Understanding the genetics of obesity- from GWAS to function in a canine model

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PhD project strategic theme: Biosciences for an integrated understanding of healthObesity is a global health problem characterised by high morbidity and mortality rates that consequently have a negative impact on public health systems. This complex disease has a high degree of heritability in humans (40-70%). Despite this, the polygenic nature of common obesity has limited researchers' ability to pinpoint genes important in the regulation of body weight and identify novel therapeutic targets. Genome wide association studies (GWAS) for body mass index (BMI) and related traits have led to the identification of >500 adiposity associated loci in humans, while still only explaining ~4% of the variation in BMI. The environmental factors implicated in human obesity such as reduced exercise and easy access to high-energy food have simultaneously become more common in their canine companion animals leading to approximately 59% of dogs being overweight or obese. Dog breeds provide a powerful genetic model for the discovery of disease genes as genetic bottlenecks have led to a reduction in heterogeneity, extensive linkage disequilibrium (LD) and increased frequency of disease-variants. Compared to humans, smaller sample sizes and fewer genetic markers are needed in within-breed GWAS. The Raffan group have previously carried out a GWAS for obesity in 127 lean or obese pug dogs with multiple loci reaching genome-wide significance, however the loci are large making it difficult to pinpoint the causal mutations. In my PhD project, this pug GWAS will be improved by imputing the samples up to a larger SNP density, performing a secondary GWAS and fine mapping the loci. We will identify candidate risk variants for obesity on the basis of functional annotation using bioinformatics approaches (e.g. gene ontology (GO) enrichment, transcription factor binding analysis, DNA element and tissue specific gene expression analysis), manual curation and literature review. The best approach to linking loci to mutations and then function relies on a multifactorial approach using bioinformatics and cellular studies. We will perform relevant experiments depending on candidate genes including techniques to measure gene expression, protein localisation, promoter activity and possibly genome editing techniques which allow direct comparison of mutations in identical genomic backgrounds.Several biological pathways have already been implicated in the regulation of body weight including a central role of the hypothalamic leptin-melanocortin pathway in controlling energy intake and expenditure. Severe obesity in humans is sometimes caused by mutations disrupting the function of the genes encoding members of this pathway including leptin, its receptor, POMC, the enzymes responsible for proteolytic cleavage of POMC, and melanocortin receptors. Three mutations in melanocortin receptors have been identified and studied to some extent in dogs. Unpublished work from Dr Raffan's lab demonstrated that all three mutations had significant effects on melanocortin signalling in response to stimulation. We predict that these functional differences will cause measurable differences in obesity phenotypes. This aim of my PhD will measure the frequency of these mutations in 30 breeds as well as mixed breed dogs. We will follow this by testing the association of these mutations to body weight, adiposity and food-motivation in affected breeds.