Multi-Tissue Transcriptome Study of Innate Immune Gene Expression Profiling Reveals Negative Energy Balance Altered the Defense and Promoted System Inflammation of Dairy Cows
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. RNA Sequencing Data and Data Grouping Information
- RNA Sequencing Data Sources
- Data grouping information
2.2. Reads Mapping and Quantification of Gene Expression
2.3. Innate Immune Gene Sets and Principal Component Analysis
2.4. Gene-Set Enrichment Analysis and Network Architecture
3. Results
3.1. Expression of Innate Immune Genes in Different Tissues of Dairy Cows
3.2. Functional Analysis Reveals Widespread Alterations of Biological Processes of Innate Immune Gene Post NEB Condition with Different Tissue
3.3. Tissue-Specific Altered Biological Functions Point to Specificity of Defensive, Metabolic, and Signaling Responses to NEB
3.4. Network Analyses of Gene Sets from Multi-Tissue Unveils Universal Changes to the Defense Response Caused by NEB
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Trait Material | Data Grouping | Sequencing Platform | Data Sources | Accession Numbers |
---|---|---|---|---|
Adipose | Normal (PreP), n = 12 NEB (PP1), n = 12 | Illumina NextSeq 500 (Bos taurus) | David Salcedo-Tacuma, 2020 | GSE159224 |
Blood | Normal, n = 10 NEB, n = 13 | Illumina HiSeq 2000 (Bos taurus) | Ze Yan, 2020 | PRJNA605719 |
Endometrium | Normal (MNEB), n = 15 NEB (SNEB), n = 9 | Illumina HiSeq 4000 (Bos taurus) | Wiruntita Chankeaw, 2021 | GSE169638 |
Hypothalamus | Normal (Restricted), n = 14 NEB (high level), n = 7 | Illumina HiSeq 4000 (Bos taurus) | Daragh Matthews, 2017 | GSE49540 |
Liver | Normal (MNEB), n = 5 NEB (SNEB), n = 6 | Illumina Genome Analyzer (Bos taurus) | Matthew McCabe, 2012 | GSE37544 |
GO Term | NES | Tissue | Regulated |
---|---|---|---|
Humoral Immune Response Mediated by Circulating Immunoglobulin | 1.8095 | Adipose | Up |
Membrane Invagination | 1.8004 | Adipose | Up |
Regulation of Humoral Immune Response | 1.7919 | Adipose | Up |
Amyloid Beta Clearance | 1.7888 | Adipose | Up |
Complement Activation | 1.7642 | Adipose | Up |
Negative Regulation of Blood Vessel Diameter | −1.6923 | Adipose | Down |
Regulation of Steroid Biosynthetic Process | −1.702 | Adipose | Down |
Regulation of Steroid Metabolic Process | −1.7112 | Adipose | Down |
Fatty Acid Metabolic Process | −1.9598 | Adipose | Down |
Sterol Metabolic Process | −2.1124 | Adipose | Down |
Myeloid Leukocyte Mediated Immunity | 2.2295 | Blood | Up |
Exocytosis | 2.1093 | Blood | Up |
Myeloid Leukocyte Activation | 1.9157 | Blood | Up |
Defense Response to Gram-Positive Bacterium | 1.8822 | Blood | Up |
Cell Activation Involved in Immune Response | 1.8773 | Blood | Up |
B Cell Activation | −1.9504 | Blood | Down |
Regulation of Fat Cell Differentiation | −2.0154 | Blood | Down |
Regulation of Immunoglobulin Production | −2.147 | Blood | Down |
B Cell Activation Involved in Immune Response | −2.2318 | Blood | Down |
Immunoglobulin Production | −2.2439 | Blood | Down |
Lymphocyte Chemotaxis | 1.9792 | Endometrium | Up |
Protein-DNA Complex Subunit Organization | 1.9613 | Endometrium | Up |
Organ Growth | 1.949 | Endometrium | Up |
Heart Growth | 1.8857 | Endometrium | Up |
Positive Regulation of Heart Growth | 1.8108 | Endometrium | Up |
Cellular Response to Virus | −1.6434 | Endometrium | Down |
Positive Regulation of Response to Cytokine Stimulus | −1.6448 | Endometrium | Down |
Sterol Metabolic Process | −1.6475 | Endometrium | Down |
Regulation of Jun Kinase Activity | −1.6754 | Endometrium | Down |
Positive Regulation of Jun Kinase Activity | −1.7641 | Endometrium | Down |
Response to Retinoic Acid | 1.9746 | Hypothalamus | Up |
Positive Regulation of CD4-Positive Alpha Beta T-Cell Differentiation | 1.8528 | Hypothalamus | Up |
Regulation of CD4-Positive Alpha Beta T-Cell Differentiation | 1.7604 | Hypothalamus | Up |
Leukocyte Homeostasis | 1.6864 | Hypothalamus | Up |
Response to Chemokine | 1.6836 | Hypothalamus | Up |
Non-canonical Wnt Signaling Pathway | −1.6246 | Hypothalamus | Down |
Calcium Ion Transmembrane Import into Cytosol | −1.6279 | Hypothalamus | Down |
Neuron Projection Organization | −1.6319 | Hypothalamus | Down |
Cellular Response to Ketone | −1.6627 | Hypothalamus | Down |
Regulation of Calcium Ion Transmembrane Transport | −1.6661 | Hypothalamus | Down |
Tissue Migration | 1.695 | Liver | Up |
Negative Regulation of Cell Adhesion | 1.6623 | Liver | Up |
Negative Regulation of Coagulation | 1.6527 | Liver | Up |
Odontogenesis | 1.65 | Liver | Up |
Positive Regulation of Cell Division | 1.6472 | Liver | Up |
Calcineurin-Mediated Signaling | −1.656 | Liver | Down |
Positive Regulation of Lipid Kinase Activity | −1.6596 | Liver | Down |
Glucose Metabolic Process | −1.6671 | Liver | Down |
Establishment of Cell Polarity | −1.7294 | Liver | Down |
Positive Regulation of Phospholipid Metabolic Process | −1.7409 | Liver | Down |
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Dai, L.; Liu, Z.; Guo, L.; Chai, Y.; Yang, Y.; Wang, Y.; Ma, Y.; Shi, C.; Zhang, W. Multi-Tissue Transcriptome Study of Innate Immune Gene Expression Profiling Reveals Negative Energy Balance Altered the Defense and Promoted System Inflammation of Dairy Cows. Vet. Sci. 2023, 10, 107. https://doi.org/10.3390/vetsci10020107
Dai L, Liu Z, Guo L, Chai Y, Yang Y, Wang Y, Ma Y, Shi C, Zhang W. Multi-Tissue Transcriptome Study of Innate Immune Gene Expression Profiling Reveals Negative Energy Balance Altered the Defense and Promoted System Inflammation of Dairy Cows. Veterinary Sciences. 2023; 10(2):107. https://doi.org/10.3390/vetsci10020107
Chicago/Turabian StyleDai, Lingli, Zaixia Liu, Lili Guo, Yuan Chai, Yanda Yang, Yu Wang, Yanfen Ma, Caixia Shi, and Wenguang Zhang. 2023. "Multi-Tissue Transcriptome Study of Innate Immune Gene Expression Profiling Reveals Negative Energy Balance Altered the Defense and Promoted System Inflammation of Dairy Cows" Veterinary Sciences 10, no. 2: 107. https://doi.org/10.3390/vetsci10020107