Suppr超能文献

基于基础模型的MHC II类抗原肽-T细胞受体结合预测

[Prediction of MHC II antigen peptide-T cell receptors binding based on foundation model].

作者信息

Xu Minrui, Zhang Siwen, Lu Manman, Gao Yuan, Zhang Menghuan, Lin Yong, Xie Lu

机构信息

School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, P. R. China.

Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200237, P. R. China.

出版信息

Sheng Wu Yi Xue Gong Cheng Xue Za Zhi. 2024 Dec 25;41(6):1243-1249. doi: 10.7507/1001-5515.202405024.

Abstract

The specific binding of T cell receptors (TCRs) to antigenic peptides plays a key role in the regulation and mediation of the immune process and provides an essential basis for the development of tumour vaccines. In recent years, studies have mainly focused on TCR prediction of major histocompatibility complex (MHC) class I antigens, but TCR prediction of MHC class II antigens has not been sufficiently investigated and there is still much room for improvement. In this study, the combination of MHC class II antigen peptide and TCR prediction was investigated using the ProtT5 grand model to explore its feature extraction capability. In addition, the model was fine-tuned to retain the underlying features of the model, and a feed-forward neural network structure was constructed for fusion to achieve the prediction model. The experimental results showed that the method proposed in this study performed better than the traditional methods, with a prediction accuracy of 0.96 and an AUC of 0.93, which verifies the effectiveness of the model proposed in this paper.

摘要

T细胞受体(TCR)与抗原肽的特异性结合在免疫过程的调节和介导中起关键作用,并为肿瘤疫苗的开发提供了重要基础。近年来,研究主要集中在主要组织相容性复合体(MHC)I类抗原的TCR预测上,而MHC II类抗原的TCR预测尚未得到充分研究,仍有很大的改进空间。在本研究中,使用ProtT5大型模型研究了MHC II类抗原肽与TCR预测的结合,以探索其特征提取能力。此外,对模型进行了微调以保留模型的潜在特征,并构建了前馈神经网络结构进行融合以实现预测模型。实验结果表明,本研究提出的方法比传统方法表现更好,预测准确率为0.96,AUC为0.93,验证了本文提出模型的有效性。

相似文献

1
[Prediction of MHC II antigen peptide-T cell receptors binding based on foundation model].
Sheng Wu Yi Xue Gong Cheng Xue Za Zhi. 2024 Dec 25;41(6):1243-1249. doi: 10.7507/1001-5515.202405024.
4
Recognition of core and flanking amino acids of MHC class II-bound peptides by the T cell receptor.
Eur J Immunol. 2002 Sep;32(9):2510-20. doi: 10.1002/1521-4141(200209)32:9<2510::AID-IMMU2510>3.0.CO;2-Q.
5
Peptide-MHC Binding Reveals Conserved Allosteric Sites in MHC Class I- and Class II-Restricted T Cell Receptors (TCRs).
J Mol Biol. 2020 Dec 4;432(24):166697. doi: 10.1016/j.jmb.2020.10.031. Epub 2020 Nov 4.
6
Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition.
PLoS One. 2018 Nov 6;13(11):e0206654. doi: 10.1371/journal.pone.0206654. eCollection 2018.
9
Coreceptor affinity for MHC defines peptide specificity requirements for TCR interaction with coagonist peptide-MHC.
J Exp Med. 2013 Aug 26;210(9):1807-21. doi: 10.1084/jem.20122528. Epub 2013 Aug 12.
10
Identification of the cognate peptide-MHC target of T cell receptors using molecular modeling and force field scoring.
Mol Immunol. 2018 Feb;94:91-97. doi: 10.1016/j.molimm.2017.12.019. Epub 2017 Dec 27.

本文引用的文献

2
iTCep: a deep learning framework for identification of T cell epitopes by harnessing fusion features.
Front Genet. 2023 May 9;14:1141535. doi: 10.3389/fgene.2023.1141535. eCollection 2023.
3
Neoantigens: promising targets for cancer therapy.
Signal Transduct Target Ther. 2023 Jan 6;8(1):9. doi: 10.1038/s41392-022-01270-x.
4
AttnTAP: A Dual-input Framework Incorporating the Attention Mechanism for Accurately Predicting TCR-peptide Binding.
Front Genet. 2022 Aug 22;13:942491. doi: 10.3389/fgene.2022.942491. eCollection 2022.
5
dbPepNeo2.0: A Database for Human Tumor Neoantigen Peptides From Mass Spectrometry and TCR Recognition.
Front Immunol. 2022 Apr 13;13:855976. doi: 10.3389/fimmu.2022.855976. eCollection 2022.
7
ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning.
IEEE Trans Pattern Anal Mach Intell. 2022 Oct;44(10):7112-7127. doi: 10.1109/TPAMI.2021.3095381. Epub 2022 Sep 14.
8
TCRdb: a comprehensive database for T-cell receptor sequences with powerful search function.
Nucleic Acids Res. 2021 Jan 8;49(D1):D468-D474. doi: 10.1093/nar/gkaa796.
9
Prediction of Specific TCR-Peptide Binding From Large Dictionaries of TCR-Peptide Pairs.
Front Immunol. 2020 Aug 25;11:1803. doi: 10.3389/fimmu.2020.01803. eCollection 2020.
10
T cell antigen discovery.
Nat Methods. 2021 Aug;18(8):873-880. doi: 10.1038/s41592-020-0867-z. Epub 2020 Jul 6.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验