Genomic Characterization of Metformin Hepatic Response.
Genomic Characterization of Metformin Hepatic Response.
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DOI：
10.1371/journal.pgen.1006449
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发表时间：
2016-11
期刊：
影响因子：
4.5
通讯作者：
Ahituv N
中科院分区：
文献类型：
--
作者：
Luizon MR;Eckalbar WL;Wang Y;Jones SL;Smith RP;Laurance M;Lin L;Gallins PJ;Etheridge AS;Wright F;Zhou Y;Molony C;Innocenti F;Yee SW;Giacomini KM;Ahituv N
二甲双胍被用作2型糖尿病（T2 D）的一线治疗，并被用于许多其他疾病。然而，其在肝脏中的作用机制尚未以系统的方式表征。为了全面鉴定与二甲双胍治疗相关的基因和调控元件，我们对来自同一供体的原代人肝细胞进行了RNA-seq和ChIP-seq（H3 K27 ac，H3 K27 me 3），所述原代人肝细胞用溶剂对照、二甲双胍或二甲双胍和化合物C（一种AMP活化蛋白激酶（AMPK）抑制剂）治疗（允许鉴定AMPK非依赖性途径）。我们鉴定了数以千计的二甲双胍反应性AMPK依赖性和AMPK非依赖性差异表达基因和调控元件。我们在功能上验证了二甲双胍诱导的启动子和增强子活性的几个元件。这些包括共济失调毛细血管扩张突变（ATM）内含子中的增强子，该内含子具有与二甲双胍治疗反应GWAS主导SNP（rs 11212617）连锁不平衡的SNP，该SNP显示相关单倍型的增强子活性增加。表达数量性状基因座（eQTL）肝脏分析和CRISPR激活表明，该增强子可能调节ATM，ATM在AMPK激活中具有已知的作用，并且可能还调节EXPH 5和DDX 10，其邻近基因。使用ChIP-seq和siRNA敲除，我们进一步表明，转录激活因子3（ATF 3），我们的二甲双胍上调AMPK依赖性基因，可能在胚胎发生抑制中发挥重要作用。我们的研究结果提供了二甲双胍肝脏反应的全基因组代表性，突出了可能与二甲双胍血糖反应个体间变异性相关的重要序列，并确定了新型T2 D治疗候选药物。二甲双胍是最广泛的处方药之一。它被用作2型糖尿病（T2 D）和其他疾病（包括癌症）的一线治疗。对二甲双胍反应的变异性很大，可能由遗传因素引起。然而，二甲双胍作用的分子机制尚不完全清楚。在这里，我们使用各种基因组测定来分析用或不用二甲双胍处理的人肝细胞，并以全基因组的方式鉴定了数千个受二甲双胍影响的差异表达基因和基因调控元件。后续功能试验鉴定了几种与二甲双胍反应相关的新基因和调控元件。这些包括ATF 3，这是一种在二甲双胍应答后显示出造血抑制的基因，也是ATM基因的一种潜在调控元件，通过全基因组关联研究与二甲双胍治疗差异相关。结合起来，这项工作确定了几个新的基因和基因调控元件，可以激活由于二甲双胍治疗，从而提供了候选序列在人类基因组中的核苷酸变异可能导致二甲双胍的反应差异。它还能够识别和优先考虑T2 D治疗的新候选药物。
Metformin is used as a first-line therapy for type 2 diabetes (T2D) and prescribed for numerous other diseases. However, its mechanism of action in the liver has yet to be characterized in a systematic manner. To comprehensively identify genes and regulatory elements associated with metformin treatment, we carried out RNA-seq and ChIP-seq (H3K27ac, H3K27me3) on primary human hepatocytes from the same donor treated with vehicle control, metformin or metformin and compound C, an AMP-activated protein kinase (AMPK) inhibitor (allowing to identify AMPK-independent pathways). We identified thousands of metformin responsive AMPK-dependent and AMPK-independent differentially expressed genes and regulatory elements. We functionally validated several elements for metformin-induced promoter and enhancer activity. These include an enhancer in an ataxia telangiectasia mutated (ATM) intron that has SNPs in linkage disequilibrium with a metformin treatment response GWAS lead SNP (rs11212617) that showed increased enhancer activity for the associated haplotype. Expression quantitative trait locus (eQTL) liver analysis and CRISPR activation suggest that this enhancer could be regulating ATM, which has a known role in AMPK activation, and potentially also EXPH5 and DDX10, its neighboring genes. Using ChIP-seq and siRNA knockdown, we further show that activating transcription factor 3 (ATF3), our top metformin upregulated AMPK-dependent gene, could have an important role in gluconeogenesis repression. Our findings provide a genome-wide representation of metformin hepatic response, highlight important sequences that could be associated with interindividual variability in glycemic response to metformin and identify novel T2D treatment candidates. Metformin is among the most widely prescribed drugs. It is used as a first line therapy for type 2 diabetes (T2D), and for additional diseases including cancer. The variability in response to metformin is substantial and can be caused by genetic factors. However, the molecular mechanisms of metformin action are not fully known. Here, we used various genomic assays to analyze human liver cells treated with or without metformin and identified in a genome-wide manner thousands of differentially expressed genes and gene regulatory elements affected by metformin. Follow up functional assays identified several novel genes and regulatory elements to be associated with metformin response. These include ATF3, a gene that showed gluconeogenesis repression upon metformin response and a potential regulatory element of the ATM gene that is associated with metformin treatment differences through genome-wide association studies. Combined, this work identifies several novel genes and gene regulatory elements that can be activated due to metformin treatment and thus provides candidate sequences in the human genome where nucleotide variation can lead to differences in metformin response. It also enables the identification and prioritization of novel candidates for T2D treatment.
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DOI：
10.1074/jbc.m111.228817
发表时间：
2011-10-21
期刊：
The Journal of biological chemistry
影响因子：
--
作者：
Birkenfeld AL;Lee HY;Majumdar S;Jurczak MJ;Camporez JP;Jornayvaz FR;Frederick DW;Guigni B;Kahn M;Zhang D;Weismann D;Arafat AM;Pfeiffer AF;Lieske S;Oyadomari S;Ron D;Samuel VT;Shulman GI
通讯作者：
Shulman GI
影响因子：
4
作者：
Caton, Paul W.;Nayuni, Nanda K.;Corder, Roger
通讯作者：
Corder, Roger
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
2.6
作者：
Gong L;Goswami S;Giacomini KM;Altman RB;Klein TE
通讯作者：
Klein TE
影响因子：
4.5
作者：
Innocenti F;Cooper GM;Stanaway IB;Gamazon ER;Smith JD;Mirkov S;Ramirez J;Liu W;Lin YS;Moloney C;Aldred SF;Trinklein ND;Schuetz E;Nickerson DA;Thummel KE;Rieder MJ;Rettie AE;Ratain MJ;Cox NJ;Brown CD
通讯作者：
Brown CD