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Kim M, Ediriweera TK, Cho E, Chung Y, Manjula P, Yu M, Macharia JK, Nam S, Lee JH. Major histocompatibility complex genes exhibit a potential immunological role in mixed Eimeria-infected broiler cecum analyzed using RNA sequencing. Anim Biosci 2024; 37:993-1000. [PMID: 38271966 PMCID: PMC11065961 DOI: 10.5713/ab.23.0412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/17/2023] [Accepted: 11/28/2023] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVE This study was conducted to investigate the differential expression of the major histocompatibility complex (MHC) gene region in Eimeria-infected broiler. METHODS We profiled gene expression of Eimeria-infected and uninfected ceca of broilers sampled at 4, 7, and 21 days post-infection (dpi) using RNA sequencing. Differentially expressed genes (DEGs) between two sample groups were identified at each time point. DEGs located on chicken chromosome 16 were used for further analysis. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis was conducted for the functional annotation of DEGs. RESULTS Fourteen significant (false discovery rate <0.1) DEGs were identified at 4 and 7 dpi and categorized into three groups: MHC-Y class I genes, MHC-B region genes, and non-MHC genes. In Eimeria-infected broilers, MHC-Y class I genes were upregulated at 4 dpi but downregulated at 7 dpi. This result implies that MHC-Y class I genes initially activated an immune response, which was then suppressed by Eimeria. Of the MHC-B region genes, the DMB1 gene was upregulated, and TAP-related genes significantly implemented antigen processing for MHC class I at 4 dpi, which was supported by KEGG pathway analysis. CONCLUSION This study is the first to investigate MHC gene responses to coccidia infection in chickens using RNA sequencing. MHC-B and MHC-Y genes showed their immune responses in reaction to Eimeria infection. These findings are valuable for understanding chicken MHC gene function.
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Affiliation(s)
- Minjun Kim
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | | | - Eunjin Cho
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134,
Korea
| | - Yoonji Chung
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Prabuddha Manjula
- Department of Animal Science, Uva Wellassa University, Badulla 90000,
Sri Lanka
| | - Myunghwan Yu
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - John Kariuki Macharia
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Seonju Nam
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
| | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134,
Korea
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134,
Korea
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Feng S, Wei G, Yang X, Zhang Z, Qu J, Wang D, Zhou T, Ni T, Liu L, Kang L. Changes in expression levels of erythrocyte and immune-related genes are associated with high altitude polycythemia. BMC Med Genomics 2023; 16:174. [PMID: 37507679 PMCID: PMC10375625 DOI: 10.1186/s12920-023-01613-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND As a chronic mountain sickness(CMS) with the highest incidence and the greatest harm, the pathogenesis of high altitude polycythemia (HAPC) is still not fully understood. METHODS 37 HAPC patients and 42 healthy subjects were selected from plateau, and peripheral venous blood samples were collected for transcriptome sequencing on Illumina NovaSeq platform. The sequenced data were analyzed by bioinformatics and phenotypic association analysis. RESULTS The results showed significant differences in multiple clinical indicators including RBC and HGB et al. existed between HAPC and control. Based on the RNA-seq data, 550 genes with significant differential expression were identified in HAPC patients. GO and KEGG pathway enrichment analysis showed that the up-regulated genes were mainly enriched in processes such as erythrocyte differentiation and development and homeostasis of number of cells, while the down-regulated genes were mainly enriched in categories such as immunoglobulin production, classical pathway of complement activation and other biological processes. The coupling analysis of differential expression genes(DEGs) and pathological phenotypes revealed that 91 DEGs were in close correlation with in the phenotype of red blood cell volume distribution (width-CV and width-SD), and they were all up-regulated in HAPC and involved in the process of erythrocyte metabolism. Combined with the functional annotation of DEGs and literature survey, we found that the expression of several potential genes might be responsible for pathogenesis of HAPC. Besides, cell type deconvolution analysis result suggested that the changes in the number of some immune cell types was significantly lower in HAPC patients than control, implying the autoimmune level of HAPC patients was affected to a certain extent. CONCLUSION This study provides an important data source for understanding the pathogenesis and screening pathogenic genes of HAPC. We found for the first time that there was a significant correlation between HAPC and the pathological phenotype of width-CV and width-SD, wherein the enriched genes were all up-regulated expressed and involved in the process of erythrocyte metabolism. Although the role of these genes needs to be further studied, the candidate genes can provide a starting point for functionally pinning down the underlying mechanism of HAPC.
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Affiliation(s)
- Siwei Feng
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous region, Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, China
| | - Gang Wei
- Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xuelin Yang
- The Second People's Hospital of Tibet Autonomous Region, Lhasa, Tibet, 850000, China
| | - Zhiying Zhang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous region, Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, China
| | - Jingfeng Qu
- The Second People's Hospital of Tibet Autonomous Region, Lhasa, Tibet, 850000, China
| | - Donglan Wang
- The Second People's Hospital of Tibet Autonomous Region, Lhasa, Tibet, 850000, China
| | - Tian Zhou
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous region, Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, China
| | - Ting Ni
- Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Lijun Liu
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous region, Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, China.
| | - Longli Kang
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous region, Key Laboratory of High Altitude Environment and Genes Related to Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, China.
