Fig. 2: Detection of immunogenic TSAs.
a, Explored antigens in CESC-1: ‘mutations’, actionable SMs; ‘predicted neo’ and ‘predicted viral’, predicted rank ≤ 2%; ‘MS neo’, MS-identified neoantigens. b, Ranking of top 50 HLA-I neoantigens tested for immunogenicity in CESC-1. Initial selection with rule-based prioritization compared to ordering of the same peptides with the ML tool (‘selection’) and to the ML, pTuneos and pVACseq prioritizations that include untested peptides (white, ‘top 50’). c, Endogenous and synthetic peptide spectral comparison of immunogenic neoantigens RPL18 p.Met53Ile and USP7 p.Glu1095Gln (cosine similarities of 0.950104 and 0.660189, respectively; mutant amino acids, red; y-ion fragments, orange; b-ion fragments, blue). d, EBV gene expression in NPC-1 through EBV cycle phases. e, IFNγ SFU per 106 cells (mean ± s.d.) from preREP and REP TILs rechallenged with EVB peptides in NCP-1 (CD8, cyan; CD4, brown). HLA alleles and predicted HLA restrictions are presented. IEDB annotations: antigen absent, white; antigen present, gray; antigen present and immunogenic on any NPC-1 HLAs, black. The EBV phase denotes the gene expression across the EBV cycle. f, Peptides derived from expressed HC-TSAs in MEL-1: predicted (rank ≤ 0.5%), blue; MS-identified, orange; immunogenic validated by IFNγ ELISpot assay, dark blue; confirmed as tumor-rejecting by TCR cloning, red. g, Comparison of ipMSDB presentation (above x axis) and binding predicted (below x axis) HLA-I (blue) and HLA-II (yellow) hotspots for MLANA and MAGEC2 for MEL-1. Binding-restricted hotspots (gray) and MS-identified and immunogenic (red) peptides are shown. h, Distribution of ipMSDB coverage of HLA-I and HLA-II predicted peptides (rank ≤ 0.5%) (HLA-I, n = 872; HLA-II, n = 464), MS-identified peptides (HLA-I, n = 110; HLA-II, n = 51), immunogenic peptides (HLA-I, n = 2) and peptides confirmed following tumor recognition assays (HLA-I, n = 4) in MEL-1 (independent one-sided t-test). i, Comparison of ipMSDB coverage across all HC-TSA predicted binder peptides annotated as immunogenic in IEDB (HLA-I, n = 91; HLA-II, n = 42) and HC-TSAs not annotated as immunogenic in IEDB (HLA-I, n = 14,721; HLA-II, n = 16,769) (independent one-sided t-test). The box plot center lines represent the median. The bounds of the box represent the 25th and 75th percentiles (interquartile range (IQR)). The whiskers extend to the smallest and largest values within 1.5× the IQRs. Individual dots represent minima and maxima beyond the whiskers.
