Figure 3.

scRNA sequencing reveals heterogeneous CD4⁺ T-cell subsets in leukemic mice. (A) CD44⁺CD4⁺ T cells from the indicated treatment arms were sorted for scRNA and scTCR sequencing (n = 4 mice/arm). Results of a single scRNAseq experiment. All cells were harvested and processed for scRNAseq simultaneously to avoid batch effects in downstream processing. Leukemia establishment and subsequent treatments were offset, relative to each other, to allow for this. (B) UMAP plots showing the subsets of CD4⁺ T cells identified. (C) UMAP feature plots showing the expression of key genes in the different clusters of CD4⁺ T cells. (D) Normalized CITE-Seq antibody expression of the indicated exhaustion markers on CD4⁺ T cells.