Follow-Up Studies of a Genome-Wide Association Analysis in Pima Indians

皮马印第安人全基因组关联分析的后续研究

• 批准号: 8939683
• 负责人: Leslie J Baier
• 金额: $ 163.98万
• 依托单位: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/8939683
• 关键词: Acute; Acyltransferase; Affect; Alleles; American Indians; Arizona; Biological Process; Body Weight; Body fat; Body mass index; Candidate Disease Gene; Caucasians; Caucasoid Race; Cell Communication; Cells; Communities; Complementary DNA; Data; Development; Disease; EGF gene; Eating; Ethnic Origin; Ethnic group; Euglycemic Clamping; Exons; Family; Fatty acid glycerol esters; Feeding behaviors; Genes; Genome; Genotype; Glucose; Glucose Clamp; Haplotypes; Homeostasis; Human; Hypothalamic structure; In Vitro; Individual; Inflammation; Insulin; Intravenous Bolus; Life; Maps; Measures; Mediating; Mitochondria; Mouse Cell Line; Native Americans; Non-Insulin-Dependent Diabetes Mellitus; Notch Signaling Pathway; Obesity; Odds Ratio; Pancreas; Pathway interactions; Peptides; Physiological; Pima Indian; Positioning Attribute; Post-Transcriptional Regulation; Predisposition; Prevalence; Publishing; Reporting; Research Design; Rivers; Role; Sampling; Siblings; Signal Pathway; Signal Transduction; Single Nucleotide Polymorphism Map; Small Interfering RNA; Techniques; Technology; Tissues; Untranslated Regions; Up-Regulation; Variant; base; cytokine; diabetic; early onset; follow-up; genome wide association study; genome-wide; islet; knock-down; lipid biosynthesis; non-diabetic; notch protein; novel; population based; response; trait

In our 1 M GWAS, among the top GWAS signals for BMI were 3 variants that mapped within the lysophosphatidylglycerol acyltransferase 1 (LPGAT1) gene. LPGAT1 belongs to a large family of acyltransferases which are involved in a variety of biological processes including pathways that regulate energy homeostasis and body weight. Therefore LPGAT1 was analyzed as a candidate gene for obesity in Pima Indians. Variants (n = 26) located within and adjacent to LPGAT1 including a novel 27 bp deletion identified by sequencing were genotyped in a population-based sample of 3391 full-heritage Pima Indians living in the Gila River Indian Community. Replication of selected variants was assessed in a second sample of 3327 mixed-heritage Native Americans from the same community. Variants with nominal associations with body mass index (BMI) in each of the two independent samples (tagged by rs112662024 and rs12058008) had associations of P = 1-4 x 10-5 in the combined sample (n = 6718). A haplotype that included a novel 27 bp deletion, which does not occur in Caucasians, showed the strongest association with BMI in full heritage Pima Indians. In vitro functional analysis provided suggestive evidence that this 27 bp deletion in the 5-UTR may affect transcriptional or post-transcriptional regulation. Analysis of LPGAT1 cDNA from human preadipocytes identified an additional exon whose sequence could potentially serve as a mitochondrial targeting peptide. In our 1 million SNP GWAS for type 2 diabetes, our strongest finding was with a SNP (rs1861612) in DNER that was associated with type 2 diabetes at genome-wide significance (odds ratio = 1.29 per copy of the T allele, P = 6.6 x 10-8). DNER (delta/notch-like EGF repeat containing) is expressed in islets and mediates notch signaling via cell-cell interaction. Notch signaling is critical for pancreatic development. We assessed the physiologic role of DNER in a mouse -cell line in which DNER was both over-expressed and knocked down by siRNA targeting. Notch pathway specific genes, Notch1, Hes1, and Neurog3 were significantly regulated by DNER (P <0.001), suggesting that alterations in DNER mediate an effect on T2D susceptibility through the notch signaling pathway. Although DNER has not been previously reported in GWASs for type 2 diabetes, NOTCH2 is a highly reproducible type 2 diabetes gene in other ethnicities. In our 1 million SNP GWAS for BMI, one of our strongest findings was identifying MAP2K3 as a new gene for obesity. This gene had not been reported as being among the top signals in published GWASs from other ethnic groups, however, we requested that the GIANT study of BMI in Caucasians look at specific SNPs in their GWAS data and several SNPs did have significant associations with BMI (P = 2 x 10-4). The effect of these variants was larger in American Indians as compared to Caucasians. Combining our American Indian data with the Caucasian data provided strong associations (P = 4 x 10-9). Functional studies on MAP2K3 showed that this gene has a role in adipogenesis, which is consistent with what is currently known about MAP signaling pathways. However, we also show that constitutive expression of MAP2K3 in the hypothalamus, a key tissue for modulating food intake, is associated with an up-regulation of genes involved in inflammation. This is an intriguing finding because several recent reports have proposed a causal role of hypothalamic inflammation in high fat induced obesity, as well as cytokines eliciting effects on feeding behavior.

