Neo-intline: integrated pipeline enables neoantigen design through the in-silico presentation of T-cell epitope

Neoantigen vaccines are one of the most effective immunotherapies for personalized tumour treatment.The current immunogen design of neoantigen vaccines is usually based on whole-genome sequencing(WGS)and bioinformatics prediction that focuses on the prediction of binding affinity between peptide and MHC molecules,ignoring other peptide-presenting related steps.This may result in a gap between high prediction accuracy and relatively low clinical effectiveness.In this study,we designed an integrated in-silico pipeline,Neo-intline,which started from the SNPs and indels of the tumour samples to simulate the presentation process of peptides in-vivo through an integrated calculation model.Validation on the benchmark dataset of TESLA and clinically validated neoantigens illustrated that neo-intline could outperform current state-of-the-art tools on both sample level and melanoma level.Furthermore,by taking the mouse melanoma model as an example,we verified the effectiveness of 20 neoantigens,including 10 MHC-I and 10 MHC-II peptides.The in-vitro and in-vivo experiments showed that both peptides predicted by Neo-intline could recruit corresponding CD4^(+)T cells and CD8^(+)T cells to induce a T-cell-mediated cellular immune response.Moreover,although the therapeutic effect of neoantigen vaccines alone is not sufficient,combinations with other specific therapies,such as broad-spectrum immune-enhanced adjuvants of granulocyte-macrophage colony-stimulating factor(GM-CSF)and polyinosinic-polycytidylic acid(poly(I:C)),or immune checkpoint inhibitors,such as PD-1/PD-L1 antibodies,can illustrate significant anticancer effects on melanoma.Neo-intline can be used as a benchmark process for the design and screening of immunogenic targets for neoantigen vaccines.