Aged intestinal stem cells propagate cell-intrinsic sources of inflammaging in mice [single-cell RNA-seq]

During ageing, cell-intrinsic and extrinsic factors lead to the decline of tissue function and organismal health. Disentangling these factors is important for developing effective strategies to prolong organismal healthspan. Here, we addressed this question in the mouse intestinal epithelium, which forms a dynamic interface with its microenvironment and receives extrinsic signals affecting its homeostasis and tissue ageing. We systematically compared transcriptional profiles of young and aged epithelial cells in vivo and ex vivo in cultured intestinal organoids. We found that all cell types of the aged epithelium exhibit an inflammation phenotype, which is marked by MHC class II upregulation and most pronounced in enterocytes. This was accompanied by elevated levels of the immune tolerance markers PD-1 and PD-L1 in the aged tissue microenvironment, indicating dysregulation of immunological homeostasis. Intestinal organoids from aged mice still showed an inflammation signature after weeks in culture, which was concurrent with increased chromatin accessibility of inflammation-associated loci. Our results reveal a cell-intrinsic, persistent inflammation phenotype in aged epithelial cells, which might contribute to systemic inflammation observed during ageing. Overall design: Combinatorial approach of bulk and single-cell RNA-Seq of epithelial cells from the proximal small intestine of 3 young (2-3 months of age) and 3 aged (20-22 months of 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)