GUT organoids and single-cell technology

Organoids, being a miniaturised and simplified version of an organ, enable studying the functioning of an organ in detail in vitro. Applying single-cell genomics approaches to organoids provides a powerful approach to obtain a detailed insight into an organ's functioning. This project focuses on establishing single-cell genomics aiming to monitor and evaluate the development of gut and other organoids.

Single-cell genomics is a powerful method to characterise and compare the cellular composition of organs and organoids. As such, single-cell genomics will allow a detailed evaluation and characterisation of new types of organoids being developed within the other complex cell systems projects.

The researchers implement single-cell technology by focusing on two different systems: immune cells and pig intestinal organoids. The first is characterised within the context of ongoing and prospected projects focussing on immune-competent organotypic gut models.

The organoids is characterised as a 2D confluent monolayer in a transwell system, which enables its future application in studies on variation in nutrient absorption rates. Moreover, optimising the growth and differentiation of stem cells into intestinal organoids in a transwell system will be the first step towards multi-organ complex cell systems.

Immune cells and intestinal organoids are well suited to studies at single-cell resolution due to their variety of cell types and relative ease of preparing individual cells by several techniques allowing isolation of arrays of individual cells. In this way, cell-specific signalling and metabolism are investigated. Furthermore, since these cell systems have already been studied in detail based on traditional methods, the researchers can benchmark their new technology.

Progress (September 2022)

The researchers are working on developing the two sytems to apply single-cell sequencing in complex cell systems.


Establishing the technique will provide a powerful addition to monitor and evaluate the planned development of complex cell systems such as airway organoids, organoids of fish intestines, and further development of intestinal organoid models for livestock species and humans.