Transcriptomic Profiling Reveals Altered Expression of Genes Involved in Metabolic and Immune Processes in NDV-Infected Chicken Embryos
Objective: The poultry industry is significantly impacted by viral infections, particularly Newcastle Disease Virus (NDV), which leads to substantial economic losses. It is essential to comprehend how the sequence of development affects biological pathways and how early exposure to infections might...
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2024-12-01
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| author | Malarmathi Muthusamy Kannaki T. Ramasamy Sunday Olusola Peters Srinivasan Palani Vasudevan Gowthaman Murali Nagarajan Sivakumar Karuppusamy Vasanthakumar Thangavelu Thiruvenkadan Aranganoor Kannan |
| author_facet | Malarmathi Muthusamy Kannaki T. Ramasamy Sunday Olusola Peters Srinivasan Palani Vasudevan Gowthaman Murali Nagarajan Sivakumar Karuppusamy Vasanthakumar Thangavelu Thiruvenkadan Aranganoor Kannan |
| author_sort | Malarmathi Muthusamy |
| collection | DOAJ |
| description | Objective: The poultry industry is significantly impacted by viral infections, particularly Newcastle Disease Virus (NDV), which leads to substantial economic losses. It is essential to comprehend how the sequence of development affects biological pathways and how early exposure to infections might affect immune responses. Methods: This study employed transcriptome analysis to investigate host–pathogen interactions by analyzing gene expression changes in NDV-infected chicken embryos’ lungs. Result: RNA-Seq reads were aligned with the chicken reference genome (Galgal7), revealing 594 differentially expressed genes: 264 upregulated and 330 downregulated. The most overexpressed genes, with logFC between 8.15 and 8.75, included C8A, FGG, PIT54, FETUB, APOC3, and FGA. Notably, downregulated genes included BPIFB3 (−4.46 logFC) and TRIM39.1 (−4.26 logFC). The analysis also identified 29 novel transcripts and 20 lncRNAs that were upregulated. Gene Ontology and KEGG pathways’ analyses revealed significant alterations in gene expression related to immune function, metabolism, cell cycle, nucleic acid processes, and mitochondrial activity due to NDV infection. Key metabolic genes, such as ALDOB (3.27 logFC), PRPS2 (2.66 logFC), and XDH (2.15 logFC), exhibited altered expression patterns, while DCK2 (−1.99 logFC) and TK1 (−2.11 logFC) were also affected. Several immune-related genes showed significant upregulation in infected lung samples, including ALB (6.15 logFC), TLR4 (1.86 logFC), TLR2 (2.79 logFC), and interleukin receptors, such as IL1R2 (3.15 logFC) and IL22RA2 (1.37 logFC). Conversely, genes such as CXCR4 (−1.49 logFC), CXCL14 (−2.57 logFC), GATA3 (−1.51 logFC), and IL17REL (−2.93 logFC) were downregulated. The higher expression of HSP genes underscores their vital role in immune responses. Conclusion: Comprehension of these genes’ interactions is essential for regulating viral replication and immune responses during infections, potentially aiding in the identification of candidate genes for poultry breed improvement amidst NDV challenges. |
| format | Article |
| id | doaj-art-e51646add6c44274b6ffdd2b861bf0f9 |
| institution | Kabale University |
| issn | 2218-1989 |
| language | English |
| publishDate | 2024-12-01 |
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| spelling | doaj-art-e51646add6c44274b6ffdd2b861bf0f92024-12-27T14:39:31ZengMDPI AGMetabolites2218-19892024-12-01141266910.3390/metabo14120669Transcriptomic Profiling Reveals Altered Expression of Genes Involved in Metabolic and Immune Processes in NDV-Infected Chicken EmbryosMalarmathi Muthusamy0Kannaki T. Ramasamy1Sunday Olusola Peters2Srinivasan Palani3Vasudevan Gowthaman4Murali Nagarajan5Sivakumar Karuppusamy6Vasanthakumar Thangavelu7Thiruvenkadan Aranganoor Kannan8Department of Animal Genetics and Breeding, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Namakkal 637002, IndiaIndian Council of Agricultural Research—Directorate of Poultry Research, Hyderabad 500030, IndiaDepartment of Animal Science, Berry College, Mount Berry, GA 30149, USADepartment of Veterinary Pathology, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Namakkal 637002, IndiaPoultry