Single-cell RNA-Sequencing of young and aged satellite cells, macrophages and fibro-adipogenic progenitor cells

The function of skeletal muscle stem cells (MuSC) declines during aging, contributing to the advent of age-related myopathies. However, whether this decline is the result of accumulating cellular damage, altered heterogeneity in stem cell populations or due to the effect of the changing niche environment remains largely unknown. By scRNA-Seq, we show that the age-related reduction in the MuSC pool is not stochastic, with different subpopulations being distinctly affected in aging. Using an in vivo allogeneic stem cell transplantation model, we show that exposure of MuSCs from old mice to a youthful niche environment significantly restores the gene expression of genes that are altered in aging. We show that age-related changes in the MuSC transcriptome are mainly driven by alterations in chromatin and transcription but are not due to posttranscriptional mechanisms affecting RNA stability. Furthermore, our data indicates that the portion of the genome that is activated in aging is significantly more responsive to restoration by niche factors compared to the repressed counterpart. Taken together, our data reveals that the niche environment plays a decisive role in controlling the transcriptional activity of MuSCs. Overall design: An aimed total of 2500 cells per mouse, composed of satellite cells, fibro-adipogenic progenitor cells and macrophages were isolated from 3 young and 4 aged male C57BL/6J mice by Fluorescence-Activated Cell Sorting. They were then processed for single-cell RNA-Sequencing using Chromium Single Cell 3' Reagent Kits (v3 Chemistry) using 10x genomics technology.