Fig. 4: Mammal cross-species comparative analysis identified human HC- and SC-enriched genes.
From: Revealing heterogeneity and damage response in the adult human utricle
a, b UMAP plots of the integrated adult human (967 cells) and mouse (2273 cells) datasets (a) with reannotated cell identities (b). c UMAP plots show known cell markers for each main cluster, genes with darker colours indicating higher expression levels. Transitional epithelial cells (TEC, ISLR+) and SC-like cells (ANKRD1+) remain distinct. d Heatmap displaying the top 10 differential gene expression of main cell clusters in (b); see Supplementary Data 3a for the full list. e–g Volcano plots of differentially expressed genes between mouse and human for hair cell type I (e), type II (f), and supporting cells (g), identified using a two-sided Wilcoxon rank-sum test; the arrowhead indicates the validated HC-human-specific gene SCGB2A1 (e, f); inset in (e) shows its relative expression in the hair cell clusters. Top genes with Padj < 0.05, log2 FC > |2| are displayed, complete lists in Supplementary Data 3c–f. h UMAP plots display the specificity of SCGB2A1 in the hair cell clusters (purple). Relative transcript counts in type II hair cell cluster for SCGB2A1 (magenta), SOX2 (cyan), and their co-expression (white) are shown, 19 is the total number of cells in this cluster. i Fluorescent in situ hybridization validated SCGB2A1 (magenta) mRNA expression in type II hair cells, counterstained with SOX2 (cyan) and DAPI (blue) in a utricle cross-section, n ≥ 3. Insets depict the colocalization of SCGB2A1 with SOX2, a marker for HC type II, in a representative nucleus marked with a white circle in the image. j UMAP plots display human-specific gene SCGB2A1 (magenta) in the hair cell clusters with pan-HC marker MYO7A (green), along with relative transcript counts across these clusters, 87 is the total number of hair cells, as shown in the inset in Fig. 2a; immunofluorescences displaying the protein expression of both markers in whole-mount utricle (63x magnification), n = 3. k Validation of hair cell marker SCGB2A1 (magenta) along with established markers SOX2 (cyan) for hair cell type II and MYO7A (green) in utricle cross-section, n ≥ 3. Representative hair cell types I and II are marked in the sensory epithelium. Scale bars = 25 μm, 2 μm (inset in i).
