Cell deconvolution-based integrated time-series network of whole blood transcriptome reveals systemic antiviral activities and cell-specific immunological changes against PRRSV infection
Abstract Porcine reproductive and respiratory syndrome (PRRS) causes significant economic losses in the swine industry. However, the molecular mechanisms behind the common and cell type-specific systemic responses during PRRS virus (PRRSV) infection are not well understood. In this study, we collect...
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BMC
2025-01-01
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| Series: | Veterinary Research |
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| Online Access: | https://doi.org/10.1186/s13567-025-01451-w |
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| author | Byeonghwi Lim Chiwoong Lim Min-Jae Jang Young-Jun Seo Do-Young Kim Christopher K. Tuggle Kyu-Sang Lim Jun-Mo Kim |
| author_facet | Byeonghwi Lim Chiwoong Lim Min-Jae Jang Young-Jun Seo Do-Young Kim Christopher K. Tuggle Kyu-Sang Lim Jun-Mo Kim |
| author_sort | Byeonghwi Lim |
| collection | DOAJ |
| description | Abstract Porcine reproductive and respiratory syndrome (PRRS) causes significant economic losses in the swine industry. However, the molecular mechanisms behind the common and cell type-specific systemic responses during PRRS virus (PRRSV) infection are not well understood. In this study, we collected viremia data, antibody levels, and whole-blood RNA-seq data obtained from eight PRRSV-infected piglets. We utilised a cell deconvolution approach to calculate cell type enrichment, constructed a time-serial gene co-expression network with differentially expressed genes, and conducted functional annotations. Three significant modules were identified within the network. The changes associated with viremia revealed an upregulated expression of genes related to antiviral activity. In the T-cell- and NK-cell-specific modules, infection led to an increased T-cell population and upregulation of genes related to T-cell defence responses. Conversely, in the monocyte- and neutrophil-specific module, genes involved in inflammatory responses were downregulated due to a decrease in monocyte proportion. This study highlights the time-series antiviral activities associated with viremia and the transcriptomic changes associated with immune responses in specific cell types. The findings provide comprehensive insights into host responses to PRRSV infection, including diagnostic biomarkers. |
| format | Article |
| id | doaj-art-50ed281f00864779ba070df71fec363d |
| institution | Kabale University |
| issn | 1297-9716 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Veterinary Research |
| spelling | doaj-art-50ed281f00864779ba070df71fec363d2025-01-26T12:47:51ZengBMCVeterinary Research1297-97162025-01-0156111210.1186/s13567-025-01451-wCell deconvolution-based integrated time-series network of whole blood transcriptome reveals systemic antiviral activities and cell-specific immunological changes against PRRSV infectionByeonghwi Lim0Chiwoong Lim1Min-Jae Jang2Young-Jun Seo3Do-Young Kim4Christopher K. Tuggle5Kyu-Sang Lim6Jun-Mo Kim7Functional Genomics & Bioinformatics Laboratory, Department of Animal Science and Technology, Chung-Ang UniversityFunctional Genomics & Bioinformatics Laboratory, Department of Animal Science and Technology, Chung-Ang UniversityFunctional Genomics & Bioinformatics Laboratory, Department of Animal Science and Technology, Chung-Ang UniversityFunctional Genomics & Bioinformatics Laboratory, Department of Animal Science and Technology, Chung-Ang UniversityFunctional Genomics & Bioinformatics Laboratory, Department of Animal Science and Technology, Chung-Ang UniversityDepartment of Animal Science, Iowa State UniversityDepartment of Animal Resources Science, Kongju National UniversityFunctional Genomics & Bioinformatics Laboratory, Department of Animal Science and Technology, Chung-Ang UniversityAbstract Porcine reproductive and respiratory syndrome (PRRS) causes significant economic losses in the swine industry. However, the molecular mechanisms behind the common and cell type-specific systemic responses during PRRS virus (PRRSV) infection are not well understood. In this study, we collected viremia data, antibody levels, and whole-blood RNA-seq data obtained from eight PRRSV-infected piglets. We utilised a cell deconvolution approach to calculate cell type enrichment, constructed a time-serial gene co-expression network with differentially expressed genes, and conducted functional annotations. Three significant modules were identified within the network. The changes associated with viremia revealed an upregulated expression of genes related to antiviral activity. In the T-cell- and NK-cell-specific modules, infection led to an increased T-cell population and upregulation of genes related to T-cell defence responses. Conversely, in the monocyte- and neutrophil-specific module, genes involved in inflammatory responses were downregulated due to a decrease in monocyte proportion. This study highlights the time-series antiviral activities associated with viremia and the transcriptomic changes associated with immune responses in specific cell types. The findings provide comprehensive insights into host responses to PRRSV infection, including diagnostic biomarkers.https://doi.org/10.1186/s13567-025-01451-wPRRS viruswhole bloodRNA sequencingcell deconvolutiontranscriptomicstime-series network |
| spellingShingle | Byeonghwi Lim Chiwoong Lim Min-Jae Jang Young-Jun Seo Do-Young Kim Christopher K. Tuggle Kyu-Sang Lim Jun-Mo Kim Cell deconvolution-based integrated time-series network of whole blood transcriptome reveals systemic antiviral activities and cell-specific immunological changes against PRRSV infection Veterinary Research PRRS virus whole blood RNA sequencing cell deconvolution transcriptomics time-series network |
| title | Cell deconvolution-based integrated time-series network of whole blood transcriptome reveals systemic antiviral activities and cell-specific immunological changes against PRRSV infection |
| title_full | Cell deconvolution-based integrated time-series network of whole blood transcriptome reveals systemic antiviral activities and cell-specific immunological changes against PRRSV infection |
| title_fullStr | Cell deconvolution-based integrated time-series network of whole blood transcriptome reveals systemic antiviral activities and cell-specific immunological changes against PRRSV infection |
| title_full_unstemmed | Cell deconvolution-based integrated time-series network of whole blood transcriptome reveals systemic antiviral activities and cell-specific immunological changes against PRRSV infection |
| title_short | Cell deconvolution-based integrated time-series network of whole blood transcriptome reveals systemic antiviral activities and cell-specific immunological changes against PRRSV infection |
| title_sort | cell deconvolution based integrated time series network of whole blood transcriptome reveals systemic antiviral activities and cell specific immunological changes against prrsv infection |
| topic | PRRS virus whole blood RNA sequencing cell deconvolution transcriptomics time-series network |
| url | https://doi.org/10.1186/s13567-025-01451-w |
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