Fig. 5: SpatialTopic captures the main dynamics in tissue architecture of normal and diseased mouse spleen.

A Six topics were identified by SpatialTopic across nine mouse spleen samples representing normal (BALBc 1-3) and different disease stages of lupus: early (MRL/lpr 4–6), intermediate (MRL/lpr 7–8), and late (MRL/lpr 9). B Heatmap shows per-topic cell type composition for the six main topics identified by SpatialTopic. Based on cell type compositions, the first three topics are labeled as red pulp, PALS (periarteriolar lymphoid sheath), and B-follicle in normal mouse spleen tissue, while the other three topics are unique to the disease stages. C Barplots shows the top 10 per-topic cell types for the six main topics identified by SpatialTopic. D Dynamic change in the topic proportion of the six topics during disease progression. Normal spleen samples are primarily characterized by topics 1 (dark blue), 2 (red), and 3 (light green), which reflect red pulp (mixed of B cells, erythroblasts, and F4/80(+) macrophages), PALS (mixed of CD8 T cells and CD4 T cells), and B-follicle (B cell dominated) respectively. There is an increase in Topic 6 (dark green) and depletion of Topic 1 in lupus-affected spleen (MRL/lpr samples), representing much fewer B cells and F4/80(+) macrophages but more granulocytes and erythroblasts in the red pulp regions. Topic 5 (mainly B220(+) DN T cells and CD4(+) T cells, pink) is enriched in lupus-affected spleen tissue at late disease stage. Topic 4 (light blue) is mainly in lupus-affected spleen (MRL/lpr samples) with high expression of CD106 in the stroma. E Dynamic change of key cell types within each topic, identified jointly by FREX(omega = 0.9) and lift metrics (See Supplementary Fig. 6). Source data are provided as a Source Data file.