SIRT6/RXRα/retinoic acid-related signaling contributes to intestinal stem cell homeostasis during aging and is modulated by Atractylenolide II

Intestinal aging is characterized by impaired intestinal stem cell (ISC) function, reduced mucosal regenerative capacity, and progressive epithelial barrier deterioration. However, the upstream metabolic and epigenetic mechanisms that regulate ISC homeostasis during aging remain poorly understood. This study aimed to determine how SIRT6 regulates ISC homeostasis during intestinal aging and to investigate whether Atractylenolide II (AT-II) can alleviate age-related ISC dysfunction. Jejunal tissues from young and aged mice, intestinal epithelial-specific Sirt6-deficient mice, and 3D intestinal organoids were used to evaluate crypt–villus morphology, ISC activity, and lineage differentiation. Mechanistic analyses included western blotting, immunofluorescence, and retinoic acid (RA) quantification, complemented by pharmacological and rescue experiments targeting RXRα activity and RA metabolic balance. The results showed that SIRT6 protein expression was markedly reduced in the aged jejunum, correlating with a decreased villus-to-crypt (V/C) ratio, impaired ISC proliferation, and altered epithelial differentiation. Intestinal epithelial deletion of Sirt6 recapitulated aging-related intestinal defects, including crypt atrophy and ISC-associated dysfunction. Consistently, aged organoids displayed reduced SIRT6 protein expression, while Sirt6^Δ/Δ organoids showed decreased SOX9 and Lgr5 expression. Mechanistically, SIRT6 physically associated with RXRα, and SIRT6 loss or inhibition was associated with increased RXRα acetylation, elevated RXRα abundance, and RA metabolic remodeling. These changes were accompanied by disrupted RA balance and aging-like ISC dysfunction. AT-II partially restored SIRT6/RXRα/RA-related molecular alterations and alleviated ISC-associated dysfunction. This study suggests that the SIRT6/RXRα/RA axis contributes to ISC homeostasis during intestinal aging and may be modulated by AT-II, offering a potential strategy for age-related intestinal barrier damage.