NetMHCpan-4.2: Improved prediction of CD8+ epitopes by use of transfer learning and structural features

Jonas Birkelund Nilsson^1*Jason Greenbaum²Bjoern Peters^2,3Morten Nielsen¹

• ¹Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
• ²Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), San Diego, California, United States
• ³Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, United States

Identification of CD8+ T cell epitopes is crucial for advancing vaccine development and immunotherapy strategies. Traditional methods for predicting T cell epitopes primarily focus on MHC presentation, leveraging immunopeptidome data. Recent advancements however suggest significant performance improvements through transfer learning and refinement using epitope data. To further investigate this, we here develop an enhanced MHC class I (MHC-I) antigen presentation predictor by integrating newly curated binding affinity and eluted ligand datasets, expanding MHC allele coverage, and incorporating novel input features related to the structural constraints of the MHC-I peptide-binding cleft. We next apply transfer learning using experimentally validated pathogen-and cancer-derived epitopes from public databases to refine our prediction method, ensuring comprehensive data partitioning to prevent performance overestimation. Our findings indicate that fine-tuning on epitope data only yields a minor accuracy boost. Moreover, the transferability between cancer and pathogen-derived epitopes is limited, suggesting distinct properties between these data types. In conclusion, while transfer learning can enhance T cell epitope prediction, the performance gains are modest and data type specific. Our final NetMHCpan-4.2 model is publicly accessible at https://services.healthtech.dtu.dk/services/NetMHCpan-4.2, providing a valuable resource for immunological research and therapeutic development.