Fig. 5: Experimental HLA-I–peptide stability assay confirms the ability of MUNIS to discriminate between binding and non-binding peptides within EBV. | Nature Machine Intelligence

Fig. 5: Experimental HLA-I–peptide stability assay confirms the ability of MUNIS to discriminate between binding and non-binding peptides within EBV.

From: Deep learning enhances the prediction of HLA class I-presented CD8+ T cell epitopes in foreign pathogens

Fig. 5: Experimental HLA-I–peptide stability assay confirms the ability of MUNIS to discriminate between binding and non-binding peptides within EBV.

a, Schematic showing the epitope prioritization pipeline for experimental validation. The top-337 ranked peptides from the BRLF1, B2LF1, EBNA1, LMP2 and EBNA3a proteins from EBV predicted to bind 1 of 17 different HLA-I alleles were chosen for downstream analysis. b, Schematic showing experimental validation of MUNIS performance on EBV epitope prediction. Stability assays on HLA-I–peptide pairs were performed using TAP-deficient monoallelic HLA-I cell lines to identify peptides that bind and are presented by HLA-I molecules. IFNγ ELISpot assays were performed on each peptide predicted to bind an HLA molecule presented by 30 HLA-haplotyped individuals to identify immunogenic peptides (data shown in Fig. 6). c, Representative data of the relative stabilization of HLA-B*35:01 by two EBV peptides predicted to bind the allele. The MFI for the DMSO negative control shown in light grey, the B*3501-specific HIV immunodominant peptide in light blue, the two predicted binders from the EBV proteome in blue and a predicted non-binder from the EBV proteome in dark grey. The higher the MFI, the greater stabilized the allele by a given peptide. d, Summary data for all predicted binders and non-binders for HLA-B*35:01. All MFIs were normalized to the HIV immunodominant peptide for the given HLA-I allele as denoted by the dashed line. Blue circles are predicted binders and grey circles are predicted non-binders. e, Summary data for all 17 HLA-I alleles evaluated for the 337 predicted peptides. Box plots are presented with medians as centre lines, 25th and 75th percentiles as lower and upper quartiles, and 1.5 times the interquartile range from the quartiles as whiskers (outliers not shown). f, Normalized anti-HLA MFI for binders versus non-binders conditioned on predicted binders with a MUNIS score greater than or equal to the given threshold score. Each point represents the median normalized anti-HLA MFI across all peptides predicted to bind or not bind a particular HLA-I allele (n = 17 HLA-I alleles). P values for pairwise comparisons between predicted binders and non-binders were calculated using the two-sided Wilcoxon rank sums test. Panels a and b created with BioRender.com.

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