Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor

The deletion of the third exon of the growth hormone receptor (GHR) is one of the most common genomic structural variants in the human genome. This deletion (GHRd3) has been linked to response to growth hormone, placenta size, birth weight, growth after birth, time of puberty, adult height, and longevity. However, its evolutionary history and the molecular mechanisms through which it affects phenotypes remain unresolved. Here, we analyzed thousands of genomes and provide evidence that this deletion was nearly fixed in the ancestral population of anatomically modern humans and Neanderthals. However, it underwent a paradoxical adaptive reduction in frequency approximately 30 thousand years ago in East Asia that roughly corresponds with the emergence of archaeological evidence for multiple modern human behaviors, dramatic changes in climate, and a concurrent population expansion. Further, we provide evidence that GHRd3 is associated with protection from edematous severe acute malnutrition primarily in males. Using a mouse line engineered to contain the deletion, we found Ghrd3's effect on the liver transcriptome of male mice grown without any calorie restriction mimics response to calorie restriction through regulation of circadian pathways. In contrast, under calorie restriction, Ghrd3 leads to the female-like gene expression in male livers. As a likely consequence, the dramatic weight difference between male and female mice disappears among GHRd3 mice under calorie restriction. Our data provide evidence for sex- and environment-dependent effects of GHRd3 and are consistent with a model in which the allele frequency of GHRd3 varies throughout human evolution as a response to fluctuations in resource availability. Liver RNAseq of 8 cohorts mice (each n=5) based on all possible combinations of sex (female or male), diet (constantly available, i.e., ad libitum (AL) or 40% calorie restricted (CR)), and genotype (wt/wt or d3/d3) under controlled settings. We raised all of the cohorts under identical conditions until weaning at 30 days old and provided the differential diets for the next 30 days.生长激素受体（growth hormone receptor, GHR）第三外显子缺失是人类基因组中最常见的基因组结构变异之一。该缺失变异（GHRd3）与生长激素应答、胎盘尺寸、出生体重、出生后生长、青春期启动时间、成年身高及寿命均存在关联。然而，其演化历史及调控表型的分子机制仍未阐明。本研究对数千个人类基因组进行分析，证实该缺失变异几乎在解剖学现代人类与尼安德特人的祖先种群中达到固定频率。但约3万年前，东亚人群中该变异的频率却出现了反常的适应性下降，这一时间节点大致与多项现代人类行为的考古证据出现、气候剧变及同期种群扩张相吻合。此外，本研究证实GHRd3主要在雄性个体中对水肿性重症急性营养不良具有保护作用。通过构建携带该缺失变异的工程化小鼠模型，我们发现：在无热量限制的饲养条件下，Ghrd3对雄性小鼠肝脏转录组的调控可通过激活昼夜节律通路模拟热量限制应答；而在热量限制条件下，Ghrd3会使雄性小鼠肝脏的基因表达模式向雌性个体趋同。这一变化的潜在结果是，在限食饲养的GHRd3小鼠中，雌雄个体间显著的体重差异消失。本研究数据为GHRd3的性别与环境依赖效应提供了直接证据，并支持以下演化模型：GHRd3的等位基因频率随人类演化进程发生动态波动，以响应资源可获得性的变化。本数据集包含8组小鼠的肝脏RNA测序（RNA-seq）数据，每组样本量n=5。实验分组覆盖性别（雌性或雄性）、饮食模式（自由采食（ad libitum, AL）或40%热量限制（calorie restricted, CR））与基因型（野生型纯合wt/wt或d3纯合d3/d3）的所有可能组合，所有实验均在可控环境中开展。所有小鼠队列均在一致条件下饲养至30日龄断奶，随后的30天内给予差异化饮食方案。