Combined analysis of gene expression and DNA variation in psoriasis

描述（由申请人提供）：银屑病是一种常见的免疫介导的炎症性和过度增殖性皮肤和关节疾病。结论性证据表明牛皮癣有遗传基础。我们最近确定HLA-Cw 6为PSORS 1的疾病等位基因，PSORS 1是银屑病易感性的主要MHC连锁成分。然而，只有大约10%的HLA-Cw 6携带者会患上银屑病，这意味着其他基因也必须起作用。已发表的和初步的数据提供了在几个非MHC基因座复制连锁或关联的证据。然而，迄今为止尚未确定非MHC易感基因。关联研究有可能识别这些基因，前提是在大样本中研究足够密度的SNP，并且通过适当的复制和精细定位研究跟踪阳性结果。这些非MHC基因的鉴定是本提案的第一个总体目标。皮肤是一个独特的可接近的器官，也是银屑病免疫系统的主要目标，导致基因表达的许多变化。以前的连锁研究的基因表达的永生化细胞系已经确定了重要的遗传元件负责控制基因表达。该项目的第二个相关的总体目标是建立银屑病皮肤的基因表达图谱，表征受影响个体的未受累和患病皮肤以及对照个体的正常皮肤的基因表达谱。除了识别差异表达的基因外，我们还将皮肤中的基因表达谱与特定的遗传位点以及可能的DNA变体联系起来。为实现这些目标，我们建议实现以下具体目标：1.收集300例早发性银屑病患者和300例对照者的皮肤活检和血液样本，并分别从这些样本中制备RNA和DNA。2.利用能够检测约500，000个单核苷酸多态性（SNP）的DNA微阵列对600例早发性银屑病病例和600例对照进行全基因组关联分析。3.对目标1中收集的300例病例和300例对照进行全局基因表达分析，并结合目标2中获得的全基因组SNP数据分析这些数据。4.在900例病例和900例对照的重复队列中随访6,000个SNP，并将我们的数据与来自德国独立的银屑病全基因组关联扫描的数据进行比较。通过在确认的关联区域进行密集SNP基因分型来细化候选关联。量化每个SNP对基因表达的影响，概率性地推断未基因分型的SNP的状态，量化它们对转录水平的影响，并组织一个公开访问的数据库。鉴定其余的银屑病易感基因将阐明这种神秘疾病的分子基础，并确定更特异和有效的治疗目标。

DESCRIPTION (provided by applicant): Psoriasis is a common, immune-mediated, inflammatory and hyperproliferative disease of the skin and joints. Conclusive evidence demonstrates psoriasis has a genetic basis. We have recently identified HLA-Cw6 as the disease allele at PSORS1, the major MHC-linked component of psoriasis susceptibility. However, only about 10% of HLA-Cw6 carriers develop psoriasis, implying that additional genes must contribute as well. Published and preliminary data provide evidence for replication of linkage or association at several non-MHC loci. However, no non-MHC susceptibility genes have been conclusively identified to date. Association studies have the potential to identify these genes, provided that a sufficiently density of SNPs is studied in a large sample, and that positive results are followed up by appropriate replication and fine-mapping studies. Identification of these non-MHC genes is the first overall goal of this proposal. The skin is a uniquely accessible organ and the major target of the immune system in psoriasis, resulting in many changes in gene expression. Prior linkage studies of gene expression in immortalized cell lines have identified important genetic elements responsible for controlling gene expression. The second, and related, overall goal of this project is to build a gene-expression map in psoriatic skin, characterizing gene expression profiles in uninvolved and diseased skin from affected individuals as well as normal skin from control individuals. In addition to identifying genes that are differentially expressed, we will relate gene expression profiles in skin to specific genetic loci, and where possible, DNA variants. To accomplish these goals, we propose to carry out the following specific aims: 1. Collect skin biopsies and blood samples from 300 early onset psoriatic cases and 300 controls, and prepare RNA and DNA, respectively, from these samples. 2. Perform whole-genome association analysis on 600 early-onset psoriatic cases and 600 controls utilizing DNA microarrays capable of assaying ~500,000 single nucleotide polymorphisms (SNPs). 3. Perform global gene expression analysis on the 300 cases and 300 controls collected in Aim 1, and analyze these data conjointly with the genome-wide SNP data obtained in Aim 2. 4. Follow-up 6,000 SNPs in a replication cohort of 900 cases and 900 controls, and compare our data with that derived from an independent whole-genome association scan of psoriasis in Germany. Refine the candidate associations by performing dense SNP genotyping in confirmed regions of association. Quantify the effect of each SNP on gene expression, probabilistically infer the state of ungenotyped SNPs, quantify their effects on transcript levels, and organize a publicly accessible database. Identification of the remaining psoriasis susceptibility genes will elucidate the molecular basis of this enigmatic disease, and identify targets for more specific and effective therapy.