Using WGCNA to analyze changes of FMDV infection pathway in cattle

doi:10.3969/j.issn.1004-1524.2021.09.06

Acta Agriculturae Zhejiangensis ›› 2021, Vol. 33 ›› Issue (9): 1617-1624.DOI: 10.3969/j.issn.1004-1524.2021.09.06

• Animal Science • Previous Articles Next Articles

Using WGCNA to analyze changes of FMDV infection pathway in cattle

YANG Shenghai¹^,²(), LIU Xilan², ZHANG Yong¹^,^*()

1. College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
2. China Agricultural Vet. Bio. Science and Technology Co., Ltd., Lanzhou 730046, China

Received:2020-06-18 Online:2021-09-25 Published:2021-10-09
Contact: ZHANG Yong

Abstract

Abstract:

In this study, GSE83514 data set was downloaded from Gene Expression Omnibus (GEO) database, and Weighted Gene Co-Expression Network Analysis (WGCNA) was used to explore the related modules and hub genes of bovine foot-and-mouth disease virus (FMDV) infection. The results showed that through constructing WGCNA co-expression network, the genes of Darkred module and Green module were found to be negatively and positively related to bovine FMDV infection respectively. MFSD4 and RHOH were the hub gene of Darkred module and Green module, respectively. Twenty Gene Ontology (GO) terms and 14 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched in those two modules. DNA replication signaling pathway was the only pathway enriched in both modules. The results of this study provided a bioinformatics basis for investigating the molecular mechanism of bovine FMDV infection, and the selected hub genes, MFSD4 and RHOH, were expected to be therapeutic biomarker for inhibiting the infection of FMDV.

Key words: foot-and-mouth disease virus of bovine, RNA-seq, weighted gene co-expression network analysis, data excavation, hub gene

CLC Number:

S858.23

YANG Shenghai, LIU Xilan, ZHANG Yong. Using WGCNA to analyze changes of FMDV infection pathway in cattle[J]. Acta Agriculturae Zhejiangensis, 2021, 33(9): 1617-1624.

Figures/Tables 5

Fig.1 Screening of soft thresholds

Fig.2 Gene clustering tree and module construction A, Cluster dendrogram; B, Dynamic tree cut; C, Merged dynamic.

Fig.3 Results of WGCNA and hub gene in each module A, Heatmap of the correlation between module eigengenes and clinical traits; B, Scatter plot of module eigengenes in the Darkred module; C, Scatter plot of module eigengenes in the Green module; D,Network of genes in Darkred module; E, Network of genes in Green module.

Fig.4 GO enrichment bubble diagram==140A, GO enrichment bubble diagram of Darkred module; B, GO enrichment bubble diagram of Green module.

Fig.5 KEGG enrichment bubble diagram A, KEGG enrichment bubble diagram of Darkred module; B,KEGG enrichment bubble diagram of Green module.

