A combined computational and experimental approach to the evolution and role of the DNA sequence environment in targeting mutations to antibody V regions

一种结合计算和实验的方法来研究 DNA 序列环境的进化和在抗体 V 区靶向突变中的作用

• 批准号: 10375356
• 负责人: ROBERT C. RIZZO
• 金额: $ 57.88万
• 依托单位: ALBERT EINSTEIN COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-03-01 至 2024-02-29
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10375356
• 关键词: Affect; Alleles; Animal Experiments; Antibodies; Antibody Affinity; Antigens; Autoimmunity; B lymphoid malignancy; B-Cell Development; B-Cell Lymphomas; B-Lymphocytes; Biological; Biology; Cell Line; Chromatin; Complementarity Determining Regions; Computer Analysis; Computer Models; DNA; DNA Sequence; Data; Databases; Development; Disease; Environment; Enzyme Activation; Evaluation; Event; Evolution; Family; Feedback; Frequencies; Future; GTP-Binding Protein alpha Subunits, Gs; Gene-Modified; Genes; Goals; HIV; Heavy-Chain Immunoglobulins; Human; Human Cell Line; Immune response; Immunity; Immunoglobulin Somatic Hypermutation; Immunoglobulins; Individual; Infection; Infectious Agent; Influenza; Influenza Hemagglutinin; Knock-in; Lead; Location; Machine Learning; Malignant Neoplasms; Mediating; Medical; Mismatch Repair; Molecular; Mus; Mutate; Mutation; Outcome; Pattern; Play; Polymerase; Process; Public Health; Research; Risk Factors; Role; Site; Solid Neoplasm; Statistical Models; Stomach; Structure of germinal center of lymph node; Techniques; Testing; Therapeutic antibodies; Time; Transgenic Mice; Validation; Variant; activation-induced cytidine deaminase; base; chromatin modification; density; experimental study; genetic variant; human data; in vivo; in vivo Model; innovation; neutralizing antibody; recruit; repair enzyme; response; spatial relationship; vaccine development; vaccine response; vaccine-induced antibodies

Project summary There is a fundamental gap in our understanding of how mutations are preferentially targeted to the variable (V) regions of the Immunoglobulin (Ig) loci during somatic hypermutation (SHM). The persistence of this gap has limited our understanding of the mutagenic mechanisms involving activation-induced deaminase (AID) in the immune response and in the role of AID in mis-targeting mutations leading to B-cell lymphomas and other cancers. The long-term goal of the proposed research is to understand the global targeting of mutations in immunity that are required to protect us from infections. As high-throughput data from human antibody immune responses became available, it provided us with new opportunities to generate hypotheses to explain the underlying mechanisms of SHM. We now propose to generate further hypotheses using computational models applied to additional databases and to validate these hypotheses using cellular and animal experiments. Our objective is to understand what directs SHM across the many human Ig heavy chain V-regions. Our central hypothesis is that the V-region SHM process is highly dependent on a DNA sequence signature(s) that drives mutations in a largely deterministic fashion. This hypothesis is supported by our preliminary results using human in vivo data from a few human V region genes and has begun to be validated using independent databases and experiments in human B cell lines. The rationale is that evaluations of computational data based upon biological mechanisms, together with appropriate biological experiments, will reveal the key differences between IGHV regions (IGHV 3-23, 4-34, 1-18, 1-02, etc.) that lead to the dominance of each of those V regions in the responses to medically important antigens. Our hypothesis will be tested by pursuing two specific aims: 1) identify the extent to which a DNA signature determines the mutation process in four individual human IGHV genes that are important in disease responses; 2) examine the relationship between AID hotspots and Polη hotspots across all the other human V region genes, thus rigorously defining a mutation targeting signature. Both aims will also entail studying human V region genes and modifications of them in human cell lines and in mice expressing a human V region to further confirm the signature and identify molecular mechanisms in vivo. Our approach is innovative because the computational models we are proposing will be mechanistically motivated focusing on the interaction between AID and Polη hotspots, thus testing molecular mechanisms as opposed to classic statistical models using whole V region sequences that ignore the underlying biology. In addition, to focus on mechanisms we will leverage new high-throughput data from human V regions that have not undergone antigen selection. Our results will be highly relevant to human IgV repertoire analyses from immune responses that are currently hard to interpret and will help future vaccine and therapeutic antibody development, as well as help to understand mutations in human malignancies where AID plays a key role.