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Seo M, Lee HJ, Kim K, Caetano-Anolles K, Jeong JY, Park S, Oh YK, Cho S, Kim H. Characterizing Milk Production Related Genes in Holstein Using RNA-seq. Asian-Australas J Anim Sci 2016; 29:343-51. [PMID: 26950864 PMCID: PMC4811784 DOI: 10.5713/ajas.15.0525] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Revised: 09/17/2015] [Accepted: 10/25/2015] [Indexed: 01/01/2023]
Abstract
Although the chemical, physical, and nutritional properties of bovine milk have been extensively studied, only a few studies have attempted to characterize milk-synthesizing genes using RNA-seq data. RNA-seq data was collected from 21 Holstein samples, along with group information about milk production ability; milk yield; and protein, fat, and solid contents. Meta-analysis was employed in order to generally characterize genes related to milk production. In addition, we attempted to investigate the relationship between milk related traits, parity, and lactation period. We observed that milk fat is highly correlated with lactation period; this result indicates that this effect should be considered in the model in order to accurately detect milk production related genes. By employing our developed model, 271 genes were significantly (false discovery rate [FDR] adjusted p-value<0.1) detected as milk production related differentially expressed genes. Of these genes, five (albumin, nitric oxide synthase 3, RNA-binding region (RNP1, RRM) containing 3, secreted and transmembrane 1, and serine palmitoyltransferase, small subunit B) were technically validated using quantitative real-time polymerase chain reaction (qRT-PCR) in order to check the accuracy of RNA-seq analysis. Finally, 83 gene ontology biological processes including several blood vessel and mammary gland development related terms, were significantly detected using DAVID gene-set enrichment analysis. From these results, we observed that detected milk production related genes are highly enriched in the circulation system process and mammary gland related biological functions. In addition, we observed that detected genes including caveolin 1, mammary serum amyloid A3.2, lingual antimicrobial peptide, cathelicidin 4 (CATHL4), cathelicidin 6 (CATHL6) have been reported in other species as milk production related gene. For this reason, we concluded that our detected 271 genes would be strong candidates for determining milk production.
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Affiliation(s)
- Minseok Seo
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-741, Korea ; CHO&KIM genomics, Seoul 151-919, Korea
| | - Hyun-Jeong Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-741, Korea ; Animal Nutritional & Physiology Team, National Institute of Animal Science, Jeonju 565-851, Korea
| | - Kwondo Kim
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea
| | | | - Jin Young Jeong
- Division of Animal Products R&D, National Institute of Animal Science, Jeonju 565-851, Korea
| | - Sungkwon Park
- Animal Nutritional & Physiology Team, National Institute of Animal Science, Jeonju 565-851, Korea . ; Department of Food Science and Technology, Sejong University, Seoul 143-747, Korea
| | - Young Kyun Oh
- Animal Nutritional & Physiology Team, National Institute of Animal Science, Jeonju 565-851, Korea
| | - Seoae Cho
- CHO&KIM genomics, Seoul 151-919, Korea
| | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-741, Korea ; CHO&KIM genomics, Seoul 151-919, Korea . ; Department of Animal Sciences, University of Illinois, Urbana, IL 61801, USA
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Song KD, Cho HW, Lee HK, Cho BW. Molecular Characterization and Expression Analysis of Equine Vascular Endothelial Growth Factor Alpha (VEGFα) Gene in Horse (Equus caballus). Asian-Australas J Anim Sci 2014; 27:743-8. [PMID: 25050010 PMCID: PMC4093191 DOI: 10.5713/ajas.2013.13821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/02/2014] [Accepted: 03/18/2014] [Indexed: 11/27/2022]
Abstract
The objective of this study was to determine the molecular characteristics of the horse vascular endothelial growth factor alpha gene (VEGFα) by constructing a phylogenetic tree, and to investigate gene expression profiles in tissues and blood leukocytes after exercise for development of suitable biomarkers. Using published amino acid sequences of other vertebrate species (human, chimpanzee, mouse, rat, cow, pig, chicken and dog), we constructed a phylogenetic tree which showed that equine VEGFα belonged to the same clade of the pig VEGFα. Analysis for synonymous (Ks) and non-synonymous substitution ratios (Ka) revealed that the horse VEGFα underwent positive selection. RNA was extracted from blood samples before and after exercise and different tissue samples of three horses. Expression analyses using reverse transcription-polymerase chain reaction (RT-PCR) and quantitative-polymerase chain reaction (qPCR) showed ubiquitous expression of VEGFα mRNA in skeletal muscle, kidney, thyroid, lung, appendix, colon, spinal cord, and heart tissues. Analysis of differential expression of VEGFα gene in blood leukocytes after exercise indicated a unimodal pattern. These results will be useful in developing biomarkers that can predict the recovery capacity of racing horses.
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Affiliation(s)
- Ki-Duk Song
- Department of Animal Science, College of Nature Resources and Life Science, Pusan National University, Miryang 627-706, Korea
| | - Hyun-Woo Cho
- Department of Animal Science, College of Nature Resources and Life Science, Pusan National University, Miryang 627-706, Korea
| | - Hak-Kyo Lee
- Department of Animal Science, College of Nature Resources and Life Science, Pusan National University, Miryang 627-706, Korea
| | - Byung Wook Cho
- Department of Animal Science, College of Nature Resources and Life Science, Pusan National University, Miryang 627-706, Korea
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