Bridging the gap between GWAS and mechanism in JIA

弥合 GWAS 和 JIA 机制之间的差距

• 批准号: 10064581
• 负责人: Peter A Nigrovic
• 金额: $ 39.38万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-12-01 至 2021-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10064581
• 关键词: Address; Affect; Alleles; Arthritis; Binding; Binding Proteins; Bioinformatics; Biological; Biology; Child; Childhood; Chronic Childhood Arthritis; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Collaborations; DNA; DNA-Protein Interaction; Data; Disease; Dissection; Experimental Genetics; Family; Frequencies; Gene Expression; Genes; Genetic Polymorphism; Genomics; Goals; Haplotypes; Human; Human Genetics; Incubated; Individual; Inflammatory; Inflammatory Arthritis; Infrastructure; Joints; Libraries; Link; Linkage Disequilibrium; Luciferases; Mass Spectrum Analysis; Mediating; Methods; Molecular Target; National Institute of Arthritis and Musculoskeletal and Skin Diseases; Nuclear Extract; Oligonucleotides; Pathogenesis; Pathway interactions; Phenotype; Positioning Attribute; Probability; Proteins; Research; Research Personnel; Rheumatoid Arthritis; Rheumatology; Risk; Role; STAT4 gene; Sampling; Single Nucleotide Polymorphism; System; TNF receptor-associated factor 1; TYK2; Techniques; Testing; Therapeutic; Therapeutic Intervention; Translating; Translational Research; Twin Multiple Birth; Untranslated RNA; Validation; Variant; Work; arthropathies; biobank; disorder risk; frontier; genetic association; genetic regulatory protein; genetic variant; genome wide association study; genome-wide; genome-wide analysis; genomic locus; innovation; insight; new therapeutic target; next generation sequencing; novel; ranpirnase; risk variant; systemic juvenile idiopathic arthritis; therapeutic target; tool; transcription factor; validation studies

Project Summary Juvenile idiopathic arthritis (JIA) is a diverse family of inflammatory arthritides that begin in childhood. Genome-wide association studies in the most common phenotype, seronegative oligoarticular plus polyarticular JIA (sometimes for simplicity termed “polygoJIA”), have identified 27 non-HLA loci associated with disease risk. GWAS of the most destructive variant, systemic JIA, has defined additional loci. Each of these “hits” marks a biological pathway in the pathogenesis of JIA. Unfortunately, pinpointing these mechanisms from GWAS data has proven difficult. GWAS hits mark large segments of DNA, termed haplotypes. Most of these haplotypes contain no SNPs (single nucleotide polymorphisms) or other variants that affect coding, suggesting that most causative polymorphisms are regulatory. Finding regulatory SNPs and the proteins that bind them has proven to be exceptionally difficult, and as a result GWAS have so far provided limited insight into JIA biology. To address this roadblock, our lab has recently developed two novel experimental methods. SNP-seq interrogates candidate regulatory variants using enzymatic restriction followed by next-generation sequencing to identify those that bind transcription factors and other regulatory proteins. Flanking Restriction Enhanced Pulldown (FREP) is an efficient method to pull down the associated protein(s) for identification by mass spectrometry, thereby linking disease-associated variants to particular cellular pathways. This tandem strategy allows us to bridge the gap between GWAS and mechanism. The hypothesis underlying this proposal is that experimental dissection of genetic associations will identify new mechanisms and thus new potential therapeutic targets in JIA. In Aim I, we will pursue SNP-seq + FREP to identify novel DNA-protein associations that drive polygoJIA risk. We screened 1,223 genetic polymorphisms in close linkage disequilibrium with 27 polygoJIA risk loci and identified multiple strong candidate functional variants, including several validated experimentally using techniques including electrophoretic mobility shift, luciferase and CRISPR. We will confirm these high-probability variants and then extend the work to other SNP-seq hits. In Aim II, beginning with an independent SNP-seq screen of the TRAF1/C5 locus, we will employ FREP and other upstream and downstream validation approaches to define how this locus drives risk of polygoJIA. We will employ SNP-seq + FREP to interrogate recently- available GWAS findings in systemic JIA to define mechanisms in this unique, highly-inflammatory disease. Together, these studies will allow us to identify DNA-protein associations that drive the pathogenesis of JIA.

项目总结