3D organoids and organoid derived monolayers from patients with inflammatory bowel disease

Scope of the method

The Method relates to
  • Human health
The Method is situated in
  • Basic Research
  • Education and training
  • Translational - Applied Research
Type of method
  • In vitro - Ex vivo
This method makes use of
  • Human derived cells / tissues / organs
Specify the type of cells/tissues/organs
Intestinal epithelial cells from human intestinal biopsies


Method keywords
  • organoids
  • ECM
  • 3D culture
  • Coculture model
  • Transwell
Scientific area keywords
  • inflammatory bowel disease
  • ulcerative colitis
  • crohn's disease
  • stem cells
  • epithelial cells
  • intestinal crypt
Method description

Intestinal organoids are cultured from intestinal biopsies obtained during routine endoscopy. The stem cell containing crypts are isolated and cultured in a 3D ECM (Matrigel) in the presence of the desired growth factors. The present stem cells will expand and give rise to all epithelial cells of the intestinal epithelium while maintaining location, disease and patient specific characteristics. 3D organoids can be used to evaluate several mechanism including responses to inflammatory stimuli, microbiota stimulation, analysis of epithelial (transport) mechanisms in the development/progress of IBD. In addition, 3D organoids can be dissociated and seeded into 2D transwells to allow access to the apical side of the cells for exposure towards different components.

Lab equipment
  • - Biosafety cabinet ;
  • - CO2 cell incubator ;
  • - Centrifuge Microscope.
Method status
  • Published in peer reviewed journal

Pros, cons & Future potential


Organoids and organoid derived monolayers maintain region, disease and patient-specific characteristics.

  • - Only epithelial cells (no immune cells) present. 
  • - Requires specialized training ECM and medium including growth factors is rather expensive.
  • - Organoids can be cultured from multiple organs.
  • - Possibilities for co-culture with other cell-types are being explored.
Future & Other applications

Organoids have/are currently been/being developed from different organs and are widely applied for the analysis of different mechanisms (drug testing, barrier function, specific mutations,..).

References, associated documents and other information


Arnauts K, Verstockt B, Santo Ramalho Veñancio A, et al. Ex vivo mimicking of inflammation in organoids derived from patients with ulcerative colitis. Gastroenterology 2020, in press. https://doi.org/10.1053/j.gastro.2020.05.064

Vancamelbeke M, Laeremans T, Vanhove W, et al. Butyrate Does Not Protect Against Inflammation-induced Loss of Epithelial Barrier Function and Cytokine Production in Primary Cell Monolayers From Patients With Ulcerative Colitis. J Crohns Colitis. 2019;13(10):1351‐1361. doi:10.1093/ecco-jcc/jjz064

Noben M, Verstockt B, de Bruyn M, et al. Epithelial organoid cultures from patients with ulcerative colitis and Crohn's disease: a truly long-term model to study the molecular basis for inflammatory bowel disease?. Gut. 2017;66(12):2193‐2195. doi:10.1136/gutjnl-2016-313667

Noben M, Vanhove W, Arnauts K, et al. Human intestinal epithelium in a dish: Current models for research into gastrointestinal pathophysiology. United European Gastroenterol J. 2017;5(8):1073‐1081. doi:10.1177/2050640617722903

Contact person

Bram Verstockt


Katholieke Universiteit Leuven (KUL)
Department of Chronic Diseases and Metabolism
Translational Research in GastroIntestinal Disorders (TARGID) - IBD Group
Flemish Region