Fig. 5: In-depth characterization of T- and B cells in lymphoid aggregates.

A Schematic overview of the analysis approach applied to the spatial transcriptomics dataset and the subsequent multiplex immunofluorescence (IF). scRNA-seq: single-cell RNA-sequencing. B Proportions of memory B cells, plasmablasts, and unassigned B cells in lymphoid aggregates (LA). C Proportions of naïve-, cytotoxic (CTL), mucosal-associated invariant T (MAIT)-, and potentially dysfunctional CD8⁺ T cells in lymphoid aggregate, mixed, and control regions. D Comparison of the deconvoluted proportions of potentially dysfunctional CD8⁺ T cells in lymphoid aggregate, mixed, and control regions (Kruskal-Wallis followed by Dunn’s multiple comparisons test). In case of multiple p-values, the upper one is associated with the Kruskal-Wallis test, while the lower ones reflects the result of Dunn’s multiple comparison test. E Representative image of the multiplex immunofluorescence analysis of a lymphoid aggregate. The names below each image indicate which antibodies are shown. The green boxes on the lower row are zoomed in on the part of the biopsy in the green box in the upper left image. F The proportion of CD3⁺CD8⁺ T cells that expressed two or three inhibitor receptors (IR⁺⁺/⁺⁺⁺) positive (or not) for granzyme B (GZMB).