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（由应用程序提供）：我们提出了一项研究培训计划，以准备一名独立的年轻研究者，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来识别引起遗传疾病的编码变化方面具有专业知识，这些技能将用于解决非编码DNA变异在癫痫中的作用。癫痫会影响全球26个人中有1人，仅在美国就有约2200万人。癫痫性脑病（EES）是所有癫痫症中最严重的，大多数对当前的治疗方法没有反应，这是新型治疗干预所必需的。设计新疗法的第一步是确定引起这种疾病的基因突变。在这方面取得了重大进展。四分之一的EE患者在20多个基因的蛋白质编码区域中具有严重的从头突变。但是，尽管尚未确定许多基因，但这些编码突变不太可能考虑所有剩余病例。最近的研究，包括NIH资助的编码项目，证明了非编码元素在控制基因表达以及何时表达基因的重要性。我们假设非编码突变通过破坏在神经发生中很重要的靶基因的表达来引起EE。检测人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，该技术可能在遗传学的未来可能很普遍。但是，对其成功的主要挑战在于OU可以区分功能性因果非编码突变和数百万个非致病性变体的能力。这一挑战需要了解非编码元件如何控制神经发生和神经元功能过程中的基因表达。该培训计划实现了表观基因组数据和解释的使用，以识别EE中重要的非编码DNA区域。 Mefford博士是人类分子遗传学研究的专家，并为了解包括癫痫在内的神经发育疾病的遗传突变做出了重要贡献。 Mefford博士将作为候选人的科学和专业发展的主要精神。此外，该候选人已经组建了一个她需要培训和心态的领域专家咨询委员会； Stamatoyannopoulos博士将支持生成表观基因组数据，并建立新的解释计算管道，Shendure博士将建议开发一种新型的靶向RNA表达方法，Doherty博士将有助于神经元细胞分化技术。此外，华盛顿大学儿科系有良好的记录，可以帮助研究员过渡到独立性。总体而言，华盛顿大学医学院是获得新的研究技能，进行教学培训并受益于从野外领导者到成为成功的独立研究员的出色心态的理想场所。该职业奖将使候选人使用我们已经定义为EE的原因作为模型的基因来制定框架来识别候选EE非编码区域。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CHD2作为模型，我们将确定该蛋白质的非编码DNA靶标，并检查这些非编码区的功能如何受CHD2损失的影响。这些不编码的DNA区域共同发展了“调节性癫痫发生地图集”，以优先考虑全基因组测序研究的变体。该实验模型可以迅速应用于引起神经发育障碍的其他基因，更广泛地有助于我们对疾病的理解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.