Enhancing tumor T cell antigen prediction by integrating deep protein representations

Cancer is a major threat to human health, and cancer immunotherapy is considered the most promising treatment option. It offers high effectiveness and precision, with fewer side effects than traditional treatments. Tumor T cell antigens (TTCA) are the proteins or protein fragments that stand on the surface of cancer cells and that are recognized by the immune system. However, physical experimental approaches to infer them might be costly and time-consuming, even though they are important for cancer immunotherapy. We propose D eep T Hybrid to predict TTCAs by combining chemically hand-designed features with deep protein representations from ProtBERT, an adapted version of the BERT large Language Model, for finding complex representations from the protein sequences. It is the first framework to incorporate these protein embeddings with complementary chemical features for this problem. After the feature extraction step, among multiple classifiers tested, we find Inception-based neural network to outperform the rest, so D eep T Hybrid includes it. We evaluate the prediction performance on multiple datasets, where D eep T Hybrid consistently outperforms the competing approaches across all datasets. For instance, on the first dataset, D eep T Hybrid achieves an accuracy of 0.76, an F1-score of 0.78, outperforming existing machine learning and state-of-the-art TTCA predictors. Across both datasets, combining deep protein embeddings with chemical attributes yields superior performance compared to using either feature type alone. We also find the mixture of deep features and chemical features more informative in terms of Shapley-based explanation values. Overall, our method is promising with its high accuracy rates and strong predictive skills. In addition to its predictive performance, D eep T Hybrid provides a fast and scalable computational screening framework that can substantially reduce the cost and time associated with biological experiments by prioritizing high-confidence tumor T cell antigen candidates for downstream experimental validation.