Fig. 5: PBMC collected at baseline, and after 1, 2 and 3 vaccinations from 20 patients for which we had sufficient cells to perform ex vivo analysis were stained with a combined immunophenotyping/dextramer panel of 29 markers (see supplementary table II).

High-dimensional single cell data analysis of the stained PBMC were performed by opt-distributed Stochastic Neighbor Embedding (optSNE) and FLOWSOM using OMIQ. a optSNE plot visualizing cluster partitions by FLOWSOM for all patient samples. b–i Frequencies of populations 3 (pop3 CD8⁺ Tcm (b)) pop5 (CD8⁺ Tn, (c) pop7 (CD4⁺Tn, (d) pop11 (DN Tn, (e) pop22 (CD4⁺ KLRG1^- Tcm, (f) pop18A (monocytes, (g) pop 18B (mMDSC, (h) and total monocytes (i) at baseline is shown as percentage of CD45⁺ cells for patients in relation to the strength of the LRPAP1_{21-30S_V}-specific CD8⁺T-cell response (left two panels) or LRPAP1_7-30V-specific (TEIPP24) CD4⁺ T-cell response (right two panels), respectively. Patients were grouped into low or high T-cell responses based on the median response (i.e. <median (gold) and > median (purple)) or based on tertiles (i.e. lowest 33% (low; red), middle 33% (intermediate; blue) or highest 33% (high; green)). Data are represented as scatter plots with bars indicating mean and dots representing individual data points (b–i). Statistical analysis by two-tailed, unpaired non-parametric Mann-Whitney U test (2 groups) or unpaired non-parametric Kruskal-Wallis with Dunn’s multiple comparisons test (3 groups). Source data are provided as a Source Data file.