References 26

[1]	QUAN M, MURPHY C M, ZHANG Z, et al. Influence of exposure intensity on the efficiency and speed of transmission of Foot-and-mouth disease[J]. Journal of Comparative Pathology, 2009, 140(4):225-237. DOI URL
[2]	ARMSTRONG R M, SAMUEL A R, CARPENTER W C, et al. A comparative study of serological and biochemical methods for strain differentiation of foot-and-mouth disease type A viruses[J]. Veterinary Microbiology, 1994, 39(3/4):285-298. DOI URL
[3]	BELSHAM G J. Translation and replication of FMDV RNA[M]//Current topics in microbiology and immunology. Berlin/Heidelberg: Springer-Verlag:43-70.
[4]	RYAN M D, BELSHAM G J, KING A M. Specificity of enzyme-substrate interactions in foot-and-mouth disease virus polyprotein processing[J]. Virology, 1989, 173(1):35-45. DOI URL
[5]	STEINBERGER J, GRISHKOVSKAYA I, CENCIC R, et al. Foot-and-mouth disease virus leader proteinase: Structural insights into the mechanism of intermolecular cleavage[J]. Virology, 2014, 468/469/470:397-408.
[6]	ACHARYA R, FRY E, STUART D, et al. The three-dimensional structure of foot-and-mouth disease virus at 2.9 A resolution[J]. Nature, 1989, 337(6209):709-716. DOI URL
[7]	HAN S C, GUO H C, SUN S Q. Three-dimensional structure of foot-and-mouth disease virus and its biological functions[J]. Archives of Virology, 2015, 160(1):1-16. DOI URL
[8]	周建华, 丛国正, 王光华, 等. 口蹄疫病毒对牦牛持续性感染的分析[J]. 浙江农业科学, 2007, 48(4):468-471.
	ZHOU J H, CONG G Z, WANG G H, et al. Analysis of persistent infection of foot-and-mouth disease virus in Yaks[J]. Journal of Zhejiang Agricultural Sciences, 2007, 48(4):468-471.(in Chinese)
[9]	韩玲玲. 口蹄疫病毒持续感染建立的分子机制探索[D]. 武汉: 武汉大学, 2018.
	HAN L L. Exploring the molecular mechanism for the establishment of persistent infection of foot-and-mouth disease virus[D]. Wuhan: Wuhan University, 2018. (in Chinese with English abstract)
[10]	STENFELDT C, DIAZ-SAN SEGUNDO F, DE LOS SANTOS T, et al. The pathogenesis of foot-and-mouth disease in pigs[J]. Frontiers in Veterinary Science, 2016, 3:41.
[11]	高雪梅. 口蹄疫病毒的致病分子机制[J]. 内蒙古电大学刊, 2008(1):50-53.
	GAO X M. Molecular mechanism of foot-and-mouth disease virus[J]. Journal of Inner Mongolia Radio & TV University, 2008(1):50-53.(in Chinese)
[12]	NFON C K, TOKA F N, KENNEY M, et al. Loss of plasmacytoid dendritic cell function coincides with lymphopenia and viremia during foot-and-mouth disease virus infection[J]. Viral Immunology, 2010, 23(1):29-41. DOI URL
[13]	SEI J J, WATERS R A, KENNEY M, et al. Effect of foot-and-mouth disease virus infection on the frequency, phenotype and function of circulating dendritic cells in cattle[J]. PLoS One, 2016, 11(3):e0152192. DOI URL
[14]	TOKA F N, GOLDE W T. Cell mediated innate responses of cattle and swine are diverse during foot-and-mouth disease virus (FMDV) infection: a unique landscape of innate immunity[J]. Immunology Letters, 2013, 152(2):135-143. DOI URL
[15]	TOKA F N, NFON C, DAWSON H, et al. Natural killer cell dysfunction during acute infection with foot-and-mouth disease virus[J]. Clinical and Vaccine Immunology, 2009, 16(12):1738-1749. DOI URL
[16]	GRANT C F, LEFEVRE E A, CARR B V, et al. Assessment of T-dependent and T-independent immune responses in cattle using a B cell ELISPOT assay[J]. Veterinary Research, 2012, 43(1):1-9. DOI URL
[17]	JULEFF N, WINDSOR M, LEFEVRE E A, et al. Foot-and-mouth disease virus can induce a specific and rapid CD4+T-cell-independent neutralizing and isotype class-switched antibody response in naïve cattle[J]. Journal of Virology, 2009, 83(8):3626-3636. DOI URL
[18]	SHARMA A K, BHATT M, SANKAR M, et al. Kinetics of Interferon gamma and Interleukin-21 response following foot and mouth disease virus infection[J]. Microbial Pathogenesis, 2018, 125:20-25. DOI URL
[19]	RODRÍGUEZ PULIDO M, SÁIZ M. Molecular mechanisms of foot-and-mouth disease virus targeting the host antiviral response[J]. Frontiers in Cellular and Infection Microbiology, 2017, 7:252. DOI URL
[20]	HAN L L, XIN X, WANG H L, et al. Cellular response to persistent foot-and-mouth disease virus infection is linked to specific types of alterations in the host cell transcriptome[J]. Scientific Reports, 2018, 8(1):1-13.
[21]	STOECKLE C, GEERING B, YOUSEFI S, et al. RhoH is a negative regulator of eosinophilopoiesis[J]. Cell Death and Differentiation, 2016, 23(12):1961-1972. DOI URL
[22]	GU Y, JASTI A C, JANSEN M, et al. RhoH, a hematopoietic-specific Rho GTPase, regulates proliferation, survival, migration, and engraftment of hematopoietic progenitor cells[J]. Blood, 2005, 105(4):1467-1475. DOI URL
[23]	ZHANG T, TIAN L F, HU G, et al. Microvascular endothelial cells play potential immunoregulatory roles in the immune response to foot-and-mouth disease vaccines[J]. Cell Biochemistry and Function, 2011, 29(5):394-399. DOI URL
[24]	KANDA M, SHIMIZU D, TANAKA H, et al. Metastatic pathway-specific transcriptome analysis identifies MFSD4 as a putative tumor suppressor and biomarker for hepatic metastasis in patients with gastric cancer[J]. Oncotarget, 2016, 7(12):13667-13679. DOI URL
[25]	ARZT J, BAXT B, GRUBMAN M J, et al. The pathogenesis of foot-and-mouth disease II: viral pathways in swine, small ruminants, and wildlife; myotropism, chronic syndromes, and molecular virus-host interactions[J]. Transboundary and Emerging Diseases, 2011, 58(4):305-326. DOI URL
[26]	MEDINA G N, SEGUNDO F D S, STENFELDT C, et al. The different tactics of foot-and-mouth disease virus to evade innate immunity[J]. Frontiers in Microbiology, 2018, 9:2644. DOI URL

Using WGCNA to analyze changes of FMDV infection pathway in cattle

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