Functional characterisation of genetic variants influencing human food preferences using bioinformatics and animal models

背景：营养是影响人类健康的重要因素之一。不健康的食物选择会导致多种疾病，如肥胖、代谢综合征、心血管疾病和某些癌症。虽然许多研究都集中在这些疾病的遗传学上，但遗传学家直到最近才开始关注食物摄入，尽管结果非常有限。在粮食供应不是问题的国家，食物偏好是推动食物选择和消费的最重要因素之一。各种研究表明，与自我报告的食物频率问卷相比，食物喜好措施更能预测实际的长期消费。我们最近的全基因组关联研究强调了与特定食物偏好差异相关的许多基因。尽管取得了这些成功，但没有一个基因编码味觉或嗅觉受体，因此它们在决定食物偏好方面的作用仍然知之甚少。该项目的目的是确定哪些已知的味觉偏好基因有可能导致代谢状态的改变，并在细胞和动物模型中对这些基因进行功能性验证。该项目有三个要素：1）定义与食物偏好相关的遗传变异对报告的食物消费量的影响-使用英国生物银行所有50万参与者的食物频率问卷及其基因型数据（2017年初上市），我们将评估先前描述的16种食物偏好遗传变异和味觉受体基因的功能变异对报告的食物消费量的影响。虽然众所周知，这些类型的调查问卷会受到报告偏差的影响，但非常大的数字提供了这样的统计能力，即使是非常小的影响也可以被检测出来。这一步对于选择携带哪些遗传变异是很重要的。2)所选遗传变异的生物信息学表征-将使用生物信息学工具表征在先前步骤中选择的变异，以制定关于它们影响哪些基因、它们如何影响基因以及在哪些组织中的假设。这一点很重要，因为在许多情况下，遗传变异并不调节最接近的基因，而是具有更长范围的影响。识别的实际目标，其组织表达，并与已知的食欲和代谢相关的途径的相互作用的潜力是制定机制假说的根本重要性。3)通过使用细胞培养物和动物模型对遗传变异体进行功能表征-将在3个主要阶段中，在动物模型和细胞培养物中对最相关的遗传变异体和基因进行功能研究。(a)在涉及食物偏好的脑回路中绘制候选基因的表达图（例如，涉及黑皮质素MC 4受体或催产素信号传导的下丘脑通路，已知与脂肪和糖偏好有关）。(b)在体外相关神经元细胞模型（例如人SH-SY 5 Y）中，在CRISPR靶向敲除或基因的变体相关调控缺失/修饰之后，对CRISPR介导的基因敲除对神经元功能和典型信号传导的影响进行建模。(c)CRISPR靶向胚胎中最有前途和/或易处理的基因，以快速生成一种新型转基因模型，用于全面体内表征基因缺失对行为食物偏好（Leng和Menzies，CIP）和体内代谢（Morton，CVS）的影响。培训成果一般流行病学超大规模食物频率问卷数据的处理和分析。遗传变异的综合生物信息学表征大型公开资源的数据挖掘新型基因/动物模型生物学的体外和体内建模，包括细胞培养、基于细胞的测定、共聚焦成像、尖端转基因工具、体内行为和代谢测定

Background: Nutrition is one of the most important factors influencing human health. Unhealthy food choices can lead to several disorders such as obesity, metabolic syndrome, cardiovascular disease and some cancers. Although many studies have focused on the genetics of these disorders, geneticists have only recently started looking at food intake, although with very limited results. In countries where food availability is not an issue, food preference is one of the most important factors driving food choice and consumption. Various studies suggest that food-liking measures are better predictors of actual long-term consumption compared to self-reported food frequency questionnaires. Our recent genome-wide association studies have highlighted numerous genes associated with differences in specific food preferences. Despite these successes, none of the genes encode taste or olfactory receptors and so their role in determining food preferences is still poorly understood. The aim of the project is to identify which of the known taste preference genes have the potential to lead to altered metabolic states and to characterise these genes functionally in cell and animal models. The project has three elements: 1) Definition of the impact of the genetic variants associated with food preferences on reported food consumption - Using the food frequency questionnaires for all 500,000 participants to UK Biobank, and their genotype data (available in early 2017), we shall assess the impact of the 16 previously described food preference genetic variants and functional variants in taste receptor genes on reported food consumption. Although it is known that these types of questionnaires are subject to reporting biases, the very large numbers provide such statistical power that even very small effects can be detected. This step will be important to select which genetic variants are carried forward. 2) Bioinformatic characterisation of the selected genetic variants - The variants selected in the previous steps will be characterized using bioinformatics tools to formulate hypotheses regarding which genes they affect, how they influence the genes and in which tissues. This is important because in many cases genetic variants do not regulate the closest gene but rather have longer range effects. The identification of the actual target, its tissue expression, and potential for interaction with known appetite- and metabolism-related pathways is of fundamental importance for formulating mechanistic hypotheses. 3) Functional characterisation of the genetic variants through the use of cell culture and animal models - The most relevant genetic variants and genes will be studied functionally in animal models and cell cultures, in 3 main stages. (a) Mapping of expression of the candidate genes in brain circuits involved in food preference (e.g. hypothalamic pathways involving the melanocortin MC4 receptor or oxytocin signalling with known links to fat and sugar preference).(b) Modelling the effects of CRISPR-mediated gene knockouts on neuronal function and canonical signalling after CRISPR-targeted knockout or variant-associated regulatory deletion/modification of the gene in a relevant neuronal cell model in vitro (e.g. human SH-SY5Y). (c) CRISPR-targeting of the most promising and/or tractable gene in embryos to rapidly generate a novel transgenic model for full in vivo characterization of the impact of gene deletion on behavioural food preferences (Leng and Menzies, CIP) and on in vivo metabolism (Morton, CVS).Training Outcomes General epidemiology Handling and analysis of very large-scale food frequency questionnaire data. Integrative bioinformatics characterisation of genetic variants Data mining of large publicly available resources In vitro and in vivo modelling of novel genes/biology of animal model, including cell culture, cell-based assays, confocal imaging, cutting-edge transgenic tools, in vivo behavioural and metabolic assays