Spatial epigenomic assay in decalcified FFPE tissues. (A) Strategy for analyzing mice paw tissues from a collagen-induced arthritis (CIA) model. (B) Representative mouse paw tissue section revealing the presence of the tibia, talus, navicular, cuneiform, and metatarsus bone. (C) H3K27-acetylation (H3K27ac) spatial epigenomic profiling performed on a mouse paw tissue section deposited on a double-barcoded DNA array (64 × 32 printed probes). (D) Number of total sequenced reads and those recovered at different stages of the primary bioinformatics analysis. (E) Violin plots displaying the number of read counts or promoter regions per SpExel. (F) Digital view of the normalized and adjusted number of read counts associated to the physical location (SpExel) of the tissue section. (G) T-distributed stochastic neighbor embedding dimensionality reduction analysis (t-SNE) displaying the presence of six clusters of SpExel; (H) Clusters’ projection on top of the physical position within the tissue. (I) Cell type gene marker association analysis performed per clusters identified in G. Relevant cell types retrieved enriched per cluster are highlighted (green boxes). (J) Example of gene promoters found enriched in H3K27ac read counts and associated to the aforementioned clusters. Cell type annotations indicated are collected from the CellMarker augmented database used for this analysis. (K) Scheme of the CIA immunization assay performed by Li et al. (2022), allowing the collection of bulk-transcriptomics data from mice paw soft tissue at different time points. (L) Heatmap revealing differential gene expression signatures from the soft-tissue transcriptomes and classified in seven gene coexpression paths. Along the public transcriptome, the detection of H3K27ac overenrichment across the decalcified FFPE mouse paw section (number of overenriched SpExel) is displayed (blue heatmap). (M) Fraction of common genes between those associated to one of the gene coexpression paths in L and those presenting a H3K27ac enrichment in the spatial epigenomic map. Notice that only H3K27ac overenriched promoters (log-fold change [LFC]>1) being present in >1%, >5%, or >10% of total SpExel across the section were considered in this analysis.
