Fig. 1

Phenotypic characterization of CD45 + cells in the cohort. a Overview of the study—Patient cohort and study samples. b Uniform Manifold Approximation and Projection (UMAP) representation and unsupervised clustering of all cells from the IMA samples (n = 3) profiled with scRNA + TCRαβ-seq. c Left: UMAP representation of the cells from ST and PB in each cluster as identified in our study. Middle: UMAP representation of the cells as per sorting strategy in each cluster as identified in our study. Right: UMAP representation of the cells representing different disease types. d Dot plot with scaled expression of top 8 DE genes between IMA phenotype clusters (Padj < 0.05, calculated as Bonferroni corrected Wilcoxon test). e Number of DE genes both upregulated and downregulated between cells from ST and PB for each cluster (Padj < 0.05, |Log2FC| > 0.5 calculated with Bonferroni corrected two-sided t-test). f Pathway enrichment analysis with GO biological processes (Hypergeometric testing). g Left: Focused UMAP of all cells with TCR from panel 1b. Right: Proportion of the cells identified as Hyperexpanded (> 9), Expanded (> 1) and Singlet as identified in the UMAP. h Cells detected as expanded versus cells detected as singlets in ST and PB in our data shows that expanded cells are enriched in ST (Padj < 0.05, Benjamini–Hochberg corrected Fisher’s one-sided exact test)