Fig. 1: T-LGLL cells show elevated cytotoxicity and exhaustion as compared to healthy hyperexpanded clonotypes.
a Schematic diagram of the study, where the left panel denotes the different cohorts, and the right panel highlights the main findings. b Uniform Manifold Approximation and Projection (UMAP) representation of CD45+ sorted cells from T-LGLL (n = 11) and healthy donor (n = 6) samples profiled with scRNA+TCRαβ-seq. Different colors indicate clusters, and cells with detected TCR are highlighted in red. c UMAP representation of the reclustered T cells and their phenotypes (left). Cells with detected TCR (right) were divided into singletons (TCR detected once), expanded (TCR detected ≥2 times), and hyperexpanded (TCR detected ≥10 times) clonotypes. d Proportion of the cells from hyperexpanded (TCR detected ≥10 times) clonotypes as compared between T-LGLL (n = 11) and healthy (n = 6). The definition of box plot visualization is stated in the Methods section Data visualization. P-value was calculated with two-sided Mann-Whitney test. e Focused UMAP of the cells with hyperexpanded TCRs from panel c without reclustering (left). Distribution of the cells from patients with T-LGLL and healthy controls are shown separately (right). f Differentially expressed genes (Padj < 0.05, calculated with a Bonferroni corrected t-test) between hyperexpanded T-LGLL and healthy clonotypes. Top 30 differentially expressed genes from T-LGLL and top 10 from healthy are labelled. X-axis denotes the average log2 fold-change between the two conditions and Y-axis denotes the Padj-value in a negative log10. Dashed line denotes Padj = 0.05. g The scaled expression of the selected top differentially expressed genes highlighted using the same UMAP representation as in panel e. h Top upregulated GO-pathways (Padj < 0.05, Benjamini-Hochberg corrected Fisher’s one-sided exact test on differentially expressed genes) in T-LGLL clonotypes in comparison to hyperexpanded clonotypes from healthy controls. Colors indicate whether the pathway can be associated to immune function by manual curation. i Protein level expression (mean fluorescence intensity, MFI) of cytotoxic proteins (GMZA, GZMB, and PRF1) from patients with T-LGLL (n = 6) and healthy controls (n = 6) in flow cytometry cohort. P-values were calculated with two-sided Mann-Whitney test. j Protein level expression (log2 fold-change of MFI) of cytokines (TNF and IFNγ) and degranulation markers (CD107a and CD107b) between TCR stimulated and unstimulated conditions. P-values were calculated with two-sided Mann-Whitney test.
