Fig. 1: scRNA-seq reveals cell heterogeneity in PAD.
a, Graphical abstract of the experimental approach used in this study. b, Representative images of H&E-stained sections of gastrocnemius muscle from non-ischemic patients (n = 8) and patients with PAD (n = 11). Scale bars, 50 µm. c,d, Quantification of fiber size in µm2 (c) and minimum feret diameter in µm (d) from b. e, Representative images of gastrocnemius muscle from non-ischemic (n = 8) and PAD (n = 11) stained for the EC marker (CD31, green) and WGA (white). Scale bars, 50 µm. f, Quantification of capillary density from e measured as the number of CD31+ cells per mm2. g, t-SNE plot of cell populations identified from human gastrocnemius muscle, color coded by the identified populations. h, Dot plot of centered log count values from cell-type-specific marker genes. Color and size of the dots indicate the centered log count value and the proportion of cells that express the gene, respectively. i, Stacked bar plots showing cluster percentage from non-ischemic patients (n = 4) and patients with PAD (n = 4), color coded by cluster. Each stack represents mean − s.e.m. j, Heatmap of centered normalized values from top high variable genes (adjusted P < 0.05) in each patient based on pseudobulk analysis between non-ischemic and PAD conditions; color indicates the centered normalized values. k, Bar plots showing normalized enrichment score of significant (adjusted P < 0.05) hallmark pathways (MSigDB) from GSEA analysis on the pseudobulk dataset; color indicates the condition. Each dot represents a single patient in c, d and f. Student’s t-test (two-tailed, unpaired, parametric, NS > 0.05, **P < 0.01) was used in c, d and f. Wald test (as implemented in the DESeq2 package) was used in j. Adaptive multilevel Monte Carlo scheme (as implemented in the fgsea package) was used in k. P = 0.4535 (c), P = 0.4585 (d), P = 0.0012 (f). NK, natural killer; NS, non-significant. Panel a created with BioRender.com.
