The role of antigen expression in shaping the repertoire of HLA presented ligands.
The role of antigen expression in shaping the repertoire of HLA presented ligands.
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DOI：
10.1016/j.isci.2022.104975
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发表时间：
2022-09-16
期刊：
影响因子：
5.8
通讯作者：
Nielsen, Morten
中科院分区：
文献类型：
--
作者：
Alvarez, Heli M. Garcia;Kosaloglu-Yalcin, Zeynep;Peters, Bjoern;Nielsen, Morten
肽的人类白细胞抗原 (HLA) 呈递是 T 细胞免疫激活的先决条件。了解定义这一事件的规则对于我们的基础免疫学知识以及免疫治疗和疫苗的合理设计具有重大意义。从历史上看，大多数可用的预测方法都只关注与抗原加工和呈递相关的信息。然而，最近的工作表明，可以通过整合与抗原丰度相关的信息来提高方法性能。在这里，我们扩展了这些后来的发现，并开发了 NetMHCpan 的扩展版本，称为 NetMHCpanExp，整合了来自 RNA-Seq 实验的抗原丰度信息。与早期的工作一致，该模型展示了 HLA 配体和癌症新抗原表位预测的性能改进。通过使用特定于样本的丰度信息可以获得最佳结果，但也可以应用参考数据集，但性能下降有限。开发的工具可从 https://services.healthtech.dtu.dk/service.php?NetMHCpanExp-1.0 获取。 NetMHCpanExp 是 NetMHCpan 的扩展，集成了抗原丰度数据 NetMHCpanExp 基于 NNAlign_MA 的修改版本构建，当使用参考而不是样本特异性 RNA-Seq 检测时，性能会出现轻微损失。生物计算方法；转录组学；生物科学工具
Human leukocyte antigen (HLA) presentation of peptides is a prerequisite of T cell immune activation. The understanding of the rules defining this event has large implications for our knowledge of basic immunology and for the rational design of immuno-therapeutics and vaccines. Historically, most of the available prediction methods have been solely focused on the information related to antigen processing and presentation. Recent work has, however, demonstrated that method performance can be boosted by integrating information related to antigen abundance. Here we expand on these later findings and develop an extended version of NetMHCpan, called NetMHCpanExp, integrating information on antigen abundance from RNA-Seq experiments. In line with earlier works, the model demonstrates improved performance for both HLA ligand and cancer neoantigen epitope prediction. Optimal results are obtained by use of sample-specific abundance information but also reference datasets can be applied with a limited performance drop. The developed tool is available at https://services.healthtech.dtu.dk/service.php?NetMHCpanExp-1.0. NetMHCpanExp, an extension of NetMHCpan, integrates antigen abundance data NetMHCpanExp is built upon a modified version of NNAlign_MA Minor performance loss when using reference instead of sample-specific RNA-Seq assays Suboptimal MHC-I binders are “rescued” if arising from highly expressed proteins Immunology; Biocomputational method; Transcriptomics; Biological sciences tools
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影响因子：
12.3
作者：
Nielsen M;Andreatta M
通讯作者：
Andreatta M
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
影响因子：
32.4
作者：
Abelin JG;Keskin DB;Sarkizova S;Hartigan CR;Zhang W;Sidney J;Stevens J;Lane W;Zhang GL;Eisenhaure TM;Clauser KR;Hacohen N;Rooney MS;Carr SA;Wu CJ
通讯作者：
Wu CJ
影响因子：
4.6
作者：
Arora, Sonali;Pattwell, Siobhan S.;Bolouri, Hamid
通讯作者：
Bolouri, Hamid
影响因子：
24.8
作者：
Faridi, Pouya;Li, Chen;Purcell, Anthony W.
通讯作者：
Purcell, Anthony W.