An epigenomic approach to identifying noncoding mutations in epilepsy

识别癫痫非编码突变的表观基因组方法

• 批准号: 8804829
• 负责人: Gemma Louise Carvill
• 金额: $ 9.11万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-30 至 2016-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8804829
• 关键词: Accounting; Address; Advisory Committees; Affect; Applications Grants; Atlases; Award; Binding; Biological Process; Cells; Child; Clustered Regularly Interspaced Short Palindromic Repeats; Code; Computational Technique; DNA; DNA Binding; Data; Development; Disease; Elements; Encephalopathies; Epigenetic Process; Epilepsy; Epileptogenesis; Experimental Models; Family; Foundations; Funding; Future; Gene Expression; Gene Expression Regulation; Gene Mutation; Gene Targeting; Generations; Genes; Genetic; Genetic Research; Genetic Transcription; Genetic Variation; Genome; Genomics; Goals; Hereditary Disease; Human; Human Genetics; Human Genome; Indium; Individual; Knowledge; Maps; Mentors; Mentorship; Methodology; Modeling; Molecular Genetics; Mutation; Neurodevelopmental Disorder; Neurons; Nucleic Acid Regulatory Sequences; Open Reading Frames; Outcome; Parents; Pathway interactions; Patients; Phase; Play; Proteins; Research; Research Personnel; Research Training; Role; Seizures; Site; Techniques; Technology; Testing; Training; Training Programs; United States National Institutes of Health; Universities; Validation; Variant; Washington; base; career; chromatin remodeling; design; embryonic stem cell; epigenomics; genome sequencing; human disease; human embryonic stem cell; interest; medical schools; neurogenesis; neuron development; next generation sequencing; novel; novel therapeutic intervention; pediatric department; proband; public health relevance; skills; sound; success

 DESCRIPTION (provided by applicant): We propose a research-training program to prepare an independent young investigator focused on understanding the genetic causes of neurodevelopmental disorders. The candidate has expertise in the use of next generation sequencing technologies to identify coding variations that cause genetic disease, these skills will be applied to addressing the role of noncoding DNA variation in epilepsy. Epilepsy affects 1 in 26 individuals across the globe, including ~22 million people in the US alone. The epileptic encephalopathies (EEs) are the most severe of all epilepsies and most do not respond to current treatments, necessitating the need for novel therapeutic interventions. The first step towards designing new treatments is to identify the genetic mutations that cause this disorder. Significant progress has been made in this regard; a quarter of patients with EE have causative de novo mutations in the protein-coding regions of over 20 genes. However, while a number of genes are yet to be identified, these coding mutations are unlikely to account for all remaining cases. Recent studies, including the NIH-funded ENCODE project, have demonstrated the importance of noncoding elements in controlling how and when genes are expressed. We hypothesize that noncoding mutations cause EE by disrupting the expression of target genes that are important in neurogenesis. The most unbiased way to detect all noncoding genetic variation in the human genome is to perform whole- genome sequencing, this technique will likely be prevalent in the future of genetics. However, a major challenge to its success lies in ou ability to differentiate between the functional causal noncoding mutation and the millions of non-pathogenic variants identified. This challenge requires an understanding of how noncoding elements control gene expression during neurogenesis and neuronal function. This training program implements the use of epigenomic data and interpretation to identify important noncoding DNA regions in EE. Dr. Mefford is an expert in human molecular genetics research and has made a significant contribution to the understanding of genetic mutation in neurodevelopmental disorders, including epilepsy. Dr. Mefford will serve as primary mentor for the scientific and professional development of the candidate. Moreover, the candidate has assembled an advisory committee of experts in the fields in which she requires training and mentorship; Dr. Stamatoyannopoulos will support generation of epigenomic data, as well as establishing novel computational pipelines for interpretation, Dr. Shendure will advise in the development of a novel targeted RNA expression methodology, and Dr. Doherty will assist in neuronal cellular differentiation techniques. Moreover, the Department of Pediatrics, University of Washington, has an excellent track record of assisting fellows' transition to independence. Overall, the University of Washington School of Medicine is an ideal setting for acquiring new research skills, performing didactic training and benefiting from excellent mentorship from field leaders towards becoming a successful independent investigator. This career award will allow the candidate to develop a framework to identify candidate EE noncoding regions, using the genes that we have already defined as causes of EE as a model. First by identifying the neuronal- specific cis-regulatory regions around known EE genes. Second, using CHD2 as a model, we will identify the noncoding DNA targets of this protein, and examine how the function of these noncoding regions is affected by CHD2 loss. Together these noncoding DNA regions move towards the development of a 'regulatory epileptogenesis atlas' for prioritizing variants from whole-genome sequencing studies. This experimental model can rapidly be applied to other genes that cause neurodevelopmental disorders, contributing more broadly to our understanding of disease and laying the foundation for the candidate's independent research plan.

