Global assessment of the acute phase response in channel catfish after infection with a Gram negative bacterium

The acute phase response (APR) is a set of metabolic and physiological reactions occurring in the host in response to tissue infection or injury and is a crucial component of the larger innate immune response. The APR is best characterized by dramatic changes in the concentration of a group of plasma proteins known as acute phase proteins (APP) which are synthesized in the liver and which function in a wide range of immunity-related activities. Utilizing a second generation high-density in situ oligonucleotide microarray for catfish, we have surveyed for the first time the APR in channel catfish liver following infection with Edwardsiella ictaluri, a fast-acting bacterial pathogen that causes enteric septicemia of catfish. Our catfish microarray design (28K) builds upon a previous 19K channel catfish array by adding recently sequenced immune transcripts from channel catfish along with 7159 unique sequences from closely-related blue catfish. Analysis of microarray results using a traditional two-fold change in gene expression cutoff and a 10% false discovery rate revealed a well-developed APR in catfish, with particularly high up-regulation (>50-fold) of genes involved in iron homeostasis (i.e. intelectin, hemopexin, haptoglobin, ferritin, and transferrin). Other classical APP upregulated greater than two-fold included coagulation factors, proteinase inhibitors, transport proteins, and complement components. Up-regulation of the majority of the complement cascade including the membrane attack complex components and complement inhibitors was observed. A number of pathogen recognition receptors (PRRs) and chemokines were also differentially expressed in the liver following infection. Validation with real-time PCR confirmed microarray results. Keywords: Disease state analysis Global gene expression in the channel catfish liver 3 days after infection with virulent Edwardsiella ictaluri was measured utilizing a new 28K catfish microarray. Three replicate pools of RNA (n=25) for control fish and three replicate pools (n=25) for infected fish were analysed on 6 separate arrays. Gene calls from at least 6 probe pairs/transcript were generated in RMA, and normalized values from treatment and control replicates were compared in SAM to identify differentially expressed genes. Criteria of two-fold expression change and a 10% FDR rate were used to determine a set of significantly up- and down-regulated genes. Representative results were confirmed by real-time RT-PCR.