High-throughput identification of antibody features for sequence-based epitope prediction

高通量鉴定抗体特征以进行基于序列的表位预测

• 批准号: 10243575
• 负责人: Nicholas C. Wu
• 金额: $ 142.74万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-17 至 2024-09-16
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10243575
• 关键词: Affinity; Amino Acid Sequence; Antibodies; Antibody Diversity; Antibody Repertoire; Antibody Specificity; Antigens; Base Sequence; Binding; Data Set; Epitopes; Genes; Genetic Recombination; Hemagglutinin; Human; Immune response; Immune system; Immunoglobulin Somatic Hypermutation; Immunoglobulin Variable Region; Influenza A virus; Influenza Hemagglutinin; Libraries; Molecular; Molecular Conformation; Process; Specificity; Structure; V(D)J Recombination; base; experimental study; interest; novel; pathogen; screening; therapeutic development; vaccine development

PROJECT SUMMARY Human antibody repertoire is highly diverse due to VDJ recombination and somatic hypermutation. VDJ recombination is a somatic recombination process that assembles the variable region of an antibody from a diverse set of gene segments, known as variable (V), diversity (D), and joining (J) genes. During the course of an immune response, antibodies will increase affinity to their antigens through somatic hypermutation. The huge diversity of antibodies enables human immune system to confer protection against various pathogens by recognizing a wide range of antigens and epitopes. Detailed molecular characterization of antibody-antigen interaction is crucial to vaccine and therapeutic development, as well as the fundamental understanding of the human immune system. The binding specificity and epitope of an antibody are determined by its structure, which in turn is determined by its amino acid sequence. As a result, information on the binding specificity and epitope of an antibody are encoded in its amino acid sequence. However, accurately predicting the epitopes of antibodies from their sequences is an extremely difficult task because our understanding of antibody sequence-function relationship is far from comprehensive. This proposal aims to develop a library-to-library screening approach to characterize antibody-antigen interaction in a high-throughput manner, with a focus on influenza A hemagglutinin (HA) as a proof-of-concept. Specifically, we will determine the HA-binding specificity and conformational epitope of hundreds of thousands of antibodies in a single experiment. Subsequently, antibody sequence features that are associated with different epitopes on HA will be systematically identified. We further aim to use these antibody features to identify HA-binding antibodies from publicly available antibody repertoire sequencing datasets as well as predict their epitopes on HA. While this proposed project focuses on influenza HA, our approach can be easily extended to any antigen of interest. This proposal will open up the possibility for antibody sequence-based epitope prediction and provides new perspectives to the understanding of human antibody repertoire.

项目概要 由于 VDJ 重组和体细胞超突变，人类抗体库具有高度多样性。虚拟DJ 重组是一种体细胞重组过程，将抗体的可变区从 不同的基因片段集，称为变量 (V)、多样性 (D) 和连接 (J) 基因。期间 在免疫反应中，抗体将通过体细胞超突变增加与其抗原的亲和力。这 抗体的巨大多样性使人类免疫系统能够通过以下方式提供针对各种病原体的保护： 识别多种抗原和表位。抗体-抗原的详细分子表征 相互作用对于疫苗和治疗的开发以及对疾病的基本理解至关重要 人体免疫系统。 抗体的结合特异性和表位由其结构决定，而结构又是 由其氨基酸序列决定。因此，有关结合特异性和表位的信息 抗体以其氨基酸序列编码。然而，准确预测抗体的表位 从它们的序列中获取是一项极其困难的任务，因为我们对抗体序列功能的理解 关系远非全面。该提案旨在开发一种图书馆到图书馆的筛选方法 以高通量方式表征抗体-抗原相互作用，重点关注甲型流感 血凝素 (HA) 作为概念验证。具体来说，我们将确定 HA 结合特异性并 在一次实验中分析数十万种抗体的构象表位。随后，抗体 与HA上不同表位相关的序列特征将被系统地识别。我们进一步 旨在利用这些抗体特征从公开的抗体库中识别 HA 结合抗体 对数据集进行测序并预测其在 HA 上的表位。虽然该拟议项目的重点是流感 HA，我们的方法可以轻松扩展到任何感兴趣的抗原。该提案将开启可能性 用于基于抗体序列的表位预测，并为理解人类抗体提供了新的视角 抗体库。

项目成果

Molecular analysis of a public cross-neutralizing antibody response to SARS-CoV-2.

对 SARS-CoV-2 公共交叉中和抗体反应的分子分析。

• DOI: 10.1101/2022.05.17.492220
• 发表时间: 2022
• 期刊: bioRxiv : the preprint server for biology
• 作者: Yuan,Meng;Wang,Yiquan;Lv,Huibin;Wilson,IanA;Wu,NicholasC
• 通讯作者: Wu,NicholasC

A large-scale systematic survey reveals recurring molecular features of public antibody responses to SARS-CoV-2.

• DOI: 10.1016/j.immuni.2022.03.019
• 发表时间: 2022-06-14
• 期刊: Immunity
• 影响因子: 32.4
• 作者: Wang Y;Yuan M;Lv H;Peng J;Wilson IA;Wu NC
• 通讯作者: Wu NC

Antigenic evolution of human influenza H3N2 neuraminidase is constrained by charge balancing.

• DOI: 10.7554/elife.72516
• 发表时间: 2021-12-08
• 期刊: eLife
• 影响因子: 7.7
• 作者: Wang Y;Lei R;Nourmohammad A;Wu NC
• 通讯作者: Wu NC

High-throughput identification of prefusion-stabilizing mutations in SARS-CoV-2 spike.

高通量鉴定 SARS-CoV-2 刺突中的融合前稳定突变。

• DOI: 10.1101/2022.09.24.509341
• 发表时间: 2022
• 期刊: bioRxiv : the preprint server for biology
• 作者: Tan,TimothyJC;Mou,Zongjun;Lei,Ruipeng;Ouyang,WenhaoO;Yuan,Meng;Song,Ge;Andrabi,Raiees;Wilson,IanA;Kieffer,Collin;Dai,Xinghong;Matreyek,KennethA;Wu,NicholasC
• 通讯作者: Wu,NicholasC

Probing the biophysical constraints of SARS-CoV-2 spike N-terminal domain using deep mutational scanning.

• DOI: 10.1126/sciadv.add7221
• 发表时间: 2022-11-25
• 期刊: Science advances
• 影响因子: 13.6