Integrative Analysis of miRNA and mRNA Expression Profiles in Mammary Glands of Holstein Cows Artificially Infected with Staphylococcus aureus
Abstract
:1. Introduction
2. Results
2.1. The Establishment of Bovine S. aureus-Induced Mastitis Model
2.2. The Pathological Observation
2.3. Differential Expressed miRNA Identification
2.4. Differential Expressed mRNA Identification
2.5. Interaction Analysis of the miRNAs and mRNAs
2.6. Functional Analysis of Differentially Expressed Genes
2.7. Validation of DE miRNAs and DEGs by qRT-PCR
3. Discussion
4. Materials and Methods
4.1. Ethics Statement and Animals Selection
4.2. Mastitis Model Construction
4.3. Sample Collection and Total RNA Extraction
4.4. Pathological Tests
4.5. Small RNA Sequencing and Data Analysis
4.6. mRNA Analysis and Data Process
4.7. miRNA–mRNA Interaction Network Construction
4.8. Functional Analysis of Differentially Expressed Genes
4.9. RT-qPCR Validation of DEGs and DE miRNAs
4.10. Statistical Analysis
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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Term ID | Term | P-Value | Gene Name | Number |
---|---|---|---|---|
GO:0071310 | cellular response to organic substance | 0.009 | CXCR1a, GFPT2, CSF3, IL17A, PTGS2, WNT2, CXCL5, IL2RA, OAS2, PTAFR, PTGIS, ABHD2, RIPOR2, SOCS3, COL1A2, GNG2, COL1A1, SCARB1, LDLR, FYN, ATP2B4, SNAI2, MSN, IRAK2, RAP1B, WASF1, CD14, COL4A1, DERL1, HSPA5, ACVR2A, LDOC1, EHD1, UFM1 | 34 |
GO:0051345 | positive regulation of hydrolase activity | 0.010 | SELE, S100A9, HTR2A, MAPRE2, AHSA2, PYCARD, ABR, CHN1, DNAJB4, ARHGAP15, SEC23A, ATP1B3, AGFG1, ASAP1 | 14 |
GO:1901701 | cellular response to oxygen-containing compound | 0.011 | CXCL5, PTAFR, COL1A2, GNG2, COL1A1, SCARB1, LDLR, FYN, ATP2B4, TXN, SNAI2, MSN, IRAK2, RAP1B, CD14, COL4A1, LDOC1, NCF1, SOD2 | 19 |
GO:0071216 | cellular response to biotic stimulus | 0.015 | CXCL5, PTAFR, SCARB1, IRAK2, CD14, HSPA5, LDOC1 | 7 |
GO:0071222 | cellular response to lipopolysaccharide | 0.015 | CXCL5, PTAFR, SCARB1, IRAK2, CD14, LDOC1 | 6 |
GO:0072676 | lymphocyte migration | 0.016 | RIPOR2, PYCARD, STK10, MSN | 4 |
GO:0032496 | response to lipopolysaccharide | 0.020 | CXCL5, PTAFR, SCARB1, IRAK2, TBXA2R, CD14, LDOC1 | 7 |
GO:0071219 | cellular response to molecule of bacterial origin | 0.021 | CXCL5, PTAFR, SCARB1, IRAK2, CD14, LDOC1 | 6 |
GO:0030334 | regulation of cell migration | 0.023 | SRPX2, PRR5L, ABHD2, RIPOR2, STC1, MAPRE2, MMP14, PYCARD, COL1A1, STK10, SNAI2, MSN, TBXA2R, ITGB1, HSPA5 | 15 |
GO:0071229 | cellular response to acid chemical | 0.028 | COL1A2, GNG2, COL1A1, LDLR, COL4A1 | 5 |
GO:0032729 | positive regulation of interferon gamma production | 0.028 | PYCARD, FAM49B, CD14 | 3 |
GO:0050900 | leukocyte migration | 0.030 | SELE, IL17A, S100A9, CXCL5, RIPOR2, PYCARD, STK10, MSN | 8 |
GO:0002237 | response to molecule of bacterial origin | 0.031 | CXCL5, PTAFR, SCARB1, IRAK2, TBXA2R, CD14, LDOC1 | 7 |
