Andrew M. Cowie

Classifying chemical mode of action using gene networks and machine learning: A case study with the herbicide linuron

The herbicide linuron (LIN) is an endocrine disruptor with an anti-androgenic mode of action. The objectives of this study were to (1) improve knowledge of androgen and anti-androgen signaling in the teleostean ovary and to (2) assess the ability of gene networks and machine learning to classify LIN as an anti-androgen using transcriptomic data. Ovarian explants from vitellogenic fathead minnows (FHMs) were exposed to three concentrations of either 5α-dihydrotestosterone (DHT), flutamide (FLUT), or LIN for 12h. Ovaries exposed to DHT showed a significant increase in 17β-estradiol (E2) production while FLUT and LIN had no effect on E2. To improve understanding of androgen receptor signaling in the ovary, a reciprocal gene expression network was constructed for DHT and FLUT using pathway analysis and these data suggested that steroid metabolism, translation, and DNA replication are processes regulated through AR signaling in the ovary. Sub-network enrichment analysis revealed that FLUT and LIN shared more regulated gene networks in common compared to DHT. Using transcriptomic datasets from different fish species, machine learning algorithms classified LIN successfully with other anti-androgens. This study advances knowledge regarding molecular signaling cascades in the ovary that are responsive to androgens and anti-androgens and provides proof of concept that gene network analysis and machine learning can classify priority chemicals using experimental transcriptomic data collected from different fish species.

Molecular responses of Walleye (Sander vitreus) embryos to naphthenic acid fraction components extracted from fresh oil sands process-affected water

Naphthenic acid fraction components (NAFCs) are constituents of oil sands process-affected water (OSPW), which is generated as a result of unconventional oil production via surface mining in the Athabasca oil sands region. NAFCs are often considered to be major drivers of OSPW toxicity to various taxa, including fishes. However, the molecular targets of these complex mixtures are not fully elucidated. Here we examined the effects in walleye (Sander vitreus) embryos after exposure to NAFCs extracted from fresh OSPW. Eleutheroembryos (exposed to 0, 4.2 or 8.3mg/L NAFCs from 1day post-fertilization to hatch) were subsampled, measured for growth and deformities, and molecular responses were assessed via real-time polymerase chain reaction (PCR). Fourteen genes were evaluated, with a focus on the aryl-hydrocarbon receptor (AhR) - cytochrome P450 pathway (arnt, cyp1a1), the oxidative stress axis (cat, gst, sod, gpx1b), apoptosis (e.g. casp3, bax and p53), growth factor signaling (e.g. insulin-like growth factors igf1, igf1b, and igf1bp), and tissue differentiation (vim). NAFC exposure was associated with an increase in the expression of cyp1a1, and a decrease in gpx1b and ribosomal protein rps40. These results indicate that NAFC effects on walleye early-life stages may be mediated through oxidative stress via pathways that include AhR.

Transcript variability and physiological correlates in the fathead minnow ovary: Implications for sample size, and experimental power.

Fundamental studies characterizing transcript variability in teleost tissues are needed if molecular endpoints are to be useful for regulatory ecotoxicology. The objectives of this study were to (1) measure transcript variability of steroidogenic enzymes and steroid receptors in the fathead minnow (FHM; Pimephales promelas) ovary to better determine normal variability and the sample sizes needed to detect specific effect sizes and to (2) determine how expression patterns related to higher level endpoints used in some regulatory ecotoxicology programs (e.g. relative gonad size). Estrogen receptor 2b (esr2b) and 5α-reductase a3 (srd5a3) showed high variability in the ovary (CV>1.0) while progesterone receptor (pgr), androgen receptor (ar), and esr2a showed comparatively low variability (CV=~0.5--0.7). Using these estimates, a power analysis revealed that sample sizes for real-time PCR experiments would need to be>20 to detect a 2-fold change for 7 of the transcripts examined; thus many molecular studies conducted in the fish ovary may have insufficient power to detect smaller effects. Two transcripts were correlated to steroid production in the ovary; cyp19a1 levels were positively correlated to in vitro E2 production, while ar levels were negatively correlated to in vitro T production. Thus, these transcripts may be informative molecular surrogates for ovarian steroid production. No transcript investigated showed any correlation to GSI, condition, or body weight/length. Molecular approaches in fish are increasingly used to assess biological impacts of chemical stressors; however additional studies are required that determine how molecular variability relates to higher level biological endpoints.

