Extended Data Fig. 8: Distinct B and plasma cell features.
a, Box plots present the abundance of cells in the nine B and plasma cell subclusters split by patients (n = 12) with a pathological complete response (pCR) and pathological non-complete response (non-pCR) and clinical response (CR, PR and SD). Data are presented as mean values +/- SEM. Brackets and numbers indicate the p-value of each cell population (cp. Fig. 3) (two-sided, Wilcoxon signed sum rank test; statistical significance determined with p < 0.05). Each box extends from the 25th (Q1, lower bound of box) to the 75th (Q3, upper bound of box) percentile, the horizontal line in the center of the box represents the median value (Q2). The whiskers extend to the 5th (min, lower bound) and the 95th percentile (max, upper bound). Dots outside the whiskers indicate outliers. b, Feature and violin plots showing the expression of selected genes in B and plasma cells: antigen presenting (Ag) (major histocompatibility complex, class II, DR alpha (HLA-DRA)), cytotoxic (Granzyme K (GZMK)) and memory (CD27) phenotypes and transcription factor of X-box binding protein 1 (XBP1) (n = 12). The violin plots illustrate the distribution of cells of each cluster. Data are presented as mean values +/- SEM. The lower and upper bound represents the 5th (min) and the 95th (max) percentiles, respectively. Dots outside the plots indicate individual outlier values. The box within each violin extends from the 25th (Q1, lower bound of the box) to the 75th percentile (Q3, upper bound of the box), with the horizontal line within the box marking the median value (Q2). c, Feature and violin plots displaying the gene expression of selected genes in B and plasma cells. B cells show cytotoxic Perforin 1 (PRF1) features, but no immunosuppressive phenotypes such as Interleukin 10 (IL10), Transforming growth factor beta 1 (TGFB1) (n = 12). Data are presented as mean values +/- SEM. The violin plots illustrate the distribution of cells of each cluster. The lower and upper bound of the violin plot represents the 5th (min) and the 95th (max) percentiles, respectively. Dots outside the plots indicate individual outlier values. The box within each violin extends from the 25th (Q1, lower bound of the box) to the 75th percentile (Q3, upper bound of the box), with the horizontal line within the box marking the median value (Q2).
