Development of intestinal organoids as tissue surrogates: cell composition and the epigenetic control of differentiation

Mol Carcinog. 2015 Mar;54(3):189-202. doi: 10.1002/mc.22089. Epub 2013 Sep 21.


Intestinal organoids are multicellular crypt-like structures that can be derived from adult intestinal stem cells (ISCs), embryonic stem cells (ESCs) or induced pluripotent stem cells (IPSCs). Here we show that intestinal organoids generated from mouse ESCs were enriched in ISCs and early progenitors. Treatment of these organoids with a γ-secretase inhibitor increased Math1 and decreased Hes1 expression, indicating Notch signaling regulates ISC differentiation in these organoids. Lgr5 and Tert positive ISCs constituted approximately 10% and 20% of the organoids. As found in native tissue, Lgr5 and Tert expressing cells resolved into two discreet populations, which were stable over time. Intestinal organoids derived from cancer-prone Apc(Min/+) mice showed similar numbers of ISCs, but had reduced Math1 expression, indicating a suppressed secretory cell differentiation potential (as found in intestinal tissue). Apc(Min/+) organoids were used to screen epigenetically active compounds for those that increased Math1 expression and organoid differentiation (including HDAC inhibitors, Sirtuin (SIRT) modulators and methyltransferase inhibitors). Broad-spectrum HDAC inhibitors increased both Math1 and Muc2 expression, indicating an ability to promote the suppressed secretory cell differentiation pathway. Other epigenetic compounds had a diverse impact on cell differentiation, with a strong negative correlation between those that activated the secretory marker Muc2 and those that activated the absorptive cell marker Fabp2. These data show that ESC-derived intestinal organoids can be derived in large numbers, contain distinct ISC types and can be used to screen for agents that promote cell differentiation through different lineage pathways.

Keywords: Apc; Math1; embryonic stem cells; histone deacetylase; intestinal stem cells.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenomatous Polyposis Coli Protein / genetics
  • Adult Stem Cells / cytology
  • Amyloid Precursor Protein Secretases / antagonists & inhibitors
  • Animals
  • Basic Helix-Loop-Helix Transcription Factors / biosynthesis
  • Cell Differentiation / genetics*
  • Cell Line
  • Embryonic Stem Cells / cytology*
  • Enzyme Activation
  • Epigenesis, Genetic*
  • Fatty Acid-Binding Proteins / metabolism
  • Histone Deacetylase Inhibitors / pharmacology
  • Homeodomain Proteins / biosynthesis
  • Induced Pluripotent Stem Cells / cytology*
  • Intestines / cytology*
  • Mice
  • Mice, Inbred C57BL
  • Mice, Transgenic
  • Mucin-2 / metabolism
  • Organoids / cytology*
  • Organoids / growth & development
  • Receptors, G-Protein-Coupled / biosynthesis
  • Receptors, Notch / metabolism
  • Telomerase / biosynthesis
  • Transcription Factor HES-1


  • Adenomatous Polyposis Coli Protein
  • Atoh1 protein, mouse
  • Basic Helix-Loop-Helix Transcription Factors
  • Fabp2 protein, mouse
  • Fatty Acid-Binding Proteins
  • Hes1 protein, mouse
  • Histone Deacetylase Inhibitors
  • Homeodomain Proteins
  • Lgr5 protein, mouse
  • Muc2 protein, mouse
  • Mucin-2
  • Receptors, G-Protein-Coupled
  • Receptors, Notch
  • Transcription Factor HES-1
  • Telomerase
  • Tert protein, mouse
  • Amyloid Precursor Protein Secretases