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Ingham AB, Osborne SA, Menzies M, Briscoe S, Chen W, Kongsuwan K, Reverter A, Jeanes A, Dalrymple BP, Wijffels G, Seymour R, Hudson NJ. RNF14 is a regulator of mitochondrial and immune function in muscle. BMC SYSTEMS BIOLOGY 2014; 8:10. [PMID: 24472305 PMCID: PMC3906743 DOI: 10.1186/1752-0509-8-10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 01/21/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND Muscle development and remodelling, mitochondrial physiology and inflammation are thought to be inter-related and to have implications for metabolism in both health and disease. However, our understanding of their molecular control is incomplete. RESULTS In this study we have confirmed that the ring finger 14 protein (RNF14), a poorly understood transcriptional regulator, influences the expression of both mitochondrial and immune-related genes. The prediction was based on a combination of network connectivity and differential connectivity in cattle (a non-model organism) and mice data sets, with a focus on skeletal muscle. They assigned similar probability to mammalian RNF14 playing a regulatory role in mitochondrial and immune gene expression. To try and resolve this apparent ambiguity we performed a genome-wide microarray expression analysis on mouse C2C12 myoblasts transiently transfected with two Rnf14 transcript variants that encode 2 naturally occurring but different RNF14 protein isoforms. The effect of both constructs was significantly different to the control samples (untransfected cells and cells transfected with an empty vector). Cluster analyses revealed that transfection with the two Rnf14 constructs yielded discrete expression signatures from each other, but in both cases a substantial set of genes annotated as encoding proteins related to immune function were perturbed. These included cytokines and interferon regulatory factors. Additionally, transfection of the longer transcript variant 1 coordinately increased the expression of 12 (of the total 13) mitochondrial proteins encoded by the mitochondrial genome, 3 of which were significant in isolated pair-wise comparisons (Mt-coxII, Mt-nd2 and mt-nd4l). This apparent additional mitochondrial function may be attributable to the RWD protein domain that is present only in the longer RNF14 isoform. CONCLUSIONS RNF14 influences the expression of both mitochondrial and immune related genes in a skeletal muscle context, and has likely implications for the inter-relationship between bioenergetic status and inflammation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Nicholas J Hudson
- CSIRO Animal, Food and Health Sciences, 306 Carmody Road, St, Lucia, Queensland, Australia.
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Yu S, Zuo Z, Cui H, Li M, Peng X, Zhu L, Zhang M, Li X, Xu Z, Gan M, Deng J, Fang J, Ma J, Su S, Wang Y, Shen L, Ma X, Ren Z, Wu B, Hu Y. Transcriptional profiling of hilar nodes from pigs after experimental infection with Actinobacillus pleuropneumoniae. Int J Mol Sci 2013; 14:23516-32. [PMID: 24351863 PMCID: PMC3876060 DOI: 10.3390/ijms141223516] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 11/12/2013] [Accepted: 11/15/2013] [Indexed: 11/16/2022] Open
Abstract
The gram-negative bacterium Actinobacillus pleuropneumoniae (APP) is an inhabitant of the porcine upper respiratory tract and the causative agent of porcine pleuropneumonia (PP). In recent years, knowledge about the proinflammatory cytokine and chemokine gene expression that occurs in lung and lymph node of the APP-infected swine has been advanced. However, systematic gene expression profiles on hilar nodes from pigs after infection with Actinobacillus pleuropneumoniae have not yet been reported. The transcriptional responses were studied in hilar nodes (HN) from swine experimentally infected with APP and the control groupusing Agilent Porcine Genechip, including 43,603 probe sets. 9,517 transcripts were identified as differentially expressed (DE) at the p ≤ 0.01 level by comparing the log2 (normalized signal) of the two groups named treatment group (TG) and controls (CG). Eight hundred and fifteen of these DE transcripts were annotated as pig genes in the GenBank database (DB). Two hundred and seventy-two biological process categories (BP), 75 cellular components and 171 molecular functions were substantially altered in the TG compared to CG. Many BP were involved in host immune responses (i.e., signaling, signal transmission, signal transduction, response to stimulus, oxidation reduction, response to stress, immune system process, signaling pathway, immune response, cell surface receptor linked signaling pathway). Seven DE gene pathways (VEGF signaling pathway, Long-term potentiation, Ribosome, Asthma, Allograft rejection, Type I diabetes mellitus and Cardiac muscle contraction) and statistically significant associations with host responses were affected. Many cytokines (including NRAS, PI3K, MAPK14, CaM, HSP27, protein phosphatase 3, catalytic subunit and alpha isoform), mediating the proliferation and migration of endothelial cells and promoting survival and vascular permeability, were activated in TG, whilst many immunomodulatory cytokines were suppressed. The significant changes in the expression patterns of the genes, GO terms, and pathways, led to a decrease of antigenic peptides with antigen presenting cells presented to T lymphocytes via the major histocompatibility complex, and alleviated immune response induced APP of HN. The immune response ability of HN in the APP-infected pigs was weakened; however, cell proliferation and migration ability was enhanced.
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Affiliation(s)
- Shumin Yu
- College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (S.Y.); (Z.Z.); (X.P.); (L.Z.); (Z.X.); (M.G.); (J.D.); (J.F.); (Y.W.); (L.S.); (X.M.); (Z.R.); (B.W.); (Y.H.)
- Laboratory of Animal Disease and Human Health, Sichuan Agricultural University, Ya’an 625014, China
| | - Zhicai Zuo
- College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (S.Y.); (Z.Z.); (X.P.); (L.Z.); (Z.X.); (M.G.); (J.D.); (J.F.); (Y.W.); (L.S.); (X.M.); (Z.R.); (B.W.); (Y.H.)
- Laboratory of Animal Disease and Human Health, Sichuan Agricultural University, Ya’an 625014, China
| | - Hengmin Cui
- College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (S.Y.); (Z.Z.); (X.P.); (L.Z.); (Z.X.); (M.G.); (J.D.); (J.F.); (Y.W.); (L.S.); (X.M.); (Z.R.); (B.W.); (Y.H.)
- Laboratory of Animal Disease and Human Health, Sichuan Agricultural University, Ya’an 625014, China
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-136-0826-4628; Fax: +86-835-2882340
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (M.L.); (M.Z.); (X.L.); (J.M.)
| | - Xi Peng
- College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (S.Y.); (Z.Z.); (X.P.); (L.Z.); (Z.X.); (M.G.); (J.D.); (J.F.); (Y.W.); (L.S.); (X.M.); (Z.R.); (B.W.); (Y.H.)
