Genetic Analysis of Complex Inflammatory Disorders

复杂炎症性疾病的遗传分析

• 批准号: 9589742
• 负责人: Daniel Kastner
• 金额: $ 134.33万
• 依托单位: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/9589742
• 关键词: Accounting; Admixture; African; African American; Age; Alabama; Algorithms; Alleles; American; Amino Acids; Antibodies; Antinuclear Antibodies; Aphthous Stomatitis; Architecture; Area; Arthritis; Autoimmune Diseases; Autoimmunity; California; Candidate Disease Gene; Cardiac; Cervical; Chicago; Child; Childhood; Chromosomes, Human, Pair 1; Chromosomes, Human, Pair 8; Chronic; Chronic Childhood Arthritis; Classification; Clinical; Collection; Complex; Computer software; Country; DNA; Data; Defect; Diffuse; Disease; Eagles; European; Family; Fever; Foundations; Gene Expression; Gene Frequency; Genes; Genetic; Genetic Risk; Genetic study; Genome; Genotype; Glutamates; Goals; HLA-DPB1 gene; HLA-DQB1; HLA-DRB1; Human; Immunologics; Immunophenotyping; Inflammatory; International; Internet; Investigation; Kidney; Lymphatic Diseases; Lymphoid Cell; MHC Class I Genes; Major Histocompatibility Complex; Medical; Michigan; Modeling; Morbidity - disease rate; Mosaicism; Myeloid Cells; National Institute of Arthritis and Musculoskeletal and Skin Diseases; New York; Operative Surgical Procedures; Organ; Oxygen Therapy Care; Paper; Pathway interactions; Patients; Pennsylvania; Periodicity; Pharyngitis; Phase; Phenotype; Population; Predisposition; Prevalence; Principal Component Analysis; Process; Publishing; Pulmonary Fibrosis; Pulmonary Hypertension; Recurrence; Regression Analysis; Regulation; Reporting; Research; Research Personnel; Rheumatism; Rheumatoid Arthritis; Rheumatology; Role; Sampling; San Francisco; Scleroderma; Secure; Single Nucleotide Polymorphism; South Carolina; Special Hospitals; Suggestion; Susceptibility Gene; Symptoms; Syndrome; TGFB3 gene; Testing; Texas; Time; Tonsil; Tonsillar Tissue; Tonsillectomy; Topoisomerase; Trisomy 8; Type I DNA Topoisomerases; Ulcer; Underserved Population; United States National Institutes of Health; Universities; University Hospitals; Variant; Vascular Diseases; Ventilator; Washington; autoinflammatory; chest computed tomography; cohort; college; conditioning; disorder risk; exome; exome sequencing; follow-up; genetic analysis; genetic risk factor; genetic variant; genome wide association study; genome-wide; illness length; improved; interest; meetings; mortality; novel; promoter; rare variant; risk variant; skin fibrosis; study population; tenure track

During the current reporting period we have focused on 3 major projects: 1) Genetics of Systemic Juvenile Idiopathic Arthritis In the previous reporting period, we focused on the MHC, and published a paper in the PNAS demonstrating that, in 6 study populations of Western European ancestry, HLA-DRB1*11 and its defining amino acid, glutamate 58, were strongly associated with sJIA. In the current reporting period, we followed up with a paper published in the Annals of the Rheumatic Diseases, reporting the results of a genome-wide association study (GWAS) of 770 children with sJIA collected in nine countries by the International Childhood Arthritis Consortium. Single nucleotide polymorphisms were tested for association with sJIA. Weighted genetic risk scores were used to compare the genetic architecture of sJIA with other JIA subtypes. The major histocompatibility complex locus and a noncoding locus on chromosome 1 each showed association with sJIA exceeding the threshold for genome-wide significance, while 23 other novel loci were suggestive of association with sJIA. Using a combination of genetic and statistical approaches, we found no evidence of shared genetic architecture between sJIA and other common JIA subtypes. The lack of shared genetic risk factors between sJIA and other JIA subtypes supports the hypothesis that sJIA is a unique disease process and argues for a different classification framework. Research to improve sJIA therapy should target its unique genetics and specific pathophysiological pathways. 2) Genetics of Scleroderma in the African-American Population Scleroderma is a chronic multisystem disease that is clinically characterized by progressive fibrosis of the skin and internal organs, vasculopathy, and autoimmunity. It is the cause of significant morbidity and mortality, and the treatment options are not nearly as effective as those available for other autoimmune diseases. Scleroderma is both more common and more severe in the African-American population. Hence, a study of scleroderma in African Americans has the potential both to identify previously unrecognized multi-ethnic scleroderma susceptibility loci, and perhaps to identify population-specific genes that could have a major impact in this underserved population with more severe disease. Through a collaborative group denoted GRASP (Genome Research in African American Scleroderma Patients), we have secured the largest collection of African American scleroderma patients ever assembled. GRASP consists of 19 centers outside of the NIH: Johns Hopkins, Georgetown, George Washington, University of Pennsylvania, University of Pittsburgh, Rutgers, New York