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Validation of the Swine Protein-Annotated Oligonucleotide Microarray.

ABSTRACT: In this study we evaluate the Swine Protein-Annotated Oligonucleotide Microarray by profiling the expression of transcripts in four porcine tissues. We validate the hybridization results by comparative analysis of expression in human orthologs, confirm expression patterns for a subset of genes by QPCR, and assess the usefulness of designed control oligonucleotides. Simple descriptive diagnostic analyses of PM/MM probe sets introduced in this paper are useful to detect non-specific hybridization. Using comparative transcriptional profiling, we found that the microarray data correlate to QPCR data for most genes detected as differentially expressed using the microarray platform. Moreover, comparison to human ortholog expression confirmed the utility of experiments based on this array in swine species as a biomedical model for human tissue specific expression.

ORGANISM(S): Sus scrofa

PROVIDER: GSE13095 | GEO | 2008/11/04

SECONDARY ACCESSION(S): PRJNA109927

REPOSITORIES: GEO

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Project description:Background: The 2009 pandemic H1N1 influenza virus emerged in swine and quickly became a major global health threat. In mouse, non-human primate, and swine infection models, the pH1N1 virus efficiently replicates in the lung and induces pro-inflammatory host responses; however, whether similar or different cellular pathways were impacted by pH1N1 virus across independent infection models remains to be further defined. To address this, we have performed a comparative transcriptomic analysis of acute host responses to a single pH1N1 influenza virus, A/California/04/2009 (CA04), in the lung of mice, macaques and swine. Results: Despite similarities in the clinical course, we observed differences in inflammatory molecules elicited, and the kinetics of their gene expression changes across all three species. The retinoid X receptor (RXR) signaling pathway controlling pro-inflammatory and metabolic processes was differentially regulated during infection in each species, though the heterodimeric RXR partner, pathway associated signaling molecules, and gene expression patterns differed in each species. Conclusions: By comparing transcriptional changes in the context of clinical and virological measures, we identified differences in the host transcriptional response to pH1N1 virus across independent models of acute infection. Antiviral resistance and the emergence of new influenza viruses have placed more focus on developing drugs that target the immune system. Underlying overt clinical disease are molecular events that suggest therapeutic targets identified in one host may not be appropriate in another. The goal of this experiment was to use global gene expression profiling to understand swine lung host responses to pandemic H1N1 influenza A/Californica/04/2009 (CA04) virus infection and compare acute host responses across independent species. Four-week-old crossbred pigs (Sus Scrofa) were inoculated intratracheally with either 10^6 TCID50/pig egg-derived 2009 pandemic influenza A/California/04/2009 virus (n = 5) or mock inoculated with non-infectious cell culture supernatant (control; n = 4). Animals were euthanized on day 7 post-infection and lung samples were used for microarray.

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Validation of the Swine Protein-Annotated Oligonucleotide Microarray.

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