- Laboratory of Animal Disease and Human Health, Sichuan Agricultural University, Ya’an 625014, China
| | - Ling Zhu
- College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (S.Y.); (Z.Z.); (X.P.); (L.Z.); (Z.X.); (M.G.); (J.D.); (J.F.); (Y.W.); (L.S.); (X.M.); (Z.R.); (B.W.); (Y.H.)
- Laboratory of Animal Disease and Human Health, Sichuan Agricultural University, Ya’an 625014, China
| | - Ming Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (M.L.); (M.Z.); (X.L.); (J.M.)
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (M.L.); (M.Z.); (X.L.); (J.M.)
| | - Zhiwen Xu
- College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (S.Y.); (Z.Z.); (X.P.); (L.Z.); (Z.X.); (M.G.); (J.D.); (J.F.); (Y.W.); (L.S.); (X.M.); (Z.R.); (B.W.); (Y.H.)
- Laboratory of Animal Disease and Human Health, Sichuan Agricultural University, Ya’an 625014, China
| | - Meng Gan
- College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (S.Y.); (Z.Z.); (X.P.); (L.Z.); (Z.X.); (M.G.); (J.D.); (J.F.); (Y.W.); (L.S.); (X.M.); (Z.R.); (B.W.); (Y.H.)
- Laboratory of Animal Disease and Human Health, Sichuan Agricultural University, Ya’an 625014, China
| | - Junliang Deng
- College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (S.Y.); (Z.Z.); (X.P.); (L.Z.); (Z.X.); (M.G.); (J.D.); (J.F.); (Y.W.); (L.S.); (X.M.); (Z.R.); (B.W.); (Y.H.)
- Laboratory of Animal Disease and Human Health, Sichuan Agricultural University, Ya’an 625014, China
| | - Jing Fang
- College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (S.Y.); (Z.Z.); (X.P.); (L.Z.); (Z.X.); (M.G.); (J.D.); (J.F.); (Y.W.); (L.S.); (X.M.); (Z.R.); (B.W.); (Y.H.)
- Laboratory of Animal Disease and Human Health, Sichuan Agricultural University, Ya’an 625014, China
| | - Jideng Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (M.L.); (M.Z.); (X.L.); (J.M.)
| | - Shengqun Su
- Library of Sichuan Agricultural University, Ya’an 625014, China; E-Mail:
| | - Ya Wang
- College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (S.Y.); (Z.Z.); (X.P.); (L.Z.); (Z.X.); (M.G.); (J.D.); (J.F.); (Y.W.); (L.S.); (X.M.); (Z.R.); (B.W.); (Y.H.)
- Laboratory of Animal Disease and Human Health, Sichuan Agricultural University, Ya’an 625014, China
| | - Liuhong Shen
- College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (S.Y.); (Z.Z.); (X.P.); (L.Z.); (Z.X.); (M.G.); (J.D.); (J.F.); (Y.W.); (L.S.); (X.M.); (Z.R.); (B.W.); (Y.H.)
- Laboratory of Animal Disease and Human Health, Sichuan Agricultural University, Ya’an 625014, China
| | - Xiaoping Ma
- College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (S.Y.); (Z.Z.); (X.P.); (L.Z.); (Z.X.); (M.G.); (J.D.); (J.F.); (Y.W.); (L.S.); (X.M.); (Z.R.); (B.W.); (Y.H.)
- Laboratory of Animal Disease and Human Health, Sichuan Agricultural University, Ya’an 625014, China
| | - Zhihua Ren
- College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (S.Y.); (Z.Z.); (X.P.); (L.Z.); (Z.X.); (M.G.); (J.D.); (J.F.); (Y.W.); (L.S.); (X.M.); (Z.R.); (B.W.); (Y.H.)
- Laboratory of Animal Disease and Human Health, Sichuan Agricultural University, Ya’an 625014, China
| | - Bangyuan Wu
- College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (S.Y.); (Z.Z.); (X.P.); (L.Z.); (Z.X.); (M.G.); (J.D.); (J.F.); (Y.W.); (L.S.); (X.M.); (Z.R.); (B.W.); (Y.H.)
- Laboratory of Animal Disease and Human Health, Sichuan Agricultural University, Ya’an 625014, China
| | - Yanchun Hu
- College of Veterinary Medicine, Sichuan Agricultural University, Ya’an 625014, China; E-Mails: (S.Y.); (Z.Z.); (X.P.); (L.Z.); (Z.X.); (M.G.); (J.D.); (J.F.); (Y.W.); (L.S.); (X.M.); (Z.R.); (B.W.); (Y.H.)
- Laboratory of Animal Disease and Human Health, Sichuan Agricultural University, Ya’an 625014, China
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Transcriptional profiling of swine lung tissue after experimental infection with Actinobacillus pleuropneumoniae. Int J Mol Sci 2013; 14:10626-60. [PMID: 23698783 PMCID: PMC3676858 DOI: 10.3390/ijms140510626] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 05/09/2013] [Accepted: 05/10/2013] [Indexed: 12/13/2022] Open
Abstract
Porcine pleuropneumonia is a highly contagious respiratory disease that causes great economic losses worldwide. In this study, we aimed to explore the underlying relationship between infection and injury by investigation of the whole porcine genome expression profiles of swine lung tissues post-inoculated with experimentally Actinobacillus pleuropneumoniae. Expression profiling experiments of the control group and the treatment group were conducted using a commercially available Agilent Porcine Genechip including 43,603 probe sets. Microarray analysis was conducted on profiles of lung from challenged versus non-challenged swine. We found 11,929 transcripts, identified as differentially expressed at the p ≤0.01 level. There were 1188 genes annotated as swine genes in the GenBank Data Base. GO term analysis identified a total of 89 biological process categories, 82 cellular components and 182 molecular functions that were significantly affected, and at least 27 biological process categories that were related to the host immune response. Gene set enrichment analysis identified 13 pathways that were significantly associated with host response. Many proinflammatory-inflammatory cytokines were activated and involved in the regulation of the host defense response at the site of inflammation; while the cytokines involved in regulation of the host immune response were suppressed. All changes of genes and pathways of induced or repressed expression not only led to a decrease in antigenic peptides presented to T lymphocytes by APCs via the MHC and alleviated immune response injury induced by infection, but also stimulated stem cells to produce granulocytes (neutrophils, eosinophils, and basophils) and monocyte, and promote neutrophils and macrophages to phagocytose bacterial and foreign antigen at the site of inflammation. The defense function of swine infection with Actinobacillus pleuropneumoniae was improved, while its immune function was decreased.
