Project 2: The Isoform repertoire and epigenome of Pediatric SLE

项目 2：儿科 SLE 的异构体库和表观基因组

• 批准号: 9194912
• 负责人: Jacques F Banchereau
• 金额: $ 64.25万
• 依托单位: BAYLOR RESEARCH INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-21 至 2017-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9194912
• 关键词: ATAC-seq; Address; Affect; Age; Alternative Splicing; Autoimmune Process; Autoimmunity; B-Lymphocytes; Biological Assay; Blood; Blood Cells; Cell physiology; Cells; Characteristics; Child; Childhood; Chromatin; Chronic Childhood Arthritis; Clinical; Clinical assessments; Communicable Diseases; Complement; Complex; Computational Biology; Coupled; DNA; Data; Data Analyses; Dermatomyositis; Development; Diagnostic; Disease; Epigenetic Process; Etiology; Gene Expression; Gene Expression Profile; Genes; Genetic Transcription; Genome; Genomics; Goals; Health; Heterogeneity; Human; Human Genome; Hybrids; Immune; Immunology; Interferons; Lupus; Messenger RNA; Methods; Modification; Molecular; Molecular Profiling; Molecular Target; Monoclonal Antibodies; Mononuclear; Monozygotic twins; Morbidity - disease rate; Myeloid Cells; Patients; Pattern; Penetrance; Plasmablast; Population; Protein Isoforms; Public Health; RNA Splicing; Reading; Research; Sampling; Seminal; Serum; Site; Subgroup; Symptoms; Systemic Lupus Erythematosus; Systems Biology; Technology; Therapeutic Intervention; Transposase; Whole Blood; autoinflammatory; base; cohort; comparative; data management; design; differential expression; disease heterogeneity; disorder subtype; epigenome; epigenomics; exon skipping; genomic data; high throughput screening; immune function; in vitro Assay; insight; knowledge base; link protein; mRNA Precursor; monocyte; nano-string; neutrophil; new therapeutic target; novel; novel marker; novel therapeutics; patient stratification; profiles in patients; promoter; research study; screening; statistics; targeted treatment; tool; transcriptome; transcriptome sequencing; transcriptomics

PROJECT SUMMARY SLE is a disease of high morbidity for which treatment options are poor. Identifying relevant targets for therapeutic intervention is difficult owing to the molecular and clinical heterogeneity of the disease. Through a large body of work, we have demonstrated that blood-based transcriptomic profiling can be used to parse out distinct transcriptional differences in immune function in health and disease. Relevant to the current application are our studies showing that SLE can be divided into seven disease subgroups based on distinct blood transcriptional signatures. More recently, we developed a sophisticated for integrated Profiling and Analysis Pipeline (iPAP) that we used to identify meaningful epigenetic and transcriptomic differences in human populations, including SLE cohorts. Building upon this knowledgebase will help us identify potential drivers of the disease, and ultimately novel biomarkers and novel therapeutic targets for SLE. We hypothesize that SLE is comprised of a spectrum of disease subtypes that can be categorized according to mutually distinct epigenomic, isoformic and transcriptomic features. The goal of this project is to characterize the repertoire of immune cell isoforms and the epigenome profiles associated with three of the seven most frequent pediatric SLE subgroups: SLE-Plasmablast (SLE-P), characterized by a plasmablast transcriptional signature and the presence of increased circulating plasmablasts; SLE-Interferon/Myeloid cells (SLE-IM), which shows an IFN and a neutrophil signature; and SLE-Plasmablast/ Interferon/Myeloid cells (SLE-PIM) displaying the three main signatures. We will use novel experimental paradigms that incorporate cutting-edge genomic technologies and build upon our established expertise in molecular immune profiling. Our project contains two Specific Aims: 1) To analyze the alternatively spliced transcriptome of blood cells from the three SLE patient subgroups, in which we will apply both short-read (Illumina HiSeq2500) and long-read (PacBio RSII) sequencing technologies to interrogate the isoform repertoire of PBMCs and select immune cell subsets; and 2) To determine the epigenome of blood cells from the three SLE subgroups, through studies capitalizing on a robust and sensitive new epigenomic assay called ATAC-seq coupled to Methyl-seq. Healthy age- matched samples will be used as controls in all experiments and, we will also examine samples from children with active juvenile dermatomyositis and systemic juvenile arthritis (n=5 per group), to identify those isoforms and signatures unique to SLE from those more generally associated with autoimmunity. Our team includes experts in immunology, genomics, epigenetics, systems biology of disease, computational biology, data management and statistics, who bring the collective expertise necessary for generating top quality genomics data and for robust data analysis using state-of-the-art methods. We will also create new tools, i.e., Nanostring probes and monoclonal antibodies, for high throughout screening assays suited to large patient cohorts. Successful completion of our project will reveal novel biomarkers of SLE and/or novel therapeutic targets.

项目摘要 SLE是一种高发病率的疾病，治疗方案很差。确定相关目标 由于该疾病的分子和临床异质性，治疗干预很困难。通过一个 大量工作，我们已经证明了基于血液的转录组分析可用于解析 健康和疾病中免疫功能的明显转录差异。与当前申请有关 我们的研究表明，基于独特的血液，SLE可以分为七个疾病亚组 转录签名。最近，我们开发了一个精致的集成分析和分析 我们用来识别人类中有意义的表观遗传和转录组差异的管道（IPAP） 种群，包括SLE队列。在此知识基础上，将帮助我们确定 该疾病，最终是新型的生物标志物和SLE的新型治疗靶标。我们假设SLE 由可以根据相互不同的疾病亚型组成 表观基因组，同基和转录组特征。该项目的目的是表征曲目 免疫细胞同工型和与七个最常见的三个相关的表观依代组曲线 小儿SLE子组：SLE-plasmablast（SLE-P），其特征是浆质转录特征 并存在增加的循环纤溶酶； SLE-Interferon/髓样细胞（SLE-IM），显示 IFN和中性粒细胞特征；和SLE-plasmablast/ Interferon/ Myeloid细胞（SLE-PIM）显示 三个主要签名。我们将使用新型的实验范例，这些范式结合了尖端的基因组 技术并以我们在分子免疫分析方面既定的专业知识为基础。我们的项目包含两个 具体目的：1）分析来自三个SLE的血细胞的剪接转录体 患者亚组，我们将同时应用短读（Illumina Hiseq2500）和长阅读（PACBIO RSII） 测序技术以询问PBMC的同工型库，并选择免疫细胞子集；和 2）通过研究资料来确定来自三个SLE亚组的血细胞的表观组 在一种强大而敏感的新表观基因组学测定中，称为atac-seq耦合到甲基序列。健康的年龄 - 匹配的样品将在所有实验中用作对照，我们还将检查儿童的样本 活跃的青少年皮肌炎和全身性少年关节炎（每组n = 5），以识别这些同工型 SLE独有的签名来自与自身免疫相关的人。我们的团队包括 免疫学，基因组学，表观遗传学，疾病系统生物学，计算生物学，数据专家 管理和统计，他们带来了产生高质量基因组学所必需的集体专业知识 数据和使用最先进方法的可靠数据分析。我们还将创建新工具，即纳米弦 探针和单克隆抗体，在整个筛选分析中，适合大型患者同类。 成功完成我们的项目将揭示SLE和/或新型治疗靶标的新型生物标志物。