DNA Methylation Analysis Validates Organoids as a Viable Model for Studying Human Intestinal Aging

BACKGROUND & AIMS: The epithelia of the intestine and colon turn over rapidly and are maintained by adult stem cells at the base of crypts. Although the small intestine and colon have distinct, well-characterized physiological functions, it remains unclear if there are fundamental regional differences in stem cell behavior or region-dependent degenerative changes during aging. Mesenchyme-free organoids provide useful tools for investigating intestinal stem cell biology in vitro and have started to be used for investigating age-related changes in stem cell function. However, it is unknown whether organoids maintain hallmarks of age in the absence of an aging niche. We tested whether stem cell–enriched organoids preserved the DNA methylation-based aging profiles associated with the tissues and crypts from which they were derived. METHODS: To address this, we used standard human methylation arrays and the human epigenetic clock as a biomarker of age to analyze in vitro–derived, 3-dimensional, stem cell–enriched intestinal organoids. RESULTS: We found that human stem cell–enriched organoids maintained segmental differences in methylation patterns and that age, as measured by the epigenetic clock, also was maintained in vitro. Surprisingly, we found that stem cell–enriched organoids derived from the small intestine showed striking epigenetic age reduction relative to organoids derived from colon. CONCLUSIONS: Our data validate the use of organoids as a model for studying human intestinal aging and introduce methods that can be used when modeling aging or age-onset diseases in vitro.