Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Development of oligonucleotide microarray to study global gene expression profile in guinea pigs in response to tuberculosis infection

ABSTRACT: In this study we developed a guinea pig oligonucleotide microarray (GPOM) comprising of a total number of 45,220 features including 43,803 valid features from different mammalian species. These features are inclusive of 2971 newly annotated probes corresponding to 344 unique genes of guinea pig. As a case study, we utilized this array to examine the gene expression profile in guinea pig lungs in response to infection with Mycobacterium tuberculosis. Studying the global gene expression profile in guinea pigs allowed identification of the disease signature of pulmonary TB infection represented by several unique genes that are differentially regulated in this model. While, 1344 unique genes exhibited marked up regulation, 1856 genes were significantly down regulated. The newly developed tool not only finds its utility in studying the global gene expression profile associated with vaccination and/or M. tuberculosis infection in this highly useful animal model but would also be immensely useful in identification of new drug targets, testing of therapies, molecular genetic analysis for diseases other than tuberculosis as well. Genotypic Technology designed Custom Cavia porcellus 4x44k Gene Expression Array (Agilent-AMADID-019424) * In order to validate the GPOM developed in this study, we compared the gene expression profile of guinea pig lungs at 10 weeks post- M. tuberculosis infection with respect to that obtained from normal uninfected animals. To address this, guinea pigs were aerosol infected with M. tuberculosis, lungs were harvested at 10 weeks post-infection and RNA obtained from infected lungs was employed for cDNA synthesis and microarray hybridization. The gene expression was compared with the RNA sample obtained from the lungs of normal uninfected guinea pigs.

ORGANISM(S): Cavia porcellus

SUBMITTER: Anil Tyagi

PROVIDER: E-GEOD-32447 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:This study used virological, histological, and global gene expression data to compare the virulence of two 2009 pH1N1 isolates from human (A/California/04/2009) and swine (A/swine/Alberta/25/2009) to that of a 1918-like classical swine influenza virus (A/swine/Iowa/1930) in a pig model of infection. The overall goal of this study was to characterize the clinical, histological, virological and global gene expression responses to three distinct influenza A isolates in an experimental pig model of influenza infection. We compared 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. Microarray was used to assess global gene expression in the lungs at 3 and 5 days post-infection. Crossbred pigs fwere obtained from a healthy herd free of SIV and porcine reproductive and respiratory syndrome virus. These studies included two experiments: the classical H1N1 SIV (IA30) study was completed at Kansas State University's biosafety level 2 (BSL-2) facility in compliance with the Institutional Animal Care and Use Committee at Kansas State University, and the pH1N1 virus study was completed at the Central States Research Center (CSRC), Inc., BSL-3 facility (Oakland, NE), in compliance with the Institutional Animal Care and Use Committee at CSRC. In each experiment, 10 pigs were inoculated with noninfectious cell culture supernatant as controls. For the classical H1N1 SIV experiment, 10 4-week-old crossbred pigs were inoculated intratracheally with 10^6 50% tissue culture infective doses (TCID50)/pig of egg-derived IA30 virus. For the pH1N1 virus experiment, 10 4-week-old crossbred pigs were inoculated intratracheally with 10^6 TCID50/pig of either egg-derived CA/09 or Alb/09 virus. Five animals per group were euthanized at 3 and 5 days postinfection (dpi), respectively.

Project description:Porcine reproductive and respiratory syndrome caused by porcine reproductive and respiratory syndrome virus (PRRSV) is an infectious disease characterized by severe reproductive deficiency in pregnant sows, respiratory symptoms in piglets, and high mortality. In this study, we employed Affymetrix microarray chip technology to compare the gene expression profiles of lung tissue samples from Dapulian (DPL) pigs (a Chinese indigenous pig breed) and Duroc×Landrace×Yorkshire (DLY) pigs after infection with PRRSV. During infection with PRRSV, the DLY pigs exhibited the range of clinical features that typify the disease, while the DPL pigs exhibited only mild signs of the disease. The percentage of CD8+ T cells in the DPL pigs was significantly higher than that in the DLY pigs at 21 days post-infection (dpi) (p< 0.05). Interleukin (IL) 1 beta (IL-1β) and IL-2 levels showed significant differences between the DPL and DLY pigs at 0 and 7 dpi (p< 0.01). For IL-10, the DLY pigs had significantly higher values than the DPL pigs at 0 and 7 dpi (p< 0.01). Significant differences were apparent between the DPL and DLY pigs in terms of their tumor necrosis factor-alpha (TNF-α) and interferon (IFN)-gamma (IFN-γ) levels at 0 and 7 dpi (p< 0.01). Microarray data revealed 16 differentially expressed genes in the lung tissue samples from the DLY and DPL pigs (q≤5%), of which LOC100516029 and LOC100523005 were up-regulated in the PRRSV-infected DPL pigs, while the other 14 genes were down-regulated in the PRRSV-infected DPL pigs compared with the PRRSV-infected DLY pigs. The expression levels of 10 of the 16 genes, namely CCDC84, C6ORF52, THYMOSIN, PRVE, HSPCB, CYP2J2, AMPD3, TOR1AIP2, PTGES3, and ACOX3, were validated by real-time quantitative RT-PCR. This study provides a platform for further investigation of the molecular mechanisms underlying the differential immune responses to PRRSV infection in different breeds or lines of pig. We investigated the response of lung tissues from Dapulian (DPL) pigs (a Chinese indigenous pig breed) and Duroc×Landrace×Yorkshire (DLY) pigs infected with porcine reproductive and respiratory syndrome virus (strain JXA1) by using the Affymetrix Porcine Genome Array. Sixteen healthy 30-day-old weaned DPL pigs were selected from the Jiaxiang Dapulian farm, Jining City, China, and 15 healthy 30-day-old weaned DLY pigs were obtained from a commercial farm with high standards of animal health. These pigs were free from PRRSV, porcine circovirus type 2 (PCV2), pseudorabies virus (PRV), and classical swine fever virus (CSFV) as determined by ELISA tests for serum antibodies; the absence of PRRSV was also confirmed by real-time quantitative reverse transcription PCR (qRT-PCR). Pigs were randomly assigned into two groups and reared in separate places: the PRRSV-infected group consisted of 11 DPL and 10 DLY pigs, and the control group consisted of five DPL and five DLY pigs. Infections in the pigs proceeded via inoculation with 2 ml of a viral suspension of PRRSV (at a tissue culture infectious dose of 105) by dripping the solution into the nasal cavity of each pig. The control group was treated with an identical volume of PBS by the same method. Rectal temperatures and clinical examinations on the pigs were recorded daily during the experiment. Anticoagulant-treated blood and untreated blood samples were collected separately at 0, 7, 14, and 21 days post-infection (dpi) from the infected and control groups for assaying CD4+, CD8+, cytokine (interleukin (IL) 1 beta (IL-1β), IL-2, IL-10, interferon (IFN)-gamma (IFN-γ), tumor necrosis factor-alpha (TNF-α), and immunoglobulin G (IgG) protein levels. Lung samples for microarray analysis and real-time qRT-PCR analysis were collected from six infected DLY and DPL pigs (three pigs for each breed) immediately post-slaughter at 28 dpi. Total RNA was isolated from lung tissue samples and purified using an RNeasy Mini kit according to the manufacturer’s protocol. RNA was prepared using the GeneChip (AFF-900623) one cycle target for the labeling and control reagents, and the labeled RNA was hybridized in an Affymetrix Hybridization Oven 640 for sequencing.

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Development of oligonucleotide microarray to study global gene expression profile in guinea pigs in response to tuberculosis infection

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