Landgraf Austin, Okada Junichi, Horton Maxwell, Liu Li, Solomon Shoshana, Qiu Yunping, Kurland Irwin J, Sidoli Simone, Pessin Jeffrey E, Shinoda Kosaku
Department of Molecular Pharmacology, The Albert Einstein College of Medicine, Bronx, NY 10461.
Department of Medicine (Division of Endocrinology), The Albert Einstein College of Medicine, Bronx, NY 10461.
bioRxiv. 2025 Apr 20:2025.04.15.649020. doi: 10.1101/2025.04.15.649020.
The mammalian liver plays a critical role in maintaining metabolic homeostasis during fasting and feeding. Liver function is further shaped by sex dimorphism and zonation of hepatocytes. To explore how these factors interact, we performed deep RNA-sequencing and label-free proteomics on periportal and pericentral hepatocytes isolated from male and female mice under fed and starved conditions. We developed a classification system to assess protein-mRNA relationship and found that gene products (mRNA or protein) for most zonation markers showed strong concordance between mRNA and protein. Although classical growth hormone regulated sex-biased gene products also exhibited concordance, ~60% of sex-biased gene products showed protein-level enrichment without corresponding mRNA differences. In contrast, transition between feeding and starvation triggered widespread changes in mRNA expression without significantly affecting protein levels. In particular, key lipogenic mRNAs (e.g. , , and ) were dramatically induced by feeding, but their corresponding proteins (ACLY, ACC1, and FAS) showed little to no change even as functional lipogenic activity increased ~28-fold in the fed state. To facilitate further exploration of these findings, we developed Discorda (https://shinoda-lab.shinyapps.io/discorda/), a web database for interactive analysis. Our findings reinforce the principle that mRNA changes do not reliably predict corresponding protein levels (and vice versa), particularly in the context of sex and acute metabolic regulation of hepatocytes, and that lipogenesis activity can be completely uncoupled from changes in protein expression.
哺乳动物肝脏在禁食和进食期间维持代谢稳态方面发挥着关键作用。肝功能还受到性别二态性和肝细胞分区的影响。为了探究这些因素如何相互作用，我们对在进食和饥饿条件下从雄性和雌性小鼠分离出的门静脉周围和中央静脉周围肝细胞进行了深度RNA测序和无标记蛋白质组学分析。我们开发了一个分类系统来评估蛋白质与mRNA的关系，发现大多数分区标记的基因产物（mRNA或蛋白质）在mRNA和蛋白质之间表现出很强的一致性。虽然经典的生长激素调节的性别偏向基因产物也表现出一致性，但约60%的性别偏向基因产物在蛋白质水平上有富集，而mRNA没有相应差异。相反，进食和饥饿之间的转变引发了mRNA表达的广泛变化，但对蛋白质水平没有显著影响。特别是，关键的脂肪生成mRNA（如 、 和 ）在进食时被显著诱导，但其相应的蛋白质（ACLY、ACC1和FAS）即使在进食状态下功能性脂肪生成活性增加约28倍时也几乎没有变化。为了便于进一步探索这些发现，我们开发了Discorda（https://shinoda-lab.shinyapps.io/discorda/），一个用于交互式分析的网络数据库。我们的发现强化了这样一个原则，即mRNA的变化不能可靠地预测相应的蛋白质水平（反之亦然），特别是在肝细胞的性别和急性代谢调节的背景下，并且脂肪生成活性可以与蛋白质表达的变化完全脱钩。
