Extended Data Fig. 8: Human lymphoid tissue T_FH phenotypes identified by core and pathogen-specific T_FH signatures.

a, Gating strategy to sort CD3⁺CD4⁺CD45RA⁻CD45RO⁺CXCR5⁺CD27⁺ human tonsillar T_FH cells from three healthy adult donors for paired scRNA-seq and CITE-seq. b, Overlay of mean ranked scores of core T_FH and T_EFF core signatures onto UMAP clusters. Mean of the ‘TotalScore’ from singscore::simpleScore function collated for each cluster. c, Distribution of T_FH cells across 11 clusters by donor. d, Proportion of pathogen-specific T_FH signatures overlapping with human cluster genes expressed differentially (one cluster vs. all other clusters). e, Overlay of mean ranked scores of each T_EFF cell pathogen-specific signature onto UMAP clusters. Mean of the ‘TotalScore’ from singscore::simpleScore function collated for each cluster. T_EFF cell pathogen-specific upregulated signature genes used. f, Gene set Enrichment and vissE analyses for the comparison Cluster 1 vs. Cluster 2. Top gene sets clusters of interest shown as barplot of DE gene counts with corresponding gene statistics (FDR as color shade) from the DE analysis. GSEA was performed using Hallmarks c2 (‘CP:REACTOME’, ‘CP:PID’, ‘CP:BIOCARTA’,‘CP:KEGG’) and c5 (‘GO:BP’,‘GO:MF’) collections from the MsigDB using a two-tailed approach correcting for multiple testing with false discovery rate (FDR) adjusted p ≤ 0.05. g, Ranked score of pathogen-specific signatures onto human dataset T_FH cells from donors in SARS-CoV-2 vaccine (n = 5), influenza vaccine (n = 1), malaria infection (adult n = 3, child n = 3), peanut allergy (n = 3), asthma (n = 4) and autoimmune contexts (healthy donor n = 6, systemic lupus erythematosus n = 8). Data are presented as mean values ± SEMs. h, Visium spatial tonsil data¹¹³ displaying ranked score of core T_FH signature. i, Xenium spatial human lymph node data displaying ranked score of core T_FH signature. j, Visium spatial tonsil data¹¹³ displaying ranked score of pathogen-specific signatures onto germinal centers highlighted by core T_FH signature.

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