tauFisher predicts circadian time from a single sample of bulk and single-cell pseudobulk transcriptomic data

Junyan Duan; Michelle N Ngo; Satya Swaroop Karri; Lam C Tsoi; Johann E Gudjonsson; Babak Shahbaba; John Lowengrub; Bogi Andersen

doi:10.1038/s41467-024-48041-6

tauFisher predicts circadian time from a single sample of bulk and single-cell pseudobulk transcriptomic data

Nat Commun. 2024 May 7;15(1):3840. doi: 10.1038/s41467-024-48041-6.

Authors

Junyan Duan^#^{1

2}, Michelle N Ngo^#^{1

2}, Satya Swaroop Karri³, Lam C Tsoi^{4

5

6

7}, Johann E Gudjonsson^{4

7}, Babak Shahbaba^{8

9}, John Lowengrub^{10

11

12}, Bogi Andersen^{13

14

15}

Affiliations

¹ Center for Complex Biological Systems, University of California Irvine, Irvine, CA, USA.
² The NSF-Simons Center for Multiscale Cell Fate Research, University of California Irvine, Irvine, CA, USA.
³ Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA.
⁴ Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA.
⁵ Department of Computational Medicine and Bioinformatics, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA.
⁶ Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA.
⁷ Mary H Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI, USA.
⁸ Center for Complex Biological Systems, University of California Irvine, Irvine, CA, USA. babaks@uci.edu.
⁹ Department of Statistics, University of California Irvine, Irvine, CA, USA. babaks@uci.edu.
¹⁰ Center for Complex Biological Systems, University of California Irvine, Irvine, CA, USA. jlowengr@uci.edu.
¹¹ Department of Mathematics, University of California, Irvine, CA, USA. jlowengr@uci.edu.
¹² Department of Biomedical Engineering, University of California Irvine, Irvine, CA, USA. jlowengr@uci.edu.
¹³ Center for Complex Biological Systems, University of California Irvine, Irvine, CA, USA. bogi@uci.edu.
¹⁴ Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA. bogi@uci.edu.
¹⁵ Department of Medicine, Division of Endocrinology, School of Medicine, University of California Irvine, Irvine, CA, USA. bogi@uci.edu.

^# Contributed equally.

Abstract

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Circadian Clocks* / genetics
Circadian Rhythm* / genetics
Computational Biology / methods
Fibroblasts / metabolism
Gene Expression Profiling / methods
Humans
Mice
Sequence Analysis, RNA / methods
Single-Cell Analysis* / methods
Skin / metabolism
Software
Transcriptome*

Abstract

Publication types

MeSH terms

Grants and funding