In Silico Analysis of the Age-Dependent Evolution of the Transcriptome of Mouse Skin Stem Cells

Abstract

The stem cells located in the hair follicle bulge area are critical for skin regeneration and repair. To date, little is known about the evolution of the transcriptome of these cells across time. Here, we have combined genome-wide expression analyses and a variety of in silico tools to determine the age-dependent evolution of the transcriptome of those cells. Our results reveal that the transcriptome of skin stem cells fluctuates extensively along the lifespan of mice. The use of both unbiased and pathway-centered in silico approaches has also enabled the identification of biological programs specifically regulated at those specific time-points. It has also unveiled hubs of highly transcriptionally interconnected genes and transcriptional factors potentially located at the core of those age-specific changes.

Functional Specificity of the Members of the Sos Family of Ras-GEF Activators: Novel Role of Sos2 in Control of Epidermal Stem Cell Homeostasis

“…We also speculate that the differential effects caused by Sos1 or Sos2 ablation in keratinocytes could be due not only to intrinsic mechanistic differences between the two Sos isoforms but also, at least in part, to their different levels of expression in this particular cell type of the skin. Indeed, we observed significantly higher levels of Sos2 RNA than Sos1 RNA in our transcriptomic analyses of actively growing keratinocyte cultures and during different developmental stages of mouse epidermal stem cells [ 30 ]. Importantly, an essential, cell-autonomous role of Sos2 in control of the homeostasis of skin keratinocytes also identifies Sos2 as a novel, potential therapy target (besides Sos1) for prevention and/or treatment of epidermal tumors.…”

“…This procedure was performed as previously described [ 30 ]. Briefly, the dorsal skin of WT and Sos2 KO (neonatal and adult) mice was excised, cleaned, and digested in 0.25% trypsin (ThermoFisher, 25200056, Waltham, MA, USA) overnight at 4 °C.…”

The Rho GTPase exchange factor Vav2 promotes extensive age-dependent rewiring of the skin stem cell transcriptome

“…This pattern can be linked to the post-mitotic telogen phase of the skin (which takes place in approx. 2.5-monthold mice) and with the subsequent acquisition of aging features by SSCs at later stages of the time-course analyzed in this study (7,18). A comprehensive description of the timedependent evolution of all these functions can be found elsewhere (18).…”

“…Thus, during the very early time point, the upregulated gene expression waves of WT SSCs encode functions related to cell growth, IGF (insulin growth factor) and mTORC signaling, extracellular matrix interaction regulators, and several metabolic routes. This spectrum of functions is probably associated with the expansion in the numbers of SSCs that is usually observed between postnatal days 18 and 30 in mice (18). In contrast, the waves associated with downregulation events contain genes encoding proteins involved in small GTPase signaling, cell adhesion, protein modification, and autophagy.…”

“…The resulting expression profiles were named according to the positions of the main positive (+) and negative (-) enrichments (peaks), i.e., 0.6 = 0.6-month-old; 1 = 1-month-old: 2.5 = 2.5-month-old; 4 = 4-month-old; 6 = 6-month-old; and 12 = 12-month-old. To evaluate how Vav2 Onc activity affects SSC transcriptional dynamics, the fluctuations of each dynamic probe set between the WT genotype (data from (18)) and the Vav2 Onc/Onc genotype (data from this study) were analyzed. Using Cytoscape software (35), the results were represented as a network, with nodes indicating expression patterns and edges (arrows) representing how dynamic transcripts behave in the Vav2 Onc context as compared to the WT.…”