Identification of causal non-coding variants in childhood genetic disorders

鉴定儿童遗传性疾病的因果非编码变异

• 批准号: 10478919
• 负责人: Yong Cheng
• 金额: $ 44.88万
• 依托单位: ST. JUDE CHILDREN'S RESEARCH HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10478919
• 关键词: Affect; Anatomy; Biology; Blood Cells; Cell physiology; Childhood; Code; Complex; DNA; DNA Sequence; Development; Disease; Elements; Enhancers; Epigenetic Process; Gene Expression; Genes; Genetic Code; Genetic Diseases; Genetic Transcription; Genetic Variation; Goals; Health; Hematological Disease; Human; Human Genome; Lead; Maps; Modification; Open Reading Frames; Pathologic; Pharmacology; Phenotype; Predisposition; Proteins; Research; Role; Single Nucleotide Polymorphism; Tissues; Untranslated RNA; Variant; Vertebral column; base; clinical application; epigenetic marker; genome wide association study; high throughput screening; individual response; insight; novel; precision medicine; prevent; promoter; trait; treatment response

PROJECT SUMMARY My long-term research goal is to understand the organization and function of Cis-regulatory modules (CRMs) in the human genome, with a focus on their impact on development and disease. CRMs, such as promoters, enhancers, and insulators, are DNA elements that regulate gene expression. Genome-wide association studies (GWAS) have shown that most variants associated with a phenotype or disease are located outside of protein- coding regions and are postulated to affect gene expression levels through CRMs. Therefore, understanding the organization and function of CRMs is key to identifying the causes of genetic diseases and providing an essential backbone for precision medicine. Even though millions of putative CRMs have recently been identified with the help of high-throughput assays, it remains challenging to pinpoint functional CRMs that regulate tissue and developmental stage-specific transcription. In fact, a large proportion of the CRM variants identified so far have no-to-mild effects on the phenotype. As a result, those insights have very limited clinical application. Over the next five years, the goal of my research is to accurately identify causal CRM variants that affect normal blood cell development and impact childhood blood disorders. Several major hurdles must be overcome to achieve this goal. First, mounting evidence indicates that the expression fluctuation is an important trait for genes. Importantly, the tolerance of expression fluctuation varies among different genes. We reason that CRMs modulating transcription of highly expression-sensitive genes tend to be essential to cell function and harbor pathological non-coding variants. However, our understanding on expression-sensitive genes and their underlying biology is still rudimentary. Secondly, different epigenetic modification markers are routinely used to map potential CRMs. However, in many loci, those epigenetic markers are not required by CRM functions. Overreliance on associative, instead of causative, markers can confuse accurate identification of biologically important CRMs. Thirdly, while the genetic code of protein-coding sequences has been discovered for decades, the similar “grammar” for non-coding sequences and CRMs in particular is still lacking. As a result, we are not able to predict how CRM variants affect their regulatory functions. Based on those challenges, we ask three fundamental questions: 1) How to systematically identify expression-sensitive genes? 2) How to decipher the causative mechanism of CRMs? 3) How can single-nucleotide variants (SNV) affect CRM functions? If successful, the proposed studies will identify functionally important CRMs controlling health-related traits and pinpoint pathological non-coding variants within those CRMs. Better understanding the anatomy and function of CRMs will facilitate precision medicine by allowing us to treat genetic diseases by manipulation of CRM function via gene editing or pharmacological approaches.

项目摘要 我的长期研究目标是了解顺式调节模块（CRM）的组织和功能， 人类基因组，重点是它们对发展和疾病的影响。CRM，如启动子， 增强子和绝缘子是调节基因表达的DNA元件。全基因组关联研究 （GWAS）已经表明，与表型或疾病相关的大多数变体位于蛋白质- 编码区，并假定通过CRM影响基因表达水平。因此了解 组织和功能的标准物质是关键，以确定遗传疾病的原因，并提供必要的 精准医疗的中坚力量即使数以百万计的推定标准物质最近已被确定与 在高通量分析的帮助下，精确定位调节组织的功能性CRM仍然具有挑战性， 发育阶段特异性转录。事实上，到目前为止确定的CRM变体中， 对表型无至轻度影响。因此，这些见解的临床应用非常有限。来 在接下来的五年里，我的研究目标是准确识别影响正常血液的因果CRM变体 细胞发育并影响儿童血液疾病。必须克服几个主要障碍才能实现 这个目标首先，越来越多的证据表明，表达波动是基因的一个重要特征。 重要的是，不同基因对表达波动的耐受性不同。我们认为CRM 调节高表达敏感基因的转录往往是细胞功能所必需的， 病理性非编码变体。然而，我们对表达敏感基因及其表达调控的理解， 基础生物学还很不成熟其次，常规使用不同的表观遗传修饰标记物来确定表观遗传修饰。 映射潜在CRM。然而，在许多基因座中，CRM功能不需要这些表观遗传标记。 过度依赖关联性而不是因果性标记会混淆生物学上的准确鉴定。 重要的CRM第三，虽然蛋白质编码序列的遗传密码已经发现了几十年， 特别是对于非编码序列和CRM，仍然缺乏类似的“语法”。因此，我们不是 能够预测CRM变体如何影响其监管功能。基于这些挑战，我们提出三个问题， 基本问题：1）如何系统地鉴定表达敏感基因？2)如何破译 CRM的成因机制？3)单核苷酸变异（SNV）如何影响CRM功能？如果 成功，拟议的研究将确定功能重要的标准物质控制健康相关的性状， 找出那些标准物质中的病理性非编码变异更好地了解解剖和功能， CRM将允许我们通过操纵CRM功能来治疗遗传性疾病，从而促进精准医疗 通过基因编辑或药理学方法。