Ontogeny and function of the circadian clock in intestinal organoids

Abstract

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 molecular mechanisms regulating circadian physiology of the intestine remain largely unknown. The lack of appropriate human model systems that enable organ-and/or diseasespecific interrogation of clock functions is a major obstacle hindering advancements of translational applications using chronotherapy. In this report, we show that both pluripotent stem cell-derived human intestinal organoids engrafted into mice and patient-derived human intestinal enteroids (HIEs) possess robust 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. RNA-Seq data show ~4% of genes are rhythmically expressed in HIEs. Remarkably, we observe anti-phasic gene expression of Rac1, a small GTPase directly inactivated by TcdB, between mouse and human enteroids. Importantly, the observed circadian time-dependent necrotic cell death response is abolished in both mouse enteroids and human intestinal organoids (HIOs) lacking robust circadian rhythms. Our findings uncover robust functions of circadian rhythms regulating critical clockcontrolled genes (CCGs) in human enteroids governing organism-specific, circadian phasedependent necrotic cell death responses. Our data highlight unique differences between mouse and human enteroids, and lay a foundation for human organ-and disease-specific investigation of clock functions using human organoids for translational applications.

The circadian clock ticks in organoids

“… The recent methodological advances have realized self‐organizing 3D culture systems that are histologically similar to a variety of human organs. Rosselot et al (2021) report that mature organoids possess circadian clocks and are susceptible to time‐controlled dosing of drugs. …”

“…One breakthrough recently occurred in this question. The current study by Rosselot et al (2021) constitutes a breakthrough, as it investigated the circadian clock in several types of artificially induced, multicellular structures that mimic the intestinal organ. The authors generated organoids that were different in terms of their maturity, cell origin, or induction process and reported that human intestinal organoids (HIO) induced from the pluripotent stem cells did not show circadian rhythm.…”

In vitro models to study Clostridioides difficile infection: current systems and future advances

“…Current studies often rely on the use of in vivo animal models -namely hamster and mouse models [8,9]. They are particularly used when studying immunological aspects of C. difficile; however, immune responses vary greatly between species and disease progression in these models is often dissimilar to that in humans [10]. Further limitations include the differences in anatomy and microbiota composition [11], plus there is a general need to reduce and refine the use of animals in research.…”

Sex Inclusion in Transcriptome Studies of Daily Rhythms

“…The greater representation of females among human studies could be related to Institutional Review Board approval and participant recruitment. In any case, recent work on organoids and diurnal rodents may lead to more species and tissue diversity in circadian data sets (Rosselot et al, 2022; Bano-Otalora et al, 2021).…”