Independent phenotypic plasticity axes define mammalian metabolic and obesity sub-types [RNA-seq, mouse]

Studies in genetically identical individuals indicate that as much as 50% of complex trait variation cannot be traced to either genetics or to the environment. The mechanisms that generate this "unexplained" phenotypic variation (UPV) remain largely unknown. Here, we identify neuronatin (NNAT) as a conserved factor that buffers against unexplained phenotypic variation. We find that Nnat deficiency in isogenic F1 mice triggers the emergence of a novel, bi-stable polyphenism, where isogenic littermates emerge into adulthood either "normal" or "overgrown", without intermediates. Mechanistically, emergence of these alternate phenotypic outcomes is mediated by an insulin-dependent overgrowth that arises from HDAC-dependent b-cell hyperproliferation. A multi-dimensional analysis of monozygotic twin discordance reveals the existence of two novel patterns of human UPV, one of which (Type-B UPV) phenocopies the NNAT-buffered polyphenism identified in mice. Specifically, monozygotic cotwins exhibiting Type-B UPV exhibit coordinate increases in fat and lean mass across the body; decreased NNAT expression; increased HDAC-responsive gene signatures; and clinical outcomes exceptionally linked to insulinemia. Type-B UPV accounts for approximately one third of all transcriptional variation in independent adult and childhood cohorts, indicating that this form of human phenotypic plasticity arises in early life and underpins a major dimension of observable human phenotypic variation. Critically, the Type-B UPV signature stratifies human cohorts into four metabolic sub-types, including two phenotypically and molecularly distinct types of obesity. Together, these data identify and characterize the first major axis regulating unexplained human phenotypic variation, and two major and novel forms of obesity. We performed bulk RNA-seq on at least 3 biological replicates of primary islets isolated from 3- or 6-weeks old mice, taken from Nnat+/-p-Light, Nnat+/-p-Heavy, and wild type littermates.针对遗传同源个体的研究表明，多达50%的复杂性状变异既无法归因于遗传因素，也无法归因于环境因素。而介导此类“无法解释的”表型变异（unexplained phenotypic variation, UPV）的具体机制，目前仍未被完全阐明。本研究将神经元素（neuronatin, NNAT）鉴定为一种可缓冲此类无法解释表型变异的保守因子。我们发现，同基因F1小鼠的Nnat缺陷会触发一种新型双稳态多态现象的出现：同基因同窝小鼠成年后会呈现两种表型——“正常”或“过度生长”，无任何中间过渡状态。从机制层面来看，这些不同表型结局的产生由胰岛素依赖性过度生长所介导，而该过度生长源于组蛋白去乙酰化酶（Histone Deacetylase, HDAC）依赖性的胰岛β细胞过度增殖。对同卵双胞胎表型不一致性的多维度分析显示，人类存在两种全新的无法解释表型变异模式，其中一种（B型无法解释表型变异，Type-B UPV）可模拟小鼠中鉴定得到的NNAT依赖性多态现象。具体而言，呈现B型UPV的同卵双胞胎同胞，其全身脂肪量与瘦体量会出现协同增加；NNAT表达水平下调；HDAC应答基因特征显著上调；且临床结局与胰岛素血症存在极强关联。在独立的成人与儿童队列中，B型UPV占全部转录变异的约三分之一，这表明该类人类表型可塑性起源于生命早期，并构成了可观测人类表型变异的核心维度之一。至关重要的是，B型UPV特征可将人类队列划分为四种代谢亚型，其中包含两种表型与分子特征均截然不同的肥胖亚型。综上，本研究鉴定并阐明了首条调控人类无法解释表型变异的核心通路，同时发现了两种全新的主要肥胖亚型。我们对从Nnat+/-p-Light、Nnat+/-p-Heavy及野生型同窝小鼠中分离的原代胰岛进行了批量RNA测序（bulk RNA-seq），每个组别的原代胰岛均至少设置3次生物学重复。