Molecular networks related to the immune system and mitochondria are targets for the pesticide dieldrin in the zebrafish (Danio rerio) central nervous system

The objectives of this study were to determine the behavioral and molecular responses in the adult zebrafish (Danio rerio) central nervous system (CNS) following a dietary exposure to the pesticide dieldrin. Zebrafish were fed pellets spiked with 0.03, 0.15, or 1.8μg/g dieldrin for 21days. Behavioral analysis revealed no difference in exploratory behaviors or those related to anxiety. Transcriptional networks for T-cell aggregation and selection were decreased in expression suggesting an immunosuppressive effect of dieldrin, consistent with other studies investigating organochlorine pesticides. Processes related to oxidative phosphorylation were also differentially affected by dieldrin. Quantitative proteomics (iTRAQ) using a hybrid quadrupole-Orbitrap identified 226 proteins that were different following one or more doses. These proteins included ATP synthase subunits (mitochondrial) and hypoxia up-regulated protein 1 which were decreased and NADH dehydrogenases (mitochondrial) and signal recognition particle 9 which were up-regulated. Thus, proteins affected were functionally associated with the mitochondria and a protein network analysis implicated Parkinsons disease (PD) and Huntingtons disease as diseases associated with altered proteins. Molecular networks related to mitochondrial dysfunction and T-cell regulation are hypothesized to underlie the association between dieldrin and PD. These data contribute to a comprehensive transcriptomic and proteomic biomarker framework for pesticide exposures and neurodegenerative diseases. BIOLOGICAL SIGNIFICANCE Dieldrin is a persistent organochlorine pesticide that has been associated with human neurodegenerative disease such as Parkinsons disease. Dieldrin is ranked 18th on the 2015 U.S. Agency for Toxic Substances and Disease Registry and continues to be a pesticide of concern for human health. Transcriptomics and quantitative proteomics (ITRAQ) were employed to characterize the molecular networks in the central nervous system that are altered with dietary exposure to dieldrin. We found that transcriptional and protein networks related to the immune system, mitochondria, and Parkinsons disease were preferentially affected by dieldrin. The study provides new insight into the mechanisms of dieldrin neurotoxicity that may explain, in part, the association between this pesticide and increased risks to neurodegeneration. These data contribute in a significant way to developing a molecular framework for pesticide induced neurotoxicity.

Validation of optimal reference genes for quantitative real time PCR in muscle and adipose tissue for obesity and diabetes research

The global incidence of obesity has led to an increasing need for understanding the molecular mechanisms that drive this epidemic and its comorbidities. Quantitative real-time RT-PCR (RT-qPCR) is the most reliable and widely used method for gene expression analysis. The selection of suitable reference genes (RGs) is critical for obtaining accurate gene expression information. The current study aimed to identify optimal RGs to perform quantitative transcriptomic analysis based on RT-qPCR for obesity and diabetes research, employing in vitro and mouse models, and human tissue samples. Using the ReFinder program we evaluated the stability of a total of 15 RGs. The impact of choosing the most suitable RGs versus less suitable RGs on RT-qPCR results was assessed. Optimal RGs differed between tissue and cell type, species, and experimental conditions. By employing different sets of RGs to normalize the mRNA expression of peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α), we show that sub-optimal RGs can markedly alter the PGC1α gene expression profile. Our study demonstrates the importance of validating RGs prior to normalizing transcriptional expression levels of target genes and identifies optimal RG pairs for reliable RT-qPCR normalization in cells and in human and murine muscle and adipose tissue for obesity/diabetes research.

Determining the mode of action of anti-mycobacterial C17 diyne natural products using expression profiling: evidence for fatty acid biosynthesis inhibition.

BackgroundThe treatment of microbial infections is becoming increasingly challenging because of limited therapeutic options and the growing number of pathogenic strains that are resistant to current antibiotics. There is an urgent need to identify molecules with novel modes of action to facilitate the development of new and more effective therapeutic agents. The anti-mycobacterial activity of the C17 diyne natural products falcarinol and panaxydol has been described previously; however, their mode of action remains largely undetermined in microbes. Gene expression profiling was therefore used to determine the transcriptomic response of Mycobacterium smegmatis upon treatment with falcarinol and panaxydol to better characterize the mode of action of these C17 diynes.ResultsOur analyses identified 704 and 907 transcripts that were differentially expressed in M. smegmatis after treatment with falcarinol and panaxydol respectively. Principal component analysis suggested that the C17 diynes exhibit a mode of action that is distinct to commonly used antimycobacterial drugs. Functional enrichment analysis and pathway enrichment analysis revealed that cell processes such as ectoine biosynthesis and cyclopropane-fatty-acyl-phospholipid synthesis were responsive to falcarinol and panaxydol treatment at the transcriptome level in M. smegmatis. The modes of action of the two C17 diynes were also predicted through Prediction of Activity Spectra of Substances (PASS). Based upon convergence of these three independent analyses, we hypothesize that the C17 diynes inhibit fatty acid biosynthesis, specifically phospholipid synthesis, in mycobacteria.ConclusionBased on transcriptomic responses, it is suggested that the C17 diynes act differently than other anti-mycobacterial compounds in M. smegmatis, and do so by inhibiting phospholipid biosynthesis.