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2009 pandemic H1N1 influenza virus causes disease and upregulation of genes related to inflammatory and immune responses, cell death, and lipid metabolism in pigs. J Virol 2011; 85:11626-37. [PMID: 21900171 DOI: 10.1128/jvi.05705-11] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
There exists limited information about whether adaptation is needed for cross-species transmission of the 2009 pandemic H1N1 influenza virus (pH1N1). Here, we compare the pathogenesis of two pH1N1 viruses, one derived from a human patient (A/CA/04/09 [CA09]) and the other from swine (A/swine/Alberta/25/2009 [Alb09]), with that of the 1918-like classical swine influenza virus (A/swine/Iowa/1930 [IA30]) in the pig model. Both pH1N1 isolates induced clinical symptoms such as coughing, sneezing, decreased activity, fever, and labored breathing in challenged pigs, but IA30 virus did not cause any clinical symptoms except fever. Although both the pH1N1 viruses and the IA30 virus caused lung lesions, the pH1N1 viruses were shed from the nasal cavities of challenged pigs whereas the IA30 virus was not. Global gene expression analysis indicated that transcriptional responses of the viruses were distinct. pH1N1-infected pigs had an upregulation of genes related to inflammatory and immune responses at day 3 postinfection that was not seen in the IA30 infection, and expression levels of genes related to cell death and lipid metabolism at day 5 postinfection were markedly different from those of IA30 infection. These results indicate that both pH1N1 isolates are more virulent due in part to differences in the host transcriptional response during acute infection. Our study also indicates that pH1N1 does not need prior adaptation to infect pigs, has a high potential to be maintained in naïve swine populations, and might reassort with currently circulating swine influenza viruses.
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Forster R, Ancian P, Fredholm M, Simianer H, Whitelaw B. The minipig as a platform for new technologies in toxicology. J Pharmacol Toxicol Methods 2010; 62:227-35. [DOI: 10.1016/j.vascn.2010.05.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 05/21/2010] [Accepted: 05/24/2010] [Indexed: 11/29/2022]
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Tuggle CK, Bearson SMD, Uthe JJ, Huang TH, Couture OP, Wang YF, Kuhar D, Lunney JK, Honavar V. Methods for transcriptomic analyses of the porcine host immune response: application to Salmonella infection using microarrays. Vet Immunol Immunopathol 2010; 138:280-91. [PMID: 21036404 DOI: 10.1016/j.vetimm.2010.10.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Technological developments in both the collection and analysis of molecular genetic data over the past few years have provided new opportunities for an improved understanding of the global response to pathogen exposure. Such developments are particularly dramatic for scientists studying the pig, where tools to measure the expression of tens of thousands of transcripts, as well as unprecedented data on the porcine genome sequence, have combined to expand our abilities to elucidate the porcine immune system. In this review, we describe these recent developments in the context of our work using primarily microarrays to explore gene expression changes during infection of pigs by Salmonella. Thus while the focus is not a comprehensive review of all possible approaches, we provide links and information on both the tools we use as well as alternatives commonly available for transcriptomic data collection and analysis of porcine immune responses. Through this review, we expect readers will gain an appreciation for the necessary steps to plan, conduct, analyze and interpret the data from transcriptomic analyses directly applicable to their research interests.
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Affiliation(s)
- C K Tuggle
- Department of Animal Science, and Center for Integrated Animal Genomics, 2255 Kildee Hall, Iowa State University, Ames, IA 50010, United States.
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Argyropoulos C, Daskalakis A, Nikiforidis GC, Sakellaropoulos GC. Background adjustment of cDNA microarray images by Maximum Entropy distributions. J Biomed Inform 2010; 43:496-509. [PMID: 20362072 DOI: 10.1016/j.jbi.2010.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Revised: 03/16/2010] [Accepted: 03/22/2010] [Indexed: 11/27/2022]
Abstract
Many empirical studies have demonstrated the exquisite sensitivity of both traditional and novel statistical and machine intelligence algorithms to the method of background adjustment used to analyze microarray datasets. In this paper we develop a statistical framework that approaches background adjustment as a classic stochastic inverse problem, whose noise characteristics are given in terms of Maximum Entropy distributions. We derive analytic closed form approximations to the combined problem of estimating the magnitude of the background in microarray images and adjusting for its presence. The proposed method reduces standardized measures of log expression variability across replicates in situations of known differential and non-differential gene expression without increasing the bias. Additionally, it results in computationally efficient procedures for estimation and learning based on sufficient statistics and can filter out spot measures with intensities that are numerically close to the background level resulting in a noise reduction of about 7%.
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Affiliation(s)
- Christos Argyropoulos
- Department of Medical Physics, School of Medicine, University of Patras, GR-26504 Rion, Greece
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Skovgaard K, Mortensen S, Boye M, Hedegaard J, Heegaard PM. Hepatic gene expression changes in pigs experimentally infected with the lung pathogen Actinobacillus pleuropneumoniae as analysed with an innate immunity focused microarray. Innate Immun 2009; 16:343-53. [DOI: 10.1177/1753425909342730] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Knowledge on gene expression in the liver during respiratory infections is limited although it is well-established that this organ is an important site of synthesis of several systemic innate immune components as response to infections. In the present study, the early transcriptional hepatic response of genes associated with innate immune responses was studied in pigs 14—18 h after intranasal inoculation with Actinobacillus pleuropneumoniae, using innate immune focused microarrays and quantitative real-time PCR (qPCR). The microarray analysis of liver tissue established that 51 genes were differentially expressed. A large group of these genes encoded proteins involved in the acute phase response, including serum amyloid A, C-reactive protein, fibrinogen, haptoglobin and tumor necrosis factor-α the expression of which were all found to be up-regulated and glutathione S-transferase, transthyretin, transferrin and albumin which were down-regulated. Additional genes associated with innate immune responses were investigated using qPCR; genes encoding interleukin-(IL-)1, IL-6, IL-8, lipopolysaccharide binding protein, lactotransferrin, and PigMAP were up-regulated and interferon 1α, α1-acid glycoprotein, mannan-binding lectin A, surfactant protein D, and surfactant protein A1 were down-regulated in the liver of infected animals. Down-regulation of α1-acid glycoprotein during infection has not been described previously in any species. These results confirm that the liver plays an important role in initiating and orchestrating the innate immune response to A. pleuropneumoniae infection.
