Learning from HIV-1 to predict the immunogenicity of T cell epitopes in SARS-CoV-2.
Learning from HIV-1 to predict the immunogenicity of T cell epitopes in SARS-CoV-2.
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DOI：
10.1016/j.isci.2021.102311
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发表时间：
2021-04-23
期刊：
影响因子：
5.8
通讯作者：
Julg B
中科院分区：
文献类型：
--
作者：
Gao A;Chen Z;Amitai A;Doelger J;Mallajosyula V;Sundquist E;Pereyra Segal F;Carrington M;Davis MM;Streeck H;Chakraborty AK;Julg B
我们描述了一个基于物理学的学习模型，用于预测来自不同病原体（包括SARS-CoV-2）的细胞毒性T淋巴细胞（CTL）表位的免疫原性。该模型是根据人类免疫缺陷病毒感染中CTL表位的相对免疫优势进行训练和优化的。它的准确性根据COVID-19患者的实验数据进行了测试。我们的模型预测，只有一些SARS-CoV-2抗原表位预测结合HLA分子是免疫原性的。预计所有SARS-CoV-2蛋白的免疫原性CTL表位都能提供广泛的人群覆盖，但仅来自SARS-CoV-2刺突蛋白的免疫原性CTL表位不太可能做到这一点。我们的模型还预测，几种免疫原性SARS-CoV-2 CTL表位与人群中流行的季节性冠状病毒相同，并且这种交叉反应性CD 8 + T细胞确实可以在大流行前的献血者中检测到，这表明在SARS-CoV-2感染前，某些个体可能存在一定水平的针对COVID-19的CTL免疫。一个基于物理学的学习模型来预测CTL表位的免疫原性在HIV中的相对CTL表位免疫优势训练并应用于SARS-CoV-2只有一部分SARS-CoV-2肽与HLA分子结合具有免疫原性免疫原性SARS-CoV-2表位与季节性冠状病毒相同已被鉴定免疫学;免疫应答;计算机生物学;人工智能
We describe a physics-based learning model for predicting the immunogenicity of cytotoxic T lymphocyte (CTL) epitopes derived from diverse pathogens including SARS-CoV-2. The model was trained and optimized on the relative immunodominance of CTL epitopes in human immunodeficiency virus infection. Its accuracy was tested against experimental data from patients with COVID-19. Our model predicts that only some SARS-CoV-2 epitopes predicted to bind to HLA molecules are immunogenic. The immunogenic CTL epitopes across all SARS-CoV-2 proteins are predicted to provide broad population coverage, but those from the SARS-CoV-2 spike protein alone are unlikely to do so. Our model also predicts that several immunogenic SARS-CoV-2 CTL epitopes are identical to seasonal coronaviruses circulating in the population and such cross-reactive CD8+ T cells can indeed be detected in prepandemic blood donors, suggesting that some level of CTL immunity against COVID-19 may be present in some individuals before SARS-CoV-2 infection. A physics-based learning model to predict CTL epitope immunogenicity across viruses Trained on relative CTL epitope immunodominance in HIV and applied to SARS-CoV-2 Only a fraction of SARS-CoV-2 peptides that bind to HLA molecules is immunogenic Immunogenic SARS-CoV-2 epitopes identical to seasonal coronaviruses were identified Immunology; Immune Respons; In Silico Biology; Artificial Intelligence
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DOI：
10.4049/jimmunol.1700893
发表时间：
2017-11-01
期刊：
Journal of immunology (Baltimore, Md. : 1950)
影响因子：
--
作者：
Jurtz V;Paul S;Andreatta M;Marcatili P;Peters B;Nielsen M
通讯作者：
Nielsen M
MHC I类的性质提出了增强免疫原性的肽。
影响因子：
4.3
作者：
Calis JJ;Maybeno M;Greenbaum JA;Weiskopf D;De Silva AD;Sette A;Keşmir C;Peters B
通讯作者：
Peters B
影响因子：
32.4
作者：
Ferguson AL;Mann JK;Omarjee S;Ndung'u T;Walker BD;Chakraborty AK
通讯作者：
Chakraborty AK
影响因子：
64.8
作者：
Daniels, Mark A.;Teixeiro, Emma;Palmer, Ed
通讯作者：
Palmer, Ed
影响因子：
3.7
作者：
Hayton EJ;Rose A;Ibrahimsa U;Del Sorbo M;Capone S;Crook A;Black AP;Dorrell L;Hanke T
通讯作者：
Hanke T