Mapping and exploring the organoid state space using synthetic biology

Semin Cell Dev Biol. 2023 May 30;141:23-32. doi: 10.1016/j.semcdb.2022.04.015. Epub 2022 Apr 22.


The functional relevance of an organoid is dependent on the differentiation, morphology, cell arrangement and biophysical properties, which collectively define the state of an organoid. For an organoid culture, an individual organoid or the cells that compose it, these state variables can be characterised, most easily by transcriptomics and by high-content image analysis. Their states can be compared to their in vivo counterparts. Current evidence suggests that organoids explore a wider state space than organs in vivo due to the lack of niche signalling and the variability of boundary conditions in vitro. Using data-driven state inference and in silico modelling, phase diagrams can be constructed to systematically sort organoids along biochemical or biophysical axes. These phase diagrams allow us to identify control strategies to modulate organoid state. To do so, the biochemical and biophysical environment, as well as the cells that seed organoids, can be manipulated.

Keywords: Bioengineering; Biophysical modelling; High-content screening; Microfluidics; Morphospace; Synthetic biology.

Publication types

  • Review
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Differentiation
  • Organoids*
  • Signal Transduction
  • Synthetic Biology*