Fig. 5: T cell cytotoxicity comparisons of select CMV-specific clonotypes from Dextramer staining and ATLAS-seq.

A Target cell killing assays: Activated TCR-transduced PBMCs were cocultured for 72 h with target CMV⁺ GFP⁺ PC3 cells (GFP⁺ PC3 cells expressing HLA-A2 and CMV pp65) or unrelated neuroblastoma SK-N-AS cells (negative for CMV pp65 peptide). Relative viability of CMV⁺ PC3 cells is measured by GFP fluorescence using the Incucyte system. Each dot: mean of n = 3 independent biological replicates. B Images of GFP-expressing CMV⁺ PC3 cells after 72-h coculturing with TCR A2, A3, A14, DL and D10 transduced PBMCs or un-transduced (UT) PBMCs. CMV⁺ GFP⁺ PC3 target cells are shown in green. Scale bar: 400μm. C Box plots showing comparison of target killing efficiencies (72-h time point) of select CMV-specific clonotypes from Dextramer staining and ATLAS-seq. Box plots feature median (center line), first and third quantiles (box boundaries), and minimum and maximum excluding outlier data points beyond 1.5x interquartile range from the first and third quartiles (whiskers). Each data point represents the target killing efficiency of a TCR-transduced PBMC sample (n = 11 for Dextramer staining clonotypes and n = 8 for ATLAS-seq clonotypes). P-values were calculated by 2-tailed Mann–Whitney U test. **p ≤ 0.01, ***p ≤ 0.001. D Secreted IFNγ and TNF concentrations after the 72-h cell killing assay. Conditioned media in the same wells were measured by IFNγ and TNF ELISA (mean ± s.d. of n = 3 independent biological replicates). Source data are provided as a Source Data file.