Systematically quantifying morphological features reveals constraints on organoid phenotypes

Abstract

Organoids recapitulate complex 3D organ structures and represent a unique opportunity to probe the principles of self-organization. While we can alter an organoid’s morphology by manipulating the culture conditions, the morphology of an organoid often resembles that of its original organ, suggesting that organoid morphologies are governed by a set of tissue-specific constraints. Here, we establish a framework to identify constraints on an organoid’s morphological features by quantifying them from microscopy images of organoids exposed to a range of perturbations. We apply this framework to Madin-Darby Canine Kidney cysts and show that they obey a number of constraints taking the form of scaling relationships or caps on certain parameters. For example, we found that the number, but not size, of cells increases with increasing cyst size. We also find that these constraints vary with cyst age and can be altered by varying the culture conditions. This quantitative framework for identifying constraints on organoid morphologies may inform future efforts to engineer organoids.

CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia

“…At the tissue level, we show that cysts can adopt a variable range of shapes beyond being symmetric spheres (Beck et al, 2022;Cerruti et al, 2013) (Fig. 2A-B, Fig.…”

“…In a biomedical context, the possibility of analyzing a very large number of samples is ideal for testing the reproducibility of epithelial organoids cultures and performing detailed comparisons between physiological and pathological conditions. Furthermore, highthroughput drug testing on animal or human epithelial organoids could take advantage of our approach to automatically analyze the effect of every drug against a target disease at the cellular level (Beck et al, 2022;Drost & Clevers, 2018;Lo et al, 2020).…”

“…Despite their simplicity, these cysts have previously been used as a suitable model system to study the establishment of cell polarity and cell junctions (Bryant & Mostov, 2008;Dukes et al, 2011;Martín-Belmonte et al, 2008;Vidal-Quadras et al, 2017;Yonemura, 2014), epithelial morphogenesis and physiology (Alfonso-Pérez et al, 2022;Guo et al, 2008;Imai et al, 2015;O'Brien et al, 2002;Wells et al, 2013;Yu et al, 2007), tumor progression (Fessenden et al, 2018;Sakurai et al, 2012;Schmeichel & Bissell, 2003;L. Yan et al, 2021), and for exploring the constraints on epithelial tissue morphogenesis (Beck et al, 2022). MDCK cysts have provided a lot of useful information to study more complex systems helping to understand the selforganization in organoids, embryoids and the early stages of mammal development (Beck et al, 2022;Carleton et al, 2022;Metzger et al, 2018).…”

“…Yan et al, 2021), and for exploring the constraints on epithelial tissue morphogenesis (Beck et al, 2022). MDCK cysts have provided a lot of useful information to study more complex systems helping to understand the selforganization in organoids, embryoids and the early stages of mammal development (Beck et al, 2022;Carleton et al, 2022;Metzger et al, 2018).…”