 描述（由申请人提供）：我们提出了一个研究培训计划，以准备一个独立的年轻研究人员专注于了解神经发育障碍的遗传原因。候选人具有使用下一代测序技术识别导致遗传疾病的编码变异的专业知识，这些技能将应用于解决癫痫中非编码DNA变异的作用。癫痫影响地球仪的1/26个体，仅在美国就有约2200万人。癫痫性脑病（EE）是所有癫痫中最严重的，并且大多数对当前的治疗没有反应，因此需要新的治疗干预。设计新疗法的第一步是确定导致这种疾病的基因突变。在这方面已经取得了重大进展;四分之一的EE患者在超过20个基因的蛋白质编码区中存在致病性从头突变。然而，虽然一些基因尚未被确定，但这些编码突变不太可能解释所有剩余病例。最近的研究，包括NIH资助的ENCODE项目，已经证明了非编码元件在控制基因表达方式和表达时间方面的重要性。我们假设非编码突变通过破坏在神经发生中重要的靶基因的表达而引起EE。检测人类基因组中所有非编码遗传变异的最无偏见的方法是进行全基因组测序，这种技术可能会在未来的遗传学中流行。然而，其成功的一个主要挑战在于区分功能性因果非编码突变和数百万非致病性变异的能力。这一挑战需要了解在神经发生和神经元功能过程中非编码元件如何控制基因表达。该培训计划实施表观基因组数据和解释的使用，以确定重要的非编码DNA区域在EE. Mefford博士是人类分子遗传学研究的专家，并作出了重大贡献的神经发育障碍，包括癫痫的基因突变的理解。Mefford博士将担任候选人科学和专业发展的主要导师。此外，候选人还组建了一个咨询委员会，由她需要培训和指导的领域的专家组成; Stamatoyannopoulos博士将支持表观基因组数据的生成，以及建立用于解释的新型计算管道，Shendure博士将建议开发一种新型靶向RNA表达方法，Doherty博士将协助神经元细胞分化技术。此外，华盛顿大学儿科系在协助研究员向独立过渡方面有着出色的记录。总的来说，华盛顿大学医学院是获得新的研究技能，进行教学培训和从优秀的指导受益的理想环境从领域领导者对成为一个成功的独立调查员。这个职业奖将允许候选人开发一个框架来识别候选EE非编码区，使用我们已经定义为EE原因的基因作为模型。首先通过鉴定已知EE基因周围的神经元特异性顺式调节区域。其次，使用CHD 2作为模型，我们将确定该蛋白质的非编码DNA靶点，并研究这些非编码区的功能如何受到CHD 2丢失的影响。这些非编码DNA区域一起朝着“调节性癫痫发生图谱”的发展方向发展，以优先考虑全基因组测序研究的变体。这种实验模型可以迅速应用于导致神经发育障碍的其他基因，更广泛地促进我们对疾病的理解，并为候选人的独立研究计划奠定基础。