Effect of age, lysosomal degradation and mitochondrial replication on mouse hematopoietic stem cell
Aging impairs the function of hematopoietic stem cells (HSCs), promotes clonal hematopoiesis and myeloid malignancies, and contributes to immune decline in the elderly. The role of lysosomes – the cell's primary degradation organelles –  beyond their passive mediation of autophagy in HSC aging remains unknown. Here, we show that lysosomes in aged HSCs are depleted, damaged, hyperacidic, and aberrantly activated compared to those in young HSCs. Using single-cell RNA sequencing (scRNA-seq) and functional analyses, we demonstrate that pharmacological inhibition of damaged hyperactivated lysosomes – by a vacuolar ATPase (v-ATPase) inhibitor  that blocks lysosomal hyperacidification – restores lysosomal integrity, as well as metabolic and epigenetic homeostasis in aged HSCs. This intervention also resolves inflammatory and interferon-related transcriptional programs by enhancing lysosomal processing of mitochondrial DNA (mtDNA) and suppressing intrinsic inflammation mediated by the cGAS–STING DNA-sensing pathway. Overall design: Freshly FACS-isolated hematopoietic stem cells [HSCs; lineage negative (Lin-) Sca1+ cKit+ (LSK) CD150+CD48- cells] from 8 weeks (young, Y) or 20 month-old (old, O) mice or HSCs cultured 16 hours in vitro in the presence of ConA (40 nM) or ddC (40uM) or non treated (NT). All conditions were assessed by scRNA-seq in addition to freshly isolated HSC from young or old mice. Note: HSC from young mice cultured 16h without drug were labelled "Old-like_mHSC_Cultured". For each samples, a barcodes.tsv, a features.tsc and a matrix.mtx are available.