Abstract P006: Novel machine-learning tools improve cost-effective development of personalised immunotherapies: Lowering false positive rates in the search for actionable (personalised and largely shared) immunogenic neoantigens
Authors: Bogaert Cedric , Pfitzer Lena , Mill Nil Adell , Fant Bruno 
Published: December 2021

Abstract
Personalised immunotherapy approaches rely on the ability of tumour-derived neoantigens to elicit a T-cell immune reaction able to recognise and kill the tumour cells expressing them. Clinical attempts to leverage the power of neoantigens have however yielded mixed results. This can mostly be attributed to the difficulty of finding truly immunogenic peptides from the set of novel peptides generated by mutations in a given cancer patient. In silico approaches can help alleviate this heavy cost by reducing the neoantigen search space, prioritising epitopes based on various parameters such as epitope expression or MHC binding likelihood. Here we present a suite of tools aimed at further assisting clinicians in selecting the most actionable peptides from a set of potential candidates. We developed neoMS, a neural network algorithm able to predict epitope presentation at the cell surface with unparalleled performance. The model achieves up to 0.61 precision at recall 0.4 on its test set, vastly outperforming the current industry standards. In addition, due to his sequence-based comparison method, neoMS exhibits extrapolation capabilities, achieving non-zero predictive power when evaluated on ground truth ligandome data derived from an HLA allele completely absent from the training set. In some cancer indications we showed, moreover, that the neoMS-predicted rate of neoantigen presentation can be used in combination with tumour mutational burden as a high-specificity predictor of response to immune checkpoint inhibitor treatment. Furthermore, the neoIM algorithm is able to discriminate, in an HLA-agnostic fashion, which of the presented peptides will elicit a T-cell immune reaction. This first-in-class algorithm is a random forest classifier specifically trained to classify short peptides of length 9-11 amino acids as immunogenic or non-immunogenic. neoIM vastly outperforms the currently available methods and can predict peptide immunogenicity with high accuracy (AUC=0.88). Interestingly, neoIM confirmed ELISPOT data obtained by Dillon et al. (2017) showing a response in 4 out of 11 breast cancer patients to a vaccine consisting of 9 MHC class-I restricted breast cancer-associated peptides. The 2 antigens that resulted in a CD8+ T-cell specific response were predicted by neoIM as the highest scoring showing its potential in finding the truly immunogenic neoantigens. Taken together, these tools decrease false positive rates significantly as they enable improved identification of immunogenic peptides and the predictions correlate with intensity of immune response and clinical benefits. As such, these tools represent a cost-efficient preliminary step in the search for actionable, immunogenic neoantigens.
Citation Format: Cedric Bogaert, Lena Pfitzer, Nil Adell Mill, Bruno Fant. Novel machine-learning tools improve cost-effective development of personalised immunotherapies: Lowering false positive rates in the search for actionable (personalised and largely shared) immunogenic neoantigens [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P006.