Epigenetic Histone Landscape Profiles in HIV

HIV 中的表观遗传组蛋白景观谱

• 批准号: 10535173
• 负责人: PAUL JOSEPH UTZ
• 金额: $ 32.99万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-21 至 2025-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10535173
• 关键词: 2019-nCoV; AIDS clinical trial group; ATAC-seq; Adjuvant; Antigens; Attenuated; Autoimmunity; BCG Live; Bacteria; Blood Cells; CD14 gene; CD34 gene; COVID-19 vaccination; COVID-19 vaccine; Cells; Cellular Indexing of Transcriptomes and Epitopes by Sequencing; ChIP-seq; Chromatin; Chronic; Communicable Diseases; Cryopreservation; Cytometry; DNA; DNA Vaccines; Data; Data Set; Dendritic Cells; Dengue; Elements; Enrollment; Epigenetic Process; Evolution; FCGR3B gene; Frequencies; Future; GTP-Binding Protein alpha Subunits, Gs; Gene Expression Profile; Genes; Genetic Transcription; Goals; HIV; HIV Infections; HIV prevention trial; Hematopoietic stem cells; Histone Deacetylation; Histones; Human; Immune; Immunity; Immunization; Immunize; Immunoglobulin G; Immunologic Memory; Immunology; Impairment; Individual; Inflammatory; Influenza; Influenza vaccination; Innate Immune Response; Interferons; Leukapheresis; Link; Maps; Measurement; Measures; Memory; Messenger RNA; Methods; Myelogenous; Myeloid Cells; Natural History; Natural Immunity; Natural Killer Cells; Outcome; Paper; Participant; Pathway interactions; Patients; Peripheral Blood Mononuclear Cell; Persons; Pfizer-BioNTech COVID-19 vaccine; Placebos; Plasma; Population; Post-Translational Protein Processing; Production; Research Personnel; Resistance to infection; Resolution; SIV; Sampling; Stains; System; T cell response; T-Lymphocyte; Testing; Time; Toll-like receptors; Training; Transcript; Transcription Factor AP-1; Vaccinated; Vaccination; Vaccinee; Vaccines; Validation; Virus; ZIKA; active method; antiviral immunity; arm; cytokine; epigenomics; influenza virus vaccine; innovation; monocyte; novel; preservation; response; seasonal influenza; simian human immunodeficiency virus; single cell analysis; transcriptomics; treatment arm; vaccine platform; vaccine trial

PROJECT SUMMARY/ABSTRACT The overarching goal of this R21 proposal is to test the hypothesis that DNA vaccines induce durable innate memory in HIV-infected humans by characterizing the evolution of the epigenetic and transcriptional landscape in subjects who have been immunized using a novel HIV DNA vaccine. We recently used a “systems immunology” approach to successfully map the epigenomic and transcriptional landscape of immunity to influenza vaccination in healthy humans. Vaccination against seasonal influenza, with or without AS03 adjuvant, resulted in persistently reduced expression of H3K27ac in monocytes and myeloid dendritic cells (mDCs), which was associated with impaired cytokine responses to toll like receptor (TLR) stimulation. Single cell analysis revealed an epigenomically-distinct subcluster of myeloid cells with reduced chromatin accessibility at activator protein-1 (AP-1) targeted loci after vaccination, persistently increased chromatin accessibility at loci targeted by interferon (IFN) response factors (IRFs), which was associated with elevated expression of antiviral genes, type 1 IFN production, and heightened resistance to infection with the heterologous viruses Zika and dengue. In another recent paper, we have shown that the Pfizer-BioNTech mRNA prime-boost vaccine (BNT162b2) resulted in enhanced innate immune responses, evidenced by a greater frequency of CD14+CD16+ inflammatory monocytes, higher plasma IFN-γ, and a transcriptional signature of innate antiviral immunity. We will replicate this “systems immunology” framework to characterize innate memory using peripheral blood mononuclear cells (PBMCs) from HIV+ subjects in the A5369 prime-boost DNA vaccine trial (NCT03560258). Induction and durability of innate memory will be studied across 3 aims in this R21. Aim 1 will identify histone posttranslational modifications (HPTMs) in PBMCs at single-cell resolution using Epigenetic Landscape Profiling using Cytometry by Time Of Flight (EpiTOF). We will test the hypothesis that antigen-specific DNA vaccination induces innate memory through epigenetic reprogramming, expands with each sequential prime and boost (week 0 < week 6 << week 26), and is preserved at week 48. Aim 2 will identify gene transcript modules, and their evolution over time, associated with innate memory. We will test the hypothesis that antigen-specific DNA vaccination induces durable innate memory through transcriptomic changes and expands with each sequential prime and boost (week 0 << week 26 > week 48). We will test the hypothesis that transcriptional modules that characterize innate memory in influenza and SARS-CoV-2 vaccination are generalizable to HIV DNA vaccines. We also expect to identify unique subsets of cells, transcripts, and pathways associated with innate memory that differ from influenza and SARS-CoV-2. Aim 3 will perform systems immunology analysis by integrating EpiTOF and transcriptomic data from Aims 1 &2, and comparing with similar data from influenza and SARS-CoV-2 vaccinated subjects testing the hypothesis that there are generalizable mechanisms underlying innate memory across vaccine platforms, and cells and pathways specific to DNA vaccines and/or HIV infection.

