DNA Binding of Human and Viral Transcription Factors is Associated with Rheumatoid Arthritis Risk Loci

人类和病毒转录因子的 DNA 结合与类风湿关节炎风险位点相关

• 批准号: 10421240
• 负责人: KENNETH M KAUFMAN
• 金额: --
• 依托单位: CINCINNATI VA MEDICAL CENTER RESEARCH
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-10-01 至 2023-09-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10421240
• 关键词: Alleles; Arthritis; Autoantibodies; Award; B-Lymphocytes; CD8-Positive T-Lymphocytes; Cell Line; Cells; ChIP-seq; Chronic; Complex; DNA; DNA Binding; Data; Degenerative polyarthritis; Dependence; Development; Diagnosis; Elements; Environment; Epstein-Barr Virus Infections; Epstein-Barr Virus latency; Etiology; Fibroblasts; Foundations; Frequencies; Future; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Genes; Genetic; Genetic Risk; Human; Human Herpesvirus 4; Immune; Immune response; Individual; Infection; Inflammatory; Inflammatory Response; Investigation; Joints; Learning; Lytic Virus; Modeling; Nature; Nuclear Antigens; Pathogenesis; Pathology; Patients; Peptides; Population; Prevention strategy; Probability; Process; Property; PubMed; Publications; Quantitative Trait Loci; Regulator Genes; Relative Risks; Rheumatoid Arthritis; Risk; Site; Specificity; Synovial Membrane; Systemic disease; T cell response; Testing; Therapeutic; Tissues; Variant; Viral; Viral Antigens; Viral Proteins; Virus; Virus Diseases; Work; base; cyclic citrullinated peptide; design; differential expression; disorder control; experience; experimental study; gene product; genomic locus; infected B cell; insight; joint destruction; medical attention; microbiome; morphogens; novel therapeutic intervention; prevent; programs; response; risk variant; single-cell RNA sequencing; small molecule libraries; transcription factor; transcriptome sequencing; viral DNA; virtual

This Merit Review application is based on our hypotheses that Fibroblast-Like Synoviocytes (FLS) from Rheumatoid Arthritis (RA) patients infected with Epstein - Barr virus (EBV) will have unique gene expression properties that alter the host immune response to EBV, and that these difference influences the risk for developing RA. These hypotheses is based on the following observations: All 12 of the FLS cell lines that we have evaluated, six from Rheumatoid Arthritis (RA) patients and six from Osteoarthritis (OA) disease controls, contained some cells infected with EBV. We discovered that FLS can be superinfected with EBV. We observed that RA (but not OA) genetic risk loci are enriched for DNA variants that are immunoprecipitated with Epstein-Barr Nuclear Antigen-2 (EBNA2) (Relative Risk (RR)=4.5, Bonferroni corrected probability (Pc)=2.4x10-14). Preliminary data showed differences between RA and OA in the expression of the genes controlled by elements in RA risk loci. These observations and the 792 publications in Pubmed, often contradictory, present many intriguing relationships between EBV and RA. In our view these observations are consistent with EBV being involved in the pathogenesis of RA. We plan three initiatives with this DVA Merit Award project. First, we will characterize the virus infection in FLS (Aim 1) by: assessing the frequency of EBV FLS infection, sequencing the EBV DNA in FLS, and comparing EBV gene expression in RA, OA, & normal (NL) FLS. We will test the hypothesis that FLS infection is common among the EBV infected human population. Second, we will explore the FLS response to EBV infection (Aim 2) by determining host gene expression with RNA-seq to assess EBV infected and secondarily influenced FLS from RA, OA, & NL subjects and by exploring allele specificity at RA loci in RA, OA, and NL FLS. Once experimental conditions are determined, single cell RNA-seq will characterize the cell population infected with EBV and the cells responding to EBV infection. These experiments will evaluate the hypotheses that RA FLS will have a different gene expression profile than the FLS from OA or NL subjects and that the expression quantitative trait loci (eQTL) will distinguish RA from OA and NL FLS. Third, we will assess the immune response to EBV infected FLS (Aim 3). Our hypothesis is that the host response to EBV infection of the FLS will differentiate RA from OA and NL subjects. In specific, our detailed working hypothesis and current model is: 1. That usually the OA & NL FLS are abortively infected with EBV, 2. That OA & NL EBV infected FLS exist at a minimal level, perhaps only expressing a few EBV latent genes, as seen in latently infected B cells, and 3. That EBV infected OA & NL FLS are usually quiescent to immune recognition. In contrast, in RA there is evidence that the early steps of the EBV lytic program are initiated with the expression of Early- Immediate EBV antigens. These changes in combination with other factors (e.g., anti-cyclic citrullinated peptide autoantibodies, possible microbiome changes, etc.) awaken the quiescent immune response and result in an overwhelming inflammatory response directed against the EBV infected RA FLS in a way that does not happen in the OA or NL synovium. As has been our experience in the previous submissions, the results obtained may contradict any of these ideas leading this work into a new conceptual and strategic direction. On the other hand, this work has the potential to provide mechanistic details of the currently unknown aspects of RA pathogenesis, which would become the basis for new therapeutic approaches and preventive strategies. Whether or not EBV is a component of RA pathogenesis, the studies proposed will provide insight into a previously unknown tissue specific site of and possible reservoir for a common chronic viral infection that infects the vast majority of human beings.

