|ZANELLA, ERALDO - Universidad De Passo Fundo|
Submitted to: Bioinformatics and Biology Insights
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/19/2015
Publication Date: 1/24/2016
Citation: Miller, L.C., Bayles, D.O., Zanella, E.L., Lager, K.M., 2016. Effects of pseudorabies virus infection on the tracheobronchial lymph node transcriptome. Bioinformatics and Biology Insights. 9(Suppl 2):25-36.
Interpretive Summary: This paper describes experiments investigating the pig's response to a PRV infection. Specifically, what changes occur in gene expression following experimental infection. We use "gene expression" to describe the regulation of the pig's metabolic processes. As a pig responds to a PRV infection changes in metabolism reflect changes in the expression of specific genes. When a gene is "expressed," a partial copy of its DNA sequence—called messenger RNA or mRNA—is used as a template to direct the synthesis of a protein. Proteins, in turn, direct all cellular function. Gene expression profiling is the process of determining which genes are active in a specific cell or group of cells. It is accomplished by measuring mRNA, the intermediary between genes and proteins. Variation in gene expression profiles can act as an important indicator of disease or predisposition to disease. By comparing gene expression patterns between cells from different environments, such as normal tissue vs. diseased tissue, one can determine which genes are active or inactive in various disease states. Characterizing these changes gives insight to how the virus affects the host, and how the host is trying to combat the infection. For example, the lymph nodes that drain the lung act as a filter that detects pathogens, and as a local control center for the immune response. In the case of respiratory disease, studying these lymph nodes provides clues to the disease process in the lung.
Technical Abstract: This study represents the first swine transcriptome hiveplots created from GSEA data and provides a novel insight into the global transcriptome changes spanning the swine genome. RNA isolated from draining tracheobronchial lymph nodes (TBLN) from 5-week old pigs clinically infected with a feral isolate of Pseudorabies virus and uninfected were interrogated using Illumina Digital Gene Expression Tag Profiling. Over 100 million tag sequences were observed, representing 4,064,189 unique 20-base sequences collected from TBLN at time points 1, 3, 6 and 14 days post-infection (dpi). Multidimensional statistical tests were applied to determine which changes in tag abundance were significant and tags were annotated. Hiveplots were created to visualize the differential expression within the swine transcriptome defined by the Broad Institute's Gene Set Enrichment Analysis reference datasets (GSEA) between infected and uninfected, allowing us to directly compare different conditions. This study represents the first swine transcriptome hiveplots created from GSEA data and provides a novel insight into the global transcriptome changes spanning the swine genome.