Fig. 5: Monitoring antigen-specific T-cell responses in CML show expansion of anti-PR1 T cells in CML, in bone marrow, and in dasatinib-treated patients. | Leukemia

Fig. 5: Monitoring antigen-specific T-cell responses in CML show expansion of anti-PR1 T cells in CML, in bone marrow, and in dasatinib-treated patients.

From: Single-cell analysis of immune recognition in chronic myeloid leukemia patients following tyrosine kinase inhibitor discontinuation

Fig. 5

a The same UMAP representation as in Fig. 3A of the pooled RNA profiles of patients with newly diagnosed CML (n = 3) CD34+ (N = 3) and CD34 + CD38- (N = 2) sorted single-cells from the bone-marrow, colored by PR1-expression score, which is a combination of PRTN3 and ELANE genes carrying the PR1 epitope. Clusters were divided into BCR-ABL1 high and low based on the clusters in Fig. 3A. P value was calculated with a two-sided Mann-Whitney. b Clonal structure of anti-PR1 T cell clonotype in individual samples. Each box within a facet is a unique clonotype, where its size corresponds to its proportion in the TCR repertoire. The same clonotypes are colored with the same color. c Network graph showing the similarity of the 231 anti-PR1 specific TCRs. Each node is a unique TCR and an edge between nodes denotes amino-acid-level similarity determined by GLIPH2. d AUROC plot showing the 10-fold cross-validation of the 231 anti-PR1 TCRs used as input for the TCRGP-classifier, where TPRS denotes true positive rates and FPRS denotes false positive rates. The mean of the AUROCs was 0.902. e The proportion of TCRGP predicted antigen-specific TCRs in CML (n = 48), healthy donors’ (n = 786), and in patients with melanoma (n = 46) peripheral blood samples. The samples were subsampled to the same sequencing depth. P-value was calculated with a two-sided Mann-Whitney test. f The proportion and number of TCRGP predicted antigen-specific TCRs in patients with CML in bone marrow (BM, n = 15) and peripheral blood (PB, n = 24). The samples were subsampled to the same sequencing depth. P-values were calculated with a two-sided Mann-Whitney test. g) The proportion of anti-PR1 T cells in patients with CML in diagnosis (n = 14), on TKI (n = 23), off TKI (n = 12), off TKI relapse (n = 7). P-values were calculated with a two-sided Mann-Whitney test. n refers to the number of patients and N to the number of samples where it differs from n. *=P < 0.05, **=P < 0.01, ***=P < 0.001, ****=P < 0.0001.

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