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.

项目总结/摘要 这项R21提案的首要目标是检验DNA疫苗诱导持久先天免疫的假设。 通过表征表观遗传和转录景观的演变， 在使用新型HIV DNA疫苗免疫的受试者中。我们最近使用了一个“系统 免疫学”的方法，成功地映射免疫的表观基因组和转录景观， 健康人接种流感疫苗。针对季节性流感的疫苗接种，有或没有AS 03佐剂， 导致单核细胞和髓样树突状细胞（mDC）中H3 K27 ac表达持续降低， 与对Toll样受体（TLR）刺激的细胞因子应答受损相关。单细胞分析 揭示了一个表观基因组学上不同的髓样细胞亚群，在激活子处染色质可及性降低， 蛋白-1（AP-1）靶向位点，持续增加染色质可及性的靶向位点， 干扰素（IFN）反应因子（IRFs）与抗病毒基因表达升高相关， 1 IFN的产生，以及对异源病毒Zika和登革热感染的增强抵抗力。在 另一篇最近的论文，我们已经表明，辉瑞BioNTech mRNA初免-加强疫苗（BNT 162 b2）， 在增强的先天性免疫应答中，通过更高频率的CD 14 + CD 16+炎性 单核细胞，更高的血浆IFN-γ和先天性抗病毒免疫的转录特征。我们将复制 这个“系统免疫学”框架使用外周血单核细胞来表征先天记忆， A5369初免-加强DNA疫苗试验（NCT 03560258）中HIV+受试者的PBMC。诱导和 在本R21中，将在3个目标中研究先天记忆的持久性。目的1将确定组蛋白翻译后 使用流式细胞术的表观遗传景观分析，以单细胞分辨率检测PBMC中的HPTM 飞行时间（EpiTOF）我们将检验抗原特异性DNA疫苗接种诱导先天性 通过表观遗传重编程的记忆，随着每个连续的启动和加强而扩展（第0周<第6周 <<第26周），并在第48周保存。目标2将确定基因转录模块，以及它们在 时间，与先天记忆有关。我们将检验抗原特异性DNA疫苗接种诱导 持久的先天记忆通过转录组的变化和扩大与每个顺序的启动和加强 (week 0 &lt;< week 26 >第48周）。我们将检验这样一个假设，即表征先天性的转录模块 流感和SARS-CoV-2疫苗接种中的记忆可推广到HIV DNA疫苗。我们也期望 识别与先天记忆相关的独特的细胞亚群，转录本和通路， 流感和SARS-CoV-2。目标3将通过整合EpiTOF和 目的1和2的转录组学数据，并与流感和SARS-CoV-2疫苗接种的类似数据进行比较 受试者测试的假设，有一个普遍的机制，潜在的先天记忆， 疫苗平台，以及对DNA疫苗和/或HIV感染特异的细胞和途径。