The Institute of Bioengineering (IBI), School of Life Science, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
F1000Res. 2020 Sep 17;9. doi: 10.12688/f1000research.26759.1. eCollection 2020.
The ability of organisms to keep track of external time, by means of the circadian clock interacting with the environment, is essential for health. The focus of this review is recent methods to detect the internal circadian time of an omics sample. Before reaching our main topic, we introduce the circadian clock, its hierarchical structure, and its main functions; we will also explain the notion of internal time, or circadian phase, and how it differs from the geophysical time. We then focus on the role played by the clock in the maintenance of human heath, in particular in the context of cancer. Thereafter, we analyze an important methodological question: how to infer the circadian phase of unlabeled omics snapshot measurements. Answering this question could both significantly increase our understanding of the circadian clock and allow the use of this knowledge in biomedical applications. We review existing methods, focusing on the more recent ones, following a historical trajectory. We explain the basic concepts underlying the methods, as well as some crucial technical aspects of each. We conclude by reporting how some of these methods have, more or less effectively, enabled furthering our understanding of the clock and given insights regarding potential biomedical applications.
生物体通过生物钟与环境相互作用来跟踪外部时间的能力对健康至关重要。本综述的重点是最近用于检测组学样本内部生物钟的方法。在进入我们的主题之前，我们将介绍生物钟、它的层次结构及其主要功能；我们还将解释内部时间或生物钟相位的概念，以及它与地理时间的不同之处。然后，我们将重点关注生物钟在维持人类健康方面的作用，特别是在癌症方面。此后，我们分析了一个重要的方法学问题：如何推断未标记的组学快照测量的生物钟相位。回答这个问题不仅可以大大提高我们对生物钟的理解，还可以将这方面的知识应用于生物医学应用中。我们回顾了现有的方法，重点介绍了更近期的方法，沿着历史轨迹进行分析。我们解释了这些方法背后的基本概念，以及每个方法的一些关键技术方面。最后，我们报告了其中一些方法如何在一定程度上有效促进了我们对生物钟的理解，并提供了关于潜在生物医学应用的见解。
