Rewiring of liver diurnal transcriptome rhythms by triiodothyronine (T3) supplementation
- Institute of Neurobiology, Center of Brain Behavior & Metabolism, University of Lübeck, Germany
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Sweden
- Department of Physiology, Institute of Bioscience, University of Sāo Paulo, Brazil
- Australian Centre for Health Services Innovation and Centre for Healthcare Transformation, School of Public Health and Social Work, Faculty of Health, Queensland University of Technology, Australia
- Institute of Experimental and Clinical Pharmacology, University Hospital Schleswig-Holstein, Germany
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Australia
- Center of Brain Behavior & Metabolism, Institute for Endocrinology and Diabetes – Molecular Endocrinology, University of Lübeck, Germany
Figures
Figure 1 with 1 supplement
Triiodothyronine (T3)-treated mice show classic effects of high thyroid hormone levels compared to control mice (CON).
(A–F) Serum levels of T3 and thyroxine (T4), 24 hr profiles of locomotor activity, body temperature, O2 consumption, and respiratory quotient are shown. Rhythm evaluation was performed by JTK_CYCLE …
Figure 1—figure supplement 1
Metabolic evaluation of control (CON) and triiodothyronine (T3) mice.
(A–D) Assessment of body temperature, food and water intake (per cage, n = 8), and body weight. (E–I) Metabolic parameters (described in the y-axis) were obtained from the third week of experiment …
Figure 2
Identification of daytime-independent differentially expressed genes (DEGs) in the liver of triiodothyronine (T3) mice.
(A) Global (all Zeitgeber times [ZTs] included) evaluation of liver transcriptomes revealed 2336 DEGs of which 1391 and 945 were considered as up- or downregulated, respectively, using a false …
Figure 3 with 2 supplements
Diurnal evaluation of liver transcriptome of triiodothyronine (T3) mice.
(A) Rhythmic probes were identified using the JTK_CYCLE algorithm (Supplementary file 5). Venn diagram represents the distribution of rhythmic probes for each group. (B) Rose plot of all rhythmic …
Figure 3—figure supplement 1
Principal component analysis (PCA) plots of shared rhythmic genes.
Each timepoint was averaged into a single replicate, and PCA were performed using the factoextra package in R and Hartigan-Wong, Lloyd, and Forgy MacQueen algorithms.
Figure 3—figure supplement 2
Validation of clock gene diurnal profile by qPCR.
CircaCompare was used to evaluate the difference in rhythmic parameters, and one-sample t-test against zero value was performed (mean 0.9069 hr, p=0.0221). Sine curve was fitted for rhythmic genes …
Figure 4
Gene expression evaluation of thyroid hormone (TH) regulators and metabolic outputs in triiodothyronine (T3) compared to control (CON).
(A, B) Genes involved in TH regulation, including transporters, Dio1, TH receptors, and well-known T3 outputs are presented. Presence (R) or absence of circadian rhythm (NR) detected by CircaCompare …
Figure 5 with 1 supplement
CircaCompare analyses of triiodothyronine (T3) (red) mice compared to control (CON) (black).
(A) Venn diagram demonstrates the number of probes that displayed differences in each rhythmic parameter (mesor, amplitude, and phase). (B) Top 5 enriched biological processes for each rhythmic …
Figure 5—figure supplement 1
Expression profile of the selected genes pertaining to biological processes identified in CircaCompare.
Diurnal profile of genes from glucose (A), fatty acid (B), and cholesterol metabolism (C). Diurnal overall gene expression was normalized by CON mesor and plotted. Sine curve was fitted for rhythmic …
Tables
Key resources table
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Gene (Mus musculus) | C57BL/6J | Janvier Labs, Germany | C57BL6JRj | |
| Strain, strain background (C57BL6JRj, male) | C57BL/6JRj | Janvier Labs, Germany | 2–3-month-old male | |
| Biological sample (M. musculus) | Liver and serum | Collected and immediately frozen in dry ice | ||
| Sequence-based reagent | RNA extraction | TRIzol, Thermo Fisher Scientific | ||
| Sequence-based reagent | RNA isolation | RNA Miniprep kit Zymo Research | ||
| Sequence-based reagent | cDNA synthesis | High-Capacity Complementary DNA Reverse Transcription Kit, Thermo Fisher | ||
| Sequence-based reagent | qPCR | GoTaq, Promega, USA | ||
| Sequence-based reagent | Microarray | WT Plus Kit, Thermo Fisher Scientific | ||
| Sequence-based reagent | qPCR primers | Integrated DNA Technologies (IDT) | Sequences are provided in the supplementary information | |
| Chemical compound, drug | T3 hormone | T6397, Sigma-Aldrich | ||
| Chemical compound, drug | BSA | A7906-50G, Sigma-Aldrich | ||
| Commercial assay or kit | T3 detection kit | DNOV053, NovaTec | ||
| Commercial assay or kit | T4 detection kit | EIA-1781, DRG Diagnostics | ||
| Commercial assay or kit | Triglycerides quantification kit | MAK266, Sigma-Aldrich | ||
| Commercial assay or kit | Cholesterol quantification kit | STA 384, Cell Biolabs | ||
| Software, algorithm | RStudio | R 4.0.3 | ||
| Software, algorithm | Prisma 9 | GraphPad |
Additional files
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Supplementary file 1
Metabolic output rhythmic evaluation by JTK_CYCLE.
- https://cdn.elifesciences.org/articles/79405/elife-79405-supp1-v4.xlsx
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Supplementary file 2
Metabolic output correlation.
- https://cdn.elifesciences.org/articles/79405/elife-79405-supp2-v4.xlsx
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Supplementary file 3
Global differentially expressed genes (DEGs).
- https://cdn.elifesciences.org/articles/79405/elife-79405-supp3-v4.xlsx
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Supplementary file 4
Differentially expressed genes (DEGs) per Zeitgeber time (ZT).
- https://cdn.elifesciences.org/articles/79405/elife-79405-supp4-v4.xlsx
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Supplementary file 5
Rhythmic evaluation by JTK_CYCLE.
- https://cdn.elifesciences.org/articles/79405/elife-79405-supp5-v4.xlsx
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Supplementary file 6
Rhythmic analyses by CircaCompare.
- https://cdn.elifesciences.org/articles/79405/elife-79405-supp6-v4.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/79405/elife-79405-mdarchecklist1-v4.docx
