Identification of key genes in bovine mammary epithelial cells challenged with <i>Escherichia coli</i> and <i>Staphylococcus aureus</i> by integrated bioinformatics analysis

Chen, Zeshi; Bian, Zhengyu; Chen, Xiuli; Li, Boling; Li, Lianbin

doi:10.37496/rbz5220220064

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Breeding and genetics • R. Bras. Zootec. 52 • 2023 • https://doi.org/10.37496/rbz5220220064 copy

Identification of key genes in bovine mammary epithelial cells challenged with Escherichia coli and Staphylococcus aureus by integrated bioinformatics analysis

Authorship SCIMAGO INSTITUTIONS RANKINGS

ABSTRACT

This study integrated four microarray datasets by Robust Rank Aggregation (RRA) method to identify the differentially expressed genes (DEG) in bovine mammary epithelial (BME) cells in response to Escherichia coli and Staphylococcus aureus infection. Furthermore, the GO function and KEGG pathway enrichment analysis of the integrated DEG were performed. Finally, the protein-protein interaction (PPI) network was constructed. A total of 72 integrated DEG were identified from the four datasets. The most significantly enriched terms within the integrated DEG were mainly involved in the immune response. The PPI network of DEG was constructed with 53 nodes. Seventeen genes, which constitute a significant module, were identified as hub genes. Among them, CD40, CXCL6, and NFKBIZ were further screened as the key genes and have the potential to become biomarkers of E. coli and S. aureus mastitis, considering the specificity of biomarkers for diseases. The identified key genes and pathways in this study can assist in the search for biomarkers for mastitis diagnosis and disease resistance breeding.

biomarkers; differentially expressed genes; E. coli; mastitis; S. aureus

Accession number	Dataset name	Pathogen	Treatment time (h)	Samples¹ (Con:Tr)	Reference
GSE24560	GSE24560E	Heat-inactivated E. coli isolates	6 and 24	18:20	Brand et al. (2011)Brand, B.; Hartmann, A.; Repsilber, D.; Griesbeck-Zilch, B.; Wellnitz, O.; Kuhn, C.; Ponsuksili, S.; Meyer, H. H. and Schwerin, M. 2011. Comparative expression profiling of E. coli and S. aureus inoculated primary mammary gland cells sampled from cows with different genetic predispositions for somatic cell score. Genetics Selection Evolution 43:24. https://doi.org/10.1186/1297-9686-43-24 https://doi.org/10.1186/1297-9686-43-24...
GSE24560	GSE24560S	Heat-inactivated S. aureus M60	6 and 24	18:20

GSE25413	GSE25413E	Heat-inactivated S. aureus strain 1027	6 and 24	6:6	Gunther et al. (2011)Gunther, J.; Esch, K.; Poschadel, N.; Petzl, W.; Zerbe, H.; Mitterhuemer, S.; Blum, H. and Seyfert, H. M. 2011. Comparative kinetics of Escherichia coli- and Staphylococcus aureus-specific activation of key immune pathways in mammary epithelial cells demonstrates that S. aureus elicits a delayed response dominated by interleukin-6 (IL-6) but not by IL-1A or tumor necrosis factor alpha. Infection and Immunity 79:695-707. https://doi.org/10.1128/IAI.01071-10 https://doi.org/10.1128/IAI.01071-10...
GSE25413	GSE25413S	Heat-inactivated E. coli strain 1303	6 and 24	6:6

Integrated DEG	Gene symbol
Upregulated	SAA3, CXCL2, GRO1, CCL20, RND1, ZC3H12A, CXCL8, CCL2, CXCL5, LTF, CCL5, NFKBIZ, S100A9, MX2, HP, IL1A, IL6, IL1B, IFI44, CD40, BCL2A1, ISG15, LOC100298356, S100A8, NFKB2, LGALS9, CFB, RTP4, MX1, TNF, CYP1A1, LTB, RSAD2, SOD2, NFKBIA, TMEM140, TNIP1, IKBKE, PLPP3, TLR2, LPO, SLC6A14, BIRC3, C2, MBP, CHI3L1, SLC46A2, PPP1R3C, ARRDC2, NOS2, USP18, LOC100847724, DHX58, DAPP1, NFKBIE, SCML4, PLAC8, CDC42EP2, TAP

Downregulated	SPTBN1, MAPKAPK5, MYO1B, ORC2, MAP2K6, CACNA2D1, TUBGCP5, NDFIP1///DIRAS3, SAFB2///SAFB, PRPF8, APP, FRMD3, ZEB1

Category	Term	P-value	Gene
BP	GO:0006954~inflammatory response	1.13E-16	CD40, CXCL8, NOS2, CCL20, CCL5, NFKBIZ, CCL2, GRO1, CXCL2, NFKB2, TLR2
	GO:0006955~immune response	6.48E-11	IL1A, CD40, CXCL8, IL1B, CCL2, GRO1, CXCL2, TNF
	GO:0070098~chemokine-mediated signaling pathway	1.55E-09	CXCL8, CCL20, CCL5, CCL2, CXCL2
	GO:0060326~cell chemotaxis	2.70E-07	CCL20, CCL2, GRO1, CXCL2
	GO:0071347~cellular response to interleukin-1	2.70E-07	IL6, CXCL8, CCL20, CCL5, CCL2

KEGG pathway	bta05134:Legionellosis	9.51E-16	NFKBIA, IL6, CXCL8, IL1B, GRO1, CXCL2, TNF, NFKB2, TLR2
	bta04668:TNF signaling pathway	3.96E-13	NFKBIA, IL6, CCL20, CCL5, IL1B, CCL2, GRO1, CXCL2, TNF
	bta05142:Chagas disease (American trypanosomiasis)	6.52E-13	NFKBIA, IL6, CXCL8, NOS2, CCL5, IL1B, CCL2, TNF, TLR2
	bta05323:Rheumatoid arthritis	1.03E-11	IL1A, IL6, CXCL8, CCL20, CCL5, IL1B, CCL2, TNF, TLR2
	bta04620:Toll-like receptor signaling pathway	2.34E-11	NFKBIA, CD40, IL6, CXCL8, CCL5, IL1B, TNF, TLR2

Gene symbol	Gene description	Mean LogFC	Degree
TNF	Tumor necrosis factor	1.8	76
IL1B	Interleukin-1 beta	2.8	60
CXCL8	Interleukin-8	3.9	60
IL6	Interleukin-6	3.0	56
GRO1	Growth-regulated protein homolog beta	3.4	52
NFKBIA	Bos taurus nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor	1.7	50
CCL2	C-C motif chemokine 20	2.3	48
CXCL2	Growth-regulated protein homolog gamma	4.4	46
CCL20	C-C motif chemokine 20	3.7	46
TLR2	Cooperates with LY96 to mediate the innate immune response to bacterial lipoproteins and other microbial cell wall components.	2.0	46
IL1A	Interleukin-1 alpha	2.7	44
CCL5	C-C motif chemokine 5	4.6	44
CD40	Receptor for TNFSF5/CD40LG	1.5	40
CXCL6	C-X-C motif chemokine 6	2.5	38
NFKB2	Nuclear factor of kappa light polypeptide gene enhancer in B-cells 2	1.2	36
NFKBIZ	NF-kappa-B inhibitor zeta	1.8	36
NOS2	Produces nitric oxide (NO)	3.6	26

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[1] * Corresponding author: lianbin@hainanu.edu.cn