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: 8465225
• 负责人: Marcus Guy Pezzolesi
• 金额: $ 11.84万
• 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/8465225
• 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; Research; Research Activity; Research Methodology; Research Training; Sampling; Source; Structure; Susceptibility Gene; Targeted Resequencing; 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 sequencing; novel; post-doctoral training; risk variant; skills; skills training; success; transcriptome sequencing

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.

描述（由申请人提供）：本指导研究科学家发展奖（K01）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，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，一个特殊的指导支持网络，以及旨在解决DN遗传学调查中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基因组中遗传变异的理解，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础基因的能力。全基因组关联（GWA）研究引领了这场革命，成功地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，仍面临许多重大挑战。在这些挑战的最前沿是精确定位在已识别关联基础上的因果功能变异，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，这导致了其他来源的猜测，包括罕见的、低频的变异，占了这种“缺失的遗传性”的一部分。这些挑战都体现在我们最近在糖尿病肾脏遗传学（GoKinD） 1型糖尿病（T1D）肾病收集中对DN的GWA扫描中。考虑到这些挑战，我建议的培训旨在以我以前的经验为基础，同时推动这一领域的研究向前发展。这将通过在群体遗传学和基因组学的分析和实验室方面的广泛教学和实践培训来实现，其中包括统计和分析技能的发展，下一代测序和基因调控的新方法的培训，以调查遗传变异和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策略的培训。我提出的研究目的是进一步研究我们在染色体1p和13q上的GoKinD集合的GWA扫描中发现的遗传关联，并确定i)致病遗传变异和ii)这些位点上关联的疾病基因。这一目标将通过两个具体目标来实现：1)在染色体1p和13q上的相关区域鉴定与DN有因果关系的DNA序列差异。为了实现这一目标，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有针对性的重测序来实现，包括包含相关变体的单倍型块/LD间隔以及1p和13q区域所有已知基因的外显子，这些区域来自GoKinD T1D肾病收集的汇总DNA样本，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、生物学和统计学意义对这些候选因果变量进行优先排序。这将使用各种标准来确定最有希望的功能候选，然后在整个GoKinD T1D肾病收集中进行后续基因分型。2)通过将候选的DN致病变异定位到其目标DN疾病基因来鉴定染色体1p和13q区域的DN易感基因。为了实现这一目标，我将a)利用RNA-Seq技术和早期DN的T1D患者的肾脏活检，建立1p和13q染色体相关区域的全面肾脏转录图谱，b)利用染色体构象捕获技术绘制13q上候选DN风险变异与其远端靶基因之间的远程相互作用图谱。c)进行体外研究，检查每个候选因果变异对1p和13q染色体区域内目标DN易感基因表达的影响。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。总之，这一目标和这些具体目标提供了一个易于处理的调查过程，建立在令人信服的初步数据。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结合起来。