New Methods to Uncover Global Transcriptional Programs for Disease Risk Variants

揭示疾病风险变异全球转录程序的新方法

• 批准号: 8644271
• 负责人: YOUSIN SUH
• 金额: $ 61.18万
• 依托单位: ALBERT EINSTEIN COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-04-05 至 2017-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8644271
• 关键词: 9p21; Address; Aging; Alleles; Alternative Splicing; Antisense Oligonucleotides; Antisense RNA; Architecture; Binding; Biological; CDKN2A gene; CDKN2B gene; Cells; Chronic Disease; Clinical; Code; Conflict (Psychology); Coronary Arteriosclerosis; Coupled; DNA Sequence; Data; Development; Disease; Disease Progression; Disease susceptibility; Endothelial Cells; Engineering; Enhancers; Epigenetic Process; Etiology; Event; Functional RNA; Gene Expression; Genes; Genetic; Genetic Transcription; Genome; Genomics; Genotoxic Stress; Genotype; Goals; Health; Higher Order Chromatin Structure; Human; Human Biology; Individual; Inflammation; Inflammatory; Investigation; Junk DNA; Laboratories; Licensing; Link; Location; Malignant Neoplasms; Maps; Methodology; Methods; Modeling; Molecular; Mus; Nature; Non-Insulin-Dependent Diabetes Mellitus; Nuclear; Nucleic Acid Regulatory Sequences; Oncogenes; Outcome; Pathway interactions; Pattern; Protein Isoforms; Proteins; Publishing; RNA; RNA Splicing; Regulation; Reporting; Risk; Role; Sequence Analysis; Signal Transduction; Site; Stress; Structure; Technology; Testing; Therapeutic; Transcript; Translating; Variant; age related; base; disease phenotype; disorder prevention; disorder risk; epigenomics; genome wide association study; genome-wide; human disease; insight; locked nucleic acid; lymphoblast; lymphoblastoid cell line; macrophage; novel; novel therapeutics; prevent; programs; promoter; response; risk variant; senescence; success; trait; transcriptome sequencing

DESCRIPTION (provided by applicant): More than 1,000 published GWAS have collectively reported significant associations of ~4,000 SNPs for more than 200 traits/diseases. The challenge is to move SNP associations to biological insights and then to translate these insights, achieving better clinical outcomes. This ambitious goal requires an inclusive and effective strategy to solve the molecular basis by which these variants confer disease susceptibility. To date, the vast majority of the associations noted in GWAS for disease phenotypes have been with variants located within gene deserts, the 99% of the genome that does not encode known proteins and where our understanding of functional consequences and causality is at best rudimentary. Recent findings indicate that altering DNA sequence in evolutionarily conserved non-coding regions can be as deleterious as altering coding regions. Therefore, it is not surprising that disease-causing variants will reside in the gene desert regions. The greatest challenge in the "post-GWAS" era is to understand the regulatory principles of risk variants in gene desert regions and the mechanisms underlying the risk conferred by these loci. The goal of this proposal is to accelerate post-GWAS functional characterization, uncovering initial global principles for the functional characterization of disease risk loci by focusing on altered function in transcription based on the actions of enhancer RNAs. Employing the 9p21 region as a model, we will establish how disease-associated common sequence variants alter the functions of regulatory regions and address the molecular mechanisms by which these effects are exerted. These studies will integrate disease susceptibility-associated sequence variations into the emerging three-dimensional network of long-distance genomic region interactions, establish local and global alterations in gene transcription, and explore the key role of enhancer-RNAs harboring sequence variations at GWAS loci. The primary significance will be the discovery of a novel functional consequences and an "epigenomic" molecular mechanism underlying GWAS loci in disease, with the opportunity for exploiting these new mechanistic and therapeutic insights for preventative approaches to the chronic diseases associated with aging.

描述（由申请人提供）：1000多个已发表的GWAS共同报道了200多个性状/疾病的约4000个snp的显著关联。挑战在于将SNP关联转化为生物学见解，然后将这些见解转化为更好的临床结果。这一雄心勃勃的目标需要一个包容性和有效的策略来解决这些变异赋予疾病易感性的分子基础。迄今为止，GWAS中所指出的疾病表型的绝大多数关联都与位于基因沙漠中的变异有关，这99%的基因组不编码已知的蛋白质，我们对功能后果和因果关系的理解充其量只是初步的。最近的研究结果表明，改变进化上保守的非编码区DNA序列可能与改变编码区一样有害。因此，致病变异存在于基因沙漠地区并不奇怪。“后gwas”时代的最大挑战是了解基因沙漠地区风险变异的调控原则以及这些基因座赋予风险的潜在机制。该提案的目标是加速gwas后的功能表征，通过关注功能改变，揭示疾病风险位点功能表征的初始全局原则