Effects of Pseudorabies Virus Infection on the Tracheobronchial Lymph Node Transcriptome

Miller, Laura C.; Bayles, Darrell O.; Zanella, Eraldo Lourenso; Lager, Kelly M.

doi:10.4137/bbi.s30522

Cited by 5 publications

(7 citation statements)

References 29 publications

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“…The use of the network lead to add 9 terms strictly related to the immune system and correctly highlighting the immunogenic effect of the virus ( Supplementary Table S5). Thus, NETGE-PLUS directly pointed out the activation of immunological processes involved in the response to virus, and like Miller et al [14] gene sets related to the cytokines and other molecular mediators of immune response were here evidenced. Supplementary Table S5.…”

Section: Effect Of the Pseudorabies Virus Infection On The Swine Transupporting

confidence: 70%

“…To characterize the host-virus interactions, Miller et al [14] investigated By using GSEA, Miller et al [14] observed the induction of the host innate immune response, including the upregulation of interferon responsive genes, inflammatory response genes, and cytokine-cytokine receptor interaction.…”

Section: Effect Of the Pseudorabies Virus Infection On The Swine Tranmentioning

confidence: 99%

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NETGE-PLUS: Standard and Network-Based Gene Enrichment Analysis in Human and Model Organisms

et al. 2020

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Omics techniques provide a spectrum of information at the genomic level, whose analysis can characterize complex traits at a molecular level. The relationship among genotype and phenotype implies that from genome information the molecular pathways and biological processes underlying a given phenotype are discovered. In dealing with this problem, gene enrichment analysis has become the most widely adopted strategy. Here we present NETGE-PLUS, a Web server for standard and networkbased functional interpretation of gene sets of human and of model organisms, including Sus scrofa, Saccharomyces cerevisiae, Escherichia coli, and Arabidopsis thaliana. NETGE-PLUS enables the functional enrichment of both simple and ranked lists of genes, introducing also the possibility of exploring relationships among KEGG pathways. A Web interface makes data retrieval complete and user-friendly. NETGE-PLUS is publicly available at http://net-ge2.biocomp.unibo.it.

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Section: Effect Of the Pseudorabies Virus Infection On The Swine Transupporting

confidence: 70%

Section: Effect Of the Pseudorabies Virus Infection On The Swine Tranmentioning

confidence: 99%

NETGE-PLUS: Standard and Network-Based Gene Enrichment Analysis in Human and Model Organisms

et al. 2020

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“…The experimental design used in the original study is described in full in Miller et al, 2015 [1] and consisted of RNA isolation from porcine tracheobronchial lymph node (TBLN) tissue from infected and non-infected pigs. Pathogen-free pigs, between 4 and 5 weeks of age ( N = 40) were split into two equal ( n = 20) treatment groups and received intranasal inoculations of either a sham inoculum or a 1 × 10 6 cell culture infectious dose (CCID 50 ) of Pseudorabies virus Florida strain isolate 268 (FS 268).…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

“…The leading edge analysis allows for the GSEA to determine which subsets (referred to as the leading edge subset) of genes contributed the most to the enrichment signal of a given gene set's leading edge or core enrichment [3] . The leading edge analysis is determined from the enrichment score (ES), which is defined as the maximum deviation from zero [1] , [3] . The analysis is accomplished by setting the GSEA software parameters to define subsets of the core genes that drive the enrichment score of the GSEA clusters.…”

Section: Transcriptome Analysismentioning

confidence: 99%

Leading edge analysis of transcriptomic changes during pseudorabies virus infection

Fleming

Miller

2016

Genomics Data

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Eight RNA samples taken from the tracheobronchial lymph nodes (TBLN) of pigs that were either infected or non-infected with a feral isolate of porcine pseudorabies virus (PRV) were used to investigate changes in gene expression related to the pathogen. The RNA was processed into fastq files for each library prior to being analyzed using Illumina Digital Gene Expression Tag Profiling sequences (DGETP) which were used as the downstream measure of differential expression. Analyzed tags consisted of 21 base pair sequences taken from time points 1, 3, 6, and 14 days' post infection (dpi) that generated 1,927,547 unique tag sequences. Tag sequences were analyzed for differential transcript expression and gene set enrichment analysis (GSEA) to uncover transcriptomic changes related to PRV pathology progression. In conjunction with the DGETP and GSEA, the study also incorporated use of leading edge analysis to help link the TBLN transcriptome data to clinical progression of PRV at each of the sampled time points. The purpose of this manuscript is to provide useful background on applying the leading edge analysis to GSEA and expression data to help identify genes considered to be of high biological interest. The data in the form of fastq files has been uploaded to the NCBI Gene Expression Omnibus (GEO) (GSE74473) database.

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“…The lymph node is the place where the innate (early, non-specific) immune response talks to the adaptive (later, specific) immune system with the TBLN working specifically to drain lymphatic fluids from virus-infected lung tissues. While the TBLN contains a number of cell types, the advantage of sampling the TBLN is that both directly effect the virus on cells in the lymph nodes, as well as indirect effects on lymph nodes draining the lungs can be examined, giving our study an indication of the real host response [12,13]. While PRRSV, PCV-2, and IAV-S can induce respiratory disease in pigs that may appear somewhat clinically similar, [13][14][15][16], the cellular specificities, kinetics of clinical disease onset and duration of infection are different for each virus.…”

Section: Introductionmentioning

confidence: 99%

Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S.

2020

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Porcine reproductive and respiratory syndrome virus (PRRSV) is a major respiratory pathogen of swine that has become extremely costly to the swine industry worldwide, often causing losses in production and animal life due to their ease of spread. However, the intracellular changes that occur in pigs following viral respiratory infections are still scantily understood for PRRSV, as well as other viral respiratory infections. The aim of this study was to acquire a better understanding of the PRRS disease by comparing gene expression changes that occur in tracheobronchial lymph nodes (TBLN) of pigs infected with either porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV-2), or swine influenza A virus (IAV-S) infections. The study identified and compared gene expression changes in the TBLN of 80 pigs following infection by PRRSV, PCV-2, IAV-S, or sham inoculation. Total RNA was pooled for each group and time-point (1, 3, 6, and 14 dpi) to make 16 libraries—analyses are by Digital Gene Expression Tag Profiling (DGETP). The data underwent standard filtering to generate a list of sequence tag raw counts that were then analyzed using multidimensional and differential expression statistical tests. The results showed that PRRSV, IAV-S and PCV-2 viral infections followed a clinical course in the pigs typical of experimental infection of young pigs with these viruses. Gene expression results echoed this course, as well as uncovered genes related to intersecting and unique host immune responses to the three viruses. By testing and observing the host response to other respiratory viruses, our study has elucidated similarities and differences that can assist in the development of vaccines and therapeutics that shorten or prevent a chronic PRRSV infection.

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Effects of Pseudorabies Virus Infection on the Tracheobronchial Lymph Node Transcriptome

Cited by 5 publications

References 29 publications

NETGE-PLUS: Standard and Network-Based Gene Enrichment Analysis in Human and Model Organisms

NETGE-PLUS: Standard and Network-Based Gene Enrichment Analysis in Human and Model Organisms

Leading edge analysis of transcriptomic changes during pseudorabies virus infection

Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S.

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