Identification of a Putative Quantitative Trait Gene for Resistance to Obesity in Mice Using Transcriptome Analysis and Causal Inference Tests

It is still challenging to identify causal genes governing obesity. Pbwg1.5, a quantitative trait locus (QTL) for resistance to obesity, was previously discovered from wild Mus musculus castaneus mice and was fine-mapped to a 2.1-Mb genomic region of mouse chromosome 2, where no known gene with an effect on white adipose tissue (WAT) has been reported. The aim of this study was to identify a strong candidate gene for Pbwg1.5 by an integration approach of transcriptome analysis (RNA-sequencing followed by real-time PCR analysis) and the causal inference test (CIT), a statistical method to infer causal relationships between diplotypes, gene expression and trait values. Body weight, body composition and biochemical traits were measured in F2 mice obtained from an intercross between the C57BL/6JJcl strain and a congenic strain carrying Pbwg1.5 on the C57BL/6JJcl background. The F2 mice showed significant diplotype differences in 12 traits including body weight, WAT weight and serum cholesterol/triglyceride levels. The transcriptome analysis revealed that Ly75, Pla2r1, Fap and Gca genes were differentially expressed in the liver and that Fap, Ifih1 and Grb14 were differentially expressed in WAT. However, CITs indicated statistical evidence that only the liver Ly75 gene mediated between genotype and WAT. Ly75 expression was negatively associated with WAT weight. The results suggested that Ly75 is a putative quantitative trait gene for the obesity-resistant Pbwg1.5 QTL discovered from the wild M. m. castaneus mouse. The finding provides a novel insight into a better understanding of the genetic basis for prevention of obesity.

鉴定调控肥胖的致病基因仍颇具挑战。Pbwg1.5是一个抗肥胖数量性状位点（quantitative trait locus, QTL），此前从野生小家鼠卡氏亚种（Mus musculus castaneus）小鼠中被发现，并被精细定位至小鼠2号染色体的2.1 Mb基因组区域内，该区域尚未见有影响白色脂肪组织（white adipose tissue, WAT）的已知基因被报道。本研究旨在通过整合转录组分析（RNA测序（RNA-sequencing）结合实时荧光定量PCR（real-time PCR）分析）与因果推断测试（causal inference test, CIT）——一种用于推断双基因型、基因表达与性状值之间因果关系的统计学方法——来鉴定Pbwg1.5的强候选基因。实验以C57BL/6JJcl品系与在C57BL/6JJcl遗传背景上携带Pbwg1.5的同类系品系杂交获得的F2代小鼠为研究对象，测定了其体重、体成分及生化性状。F2代小鼠在包括体重、白色脂肪组织重量以及血清胆固醇/甘油三酯水平在内的12项性状上均表现出显著的双基因型差异。转录组分析显示，肝脏中Ly75、Pla2r1、Fap及Gca基因存在差异表达，而白色脂肪组织中Fap、Ifih1及Grb14基因存在差异表达。然而，因果推断测试结果显示，仅有肝脏中的Ly75基因介导了基因型与白色脂肪组织重量之间的关联。Ly75的表达水平与白色脂肪组织重量呈负相关。研究结果表明，Ly75是从野生小家鼠卡氏亚种小鼠中发现的抗肥胖Pbwg1.5数量性状位点的推定数量性状基因。本发现为深入理解肥胖预防的遗传基础提供了新的视角。