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Affiliation(s)
- Kerstin Skovgaard
- National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark,
| | - Shila Mortensen
- National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Mette Boye
- National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
| | - Jakob Hedegaard
- Faculty of Agricultural Sciences, Aarhus University, Tjele, Denmark
| | - Peter M.H. Heegaard
- National Veterinary Institute, Technical University of Denmark, Copenhagen, Denmark
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Bioinformatics annotation of the hypothetical proteins found by omics techniques can help to disclose additional virulence factors. Curr Microbiol 2009; 59:451-6. [PMID: 19636617 DOI: 10.1007/s00284-009-9459-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 07/07/2009] [Indexed: 01/17/2023]
Abstract
The advent of genomics should have facilitated the identification of microbial virulence factors, a key objective for vaccine design. When the bacterial pathogen infects the host it expresses a set of genes, a number of them being virulence factors. Among the genes identified by techniques as microarrays, in vivo expression technology, signature-tagged mutagenesis and differential fluorescence induction there are many related to cellular stress, basal metabolism, etc., which cannot be directly involved in virulence, or at least cannot be considered useful candidates to be deleted for designing a live attenuated vaccine. Among the genes disclosed by these methodologies there are a number of hypothetical or unknown proteins. As they can hide some true virulence factors, we have reannotated all of these hypothetical proteins from several respiratory pathogens by a careful and in-depth analysis of each one. Although some of the re-annotations match with functions that can be related to microbial virulence, the identification of virulence factors remains difficult.
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Toro MA, Fernández J, Caballero A. Molecular characterization of breeds and its use in conservation. Livest Sci 2009. [DOI: 10.1016/j.livsci.2008.07.003] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ferraz ALJ, Ojeda A, López-Béjar M, Fernandes LT, Castelló A, Folch JM, Pérez-Enciso M. Transcriptome architecture across tissues in the pig. BMC Genomics 2008; 9:173. [PMID: 18416811 PMCID: PMC2335121 DOI: 10.1186/1471-2164-9-173] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Accepted: 04/16/2008] [Indexed: 11/24/2022] Open
Abstract
Background Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues? Results In order to gain insight on these issues, we conducted microarray expression profiling of 16 different tissues from four animals of two extreme pig breeds, Large White and Iberian, two males and two females. Mixed model analysis and neighbor – joining trees showed that tissues with similar developmental origin clustered closer than those with different embryonic origins. Often a sound biological interpretation was possible for overrepresented gene ontology categories within differentially expressed genes between groups of tissues. For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively. Tissue accounted for ~11 times more variability than sex or breed. Nevertheless, we were able to confidently identify genes with differential expression across tissues between breeds (33 genes) and between sexes (19 genes). The genes primarily affected by sex were overall different than those affected by breed or tissue. Interaction with tissue can be important for differentially expressed genes between breeds but not so much for genes whose expression differ between sexes. Conclusion Embryonic development leaves an enduring footprint on the transcriptome. The interaction in gene × tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome.
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Affiliation(s)
- André L J Ferraz
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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Ojha S, Kostrzynska M. Examination of animal and zoonotic pathogens using microarrays. Vet Res 2007; 39:4. [DOI: 10.1051/vetres:2007042] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Accepted: 07/27/2007] [Indexed: 01/13/2023] Open
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Byrne KA, Wang YH, Lehnert SA, Harper GS, McWilliam SM, Bruce HL, Reverter A. Gene expression profiling of muscle tissue in Brahman steers during nutritional restriction. J Anim Sci 2007; 83:1-12. [PMID: 15583036 DOI: 10.2527/2005.8311] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Expression profiling using microarrays allows for the detailed characterization of the gene networks that regulate an animal's response to environmental stresses. During nutritional restriction, processes such as protein turnover, connective tissue remodeling, and muscle atrophy take place in the skeletal muscle of the animal. These processes and their regulation are of interest in the context of managing livestock for optimal production efficiency and product quality. Here we expand on recent research applying complementary DNA (cDNA) microarray technology to the study of the effect of nutritional restriction on bovine skeletal muscle. Using a custom cDNA microarray of 9,274 probes from cattle muscle and s.c. fat libraries, we examined the differential gene expression profile of the LM from 10 Brahman steers under three different dietary treatments. The statistical approach was based on mixed-model ANOVA and model-based clustering of the BLUP solutions for the gene x diet interaction effect. From the results, we defined a transcript profile of 156 differentially expressed array elements between the weight loss and weight gain diet substrates. After sequence and annotation analyses, the 57 upregulated elements represented 29 unique genes, and the 99 downregulated elements represented 28 unique genes. Most of these co-regulated genes cluster into groups with distinct biological function related to protein turnover and cytoskeletal metabolism and contribute to our mechanistic understanding of the processes associated with remodeling of muscle tissue in response to nutritional stress.
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Affiliation(s)
- K A Byrne
- Cooperative Research Centre for Cattle and Beef Quality, CSIRO Livestock Industries, Queensland Bioscience Precinct, St. Lucia, Queensland 4067, Australia
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Moser RJ, Reverter A, Lehnert SA. Gene expression profiling of porcine peripheral blood leukocytes after infection with Actinobacillus pleuropneumoniae. Vet Immunol Immunopathol 2007; 121:260-74. [PMID: 18054086 DOI: 10.1016/j.vetimm.2007.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Revised: 08/02/2007] [Accepted: 10/11/2007] [Indexed: 01/15/2023]
Abstract
The gene expression profile of peripheral blood leukocytes (PBL) from extreme performing pigs after infection with Actinobacillus pleuropneumoniae was analysed using a custom complementary DNA (cDNA) microarray and quantitative reverse transcription-PCR (qRT-PCR). Four high performing animals with low disease-score (HP), three low performing animals with high disease-score (LP) and one medium performing animal with medium disease-score (MP) were selected for microarray profiling. PBL RNA from these eight pigs collected before and at 24h after APP infection, was examined. The study identified 92 genes that were up-regulated and four genes that were down-regulated in PBL RNA from HP pigs compared to LP pigs. The majority of differentially expressed (DE) genes were identified by virtue of their elevated expression in the HP animals at 24h post-infection. A large number of annotated DE genes are involved in innate immune response pathways. The gene expression profile of 10 DE candidate genes was further explored across the entire pig population in the same infection trial using qRT-PCR. Considerable animal-to-animal variation in PBL gene expression was observed, especially in the LP group. The qRT-PCR analysis suggested that only one true LP pig might be present in this study, which contributes significantly to the differential expression profile of the selected genes in HP animals following APP infection. This study has therefore identified a set of genes which could serve as molecular indicators for an effective immune response to APP in pigs and which could also serve as source for gene marker development in molecular genetics studies of heritable immune traits.
