Integrated Transcriptomics and Metabolomics Reveal Changes in Cell Homeostasis and Energy Metabolism in Trachinotus ovatus in Response to Acute Hypoxic Stress
Abstract
:1. Introduction
2. Results
2.1. Transcriptomics Analysis
2.1.1. Sequencing Quality and Sample Relationship
2.1.2. Identification of Differentially Expressed Genes (DEGs)
2.1.3. Gene Expression Trends
2.1.4. Gene Co-Expression Network Construction
2.1.5. Kyoto Encyclopedia of Genes and Genomes (KEGG) Enrichment Analysis
2.1.6. Gene Ontology (GO) Enrichment Analysis
2.1.7. Protein–Protein Interaction (PPI) Network Analysis
2.2. Metabolomics Analysis
2.2.1. Metabolite Identification and Multivariate Statistical Analysis
2.2.2. Identification of Differentially Expressed Metabolites (DEMs)
2.2.3. KEGG Enrichment Analysis of DEMs
2.3. Integrated KEGG Enrichment Analysis of Transcriptomics and Metabolomics
2.4. Key Genes, Metabolites, and Biological Pathways
2.5. Key Gene Expression Analysis during Acute Hypoxic Stress and Re-Oxygenation
2.6. Quantitative Real-Time PCR (qRT-PCR) Validation of Key Genes
3. Discussion
3.1. Hub Genes in Response to Hypoxia Adaptation
3.2. Cell Growth and Death in Response to Acute Hypoxic Stress and Re-Oxygenation
3.2.1. Cell Cycle Arrest during the Hypoxia Stage
3.2.2. Balance of Both Pro-Apoptosis and Anti-Apoptosis Processes under Acute Hypoxic Stress
3.2.3. Continuous Apoptosis after Re-Oxygenation
3.3. Carbohydrate Metabolism, Amino Acid Metabolism, and Lipid Metabolism in Response to Acute Hypoxic Stress and Re-Oxygenation
3.3.1. Enhancing Anaerobic Glycolysis and Lactate Transport for Hypoxia Adaptation
3.3.2. Enhancing Gluconeogenesis and Glycogen Synthesis for Hypoxia Adaptation
3.3.3. Enhancing Amino Acid Metabolism for Hypoxia Adaption
3.3.4. Enhancing Fat Mobilization and Fatty Acid Biosynthesis for Hypoxia Adaption
3.3.5. Activating Fatty Acid β-Oxidation and Aerobic Metabolism after Re-Oxygenation
3.4. Key Periods for Acute Hypoxic Stress and Re-Oxygenation in T. ovatus
4. Materials and Methods
4.1. Ethics Statement and Fish Management
4.2. Experimental Design and Sample Collection
4.3. Transcriptomics Analysis
4.4. Metabolomics Analysis
4.5. Integrated Analysis of Transcriptomics and Metabolomics
4.6. qRT-PCR Validation for Key Genes
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample Name | Hy0 | Hy1 | Hy6 | Ro12 | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Hy0-1 | Hy0-2 | Hy0-3 | Hy1-1 | Hy1-2 | Hy1-3 | Hy6-1 | Hy6-2 | Hy6-3 | Ro12-1 | Ro12-2 | Ro12-3 | |
Raw reads (×106) | 39.06 | 43.39 | 38.85 | 40.63 | 41.55 | 40.95 | 42.33 | 41.99 | 41.23 | 41.33 | 59.29 | 44.58 |
Clean reads (×106) | 38.43 | 42.74 | 38.28 | 39.97 | 40.83 | 40.39 | 41.70 | 41.23 | 40.73 | 40.74 | 58.25 | 43.53 |
Clean reads rate (%) | 98.39 | 98.50 | 98.53 | 98.38 | 98.27 | 98.63 | 98.51 | 98.19 | 98.79 | 98.57 | 98.25 | 97.64 |
Raw bases (×109 bp) | 5.86 | 6.51 | 5.83 | 6.10 | 6.23 | 6.14 | 6.35 | 6.30 | 6.18 | 6.20 | 8.89 | 6.69 |
