用新方法设计能激活T细胞的肽,助力癌症和病毒疫苗研发。
T-cell receptor specificity landscape revealed through de novo peptide design
- 基于物理引导的机器学习模型预测T细胞识别肽
- 新设计肽在实验中50%成功率激活T细胞
- 可解析人类与小鼠T细胞特异性,适合免疫治疗设计
T细胞通过识别主要组织相容性复合体(MHC)呈递的病原体肽来启动适应性免疫反应。然而,由于缺乏T细胞反应的功能数据,预测T细胞受体(TCR)与肽的相互作用仍具挑战。本文提出一种计算方法,用于预测TCR与MHC I类等位基因呈递肽的结合亲和力,并设计针对特定TCR-MHC复合物的新免疫原性肽。该方法利用HERMES模型——一个基于结构、物理引导的机器学习模型,在蛋白质宇宙上训练以预测局部结构环境下的氨基酸偏好。尽管未直接训练于TCR-pMHC数据,其隐含的物理推理使模型在多种病毒表位和癌症新抗原上准确预测了结合亲和力与T细胞活性,最高相关性达0.72。基于此识别模型,我们开发了从头设计免疫原性肽的计算流程。在三个针对病毒和癌症肽的TCR-MHC系统中,经实验验证,最多含五处突变的设计肽成功激活T细胞,最高成功率50%。最后,利用生成框架量化了不同TCR-MHC复合物的肽识别景观多样性,为人类和小鼠T细胞特异性提供关键见解。本方法为免疫原性肽和新抗原设计、TCR特异性评估提供了计算平台,有助于工程化T细胞疗法与疫苗开发。
原文摘要 · Abstract (English)
T-cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. An effective binding between T-cell receptors (TCRs) and pathogen-derived peptides presented on Major Histocompatibility Complexes (MHCs) mediate an immune response. However, predicting these interactions remains challenging due to limited functional data on T-cell reactivities. Here, we introduce a computational approach to predict TCR interactions with peptides presented on MHC class I alleles, and to design novel immunogenic peptides for specified TCR-MHC complexes. Our method leverages HERMES, a structure-based, physics-guided machine learning model trained on the protein universe to predict amino acid preferences based on local structural environments. Despite no direct training on TCR-pMHC data, the implicit physical reasoning in HERMES enables us to make accurate predictions of both TCR-pMHC binding affinities and T-cell activities across diverse viral epitopes and cancer neoantigens, achieving up to 0.72 correlation with experimental data. Leveraging our TCR recognition model, we develop a computational protocol for de novo design of immunogenic peptides. Through experimental validation in three TCR-MHC systems targeting viral and cancer peptides, we demonstrate that our designs -- with up to five substitutions from the native sequence -- activate T-cells at success rates of up to 50%. Lastly, we use our generative framework to quantify the diversity of the peptide recognition landscape for various TCR-MHC complexes, offering key insights into T-cell specificity in both humans and mice. Our approach provides a platform for immunogenic peptide and neoantigen design, as well as for evaluating TCR specificity, offering a computational framework to inform design of engineered T-cell therapies and vaccines.
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