A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation

Jenny Ostrop; Rosalie T Zwiggelaar; Marianne Terndrup Pedersen; François Gerbe; Korbinian Bösl; Håvard T Lindholm; Alberto Díez-Sánchez; Naveen Parmar; Silke Radetzki; Jens Peter von Kries; Philippe Jay; Kim B Jensen; Cheryl Arrowsmith; Menno J Oudhoff

doi:10.3389/fcell.2020.618552

A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation

Front Cell Dev Biol. 2021 Jan 21:8:618552. doi: 10.3389/fcell.2020.618552. eCollection 2020.

Authors

Jenny Ostrop¹, Rosalie T Zwiggelaar¹, Marianne Terndrup Pedersen^{2

3}, François Gerbe⁴, Korbinian Bösl⁵, Håvard T Lindholm¹, Alberto Díez-Sánchez¹, Naveen Parmar¹, Silke Radetzki⁶, Jens Peter von Kries⁶, Philippe Jay⁴, Kim B Jensen^{2

3}, Cheryl Arrowsmith^{7

8

9}, Menno J Oudhoff¹

Affiliations

¹ Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway.
² BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
³ Novo Nordisk Foundation Center for Stem Cell Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
⁴ Cancer Biology Department, Institute of Functional Genomics, University of Montpellier, Montpellier, France.
⁵ Department of Bioinformatics, Computational Biological Unit, University of Bergen, Bergen, Norway.
⁶ Screening Unit, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.
⁷ Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.
⁸ Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
⁹ Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.

Abstract

Intestinal organoids are an excellent model to study epithelial biology. Yet, the selection of analytical tools to accurately quantify heterogeneous organoid cultures remains limited. Here, we developed a semi-automated organoid screening method, which we applied to a library of highly specific chemical probes to identify epigenetic regulators of intestinal epithelial biology. The role of epigenetic modifiers in adult stem cell systems, such as the intestinal epithelium, is still undefined. Based on this resource dataset, we identified several targets that affected epithelial cell differentiation, including HDACs, EP300/CREBBP, LSD1, and type I PRMTs, which were verified by complementary methods. For example, we show that inhibiting type I PRMTs, which leads enhanced epithelial differentiation, blocks the growth of adenoma but not normal organoid cultures. Thus, epigenetic probes are powerful tools to study intestinal epithelial biology and may have therapeutic potential.

Keywords: CREBBP; EP300; PRMT1; bioimage analysis; epigenetic modifiers; intestinal stem cell biology; organoids.