Clean bases (×109 bp) | 5.73 | 6.38 | 5.72 | 5.97 | 6.09 | 6.03 | 6.23 | 6.15 | 6.08 | 6.09 | 8.70 | 6.49 |
GC content (%) | 49.25 | 49.00 | 49.22 | 49.29 | 49.09 | 49.44 | 49.64 | 49.78 | 49.45 | 49.69 | 49.05 | 49.87 |
Q20 (%) | 97.80 | 97.63 | 97.68 | 97.68 | 97.65 | 97.69 | 97.73 | 97.72 | 97.90 | 97.89 | 97.41 | 97.74 |
Q30 (%) | 93.79 | 93.37 | 93.50 | 93.54 | 93.45 | 93.50 | 93.63 | 93.61 | 94.00 | 94.02 | 92.93 | 93.69 |
High-quality reads (×106) | 38.41 | 42.72 | 38.27 | 39.94 | 40.81 | 40.37 | 41.67 | 41.21 | 40.71 | 40.72 | 58.22 | 43.51 |
Total mapped (×106) | 35.83 | 40.02 | 35.80 | 37.46 | 38.15 | 38.06 | 39.18 | 36.97 | 38.35 | 37.54 | 54.07 | 40.79 |
Total mapped rate (%) | 93.29 | 93.67 | 93.57 | 93.78 | 93.48 | 94.28 | 94.03 | 89.73 | 94.20 | 92.20 | 92.87 | 93.74 |
Unique mapped (×106) | 34.09 | 37.80 | 33.91 | 35.53 | 36.41 | 35.93 | 37.04 | 35.36 | 36.57 | 35.80 | 51.30 | 38.51 |
Unique mapped rate (%) | 88.75 | 88.50 | 88.62 | 88.95 | 89.22 | 89.01 | 88.90 | 85.81 | 89.84 | 87.92 | 88.11 | 88.51 |
Genes/Metabolites | Description | Log2 (Fold Change) | |||
---|---|---|---|---|---|
Hy0 vs. Hy1 | Hy0 vs. Hy6 | Hy0 vs. Ro12 | Hy6 vs. Ro12 | ||
Signal transduction | |||||
FOS | proto-oncogene c-Fos | 9.16 ** | 7.05 ** | −0.18 | −7.22 ** |
JUN | proto-oncogene c-Jun | 6.43 ** | 5.03 ** | 0.08 | −4.95 ** |
Cell cycle arrest | |||||
GADD45B | growth arrest and DNA damage-inducible protein GADD45 beta | 5.17 ** | 3.42 ** | 1.70 ** | −1.72 |
CDKN1A | cyclin-dependent kinase inhibitor 1A | 1.18 ** | 1.52 ** | 0.25 | −1.28 * |
Pro-apoptosis (intrinsic pathway) | |||||
BAX | Bcl-2-associated X | 0.62 | 1.25 ** | 0.21 | −1.04 * |
CYC-B | cytochrome c-b | 2.13 ** | 4.73 ** | 1.39 * | −3.35 ** |
CASP3 | caspase-3 | −0.42 | 0.64 * | 0.97 ** | 0.34 |
Pro-apoptosis (extrinsic pathway) | |||||
TNFRSF10A | tumor necrosis factor receptor superfamily member 10A | 1.84 ** | 1.72 ** | 0.15 | −1.57 ** |
Pro-apoptosis (glutathione metabolism) | |||||
GPX7 | glutathione peroxidase 7 | −1.37 | −2.92 ** | 0.00 | 2.92 * |
GGT5 | glutathione hydrolase 5 | 0.59 | 1.34 * | 1.91 ** | 0.57 |
Glutathione | – | −2.40 # | −1.67 # | 0.58 | 2.25 # |
L-Glutamic acid | – | −0.63 # | −0.90 # | −0.63 # | 0.27 |
γ-Glutamylcysteine | – | 3.16 # | 1.38 | 0.06 | −1.32 |
L-Cysteine | – | 0.31 | 1.17 | 2.93 # | 1.76 # |
Pro-apoptosis (sphingosine metabolism) | |||||
CERS6 | ceramide synthase 6 | 0.30 | −1.14 | 1.51 * | 2.65 ** |
Sphingosine | – | 1.28 | 0.60 | 3.20 # | 2.60 # |
Anti-apoptosis | |||||
MCL1 | myeloid leukemia cell differentiation protein Mcl-1 | 1.48 ** | 1.77 ** | 0.07 | −1.70 ** |
HSP70 | heat shock protein 70 | 8.28 ** | 9.83 ** | 2.00 | −7.83 ** |
MDM2 | murine double minute 2 | 0.47 * | 1.32 ** | −0.41 | −1.72 ** |
Glycolysis | |||||
HK1 | hexokinase 1 | 1.42 ** | 2.28 ** | 0.95 | −1.33 * |
PFKL | ATP-dependent 6-phosphofructokinase, liver type | −0.08 | 2.05 ** | 0.86 ** | −1.19 * |
ALDOA | fructose-bisphosphate aldolase A | 1.52 ** | 3.22 ** | 1.40 ** | −1.82 ** |
