Extended Data Fig. 4: Patient-level T cell immunophenotyping and intracellular cytokine production, and Impact of tumor-intrinsic and -extrinsic features on antigen immunogenicity.

a, Per-patient CD4+ and CD8+ composition of vaccine-reactive (IFNγ+) T cells for each vaccine peptide pool and each patient (week 16 after vaccination). n.d., not detectable (the absolute number of IFNγ+ cells were too low for evaluation, or the frequency of IFNγ was not at least 1.5-fold higher than the negative control, HIV gag protein). * The additional negative control, HIV gag, was not available for patient 110 analysis. The results are reported here for reference, but not included in the overall summary. b, Per-patient and per-vaccine pool assessment of cytokine production. For each patient, the median fluorescence intensity (MFI) of (c) PD-1 (d) CD45RO for vaccine-reactive (IFNγ+) CD4+ T cells compared to naïve T cells (CD45RA+CD27+) is shown. e-i, the immunogenicity of each neoantigen-containing vaccine peptide was assessed by stimulation of week 16 PBMCs (in vitro stimulation) and measurement of IFNγ+ by ELISpot. For tumor-intrinsic features, the immunogenicity of each vaccine peptide was examined based on (e) the clonality of the underlying mutation in the tumor and (f) the expression of that gene (measured in transcripts per million; TPM). For tumor-extrinsic features, the immunogenicity of each vaccine peptides was examined based on (g) whether the predicted T cell epitope was inferred as a strong (rank <0.5) or weak (rank <2) HLA class I binder, (h) which HLA class I allele the epitope was predicted to bind to, and (i) whether the neoantigen was derived from an SNV or an indel.

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