Metals Toxicity as Seen from The Rainbow Trout Transcriptome
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Although lethal toxicity of cationic metals in fish has been well-studied, the molecular determinants of how toxicity varies across metal, exposure concentration, and exposure duration are not well understood. Therefore, we compared transcriptome changes in gill and liver of juvenile rainbow trout (Oncorhynchus mykiss) exposed to copper (Cu), cadmium (Cd), or zinc (Zn) to control laboratory waters, 17, or 50% of available metal-specific 96-hour LC50 concentrations for 48 and 96 hours (N=6 within each of 36 sample groups). From 190 of 216 fish, 15,305,931 ± 25,483 trimmed Illumina reads/sample were aligned to an Omyk_RefSeq template consisting of 79,244 transcripts. Expression levels compared to controls were normalized with DESeq2, and a combined set of 4664 differentially expressed genes (DEGs) were identified (i.e., ≥2-fold change, corrected P ≤0.05 & 95% confidence). The number of DEGs differed by metal (P<0.05); Cu (3751), Zn (1047), and Cd (24), with only a single DEG shared by all 3 metals. While Cu primarily affected gene expression in the liver, Cd and Zn effects were concentrated within gill tissue. The total number of DEGs increased with exposure duration (P<0.05), but not exposure concentration (P=0.864). Principal components analysis showed that PC1 accounted for 63.6% of the variation in the expression data and was associated with tissue differences, with the influence of metal being secondary. Gene Ontology (GO) enrichment analyses were performed for all up and down regulated DEG sets (corrected P≤0.05, FDR ≤ 0.05). A total of 1484 GOs were enriched for 18 DEG sets. Interestingly, the single shared transcript had 76 GO annotations plus 3 enzyme codes related to transferring phosphorous-containing groups. Altered expression of DEGs coding for enzymes occurred in 112 KEGG pathways. Six of the pathways were affected by 10 or more treatment conditions. Most notably, expression of genes for multiple enzymes in purine and thiamine metabolism pathways were variously changed for 15 and 13 of the DEG sets, respectively, which spanned all metals, durations, concentrations, and tissues. The unique gene expression patterns across metals and tissues suggests that each metal may bind tissue sites differently during exposure; however, there appears to be some convergence among impacted downstream biochemical pathways that warrants further investigation.