University, Hospital for Special Surgery, Medical University of South Carolina, Emory, Miami, University of Alabama at Birmingham, Tulane, Northwestern, University of Chicago, Michigan, University of Texas at Houston, University of California San Francisco, and Stanford. With help from the Scleroderma Research Foundation, in the first phase of the project we have collected DNA samples from 1052 African American scleroderma patients, and we have identified 1039 antinuclear antibody (ANA) negative African-American controls provided by Charles Rotimi. During the current reporting period, we have completed three separate studies that will be reported as podium presentations at the 2017 American College of Rheumatology meeting. The first of these three studies compared the phenotypic manifestations of scleroderma in 1009 subjects in the GRASP cohort to that reported in the European League Against Rheumatism Scleroderma Trials and Research (EUSTAR) cohort. 945 (94 percent) patients met the 2013 ACR/EULAR classification criteria for scleroderma, with the remaining 64 (6 percent) meeting the 1980 ACR or CREST criteria. The majority (57 percent) had the more diffuse subtype and a young age at symptom onset, in marked contrast to the EUSTAR cohort. 1 in 10 patients had a severe Medsger cardiac score of 4. Pulmonary fibrosis evident on computed tomography of the chest was present in 43 percent of patients, and was significantly associated with anti-topoisomerase I positivity. 38 percent of patients with CT evidence of pulmonary fibrosis had a severe restrictive ventilator defect. 1 in 6 GRASP patients required oxygen therapy, compared to 3 percent in the EUSTAR cohort. A significant association was noted between longer disease duration and higher odds of pulmonary hypertension. The prevalence of potentially fatal scleroderma renal crisis was 3.5 times higher than that reported in the EUSTAR cohort. In the second study, we used the Illumina MEGA array to conduct the first genome-wide association study (GWAS) in African-American scleroderma. 1.7 million variants were genotyped and then imputed using Beagle software and 1000 Genomes as the reference population. Admixture and principal component analysis (PCA) confirmed that the patients and controls were well-matched, with a lambdaGC of 1.03. Association analysis was performed on the imputed data in 934 patients and 946 controls. The MHC region demonstrated the strongest association after accounting for the top 10 PCAs. rs35915063 was the top variant in the HLA-DQB1 gene (P=2.2 x 10e-17, OR=1.96). Stepwise conditional regression analysis using an additive model revealed the DQA gene variant rs9271620 and the DPB1 variant rs2071354 as the next 2 independent risk variants. The rs59063398 variant showed the strongest non-MHC association with P=2.2 x 10e-8, OR=0.47). This variant is part of an evolutionarily conserved halpoblock in the IFT43 gene region that is African ancestry specific. This gene region includes the promoter for TGFB3, suggesting potential alteration of TGFB3 promoter activity and hence regulation of TGFB3 expression. In the third study, we used MHC region genotypes from the MEGA array to impute classical HLA types and analyzed their associations with scleroderma in the GRASP cohort. We extracted the genotypes of 25,256 markers from 20 Mb encompassing the greater MHC region and used the Michigan Imputation Server with 1000G Phase 3 v5 reference and Eagle phasing algorithm to obtain input data for the HLA*IMP:03 web server. The most significantly scleroderma-associated HLA type was a predominantly African allele, HLA-DRB1*08:04, OR=2.95. Regression analysis conditioning on the disease-associated alleles identified another African DRB1 allele, *11:02, as well as HLA-DPB1*13:01, and HLA-DRB4*01:01 as independent contributors to disease risk, but no association was found for MHC class I alleles. 34.6 percent of GRASP cases carry either DRB1*08:04 or *11:02 compared with 16.3 percent of controls. Analysis of 246 anti-topoisomerase antibody positive cases revealed a strong disease risk conferred by HLA-DPB1*13:01 (OR=4.1). 30.5 percent of anti-topoisomerase Ab cases carry HLA-DPB1*13:01, compared with 9.7 percent of controls. 3) Genetics of PFAPA We are also studying the genetic and immunologic underpinnings of PFAPA syndrome, the most common periodic fever syndrome in children. We are searching for rare, causative variants by whole exome sequencing of familial cases. Our results suggest that PFAPA is a polygenic disease, and we are now assessing allele frequencies of candidate genes involved in other complex ulcerative autoinflammatory diseases in a cohort of PFAPA patients. Tonsillectomy is curative in many patients with PFAPA; therefore, we are characterizing lymphoid and myeloid cell populations in the tonsils of patients with PFAPA with immunophenotyping, comparisons of gene expression, and functional studies. In addition, we have observed that patients with trisomy 8 mosaicism and chromosome 8 duplications have a propensity to autoinflammatory disease with recurrent fever and severe mucocutaneous ulcers; studies to identify causal genes are underway.

