Microarray gene expression analysis in atrophying rainbow trout muscle: An unique non-mammalian muscle degradation model

Muscle atrophy is a physiological response to diverse physiological and pathological conditions that trigger muscle deterioration through distinct cellular stimuli. Despite different physiological signals, the resulting biochemical changes in atrophying muscle share many common cascades. Muscle deterioration as a physiological response to the energetic demands of fish spawning represents a unique model for studying the mechanisms of muscle degradation in non-mammalian animals. A salmonid microarray, containing 16,006 cDNAs, was used to study the transcriptome response to atrophying fast-switch muscles from gravid rainbow trout in comparison to sterile fish. A total of 202 unique transcripts were reproducibly identified as 82 up- and 120 down-regulated genes in atrophying muscles. Transcripts having gene ontology biological process identifiers were grouped according to their functions. Muscle deterioration was associated with elevated expression of genes involved in the catheptic and collagenase proteolytic pathways, the aerobic ATP production, buffering, utilization and growth arrest. Whereas, atrophying muscle showed down-regulation of genes encoding serpin (a serine proteinase inhibitor), enzymes of anaerobic respiration, muscle proteins as well as genes required for RNA and protein biosynthesis/processing. Therefore, gene transcription of atrophying trout muscle changed in a manner similar to mammalian muscle atrophy. These changes result in an arrest of normal cell growth, net protein loss, and a decreased dependence on glycolytic cellular respiration characteristic of fast-switch muscle to aerobic respiratory mechanisms. Other changes/mechanisms unique to the fish model were discussed including genes associated with muscle atrophy reported for the first time. Keywords: muscle atrophy Mature female, fertile (diploid) and sterile (triploid) rainbow trout were collected from Flowing Springs Trout Farm (Delray, WV) during the fall spawning season in early October. Fish from each group were cultured in identical raceways receiving water from a common spring at temperature of 13±3 oC. Fish were fed ad libitum using demand-feeders. As confirmed by dissection, fertile fish were gravid with a gonado-somatic index (GSI) of 15.8 ± SD 0.3 (n=5). The GSI of sterile fish was 0.3± SD 0.2 (n=5). White muscle samples from five fish of each group were collected from the dorsal musculature and flash frozen in liquid nitrogen and stored at -80 oC until RNA extraction. Total RNA was isolated using the Trizol reagent (Invitrogen) according to manufacturer’s instruction. Poly(A)+ RNA was purified using Oligotex mRNA Mini Kit (Qiagen) according to manufacturer’s instruction. A salmonid microarray containing cDNAs representing 16,006 genes selected from atlantic salmon and rainbow trout expressed sequence tag databases was used to profile changes of gene expression in spawning-induced atrophying muscles.