Molecular analysis of bipolar and schizophrenia candidate genes

双相情感障碍和精神分裂症候选基因的分子分析

• 批准号: 8040802
• 负责人: HERBERT M LACHMAN
• 金额: $ 40.84万
• 依托单位: ALBERT EINSTEIN COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-08-01 至 2013-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8040802
• 关键词: Active Sites; Address; Antibodies; Binding; Binding Sites; Biological; Biological Assay; Biological Process; Bipolar Disorder; Brain; CTNNB1 gene; Candidate Disease Gene; Chromatin; Code; DNA; DNA Resequencing; Disease; Disease susceptibility; Distal; EP300 gene; Enhancers; Enzymes; Evolution; Functional RNA; Functional disorder; Future; Gene Expression Regulation; Gene Frequency; Genes; Genetic; Genetic Enhancer Element; Genetic Variation; Genome; Grant; Histones; Human; Human Genome; Intercistronic Region; Introns; Lead; Linkage Disequilibrium; Lithium; Mental disorders; Methods; Minority; Molecular; Molecular Analysis; Mutation; Neurons; Nucleic Acid Regulatory Sequences; Pathogenesis; Pathway interactions; Patients; Phase; Proteins; Regulatory Element; Research Personnel; Resources; Salts; Schizophrenia; Screening procedure; Signal Transduction; Site; Source; Subgroup; Thumb structure; Variant; autism spectrum disorder; base; chromatin immunoprecipitation; cis acting element; developmental disease; disease-causing mutation; disorder risk; genetic variant; genome wide association study; genome-wide; induced pluripotent stem cell; neurodevelopment; neuropsychiatry; novel; promoter; research study; tool; transcription factor; treatment strategy

DESCRIPTION (provided by applicant): Although there have been major advances in understanding the genetic basis of schizophrenia (SZ) and bipolar disorder (BD) using genome-wide association studies (GWAS), identifying disease causing functional variants in patients remains a problem. An exception is the finding of structural alterations, such as patient-specific copy number variants (CNVs), which have been found a sizeable minority of patients with SZ and autism spectrum disorders (ASD), especially do novo cases. Disease-associated SNPs identified in GWAS are usually not functional variants on their own, but are presumably in linkage disequilibrium (LD) with bona fide disease-causing functional mutations. However, identifying such variants is difficult, especially when associated SNPs are found in non-coding regions - deep within introns or in intergenic regions far removed from the nearest annotated genes, which has been a common theme in GWAS. A reasonable assumption, considering that significant LD is maintained for only ~10-20 kb, is that many disease-causing mutations are occurring in regulatory elements that are far removed from a candidate gene's coding region, such as distal enhancers, suppressors and promoters of non-coding RNAs. A feature of many regulatory elements is sequence conservation. However, sequence conservation alone is not sufficient to establish biological function and human-specific enhancer elements have been observed. What are the regulatory elements that control the regulation of genes involved in psychiatric disorders? Does genetic variation in these regions contribute to disease risk? Are the positive association signals identified in GWAS due to LD with these features? One strategy we successfully implemented in the initial grant period was to use a chromatin immunoprecipitation based method - ChIP-chip - as a screening tool to identify novel regulatory elements in SZ and BD candidate genes. The basic ChIP-chip strategy involves immunoprecipitation of chromatin using antibodies (Ab) to proteins, such as covalently modified histones, that bind to DNA and are enriched in regulatory domains. These regions can then be assayed for biological activity and, if such activity can be demonstrated, resequenced to identify rare patient-specific variants or SNPs that have higher allele frequencies in patients compared with controls. Such potential disease- causing variants can also be subjected to functional analysis to establish biological activity. However, ChIP-chip is limiting by the number of genes and amount of DNA that can be interrogated. A much more comprehensive analysis for regulatory domain screening is ChIP-Seq, the primary advantage of which is that it provides unbiased, genomewide coverage. Thus, ChIP-Seq has the potential to identify regulatory elements in all previously characterized candidate genes, as well as those identified in the future, providing researchers with biologically active sites that can be efficiently screened to identify patient-specific mutations. The ChIP-Seq approach will also be used to identify binding sites, throughout the entire human genome, of transcription factors relevant to SZ and BD pathophysiology. PUBLIC HEALTH RELEVANCE: This proposal describes experiments that will help identify regions of the genome involved in regulating the expression of candidate genes for schizophrenia, bipolar disorder, autism spectrum disorders and other neuropsychiatric disorders. Understanding how these genes are regulated may lead to novel treatment strategies. Furthermore, mutations in these regulatory regions may be responsible for disease susceptibility in a subgroup of patients.

描述（由申请人提供）：尽管利用全基因组关联研究（GWAS）在理解精神分裂症（SZ）和双相情感障碍（BD）的遗传基础方面取得了重大进展，但在患者中识别导致功能变异的疾病仍然是一个问题。一个例外是发现了结构改变，例如患者特异性拷贝数变异（CNVs），这在相当大的少数SZ和自闭症谱系障碍（ASD）患者中被发现，特别是新生病例。在GWAS中发现的与疾病相关的snp通常本身不是功能变异，但可能是连锁不平衡（LD），具有真正的致病功能突变。然而，识别这样的变异是困难的，特别是当相关的snp发现于非编码区域时——在内含子深处或在远离最近的注释基因的基因间区域，这是GWAS的一个共同主题。考虑到显著LD仅维持约10-20 kb，一个合理的假设是，许多致病突变发生在远离候选基因编码区的调控元件中，如非编码rna的远端增强子、抑制子和启动子。许多调控元件的一个特点是序列保守。然而，序列保守本身并不足以建立生物学功能，并且已经观察到人类特异性增强子元件。控制与精神疾病有关的基因调控的调控因素是什么？这些区域的遗传变异会增加疾病风险吗？在GWAS中，由于LD的阳性关联信号是否具有这些特征？我们在最初的资助期成功实施的一个策略是使用基于染色质免疫沉淀的方法- ChIP-chip -作为筛选工具来识别SZ和BD候选基因中的新调控元件。ChIP-chip的基本策略包括使用针对蛋白质的抗体（Ab）对染色质进行免疫沉淀，如共价修饰的组蛋白，这些组蛋白与DNA结合并在调节区域富集。然后可以分析这些区域的生物活性，如果这种活性可以被证明，就可以对其进行重新测序，以确定罕见的患者特异性变异或snp，这些变异或snp在患者中具有比对照组更高的等位基因频率。这种潜在的致病变异也可以进行功能分析以确定生物活性。然而，ChIP-chip受到基因数量和DNA数量的限制。ChIP-Seq是一种更全面的调控域筛选分析方法，其主要优势在于它提供了无偏倚的全基因组覆盖。因此，ChIP-Seq有潜力鉴定所有先前鉴定的候选基因中的调控元件，以及未来鉴定的那些，为研究人员提供可以有效筛选的生物活性位点，以鉴定患者特异性突变。ChIP-Seq方法还将用于在整个人类基因组中识别与SZ和BD病理生理相关的转录因子的结合位点。