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: 8931100
• 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/8931100
• 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; DNA Sequence Alteration; Data; Development; Disease; Elements; Encephalopathies; Epigenetic Process; Epilepsy; Epileptogenesis; Experimental Models; Family; Foundations; Funding; Future; Gene Expression; Gene Expression Regulation; Gene Targeting; Generations; Genes; Genetic; Genetic Research; Genetic Transcription; Genetic Variation; Genomic Segment; Goals; Health; 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 editing; genome sequencing; human disease; human embryonic stem cell; interest; medical schools; neurogenesis; neuron development; next generation sequencing; novel; novel therapeutic intervention; pediatric department; proband; 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，以培养一名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。候选人在使用下一代测序技术识别导致遗传病的编码变异方面具有专业知识，这些技能将应用于解决非编码DNA变异在癫痫中的作用。全球每26个人中就有一个患有癫痫，其中仅美国就有约2200万人。癫痫脑病(EES)是所有癫痫中最严重的，大多数对目前的治疗没有反应，需要新的治疗干预措施。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20多个基因的蛋白质编码区有致病的从头突变。然而，虽然许多基因尚未确定，但这些编码突变不太可能解释所有剩余的病例。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的方式和时间方面的重要性。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导致EE。检测人类基因组中所有非编码遗传变异的最公正的方法是进行全基因组测序，这项技术很可能在未来的遗传学中盛行。然而，其成功的一个主要挑战在于我们区分功能性原因非编码突变和已识别的数百万非致病变异体的能力。这一挑战需要了解非编码元件在神经发生和神经元功能过程中如何控制基因表达。该培训计划使用表观基因组数据和解释来识别EE中重要的非编码DNA区域。梅福德博士是人类分子遗传学研究方面的专家，在了解包括癫痫在内的神经发育障碍的基因突变方面做出了重大贡献。梅福德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由她需要培训和指导的领域的专家组成的咨询委员会；斯塔马托扬诺普洛斯博士将支持表观基因组数据的生成，并建立用于解释的新的计算管道；Shendure博士将为开发新的靶向RNA表达方法提供建议，Doherty博士将协助神经细胞分化技术。此外，华盛顿大学儿科系在帮助研究员向独立过渡方面有着良好的记录。总体而言，华盛顿大学医学院是一个理想的环境，可以获得新的研究技能，进行教学培训，并受益于领域领导人的出色指导，从而成为一名成功的独立调查员。这个职业奖项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病因的基因作为模型。首先，通过识别已知EE基因周围的神经元特异性顺式调节区。其次，以CHD2为模型，我们将确定该蛋白的非编码区DNA靶标，并研究CHD2缺失对这些非编码区功能的影响。这些非编码的DNA区域共同发展出一种用于优先处理全基因组测序研究中的变异体的“癫痫发生调控图谱”。这一实验模型可以迅速应用于导致神经发育障碍的其他基因，有助于我们更广泛地了解疾病，并为候选人的独立研究计划奠定基础。

项目成果

Refining analyses of copy number variation identifies specific genes associated with developmental delay.

• DOI: 10.1038/ng.3092
• 发表时间: 2014-10
• 期刊: NATURE GENETICS
• 影响因子: 30.8
• 作者: Coe, Bradley P.;Witherspoon, Kali;Rosenfeld, Jill A.;van Bon, Bregje W. M.;Vulto-van Silfhout, Anneke T.;Bosco, Paolo;Friend, Kathryn L.;Baker, Carl;Buono, Serafino;Vissers, Lisenka E. L. M.;Schuurs-Hoeijmakers, Janneke H.;Hoischen, Alex;Pfundt, Rolph;Krumm, Nik;Carvill, Gemma L.;Li, Deana;Amaral, David;Brown, Natasha;Lockhart, Paul J.;Scheffer, Ingrid E.;Alberti, Antonino;Shaw, Marie;Pettinato, Rosa;Tervo, Raymond;de Leeuw, Nicole;Reijnders, Margot R. F.;Torchia, Beth S.;Peeters, Hilde;O'Roak, Brian J.;Fichera, Marco;Hehir-Kwa, Jayne Y.;Shendure, Jay;Mefford, Heather C.;Haan, Eric;Gecz, Jozef;de Vries, Bert B. A.;Romano, Corrado;Eichler, Evan E.
• 通讯作者: Eichler, Evan E.