Dieldrin Augments mTOR Signaling and Regulates Genes Associated with Cardiovascular Disease in the Adult Zebrafish Heart (Danio rerio)

Dieldrin is a legacy organochlorine pesticide that is persistent in the environment, despite being discontinued from use in North America since the 1970s. Some epidemiologic studies suggest that exposure to dieldrin is associated with increased risks of neurodegenerative disease and breast cancer by inducing inflammatory responses in tissues as well as oxidative stress. However, the direct effects of organochlorine pesticides on the heart have not been adequately addressed to date given that these chemicals are detectable in human serum and are environmentally persistent; thus, individuals may show latent adverse effects in the cardiovascular system due to long-term, low-dose exposure over time. Our objective was to determine whether low-level exposure to dieldrin at an environmentally relevant dose results in aberrant molecular signaling in the vertebrate heart. Using transcriptomic profiling and immunoblotting, we determined the global gene and targeted protein expression response to dieldrin treatment and show that dieldrin affects gene networks in the heart that are associated with processes related to cardiovascular disease, specifically cardiac arrest and ventricular fibrillation. We report that genes regulating inflammatory responses, a significant risk factor for cardiovascular disease, are upregulated by dieldrin whereas transcripts related to lysosomal function are significantly downregulated. To verify these findings, proteins in these pathways were examined with immunoblotting, and our results demonstrate that dieldrin constitutively activates Akt/mTOR signaling and downregulates lysosomal genes, participating in autophagy. Our data demonstrate that dieldrin induces genes associated with cardiovascular dysfunction and compromised lysosomal physiology, thereby identifying a novel mechanism for pesticide-induced cardiotoxicity.

The pesticide dieldrin disrupts proteins related to oxidative respiration and mitochondrial stress in the central nervous system

Quantitative proteins analysis was carried out in the hypothalamus of zebrafish following dietary exposure to the legacy pesticide dieldrin. Data were collected using iTRAQ labeling methodology and data were acquired using a hybrid quadrupole Orbitrap (Q Exactive) MS system (Thermo Fisher Scientific, Bremen, Germany). There were 3941 proteins identified in the hypothalamus of zebrafish, and these proteins comprised 23 unique expression patterns for proteins based on the three doses of dieldrin. There were 226 proteins that were regulated in one or more doses of dieldrin and 3715 proteins that were not affected. Thus, 5.7% of the proteins detected responded to the treatment. Many proteins that were differentially expressed were those found in, or associated with, the mitochondria. The proteomics data described in this article is associated with a research article, “Transcriptomic and proteomic analysis implicates the immune system and mitochondria as molecular targets of dieldrin in the zebrafish (Danio rerio) central nervous system” (A.M. Cowie, K.I. Sarty, A. Mercer, J. Koh, K.A. Kidd, C.J. Martyniuk, submitted) [1], and serves as a resource for researchers working in the field of pesticide exposures and protein biomarkers.

Response of oxidative stress transcripts in the brain of wild yellow perch (Perca flavescens) exposed to an environmental gradient of methylmercury

Methylmercury (MeHg) exposure and adverse health effects in fishes have been documented, but the molecular mechanisms involved in toxicity have not been fully characterized. The objectives of the current study were to (1) determine whether total Hg (THg) in the muscle was predictive of MeHg concentrations in the brain of wild female yellow perch (Perca flavescens) collected from four lakes in Kejimkujik National Park, a known biological mercury (Hg) hotspot in Nova Scotia, Canada and (2) to determine whether transcripts involved in the oxidative stress response were altered in abundance in fish collected across five lakes representing a MeHg gradient. In female yellow perch, MeHg in whole brain (0.38 to 2.00μg/g wet weight) was positively associated with THg in muscle (0.18 to 2.13μg/g wet weight) (R2=0.61, p<0.01), suggesting that muscle THg may be useful for predicting MeHg concentrations in the brain. Catalase (cat) mRNA levels were significantly lower in brains of perch collected from lakes with high Hg when compared to those individuals from lakes with relatively lower Hg (p=0.02). Other transcripts (cytochrome c oxidase, glutathione peroxidase, glutathione-s-transferase, heat shock protein 70, protein disulfide isomerase, and superoxide dismutase) did not show differential expression in the brain over the gradient. These findings suggest that MeHg may be inversely associated with catalase mRNA abundance in the central nervous system of wild fishes.