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Comprehensive analysis of cold exposure-associated transcriptional and metabolic changes in the liver
doi: 10.1515/fzm-2025-0024
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Abstract:
Background Cold exposure is associated with metabolic alterations. This study aims to investigate the effects and mechanisms of cold exposure on liver metabolism through the integration of transcriptomics and metabolomics. Methods Liver tissues from mice exposed to cold were subjected to RNA sequencing and liquid chromatography-mass spectrometry (LC-MS) for transcriptomic and metabolomic profiling, respectively. Differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) were identified. mRNA expression levels were validated by real-time polymerase chain reaction (RT-PCR). Gene ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG), and Reactome enrichment analyses were performed. Finally, transcriptomic and metabolomic data were integrated and analyzed. Results Cold exposure altered the transcriptomic and metabolomic profiles in the liver in cold exposed mice. Enrichment analyses were of DEGs and DEMs. Enrichment analyses of DEGs and DEMs revealed that DEGs were involved in pathways such as the PI3K-Akt signaling pathway, cytokine-cytokine receptor interaction, and cell adhesion molecules. DEMs were enriched in pathways related to membrane transport, nucleotide metabolism, and the metabolism of cofactors and vitamins. The integration of transcriptomic and metabolomic data identified several pathways potentially associated with cold exposure, such as the PI3K-Akt signaling pathway. Conclusion Cold exposure alters liver transcriptomic and metabolomic profiles in mice. The integrative analysis of transcriptomic and metabolomic data highlights the complexity of the liver's response to cold exposure and identifies potential targets for further investigation. -
Key words:
- cold exposure /
- liver metabolism /
- transcriptome /
- metabolome
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Figure 1. Cold exposure alters gene expression profiles in the mouse liver
(A) Gene expression heatmap between the control and day groups. (B) Gene expression heatmap between the control and night groups. (C) The volcano plots of differentially expressed genes between the control and day groups. (D) The volcano plots of differentially expressed genes between the control and night groups. (E) The number of DEGs between the control and night groups. (F) The number of DEGs between the control and day groups. (G) Radar Chart of differentially expressed genes between the control and day groups. (H) Radar Chart of differentially expressed genes between the control and night groups. (I) Acot1 mRNA expression in the control and day groups. (J) Acot1 mRNA expression in the control and night groups. (K) Cry1 mRNA expression in the control and day groups. (L) Cry1 mRNA expression between the control and day groups. CTL, control. *P < 0.05. **P < 0.01.
Figure 2. Enrichment analysis of differentially expressed genes (DEGs) in the mouse liver
(A) The bar chart of gene ontology enrichment analysis of DEGs between the control and day groups. (B) Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis of DEGs between the control and day groups. (C) Reactome enrichment analysis of DEGs between the control and day groups. (D) GO enrichment analysis of DEGs between the control and night groups. (E) KEGG enrichment analysis of DEGs between the control and night groups. (F) Reactome enrichment analysis of DEGs between the control and night groups. (G) The overlapped DEGs across the three groups. (H) KEGG pathway of DEGs is upregulated following cold exposure. (I) KEGG pathway of DEGs is downregulated following cold exposure. CTL, control.
Figure 3. Enrichment analysis of differentially expressed metabolites (DEMs) in the mouse liver tissue
(A) Orthogonal partial least squares discriminant analysis (OPLS-DA) analysis of the cardiometabolic group between the control and day positive ion (POS) mode. (B) OPLS-DA of the cardiometabolic group between the control and night in POS mode. (C) Permutation test evaluating the accuracy of the OPLS-DA model for the control and day group. (D) Permutation test evaluating the accuracy of the OPLS-DA model for the control and night group. (E) Heatmap of DEMs between the con-trol and day groups. (F) Heatmap of DEMs between the control and night groups. (G) Volcano plots of DEMs between the control and day groups. (H) Volcano plots of DEMs between the control and night groups. (I) Lollipop chart of DEMs between the control and day groups. (J) Lollipop chart of DEMs between the control and night groups. (K) Venn diagram of DEMs across the three groups. CTL, control.
Figure 4. Enrichment analysis of the differentially expressed metabolites (DEMs) in liver of cold-exposed mice
(A) KEGG enrichment analysis of DEMs between the control and day groups. (B) Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis of the upregulated and downregulated DEMs between the control and day groups. (C) Reactome enrichment analysis of DEMs between the control and day groups. (D) KEGG enrichment analysis of DEMs between the control and night groups. (E) KEGG enrichment analysis of the upregulated and downregulated DEMs between the control and night groups. (F) Reactome enrichment analysis of DEMs between the control and night groups. (G) Gene set enrichment analysis (GSEA) enrichment analysis of Purine metabolism pathway between the control and day groups. (H) GSEA enrichment analysis of Purine metabolism pathway between the control and night groups. (I) GSEA enrichment analysis of ABC transporters pathway between the control and day groups. CTL, control.
Figure 5. Combined analysis of transcriptome and metabolome
(A) Number of differentially expressed metabolites (DEMs) and differentially expressed metabolites (DEMs) between the control and day groups enriched Kyoto encyclopedia of genes and genomes (KEGG) pathways. (B) Number of overlapped KEGG pathways between the control and day groups. (C) Overlapping pathways between the control and day groups. (D) Number of DEGs and DEMs between the control and night groups enriched KEGG pathways. (E) Number of overlapping KEGG pathways between the control and night groups. (F) Overlapping pathways between the control and night groups. (G) Interaction network diagram of the overlapping pathways between the control and day groups. (H) Interaction network diagram of overlapping pathways between the control and night groups. (I) Enriched pathways associated with cold exposure. CTL, control.
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