在当前的报告期内，我们专注于3个主要项目： 1）全身少年特发性关节炎的遗传学 在上一个报告时期，我们专注于MHC，并在PNA中发表了一篇论文，表明，在西欧血统的6个研究人群中，HLA-DRB1*11及其定义的氨基酸58与SJIA密切相关。在当前的报告期间，我们随后发表了一篇发表在风湿病史上的论文，报道了全基因组协会研究（GWAS）的结果，该研究的结果是，国际儿童关节炎联盟在9个国家收集的770名SJIA儿童。测试了单核苷酸多态性与SJIA关联。加权遗传风险评分比较了SJIA的遗传结构与其他JIA亚型的遗传结构。染色体1上的主要组织相容性复合物基因座和一个非编码基因座都显示与SJIA的关联超过全基因组显着性的阈值，而其他23个新型基因座则暗示与SJIA相关。使用遗传和统计方法的结合，我们没有发现SJIA和其他常见JIA亚型之间共享遗传结构的证据。 SJIA和其他JIA亚型之间缺乏共同的遗传危险因素支持以下假设：SJIA是一个独特的疾病过程，并主张不同的分类框架。改善SJIA治疗的研究应针对其独特的遗传学和特定的病理生理途径。 2）在非裔美国人人口中硬皮病的遗传学 硬皮病是一种慢性多系统疾病，其在临床上以皮肤和内脏，血管病和自身免疫性的进行性纤维化为特征。这是发病率和死亡率重大的原因，治疗方案的效果不如其他自身免疫性疾病的效果。在非裔美国人人口中，硬皮病更为普遍，更严重。因此，一项对非裔美国人硬皮病的研究有可能识别先前未识别的多种族硬皮病易感基因座，也许可以鉴定出可能在患有更严重疾病的人群中产生重大影响的人群特异性基因。 通过一个协作小组表示GRASP（非裔美国人硬皮病患者的基因组研究），我们获得了有史以来最大的非裔美国人硬皮病患者收集的收集。掌握由NIH以外的19个中心组成：约翰·霍普金斯（Johns Hopkins），乔治·华盛顿（Georgeown），乔治·华盛顿（Georgeown），宾夕法尼亚大学，匹兹堡大学，匹兹堡大学，纽约大学，纽约大学，南卡罗来纳州医科大学，埃默里医科大学，埃默里，埃默里，迈阿密，迈阿密，迈阿密，阿拉巴马州，伯明翰，伯明翰，北部，乔治，乔尼亚，乔尼亚，乔尼亚，乔尼亚，乔尼亚，乔尼亚，乔尼亚，乔尼亚，乔尼亚，乔尼亚，科学，科学，科学，乔尼亚，科学，乔尼亚，科学，乔尼亚，科学，乔尼亚，科学，科学，乔尼亚，科学，乔尼亚，科学，乔尼亚，科学，科学，乔尼亚。旧金山和斯坦福大学。在硬皮病研究基金会的帮助下，在该项目的第一阶段，我们收集了来自1052名非裔美国硬皮病患者的DNA样品，我们已经确定了1039种抗核抗体（ANA）Charles Rotimi提供的负面非裔美国人对照。在当前的报告期间，我们已经完成了三项单独的研究，这些研究将在2017年美国风湿病学院会议上报道为讲台。 这三项研究中的第一项比较了欧洲对抗风湿病的硬皮病性硬皮试验和研究（Eustar）同伙的1009名受试者的硬皮病的表型表现。 945（94％）患者符合硬皮病的2013年ACR/EULAR分类标准，其余64（6％）符合1980年的ACR或Crest标准。大多数（57％）的亚型较高，并且在症状发作时年轻，与Eustar队列形成鲜明对比。十分之一的患者中有1例严重的MEDSGER心脏评分为4。胸部计算机断层扫描在43％的患者中存在明显的肺纤维化，并且与抗昆虫异构酶I的阳性显着相关。