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Affiliation(s)
- Ralf J Moser
- CSIRO Livestock Industries, St Lucia 4067, Australia.
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15
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Qu A, Rothschild MF, Stahl CH. Effect of dietary phosphorus and its interaction with genetic background on global gene expression in porcine muscle. J Anim Breed Genet 2007; 124:214-24. [PMID: 17651324 DOI: 10.1111/j.1439-0388.2007.00655.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Environmental concerns and costs associated with dietary phosphorus (P) supplementation have lead to attempts to minimize the amount of P added to swine diets. In addition to its requirement for bone growth, dietary P is also necessary for muscular growth. To examine the effects of genetic background and dietary P on global gene expression in the muscle of young pigs, we utilized muscle tissue from 36 gilts sired from two different sire lines. These animals were fed either a P adequate, P deficient or P repletion diets for 14 days and showed differences in growth performance and bone integrity in response to the interaction of genetic background and dietary P. Total RNA from the loin muscle of these animals was obtained for microarray analysis. Significant differences (p<0.01) in gene expression were seen based on the effect of sire line (339 genes), dietary P (18 genes) and the interaction between sire line and dietary P (31 genes). The microarray data were validated by semi-quantitative real-time PCR. These results support our hypothesis that genetic background and dietary P treatment can affect the homeorhetic control of P metabolism in pigs. Genes identified as differentially expressed in this study may be excellent candidate genes for additional work to elucidate genotype specific P requirements as well as to identify a genetic background that can maintain superior growth in a more environmentally friendly manner.
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Affiliation(s)
- A Qu
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
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16
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Skovgaard K, Mortensen S, Poulsen KT, Angen Ø, Heegaard PMH. Validation of putative reference genes for qRT-PCR normalization in tissues and blood from pigs infected with Actinobacillus pleuropneumoniae. Vet Immunol Immunopathol 2007; 118:140-6. [PMID: 17544155 DOI: 10.1016/j.vetimm.2007.04.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Revised: 03/19/2007] [Accepted: 04/26/2007] [Indexed: 11/20/2022]
Abstract
The quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) is a sensitive and very efficient technique for quantification of gene expression. However, qRT-PCR relies on accurate normalization of gene expression data, as RNA recovery and cDNA synthesis efficiency might vary from sample to sample. In the present study, six putative reference genes were validated for normalization of gene expression in three different tissues and in white blood cells from pigs experimentally infected with the common respiratory pathogen Actinobacillus pleuropneumoniae. Two dedicated validation programs (geNorm and Normfinder) were used to rank the six reference genes from best to worst. qRT-PCR data for the proinflammatory cytokine IL-6 was normalized using the proposed genes from geNorm and Normfinder as well as the commonly used reference gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH). IL-6 expression was quantified in white blood cells, liver, lymph nodes and tonsils from 10 infected pigs and 5 control pigs. After normalization using either geNorm or Normfinder IL-6 was shown to be significantly up-regulated (P<0.05) in all of the tissues from infected animals compared to non-infected control animals with a good agreement of expression differences between the two programs. On the contrary, normalization of IL-6 expression data from blood using GAPDH rendered the difference between infected and non-infected groups non-significant, and resulted in significantly different values compared to geNorm (P=0.01). Based on these results, we recommend to validate putative reference genes before normalization.
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Affiliation(s)
- Kerstin Skovgaard
- Department of Veterinary Diagnostics and Research, National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, DK-1790 Copenhagen, Denmark.
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17
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Hedegaard J, Skovgaard K, Mortensen S, Sørensen P, Jensen TK, Hornshøj H, Bendixen C, Heegaard PMH. Molecular characterisation of the early response in pigs to experimental infection with Actinobacillus pleuropneumoniae using cDNA microarrays. Acta Vet Scand 2007; 49:11. [PMID: 17466061 PMCID: PMC1868913 DOI: 10.1186/1751-0147-49-11] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2006] [Accepted: 04/27/2007] [Indexed: 12/02/2022] Open
Abstract
Background The bacterium Actinobacillus pleuropneumoniae is responsible for porcine pleuropneumonia, a widespread, highly contagious and often fatal respiratory disease of pigs. The general porcine innate immune response after A. pleuropneumoniae infection is still not clarified. The objective of this study was hence to characterise the transcriptional response, measured by using cDNA microarrays, in pigs 24 hours after experimental inoculation with A. pleuropneumoniae. Methods Microarray analyses were conducted to reveal genes being differentially expressed in inflamed versus non-inflamed lung tissue sampled from inoculated animals as well as in liver and tracheobronchial lymph node tissue sampled from three inoculated animals versus two non-inoculated animals. The lung samples were studied using a porcine cDNA microarray with 5375 unique PCR products while liver tissue and tracheobronchial lymph node tissue were hybridised to an expanded version of the porcine microarray with 26879 unique PCR products. Results A total of 357 genes differed significantly in expression between infected and non-infected lung tissue, 713 genes differed in expression in liver tissue from infected versus non-infected animals and 130 genes differed in expression in tracheobronchial lymph node tissue from infected versus non-infected animals. Among these genes, several have previously been described to be part of a general host response to infections encoding immune response related proteins. In inflamed lung tissue, genes encoding immune activating proteins and other pro-inflammatory mediators of the innate immune response were found to be up-regulated. Genes encoding different acute phase reactants were found to be differentially expressed in the liver. Conclusion The obtained results are largely in accordance with previous studies of the mammalian immune response. Furthermore, a number of differentially expressed genes have not previously been associated with infection or are presently unidentified. Determination of their specific roles during infection may lead to a better understanding of innate immunity in pigs. Although additional work including more animals is clearly needed to elucidate host response to porcine pleuropneumonia, the results presented in this study demonstrate three subsets of genes consistently expressed at different levels depending upon infection status.
