Fig. 6: Expanded memory CD4⁺ T cell clones in malaria protected patients exhibit a cytolytic gene expression signature.

(A) Frequency of each expanded memory CD4⁺ T cell clone expressing an identical TCR clonotype among all memory CD4⁺ T cells in patient 1 (n=10, Orange), patient 2 (n=6, Green), patient 3 (n=9, Blue), as defined by single-cell TCR-seq. (B) Expanded memory CD4⁺ T cell clones (at least 10 cells sequenced with the exact same TCRα and TCRβ chains) in each of the 3 participants, highlighted on the concatenated UMAP visualization shown in Fig. 5A. (C) Pie-chart of expanded memory CD4⁺ T cell clone proportions across distinct transcriptional clusters defined in Fig. 5A and across the 3 protected participants. (D) Distribution of individual clones with identical TCR clonotype across memory CD4⁺ T cell cluster 1, 2, 3 and 4 (as defined in Fig. 5) and across the 3 protected participants. (E) Pseudotime analysis of the memory CD4⁺ T cell subsets of Fig. 5A. (F) Cumulative proportion of expanded memory CD4⁺ T cell clones expressing indicated gene-encoding transcripts across the 3 participants. (G) Proportion of cells that express ZEB2 or (Granzyme B (GZMB) transcripts among all memory CD4⁺ T cells or only among expanded T cell clones (n=3). Pool of three independent experiments represented as individual data and means ± SEM (A, F, G).