Functional Dissection of CNVs in Neurodevelopmental Traits

神经发育特征中 CNV 的功能剖析

基本信息

批准号：
10491188
负责人：
Erica Ellen Davis
金额：
$ 52.62万
依托单位：
LURIE CHILDREN'S HOSPITAL OF CHICAGO
依托单位国家：
美国
项目类别：
财政年份：
2015
资助国家：
美国
起止时间：
2015-03-01 至 2026-08-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10491188
关键词：
16p11.2 19p13.1 Affect Animal Model Area Attention Biological Biological Assay Biology Cartilage Cells Collaborations Complex Copy Number Polymorphism Data Data Set Disease Disease susceptibility Dissection Equilibrium Face Funding Gene Combinations Gene Dosage Gene Expression Profile Genes Genetic Genetic Epistasis Genetic Transcription Genomics Histone Deacetylase Human Human Pathology Individual Knowledge Maps Measures Methods Modeling Molecular Mus Mutation Neurodevelopmental Disorder Neurons Pathogenicity Pathology Pathway Analysis Pathway interactions Pharmaceutical Preparations Phenocopy Phenotype Physiological Probability Property Protocols documentation RORA gene Rattus Repressor Proteins Role Safety Syndrome Testing Therapeutic Therapeutic Intervention Transcript Transcription Repressor Transcriptional Regulation Translating Validation Work Zebrafish biological systems burden of illness cell type combinatorial craniofacial craniofacial development dosage drug candidate drug development drug discovery drug repurposing efficacy testing genetic architecture genetic corepressor genomic data genomic locus in vivo inhibitor neurodevelopment novel phenotypic data safety testing therapeutic candidate therapeutic development tool trait transcriptome transcriptomics

项目摘要

Understanding the contribution of copy number variants (CNVs) to human pathology remains challenging, in part because of the complex and varied influence of loci within them. In some cases, a single dosage-sensitive locus drives pathology. In other examples, multiple genes contribute to phenotypes through additive effects and through complex genetic interactions. In the previous funding period, we focused on deletion syndromes and reciprocal CNVs and asked whether we could develop tools to aid the identification of driver genes. Progress in that work has informed several areas of pathology. For example, the identification of SIN3B as a driver of a non-recurrent 230 kb deletion on 19p13.1 that causes a complex neurodevelopmental phenotype reinforced the role of the Sin3/HDAC transcriptional corepressor complex in neurodevelopment and facilitated the identification of Mendelian mutations that phenocopy the CNV. In the case of the 17q24.2 CNV, we learned about the synthetic CNV phenotype likely caused by dosage imbalance of both BPTF and PSMD12. Finally, modeling of multiple phenotypes associated with the 16p11.2 CNV showed how: (a) key neurodevelopmental and craniofacial pathologies were conserved from humans, to mice, to rats, to zebrafish; (b) demonstrated discrete epistatic interactions between loci; and (c) generated a host of surrogate model organisms in which to perform both pathway analysis and drug discovery. Overall, the genetic and functional dissection of CNV exemplars has underscored three observations: (a) not all genes in a CNV are dosage sensitive (suspected, but now supported by experimental evidence); (b) some genes are dosage sensitive in one direction (gain, loss, but not both); and (c) non-driver genes can participate in distinct genetic interactions. The knowledge and experimental tools gained affords us the opportunity to expand our ambition. We still do not understand how intra-CNV combinatorial dosage influences phenotype, and whether the lessons learned from prior work are broadly generalizable. Moreover, given the non-trivial contribution of CNVs to disease burden, it is crucial that we pay attention to the development of therapeutic avenues. We propose three Aims: (1) We will dissect a unique set of CNVs, in which the phenotype is driven only by duplication to identify triplosensitive genes and ask whether disease susceptibility is driven by a threshold effect as a means to understanding why only a subset of human genes are dosage sensitive. (2) We will harness our existing zebrafish models to characterize the molecular properties of epistatic effects using the neuronal and facial cartilage phenotypes of the 16p11.2 CNV and ask whether we can detect epistasis at the level of transcriptional regulation. (3) We will combine our extensive repertoire of zebrafish models of CNV drivers with the Connectivity Map (CMap) Touchstone dataset and a newly developed safety/efficacy protocol to identify candidate therapeutics. Together, our studies will refine the genetic architecture of genomic disorders, inform the molecular basic of genetic interactions, and chart a systematic path toward therapeutics for neurodevelopmental traits.

了解拷贝数变异 (CNV) 对人类病理学的贡献仍然具有挑战性，部分原因是它们内部基因座的复杂且多样的影响。在某些情况下，单一剂量敏感基因座驱动病理学。在其他例子中，多个基因通过加性效应对表型做出贡献并通过复杂的遗传相互作用。在之前的资助期间，我们专注于缺失综合症和相互的 CNV，并询问我们是否可以开发工具来帮助识别驱动基因。这项工作的进展为病理学的多个领域提供了信息。例如，将 SIN3B 识别为 19p13.1 上非重复性 230 kb 缺失的驱动因素，导致复杂的神经发育表型增强了 Sin3/HDAC 转录辅阻遏物复合物在神经发育中的作用并促进鉴定对 CNV 进行表型复制的孟德尔突变。在 17q24.2 CNV 的情况下，我们了解到关于可能由 BPTF 和 PSMD12 剂量不平衡引起的合成 CNV 表型。最后，与 16p11.2 CNV 相关的多种表型建模显示：(a) 关键的神经发育人类、小鼠、大鼠和斑马鱼的颅面部病变均保留； (b) 证明位点之间离散的上位相互作用； (c) 产生了许多替代模型生物体进行通路分析和药物发现。总体而言，CNV 的遗传和功能解剖范例强调了三个观察结果：（a）并非 CNV 中的所有基因都对剂量敏感（怀疑，但现在有实验证据支持）； (b) 一些基因在一个方向上对剂量敏感（增益、损失，但不是两者都有）； (c)非驱动基因可以参与不同的遗传相互作用。知识和获得的实验工具为我们提供了扩大我们的雄心的机会。我们仍然不明白如何 CNV 内组合剂量影响表型，以及从先前工作中吸取的教训是否有效具有广泛的概括性。此外，鉴于 CNV 对疾病负担的重要贡献，至关重要的是我们关注治疗途径的发展。我们提出三个目标：（1）我们将剖析一组独特的 CNV，其中表型仅由重复驱动以识别三倍敏感基因和询问疾病易感性是否由阈值效应驱动，以此作为理解为什么只有人类基因的子集对剂量敏感。 (2) 我们将利用现有的斑马鱼模型来表征使用 16p11.2 的神经元和面部软骨表型的上位效应的分子特性 CNV 并询问我们是否可以在转录调控水平上检测上位性。 (3) 我们将结合我们的具有连接图 (CMap) Touchstone 数据集的 CNV 驱动器斑马鱼模型的广泛库以及新开发的安全性/有效性协议来确定候选疗法。一起，我们的研究将完善基因组疾病的遗传结构，了解遗传相互作用的分子基础，以及绘制神经发育特征治疗的系统路径。