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.

此优点评估应用程序基于我们的假设，即成纤维细胞样滑膜细胞(FLS)来自 感染EB病毒的类风湿关节炎(RA)患者将拥有独特的基因 改变宿主对EBV的免疫反应的表达特性，以及这些差异影响风险 用于发展RA。这些假设基于以下观察：所有12个FLS细胞系 我们已经评估了6名类风湿性关节炎(RA)患者和6名骨关节炎(OA)患者 对照组，含有一些感染EBV的细胞。我们发现FLS可以重叠感染EBV。我们 观察到RA(而不是OA)遗传风险基因座富含DNA变异，这些DNA变异是免疫沉淀的 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，RA和OA在基因表达上存在差异 受类风湿性关节炎风险基因座中的元素控制。这些观察结果和发表在Pubmed上的792篇论文经常 EB病毒和类风湿性关节炎之间存在许多相互矛盾的关系。在我们看来，这些观察结果是 与EB病毒参与类风湿关节炎的发病机制一致。 我们计划通过这个DVA优秀奖项目实施三项举措。首先，我们将描述病毒感染的特征 FLS(目标1)：评估EBV FLS感染频率，对FLS中的EBV DNA进行测序，以及 比较EB病毒基因在类风湿关节炎、骨性关节炎和正常(NL)FLS中的表达。我们将检验FLS感染的假设 在EBV感染人群中很常见。第二，我们将探索FLS对EBV的反应 感染(目标2)用RNA-seq测定宿主基因表达以评估EBV感染和继发性 RA、OA和NL受试者对FLS的影响以及RA、OA和NL中RA基因座的等位基因特异性 FLS。一旦实验条件确定，单细胞rna-seq将确定细胞群体的特征。 EBV感染和对EBV感染有反应的细胞。这些实验将对假设进行评估 RA FLS将具有与OA或NL受试者的FLS不同的基因表达谱，并且 表达数量性状基因座(EQTL)可以区分RA、OA和NL FLS。第三，我们将评估 对EB病毒感染的FLS的免疫应答(目标3)。我们的假设是宿主对EBV感染的反应 FLS将RA与OA和NL受试者区分开来。具体地说，我们详细的工作假设和当前 模型为：1.通常OA&NL FL流产感染EBV；2.OA&NL EB病毒感染 FL的存在水平很低，可能只表达几个EBV潜伏基因，就像在潜伏感染的B组中所看到的那样 EBV感染的OA和NL FL通常处于静止状态，不能进行免疫识别。相比之下，在RA 有证据表明，EBV裂解计划的早期步骤是通过表达早期- 即刻EBV抗原。这些变化与其他因素(如抗环瓜氨酸)相结合 多肽自身抗体、可能的微生物组变化等)唤醒静止的免疫反应， 导致针对EBV感染的RA FLS的压倒性炎症反应 不发生在OA或NL滑膜。正如我们在之前提交的材料中的经验一样，结果 所取得的成果可能与这些想法中的任何一个相矛盾，从而将这项工作引向一个新的概念和战略方向。在……上面 另一方面，这项工作有可能提供目前未知的方面的机械细节 RA的发病机制，这将成为新的治疗方法和预防策略的基础。 无论EBV是否是RA发病机制的组成部分，所提出的研究将为深入了解 以前未知的常见慢性病毒感染的特定组织部位和可能的储蓄者 感染了绝大多数人类。