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18
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Tuggle CK, Wang Y, Couture O. Advances in swine transcriptomics. Int J Biol Sci 2007; 3:132-52. [PMID: 17384733 PMCID: PMC1802012 DOI: 10.7150/ijbs.3.132] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Accepted: 01/02/2007] [Indexed: 01/23/2023] Open
Abstract
The past five years have seen a tremendous rise in porcine transcriptomic data. Available porcine Expressed Sequence Tags (ESTs) have expanded greatly, with over 623,000 ESTs deposited in Genbank. ESTs have been used to expand the pig-human comparative maps, but such data has also been used in many ways to understand pig gene expression. Several methods have been used to identify genes differentially expressed (DE) in specific tissues or cell types under different treatments. These include open screening methods such as suppression subtractive hybridization, differential display, serial analysis of gene expression, and EST sequence frequency, as well as closed methods that measure expression of a defined set of sequences such as hybridization to membrane arrays and microarrays. The use of microarrays to begin large-scale transcriptome analysis has been recently reported, using either specialized or broad-coverage arrays. This review covers published results using the above techniques in the pig, as well as unpublished data provided by the research community, and reports on unpublished Affymetrix data from our group. Published and unpublished bioinformatics efforts are discussed, including recent work by our group to integrate two broad-coverage microarray platforms. We conclude by predicting experiments that will become possible with new anticipated tools and data, including the porcine genome sequence. We emphasize that the need for bioinformatics infrastructure to efficiently store and analyze the expanding amounts of gene expression data is critical, and that this deficit has emerged as a limiting factor for acceleration of genomic understanding in the pig.
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Affiliation(s)
- Christopher K Tuggle
- Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA
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19
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Ponsuksili S, Murani E, Walz C, Schwerin M, Wimmers K. Pre- and postnatal hepatic gene expression profiles of two pig breeds differing in body composition: insight into pathways of metabolic regulation. Physiol Genomics 2007; 29:267-79. [PMID: 17264241 DOI: 10.1152/physiolgenomics.00178.2006] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The liver plays a central role in the regulation of the metabolic status, partitioning of nutrients, and expenditure of energy. To gain insight into hepatic metabolic pathways and key transcripts affecting traits related to body composition, liver expression profiles were compared of pigs of two breeds, the obese German Landrace (DL) and the lean Pietrain (Pi). Porcine oligonucleotide microarray were hybridized with liver cRNAs obtained at peripubertal age (180 days of age) and prenatal stages (35, 63, and 91 days postconception) that represent three developmental stages of liver, i.e., period of differentiation, period of metabolic activity, and period of glycogen accumulation. In terms of the number of genes regulated between DL and Pi, the most striking distinctions were found at peripubertal age with upregulation of key genes of lipid metabolism pathways (FASN, ACSS2, ACACA) in obese DL pigs and upregulation of genes of cell growth and/or maintenance, and protein syntheses, as well as cell proliferation pathways (PPARD, POU1F1, IGF2R), in lean Pi pigs. Moreover, time course analysis of breed-dependent expression profiles revealed breed-typical temporal regulation from prenatal stages to peripubertal age of genes assigned to biological processes involving lipid pathways and cell activity, i.e., breed differences are already initiated during early prenatal development. Information about mRNA expression levels of the two breeds differing in body composition, partitioning and utilization of nutrients and energy reveals functional candidate genes for traits related to obesity and leanness.
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Affiliation(s)
- Siriluck Ponsuksili
- Research Group Functional Genomics, Research Institute for the Biology of Farm Animals, FBN, Dummerstorf, Germany
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20
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Reverter A, Wang YH, Byrne KA, Tan SH, Harper GS, Lehnert SA. Joint analysis of multiple cDNA microarray studies via multivariate mixed models applied to genetic improvement of beef cattle. J Anim Sci 2006; 82:3430-9. [PMID: 15537761 DOI: 10.2527/2004.82123430x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In functional genomic laboratories, it is common to use the same microarray slide across studies, each investigating a unique biological question, and each analyzed separately due to computational limitations and/or because there is no hybridization of samples from different studies on one slide. However, the question of analyzing data from multiple studies is a major current issue in microarray data analysis because there are gains to be made in the accuracy of estimated effects by exploiting a covariance structure between gene expression data across studies. We propose an approach for combining multiple studies using multivariate mixed models, with the assumption of a nonzero correlation among genes across experiments, while imposing a null residual covariance. We applied this method to jointly analyze three experiments in genetics of cattle with a total of 54 arrays, each with 19,200 spots and 7,638 elements. The resulting seven-variate model contains 752,476 equations and 56 covariances. To identify differentially expressed genes, we applied model-based clustering to a linear combination of the random gene x variety interaction effect. We enhanced the biological interpretation of the results by applying an iterative algorithm to identify the gene ontology classes that significantly changed in each experiment. We found 118 elements with coordinate expression that clustered into distinct biological functions such as adipogenesis and protein turnover. These results contribute to our understanding of the mechanistic processes involved in adipogenesis and nutrient partitioning.
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Affiliation(s)
- A Reverter
- The Cooperative Research Centre for Cattle and Beef Quality, CSIRO Livestock Industries, Queensland Bioscience Precinct, St. Lucia, Queensland 4067, Australia.
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21
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Zhao SH, Kuhar D, Lunney JK, Dawson H, Guidry C, Uthe JJ, Bearson SMD, Recknor J, Nettleton D, Tuggle CK. Gene expression profiling in Salmonella Choleraesuis-infected porcine lung using a long oligonucleotide microarray. Mamm Genome 2006; 17:777-89. [PMID: 16845603 DOI: 10.1007/s00335-005-0155-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Accepted: 03/07/2006] [Indexed: 12/19/2022]
Abstract
Understanding the transcriptional response to pathogenic bacterial infection within food animals is of fundamental and applied interest. To determine the transcriptional response to Salmonella enterica serovar Choleraesuis (SC) infection, a 13,297-oligonucleotide swine array was used to analyze RNA from control, 24-h postinoculation (hpi), and 48-hpi porcine lung tissue from pigs infected with SC. In total, 57 genes showed differential expression (p < 0.001; false discovery rate = 12%). Quantitative real-time PCR (qRT-PCR) of 61 genes was used to confirm the microarray results and to identify pathways responding to infection. Of the 33 genes identified by microarray analysis as differentially expressed, 23 were confirmed by qRT-PCR results. A novel finding was that two transglutaminase family genes (TGM1 and TGM3) showed dramatic increases in expression postinoculation; combined with several other apoptotic genes, they indicated the induction of apoptotic pathways during SC infection. A predominant T helper 1-type immune response occurred during infection, with interferon gamma (IFNG) significantly increased at 48 hpi. Genes induced by IFNs (GBP1, GBP2, C1S, C1R, MHC2TA, PSMB8, TAP1, TAP2) showed increased expression during porcine lung infection. These data represent the first thorough investigation of gene regulation pathways that control an important porcine respiratory and foodborne bacterial infection.
