Altered Vγ9Vδ2-T–cell transcriptional profile in CLL patients. RNA sequencing was performed on paired Vγ9Vδ2-T cells from 4 CLL patients and 4 HCs, directly after thawing and after autologous moDC-based expansion. (A) Multidimensional scaling plot of gene-expression data. Each circle represents an individual donor. (B) Number of genes differentially expressed (false discovery rate < 0.05) in the indicated comparisons. (C) Gene set enrichment analysis of CLL vs HC Vγ9Vδ2-T cells, before (x-axis) and after (y-axis) ex vivo expansion. Each circle represents a gene set [derived from the Hallmark (H) or BioCarta (B) gene sets from the Molecular Signatures Database or self-generated gene sets]. Gene sets differentially expressed (P < .01) before, but not after (P > .1), expansion are highlighted in orange and purple. (D) Gene set enrichment analysis of CLL vs HC Vγ9Vδ2-T cells directly prior to ex vivo expansion. The red dashed line indicates P = .05. Also shown is whether each gene set is up- or downregulated in CLL in comparison with HC Vγ9Vδ2-T cells. (E-F) The gene expression of CLL Vγ9Vδ2-T cells was compared with HC Vγ9Vδ2-T cells. Each circle represents an individual gene. Genes related to synapse and adhesion (E) or inhibitory and exhaustion (F) molecules are highlighted in red. Genes with a P value < .05 and/or a fold change ≤ −1.75 or ≥ 1.75 are annotated. FC, fold change; NK, natural killer cell.