Combined analysis of gene expression and DNA variation in psoriasis

描述(申请人提供)：牛皮癣是一种常见的，免疫调节，炎性和过度增殖的皮肤和关节疾病。确凿的证据表明，牛皮癣有遗传基础。我们最近已确定PSORS1的疾病等位基因为人类白细胞抗原-CW6，PSORS1是银屑病易感性的主要MHC连锁成分。然而，只有大约10%的HLA-CW6携带者会患上银屑病，这意味着额外的基因也必须起作用。已发表的和初步的数据为在几个非MHC基因座上复制连锁或关联提供了证据。然而，到目前为止，还没有确定非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了足够密度的SNPs，并且在阳性结果之后进行了适当的复制和精细定位研究。鉴定这些非MHC基因是这项提案的第一个总体目标。皮肤是唯一可接触的器官，也是银屑病免疫系统的主要靶点，导致基因表达的许多变化。先前对永生化细胞系中基因表达的连锁研究已经确定了负责控制基因表达的重要遗传因素。该项目的第二个和相关的总体目标是建立银屑病患者皮肤的基因表达图谱，表征患者未受累和患病皮肤以及对照组正常皮肤的基因表达谱。除了识别差异表达的基因外，我们还将把皮肤中的基因表达谱与特定的遗传位点联系起来，并在可能的情况下，将DNA变异联系起来。为了实现这些目标，我们提出了以下具体目标：1.收集300例早发性银屑病患者和300例对照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DNA微阵列技术对600例早发性银屑病患者和600例对照进行了全基因组关联分析。3.对AIM 1收集的300例银屑病患者和300例对照进行全局基因表达分析，并结合AIM 2中获得的全基因组SNP数据进行分析。4.对900例银屑病患者和900名对照的重复队列中的6000个SNP进行随访，并将我们的数据与德国独立的银屑病全基因组联合扫描的数据进行比较。通过在已确认的关联区域进行密集SNP基因分型来提炼候选关联。量化每个SNP对基因表达的影响，以概率推断未分型SNP的状态，量化它们对转录水平的影响，并组织一个可公开访问的数据库。识别剩下的银屑病易感基因将阐明这种神秘疾病的分子基础，并为更具体和有效的治疗确定靶点。

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.