In-depth comparison and feasibility assessment of an integrated pipeline for neoantigen identification and HLA ligandome sequencing in a clinical setting
Each year 4500 individuals are diagnosed with lung cancer in Flanders alone. Five years later, 85% of these individuals will have died despite intensive treatment. Moreover, current treatments are either highly toxic or susceptible to rapid development of resistance. Recently however, a new therapy was discovered: immune checkpoint blockers (ICB), which prevent the downregulation of the natural immune activity towards cancer cells. Despite their proven effectiveness, only a small percentage of patients respond to treatment with ICB. Therefore, a proof-of-concept clinical trial is in development at the labs of prof. Menten and prof. Vandekerckhove, which aims to combine ICBs with an active vaccination strategy. For this vaccine, tumor specific targets will be identified for each patient. These targets are known as neoantigens which are small peptides derived from tumor specific mutations that arose during tumor formation. This proposal aims to develop a fully integrated and accurate pipeline for the identification of these neoantigen targets for use in a clinical setting. Therefore, we will employ current state-of-the-art sequencing technologies and computer algorithms and compare their predictions with the newly developed HLA ligandome sequencing. Moreover, we will evaluate their feasibility and potential to elicit an immune response during our clinical trial. Based on this evaluation, we will uncover new insights into neoantigens predictions that can improve treatment.