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Affiliation(s)
- Shu-Hong Zhao
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, 50011, USA
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22
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Kerr CA, Bunter KL, Seymour R, Shen B, Reverter A. The heritability of the expression of two stress-regulated gene fragments in pigs. J Anim Sci 2006; 83:1753-65. [PMID: 16024694 DOI: 10.2527/2005.8381753x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pigs reared in commercial production units sometimes encounter stressors that significantly decrease growth performance. It is hypothesized that response to stress challenges could potentially be used as selection criteria. This study aimed to investigate, in a commercial setting, the heritability of two target genes previously shown to be induced in response to stress, and related to growth performance, in an experimental situation. Blood samples (n = 2,392) were collected from three separate breeding lines of pedigreed and performance-tested boars between 24 to 25 wk of age. The expression levels of a novel fragment, '29a,' and the calcitonin receptor gene (CTR) were quantified using quantitative real-time PCR (qRT-PCR) on a subset (n = 709) of the blood samples. Gene expression levels were corrected for the efficiency of PCR reactions and also computed directly from threshold cycle (Ct) values. Resulting data showed a skewed nonnormal distribution of expression levels for the target genes relative to the endogenous control, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and were highly variable. Analyses were subsequently performed using untransformed and log-transformed data, with outliers identified and deleted in edited data sets. Regardless of the transformation or editing procedures for outliers applied, there was negligible genetic variation for the expression of target genes relative to GAPDH. In contrast, repeatabilities of replicate samples were generally high (between 0.54 and 0.67). Absolute expression levels for GAPDH and 29a were lowly heritable (h2 of about 0.04), although estimates did not exceed their SE. Subsetting the data according to whether the target gene had a higher or lower level of expression than GAPDH was then performed using the relevant Ct values. In the subset where the target gene was more highly expressed than GAPDH, a moderate estimate of heritability (0.18 +/- 0.10) for the log-transformed absolute expression level of 29a was obtained, whereas the estimate for its expression relative to GAPDH was lower (0.09 +/- 0.07). Estimates of heritability did not increase in the subset of low expression data. The limitations of using gene expression measures as potential selection criteria in commercial situations are discussed.
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Affiliation(s)
- C A Kerr
- CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia.
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Kadarmideen HN, von Rohr P, Janss LLG. From genetical genomics to systems genetics: potential applications in quantitative genomics and animal breeding. Mamm Genome 2006; 17:548-64. [PMID: 16783637 PMCID: PMC3906707 DOI: 10.1007/s00335-005-0169-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Accepted: 02/21/2006] [Indexed: 11/04/2022]
Abstract
This article reviews methods of integration of transcriptomics (and equally proteomics and metabolomics), genetics, and genomics in the form of systems genetics into existing genome analyses and their potential use in animal breeding and quantitative genomic modeling of complex traits. Genetical genomics or the expression quantitative trait loci (eQTL) mapping method and key findings in this research are reviewed. Various procedures and potential uses of eQTL mapping, global linkage clustering, and systems genetics are illustrated using actual analysis on recombinant inbred lines of mice with data on gene expression (for diabetes- and obesity-related genes), pathway, and single nucleotide polymorphism (SNP) linkage maps. Experimental and bioinformatics difficulties and possible solutions are discussed. The main uses of this systems genetics approach in quantitative genomics were shown to be in refinement of the identified QTL, candidate gene and SNP discovery, understanding gene-environment and gene-gene interactions, detection of candidate regulator genes/eQTL, discriminating multiple QTL/eQTL, and detection of pleiotropic QTL/eQTL, in addition to its use in reconstructing regulatory networks. The potential uses in animal breeding are direct selection on heritable gene expression measures, termed “expression assisted selection,” and genetical genomic selection of both QTL and eQTL based on breeding values of the respective genes, termed “expression-assisted evaluation.”
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Affiliation(s)
- Haja N Kadarmideen
- Statistical Animal Genetics Group, Institute of Animal Science, Swiss Federal Institute of Technology, ETH Zentrum (UNS D7), Universitaetstrasse 65, CH 8092 Zürich, Switzerland.
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Tan SH, Reverter A, Wang Y, Byrne KA, McWilliam SM, Lehnert SA. Gene expression profiling of bovine in vitro adipogenesis using a cDNA microarray. Funct Integr Genomics 2006; 6:235-49. [PMID: 16470362 DOI: 10.1007/s10142-005-0016-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2005] [Revised: 10/04/2005] [Accepted: 10/08/2005] [Indexed: 12/16/2022]
Abstract
The gene expression profile of bovine bone marrow stromal cells undergoing adipogenesis was established using a custom cDNA microarray. Cells that were treated with adipogenic stimulants and those that were not were collected at each of the six time points, and gene expression differences between the treated and untreated samples within each time point were compared using a microarray. Statistical analyses revealed that 158 genes showed a minimum fold change of 2 in at least one of the five post-differentiation time points. These genes are involved in various cellular pathways and functions, including lipogenesis, glycolysis, cytoskeleton remodelling, extracellular matrix, transcription as well as various signalling pathways such as insulin, calcium and wingless signalling. The experiment also identified 17 differentially expressed (DE) microarray elements with no assigned function. Quantitative real-time PCR was employed to validate eight DE genes, and the PCR data were found to reproduce the microarray data for these eight genes. Subsequent gene ontology annotation was able to provide a global overview of the molecular function of DE genes during adipogenesis. This analysis was able to indicate the importance of different gene categories at various stages of adipogenic conversion, thereby providing further insights into the molecular changes during bovine adipogenesis.
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Affiliation(s)
- Siok Hwee Tan
- The Cooperative Research Center for Cattle and Beef Quality, CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Qld 4067, Australia.
