes of these techniques are described in the following table

Techniques Attributes Low attachment microplates
Microfluidics systems
Product Description (Corning® Spheroids Plates) (CellASIC ONIX Gradient Plate) (Corning® Spinner Flask or Roller Bottles)
Long term culture ++ +++ +++
Cell retrieval  +++  -  +++
Image analysis  +++ +++   -
Cost effectiveness  ++  -  -
HCS/HTS analysis  +++  -  +

Suitability : +++ = High; ++ = Medium; + = Low; - = Unsuitable

Table 3:  Scaffold-free 3D technique overview with attributes


The evolution of 3D cell culture has the potential to bridge the gap between in vitro and in vivo experiments. The convenience of handling cells in vitro while obtaining results that reflect in-vivo condition and avoiding ethical concerns of animal usage is making 3D cell culture techniques increasingly popular among researchers, but choosing the right system to develop a 3D cell culture model is not a trivial question.

The future will see the emerging of some more complex and advanced technologies like 3D bioprinting, an offshoot of 3D printing, helpful to print both biomaterials and living cells. 3D bioprinting has a wide medical application like skin grafting, which avoids a second wound site, characteristic of the traditional grafting methods. The major components for 3D bioprinting, like bio-inks, scaffold material, and biomaterials, are relatively well known to the scientific world. By configuring the order and position of these components various tissue products can be developed while simulating the physiological environment19. At the moment, the technique is in the early stage but has the potential to evolve as an indispensable tool for drug discovery and toxicity studies.




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