Genetic Variation Determines PPARγ Function and Antidiabetic Drug Response In Vivo [RNA-seq]

SNPs affecting disease risk often reside in non-coding genomic regions. Here we show that SNPs are highly enriched at mouse strain-selective adipose tissue binding sites for PPARγ, a nuclear receptor for antidiabetic drugs. Many such SNPs alter binding motifs for PPARγ or cooperating factors, and functionally regulate nearby genes whose expression is strain-selective and imbalanced in heterozygous F1 mice. Moreover, genetically-determined binding of PPARγ accounts for mouse strain-specific transcriptional effects of TZD drugs, providing proof-of- concept for personalized medicine related to nuclear receptor genomic occupancy. In human fat, motif-altering SNPs cause differential PPARγ binding, provide a molecular mechanism for some expression quantitative trait loci, and are risk factors for dysmetabolic traits in genome- wide association studies. One PPARγ motif-altering SNP is associated with HDL levels and other metabolic syndrome parameters. Thus, natural genetic variation in PPARγ genomic occupancy determines individual disease risk and drug response. Comparison of 5 RNA-seq experiments between 2 strains of mice differing in diet and fat depot. One of the experiments was evaluation of the response to a drug Rosiglitazone. Our RNA-seq data comprises primarily of 4 main experiments: The first experiment consists of samples taken from 2 strains of mice and their F1 progeny The samples are all taken from the same depot and when the mice were fed the same chow diet The second experiment has 2 parts, the first one involves samples taken from the 2 strains from the same eWAT depot when they were kept on a Low Fat Diet (LFD) This first part serves as a control for the second one in which the mice were treated with a drug, rosiglitazone in conjunction with a LFD The third experiment consists of samples taken from mice being fed on LFD. The samples are taken from the eWAT depot for both the strains. The fourth experiment consists of samples taken from mice being fed on LFD. The samples are taken from the iWAT depot for both the strains. We also have a solitary sample from a GRO-seq experiment which was done on eWAT in a B6 strain of mice being fed a LFD eWAT: epididymal White Adipose Tissue iWAT: inguinal White Adipose Tissue LFD-12w: mice were fed a control low fat diet (Research Diet D12450B) chow: mice were fed standard rodent chow Diet LFD w/rosiglitazone: Drug rosiglitazone (Cayman Chemicals) was incorporated into low fat diet D12450B by Research Diets at 36mg/kg of diet. Mice received control low fat diet for 10 weeks (age 6-16 weeks), and the rosiglitazone-containing diet versus control diet for the final 2 weeks (until sacrifice at 18 weeks) LFD control for rosi: mice were fed a control low fat diet (Research Diet D12450B)

影响疾病风险的单核苷酸多态性（Single Nucleotide Polymorphisms，SNPs）通常位于非编码基因组区域。本研究发现，SNPs在小鼠品系选择性的脂肪组织过氧化物酶体增殖物激活受体γ（PPARγ）结合位点处高度富集——PPARγ是一类抗糖尿病药物的核受体。此类SNPs多可改变PPARγ或其协同结合因子的DNA结合基序，并对邻近基因实施功能性调控；这些邻近基因的表达呈现品系特异性，且在杂合F1小鼠中存在等位基因表达失衡现象。此外，由遗传因素决定的PPARγ基因组结合特征，可解释噻唑烷二酮类（Thiazolidinediones，TZD）药物的小鼠品系特异性转录效应，为针对核受体基因组结合占据特征的个性化医疗提供了概念验证。

在人类脂肪组织中，改变结合基序的SNPs可导致PPARγ结合出现差异，为部分表达数量性状位点（expression quantitative trait loci，eQTL）提供了分子机制，同时在全基因组关联研究中被认定为代谢异常性状的风险因子。其中一个改变PPARγ结合基序的SNP与高密度脂蛋白（High-Density Lipoprotein，HDL）水平及其他代谢综合征参数存在显著关联。综上，PPARγ基因组结合占据特征的自然遗传变异，决定了个体的疾病风险与药物应答反应。

本数据集包含针对2种饮食与脂肪垫存在差异的小鼠品系的5组RNA测序（RNA-seq）实验对比数据，其中1组实验用于评估罗格列酮（Rosiglitazone）的药物应答效果。本研究的RNA-seq数据主要包含4组核心实验：
1. 第一组实验的样本取自2种小鼠品系及其F1代子代，所有样本均采集自同一脂肪垫，且实验小鼠均饲喂相同的标准啮齿类饲料。
2. 第二组实验包含2个亚组：其一为2种品系小鼠在饲喂低脂饮食（Low Fat Diet，LFD）时，采集自同一附睾白色脂肪垫（epididymal White Adipose Tissue，eWAT）的样本；该亚组作为第二亚组的对照，第二亚组中小鼠在饲喂低脂饮食的同时接受罗格列酮药物处理。
3. 第三组实验的样本取自饲喂低脂饮食的2种品系小鼠，采集部位为附睾白色脂肪垫（eWAT）。
4. 第四组实验的样本取自饲喂低脂饮食的2种品系小鼠，采集部位为腹股沟白色脂肪垫（inguinal White Adipose Tissue，iWAT）。

此外，本数据集还包含1组单独的全局转录延伸测序（Global Run-On Sequencing，GRO-seq）实验样本，该实验以饲喂低脂饮食的B6品系小鼠的附睾白色脂肪垫为研究对象。

### 术语与实验饲养细节说明
- eWAT：附睾白色脂肪垫（epididymal White Adipose Tissue）
- iWAT：腹股沟白色脂肪垫（inguinal White Adipose Tissue）
- LFD-12w：饲喂对照低脂饲料（Research Diet D12450B）的小鼠
- chow：饲喂标准啮齿类维持饲料的小鼠
- LFD联合罗格列酮组：将罗格列酮药物（Cayman Chemicals）以36mg/kg饲料的浓度掺入低脂饲料D12450B中进行饲喂。实验小鼠先饲喂对照低脂饲料10周（6至16周龄），最后2周更换为含罗格列酮的低脂饲料或对照低脂饲料，直至18周龄时处死取材
- 罗格列酮对照低脂饮食组：饲喂Research Diet D12450B配方对照低脂饲料的小鼠