有38％的CT肺纤维化证据患者患有严重的限制性呼吸机缺陷。六分之一的掌握患者需要氧气治疗，而尤斯塔尔队列中则为3％。在较长的疾病持续时间和较高的肺动脉高压几率之间存在显着关联。潜在的致命性硬皮病肾脏危机的患病率是Eustar队列中报道的3.5倍。 在第二项研究中，我们使用Illumina Mega阵列在非裔美国人的硬皮病中进行了首个全基因组关联研究（GWAS）。将170万种变体用于基因分型，然后使用Beagle软件和1000个基因组作为参考群体进行估算。混合物和主成分分析（PCA）证实，患者和对照组的lambdagc为1.03。对934例患者和946例对照的估算数据进行了关联分析。 MHC地区在占10位PCA的情况下表现出最强的关联。 RS35915063是HLA-DQB1基因的最高变体（p = 2.2 x 10e-17，或= 1.96）。使用添加剂模型的逐步条件回归分析揭示了DQA基因变体RS9271620和DPB1变体RS2071354作为接下来的2个独立风险变体。 RS59063398变体显示出与p = 2.2 x 10e-8的最强非MHC关联，OR = 0.47）。该变体是非洲血统特有的IFT43基因区域中进化保守的halpoblock的一部分。该基因区域包括用于TGFB3的启动子，表明TGFB3启动子活性的潜在改变，从而调节TGFB3表达。 在第三项研究中，我们使用了来自巨型阵列的MHC区域基因型来估算经典的HLA类型，并分析了它们与Grasp队列中的硬皮病的关联。我们从20 MB中提取了25,256个标记的基因型，其中包含更大的MHC区域，并使用了Michigan插入服务器，其中具有1000G阶段3 V5参考和Eagle phasing Algorithm的基因型，以获取HLA*IMP*IMP：03 Web服务器的输入数据。硬皮病相关的HLA类型最显着的是主要是非洲等位基因，HLA-DRB1*08：04，或= 2.95。对疾病相关等位基因的回归分析条件确定了另一个非洲DRB1等位基因，*11：02，以及HLA-DPB1*13：01，HLA-DRB4*01：01是疾病风险的独立贡献者，但没有发现MHC I类的关联。 34.6％的GRASP病例携带DRB1 *08：04或 *11：02，而对照组的16.3％。对246例抗昆虫异构酶抗体阳性病例的分析表明，HLA-DPB1*13：01（OR = 4.1）赋予了强烈的疾病风险。 30.5％的抗昆虫异构酶AB病例携带HLA-DPB1*13：01，而对照组为9.7％。 3）PFAPA的遗传学 我们还研究了PFAPA综合征的遗传和免疫学基础，PFAPA综合征是儿童最常见的周期性发烧综合征。我们正在通过对家族病例的整个外显子组测序进行罕见的，因果变体。我们的结果表明，PFAPA是一种多基因疾病，我们现在正在评估一组PFAPA患者中参与其他复杂性溃疡自身炎症性疾病的候选基因的等位基因频率。扁桃体切除术在许多PFAPA患者中是治愈性的。因此，我们正在表征PFAPA患者具有免疫表型，基因表达比较和功能研究的PFAPA患者的扁桃体中的淋巴样和髓样细胞群。此外，我们已经观察到，三体三体镶嵌和8染色体的患者具有复发性发烧和严重的粘膜溃疡的自发性疾病的倾向。鉴定因果基因的研究正在进行中。