Dissecting the role of disease-associated variants in the regulation of TMEM106B

 描述(申请人提供)：额颞叶变性(FTLD)占65岁以下痴呆症患者的10%-20%，是一种致命的疾病，没有可用的治疗方法。全基因组关联研究发现，TMEM106B基因座上的三个单核苷酸多态(SNPs)与FTLD-TDP的风险增加有关，FTLD-TDP是FTLD最常见的神经病理亚型。在患者的脑和淋巴母细胞系(LCLS)中，顶级GWASNP的风险等位基因rs1990622与TMEM106B水平的升高相关，这表明风险等位基因携带者可能由于TMEM106B在一种或多种脑细胞类型中表达的增加而更容易患上疾病。FTLD-TDP组的TMEM106B水平也高于神经学正常对照组，进一步证实了TMEM106B表达在疾病中的重要性。有趣的是，TMEM106B的基因型和表达也与原颗粒有关，原颗粒是一种重要的分泌型神经营养因子。原颗粒蛋白基因(GRN)功能缺失突变是家族性FTLD-TDP的常见原因，TMEM106B在细胞培养系统中的过表达会影响细胞内外原颗粒蛋白水平。此外，携带TMEM106B SNP rs1990622风险等位基因的个体降低了血浆原颗粒水平。因此，TMEM106B的风险等位基因可能通过影响TMEM106B对原颗粒蛋白的表达水平而影响疾病的风险。这项建议的目的是确定导致风险等位基因携带者TMEM106B水平升高的确切分子机制，以便确定可以靶向调节TMEM106B水平的调控途径。基于TMEM106B基因座的连锁不平衡结构和LCL eQTL信号的精细定位，根据ENCODE实验数据评估的调控功能的可能性，对候选遗传变异进行了优先排序。这种全面的、不偏不倚的变异优先顺序导致了位于预测的绝缘子区域的两个首选候选SNP的识别，该SNP在基于细胞的报告构建分析中显示出单倍型依赖的增强子阻断活性。基于这一初步数据，提出了两个主要目标：1)确定该区域在体内基因组编辑调控TMEM106B中的作用；2)确定导致绝缘子功能单倍型效应的SNP(S)，以及 涉及的分子机制。阐明TMEM106B基因与表达水平以及疾病风险之间关系的确切分子机制，将揭示可以针对TMEM106B水平操纵的上游调控途径。

 DESCRIPTION (provided by applicant): Frontotemporal lobar degeneration (FTLD) accounts for 10-20% of dementia cases in individuals under age 65, and is a fatal disease with no available treatments. Three single nucleotide polymorphisms (SNPs) at the TMEM106B locus have been associated with increased risk of FTLD-TDP, the most common neuropathological subtype of FTLD, by genome-wide association study (GWAS). The risk allele of the top GWAS SNP, rs1990622, has been associated with increased TMEM106B levels in patient brain and lymphoblastoid cell lines (LCLs), suggesting that risk allele carriers may be more susceptible to disease due to increased TMEM106B expression in one or more brain cell types. TMEM106B levels are also increased in FTLD-TDP brains compared to neurologically normal controls, further establishing the importance of TMEM106B expression in disease. Intriguingly, TMEM106B genotype and expression have also been linked to progranulin, an important secreted neurotrophic factor. Loss-of-function mutations in the progranulin gene (GRN) are a common cause of familial FTLD-TDP, and overexpression of TMEM106B in cell culture systems affects intra- and extracellular levels of progranulin. Furthermore, individuals with the risk allee of the TMEM106B SNP rs1990622 have decreased plasma progranulin levels. Therefore, the risk allele of TMEM106B may influence risk for disease through an effect of TMEM106B expression levels on progranulin. The goal of this proposal is to identify the precise molecular mechanisms responsible for the increased TMEM106B levels seen in risk allele carriers, in order to identify regulatory pathways that can be targeted to modulate TMEM106B levels. Based on the linkage disequilibrium structure at the TMEM106B locus and fine-mapping of the LCL eQTL signal, candidate genetic variants were prioritized based on likelihood of regulatory function as assessed by ENCODE experimental data. This comprehensive, unbiased prioritization of variants resulted in the identification of two top candidate SNPs located in a predicted insulator region, which displays haplotype-dependent enhancer-blocking activity in cell-based reporter construct assays. Two major aims based on this preliminary data are proposed: 1) Determine the role of this region in the regulation of TMEM106B by in vivo genome editing, and 2) Identify the SNP(s) responsible for the haplotype effect on insulator function, and the molecular mechanisms involved. Elucidation of the precise molecular mechanisms underlying the association of TMEM106B genotype with expression levels, and by extension, disease risk, will reveal upstream regulatory pathways that can be targeted to manipulate TMEM106B levels.