Extended Data Fig. 6: β-cell heterogeneity in healthy mice.
From: Targeted pharmacological therapy restores β-cell function for diabetes remission
a, Endocrine cell annotation is based on the hormone expression of insulin (Ins), glucagon (Gcg), somatostatin (Sst), and pancreatic polypeptide (PP). b, UMAP plot showing all endocrine cells (7578 cells in total) from healthy mice. The cell number and proportion of each endocrine cluster is indicated. c, Redefined clustering of the Ins+ β cells revealed two main β-cell subpopulations. d, Expression changes of genes from selected pathways along a pseudotime trajectory from β2- to β1 cells. β1-cells were downsampled to 1000 cells for better visualisation. e, GO term and KEGG pathway enrichment analysis of up- (log(fold change) > 0.25) and downregulated (log(fold change) < -0.25) genes in β2- (278 cells) compared to β1 cells (5380 cells). Cells were pooled from n = 3 mice. Representative terms from Supplementary table 2 are depicted. We used limma-trend to find differentially expressed genes (M&M). Gene enrichment was done with EnrichR using Fisher’s exact test to identify regulated ontologies/pathways (M&M). f, Violin plots showing the distribution of the expression of proliferation and β-cell maturation genes suggesting an immature phenotype of cycling β-cells. Accordingly, 16/403 of the β2 cells, whereas only 2/5319 of the mature β1 cells were classified as cycling (M&M). Cells were pooled from n = 3 mice. Violin shows the distribution as a kernel density estimate fit. Points in violin interior show individual data points. Boxplot in violin interior shows median, quartile and whisker values. g, Measured proportion and expected doublet frequency of polyhormonal cell clusters. Expected doublet frequency is calculated given a doublet rate of 10% (M&M). h, Boxplot displaying the doublet score distribution of mono- and polyhormonal cell clusters. A high score indicates a high doublet probability. Cells were pooled from n = 3 mice. Boxplot shows the quartile values and extreme values. Whiskers extend to 1.5 IQRs of the lower and upper quartile. Outliers are displayed individually.
