Intestinal stem cells: you can’t teach an old dog new tricks

Xuan Zheng, Jeroen van Zon, Sander Tans and colleagues base that conclusion on the behaviour of cells in intestinal organoids. These mini-organs, cultured in vitro, were originally developed by Hans Clevers and colleagues at the Hubrecht Institute in Utrecht. At AMOLF, they have since been further refined to more closely resemble genuine intestinal tissue.

The crux of the current research is that such an organoid is monitored over 60 days using a confocal microscope that captures a 3D image every 12 seconds. Afterwards, once the intestinal stem cells have divided numerous times, the recordings are entrusted to AI software that traces back the trail: where did the cells present at the end of the experiment originally come from?

TypeTracker

The first version of this OrganoidTracker software, introduced three years ago, tracked only the cell nuclei without examining them more closely. PhD candidate Zheng has now expanded this into a TypeTracker that can also distinguish between different cell types. This is achieved by selectively labelling proteins secreted by the intestinal cells with fluorescent antibodies. In this way, it is possible to determine retrospectively at what point the cells had become sufficiently specialised to begin producing these proteins.

Specialising

Often, that turns out to be earlier than previously thought. The cells differentiate whilst still safely enclosed in stem cell form within the recesses (crypts) of the intestinal wall. Only thereafter do they migrate to the protrusions (villi, singular villus) that are in contact with the intestinal contents. How they find their way in doing so remains unclear. However, the obvious hypothesis that they only specialise upon arrival, under the influence of the local environment, does not appear to hold true.

New model

The researchers call their new model commit-then-sort. They concede that there remain considerable differences between organoids and ‘real’ intestinal tissue, yet it is difficult to imagine that the process would work in an entirely different manner there. It is noted, moreover, that the research method should be straightforwardly adaptable to other organoids, which serve as models for a whole range of tissue types.

Xuan Zheng, et al., Organoid cell fate dynamics in space and time, Science Advances (2023)