Extending Immunological Profiling in the Gilthead Sea Bream, Sparus aurata, by Enriched cDNA Library Analysis, Microarray Design and Initial Studies upon the Inflammatory Response to PAMPs

Abstract

21 páginas, 7 figuras, 3 tablas.-- Sebastian Boltaña ... et al.-- This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) licenseThis study describes the development and validation of an enriched oligonucleotide-microarray platform for Sparus aurata (SAQ) to provide a platform for transcriptomic studies in this species. A transcriptome database was constructed by assembly of gilthead sea bream sequences derived from public repositories of mRNA together with reads from a large collection of expressed sequence tags (EST) from two extensive targeted cDNA libraries characterizing mRNA transcripts regulated by both bacterial and viral challenge. The developed microarray was further validated by analysing monocyte/macrophage activation profiles after challenge with two Gram-negative bacterial pathogen-associated molecular patterns (PAMPs; lipopolysaccharide (LPS) and peptidoglycan (PGN)). Of the approximately 10,000 EST sequenced, we obtained a total of 6837 EST longer than 100 nt, with 3778 and 3059 EST obtained from the bacterial-primed and from the viral-primed cDNA libraries, respectively. Functional classification of contigs from the bacterial- and viral-primed cDNA libraries by Gene Ontology (GO) showed that the top five represented categories were equally represented in the two libraries: metabolism (approximately 24% of the total number of contigs), carrier proteins/membrane transport (approximately 15%), effectors/modulators and cell communication (approximately 11%), nucleoside, nucleotide and nucleic acid metabolism (approximately 7.5%) and intracellular transducers/signal transduction (approximately 5%). Transcriptome analyses using this enriched oligonucleotide platform identified differential shifts in the response to PGN and LPS in macrophage-like cells, highlighting responsive gene-cassettes tightly related to PAMP host recognition. As observed in other fish species, PGN is a powerful activator of the inflammatory response in S. aurata macrophage-like cells. We have developed and validated an oligonucleotide microarray (SAQ) that provides a platform enriched for the study of gene expression in S. aurata with an emphasis upon immunity and the immune responseThis study was supported by the Consolider-Ingenio Programme 2010, project CSD2007-0002 funded by the Spanish Ministry of Science and Education, Spain to SM, and FONDAP (15110027) and FONDECYT 1150585 awarded by CONICYT-Chile to Sebastian BoltañaWe acknowledge support by the CSIC Open Access Publication Initiative through its Unit of Information Resources for Research (URICI).This study was supported by the Consolider-Ingenio Programme 2010, project CSD2007-0002 funded by the Spanish Ministry of Science and Education, Spain to SM, and FONDAP (15110027) and FONDECYT 1150585 awarded by CONICYT-Chile to Sebastian Boltaña.Peer reviewe