Fig. 2: Multiomics spatial analysis enhances niche characterization in tonsil tissues.

a, Tonsil tissue sample with cells color-coded by cell type. b, Niche characterization results based on cellular composition (left), local average protein expression (middle), and local average RNA expression (right, enabled by the fusion algorithm MaxFuse). We observed enhanced spatial delineation of neighborhoods, labeled as neighborhoods 0 (blue), 1 (orange) and 3 (red) in the middle and right panels, that consistently emerge within the germinal centers, which are identified only as neighborhood 1 (orange) in the left panel. c, A zoom-in visualization at one of the germinal centers (circled by dotted lines). The entropy values (calculated as the Shannon diversity index: \(H=-\sum p(x)\log p(x)\), where p(x) is the proportion of cells in each neighborhood) quantify the granularity of neighborhood characterization, with higher values indicating increased delineation. Primarily composed of B cells, as shown in subpanel i, this germinal center corresponds to the neighborhood labeled as 1 and colored orange in subpanel ii. MESA reveals that it can be subdivided into more granular neighborhoods, colored orange, red and blue in subpanels iii and iv, and this pattern emerges consistently across multiple germinal centers. d, Heatmap visualizing cellular composition versus protein and mRNA expression levels. The red box highlights that, despite comparable cellular makeups in neighborhoods 0, 1 and 3, notable variances exist in protein and mRNA expression profiles. The values are normalized to 0 and 1 for visualization. e, DE and GSEA were conducted on the newly emerged neighborhoods (0 and 3), revealing distinct B cell developmental states within the germinal center’s dark and light zones. DE analysis was performed using two-sided exact test with P values adjusted for multiple testing using the Benjamini–Hochberg (BH) procedure. The adjusted P value threshold was set at 0.05, and the effect size (log fold-change) threshold at 0.1. In the GSEA plot, the pathways colored blue are significantly enriched in neighborhood 0, red in neighborhood 3 and gray indicates no statistical significance after false delivery rate (FDR) correction. GSEA was conducted using normalized enrichment scores with permutation-based two-sided tests and P values adjusted using the BH procedure. The adjusted P value threshold was set at 0.05.