GO:0030593 | neutrophil chemotaxis | 0.034 | S100A9, CXCL5, RIPOR2 | 3 |
GO:0072678 | T cell migration | 0.034 | RIPOR2, PYCARD, MSN | 3 |
GO:0006954 | inflammatory response | 0.038 | IL17A, S100A9, THBS1, PTGS2, ALOX5AP, CD163, PTGS1, PTAFR, PTGIS, SOCS3, PYCARD, LDLR, IRAK2, CYBB | 14 |
GO:0030203 | glycosaminoglycan metabolic process | 0.040 | LYVE1, DSE, SLC35D1, UGDH | 4 |
GO:0050954 | sensory perception of mechanical stimulus | 0.040 | RIPOR2, COL1A1, FYN, SNAI2 | 4 |
GO:0071230 | cellular response to amino acid stimulus | 0.041 | COL1A2, COL1A1, COL4A1 | 3 |
GO:0006935 | chemotaxis | <0.001 | CXCL11b, CXCL10, F2RL1, CXCL9, MSTN, NFIB, MET, CCL5, PDGFA, CXCR3, SCN1B | 11 |
GO:0050921 | positive regulation of chemotaxis | <0.001 | CXCL10, F2RL1, MSTN, MET, CCL5, CXCR3 | 6 |
GO:0050920 | regulation of chemotaxis | <0.001 | CXCL10, F2RL1, MSTN, MET, CCL5, CXCR3 | 6 |
GO:0032103 | positive regulation of response to external stimulus | 0.001 | CXCL10, F2RL1, MSTN, C3, MET, CCL5, CXCR3 | 7 |
GO:0050900 | leukocyte migration | 0.001 | CXCL11, CXCL10, F2RL1, MSTN, GATA3, CCL5, CXCR3 | 7 |
GO:0060326 | cell chemotaxis | 0.004 | CXCL11, CXCL10, MSTN, MET, CCL5 | 5 |
GO:0002690 | positive regulation of leukocyte chemotaxis | 0.005 | CXCL10, MSTN, CCL5 | 3 |
GO:1990868 | response to chemokine | 0.005 | CX3CR1, CCL5, CXCR3 | 3 |
GO:1990869 | cellular response to chemokine | 0.005 | CX3CR1, CCL5, CXCR3 | 3 |
GO:0032101 | regulation of response to external stimulus | 0.006 | CXCL10, F2RL1, MSTN, S100B, C3, GATA3, MET, CCL5, PDGFA, CXCR3 | 10 |
GO:0002688 | regulation of leukocyte chemotaxis | 0.010 | CXCL10, MSTN, CCL5 | 3 |
GO:0002685 | regulation of leukocyte migration | 0.012 | CXCL10, MSTN, CCL5, CXCR3 | 4 |
GO:0030595 | leukocyte chemotaxis | 0.013 | CXCL11, CXCL10, MSTN, CCL5 | 4 |
GO:0002687 | positive regulation of leukocyte migration | 0.016 | CXCL10, MSTN, CCL5 | 3 |
GO:0007606 | sensory perception of chemical stimulus | 0.027 | SCNN1G, SCNN1B | 2 |
GO:0036230 | granulocyte activation | 0.027 | F2RL1, CCL5 | 2 |
GO:0071622 | regulation of granulocyte chemotaxis | 0.027 | MSTN, CCL5 | 2 |
GO:1905517 | macrophage migration | 0.027 | MSTN, CCL5 | 2 |
GO:0002673 | regulation of acute inflammatory response | 0.032 | S100B, C3 | 2 |
GO:0050918 | positive chemotaxis | 0.034 | CXCL10, MET, CCL5 | 3 |
GO:0009605 | response to external stimulus | 0.039 | CXCL11, CXCL10, F2RL1, CXCL9, MSTN, S100B, C3, NFIB, REEP6, GATA3, AQP3, MET, IKZF3, CCL5, PDGFA, CXCR3, SCN1B | 17 |
GO:0072678 | T cell migration | 0.043 | CXCL11, CXCL10 | 2 |
GO:2000401 | regulation of lymphocyte migration | 0.048 | CXCL10, CCL5 | 2 |
GO:1904062 | regulation of cation transmembrane transport | 0.048 | CXCL11, CXCL10, CXCL9, CXCR3 | 4 |
GO:0042379 | chemokine receptor binding | <0.001 | CXCL11, CXCL10, CXCL9, CCL5 | 4 |
