Berardi Domenica, Farrell Gillian, AlSultan Abdullah, McCulloch Ashley, Hall Nicole M, Sousa Rui Pedro Pereira, Jimenez Melanie, Selman Colin, Bellantuono Ilaria, Johnson Caroline H, Rattray Zahra, Rattray Nicholas J W
Department of Environmental Health Sciences, Yale School of Public Health, Yale University, New Haven, Connecticut, USA.
Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow, UK.
Aging Cell. 2025 Aug;24(8):e70127. doi: 10.1111/acel.70127. Epub 2025 Jun 18.
The relationship between in vitro senescence cell induction and intracellular biomolecular dysregulation is still poorly understood. In this study, we have found that a range of metabolic subphenotypes exists and is dependent on the induction method that is used. To develop understanding of these subphenotypes, we developed and employed a novel bioanalytical pipeline integrating untargeted metabolomics, label-free proteomics, and stable isotope tracing alongside cellular deformability measurements and established senescence biomarkers. Initially, standard senescent markers indicated all induction methods were consistent by showing elevated SA-β-Gal expression, p21 levels, and γH2AX DNA damage markers alongside a decrease in Ki67 and an increase in shape, volume, and deformability. However, when probed at the metabolic and protein levels, all senescence models indicated both shared and unique biomolecular responses. A metabolic shift toward reductive pathways (driven by serine and taurine rewiring) and impaired proteostasis was an observed shared response. These findings suggest that targeting metabolic redox circuits, alongside serine and taurine metabolic processes, presents novel therapeutic strategies for addressing senescence and aging. But importantly, alongside this general shift, we found that significant metabolic and proteomic heterogeneity also exists across different senescence induction methods. This demonstrates that the method of senescence induction significantly influences cell metabolic and proteomic profiles. Critically, methods of senescence induction are not interchangeable, and careful consideration is needed when choosing between different induction methods and when comparing cellular phenotypes across different in vitro senescence experiments.
体外衰老细胞诱导与细胞内生物分子失调之间的关系仍未得到充分理解。在本研究中,我们发现存在一系列代谢亚表型,且这些亚表型取决于所使用的诱导方法。为深入了解这些亚表型,我们开发并采用了一种新型生物分析流程,该流程整合了非靶向代谢组学、无标记蛋白质组学、稳定同位素示踪以及细胞变形性测量,并建立了衰老生物标志物。最初,标准衰老标志物显示所有诱导方法均一致,表现为SA-β-Gal表达升高、p21水平升高、γH2AX DNA损伤标志物升高,同时Ki67降低,细胞形状、体积和变形性增加。然而,当在代谢和蛋白质水平进行探究时,所有衰老模型均显示出共同和独特的生物分子反应。观察到的共同反应是代谢向还原途径转变(由丝氨酸和牛磺酸重排驱动)以及蛋白质稳态受损。这些发现表明,针对代谢氧化还原回路以及丝氨酸和牛磺酸代谢过程,为解决衰老问题提供了新的治疗策略。但重要的是,除了这种普遍转变外,我们还发现不同衰老诱导方法之间存在显著的代谢和蛋白质组学异质性。这表明衰老诱导方法会显著影响细胞代谢和蛋白质组学谱。至关重要的是,衰老诱导方法不可互换,在选择不同诱导方法以及比较不同体外衰老实验中的细胞表型时需要仔细考虑。
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