Fig. 3.

Compositional and clonal analysis of B lymphocytes following CAR-T cell therapy. (A) UMAP plots showing re-clustering of B cells colored by six subsets, annotated as immature, naive, non-switched memory (NS mem), switched memory (Sw mem), double negative (DN) B cells, and plasmablasts and plasma cells (PB/PCs). UMAP plot of B cell subsets colored by clone size (number of cells belonging to a specific clone type), showing significant clonal expansion. (B) Dot plot showing cell clusters denoted by gene expression of known markers. (C) UMAP plots showing cell distribution of B cells integrated from the patient with IMNM at baseline, at 1 mo, at 3 mo, at 6 mo, at 9 mo, at 12 mo, at 15 mo, and at 18 mo post-infusion. (D) Individual repertories from B cells integrated from the patient with IMNM at baseline, at 1 mo, at 3 mo, at 6 mo, at 9 mo, at 12 mo, at 15 mo, and at 18 mo post-infusion. For the inner circle, colored wedges represent expanded clones and gray area represents singleton sequence. For the outer circle, colored edges represent immunoglobulin classes. (E) Scatterplot comparing BCR clone frequencies between B cells integrated from the patient with IMNM at baseline and at 12 mo/15 mo/18 mo, respectively. (F) Volcano plot showing differential expression analysis comparing B cells integrated from the patient with IMNM at baseline to those at 18 mo post-infusion. (G) GSEA analysis showing significantly changed pathways comparing B cells integrated from the patient with IMNM at baseline to those at 18 mo post-infusion. (H) Dot plots of genes related to adaptive immune response, B cell activation, B cell-mediated immunity, and Ig production of B cells integrated from the patient with IMNM at baseline, at 1 mo, at 3 mo, at 6 mo, at 9 mo, at 12 mo, at 15 mo, and at 18 mo post-infusion.