此优点审查申请是基于我们的假设，该假设是从 感染爱泼斯坦 - 巴尔病毒（EBV）的类风湿关节炎（RA）患者将具有独特的基因 改变宿主免疫反应EBV的表达特性，这些差异会影响风险 用于开发RA。这些假设基于以下观察结果：所有12个FLS细胞系 我们已经评估了六例类风湿关节炎（RA）患者，六名来自骨关节炎（OA）疾病 对照包含一些感染EBV的细胞。我们发现可以将FLS与EBV息息。我们 观察到RA（而非OA）遗传风险基因座富含与与 Epstein-Barr核抗原2（EBNA2）（相对风险（RR）= 4.5，Bonferroni校正概率 （PC）= 2.4x10-14）。初步数据显示了RA和OA在基因表达中的差异 由RA风险基因座中的元素控制。这些观察结果和PubMed中的792个出版物，通常 矛盾的是，EBV与RA之间的许多有趣的关系。我们认为这些观察是 与EBV一致参与RA的发病机理。 我们通过此DVA优异奖项目计划三个计划。首先，我们将表征病毒感染 FLS（AIM 1）by：评估EBV FLS感染的频率，对FL中的EBV DNA进行排序，然后 比较RA，OA和正常（NL）FL中的EBV基因表达。我们将检验FLS感染的假设 在EBV感染的人群中很常见。第二，我们将探索FLS对EBV的反应 通过用RNA-seq确定宿主基因表达来评估感染的EBV，其次是感染（AIM 2） 受到RA，OA和NL受试者的FL，并通过探索RA，OA和NL的RA基因座的等位基因特异性 佛罗里达州。一旦确定了实验条件，单细胞RNA-seq将表征细胞群体 感染了EBV和对EBV感染反应的细胞。这些实验将评估假设 RA FLS的基因表达谱将与OA或NL受试者的FL不同，并且 表达定量性状基因座（EQTL）将将RA与OA和NL FL区分开。第三，我们将评估 对EBV感染的FL的免疫反应（AIM 3）。我们的假设是宿主对EBV感染的反应 FLS将使RA与OA和NL受试者区分开。具体而言，我们详细的工作假设和当前 型号为：1。通常OA＆NL FL被EBV堕胎，2。 FL的存在最小的水平，也许只能表达一些EBV潜在基因，如潜在感染的B 细胞，3。感染EBV的OA和NL FL通常会静止不动。相反，在RA中 有证据表明，EBV裂解程序的早期步骤是通过早期表达的 立即使用EBV抗原。这些与其他因素结合的变化（例如，抗环状柑橘类 肽自身抗体，可能的微生物组变化等）唤醒了静止的免疫反应和 导致针对EBV感染的RA FL的压倒性炎症反应以某种方式 在OA或NL滑膜中不发生。就像我们在先前提交的经验一样，结果 所获得的可能与这些想法中的任何一个相矛盾，这将这项工作朝着新的概念和战略方向发展。在 另一方面，这项工作有可能提供当前未知方面的机械细节 RA发病机理，这将成为新的治疗方法和预防策略的基础。 EBV是否是RA发病机理的组成部分，提出的研究将提供有关A 以前未知的组织特异性部位和可能的储存库，用于常见的慢性病毒感染 感染绝大多数人。