在我们的 1 M GWAS 中，BMI 的最重要 GWAS 信号中有 3 个变异，映射在溶血磷脂酰甘油酰基转移酶 1 (LPGAT1) 基因内。 LPGAT1 属于酰基转移酶大家族，参与多种生物过程，包括调节能量稳态和体重的途径。因此LPGAT1被分析为皮马印第安人肥胖的候选基因。位于 LPGAT1 内部和附近的变体 (n = 26)，包括通过测序鉴定出的新的 27 bp 缺失，在居住在希拉河印第安社区的 3391 名全遗产皮马印第安人的群体样本中进行了基因分型。在来自同一社区的 3327 名混合遗传美洲原住民的第二个样本中评估了所选变体的复制情况。在两个独立样本（由 rs112662024 和 rs12058008 标记）中，与体重指数 (BMI) 名义相关的变异在组合样本 (n = 6718) 中具有 P = 1-4 x 10-5 的相关性。包含新的 27 bp 缺失的单倍型（这种情况在白种人中不存在）显示出与纯种皮马印第安人的 BMI 最强相关。体外功能分析提供了提示性证据，表明 5-UTR 中的 27 bp 缺失可能会影响转录或转录后调节。对人类前脂肪细胞 LPGAT1 cDNA 的分析发现了一个额外的外显子，其序列可能作为线粒体靶向肽。 在我们针对 2 型糖尿病的 100 万个 SNP GWAS 中，我们最有力的发现是 DNER 中的一个 SNP (rs1861612)，该 SNP 在全基因组范围内与 2 型糖尿病相关（比值比 = 每个 T 等位基因拷贝 1.29，P = 6.6 x 10-8)。 DNER（含有 δ/Notch 样 EGF 重复序列）在胰岛中表达，并通过细胞间相互作用介导 Notch 信号传导。 Notch 信号传导对于胰腺发育至关重要。我们评估了 DNER 在小鼠细胞系中的生理作用，其中 DNER 过表达并被 siRNA 靶向敲低。 Notch 通路特异性基因 Notch1、Hes1 和 Neurog3 受 DNER 显着调节（P <0.001），表明 DNER 的改变通过 Notch 信号通路介导对 T2D 易感性的影响。尽管之前在 2 型糖尿病的 GWAS 中尚未报道过 DNER，但 NOTCH2 是其他种族中高度可重复的 2 型糖尿病基因。 在我们针对 BMI 的 100 万个 SNP GWAS 中，我们最有力的发现之一是将 MAP2K3 确定为一种新的肥胖基因。在已发表的其他种族群体的 GWAS 中，该基因尚未被报道为最重要的信号之一，但是，我们要求白种人 BMI 的 GIANT 研究查看其 GWAS 数据中的特定 SNP，并且一些 SNP 确实与 BMI 存在显着关联（ P = 2 x 10-4)。与白种人相比，这些变异对美洲印第安人的影响更大。将我们的美洲印第安人数据与高加索人数据相结合，得出了很强的关联性 (P = 4 x 10-9)。对 MAP2K3 的功能研究表明，该基因在脂肪生成中发挥作用，这与目前已知的 MAP 信号通路一致。然而，我们还表明，下丘脑（调节食物摄入的关键组织）中 MAP2K3 的组成型表达与炎症相关基因的上调有关。这是一个有趣的发现，因为最近的几份报告提出了下丘脑炎症在高脂肪诱导的肥胖中的因果作用，以及细胞因子对进食行为的影响。