Fig. 2: Single-cell Immune Atlas of samples from participants with MM.
a, UMAP embedding of 1,149,344 CD138− BMME cells collected from participants with MM. A total of 106 clusters were observed, spanning five major compartments defined by canonical markers: T and NK cells, B cells and erythroblasts, myeloid cells, erythrocytes and plasma cells. Populations identified as doublets are colored gray. b, Feature plots displaying the normalized gene expression for a selection of lineage-specific markers. UMAPs and per-aliquot cluster compositions to depict the effects of batch correction for major lineages are shown in Extended Data Fig. 2. c, A stacked bar chart displaying the average per-participant cell type composition at baseline. Clusters are colored by their lineage and shaded by subtype. Doublet populations are omitted. d, UMAP of the T lymphocyte and NK compartment. Cells are colored by individual cell type, with shaded boundaries representing regions predominantly containing CD4+ (purple), CD8+ (orange) or NK (green) cells. The color for specific cell types is included in the corresponding dot plots (f–h). An extended dot plot for precise annotation of different T and NK cell subtypes is shown in Extended Data Fig. 3a. UMAPs for only the CD8+ and CD4+ T cells are also shown in Extended Data Fig. 3b,c. e, Feature plots displaying the normalized gene expression per cell for markers to distinguish CD4+, CD8+ and NK cells. f–h, Dot plots displaying the average scaled expression of select marker genes used for precise cluster annotation. Expression is visualized on a red–blue color scale, with the size of each dot corresponding to the percentage expression. Dot plots are split by lineage into NK cells (f), CD8+ T cells (g) and CD4+ T cells (h). The colored triangle next to the cluster name matches the cluster color in the corresponding UMAP (d). Percent.mt refers to the percentage of mitochondrial transcripts. i, UMAP of the myeloid compartment. Cells are shaded by their subtype. Doublet populations are colored gray. j, Dot plot displaying the average scaled expression of select marker genes for precise cluster annotation in the myeloid compartment. Expression is visualized on a red–blue color scale, with the size of each dot corresponding to the percentage expression. The triangle next to the cluster name matches the cluster color in the corresponding UMAP. k, UMAP of the B cell and erythroblast compartment. Cells are colored by their lineage (B cells, cyan; erythrocytes, red; others, dark blue), shaded by subtype. Doublet populations are colored gray. l, Dot plot displaying the average scaled expression of select marker genes used for precise cluster annotation in the B cell and erythroblast compartment. Expression is visualized on a red–blue color scale, with the size of each dot corresponding to the percentage expression.
