Fig. 6: Single-cell RNA-seq analyses reveal gene signatures in the mutant ECs.

a Uniform Manifold Approximation and Projection (UMAP) for single-cell transcriptomes in ECs from WT, Tfam^ECKO, Cox10^ECKO, and Trx2^ECKO retinas colored accordingly to identified clusters. b Dotplots for specific marker genes in each cluster. c The representative GO pathways for each cluster. False discovery rate (FDR) was adjusted by p.adjust function in R with “method = ”BH”” parameter. d Percentage of cells for each cluster in WT and mutant retinas. Clusters 3, 4, and 5 in the mutant retinas were evidently altered compared to WT are indicated. e Heatmap of the log2 fold changes of the gene expression of the common differentially expressed genes (Common DEGs) (n = 138, adjusted p-value < 0.05) between each mutant and the WT. f–i Heatmaps of the log2 fold changes of specific groups of genes (Transporters, ECM, and TGFβ signaling) from the 138 DEGs. n = 3 mice. Genes were considered significantly differentially expressed when the two-sided Wilcoxon Rank Sum test adjusted p-value, based on Bonferroni correction using the total number of genes in the dataset, was below 0.05. j, k Visualization of p-SMAD2. P15 Tfam^ECKO retinas were subjected to whole mount co-staining with p-SMAD2 and CD31. j Low power images of vascular plexi at top and high-power images at bottom. Arrowheads and arrows indicate p-SMAD2^- normal vessels in WT and p-SMAD2/3⁺ vessels in the mutant retinas, respectively. (k) SMAD2⁺ ECs and p^-SMAD2⁺ microaneurysm were quantified. n = 6 mice per group. Data are means ± SEM. P values are indicated, using unpaired, two-tailed Student’s t test. Source data are provided as a Source Data file.