Disease Diagnosis and Surveillance Laboratory, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Namakkal 637002, IndiaAlambadi Cattle Breed Research Centre, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Dharmapuri 635111, IndiaFaculty of Food and Agriculture, The University of the West Indies, St. Augustine 999183, Trinidad and TobagoVeterinary University Training and Research Centre, Karur 639006, IndiaDepartment of Animal Genetics and Breeding, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University (TANUVAS), Namakkal 637002, IndiaObjective: The poultry industry is significantly impacted by viral infections, particularly Newcastle Disease Virus (NDV), which leads to substantial economic losses. It is essential to comprehend how the sequence of development affects biological pathways and how early exposure to infections might affect immune responses. Methods: This study employed transcriptome analysis to investigate host–pathogen interactions by analyzing gene expression changes in NDV-infected chicken embryos’ lungs. Result: RNA-Seq reads were aligned with the chicken reference genome (Galgal7), revealing 594 differentially expressed genes: 264 upregulated and 330 downregulated. The most overexpressed genes, with logFC between 8.15 and 8.75, included C8A, FGG, PIT54, FETUB, APOC3, and FGA. Notably, downregulated genes included BPIFB3 (−4.46 logFC) and TRIM39.1 (−4.26 logFC). The analysis also identified 29 novel transcripts and 20 lncRNAs that were upregulated. Gene Ontology and KEGG pathways’ analyses revealed significant alterations in gene expression related to immune function, metabolism, cell cycle, nucleic acid processes, and mitochondrial activity due to NDV infection. Key metabolic genes, such as ALDOB (3.27 logFC), PRPS2 (2.66 logFC), and XDH (2.15 logFC), exhibited altered expression patterns, while DCK2 (−1.99 logFC) and TK1 (−2.11 logFC) were also affected. Several immune-related genes showed significant upregulation in infected lung samples, including ALB (6.15 logFC), TLR4 (1.86 logFC), TLR2 (2.79 logFC), and interleukin receptors, such as IL1R2 (3.15 logFC) and IL22RA2 (1.37 logFC). Conversely, genes such as CXCR4 (−1.49 logFC), CXCL14 (−2.57 logFC), GATA3 (−1.51 logFC), and IL17REL (−2.93 logFC) were downregulated. The higher expression of HSP genes underscores their vital role in immune responses. Conclusion: Comprehension of these genes’ interactions is essential for regulating viral replication and immune responses during infections, potentially aiding in the identification of candidate genes for poultry breed improvement amidst NDV challenges.https://www.mdpi.com/2218-1989/14/12/669NDVchickenimmune genesmetabolic genesAPOC3ALDOB |
| spellingShingle | Malarmathi Muthusamy Kannaki T. Ramasamy Sunday Olusola Peters Srinivasan Palani Vasudevan Gowthaman Murali Nagarajan Sivakumar Karuppusamy Vasanthakumar Thangavelu Thiruvenkadan Aranganoor Kannan Transcriptomic Profiling Reveals Altered Expression of Genes Involved in Metabolic and Immune Processes in NDV-Infected Chicken Embryos Metabolites NDV chicken immune genes metabolic genes APOC3 ALDOB |
| title | Transcriptomic Profiling Reveals Altered Expression of Genes Involved in Metabolic and Immune Processes in NDV-Infected Chicken Embryos |
| title_full | Transcriptomic Profiling Reveals Altered Expression of Genes Involved in Metabolic and Immune Processes in NDV-Infected Chicken Embryos |
| title_fullStr | Transcriptomic Profiling Reveals Altered Expression of Genes Involved in Metabolic and Immune Processes in NDV-Infected Chicken Embryos |
| title_full_unstemmed | Transcriptomic Profiling Reveals Altered Expression of Genes Involved in Metabolic and Immune Processes in NDV-Infected Chicken Embryos |
| title_short | Transcriptomic Profiling Reveals Altered Expression of Genes Involved in Metabolic and Immune Processes in NDV-Infected Chicken Embryos |
| title_sort | transcriptomic profiling reveals altered expression of genes involved in metabolic and immune processes in ndv infected chicken embryos |
| topic | NDV chicken immune genes metabolic genes APOC3 ALDOB |
| url | https://www.mdpi.com/2218-1989/14/12/669 |
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