Fig. 4

Neoantigen-specific T cells in atezolizumab responders are skewed towards a late differentiated CMV-like phenotype. a PCA of all neoantigen-and virus-specific CD8+ T cells hits identified in this study. PCA is based on phenotypic profiling (percent of antigen-specific CD8+ T cells positive for the markers shown in Fig. 3a). The distribution pattern of all hits across the first two principal components allows for an annotation of three distinct clusters. b The majority of the neoantigen-specific T cells from the responder group are located within Cluster 1 and 3, whereas most of the neoantigen-specific T cells from non-responder patients are detected in Cluster 2. CMV-specific T cells were mostly found in Cluster 1, EBV- and influenza-specific T cells mapped within Cluster 2 and 3. Labels are according to patient response and virus-specificity. c Pie chart summarizing the data shown in 4B: top, number of neoantigen hits; bottom, number of viral hits for each PCA cluster. d Graphical representation of the most differentially expressed markers of all virus-specific CD8+ T cells in the three PCA clusters; Bubble size is proportional to mean frequencies of all virus-specific CD8+ T cells positive for the indicated marker in any given cluster