Fig. 5: Single-cell transcriptomics analysis uncovers injury-induced spatiotemporal reprogramming of p57+ cells. | Nature Communications

Fig. 5: Single-cell transcriptomics analysis uncovers injury-induced spatiotemporal reprogramming of p57+ cells.

From: Spatiotemporal reprogramming of differentiated cells underlies regeneration and neoplasia in the intestinal epithelium

Fig. 5

a Schematic representation of the experimental procedure for scRNA-seq analysis of normal and regenerating crypt cells from the small intestine of p57-DTR-Venus mice (n = 2 biological replicates for each condition, with two mice for each replicate). b A t-SNE projection for 567 p57-Venus+ (purple) and 1055 p57-Venus‒ (pink) crypt cells from p57-DTR-Venus mice at 3 days after injection of 5-FU as well as for 472 p57-Venus+ (green) and 923 p57-Venus‒ (cyan) crypt cells from normal p57-DTR-Venus mice is shown in the left panel. Unsupervised clusters are color coded and overlaid on the t-SNE map in the right panel. The indicated cellular identity of each cluster is based on the expression of known cell-type-specific genes (Supplementary Fig. 4d, e). c Heat map for the mean expression level of the indicated Clu+ revSC marker genes shown on the t-SNE projection. d Volcano plot showing log2(fold change) and –log10(P value) for differentially expressed genes (DEGs) in the Regenerating 1 group (clusters 4, 10, 17, and 18) relative to all other cell clusters. Points colored red indicate the top 100 genes with regard to –log10(P value). Typical revSC- or fetal intestine-specific genes (orange), adult stomach-specific genes (green), and adult intestine-specific genes (blue) are highlighted. e, f Heat maps for the mean expression level of fetal intestine signature genes (e) or of adult stomach signature genes (f) shown on the t-SNE projection. g, h Heat maps for the abundance of Nkx6-3 (g) and Ascl2 (h) mRNAs shown on the t-SNE projection. FC, fold change. i RT-qPCR analysis of relative mRNA abundance for representative marker genes of revSCs or fetal intestine, or for those of adult stomach, in sorted normal and postinjury p57-Venus+ cells. Data are means + SEM (n = 3 mice). NS (not significant), *P < 0.05, **P < 0.01, ****P < 0.001 (two-tailed Student’s t test). Individual genes for each signature are listed in Supplementary Table 1. Source data are provided as a Source Data file.

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