Extended Data Fig. 12: Transcriptional correlates of neutralizing antibody and T cell responses.

a, BTMs (day 22 relative to day 21) associated with the neutralizing antibody or CD8 IFNγ T cell response to BNT162b2. GSEA was run using BTMs on gene lists ranked by correlation with either day-42 neutralizing antibody titres or day-28 antigen-specific CD8⁺IFNγ⁺ T cell frequencies. Modules shown are those with NES > 2 and FDR < 0.05. b, Correlation of genes in M75, an antiviral BTM, on day 22 with the day-42 neutralizing antibody response (top) or day-28 antigen-specific CD8⁺IFNγ⁺ T cell frequencies (bottom). Colour represents two-sided Pearson correlation coefficient. Each edge (grey line) represents a co-expression relationship, as previously described¹⁸. c, BTMs correlated with cross-neutralization index, ratio of B.1.351:WA1 neutralizing antibody titres, analysed as in a. Modules shown are those with NES > 2 and FDR < 0.05. d, Frequency of classical monocytes (Lin⁻HLA-DR⁺CD14⁺CD16⁻ cells) in whole-blood samples analysed by CyTOF. e, f, Scatter plots of two-sided Spearman’s correlation between cross-neutralization index and peak (day 23) classical monocyte frequency (e) or a gene score created in the bulk RNA-sequencing data using the cluster-defining genes of the classical monocyte cluster, C3, in CITE-seq (f). The error bands represent 95% confidence limits. Each dot represents an individual in all plots. Blue and red colour denote female and male participants, respectively in d–f. Boxes show median and 25th–75th percentiles, and whiskers show the range in d.