Ontogeny and function of the circadian clock in intestinal organoids

EMBO J. 2022 Dec 17;41(2):e106973. doi: 10.15252/embj.2020106973. Epub 2021 Oct 27.


Circadian rhythms regulate diverse aspects of gastrointestinal physiology ranging from the composition of microbiota to motility. However, development of the intestinal circadian clock and detailed mechanisms regulating circadian physiology of the intestine remain largely unknown. In this report, we show that both pluripotent stem cell-derived human intestinal organoids engrafted into mice and patient-derived human intestinal enteroids possess circadian rhythms and demonstrate circadian phase-dependent necrotic cell death responses to Clostridium difficile toxin B (TcdB). Intriguingly, mouse and human enteroids demonstrate anti-phasic necrotic cell death responses to TcdB. RNA-Seq analysis shows that ~3-10% of the detectable transcripts are rhythmically expressed in mouse and human enteroids. Remarkably, we observe anti-phasic gene expression of Rac1, a small GTPase directly inactivated by TcdB, between mouse and human enteroids, and disruption of Rac1 abolishes clock-dependent necrotic cell death responses. Our findings uncover robust functions of circadian rhythms regulating clock-controlled genes in both mouse and human enteroids governing organism-specific, circadian phase-dependent necrotic cell death responses, and lay a foundation for human organ- and disease-specific investigation of clock functions using human organoids for translational applications.

Keywords: Rac1; Clostridium difficile toxin B; circadian rhythms; human enteroids; intestinal organoids.

Publication types

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

MeSH terms

  • Animals
  • Bacterial Proteins / toxicity
  • Bacterial Toxins / toxicity
  • Cell Death
  • Cells, Cultured
  • Circadian Clocks*
  • Humans
  • Jejunum / cytology*
  • Mice
  • Mice, Inbred C57BL
  • Organoids / drug effects
  • Organoids / metabolism*
  • Organoids / physiology
  • rac1 GTP-Binding Protein / genetics
  • rac1 GTP-Binding Protein / metabolism


  • Bacterial Proteins
  • Bacterial Toxins
  • RAC1 protein, human
  • toxB protein, Clostridium difficile
  • rac1 GTP-Binding Protein

Associated data

  • GEO/GSE179028