Fig. 1: Immune dysregulation is established early in the course of WM with disease-specific immune hallmarks.

A Uniform manifold approximation and projection (UMAP) embeddings of myeloid cells (n = 53,172), T cells (n = 95,754), NK cells (n = 24,219), and progenitor cells (n = 36,582). B–D Volcano plot of proportion changes in the BM of patients with AWM (B, n = 25), SMM (C, n = 24), and IgM MGUS (D, n = 6), compared to HD (n = 18). Patients with at least 100 immune cells were included. P-values were computed with two-sided Wilcoxon’s rank-sum test and corrected using the Benjamini-Hochberg approach. E Heatmap of cell type proportions in patients with IgM MGUS (n = 6, light yellow), SWM (n = 19, orange), WM (n = 3, red), and HD (n = 18, blue) (x-axis). Patients with at least 100 immune cells were included. Cell types that changed significantly between patients with AWM and HD, excluding progenitor cells, were visualized (y-axis) and the log₂ fold-change was depicted in a bar (right). F Box plots, violin plots, and scatter plots visualizing the proportion of Tregs in patients with IgM MGUS (n = 6) compared to SWM (n = 19). Violin outline width represents density. Box: 1st quartile, median, 3rd quartile; whiskers: +/− 1.5*interquartile range (IQR). The p-value was computed with two-sided T-test. G Box plots, violin plots, and scatter plots comparing the proportion of activated and IFN-stimulated T and NK cells in the BM microenvironment of HD (n = 18), patients with SMM (n = 24), IgM MGUS (n = 6), and SWM (n = 19). Violin outline width represents density. Box: 1st quartile, median, 3rd quartile; whiskers: +/− 1.5*IQR. P-values were computed with two-sided Wilcoxon’s rank-sum test and corrected with the Benjamini-Hochberg approach. H Scatter plots of genes differentially expressed in patients with AWM compared to HD (x-axis) and in patients with AWM compared to patients with SMM (y-axis) in myeloid cells. Genes whose log₂ fold-change between patients with AWM and HD is higher than that between AWM and SMM are colored in red; genes whose log₂ fold-change is lower are colored in blue; genes discussed in the main text are presented in bold. I UMAP embedding of myeloid cells in HD (n = 15,957), and patients with SMM (n = 5634) and AWM (n = 23,521) colored by MNDA expression levels. J Scatter plots of genes differentially expressed in patients with AWM compared to HD (x-axis) and in AWM compared to SMM (y-axis) in T cells. Genes whose log₂ fold-change between patients with AWM and HD is higher than that between AWM and SMM are colored in red; genes whose log₂ fold-change is lower are colored in blue; genes discussed in the main text are presented in bold. K Box plots, violin plots, and scatter plots of IFN-γ expression measured by ELISPOT in PB T cells from patients with AWM (n = 3), SMM (n = 10), and HD (n = 10) post-stimulation with CERI peptides in vitro compared to DMSO. Each dot represents the mean of two replicates from an individual patient. Violin outline width represents density. Box: 1st quartile, median, 3rd quartile; whiskers: +/− 1.5*IQR. P-values were computed with two-sided Wilcoxon’s rank-sum test and corrected with the Benjamini-Hochberg approach. L Principal component embedding of BM samples from patients with AWM (n = 25), SMM (n = 24), and HD (n = 18). Patients with at least 100 immune cells were included in this analysis. M Confusion matrix visualizing the accuracy of an SVM classifier trained using 5-fold cross-validation on BM samples from patients with AWM (n = 25), SMM (n = 24), and HDs (n = 17). Patients with at least 100 immune cells excluding progenitor cells were included in this analysis. The classifier’s performance in the held-out subsets (n = 66) was visualized. Source data are provided as a Source Data file.