Maintenance of the mammalian intestine throughout life relies on rapidly dividing stem cells located at the base of invaginating crypts in both the small intestine and the colon. These crypts constitute a protective niche to provide signals conducive to stem cell proliferation and maintenance, while preventing exposure to harmful toxins that may be present in the gut lumen. During homeostasis, gut stem cells respond to signals from the niche to either self-renew or differentiate to generate specialized epithelial cells. Intestinal and colonic stem cells are both specifically marked by the Wnt target gene Lgr5. While much has been learned about intestinal stem cell biology through the use of Lgr5-labeled transgenic mouse models, relatively little is known about how stem cell behavior differs between small intestine and colon, particularly in human. Colon cancer is far more common than small intestinal cancers and is thought to arise from malignant transformation of gut stem cells during aging. Yet how the stem cells of small intestine and colon differ molecularly under homeostatic conditions and during aging remains unclear. Three-dimensional organoids, which permit long-term self-renewal of mammalian gut stem cells in vitro, provide a convenient and accessible system for investigating regional differences in stem cell behavior. Additionally, the epigenetic clock – a measure of age based on age-dependent DNA methylation changes – provides a quantitative tool for analyzing aging of different tissues and cell types.

Here, we show that colon stem cells grown in culture proliferate slower than small intestinal stem cells, have decreased stem cell function, and have a greater tendency to differentiate. In addition to stem cell behavioral differences in culture, we find that human small intestine and colon exhibit different aging profiles as measured by the epigenetic clock. We demonstrate that small intestine crypt cells have decreased epigenetic clock aging rates compared to colon crypts and to surrounding small intestine mucosal cells, and these regional differences in epigenetic aging appear to be maintained in vitro.