ALDOCB | fructose-bisphosphate aldolase C-B | 0.95 ** | 2.86 ** | 1.07 ** | −1.79 ** |
GAPDH-2 | glyceraldehyde 3-phosphate dehydrogenase isoform 2 | 0.50 | 2.01 ** | 1.30 ** | −0.71 * |
PGAM1 | phosphoglycerate mutase 1 | 1.27 * | 3.16 ** | 2.13 * | −1.03 |
ENO1 | alpha-enolase | −0.15 | 1.97 ** | 1.55 ** | −0.42 |
LDHA | lactate dehydrogenase A | 2.73 ** | 4.16 ** | 1.44 ** | −2.71 ** |
Lactate transport | |||||
SLC16A3 | solute carrier family 16 member 3 | 3.25 ** | 4.44 ** | 1.56 | −2.88 ** |
Gluconeogensis | |||||
G6PC | glucose-6-phosphatase | 2.02 ** | 1.29 ** | −0.26 | −1.56 ** |
PCK1 | cytosolic phosphoenolpyruvate carboxykinase 1 | 4.95 ** | 4.70 ** | 1.39 * | −3.31 ** |
Liver glycogen synthesis | |||||
GYG2 | glycogenin-2 | 0.01 | 1.22 ** | −0.49 | −1.71 ** |
GYS2 | glycogen synthase, liver | 0.18 | 0.86 ** | 0.39 | −0.47 |
PHKA2 | phosphorylase b kinase regulatory subunit alpha, liver isoform | −0.61 | −1.85 ** | −0.95 * | 0.90 |
PYGL | glycogen phosphorylase, liver form | −0.72 | −1.42 * | −0.59 | 0.83 |
Amino acid metabolism | |||||
GOT2 | L-aspartic acid aminotransferase 2 | 0.74 * | 1.62 ** | 0.29 | −1.33 ** |
L-Aspartic acid | – | −0.37 # | −0.75 # | −0.56 # | 0.19 |
Fat mobilization | |||||
PNPLA2 | patatin-like phospholipase domain-containing protein 2 | 0.90 ** | 1.83 ** | −0.56 | −2.39 ** |
LIPE | hormone-sensitive lipase-like | 0.98 * | 1.90 ** | −0.80 | −2.69 ** |
Fatty acid biosynthesis | |||||
ACSL4 | long-chain-fatty-acid-CoA ligase 4 | 2.19 * | 4.09 ** | −4.62 ** | −0.53 |
ACLY | ATP-citrate lyase | 0.94 | 2.25 ** | 0.53 | −1.72 * |
Fatty acid β-oxidation | |||||
CPT1A | carnitine O-palmitoyltransferase 1, liver isoform | 0.35 | −0.05 | 1.17 ** | 1.22 * |
CPT2 | carnitine O-palmitoyltransferase 2, mitochondrial | −0.80 * | −1.26 ** | 0.07 | 1.33 ** |
TCA cycle | |||||
Oxoglutaric acid | – | 0.48 | 0.30 | 1.01 # | 0.70 |
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Wang, Q.-H.; Wu, R.-X.; Ji, J.-N.; Zhang, J.; Niu, S.-F.; Tang, B.-G.; Miao, B.-B.; Liang, Z.-B. Integrated Transcriptomics and Metabolomics Reveal Changes in Cell Homeostasis and Energy Metabolism in Trachinotus ovatus in Response to Acute Hypoxic Stress. Int. J. Mol. Sci. 2024, 25, 1054. https://doi.org/10.3390/ijms25021054
Wang Q-H, Wu R-X, Ji J-N, Zhang J, Niu S-F, Tang B-G, Miao B-B, Liang Z-B. Integrated Transcriptomics and Metabolomics Reveal Changes in Cell Homeostasis and Energy Metabolism in Trachinotus ovatus in Response to Acute Hypoxic Stress. International Journal of Molecular Sciences. 2024; 25(2):1054. https://doi.org/10.3390/ijms25021054
Chicago/Turabian StyleWang, Qing-Hua, Ren-Xie Wu, Jiao-Na Ji, Jing Zhang, Su-Fang Niu, Bao-Gui Tang, Ben-Ben Miao, and Zhen-Bang Liang. 2024. "Integrated Transcriptomics and Metabolomics Reveal Changes in Cell Homeostasis and Energy Metabolism in Trachinotus ovatus in Response to Acute Hypoxic Stress" International Journal of Molecular Sciences 25, no. 2: 1054. https://doi.org/10.3390/ijms25021054