Fig. 2: T-LGLL clones are phenotypically heterogeneous and wild-type STAT3 clones are more cytotoxic than mutated STAT3 clones.
a Clonal expansion of clonotypes in T-LGLL (n = 11) and one representative healthy control. Each box denotes a unique T cell clonotype in a sample as detected with scTCRαβ-seq and the size of the box corresponds to its frequency in the repertoire occupancy. b UMAP representation of the transcriptomes of the selected 18 T-LGLL clonotypes highlighted in panel a from 11 T-LGLL samples (n = 9 patients). c Scaled expression of selected differentially expressed genes between T-LGLL clusters highlighted in the same UMAP representation as in panel b. d Heatmap showing scaled expression of differentially expressed genes (Padj < 0.05, calculated with Bonferroni corrected two-sided t-test) between T-LGLL phenotype clusters. Cluster (cl) numbers referring to panel b are marked on right side of the heatmap. e Proportion of the different patient-specific T-LGLL clonotypes in different clusters. Each bar represents an individual T-LGLL clone. f The imputed and detected STAT3 mutation status presented in the UMAP representation. The inferred STAT3 mutation status was obtained clonotype-wise as in panel a (shown in the panel on the left) and the detected STAT3 mutation status was retrieved from the scRNA-seq data using a variant detection tool Vartrix (shown in the panel on the right). g Differentially expressed genes between (Padj < 0.05, calculated with Bonferroni corrected two-sided t-test) the mutated and wild-type STAT3 T-LGLL clones. Top 20 genes from each condition are labeled. X-axis denotes the average log2 fold-change between the two conditions and Y-axis denotes the Padj-value in a negative log10 transformed scale. h Top upregulated GO-pathways (Padj < 0.05, Benjamini-Hochberg corrected Fisher’s one-sided exact test on differentially expressed genes) in wild-type STAT3 in comparison to mutated STAT3 clonotypes. i Cytotoxicity score of individual cells in wild-type STAT3 clones in comparison to mutated STAT3 clones in scRNA-seq. P-value was calculated with two-sided Mann-Whitney test. j Principal component analysis (PCA) plot from bulk-RNA-sequencing data from 10 mutated and 5 wild-type STAT3 T-LGLL patients’ and 5 healthy donors’ CD8+-sorted T cells. k Cytotoxicity score of the wild-type STAT3 patients (n = 5) as compared to the STAT3 mutated (n = 10) patients’ scores in the bulk-RNA-seq validation cohort. P-value was calculated with two-sided Kruskal-Wallis test.
