Fig. 4: Spatial transcriptomic analysis of CD68+ myeloid cells in BRL lesion rims, mixed-lesion rims and active lesion centers compared to NAWM.
a, PCA of the normalized expression data for the three lesion types (active center, BRL rim, mixed rim). b, Venn diagram of DEGs (each lesion type compared to the respective NAWM) of all three lesion types. c, Volcano plot of DEGs (BRL rim over NAWM) that are exclusively upregulated in BRLs but not in other lesion types. The blue dots indicate genes with significant differential enrichment between conditions (Padj < 0.05). Relevant genes of interest are annotated. All comparisons used moderated two-sided t-statistics with Benjamini–Hochberg adjustments for multiple comparisons; non-exclusive, overlapping DEGs were removed. d, GSEA based on DEGs (lesional CD68+ cells over corresponding NAWM) that are shared between all three lesion types, with GO Biological Processes (BP) gene sets as signatures; clusterProfiler’s implementation of a one-sided Fisher’s exact test was used for the enrichment analysis, with Benjamini–Hochberg correction for multiple comparisons. Only significantly enriched terms of biological interest were selected for dot plot visualization. The full set of significant GO terms is displayed in Supplementary Table 5. The colors indicate Padj values; the dot size depicts the geneRatio (the percentage of genes with core enrichment relative to the size of the full gene set). e, GSEA based on DEGs (lesional CD68+ cells over corresponding NAWM) uniquely overexpressed in BRLs, with GO BP gene sets as signatures; clusterProfiler’s implementation of a one-sided Fisher’s exact test was used for the enrichment analysis, with Benjamini–Hochberg correction for multiple comparisons. Only significantly enriched terms of biological interest were selected for dot plot visualization; the full set of significant GO terms is displayed in our Supplementary Table 5. The colors indicate Padj values; the dot size depicts the geneRatio. f,g, GSEA plots based on the GSEA GO term analysis depicted in d,e, respectively; the relevant gene sets were grouped according to relevant functions and genes with core enrichment were combined to form the representative signatures. All P values were calculated with the clusterProfiler GSEA permutation test and adjusted for multiple hypothesis testing with the Benjamini–Hochberg method. MHC, major histocompatibility complex.
