Fig. 3: Identification of conserved T_FH and T_FR signatures.

a–j, Bulk RNA-seq of sorted CD4⁺CD44⁺PD-1⁺CXCR5⁺FoxP3-RFP⁻IL-21–GFP⁺ T_FH, CD4⁺CD44⁺PD-1⁺CXCR5⁺FoxP3-RFP⁻IL-21–GFP⁻ T_FH, CD4⁺CD44⁺PD-1⁺CXCR5⁺FoxP3-RFP⁺IL-21–GFP⁺ T_FR, and CD4⁺CD44⁺PD-1⁻CXCR5⁻FoxP3-RFP⁻IL-21–GFP⁻ T_eff cells from the draining lymph nodes of the mice infected with pathogens described in Fig. 1. MA plot visualizing the log fold change (FC) in the mean expression of genes expressed differentially between the T_FH and T_eff populations for the five infections (a). UpSet plot showing intersections of genes differentially expressed between the T_FH and T_eff populations for each infection (b). Common DE genes across three or more infections were used to derive the core T_FH signature. False discovery rate (FDR) < 0.05. Heatmap of core T_FH signature genes (row-based z scores of normalized log₂ counts per million) for cytokine and cell surface receptor genes (c) and transcriptional regulator genes (d). GSEA of differentially expressed genes in T_FH (T_FH versus T_eff comparison), T_FR (T_FR versus T_eff), and T_eff cells (T_eff versus T_FH) for all infections (e,f). NES of T_FH, non-T_FH, GC T_FH, GC B, human T_FH and cancer-associated T_FH cell programs (e) and precursors of exhausted (T_PEX), exhausted progenitor (T_PROG) and long-term hematopoietic stem cell (HSC-LT) gene programs in the T_FH, T_FR and T_eff populations (f). The NES score represents the enrichment of genes (sets) relative to each comparison, correcting for multiple testing. UpSet plot of the T_FR signature showing intersections of upregulated genes expressed differentially between the T_FR versus T_FH cell contrast population and the T_FR versus T_eff cell contrast population for five infections (g). FDR < 0.05. Heatmap of T_FR signature genes shared across contrasts (T_FR versus T_FH and T_FR versus T_eff) (row-based z score of normalized log₂ counts per million) for cytokine and cell surface receptor genes (h) and transcriptional regulator genes (i). Bubble plot of Bcl-6 network transcriptional regulator genes in the T_FH core showing log₂FC differences in the T_FH (T_FH versus T_eff contrast) and T_FR (T_FR versus T_eff contrast) populations (j). The size of the bubble represents the −log₁₀(FDR), and the color indicates the log₂FC compared to T_eff cells. The colored bar indicates genes present in the T_FH core and Bcl-6 gene sets from Extended Data Fig. 5g. Novel genes proposed to be independent of the Bcl-6 network are indicated with gray bars. The data represent independent samples of 2–3 per cell type per infection.

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