Unbiased Characterization of Peptide-HLA Class II Interactions Based on Large-Scale Peptide Microarrays; Assessment of the Impact on HLA Class II Ligand and Epitope Prediction.

Mareike Wendorff,Hesham Elabd,Thomas Østerbye,Søren Buus,Frauke Degenhardt,Elisa Rosati,Andre Franke,Heli M Garcia Alvarez,Morten Nielsen

doi:10.3389/fimmu.2020.01705

Abstract

Human Leukocyte Antigen class II (HLA-II) molecules present peptides to T lymphocytes and play an important role in adaptive immune responses. Characterizing the binding specificity of single HLA-II molecules has profound impacts for understanding cellular immunity, identifying the cause of autoimmune diseases, for immunotherapeutics, and vaccine development. Here, novel high-density peptide microarray technology combined with machine learning techniques were used to address this task at an unprecedented level of high-throughput. Microarrays with over 200,000 defined peptides were assayed with four exemplary HLA-II molecules. Machine learning was applied to mine the signals. The comparison of identified binding motifs, and power for predicting eluted ligands and CD4+ epitope datasets to that obtained using NetMHCIIpan-3.2, confirmed a high quality of the chip readout. These results suggest that the proposed microarray technology offers a novel and unique platform for large-scale unbiased interrogation of peptide binding preferences of HLA-II molecules.

Highlights

The highly diverse major histocompatibility complex (MHC) proteins play a major role in the adaptive immune system
The results suggest that the inclusion of elution data has a positive impact on the predictive power of in-silico methods in particular for the prediction of human leukocyte antigen (HLA) antigen presentation [10,11,12,13,14,15]
We evaluated the consistency of the triplicates using the coefficient of variation (CoV) and the Pearson Correlation Coefficient (PCC) between three replicates

Summary

Introduction

The highly diverse major histocompatibility complex (MHC) proteins play a major role in the adaptive immune system. The HLA locus is highly polymorphic, resulting in different HLA molecules having a specific peptide binding preference and specific peptidomes. The HLA is an important susceptibility locus in genetic studies of many immune-related diseases, often with multiple HLA alleles playing a role [2,3,4]. Beyond the suggested association, these studies do not inform about the causes of a disease, i.e., the antigen/epitope that binds to associated HLA proteins and potentially drive the disease onset.

Methods

Results

Conclusion