Fig. 4: ALFQA and alum-induced cytokine and chemokine milieu.

a, b Principal component analysis (PCA) of absolute levels (pg/ml) of cytokines, chemokines and other proteins measured in plasma collected at (a) week 12 + 24 h and b week 13 from alum (n = 17 at week 12 + 24 h and n = 12 at week 13) and ALFQA (n = 12 at both timepoints) animals. Arrows indicate the top drivers (loadings) for PC1 and PC2. c, d Volcano plots summarizing two-tailed Mann–Whitney differences in the plasma proteome between alum and ALFQA groups at c week 12 + 24 hs and d week 13 from Alum (n = 17 at week 12 + 24 h and n = 12 at week 13) and ALFQA (n = 12 at both timepoints) animals. The x-axis indicates the difference between the medians of each target level for each group, while the y-axis indicates the −log₁₀ (p values) of the ALFQA vs alum comparisons. Unadjusted p values are reported. The x-axis values are calculated as log₁₀ (absolute value (median of outer differences)) * sign of median of outer differences, as described in the methods. Only targets significantly different between the groups (p < 0.05) are labeled. Targets higher in the ALFQA group are marked in red, whereas targets higher in the Alum group are marked in blue. e Alluvial diagram summarizing the pattern of two-tailed Mann–Whitney significance (p < 0.05) over time. Targets that differ between the groups at baseline have been omitted. At each timepoint, targets are colored according to their direction of Mann–Whitney difference p < 0.05. Alluvial flow between the timepoints connect the same target at week 12 + 24 h and week 13 and are colored according to their pattern at week 12 + 24 h. (f–k) Absolute levels (pg/ml) of C-C motif chemokine ligand 2 (CCL2) at f week 12 + 24 h and i week 13, Interleukin 18 (IL-18) at g week 12 + 24 h and h week 13, and Lymphotoxin-alpha (LTA) at j week 12 + 24 h and k week 13, in plasma of Alum (n = 17 at week 12 + 24 h and n = 12 at week 13) and ALFQA (n = 12 at both timepoints). Comparisons: f–k two-tailed Mann–Whitney U-test with median. In panels a, b and f–k, SIV-immunized alum and ALFQA animals are depicted as black circles filled in blue and red, respectively. Source data are provided as a Source Data file.