MHC and KIR Region Genomics in Psoriasis

银屑病的 MHC 和 KIR 区域基因组学

• 批准号: 9115532
• 负责人: Wilson Liao
• 金额: $ 70.54万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-07-24 至 2020-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9115532
• 关键词: Accounting; Address; Affect; Alleles; American; Arthritis; Asians; Autoimmune Diseases; Bioinformatics; Cells; Comorbidity; Conflict (Psychology); DNA Sequence; Data; Data Set; Development; Digit structure; Disease; Disease Progression; Disease susceptibility; Ethnic group; European; Exhibits; Flow Cytometry; Genes; Genetic; Genetic Models; Genetic Variation; Genetic study; Genomic Segment; HLA-C Antigens; Health; Immune; Immunogenetics; Immunoglobulins; Immunologist; Individual; Inflammation; Inflammatory; Inflammatory Bowel Diseases; Interleukin-12; International; Killer Cells; Lead; Ligands; Light; Linkage Disequilibrium; Major Histocompatibility Complex; Major Histocompatibility Complex Gene; Mediating; Methods; Modeling; Myocardial Infarction; Nature; Non-Insulin-Dependent Diabetes Mellitus; Obesity; Onset of illness; Outcome; Pathogenesis; Pathway interactions; Patients; Population; Predisposition; Problem Solving; Protocols documentation; Psoriasis; Psoriatic Arthritis; Receptor Gene; Refractory; Reporting; Research Design; Residual state; Resolution; Role; SNP array; SNP genotyping; Sample Size; Severities; Signal Transduction; Skin; Sorting - Cell Movement; Stroke; Susceptibility Gene; Systemic disease; Systems Biology; TNF gene; Techniques; Technology; Time; United States; Variant; Work; cohort; cost; deep sequencing; genetic association; genetic variant; genome wide association study; improved; innovation; multidisciplinary; next generation sequencing; novel; novel therapeutics; population health; receptor; response; skin disorder; tool; transcriptome; transcriptome sequencing

 DESCRIPTION (provided by applicant): Psoriasis is a common, immune-mediated, inflammatory skin disease associated with arthritis and systemic inflammation. Genome-wide association studies of psoriasis have identified over 40 susceptibility loci implicating both innat and adaptive immune pathways. The genetic locus exhibiting the greatest association with psoriasis is the MHC, with HLAC:06:02 showing very strong association in multiple ethnic groups. However, significant residual genetic signal remains in the MHC after accounting for the effects of HLAC:06:02 and it is not clear whether the residual signal resides in other HLA alleles, additional nearby genes, or regulatory variants. There is also evidence to suggest psoriasis susceptibility may be influenced by the interaction of killer cell immunoglobulin-like receptors (KIR) with HLA class I ligands; however, studies to date of HLA-KIR in psoriasis have generally been hampered by the time-consuming nature and high cost of HLA and KIR typing. Finally, although HLAC:06:02 is known to associate significantly with psoriasis and HLAC:06:02-positive psoriasis patients show differences in disease onset, severity, and response to therapy compared to HLAC:06:02-negative psoriasis patients, the mechanism by which HLAC:06:02 contributes to psoriasis has not been well studied. In this application, we utilize a variety of innovative approaches to address these questions. First, we perform high fidelity next-generation sequencing of the extended MHC in a psoriasis reference cohort and impute identified variants into European and Asian GWAS cohorts totaling over 8,500 cases and 17,000 controls. We construct a comprehensive genetic model to best explain the genetic association within the MHC using multiple model inputs including 4-digit resolution calls for 26 HLA/MICA/MICB/TAP genes, SNPs, indels, and functional variables. Second, we optimize a novel KIR imputation method that uses SNP array data to accurately call KIR copy number and apply this method to examine HLA-KIR associations in psoriasis using a large cohort. Finally, we utilize a novel flow cytometry protocol to sort psoriasis-relevant cell populations from the ski of HLAC:06:02-positive and HLAC:06:02- negative psoriasis patients, perform whole transcriptome RNA-sequencing on individual cell populations, and use systems biology analytical approaches to better understand the contribution of HLAC:06:02 to psoriasis pathogenesis. Together, the proposed work will identify causal variants in psoriasis, shed light on functional mechanisms, and potentially identify novel therapeutic pathways. The approaches and tools developed here will greatly facilitate the study of other immune-mediated diseases.

 描述(申请人提供)：牛皮癣是一种常见的，免疫调节的炎症性皮肤病，与关节炎和全身炎症有关。银屑病的全基因组关联研究已经确定了40多个易感基因，这些易感基因涉及天然免疫和获得性免疫途径。与银屑病关联最大的遗传基因座是MHC，HLAC：06：02在多个民族中显示出非常强的关联性。然而，在考虑了HLAC：06：02的影响后，显著的残留遗传信号仍然存在于MHC中，并且尚不清楚残留信号是否驻留在其他HLA等位基因中， 其他附近的基因，或调节变种。也有证据表明银屑病的易感性可能受到杀伤细胞免疫球蛋白样受体(KIR)与HLAI类配体的相互作用的影响；然而，迄今为止关于HLAKIR在银屑病中的研究普遍受到耗时和昂贵的HLAKIR配型的阻碍。最后，尽管已知HLAC：06：02与银屑病显著相关，HLAC：06：02阳性的银屑病患者与HLAC：06：02阴性的银屑病患者相比，在发病、严重程度和治疗反应方面存在差异，但HLAC：06：02导致银屑病的机制尚未得到很好的研究。在本应用程序中，我们利用各种创新方法来解决这些问题。首先，我们对银屑病参考队列中扩展的MHC进行高保真的下一代测序，并将已识别的变异归因于欧洲和亚洲的GWA群，总计超过8,500例和17,000名对照。我们构建了一个全面的遗传模型，以最好地解释MHC内的遗传关联，使用多个模型输入，包括26个HLA/MICA/MICB/TAP基因、SNPs、INDELs和功能变量的4位数分辨率调用。其次，我们优化了一种新的KIR定位方法，该方法使用SNP阵列数据来准确地调用KIR拷贝数，并将该方法应用于使用大队列来检验银屑病患者的人类白细胞抗原-KIR相关性。最后，我们利用一种新的流式细胞术方法从HLAC：06：02阳性和HLAC：06：02阴性的银屑病患者中筛选出与银屑病相关的细胞群体，对单个细胞群体进行完整的转录组RNA测序，并使用系统生物学分析方法更好地了解HLAC：06：02在银屑病发病机制中的作用。总之，这项拟议的工作将识别牛皮癣的因果变异，阐明作用机制，并可能确定新的治疗途径。这里开发的方法和工具将极大地促进其他免疫介导性疾病的研究。