Dynamic Zebrafish Interactome Reveals Transcriptional Mechanisms of Dioxin Toxicity

Abstract

BackgroundIn order to generate hypotheses regarding the mechanisms by which 2,3,7,8-tetrachlorodibenzo-p-dioxin (dioxin) causes toxicity, we analyzed global gene expression changes in developing zebrafish embryos exposed to this potent toxicant in the context of a dynamic gene network. For this purpose, we also computationally inferred a zebrafish (Danio rerio) interactome based on orthologs and interaction data from other eukaryotes.Methodology/Principal FindingsUsing novel computational tools to analyze this interactome, we distinguished between dioxin-dependent and dioxin-independent interactions between proteins, and tracked the temporal propagation of dioxin-dependent transcriptional changes from a few genes that were altered initially, to large groups of biologically coherent genes at later times. The most notable processes altered at later developmental stages were calcium and iron metabolism, embryonic morphogenesis including neuronal and retinal development, a variety of mitochondria-related functions, and generalized stress response (not including induction of antioxidant genes). Within the interactome, many of these responses were connected to cytochrome P4501A (cyp1a) as well as other genes that were dioxin-regulated one day after exposure. This suggests that cyp1a may play a key role initiating the toxic dysregulation of those processes, rather than serving simply as a passive marker of dioxin exposure, as suggested by earlier research.Conclusions/SignificanceThus, a powerful microarray experiment coupled with a flexible interactome and multi-pronged interactome tools (which are now made publicly available for microarray analysis and related work) suggest the hypothesis that dioxin, best known in fish as a potent cardioteratogen, has many other targets. Many of these types of toxicity have been observed in mammalian species and are potentially caused by alterations to cyp1a.

The Involvement of Cholesterol in Sepsis and Tolerance to Lipopolysaccharide Highlighted by the Transcriptome Analysis of Zebrafish (Danio rerio)

“…The interactome backbone contains 5,760 nodes (protein-protein and protein-DNA interactions) and 99,573 relationships between these proteins (interactions). The designation of protein properties was drawn from Alexeyenko et al 2010 18 NCBI gene name attributes were used to unify the protein list and were imported through the Biomart plugin. The network for the zebrafish challenges was built from within the Danio_rerio_CS interactome.…”

Toxicogenomic investigation of Tetrahymena thermophila exposed to dichlorodiphenyltrichloroethane (DDT), tributyltin (TBT), and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)

“…Although high-throughput methods have been used widely for years, they have primarily been used to screen a few responding genes rather than for network analysis at the genome level. Taking the three toxicants we investigated as examples, recent studies on network analysis of environmental pollutants have primarily focused on classical genes and pathways [45][46][47][48][49][50][51]. Thus, a suitable model and a corresponding method for network analysis at the genome level are required.…”

Regulation of Ahr signaling by Nrf2 during development: Effects of Nrf2a deficiency on PCB126 embryotoxicity in zebrafish (Danio rerio)

“…In zebrafish for example, while nrf2a has been shown to be up-regulated by TCDD (Hahn, et al, 2014), zebrafish embryos sampled immediately after a 6 h exposure to TCDD showed no evidence of altered expression of other genes typically found in the oxidative stress response at 4 dpf, and there was an increase in gstp1 expression only after 48 h of a TCDD exposure that began at 24 hours post fertilization (hpf) (Hahn, et al, 2014). An oxidative stress response was not observed in response to TCDD at least two other studies (Alexeyenko et al ., 2010; Wang et al ., 2013). This may be due to many factors including differences in timing, dose, developmental stage, species sensitivity to Ahr ligand binding, or exposure duration, or it is possible that ROS generation may not always be sufficient to alter redox signaling or activate an oxidative stress response.…”