title: Long-term gene expression profile dynamics following cecal ligation and puncture in the rat.
abstract: BACKGROUND
  Despite the fact that the treatment options for septic patients have been significantly improved, the pathophysiologic changes caused by various septic cases have not been well understood. One commonly observed clinical phenomenon is the onset of a polymicrobial infection caused by bacteria that originate in the intestine but enter the peritoneum via translocation from the gut. This triggers a systemic inflammatory response via the innate immune system, which needs to be well characterized. Cecal ligation and puncture (CLP) is considered to be the gold-standard animal model by establishing infection with mixed bacterial flora and necrotic tissue to induce an inflammatory response. The aim of this study is to analyze the long-term gene expression dynamics in the rats subject to CLP in order to characterize the impact of sepsis upon liver function over an 8-d time period.
  
  
  METHODS
  Rats received CLP or its control, sham CLP (SCLP), and then they were sacrificed at 9 am on days 0 (no treatment), 1, 2, 5, and 8 post injury to collect liver samples for microarray analysis. Differentially expressed probe sets in CLP versus SCLP (q value <0.001 and P value <0.001) were combined to form one single matrix, which was then clustered using the approach of "consensus clustering" to identify subsets of transcripts with coherent expression patterns. Finally, the gene expression patterns of the clusters were further transformed into principal components, which account for 65% of the total data.
  
  
  RESULTS
  Three major clusters were obtained. The first cluster, which is mainly related to genes of anti-inflammatory response and antioxidative properties, is suppressed early in the CLP condition and later upregulated compared to the SCLP condition. Cluster 2 represents pro-inflammatory responses and signaling, along with amino acid metabolism. Cluster 3 is also associated with pro-inflammatory response. The genes of toll-like receptor signaling and hypermetabolism were identified in this cluster as well. Clusters 2 and 3 are both suppressed in the long-term response following CLP. Clusters 1 and 2 acting in concert return to the time 0 baseline in both groups, indicating resolution of both the anti-inflammatory and pro-inflammatory response; however, the SCLP response in cluster 3 shows persistent downregulation.
  
  
  CONCLUSIONS
  Characterization of long-term hepatic responses to injury is critical to understanding the dynamics of transcriptional changes following the induction of the inflammatory response, and to monitoring its effective resolution. These results showed that each condition has unique dynamics that indicate fundamental differences in the response. Furthermore, the gene ontologies suggest a link to oxidative stress over the long term that may be able to be explored for clinical treatments.
authors.affiliation: Department of Chemical and Biochemical Engineering, Rutgers, State University of New Jersey, Piscataway, NJ 08854, USA.
authors.forename: John S A
authors.initials: JS
authors.lastname: Mattick
authors.forename: Qian
authors.initials: Q
authors.lastname: Yang
authors.forename: Mehmet A
authors.initials: MA
authors.lastname: Orman
authors.forename: Marianthi G
authors.initials: MG
authors.lastname: Ierapetritou
authors.forename: Francois
authors.initials: F
authors.lastname: Berthiaume
authors.forename: Ioannis P
authors.initials: IP
authors.lastname: Androulakis
mesh_terms: D000818:Animals; D002432:Cecum / Q000293:injuries*; D004195:Disease Models, Animal; D007113:Immunity, Innate / Q000235:genetics*; D008026:Ligation; D008099:Liver / Q000502:physiology; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D051381:Rats; D017207:Rats, Sprague-Dawley; D018805:Sepsis / Q000235:genetics* / Q000276:immunology; D013995:Time; D059467:Transcriptome; D014951:Wounds, Stab / Q000235:genetics / Q000276:immunology