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Zhao SH, Recknor J, Lunney JK, Nettleton D, Kuhar D, Orley S, Tuggle CK. Validation of a first-generation long-oligonucleotide microarray for transcriptional profiling in the pig. Genomics 2005; 86:618-25. [PMID: 16216716 DOI: 10.1016/j.ygeno.2005.08.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2005] [Revised: 07/27/2005] [Accepted: 08/01/2005] [Indexed: 10/25/2022]
Abstract
A first-generation porcine oligonucleotide set, representing 13,297 cDNAs and ESTs, has been designed by Qiagen-Operon for transcriptional profiling. To validate this set, microarrays containing each 70-mer oligonucleotide, referred to as the Qiagen-NRSP8 array, were hybridized with targets from porcine adult liver, lung, muscle, or small intestine. Transcriptome analyses showed that 11,328 of the oligonucleotides demonstrated expression in at least one tissue. Statistical analyses revealed that 1810 genes showed differential expression among tissues (Bonferroni adjusted p < 0.05). Biological pathways identified by DAVID/EASE analysis using a list of 423 tissue-selective genes matched archetypal pathways in the corresponding human or mouse tissue. Real-time quantitative PCR confirmed expression patterns for 9 of 11 genes tested. Our results demonstrate that this first-generation porcine oligonucleotide array is informative and the specificity is high. This is essential validation for investigators using the Qiagen-NRSP8 array for porcine functional genomics and for using the pig in modeling important physiological problems.
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Affiliation(s)
- Shu-Hong Zhao
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011, USA
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26
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Ponsuksili S, Murani E, Schellander K, Schwerin M, Wimmers K. Identification of functional candidate genes for body composition by expression analyses and evidencing impact by association analysis and mapping. ACTA ACUST UNITED AC 2005; 1730:31-40. [PMID: 16005530 DOI: 10.1016/j.bbaexp.2005.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Revised: 05/27/2005] [Accepted: 06/02/2005] [Indexed: 11/28/2022]
Abstract
This study aims to identify hepatic genes affecting traits related to muscularity and obesity by combining expression analyses, association studies, and gene mapping. Functional candidate genes with trait-associated expression were obtained by hybridising custom made application-specific cDNA microarrays with targets of discordant sib pairs of a porcine experimental population. Out of 238 genes addressed, nine genes were regulated by the factor>or=2 between the sib pairs. Differential gene expression was independently confirmed for selected genes by real time RT-PCR. Transcript levels of four genes (APOH, PEDF, SLCO1B3, TBG) were significantly different between the phenotype groups. Screening for trait associated markers within TBG and APOH by comparative sequencing of discordant sib pairs revealed a SNP at position nt 778 (A>C) (N229H) of TBG. No polymorphism in APOH was detected. Association analysis confirmed effects of TBG on carcass traits statistically. Allocating TBG to a QTL region on chromosome X revealed genetic evidence for the effect. Moreover, our results indicate that there are probably two polymorphisms segregating-one (N229H) altering binding capability of TBG and another still to be detected altering the transcription rate of TBG.
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Affiliation(s)
- Siriluck Ponsuksili
- Institute of Animal Breeding and Genetics, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany; Research Institute for the Biology of Farm Animals, Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
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27
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Donaldson L, Vuocolo T, Gray C, Strandberg Y, Reverter A, McWilliam S, Wang Y, Byrne K, Tellam R. Construction and validation of a Bovine Innate Immune Microarray. BMC Genomics 2005; 6:135. [PMID: 16176586 PMCID: PMC1261263 DOI: 10.1186/1471-2164-6-135] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Accepted: 09/22/2005] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Microarray transcript profiling has the potential to illuminate the molecular processes that are involved in the responses of cattle to disease challenges. This knowledge may allow the development of strategies that exploit these genes to enhance resistance to disease in an individual or animal population. RESULTS The Bovine Innate Immune Microarray developed in this study consists of 1480 characterised genes identified by literature searches, 31 positive and negative control elements and 5376 cDNAs derived from subtracted and normalised libraries. The cDNA libraries were produced from 'challenged' bovine epithelial and leukocyte cells. The microarray was found to have a limit of detection of 1 pg/microg of total RNA and a mean slide-to-slide correlation co-efficient of 0.88. The profiles of differentially expressed genes from Concanavalin A (ConA) stimulated bovine peripheral blood lymphocytes were determined. Three distinct profiles highlighted 19 genes that were rapidly up-regulated within 30 minutes and returned to basal levels by 24 h; 76 genes that were up-regulated between 2-8 hours and sustained high levels of expression until 24 h and 10 genes that were down-regulated. Quantitative real-time RT-PCR on selected genes was used to confirm the results from the microarray analysis. The results indicate that there is a dynamic process involving gene activation and regulatory mechanisms re-establishing homeostasis in the ConA activated lymphocytes. The Bovine Innate Immune Microarray was also used to determine the cross-species hybridisation capabilities of an ovine PBL sample. CONCLUSION The Bovine Innate Immune Microarray has been developed which contains a set of well-characterised genes and anonymous cDNAs from a number of different bovine cell types. The microarray can be used to determine the gene expression profiles underlying innate immune responses in cattle and sheep.
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Affiliation(s)
- Laurelea Donaldson
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia 4067, QLD, Australia
- Co-operative Research Centre for Innovative Dairy Products, Level 1, 84 William St, Melbourne, 3000, VIC, Australia
| | - Tony Vuocolo
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia 4067, QLD, Australia
- Co-operative Research Centre for Innovative Dairy Products, Level 1, 84 William St, Melbourne, 3000, VIC, Australia
| | - Christian Gray
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia 4067, QLD, Australia
- Co-operative Research Centre for Innovative Dairy Products, Level 1, 84 William St, Melbourne, 3000, VIC, Australia
| | - Ylva Strandberg
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia 4067, QLD, Australia
- Co-operative Research Centre for Innovative Dairy Products, Level 1, 84 William St, Melbourne, 3000, VIC, Australia
| | - Antonio Reverter
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia 4067, QLD, Australia
- Co-operative Research Centre for Innovative Dairy Products, Level 1, 84 William St, Melbourne, 3000, VIC, Australia
| | - Sean McWilliam
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia 4067, QLD, Australia
- Co-operative Research Centre for Innovative Dairy Products, Level 1, 84 William St, Melbourne, 3000, VIC, Australia
| | - YongHong Wang
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia 4067, QLD, Australia
| | - Keren Byrne
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia 4067, QLD, Australia
| | - Ross Tellam
- CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd., St Lucia 4067, QLD, Australia
- Co-operative Research Centre for Innovative Dairy Products, Level 1, 84 William St, Melbourne, 3000, VIC, Australia
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2004. [PMCID: PMC2447433 DOI: 10.1002/cfg.356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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