研究动态
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哺乳动物肺组织快照数据中昼夜节律的量化。

Quantification of circadian rhythms in mammalian lung tissue snapshot data.

发表日期:2024 Jul 14
作者: Saskia Grabe, Bharath Ananthasubramaniam, Hanspeter Herzel
来源: GENES & DEVELOPMENT

摘要:

健康的哺乳动物细胞具有生物钟,这是一个基因调控网络,使它们能够将其生理过程安排在一天中的最佳时间。当健康细胞转变为癌细胞时,生物钟常常会受到癌症的特别干扰,因此从癌症的基因表达数据中提取昼夜节律特征引起了人们的兴趣。这是具有挑战性的,因为癌症的临床基因表达样本是快照状的,并且最好使用基因表达时间序列来检查生物钟。在这项研究中,我们获得了小鼠和狒狒肺组织的公共基因表达时间序列数据中交叉的昼夜节律基因列表。我们的昼夜节律基因列表基于昼夜节律基因的基因表达水平的相关性,这与它们之间的相位差密切相关。结合不同年龄的昼夜物种的昼夜节律基因表达模式,提供了在健康和癌性人类肺组织中也很重要的昼夜节律基因。我们通过基于 PCA 的小鼠和狒狒样本的昼夜节律时间重建来测试基因列表中生物钟的表示质量。然后,我们为人体肺组织样本分配了潜在的昼夜节律时间,并在健康的人体肺组织中发现了完整的生物钟,但在邻近的癌性肺组织中发现了一个改变的、微弱的生物钟。© 2024。作者。
Healthy mammalian cells have a circadian clock, a gene regulatory network that allows them to schedule their physiological processes to optimal times of the day. When healthy cells turn into cancer cells, the circadian clock often becomes cancer specifically disturbed, so there is an interest in the extraction of circadian features from gene expression data of cancer. This is challenging, as clinical gene expression samples of cancer are snapshot-like and the circadian clock is best examined using gene expression time series. In this study, we obtained lists of intersecting circadian genes in public gene expression time series data of lung tissue of mouse and baboon. We base our circadian gene lists on correlations of gene expression levels of circadian genes, which are closely associated to the phase differences between them. Combining circadian gene expression patterns of diurnal and nocturnal species of different ages provides circadian genes that are also important in healthy and cancerous human lung tissue. We tested the quality of the representation of the circadian clock in our gene lists by PCA-based reconstructions of the circadian times of the mouse and baboon samples. Then we assigned potential circadian times to the human lung tissue samples and find an intact circadian clock in the healthy human lung tissue, but an altered, weak clock in the adjacent cancerous lung tissue.© 2024. The Author(s).