title: Analysis of porcine transcriptional response to Salmonella enterica serovar Choleraesuis suggests novel targets of NFkappaB are activated in the mesenteric lymph node.
abstract: BACKGROUND
  Specific knowledge of the molecular pathways controlling host-pathogen interactions can increase our understanding of immune response biology as well as provide targets for drug development and genetic improvement of disease resistance. Toward this end, we have characterized the porcine transcriptional response to Salmonella enterica serovar Choleraesuis (S. Choleraesuis), a Salmonella serovar that predominately colonizes swine, yet can cause serious infections in human patients. Affymetrix technology was used to screen for differentially expressed genes in pig mesenteric lymph nodes (MLN) responding to infection with S. Choleraesuis at acute (8 hours (h), 24 h and 48 h post-inoculation (pi)) and chronic stages (21 days (d) pi).
  
  
  RESULTS
  Analysis of variance with false discovery rate control identified 1,853 genes with significant changes in expression level (p-value < 0.01, q-value < 0.26, and fold change (FC) > 2) during infection as compared to un-inoculated control pigs. Down-regulation of translation-related genes at 8 hpi and 24 hpi implied that S. Choleraesuis repressed host protein translation. Genes involved in the Th1, innate immune/inflammation response and apoptosis pathways were induced significantly. However, antigen presentation/dendritic cell (DC) function pathways were not affected significantly during infection. A strong NFkappaB-dependent response was observed, as 58 known NFkappaB target genes were induced at 8, 24 and/or 48 hpi. Quantitative-PCR analyses confirmed the microarray data for 21 of 22 genes tested. Based on expression patterns, these target genes can be classified as an "Early" group (induced at either 8 or 24 hpi) and a "Late" group (induced only at 48 hpi). Cytokine activity or chemokine activity were enriched within the Early group genes GO annotations, while the Late group was predominantly composed of signal transduction and cell metabolism annotated genes. Regulatory motif analysis of the human orthologous promoters for both Early and Late genes revealed that 241 gene promoters were predicted to contain NFkappaB binding sites, and that of these, 51 Early and 145 Late genes were previously not known to be NFkappaB targets.
  
  
  CONCLUSIONS
  Our study provides novel genome-wide transcriptional profiling data on the porcine response to S. Choleraesuis and expands the understanding of NFkappaB signaling in response to Salmonella infection. Comparison of the magnitude and timing of porcine MLN transcriptional response to different Salmonella serovars, S. Choleraesuis and S. Typhimurium, clearly showed a larger but later transcriptional response to S. Choleraesuis. Both microarray and QPCR data provided evidence of a strong NFkappaB-dependent host transcriptional response during S. Choleraesuis infection. Our data indicate that a lack of strong DC-mediated antigen presentation in the MLN may cause S. Choleraesuis infected pigs to develop a systemic infection, and our analysis predicts nearly 200 novel NFkappaB target genes which may be applicable across mammalian species.
authors.affiliation: Department of Animal Science, and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, IA 50010, USA. yanfangw@hotmail.com
authors.forename: Yanfang
authors.initials: Y
authors.lastname: Wang
authors.forename: Oliver P
authors.initials: OP
authors.lastname: Couture
authors.forename: Long
authors.initials: L
authors.lastname: Qu
authors.forename: Jolita J
authors.initials: JJ
authors.lastname: Uthe
authors.forename: Shawn M D
authors.initials: SM
authors.lastname: Bearson
authors.forename: Daniel
authors.initials: D
authors.lastname: Kuhar
authors.forename: Joan K
authors.initials: JK
authors.lastname: Lunney
authors.forename: Dan
authors.initials: D
authors.lastname: Nettleton
authors.forename: Jack C M
authors.initials: JC
authors.lastname: Dekkers
authors.forename: Christopher K
authors.initials: CK
authors.lastname: Tuggle
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling; D054884:Host-Pathogen Interactions; D008198:Lymph Nodes / Q000378:metabolism*; D008643:Mesentery / Q000378:metabolism; D016328:NF-kappa B / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012481:Salmonella Infections, Animal / Q000235:genetics / Q000382:microbiology; D019779:Salmonella enterica / Q000502:physiology*; D013552:Swine; D013553:Swine Diseases / Q000235:genetics / Q000382:microbiology; D014158:Transcription, Genetic
chemical_list: D016328:NF-kappa B