A systems biology approach to developmental toxicology

Exposure to Concentrated Ambient PM2.5 Shortens Lifespan and Induces Inflammation-Associated Signaling and Oxidative Stress in Drosophila

Exposure to ambient PM 2.5 is associated with human premature mortality. However, it has not yet been toxicologically replicated, likely due to the lack of suitable animal models. Drosophila is frequently used in longevity research due to many incomparable merits. The present study aims to validate Drosophila models for PM 2.5 toxicity study through characterizing their biological responses to exposure to concentrated ambient PM 2.5 (CAP). The survivorship curve demonstrated that exposure to CAP markedly reduced lifespan of Drosophila. This antilongevity effect of CAP exposure was observed in both male and female Drosophila, and by comparison, the male was more sensitive [50% survivals: 20 and 48 days, CAP- and filtered air (FA)-exposed males, respectively; 21 and 40 days, CAP- and FA-exposed females, respectively]. Similar to its putative pathogenesis in humans, CAP exposure-induced premature mortality in Drosophila was also coincided with activation of pro-inflammatory signaling pathways including Jak, Jnk, and Nf-κb and increased systemic oxidative stress. Furthermore, like in humans and mammals, exposure to CAP significantly increased whole-body and circulating glucose levels and increased mRNA expression of Ilp2 and Ilp5 , indicating that CAP exposure induces dysregulated insulin signaling in Drosophila. Similar to effects on humans exposure to CAP leads to premature mortality likely through induction of inflammation-associated signaling, oxidative stress, and metabolic abnormality in Drosophila, strongly supporting that it can be a useful model organism for PM 2.5 toxicity study.

Molecular profiling of marine fauna: integration of omics with environmental assessment of the world's oceans

Many species that contribute to the commercial and ecological richness of our marine ecosystems are harbingers of environmental change. The ability of organisms to rapidly detect and respond to changes in the surrounding environment represents the foundation for application of molecular profiling technologies towards marine sentinel species in an attempt to identify signature profiles that may reside within the transcriptome, proteome, or metabolome and that are indicative of a particular environmental exposure event. The current review highlights recent examples of the biological information obtained for marine sentinel teleosts, mammals, and invertebrates. While in its infancy, such basal information can provide a systems biology framework in the detection and evaluation of environmental chemical contaminant effects on marine fauna. Repeated evaluation across different seasons and local marine environs will lead to discrimination between signature profiles representing normal variation within the complex milieu of environmental factors that trigger biological response in a given sentinel species and permit a greater understanding of normal versus anthropogenic-associated modulation of biological pathways, which prove detrimental to marine fauna. It is anticipated that incorporation of contaminant-specific molecular signatures into current risk assessment paradigms will lead to enhanced wildlife management strategies that minimize the impacts of our industrialized society on marine ecosystems.

Toxicity testing in the 21st century: a vision and a strategy

With the release of the landmark report Toxicity Testing in the 21st Century: A Vision and a Strategy, the U.S. National Academy of Sciences, in 2007, precipitated a major change in the way toxicity testing is conducted. It envisions increased efficiency in toxicity testing and decreased animal usage by transitioning from current expensive and lengthy in vivo testing with qualitative endpoints to in vitro toxicity pathway assays on human cells or cell lines using robotic high-throughput screening with mechanistic quantitative parameters. Risk assessment in the exposed human population would focus on avoiding significant perturbations in these toxicity pathways. Computational systems biology models would be implemented to determine the dose-response models of perturbations of pathway function. Extrapolation of in vitro results to in vivo human blood and tissue concentrations would be based on pharmacokinetic models for the given exposure condition. This practice would enhance human relevance of test results, and would cover several test agents, compared to traditional toxicological testing strategies. As all the tools that are necessary to implement the vision are currently available or in an advanced stage of development, the key prerequisites to achieving this paradigm shift are a commitment to change in the scientific community, which could be facilitated by a broad discussion of the vision, and obtaining necessary resources to enhance current knowledge of pathway perturbations and pathway assays in humans and to implement computational systems biology models. Implementation of these strategies would result in a new toxicity testing paradigm firmly based on human biology.

Differential toxicity of carbon nanomaterials in Drosophila: larval dietary uptake is benign, but adult exposure causes locomotor impairment and mortality

Rapid growth in nanomaterial manufacturing is raising concerns about potential adverse effects on the environment. Nanoparticle contact with intact organisms in the wild may lead to different biological responses than those observed in laboratory cell-based toxicity assays. In nature, the scale and chemistry of nanoparticles coupled with the surface properties, texture, and behaviors of the organisms will influence biologically significant exposure and ultimate toxicity. We used larval and adult Drosophila melanogaster to study the effects of carbon nanomaterial exposure under several different scenarios. Dietary uptake of fullerene C60, carbon black (CB), or single-walled or multiwalled nanotubes (SWNTs, MWNTs) delivered through the food to the larval stage had no detectable effect on egg to adult survivorship, despite evidence that the nanomaterials are taken up and become sequestered in tissue. However, when these same nanocarbons were exposed in dry form to adults, some materials (CB, SWNTs) adhered extensively to fly surfaces, overwhelmed natural grooming mechanisms, and led to impaired locomotor function and mortality. Others (C60, MWNT arrays) adhered weakly, could be removed by grooming, and did not reduce locomotor function or survivorship. Evidence is presented that these differences are primarily due to differences in nanomaterial superstructure, or aggregation state, and that the combination of adhesion and grooming can lead to active fly borne nanoparticle transport.

