Journal: Aging Cell
Article Title: Transcriptional Profiling at Single‐Cell Resolution Reveals Diversity and Regulatory Networks of Primary and Secondary Senescent Cells
doi: 10.1111/acel.70540
Figure Lengend Snippet: Transcriptional heterogeneity and lineage‐resolved progression in primary senescence at single‐cell level. (A) Experimental overview. Renal epithelial cells were irradiated (IR; 10 Gy, 10 days) to induce primary senescence, with quiescent controls (QUI; 0.01% serum, 3 days) processed for scRNA‐seq. (B) Expression levels of senescence and SASP‐related genes in senescent relative to the controls (QUI, n = 3; IR, n = 3). (C) Secreted IL‐6 levels in CM measured using ELISA (QUI, n = 6; IR, n = 6). Data are presented as the means ± the standard error of the mean (unpaired two‐tailed t ‐test; * p < 0.05, ** p < 0.01, *** p < 0.001). (D) UMAP of primary dataset showing clusters grouped into non‐senescent (C4 and C9), intermediate (C0, C1, C3, and C7), and fully senescent states (C5, C6, and C8) (left). Each bar represents either IR or QUI, and each colored segment's height indicates the fraction of one of the three senescence states within that group (middle). Stacked bar chart showing the proportions of IR and QUI cells across each cluster (right). (E) Feature plots showing expression levels of proliferation and senescence‐associated genes. (F) Heatmap of pathway activity across clusters scored via gene set variation analysis, with Z ‐score normalization. (G) UMAP trajectory analysis using Slingshot identifying three senescence progression lineages. Trajectory lines overlaid on UMAP. Cell clusters are colored by pseudotime progression. (H, I) Boxplots of normalized pathway scores for DNA repair (H) and SASP‐related gene sets (I) across clusters (Kruskal–Wallis test, with pairwise Wilcoxon rank‐sum test; adjusted p‐values as shown). (J) Enriched pathways of non‐senescent, intermediate, and fully senescent states in the primary SnCs. p‐values were calculated using a hypergeometric distribution. (K) TradeSeq‐based heatmap of temporally regulated top 500 genes along the pseudotime trajectory for lineage 3 ( p < 0.05), with representative late‐pseudotime genes highlighted.
Article Snippet: Human renal epithelial cells (ATCC; PCS‐400‐011) were cultured in Renal Epithelial Cell Basal Medium (ATCC; PCS‐400‐030) supplemented with the Renal Epithelial Cell Growth Kit (ATCC; PCS‐400‐040), which maintains the cultures at a final serum concentration of 0.5% and incubated at 37°C in 10% CO 2 and 3% O 2 .
Techniques: Single Cell, Irradiation, Expressing, Enzyme-linked Immunosorbent Assay, Two Tailed Test, Activity Assay