Figure 4.

scRNA-seq analysis reveals BCR-driven TIL-B activatory signatures, and B lymphocyte functional trait gene markers predict positive survival outcome. A, UMAP visualization according to global GEx of single B lymphocytes pooled from the peripheral blood (1,476 cells) and tumors (1,021 cells) of eight patients (single-cell cohort), colored by relative normalized gene expression levels for CD20 and CD27. B, The detection of differentially expressed genes [DEG; on cells originally annotated by Azizi and colleagues (22) as B cells] demonstrates elevated expression of FOS, JUN, RGS1, and CD69, indicated by fold change (FC; determined using Wilcoxon rank sum test). C, Gene set enrichment analysis of TIL-B relative to circulating B lymphocytes using hallmark gene sets. Red, positive normalized enrichment scores (hallmark expression enhanced in TIL-B). D, Survival analysis in KM Plotter of determined ER⁻HER2⁻/basal surrogate, HER2⁺, luminal A, and luminal B subtype KM plotter surrogate subgroups (KM plotter cohort; ref. 19) for expression of gene signatures positively regulating key B lymphocyte properties (activation, proliferation, and differentiation). Representative genes listed for B lymphocyte proliferation (44 total in set). Signatures from all three functions carry positive prognostic value in the basal-like cancer subtype. Individual genes were evaluated in combination with each other gene (left) and gene set as a whole (right). E, CellPhoneDB (25) was applied to analyze B-cell–T-cell interactions (single-cell cohort). After FDR (FDR < 0.001) correction, communication pathways identified included lymphoid assembly, cytokine signaling, costimulation, T-cell–dependent B-cell activation, and cytotoxic T lymphocyte (CTL) activation. Circle sizes indicate P value, whereas color-coding represents the average expression level of interacting molecule 1 in cluster 1 and interacting molecule 2 in cluster 2. ****, P < 0.0001.