项目摘要/摘要 这项R21提案的首要目标是检验DNA疫苗能够诱导持久的先天免疫的假设 通过表征表观遗传和转录格局的演变来描述HIV感染者的记忆 在使用新型艾滋病毒DNA疫苗进行免疫的受试者中。我们最近使用了一个“系统” 成功地将免疫的表观基因组和转录图谱映射到 在健康人中接种流感疫苗。接种季节性流感疫苗，加或不加AS03佐剂， 导致单核细胞和髓系树突状细胞(MDCs)H3K27ac表达持续减少 与Toll样受体(TLR)刺激的细胞因子反应受损有关。单细胞分析 发现一个表观上不同的髓系细胞亚群，在激活剂处染色质可及性降低 蛋白-1(AP-1)靶向基因座接种后，持续增加了靶向基因座的染色质可及性 干扰素(干扰素)反应因子(IRF)，与抗病毒基因表达升高相关，类型 1产生干扰素，并增强对异源寨卡病毒和登革热病毒感染的抵抗力。在……里面 我们最近的另一篇论文表明，辉瑞-BioNTech mRNA Prime-Boost疫苗(BNT162b2)导致了 在增强的先天免疫反应中，CD14+CD16+炎性细胞的频率更高 单核细胞，较高的血浆干扰素-γ，以及先天抗病毒免疫的转录特征。我们将复制 利用外周血单核细胞来表征先天记忆的“系统免疫学”框架 A5369 PRIME-Boost DNA疫苗试验(NCT03560258)中HIV+受试者的(PBMC)。归纳法和 先天记忆的持久性将在R21中的三个目标上进行研究。目标1将确定组蛋白翻译后 用细胞计数法在单细胞分辨率下利用表观遗传景观分析对PBMC进行修饰(HPTM) 按飞行时间(EpiTOF)。我们将检验一种假设，即抗原特异性DNA疫苗可以诱导先天的 记忆通过表观遗传重新编程，随着每个连续的质数和升压而扩展(第0周和第6周 &lt；&lt；26周)，并在48周保存。目标2将确定基因转录模块及其进化过程 时间与与生俱来的记忆有关。我们将测试抗原特异性DNA疫苗诱导的假设 持久的先天记忆通过转录改变并随着每一次连续的素数和增强而扩展 (第0&lt；&lt；周26和48周)。我们将测试这样一种假设，即表征先天的转录模块 流感和SARS-CoV-2疫苗的记忆可以推广到艾滋病毒DNA疫苗。我们也期待着 识别与先天记忆相关的细胞、转录本和通路的独特子集，这些不同于 流感和SARS-CoV-2。AIM 3将通过整合EpiTOF和 AIMS 1和2的转录数据，并与流感和SARS-CoV-2疫苗接种的相似数据进行比较 受试者测试假设，即存在潜在的先天记忆的可概括机制 疫苗平台，以及针对DNA疫苗和/或艾滋病毒感染的细胞和途径。