项目概要 我们对突变如何优先针对变量的理解存在根本差距 (V) 体细胞超突变 (SHM) 期间免疫球蛋白 (Ig) 基因座的区域。这种差距的持续存在 限制了我们对涉及激活诱导脱氨酶（AID）的诱变机制的理解 免疫反应以及 AID 在导致 B 细胞淋巴瘤的错误靶向突变中的作用 其他癌症。拟议研究的长期目标是了解全球目标 保护我们免受感染所需的免疫突变。作为来自人类的高通量数据 抗体免疫反应的出现，为我们提供了产生新的机会 解释 SHM 潜在机制的假设。我们现在建议产生进一步的假设 使用应用于其他数据库的计算模型并使用细胞验证这些假设 和动物实验。我们的目标是了解是什么引导 SHM 跨越许多人类 Ig 重链 链V区。我们的中心假设是 V 区 SHM 过程高度依赖于 DNA 以很大程度上确定性的方式驱动突变的序列签名。这个假设得到支持 根据我们的初步结果，使用来自一些人类 V 区基因的人体数据，并已开始 使用独立数据库和人类 B 细胞系实验进行验证。理由是 基于生物机制的计算数据的评估，以及适当的生物 实验，将揭示 IGHV 区域（IGHV 3-23、4-34、1-18、1-02 等）之间的关键差异， 导致每个 V 区在对医学上重要抗原的反应中占主导地位。我们的 假设将通过追求两个具体目标来检验：1）确定 DNA 特征的程度 确定四个对疾病很重要的人类 IGHV 基因的突变过程 回应； 2）检查所有其他人类的 AID 热点和 Polη 热点之间的关系 V 区基因，从而严格定义突变靶向特征。这两个目标还需要学习 人类V区基因及其在人类细胞系和表达人类V区的小鼠中的修饰 区域以进一步确认特征并确定体内分子机制。我们的方法是 创新，因为我们提出的计算模型将是机械驱动的聚焦 关于 AID 和 Polη 热点之间的相互作用，从而测试分子机制，而不是 使用整个 V 区序列的经典统计模型忽略了潜在的生物学。此外 重点关注我们将利用来自人类 V 区的新高通量数据的机制，这些数据尚未 经过抗原选择。我们的结果将与人类 IgV 库分析高度相关 目前难以解释的免疫反应将有助于未来的疫苗和治疗性抗体 发展，并有助于了解 AID 在人类恶性肿瘤中发挥关键作用的突变。

项目成果

Mutational pressure by host APOBEC3s more strongly affects genes expressed early in the lytic phase of herpes simplex virus-1 (HSV-1) and human polyomavirus (HPyV) infection.

宿主 APOBEC3 的突变压力更强烈地影响单纯疱疹病毒 1 (HSV-1) 和人多瘤病毒 (HPyV) 感染裂解期早期表达的基因。

• DOI: 10.1371/journal.ppat.1009560
• 发表时间: 2021-04
• 期刊: PLoS pathogens
• 影响因子: 6.7
• 作者: Shapiro M;Krug LT;MacCarthy T
• 通讯作者: MacCarthy T

AID Overlapping and Polη Hotspots Are Key Features of Evolutionary Variation Within the Human Antibody Heavy Chain (IGHV) Genes.

AID 重叠和 PolÎ 热点是人类抗体重链 (IGHV) 基因内进化变异的关键特征。

• DOI: 10.3389/fimmu.2020.00788
• 发表时间: 2020
• 期刊: Frontiers in immunology
• 影响因子: 7.3
• 作者: Tang,Catherine;Bagnara,Davide;Chiorazzi,Nicholas;Scharff,MatthewD;MacCarthy,Thomas
• 通讯作者: MacCarthy,Thomas

STAT3 imparts BRCAness by impairing homologous recombination repair in Epstein-Barr virus-transformed B lymphocytes.

STAT3 通过损害 Epstein-Barr 病毒转化的 B 淋巴细胞的同源重组修复来赋予 BRCAness。

• DOI: 10.1371/journal.ppat.1008849
• 发表时间: 2020-10
• 期刊: PLoS pathogens
• 影响因子: 6.7
• 作者: McIntosh MT;Koganti S;Boatwright JL;Li X;Spadaro SV;Brantly AC;Ayers JB;Perez RD;Burton EM;Burgula S;MacCarthy T;Bhaduri-McIntosh S
• 通讯作者: Bhaduri-McIntosh S

The cytidine deaminase under-representation reporter (CDUR) as a tool to study evolution of sequences under deaminase mutational pressure.

• DOI: 10.1186/s12859-018-2161-y
• 发表时间: 2018-05-02
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Shapiro M;Meier S;MacCarthy T
• 通讯作者: MacCarthy T

Post-Transformation IGHV-IGHD-IGHJ Mutations in Chronic Lymphocytic Leukemia B Cells: Implications for Mutational Mechanisms and Impact on Clinical Course.

• DOI: 10.3389/fonc.2021.640731
• 发表时间: 2021
• 期刊: Frontiers in oncology
• 影响因子: 4.7
• 作者: Bagnara D;Tang C;Brown JR;Kasar S;Fernandes S;Colombo M;Vergani S;Mazzarello AN;Ghiotto F;Bruno S;Morabito F;Rai KR;Kolitz JE;Barrientos JC;Allen SL;Fais F;Scharff MD;MacCarthy T;Chiorazzi N
• 通讯作者: Chiorazzi N