Extended Data Fig. 2: Identification of the pre-vaccination endotypes.

(a) Gap statistic for different number of clusters (k). The 95% confidence interval were estimated by 100 Monte Carlo iterations. (b) Boxplot and barplot of age, sex and pre-vaccination antibody titers as a function of the inflammatory endotypes. For each boxplot, the vertical line indicates the median, the box indicates the interquartile range, and the whiskers indicate 1.5 times the interquartile range. (c) Lineplot showing the differences in expression of inflammatory pathways between 7 days before vaccination compared to just before vaccination. (d) Monocytes/dendritic cell markers expression in blood of pre-vaccinated individuals. PBMCs from 20 healthy participants profiled by CITE-seq¹⁰. The heatmap shows the average expression of monocyte and dendritic cell markers identified in bulk meta-analysis associated with the high inflammatory state, scale shown is the z-score of the gene across protein-based cell subsets. (e) Scatter plot showing inferred frequencies of immune cells estimate by CIBERSORT as a function of cell counts measured by flow cytometry (FCM) for three separate study. Linear fit (lines) is drawn for each study. (f) Frequencies of immune cells, estimated by deconvolution, in the three pre-vaccination states. For each boxplot, the vertical line indicates the median, the box indicates the interquartile range, and the whiskers indicate 1.5 times the interquartile range. Wilcoxon rank-sum test between two endotypes: p-values less than 0.05 are flagged with one star (*), p-values less than 0.01 are flagged with 2 stars (**), and p-values less than 0.001 are flagged with three stars (***).