Identification of novel candidate neural genes for diet-induced obesity in outbred heterogeneous stock rats

Background Obesity is caused by genetics, the environment (e.g., diet) and their interactions. The brain, specifically the hypothalamus, plays an important role in obesity, but controlled studies using human brain tissue are not possible. The goal of this study was to conduct a genome wide association study using outbred heterogeneous stock (HS) rats to map genetic loci associated with diet-induced obesity. This was followed by RNAseq in the ventromedial hypothalamus (VMH) to identify candidate causal obesity genes. Methods We measured multiple metabolic traits (including fat and lean mass, fasting glucose, insulin, and lipids, glucose tolerance, food intake and activity levels) after long-term consumption of a low-fat (LFD) or high-fat diet (HFD) in 2000 HS rats, split equally by sex and diet. Rats were genotyped using low-coverage whole genome sequencing. RNAseq data was obtained from the VMH of a sub-set of 400 HS rats split equally by sex and diet. We used linear mixed models to detect physiological and expression quantitative trait loci (pQTLs and eQTLs, respectively) in the full dataset and separately by diet and sex. Genes with cis-eQTLs that overlapped pQTLs were assessed as candidate causal genes through mediation analysis. We also identified VMH genes differentially expressed by diet in both sexes, followed by pathway analysis. Results We identified 47 pQTLs where six mapped multiple traits, 11 were diet-specific and 13 were sex-specific. We identified nine candidate causal genes, including Pcare , Rbks, Mpv17 and Gpn1 within a pleiotropic pQTL for multiple adiposity traits on rat chr. 6 and Tnsfs9 within a pQTL for fat pad weight on rat chr. 9. We also identified Ccdc77 as a candidate gene within a LFD-specific pQTL for activity levels and Rtel1 and Polr3k within a male-specific pQTL for fatty liver. Genes involved in extracellular matrix and inflammation were dysregulated by diet, particularly in females, while males on HFD showed upregulation of several addiction pathways. Conclusions We identified novel candidate genes as neural regulators of diet-induced obesity and related traits and confirmed the importance of accounting for diet and sex in genetic studies of obesity.