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）：我们提出了一项研究培训计划，旨在培养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。该候选人拥有使用下一代测序技术来识别导致遗传疾病的编码变异的专业知识。 ，这些技能将用于解决非编码 DNA 变异在癫痫中的作用，全球每 26 个人中就有 1 人患有癫痫，其中仅美国就有约 2200 万人。 (EE) 是所有癫痫中最严重的一种，大多数对当前的治疗没有反应，因此需要新的治疗干预措施，设计新治疗方法的第一步是识别导致这种疾病的基因突变。在这方面；四分之一的 EE 患者在 20 多个基因的蛋白质编码区域有致病性的新生突变。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。 。最近的包括 NIH 资助的 ENCODE 项目在内的研究已经证明了非编码元件在控制基因表达方式和时间方面的重要性，我们发现非编码突变通过破坏神经发生中重要的靶基因的表达来导致 EE。检测人类基因组中所有非编码遗传变异的方法是进行全基因组测序，这项技术可能会在未来的遗传学中普及，然而，其成功的一个主要挑战在于区分功能因果关系的能力。这一挑战需要了解非编码元件如何在神经发生和神经元功能过程中控制基因表达。该培训计划使用表观基因组数据和解释来识别 EE 中的重要非编码 DNA 区域。梅福德博士是人类分子遗传学研究专家，为理解神经发育障碍（包括癫痫）的基因突变做出了重大贡献。梅福德博士将担任该领域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；Stamatoyannopoulos 博士将支持表观基因组数据的生成，并建立新的解释计算管道，Shendure 博士将在以下方面提供建议：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，华盛顿大学儿科在帮助研究员过渡到独立方面有着出色的记录。华盛顿大学医学院是获得新研究技能、进行教学培训并受益于领域领导者的优秀指导，成为一名成功的独立研究者的理想场所。该职业奖将使候选人能够开发一个框架来识别候选人 EE。首先，通过识别已知 EE 基因周围的神经元特异性顺式调控区域，使用 CHD2 作为模型，我们将识别非编码 DNA 靶标。这个的蛋白质，并检查这些非编码区的功能如何受到 CHD2 丢失的影响，这些非编码 DNA 区一起朝着开发“调控癫痫发生图谱”的方向发展，以优先考虑全基因组测序研究中的变异。与导致神经发育障碍的其他基因相关，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。

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.