Transcriptomic profiling in fins of Atlantic salmon parasitized with sea lice: Determining the differentially expressed transcripts in fins of lice-infected salmon at 8 days post-infection

Sea lice (e.g., Lepeophtheirus salmonis) are parasites causing costly disease outbreaks in salmon farming globally. Despite the currently available controlling practices, molecular insights into the parasite-induced host immune responses and host-pathogen interaction will provide the basis for improved and innovative treatment strategies. We investigated the early transcriptomic responses in the fins of Atlantic salmon parasitized with sea lice at the chalimus stage (8 days post-infection). Fin tissue collected from non-infected (PRE) control and at (ATT) and adjacent (ADJ) to chalimus-attachment sites from infected fish were used in profiling the global gene expression using a 44K microarray platform. Microarray analyses indicated that global transcriptomic changes resulted in 6,568 differentially expressed probes (DEPs, FDR < 5%) that include 1928 shared DEPs between ATT and ADJ compared to PRE. A direct comparison of ATT vs. ADJ revealed 90 DEPs, all of which were up-regulated in ATT. Atlantic salmon were acclimated for 14 weeks. Prior to infecting them with sea lice copipodids, pelvic fin tip samples were collected from ~5 fish from each tank (duplicate tanks). Fish were then bath-infected with L. salmonis by adding ~50 copepodids per fish to each tank for 2 h. Tissue from pelvic fin tips at (an area of the fin with lice ‘attached’, ATT) and ‘adjacent’ area (with no signs of previous lice attachment, ADJ) from chalimus attachment sites were excised at 8 days post-infection (dpi) and 30 dpi (when most lice were at their chalimus and pre-adult stages, respectively). A universal reference design was used for the microarray experiment. For the test samples, RNA was used from individual fins of fish from the 3 treatment groups. For each treatment group, we used 6 biological replicates (3 fish from each of 2 tanks). All test samples were labeled with Cy5. The common reference was a pool of 18 RNA samples from the fins of fish from all individuals invovled in microarray experiment. The common reference was labeled with Cy3. Each individual test sample was hybridized together with the common reference sample on an array, so the experiment consisted of 18 arrays.