Search of Diabetes Nephropathy Genes in Type 1 Diabetes

1 型糖尿病中糖尿病肾病基因的搜索

• 批准号: 8189702
• 负责人: Marcus Guy Pezzolesi
• 金额: $ 11.7万
• 依托单位: JOSLIN DIABETES CENTER
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-08-01 至 2016-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8189702
• 关键词: 13q; Accounting; Address; Aging; Albuminuria; Architecture; Area; Award; Bioinformatics; Biological; Biopsy; Cataloging; Catalogs; Chromosomes; Code; Collection; Complex; Consent; DNA; DNA Resequencing; DNA Sequence; Data; Development; Development Plans; Diabetes Mellitus; Diabetic Nephropathy; Disease; Distal; Exons; Foundations; Frequencies; Future; Gene Expression Regulation; Gene Targeting; Genes; Genetic; Genetic Variation; Genome; Genomics; Genotype; Goals; Haplotypes; Hereditary Disease; Heritability; In Vitro; Insulin-Dependent Diabetes Mellitus; Intercistronic Region; Investigation; Kidney; Kidney Diseases; Laboratories; Maps; Mentored Research Scientist Development Award; Mentors; Methodology; Mind; Molecular Conformation; Mus; Myosin Heavy Chains; Non-Insulin-Dependent Diabetes Mellitus; Pathogenesis; Patients; Population Genetics; Predisposition; Proteins; RNA; Research; Research Activity; Research Methodology; Research Training; Risk; Sampling; Source; Structure; Susceptibility Gene; Technology; Training; Training Activity; Transcript; Variant; base; career; career development; diabetes mellitus genetics; experience; follow-up; genetic association; genetic variant; genome wide association study; human IRS2 protein; human disease; interest; knowledge base; neuronal growth; next generation; novel; post-doctoral training; skills; skills training; success

DESCRIPTION (provided by applicant): This Mentored Research Scientist Development Award (K01) application aims to expand upon the base knowledge I have acquired during my post-doctoral training in the genetics of diabetic nephropathy (DN) and develop expertise in both analytical and laboratory skills that will prepare me for a long and impactful career in research on the genetics of diabetes and its complications. Through carefully structured career development and training activities, an exceptional network of mentored support, and a research plan aimed at addressing specific challenges in investigations on the genetics of DN, I fully expect to accomplish this goal. Recent advances in population genetics and genomics have expanded our understanding of genetic variation across our genome and facilitated cutting-edge technologies that have transformed our ability to identify genes that underlie human disease. Genome-wide association (GWA) studies have spearheaded this revolution, successfully identifying hundreds of common genetic variants associated with complex disease. Despite these successes, a number of important challenges lie ahead to fully appreciate the genetic basis of these complex diseases. At the forefront of these challenges is pinpointing the causal functional variants that underlie the identified associations, a task that is particularly formidable when the associated SNP is localized to a region devoid of evidence of protein-coding genes. Additionally, somewhat surprisingly, the first wave of GWA studies has shown that the effect size of common variants is more modest than previously suspected, leading to speculation that other sources, including rare, low frequency variants, account for a portion of this 'missing heritability'. Each of these challenges was manifest in our recent GWA scan of DN in the Genetics of Kidneys in Diabetes (GoKinD) type 1 diabetes (T1D) Nephropathy Collection. With these challenges in mind, my proposed training seeks to build on my previous experience while moving this area of research forward. This will be accomplished through extensive didactic and hands-on training in both analytical and laboratory aspects of population genetics and genomics that includes the development of statistical and analytical skills, training in new methodologies of next-generation sequencing and gene regulation to investigate the relationship between genetic variations and disease predisposition, and training in analytical methodologies and research strategies for investigating complex disease. My proposed research aims to further investigate genetic associations identified in our GWA scan of the GoKinD collection on chromosomes 1p and 13q and identify both i) the causative genetics variants and ii) the disease genes underlying the associations at each of these loci. This goal will be accomplished through two Specific Aims. 1) To identify DNA sequence differences that are causally related to DN in the associated regions on chromosomes 1p and 13q. To accomplish this, I will a) establish a comprehensive catalog of all DNA sequence differences located in the intervals containing the associated SNPs using next-generation sequencing technology. This will be accomplished by targeted resequencing of these regions, including the haplotype blocks/LD intervals containing the associated variants and the exons of all known genes in the 1p and 13q regions, in pooled DNA samples from the GoKinD T1D Nephropathy Collection using filter-based hybridization capture followed by massively parallel DNA resequencing. I will then b) prioritize these candidate causal variants based on their bioinformatic, biological, and statistical significance. This will be accomplished using a variety of criteria to identify the most promising functional candidates followed by follow-up genotyping in the entire GoKinD T1D Nephropathy Collection. 2) To identify the DN susceptibility genes at the chromosome 1p and 13q regions by mapping the candidate causal variants to their target DN disease gene. To accomplish this I will a) establish a comprehensive renal transcript map for the associated regions on chromosome 1p and 13q using RNA-Seq technology and kidney biopsies obtained from T1D patients with early DN, b) map the long-range interaction between the candidate DN risk variants on 13q and its distal target gene using Chromosome Conformation Capture technology, and c) perform in vitro studies to examine the impact of each candidate causal variant on the expression of their target DN susceptibility gene within the 1p and 13q chromosomal regions. These targeted studies will be the foundation for future, more detailed functional studies. Together, this goal and these Specific Aims offer a tractable course of investigation that builds on convincing preliminary data. They will have a profound impact on our understanding of the allelic architecture of DN and its underlying mechanism. Importantly, they also faithfully integrate highly-focused research activities with my overall training and career development goals. PUBLIC HEALTH RELEVANCE: The proposed training aims to expand upon the base knowledge I have acquired during my post-doctoral training in the genetics of diabetic nephropathy (DN) and develop expertise in both analytical and laboratory skills that will prepare me for a long and impactful career in research on the genetics of diabetes and its complications. This will be accomplished through extensive didactic and hands-on training in both analytical and laboratory aspects of population genetics and genomics. The proposed research strategy will have a profound impact on our understanding of the allelic architecture of DN and its underlying mechanism while faithfully integrating highly-focused research activities with my overall training and career development goals.

