Promoter interactome-aided mapping of unexplored CVID genetic landscapes

未探索的 CVID 遗传景观的启动子相互作用组辅助绘图

• 批准号: 10640143
• 负责人: NEIL David ROMBERG
• 金额: $ 57.02万
• 依托单位: CHILDREN'S HOSP OF PHILADELPHIA
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-16 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10640143
• 关键词: 3-Dimensional; ATAC-seq; Affinity; Antibodies; Architecture; Autoimmune Diseases; B-Lymphocytes; BLR1 gene; Blood specimen; CD19 gene; CD4 Positive T Lymphocytes; Cataloging; Catalogs; Cell Differentiation process; Cell Line; Cell physiology; Cells; Cessation of life; Chromatin; Coculture Techniques; Code; Combinatorics; Common Variable Immunodeficiency; Communicable Diseases; Complement 3d Receptors; Copy Number Polymorphism; DNA; Data; Data Set; Disease; Environment; Epigenetic Process; Euchromatin; Fostering; Functional disorder; Gene Expression; Genes; Genetic; Genetic Transcription; Genetic Variation; Genome; Genome Mappings; Genomic Segment; Genotype; Goals; Grant; Helper-Inducer T-Lymphocyte; Homeostasis; Hyperplasia; Immunocompetent; Immunoglobulin Class Switching; Immunoglobulin D; Immunologic Deficiency Syndromes; Individual; Inherited; Investigation; Linkage Disequilibrium; Lymph Node Dissections; Lymphocyte; Lymphocyte Function; Lymphoid Tissue; Maps; Measures; Mendelian disorder; Methods; Pathogenesis; Pathology; Patients; Phenotype; Predisposition; Proteins; Proxy; Publishing; Quantitative Trait Loci; RNA library; Sampling; Sentinel; Single Nucleotide Polymorphism; Sorting; Spliced Genes; Structure; Structure of germinal center of lymph node; Symptoms; T-Lymphocyte; Technology; Testing; Tissues; Tonsil; Transcript; Transcriptional Regulation; Untranslated RNA; Validation; Variant; Work; cell type; chromosome conformation capture; clinically significant; common symptom; congenital immunodeficiency; exome; gene interaction; genetic variant; genetically modified cells; genome wide association study; genome-wide; innovation; interleukin-21; lymph node biopsy; lymph nodes; novel diagnostics; novel therapeutics; personalized medicine; programs; promoter; response; transcriptome; whole genome

PROJECT SUMMARY/ABSTRACT Common variable immunodeficiency (CVID) is a primary disease of germinal center (GC) dysfunction, yet most CVID mechanistic investigations have utilized patient blood samples, which do not contain bona fide GC cells. Similarly, genome-wide association studies (GWAS) of CVID patients have identified many disease-associated single nucleotide polymorphisms (SNPs), yet most lie in non-coding DNA and are of unclear relevance to disease pathogenesis. The long-range goal of the proposed work is to determine the full genetic basis of CVID. The objective of this grant is to determine which non-coding regions of DNA contribute to GC dysfunction. The working hypothesis is that CVID GWAS SNPs point to important non-coding genomic regions that interact with promoters of genes key to GC lymphocyte function. Further, genetic variation altering gene promoter interactions, or damage to these genes themselves, will lead to GC dysfunction and eventually the symptoms of CVID. Our rationale is that identifying gene promoter interactions critical to GC homeostasis will provide new diagnostic and therapeutic opportunities for patients suffering from diseases of GC dysfunction including, but not limited to, CVID. Our specific aims will test the following hypotheses: (Aim 1) CVID GWAS associated regions euchromatically interact with gene promoters in T follicular helper cells (Tfh) and/or follicular B cells (FO B cells); (Aim 2) these interactions influence gene expression; (Aim 3) non-coding variants altering gene expression or variants damaging coding genes are enriched in CVID patients and that rhese variants alter Tfh and FO B cell function. The contribution is significant because cataloguing the genes and gene promoter contacts vital to GC homeostasis/dysfunction will offer new disease discovery opportunities and provide new molecules to target with personalized therapies. The proposed work is innovative because we are reinterpreting published GWAS with a suite of interlocking genome-scale technologies capable of annotating individual SNPs with overlapping layers of cell type-specific epigenetic information including promoter contacts, chromatin availability and gene expression. Further, we are verifying our findings in CVID exomes and genomes, with genetically modified cell-lines, with patient lymph nodes and in co-cultures that recapitulate key transcriptional features of the GC environment.

项目概要/摘要 常见变异型免疫缺陷（CVID）是生发中心（GC）功能障碍的原发性疾病，但大多数 CVID 机制研究使用了患者血液样本，其中不含真正的 GC 细胞。 同样，CVID 患者的全基因组关联研究 (GWAS) 也发现了许多与疾病相关的疾病。 单核苷酸多态性 (SNP)，但大多数存在于非编码 DNA 中，与疾病相关性尚不清楚 疾病发病机制。这项工作的长期目标是确定 CVID 的完整遗传基础。 此项资助的目的是确定 DNA 的哪些非编码区域会导致 GC 功能障碍。这 工作假设是 CVID GWAS SNP 指向重要的非编码基因组区域，这些区域与 GC 淋巴细胞功能关键基因的启动子。此外，遗传变异改变基因启动子 这些基因本身的相互作用或损伤将导致 GC 功能障碍，并最终导致症状 CVID。我们的理由是，识别对 GC 稳态至关重要的基因启动子相互作用将提供新的 为患有 GC 功能障碍疾病的患者提供诊断和治疗机会，包括但 不限于CVID。我们的具体目标将测试以下假设：（目标 1）CVID GWAS 相关 常染色质区域与滤泡辅助细胞 (Tfh) 和/或滤泡 B 细胞中的基因启动子相互作用 （FO B 细胞）； （目标 2）这些相互作用影响基因表达； （目标 3）改变基因的非编码变异 破坏性编码基因的表达或变异在 CVID 患者中丰富，并且这些变异会改变 Tfh 和 FO B 细胞功能。这一贡献是显着的，因为对基因和基因启动子进行了编目 对 GC 稳态/功能障碍至关重要的接触将提供新的疾病发现机会并提供新的 个性化治疗的靶向分子。拟议的工作具有创新性，因为我们正在重新解释 发布了 GWAS，其中包含一套能够注释单个 SNP 的连锁基因组规模技术 具有细胞类型特异性表观遗传信息的重叠层，包括启动子接触、染色质 可用性和基因表达。此外，我们正在验证我们在 CVID 外显子组和基因组中的发现， 转基因细胞系，与患者淋巴结和共培养物一起重述关键转录 GC 环境的特点。