Center for Complex Biological Systems, University of California Irvine, Irvine, CA, USA.
The NSF-Simons Center for Multiscale Cell Fate Research, University of California Irvine, Irvine, CA, USA.
Nat Commun. 2024 May 7;15(1):3840. doi: 10.1038/s41467-024-48041-6.
As the circadian clock regulates fundamental biological processes, disrupted clocks are often observed in patients and diseased tissues. Determining the circadian time of the patient or the tissue of focus is essential in circadian medicine and research. Here we present tauFisher, a computational pipeline that accurately predicts circadian time from a single transcriptomic sample by finding correlations between rhythmic genes within the sample. We demonstrate tauFisher's performance in adding timestamps to both bulk and single-cell transcriptomic samples collected from multiple tissue types and experimental settings. Application of tauFisher at a cell-type level in a single-cell RNAseq dataset collected from mouse dermal skin implies that greater circadian phase heterogeneity may explain the dampened rhythm of collective core clock gene expression in dermal immune cells compared to dermal fibroblasts. Given its robustness and generalizability across assay platforms, experimental setups, and tissue types, as well as its potential application in single-cell RNAseq data analysis, tauFisher is a promising tool that facilitates circadian medicine and research.
由于生物钟调节着基本的生物过程，因此在患者和病变组织中经常观察到生物钟紊乱。在生物钟医学和研究中，确定患者或关注组织的生物钟时间至关重要。在这里，我们介绍了 tauFisher，这是一种计算管道，通过在样本中找到节律基因之间的相关性，从单个转录组样本中准确预测生物钟时间。我们展示了 tauFisher 在为来自多种组织类型和实验设置的批量和单细胞转录组样本添加时间戳方面的性能。在从小鼠皮肤真皮中收集的单细胞 RNAseq 数据集上应用 tauFisher 进行细胞类型水平分析表明，与真皮成纤维细胞相比，真皮免疫细胞中核心时钟基因表达的集体节律可能解释了更为明显的生物钟相位异质性。鉴于其在检测平台、实验设置和组织类型方面的稳健性和通用性，以及在单细胞 RNAseq 数据分析中的潜在应用，tauFisher 是一种很有前途的工具，可促进生物钟医学和研究。