该指导研究科学家发展奖（K 01）申请旨在扩展我在糖尿病肾病（DN）遗传学博士后培训期间获得的基础知识，并发展分析和实验室技能方面的专业知识，这将为我在糖尿病及其并发症遗传学研究方面的长期而有影响力的职业生涯做好准备。通过精心组织的职业发展和培训活动，一个特殊的辅导支持网络，以及一个旨在解决DN遗传学调查中的具体挑战的研究计划，我完全期望实现这一目标。 群体遗传学和基因组学的最新进展扩大了我们对整个基因组遗传变异的理解，并促进了尖端技术的发展，这些技术改变了我们识别人类疾病基因的能力。全基因组关联（GWA）研究引领了这场革命，成功识别了数百种与复杂疾病相关的常见遗传变异。 尽管取得了这些成功，但要充分了解这些复杂疾病的遗传基础，还面临着一些重要的挑战。在这些挑战的最前沿，是精确定位所确定的关联背后的因果功能变体，当相关SNP定位于缺乏蛋白质编码基因证据的区域时，这项任务尤其艰巨。此外，有些令人惊讶的是，第一波GWA研究表明，常见变异的效应大小比以前怀疑的要小，这导致人们猜测其他来源，包括罕见的低频变异，也是这种“缺失遗传性”的一部分。这些挑战中的每一个都在我们最近的糖尿病肾脏遗传学（GoKinD）1型糖尿病（T1 D）肾病集合中的DN GWA扫描中表现出来。 考虑到这些挑战，我提出的培训旨在建立在我以前的经验，同时推动这一领域的研究向前发展。这将通过在人口遗传学和基因组学的分析和实验室方面进行广泛的教学和实践培训来实现，包括发展统计和分析技能，培训下一代测序和基因调控的新方法，以调查遗传变异与疾病易感性之间的关系，以及调查复杂疾病的分析方法和研究战略方面的培训。 我提出的研究旨在进一步研究我们在1 p和13 q染色体上的GoKinD集合的GWA扫描中确定的遗传关联，并确定i）致病遗传变异和ii）这些基因座中每个基因座关联的疾病基因。 这一目标将通过两个具体目标来实现。1)确定染色体1 p和13 q相关区域中与DN因果相关的DNA序列差异。为了实现这一点，我将a）使用下一代测序技术建立一个位于包含相关SNP的间隔中的所有DNA序列差异的综合目录。这将通过对这些区域进行靶向重测序来实现，包括在GoKinD T1 D Nephropathy Collection的合并DNA样本中含有相关变体的单倍型区块/LD间隔以及1 p和13 q区域中所有已知基因的外显子，使用基于过滤器的杂交捕获，然后进行大规模平行DNA重测序。然后，我将B）根据其生物信息学、生物学和统计学显著性对这些候选因果变异体进行优先排序。这将使用各种标准来确定最有希望的功能候选人，然后在整个GoKinD T1 D肾病集合中进行后续基因分型。2)通过将候选致病变异体定位到其靶DN疾病基因上，鉴定染色体1 p和13 q区域的DN易感基因。为了实现这一目标，我将a）使用RNA-Seq技术和从患有早期DN的T1 D患者中获得的肾脏活检，建立染色体1 p和13 q相关区域的全面肾脏转录图谱，B）绘制候选DN之间的长期相互作用使用染色体构象捕获技术，13 q上的DN风险变体及其远端靶基因，和c）进行体外研究以检查每种候选致病变体对它们的靶DN易感性基因在1 p和13 q染色体区域内的表达的影响。这些有针对性的研究将为未来更详细的功能研究奠定基础。 这一目标和这些具体目标一起提供了一个建立在令人信服的初步数据基础上的易于处理的调查过程。它们将对我们理解DN的等位基因结构及其潜在机制产生深远的影响。重要的是，他们还忠实地将高度集中的研究活动与我的整体培训和职业发展目标相结合。 公共卫生相关性：拟议的培训旨在扩展我在糖尿病肾病（DN）遗传学博士后培训期间获得的基础知识，并发展分析和实验室技能方面的专业知识，这将使我为糖尿病及其并发症遗传学研究的长期而有影响力的职业生涯做好准备。这将通过在群体遗传学和基因组学的分析和实验室方面进行广泛的教学和实践培训来实现。拟议的研究策略将对我们理解DN的等位基因结构及其潜在机制产生深远的影响，同时忠实地将高度集中的研究活动与我的整体培训和职业发展目标相结合。