Pathway ID | Pathway | P-Value | Gene Name | Number |
---|---|---|---|---|
bta04666 | Fc gamma R-mediated phagocytosis | <0.001 | PLA2G4Aa, MARCKSL1, VASP, SYK, PIK3R3, FCGR1A, WASF1, CFL1, ASAP1, NCF1, ARPC5, LYN, ARPC2, MAP2K1 | 14 |
bta04668 | TNF signaling pathway | <0.001 | CXCL2, SELE, MMP3, PTGS2, CXCL6, VEGFC, SOCS3, MMP14, CASP3, LIF, CSF1, PIK3R3, MAP3K8, TNFAIP3, MAP2K3, MAP2K1 | 16 |
bta04066 | HIF-1 signaling pathway | <0.001 | SERPINE1, LDHA, PFKFB3, PGK1, HIF1A, PFKP, TFRC, PIK3R3, MKNK1, ALDOA, ENO1, ENO2, CYBB, MAP2K1 | 14 |
bta04015 | Rap1 signaling pathway | <0.001 | ITGAM, THBS1, PDGFRA, ID1, ITGB3, PDGFD, VEGFC, APBB1IP, FYB, PDGFRB, VASP, CSF1, PIK3R3, SIPA1L2, RAP1B, PFN1, MAP2K3, ITGB1, TLN1, PRKD3, MAP2K1 | 21 |
bta04657 | IL-17 signaling pathway | <0.001 | CXCL2, CSF3, IL17A, MMP3, S100A9, FOSL1, PTGS2, CXCL6, MMP1, CASP3, TNFAIP3, MAPK6 | 12 |
bta05020 | Prion diseases | 0.001 | NCAM1, LAMC1, FYN, PRKACB, HSPA5, MAP2K1 | 6 |
bta04664 | Fc epsilon RI signaling pathway | 0.002 | ALOX5AP, FCER1A, PLA2G4A, FYN, SYK, PIK3R3, MAP2K3, LYN, MAP2K1 | 9 |
bta04151 | PI3K–Akt signaling pathway | 0.002 | CSF3, THBS2, BDNF, THBS1, ITGA5, IL2RA, PDGFRA, EPOR, ITGB3, PDGFD, VEGFC, COL1A2, LAMA4, ITGA9, LAMC1, GNG2, COL1A1, PDGFRB, CSF1, SYK, PIK3R3, YWHAG, GNB4, COL4A1, ITGB1, CDK2, MAP2K1 | 27 |
bta05134 | Legionellosis | 0.002 | CXCL2, ITGAM, NAIP, CASP3, PYCARD, HSPA8, CD14, SAR1A | 8 |
bta05146 | Amoebiasis | 0.002 | SERPINB4, CXCL2, ITGAM, COL1A2, CASP3, LAMA4, LAMC1, COL1A1, PRKACB, PIK3R3, CD14, COL4A1 | 12 |
bta04670 | Leukocyte transendothelial migration | 0.005 | ITGAM, MMP2, JAM3, VASP, PIK3R3, MSN, RAP1B, PTPN11, ITGB1, NCF1, CYBB | 11 |
bta04062 | Chemokine signaling pathway | 0.007 | CXCR2, CXCL2, CCR1, CXCL6, CCL16, PREX1, GNG2, ARRB2, PRKACB, PIK3R3, RAP1B, GNB4, NCF1, LYN, MAP2K1 | 15 |
bta05100 | Bacterial invasion of epithelial cells | 0.008 | ITGA5, CBL, PIK3R3, WASF1, DNM3, ITGB1, ARPC5, ARPC2 | 8 |
bta04145 | Phagosome | 0.008 | THBS2, ITGAM, THBS1, ITGA5, ITGB3, SCARB1, TUBB3, TFRC, FCGR1A, CD14, ITGB1, ATP6V1C1, NCF1, CYBB | 14 |
bta05165 | Human papillomavirus infection | 0.011 | THBS2, THBS1, PTGS2, WNT2, ITGA5, ITGB3, PKM, COL1A2, CASP3, LAMA4, ITGA9, LAMC1, COL1A1, PDGFRB, PRKACB, NOTCH2, PIK3R3, COL4A1, MX2, ITGB1, ATP6V1C1, CDK2, MAP2K1 | 23 |
bta05167 | Kaposi sarcoma-associated herpesvirus infection | 0.023 | CXCL2, CCR1, PTGS2, E2F3, CASP3, PREX1, GNG2, HIF1A, RCAN1, SYK, PIK3R3, GNB4, MAPKAPK2, LYN, MAP2K1 | 15 |
bta05323 | Rheumatoid arthritis | 0.023 | CXCL2, IL17A, MMP3, CXCL6, MMP1, CD80, CSF1, ATP6V1C1, IL11 | 9 |
bta04392 | Hippo signaling pathway- multiple species | 0.026 | RASSF2, WTIP, TEAD3, WWTR1 | 4 |
bta04014 | Ras signaling pathway | 0.030 | BDNF, PDGFRA, PDGFD, VEGFC, PLA2G4A, GNG2, PDGFRB, PRKACB, CSF1, PIK3R3, RAP1B, GNB4, ABL1, PTPN11, ABL2, MAP2K1 | 16 |