Using a comparative in vivo DNase I footprinting technique to analyze changes in protein–DNA interactions following phthalate exposure

Exposure to environmental chemicals often induces changes in gene expression leading to a variety of developmental and physiological problems. Understanding the underlying mechanism of these changes will aid in assessing human risk to these chemicals. Traditional methods for analyzing protein-DNA interactions include in vivo footprinting and chromatin immunoprecipitation (ChIP). However, ChIP does not provide binding location, and conventional footprinting is too subjective and time consuming for comparing protein binding in toxicological studies. Here, in vivo DNase I footprinting is adapted for use with the automated DNA sequencer to provide a semiquantitative map of changes in DNA-protein interactions in the promoter of steroidogenic acute regulatory (StAR) protein. StAR is the rate-limiting step in testosterone biosynthesis and is downregulated following in utero di-butyl phthalate (DBP) treatment in rats through an unknown mechanism. In vivo footprinting identified three regions of altered DNase digestibility following DBP treatment, and EMSA identified the corresponding transcription factors as SF-1, c/ebp beta, and GATA4. ChIP assays confirmed changes in protein-binding activity of SF-1 and c/ebp beta, but only c/ebp beta gesponds to only DBP. This suggests that c/ebp beta ginding is involved in DBP-induced transcriptional changes. By tailoring in vivo footprinting for toxicological studies, it can provide a detailed and accurate map of protein-DNA interactions and is an excellent first step in determining the changes in the structure of transcriptional machinery following an exogenous chemical treatment.

Integrative database management for mouse development: Systems and concepts

Cells in the developing embryo must integrate complex signals from the genome and environment to make decisions about their behavior or fate. The ability to understand the fundamental biology of the decision-making process, and how these decisions may go awry during abnormal development, requires a systems biology paradigm. Presently, the ability to build models with predictive capability in birth defects research is constrained by an incomplete understanding of the fundamental parameters underlying embryonic susceptibility, sensitivity, and vulnerability. Key developmental milestones must be parameterized in terms of system structure and dynamics, the relevant control methods, and the overall design logic of metabolic and regulatory networks. High-content data from genome-based studies provide some comprehensive coverage of these operational processes but a key research challenge is data integration. Analysis can be facilitated by data management resources and software to reveal the structure and function of bionetwork motifs potentially associated with an altered developmental phenotype. Borrowing from applied mathematics and artificial intelligence, we conceptualize a system that can help address the new challenges posed by the transformation of birth defects research into a data-driven science.

Risk assessment of chemicals potentially affecting male fertility

Male reproductive toxicity involves a broad range of targets and mechanisms such as direct effects on the seminiferous epithelium and/or on Leydig and Sertoli cells supporting spermatogenesis, epididymal sperm maturation as well as endocrine disruption. Direct effects on spermatogenesis may be adequately revealed through both reproduction and repeated-dose toxicity studies; however, more research is needed on early markers of effect and on long-term sequelae of short-term exposures. Endocrine-related mechanisms are particularly relevant to subtle, but persistent effects on reproductive development due to altered early programming; the two-generation study is the test of choice, whereas targeted studies on the prepubertal phase are also desirable. Studies using in vitro methods as well as toxicogenomics are increasing; although gaps exist and much validation work is needed, in perspective, such approaches may be important in order to select compound, understand mechanisms, as well identify biomarkers of potential use also in human studies.

A Systems-Based Computational Model for Dose-Response Comparisons of Two Mode of Action Hypotheses for Ethanol-Induced Neurodevelopmental Toxicity

Investigations into the potential mechanisms for ethanol-induced developmental toxicity have been ongoing for over 30 years since Fetal Alcohol Syndrome (FAS) was first described. Neurodevelopmental endpoints are particularly sensitive to in utero exposure to alcohol as suggested by the more prevalent alcohol-related neurodevelopmental disorder (ARND). The inhibition of proliferation during neurogenesis and the induction of apoptosis during the period of synaptogenesis have been identified as potentially important mechanisms for ARND. However, it is unclear how these two mechanisms quantitatively relate to the dose and timing of exposure. We have extended our model of neocortical neurogenesis to evaluate apoptosis during synaptogenesis. This model construct allows quantitative evaluation of the relative impacts on neuronal proliferation versus apoptosis during neocortical development. Ethanol-induced lengthening of the cell cycle of neural progenitor cells during rat neocortical neurogenesis (G13-G19) is used to compute the number of neurons lost after exposure during neurogenesis. Ethanol-induced dose-dependent increases in cell death rates are applied to our apoptosis model during rat synaptogenesis (P0-P14), when programmed cell death plays a major role in shaping the future neocortex. At a human blood ethanol concentration that occurs after 3-5 drinks ( approximately 150 mg/dl), our model predicts a 20-30% neuronal deficit due to inhibition of proliferation during neurogenesis, while a similar exposure during synaptogenesis suggests a 7-9% neuronal loss through induction of cell death. Experimental in vitro and in vivo dose-response research and stereological research on long-term neuronal loss after developmental exposure to ethanol is compared to our model predictions. Our computational model allows for quantitative, systems-level comparisons of mechanistic hypotheses for perturbations during specific neurodevelopmental periods.