YWHAH, a member of 14-3-3 family proteins, and PSME2, the proteasome activator subunit 2, are key host factors of Japanese encephalitis virus infection
Abstract Background Host response to virus infection is key to the effective control and eventual elimination of viruses or infected cells; however, the underlying mechanism of Japanese encephalitis virus (JEV) infection remains unclear. Methods In the present study, short time-series expression was...
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| Format: | Article |
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BMC
2023-07-01
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| Series: | BMC Medical Genomics |
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| Online Access: | https://doi.org/10.1186/s12920-023-01589-6 |
| _version_ | 1797778620028026880 |
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| author | Chaoyue Liu Yanhong Yang Qianqian Li Weimin Hu Jinxia Chang Rong Chen Hong Zhu Mingfei Xu |
| author_facet | Chaoyue Liu Yanhong Yang Qianqian Li Weimin Hu Jinxia Chang Rong Chen Hong Zhu Mingfei Xu |
| author_sort | Chaoyue Liu |
| collection | DOAJ |
| description | Abstract Background Host response to virus infection is key to the effective control and eventual elimination of viruses or infected cells; however, the underlying mechanism of Japanese encephalitis virus (JEV) infection remains unclear. Methods In the present study, short time-series expression was analyzed by R software to obtain two groups of differentially expressed genes (DEGs) [upregulated/downregulated] during the entire process of JEV infection based on the data in the Gene Expression Omnibus database. GO enrichment and KEGG pathway, protein interactions and hub genes selection were analyzed by DAVID, STRING and Cytoscape respectively. Interactions of the JEV and host proteins, and the microRNAs that target Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activating protein Eta (YWHAH) and Proteasome activator subunit 2(PSME2) were predicted by P-hipster and ENCORI, respectively. Expression levels of YWHAH and PSME2 were analyzed using the HPA database and RT-qPCR assay. Results Two groups of continuously changed DEGs during entire process of JEV infection were obtained. Continuously upregulated cluster was mainly related to regulation of transcription, immune response and inflammatory response; and the continuous downregulated group mainly including intracellular protein transport and signal transduction, several proteolysis pathways. As targets of several microRNAs, the downregulated-YWHAH and the upregulated-PSME2 were related to host and JEV proteins to affect several pathways after JEV infection. Conclusions YWHAH and PSME2 are key host factors of JEV infection based on their continuously differentially expressed pattern, interactions with multiple JEV proteins, and as members of the hub genes. Our results provide valuable information for further studies on the interactions between viruses and host. |
| first_indexed | 2024-03-12T23:20:03Z |
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| id | doaj.art-20ddcb111b24422d9bc4d9c9e03e1eb5 |
| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-12T23:20:03Z |
| publishDate | 2023-07-01 |
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| series | BMC Medical Genomics |
| spelling | doaj.art-20ddcb111b24422d9bc4d9c9e03e1eb52023-07-16T11:30:53ZengBMCBMC Medical Genomics1755-87942023-07-0116111310.1186/s12920-023-01589-6YWHAH, a member of 14-3-3 family proteins, and PSME2, the proteasome activator subunit 2, are key host factors of Japanese encephalitis virus infectionChaoyue Liu0Yanhong Yang1Qianqian Li2Weimin Hu3Jinxia Chang4Rong Chen5Hong Zhu6Mingfei Xu7Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical CollegeInstitute of Basic Medicine and Forensic Medicine, North Sichuan Medical CollegeInstitute of Basic Medicine and Forensic Medicine, North Sichuan Medical CollegeInstitute of Basic Medicine and Forensic Medicine, North Sichuan Medical CollegeInstitute of Basic Medicine and Forensic Medicine, North Sichuan Medical CollegeInstitute of Basic Medicine and Forensic Medicine, North Sichuan Medical CollegeInstitute of Basic Medicine and Forensic Medicine, North Sichuan Medical CollegeInstitute of Basic Medicine and Forensic Medicine, North Sichuan Medical CollegeAbstract Background Host response to virus infection is key to the effective control and eventual elimination of viruses or infected cells; however, the underlying mechanism of Japanese encephalitis virus (JEV) infection remains unclear. Methods In the present study, short time-series expression was analyzed by R software to obtain two groups of differentially expressed genes (DEGs) [upregulated/downregulated] during the entire process of JEV infection based on the data in the Gene Expression Omnibus database. GO enrichment and KEGG pathway, protein interactions and hub genes selection were analyzed by DAVID, STRING and Cytoscape respectively. Interactions of the JEV and host proteins, and the microRNAs that target Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activating protein Eta (YWHAH) and Proteasome activator subunit 2(PSME2) were predicted by P-hipster and ENCORI, respectively. Expression levels of YWHAH and PSME2 were analyzed using the HPA database and RT-qPCR assay. Results Two groups of continuously changed DEGs during entire process of JEV infection were obtained. Continuously upregulated cluster was mainly related to regulation of transcription, immune response and inflammatory response; and the continuous downregulated group mainly including intracellular protein transport and signal transduction, several proteolysis pathways. As targets of several microRNAs, the downregulated-YWHAH and the upregulated-PSME2 were related to host and JEV proteins to affect several pathways after JEV infection. Conclusions YWHAH and PSME2 are key host factors of JEV infection based on their continuously differentially expressed pattern, interactions with multiple JEV proteins, and as members of the hub genes. Our results provide valuable information for further studies on the interactions between viruses and host.https://doi.org/10.1186/s12920-023-01589-6Japanese encephalitis virusHost responseDifferential ExpressionBioinformatics |
| spellingShingle | Chaoyue Liu Yanhong Yang Qianqian Li Weimin Hu Jinxia Chang Rong Chen Hong Zhu Mingfei Xu YWHAH, a member of 14-3-3 family proteins, and PSME2, the proteasome activator subunit 2, are key host factors of Japanese encephalitis virus infection BMC Medical Genomics Japanese encephalitis virus Host response Differential Expression Bioinformatics |
| title | YWHAH, a member of 14-3-3 family proteins, and PSME2, the proteasome activator subunit 2, are key host factors of Japanese encephalitis virus infection |
| title_full | YWHAH, a member of 14-3-3 family proteins, and PSME2, the proteasome activator subunit 2, are key host factors of Japanese encephalitis virus infection |
| title_fullStr | YWHAH, a member of 14-3-3 family proteins, and PSME2, the proteasome activator subunit 2, are key host factors of Japanese encephalitis virus infection |
| title_full_unstemmed | YWHAH, a member of 14-3-3 family proteins, and PSME2, the proteasome activator subunit 2, are key host factors of Japanese encephalitis virus infection |
| title_short | YWHAH, a member of 14-3-3 family proteins, and PSME2, the proteasome activator subunit 2, are key host factors of Japanese encephalitis virus infection |
| title_sort | ywhah a member of 14 3 3 family proteins and psme2 the proteasome activator subunit 2 are key host factors of japanese encephalitis virus infection |
| topic | Japanese encephalitis virus Host response Differential Expression Bioinformatics |
| url | https://doi.org/10.1186/s12920-023-01589-6 |
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