Identification of CD8+ T cell epitopes through proteasome cleavage site predictions

Abstract

Background: We previously introduced PCPS (Proteasome Cleavage Prediction Server), a web-based tool to predict proteasome cleavage sites using n-grams. Here, we evaluated the ability of PCPS immunoproteasome cleavage model to discriminate CD8⁺ T cell epitopes.

Results: We first assembled an epitope dataset consisting of 844 unique virus-specific CD8⁺ T cell epitopes and their source proteins. We then analyzed cleavage predictions by PCPS immunoproteasome cleavage model on this dataset and compared them with those provided by a related method implemented by NetChop web server. PCPS was clearly superior to NetChop in term of sensitivity (0.89 vs. 0.79) but somewhat inferior with regard to specificity (0.55 vs. 0.60). Judging by the Mathew's Correlation Coefficient, PCPS predictions were overall superior to those provided by NetChop (0.46 vs. 0.39). We next analyzed the power of C-terminal cleavage predictions provided by the same PCPS model to discriminate CD8⁺ T cell epitopes, finding that they could be discriminated from random peptides with an accuracy of 0.74. Following these results, we tuned the PCPS web server to predict CD8⁺ T cell epitopes and predicted the entire SARS-CoV-2 epitope space.

Conclusions: We report an improved version of PCPS named iPCPS for predicting proteasome cleavage sites and peptides with CD8⁺ T cell epitope features. iPCPS is available for free public use at https://imed.med.ucm.es/Tools/pcps/ .

Keywords: CD8+ T cell epitope; Immunoproteasome; Peptide; Prediction; Proteasome; SARS-CoV-2.

Fig. 1

Discrimination of CD8⁺ T cell epitopes using PCPS immunoproteasome cleavage predictions. Graph depicts the accuracy (ACC) of PCPS immunoproteasome model to distinguishing CD8⁺ T cell epitopes by their C-terminus at different thresholds (0.35–0.6). The analysis to compute ACC was repeated 5 times with different 9-mer peptides selected randomly from the same source proteins than the epitopes. Average values of ACC are represented with standard deviations as errors bars

Fig. 2

Discrimination of CD8⁺ T cell epitopes by immunoproteasome cleavage predictions considering HLA I restriction. Figure shows the accuracy (ACC) of C-terminus immunoproteasome cleavage predictions discriminating virus-specific CD8⁺ T cell epitopes restricted by specific HLA I molecules (columns) from 9-mer peptides, selected randomly from the same source proteins than the epitopes. The analysis was carried out using PCPS immunoproteasome model at a threshold of 0.5 and the represented ACC corresponds to means ± SD obtained after repeating the analysis five times with different random 9-mer peptides

Fig. 3

Improved Proteasome Cleavage Prediction Server (iPCPS). a Web interface of iPCPS. The interface of iPCPS is divided in three sections for intuitive use. In the first section (models), users select the immunoproteasome and/or proteasome model and the threshold. In input, users paste or upload their sequence/s in FASTA format and in output select to get cleavage sites per residue or peptides with C-terminus generated by the proteasome. Users can set the size of the peptide, discard those with internal cleavage sites and obtain a graphical display. b iPCPS output. Figure shows a representative iPCPS peptide output obtained selecting the proteasome and immunoproteasome model and graphics display. Ticks indicate that peptides have a C-terminus generated by the proteasomes and green zero symbols are for peptides without internal cleavage sites for the selected threshold. Peptides with red cross symbols do have internal cleavage sites

Fig. 4

Predicted SARS-CoV-2-specific CD8⁺ T cell epitopes using iPCPS. a The figure represents the number of predicted CD8⁺ T cell epitopes in SARS-CoV-2 proteome using iPCPS with different settings indicated in the abscissa: 9-mer, total 9-mer peptides in the SARS-CoV-2 proteome; IP, immunoproteasome model; IP w/o, immunoproteasome model discarding peptides with internal cleavage sites; IP + P, immunoproteasome and proteasome models; IP + P w/o, immunoproteasome and proteasome models discarding peptides with internal cleavage sites. b Percentage of SARS-CoV-2 CD8⁺ T cell epitopes predicted by peptide-HLA I binding predictions reported by Grifoni et al. [31] included in those anticipated by iPCPS with settings indicated in panel A

Fig. 5

iPCPS graphic work. The figure depicts the suitability of iPCPS to predict potential CD8⁺ T cell epitopes covering all HLA I molecules