bta04061 | Viral protein interaction with cytokine and cytokine receptor | 0.033 | CXCR2, CXCL2, CCR1, CXCL6, IL2RA, CCL16, IL10RA, CSF1 | 8 |
bta05140 | Leishmaniasis | 0.033 | ITGAM, PTGS2, MARCKSL1, FCGR1A, ITGB1, NCF1, CYBB | 7 |
bta05145 | Toxoplasmosis | 0.035 | IL10RA, CASP3, LAMA4, LAMC1, LDLR, SOCS1, MAP2K3, HSPA8, ITGB1 | 9 |
bta04060 | Cytokine–cytokine receptor interaction | <0.001 | CXCL11b, CX3CR1, CXCL10, CXCL9, NGFR, CXCL14, MSTN, XCL1, IL17RE, BMP3, TNFRSF9, TNFSF10, GHR, CXCR6, CCL5, TNFRSF19, CXCR3, TGFB2 | 18 |
bta04061 | Viral protein interaction with cytokine and cytokine receptor | <0.001 | CXCL11, CX3CR1, CXCL10, CXCL9, CXCL14, XCL1, TNFSF10, CCL5, CXCR3 | 9 |
bta04062 | Chemokine signaling pathway | 0.001 | CXCL11, CX3CR1, CXCL10, CXCL9, CXCL14, XCL1, ITK, PRKCZ, CXCR6, CCL5, CXCR3 | 11 |
bta04015 | Rap1 signaling pathway | 0.004 | FGFR4, NGFR, PRKCZ, FGFR2, MET, LPAR2, TLN2, INSR, PDGFA, MAGI3, CTNND1 | 11 |
bta04670 | Leukocyte trans endothelial migration | 0.007 | CLDN1, ITK, OCLN, CLDN3, TXK, EZR, CTNND1 | 7 |
bta05340 | Primary immunodeficiency | 0.009 | CD8A, BLNK, CIITA, TAP1 | 4 |
bta01521 | EGFR tyrosine kinase inhibitor resistance | 0.020 | ERBB3, FGFR2, MET, PDGFA, GAB1 | 5 |
bta04010 | MAPK signaling pathway | 0.028 | FGFR4, ERBB3, NGFR, RPS6KA6, FGFR2, MET, INSR, MAP3K13, PDGFA, MAP3K1, TGFB2 | 11 |
bta04390 | Hippo signaling pathway | 0.034 | RASSF6, PRKCZ, DLG3, PPP2R2B, TCF7, TCF7L2, TGFB2 | 7 |
bta04151 | PI3K–Akt signaling pathway | 0.035 | FGFR4, ERBB3, NGFR, GHR, FGFR2, PPP2R2B, MET, LPAR2, INSR, ITGA6, LAMC2, PDGFA, ITGA3 | 13 |
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Wang, X.; Fan, Y.; He, Y.; Han, Z.; Gong, Z.; Peng, Y.; Meng, Y.; Mao, Y.; Yang, Z.; Yang, Y. Integrative Analysis of miRNA and mRNA Expression Profiles in Mammary Glands of Holstein Cows Artificially Infected with Staphylococcus aureus. Pathogens 2021, 10, 506. https://doi.org/10.3390/pathogens10050506
Wang X, Fan Y, He Y, Han Z, Gong Z, Peng Y, Meng Y, Mao Y, Yang Z, Yang Y. Integrative Analysis of miRNA and mRNA Expression Profiles in Mammary Glands of Holstein Cows Artificially Infected with Staphylococcus aureus. Pathogens. 2021; 10(5):506. https://doi.org/10.3390/pathogens10050506
Chicago/Turabian StyleWang, Xiaolong, Yongliang Fan, Yifan He, Ziyin Han, Zaicheng Gong, Yalan Peng, Yining Meng, Yongjiang Mao, Zhangping Yang, and Yi Yang. 2021. "Integrative Analysis of miRNA and mRNA Expression Profiles in Mammary Glands of Holstein Cows Artificially Infected with Staphylococcus aureus" Pathogens 10, no. 5: 506. https://doi.org/10.3390/pathogens10050506
APA StyleWang, X., Fan, Y., He, Y., Han, Z., Gong, Z., Peng, Y., Meng, Y., Mao, Y., Yang, Z., & Yang, Y. (2021). Integrative Analysis of miRNA and mRNA Expression Profiles in Mammary Glands of Holstein Cows Artificially Infected with Staphylococcus aureus. Pathogens, 10(5), 506. https://doi.org/10.3390/pathogens10050506