Extended Data Fig. 8: Flow cytometry analysis on patient PBMCs compared by S.copri levels and analysis of cytokine/chemokines levels in patient plasma.

A, Frequency of TC1 subpopulations in the PBMCs of S. copri high (n = 8) and S. copri low (n = 5) patients. B, Frequency and memory (CD45RA⁻CD45RO⁺) and naïve (CD45RA⁺CD45RO⁻) conventional CD4⁺ cells and CD8⁺ cells between S.copri high (n = 8) and S. copri low patients (n = 5). C, Flow cytometry representation of unsupervised t-SNE plots on monocytes. DNAM1⁺ cells at each sampling time point are represented overlaid in blue. D, Frequency of DNAM1⁺ cells in classical, intermediate, and non-classical monocytes in S.copri high and S. copri low patients between S. copri high (n = 8) and S. copri low patients (n = 5). E, Frequency of CD163 and F, CD33 expression on intermediate monocytes, and G, frequency of CD56⁺⁺CD16⁻ cells between S. copri high (n = 8) and S. copri low patients (n = 5). Quantification of cytokines and chemokines in patient plasma, compared by the H, presence (n = 10) or absence (n = 10) of grade 3 irAEs, I, response (n = 9 non-responder, n = 9 responders), and J, S. copri levels (n = 8 high, n = 5 low). Boxplot bounds represent the 25th and 75th percentiles, with whiskers representing the minimum and maximum values and the central line representing the median. Statistical analysis was conducted using a two-sided unpaired Wilcoxon rank-sum test for comparisons at T5 or the two-sided Wilcoxon matched-pairs signed-rank test with Benjamini-Hochberg correction for multiple within-group comparisons; *p < 0.05.