Unlocking insights into cellular senescence through single cell transcriptomics of ageing mesenchymal stem cells
Atefeh Taherian Fard,Jessica Mar Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, QLD 4072, Australia
Abstract
Aging is a complex biological process. The heterogeneity of ageing phenotype is driven by the complex and dynamic nature through which several key molecular and cellular traits arise and interact. To understand the heterogeneity associated with aging, and the complications associated with age-related diseases, research into clinical treatments, including Mesenchymal Stem Cell (MSC) therapy, is underway. For a proper use of MSCs in clinical applications, and in order to develop therapeutic intervention to slow down age-related degenerative changes in aging tissue, it is crucial to have a general understanding of the biological mechanism controlling MSC survival, proliferation, differentiation and senescence. Here for the first time, single cell RNA-seq data was generated to investigate the gene expression heterogeneity of MSCs undergoing replicative senescence. We extracted RNA from three different time-points, capturing the proliferative, quiescent and the senescent state of the MSCs under controlled culture conditions. By utilising our implemented pipeline in R, we characterised different MSCs sub-populations at the different stages of cell cycle, compared the transcription profile of cells going from a proliferative to a senescent state and identified the key factors driving this transitional process. We used libraries in Bioconductor (DropletUtils for doublet identification and Slingshot for trajectory inference), CRAN and an in-house R package for identifying differentially distributed genes. We found that, under controlled condition, there are atleast three different senescent phenotypes in the aging MSCs. These phenotypes are linked to SASP induced senescence, oncogene induced senesce and SASP-induced senescence escapees. The result from this study enabled us to identify potential alternative pathways and their associated key drivers that lead to different senescent states and unravel the heterogeneity associated with the aging MSCs.
Keywords: Senescence,MSC,single-cell RNA sequencing,heterogeneity