Variation of gene expression in the liver of Nile tilapia at different time points of sub-chronic exposure to Benzo(a)pyrene
Nacira Anahi Albornoz-Abud,Rossana del Pilar Rodriguez-Canul,Reyna Cristina Colli-Dula
Cinvestav del IPN Unidad Mérida
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are pollutants of environmental concern because they are widely distributed in aquatic systems around the world. Although, benzo(a)pyrene (BaP) is a model PAH known for its carcinogenic effects in vertebrates, information on its molecular toxicity in aquatic organisms is still lacking. In teleost fish, both field and laboratory investigations have reported the impact of PAHs on reproduction, development, cardiac problems, among others. This study aimed to test for differences in gene expression in the liver of Oreochromis niloticus (Nile tilapia) between different BaP exposure times. For this purpose, total RNA sequencing expression data from liver samples of adult male tilapia sub chronically exposed to BaP for 26 and 56 days were analyzed. Tilapia were exposed intraperitoneally (ip) to repeated doses of 3 mg/kg BaP (each fish was injected every 6 days), two days after the fourth injection 26 d and the tenth injection 56 d with BaP or with carrier solution (for control organisms), the liver was excised and stored at -80° until analysis, then total RNA was extracted and sequenced. Differential expression (DE) analysis and gene set enrichment analysis (GSEA) were carried out with the help of Bioconductor packages: Rsubread, DESeq2, BioMart and ClusterProfiler. To test for any differences in gene expression at the different time points, the likelihood ratio test (LRT) from the DESeq2 package was performed, using the interaction of the factor condition and time. The results showed only 28 DE genes were significant (p < 0.05) in BaP-treated organisms of which 20 genes were over-regulated and 8 were down-regulated at 56 d compared to those at 26 d. The most significant genes were solute carrier family 25 member 36-A (SLC25A36) and methylmalonate-semialdehyde dehydrogenase [acylating] mitochondrial (ALDH6A1). Also, we observed a decrease in the thioredoxin domain containing 5 (TXNDC5) gene that has a role in protecting hypoxic cells from apoptosis. The GSEA using the KEGG database for tilapia yielded nine enriched pathways. While the taurine and hypotaurine metabolism, progesterone-mediated oocyte maturation, oocyte meiosis, mTOR signaling pathway, galactose metabolism, cell cycle and oxidative phosphorylation pathways were activated, only the ribosome and phototransduction pathway were suppressed. The deregulation of cell cycle-related pathways and activation of progesterone-mediated oocyte maturation and oocyte meiosis pathways are linked to liver cancer and cirrhosis. In this research, we emphasize how the use of Bioconductor packages allowed us to identify the differences in gene expression between two BaP exposure times and to recognize those pathways that were significantly affected and related to toxic changes in the liver of a non-model organism such as Nile tilapia. This indicates probable damage to this organ and consequently would not only impact the development and growth but possibly tilapia’s survivability.