Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice [Capture-C]

Low-grade chronic inflammation is considered a hallmark of ageing and associated with impaired tissue function and development of disease. However, how cell-intrinsic and -extrinsic factors interact to establish this phenotype, termed inflammaging, remains poorly understood. We addressed this question in the mouse intestinal epithelium, using organoid cultures to dissect stem cell-intrinsic and -extrinsic sources of increased inflammatory signaling upon ageing. At the single-cell level, we found that inflammaging establishes differently in cells along the crypt-villus axis, including intestinal stem cells (ISCs). Importantly, the inflammaging phenotype was stably propagated by aged ISCs in organoid cultures and associated with increased chromatin accessibility of inflammation-associated loci in vivo and ex vivo, indicating a cell-intrinsic memory of inflammation. Mechanistically, we show that expression of inflammaging genes is dependent on STAT1 signaling. Together, our data reveal that inflammaging in the intestine is promoted by a cell-intrinsic mechanism, stably propagated by ISCs and associated with a disbalance in immune homeostasis. Overall design: Combinatorial approach of bulk and single-cell RNA-Seq on epithelial cells from the proximal small intestine of 3 young (2-3 months of age) and 3 aged (20-22 months fo age) mice; cells were freshly isolated by tissue digest and following FACS-based cell sorting. Complementary bulk RNA-Seq & ATAC-Seq was performed from small intestinal organoids derived from young (2-3 months of age) and aged (20-22 months fo age) mice. (Bulk RNA-Seq: n=6 per age, ATAC-Seq: n=3 per age)