RIGERR: Resources for Investigating Genetic and Epigenetic Regulation of Renal Disease

摘要 识别疾病相关功能变异的功能序列变异和效应基因，了解这些变异如何影响效应基因和疾病，并利用这些信息来推进精确医学，是当前常见疾病遗传学研究中最重要但也是最艰巨的挑战之一。全基因组关联研究发现的序列变异对基因表达有重要影响，识别全基因组关联研究中的效应基因及其作用机制具有重要的临床和科学意义。慢性肾脏疾病的发病率超过总人口的10%。在多达100万人中发现了200多个与肾功能、慢性肾脏疾病或尿白蛋白/肌酐比率相关的基因组基因座。这些基因座的连锁不平衡(LD)单倍型包含7,000多个独特的单核苷酸多态(SNPs)。很少有研究超越相关性来确定肾脏相关SNPs对基因表达的影响或调查相关机制。这样的研究将必须克服重大挑战，包括调节性SNPs对基因表达的影响具有组织特异性。许多LD区有数千个碱基对长，可能包含数十个SNP。这些长LD区域尤其难以研究。 我们开发了一种独特的方法和创新方法，用于明确和机械地将单倍型变体(包括长单倍型)与特定疾病相关细胞类型中的基因联系起来。在RIGERR(研究肾脏疾病的遗传和表观遗传调控的资源)中，我们建议使用这套复杂的技术来产生大量的创新工具和资源，以广泛地改变肾脏疾病的遗传和表观遗传研究。RIGERR的目标1是通过基因工程产生100多株人类诱导的多能干细胞，以包含与肾脏功能或疾病相关的易于编辑或精确重组的单倍型或高外显性变异。这些编辑后的细胞系将被提供给研究团体，用于广泛的肾脏疾病的分子、功能或药物测试研究。在目标2中，我们将产生新的数据集，并建立一个利用这些前所未有的资源进行肾脏功能和疾病的机械性和活体研究的工作流程，以蛋白尿为例。我们获得了令人振奋的初步数据，这些数据有力地支持了RIGERR在概念和技术上的可行性。

SUMMARY Identifying functional sequence variants and effector genes for disease-associated functional variants, understanding how the variants influence effector genes and disease, and utilizing this information to advance precision medicine are among the most important yet formidable challenges in current genetic research of common diseases. Sequence variants identified by genome-wide association studies (GWAS) can have substantial effects on gene expression, and identification of GWAS effector genes and the mechanisms involved has important clinical and scientific implications. Chronic kidney disease occurs in more than 10% of the general population. GWAS in up to 1 million people have identified more than 200 genomic loci associated with renal function, chronic kidney disease, or urinary albumin-to-creatinine ratio. Haplotypes in linkage disequilibrium (LD) at these loci contain more than 7,000 unique single nucleotide polymorphisms (SNPs). Very few studies have gone beyond associations to ascertain the effect of kidney-associated SNPs on gene expression or investigate the mechanisms involved. Such studies would have to overcome substantial challenges including the tissue-specific nature of the effect of regulatory SNPs on gene expression. Many LD regions are thousands of base pairs long and may contain dozens of SNPs. These long LD regions are particularly difficult to study. We have developed a unique approach and innovative methods for definitively and mechanistically linking haplotype variants, including long haplotypes, to genes in specific disease-relevant cell types. In RIGERR (Resources for Investigating Genetic and Epigenetic Regulation of Renal Disease), we propose to use this suite of sophisticated technologies to generate a large collection of innovative tools and resources to transform genetic and epigenetic research of kidney disease broadly. Aim 1 of RIGERR is to generate more than 100 lines of human induced pluripotent stem cells genetically engineered to contain readily editable or precisely reconstituted haplotypes or high-penetrance variants associated with kidney function or disease. These edited cell lines will be provided to the research community for a wide range of molecular, functional, or drug testing studies for kidney disease. In Aim 2, we will produce novel datasets and establish a workflow for utilizing these unprecedented resources to conduct mechanistic and in vivo studies of kidney function and disease, using albuminuria as an example. We have obtained exciting preliminary data that strongly support the conceptual and technical feasibility of RIGERR.