Use of comparative genomics approaches to characterize interspecies differences in response to environmental chemicals: challenges, opportunities, and research needs

Cell-assembled extracellular matrix (CAM) sheet production: Translation from using human to large animal cells

We have created entirely biological tissue-engineered vascular grafts (TEVGs) using sheets of cell-assembled extracellular matrix (CAM) produced by human fibroblasts in vitro. A large animal TEVG would allow long-term pre-clinical studies in a clinically relevant setting (graft size and allogeneic setting). Therefore, canine, porcine, ovine, and human skin fibroblasts were compared for their ability to form CAM sheets. Serum sourcing greatly influenced CAM production in a species-dependent manner. Ovine cells produced the most homogenous and strongest animal CAM sheets but remained ≈3-fold weaker than human sheets despite variations of serum, ascorbate, insulin, or growth factor supplementations. Key differences in cell growth dynamics, tissue development, and tissue architecture and composition were observed between human and ovine. This study demonstrates critical species-to-species differences in fibroblast behavior and how they pose a challenge when attempting to substitute animal cells for human cells during the development of tissue-engineered constructs that require long-term cultures.

Use cases, best practice and reporting standards for metabolomics in regulatory toxicology

Metabolomics is a widely used technology in academic research, yet its application to regulatory science has been limited. The most commonly cited barrier to its translation is lack of performance and reporting standards. The MEtabolomics standaRds Initiative in Toxicology (MERIT) project brings together international experts from multiple sectors to address this need. Here, we identify the most relevant applications for metabolomics in regulatory toxicology and develop best practice guidelines, performance and reporting standards for acquiring and analysing untargeted metabolomics and targeted metabolite data. We recommend that these guidelines are evaluated and implemented for several regulatory use cases.

A risk assessment-driven quantitative comparison of gene expression profiles in PBMCs and white adipose tissue of humans and rats after isoflavone supplementation

Quantitative insight into species differences in risk assessment is expected to reduce uncertainty and variability related to extrapolation from animals to humans. This paper explores quantification and comparison of gene expression data between tissues and species from intervention studies with isoflavones. Gene expression data from peripheral blood mononuclear cells (PBMCs) and white adipose tissue (WAT) after 8wk isoflavone interventions in postmenopausal women and ovariectomized F344 rats were used. A multivariate model was applied to quantify gene expression effects, which showed 3-5-fold larger effect sizes in rats compared to humans. For estrogen responsive genes, a 5-fold greater effect size was found in rats than in humans. For these genes, intertissue correlations (r = 0.23 in humans, r = 0.22 in rats) and interspecies correlation in WAT (r = 0.31) were statistically significant. Effect sizes, intertissue and interspecies correlations for some groups of genes within energy metabolism, inflammation and cell cycle processes were significant, but weak. Quantification of gene expression data reveals differences between rats and women in effect magnitude after isoflavone supplementation. For risk assessment, quantification of gene expression data and subsequent calculation of intertissue and interspecies correlations within biological pathways will further strengthen knowledge on comparability between tissues and species.

A genomics-based framework for identifying biomarkers of human neurodevelopmental toxicity

Human embryonic stem cell (hESC) neural differentiation models have tremendous potential for evaluating environmental compounds in terms of their ability to induce neurodevelopmental toxicity. Genomic based-approaches are being applied to identify changes underlying normal human development (in vitro and in vivo) and the effects of environmental exposures. Here, we investigated whether mechanisms that are shared between hESC neural differentiation model systems and human embryos are candidate biomarkers of developmental toxicities for neurogenesis. We conducted a meta-analysis of transcriptomic datasets with the goal of identifying differentially expressed genes that were common to the hESC-model and human embryos. The overlapping NeuroDevelopmental Biomarker (NDB) gene set contained 304 genes which were enriched for their roles in neurogenesis. These genes were investigated for their utility as candidate biomarkers in the context of toxicogenomic studies focused on the effects of retinoic acid, valproic acid, or carbamazepine in hESC models of neurodifferentiation. The results revealed genes, including 13 common targets of the 3 compounds, that were candidate biomarkers of neurotoxicity in hESC-based studies of environmental toxicants.

Uncertainties in human health risk assessment of environmental contaminants: A review and perspective

Addressing uncertainties in human health risk assessment is a critical issue when evaluating the effects of contaminants on public health. A range of uncertainties exist through the source-to-outcome continuum, including exposure assessment, hazard and risk characterisation. While various strategies have been applied to characterising uncertainty, classical approaches largely rely on how to maximise the available resources. Expert judgement, defaults and tools for characterising quantitative uncertainty attempt to fill the gap between data and regulation requirements. The experiences of researching 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) illustrated uncertainty sources and how to maximise available information to determine uncertainties, and thereby provide an 'adequate' protection to contaminant exposure. As regulatory requirements and recurring issues increase, the assessment of complex scenarios involving a large number of chemicals requires more sophisticated tools. Recent advances in exposure and toxicology science provide a large data set for environmental contaminants and public health. In particular, biomonitoring information, in vitro data streams and computational toxicology are the crucial factors in the NexGen risk assessment, as well as uncertainties minimisation. Although in this review we cannot yet predict how the exposure science and modern toxicology will develop in the long-term, current techniques from emerging science can be integrated to improve decision-making.

Are adverse outcome pathways here to stay?

Social pressure to minimize the use of animal testing and the ever-increasing concern on animal welfare, together with the need for more human-relevant and more predictive toxicity tests, are some of the drivers for new approaches to chemical screening. These approaches must also be able to accelerate the screening and assessment of the thousands of chemicals that are currently in use and in development for potential hazards to human and ecological health. Ideally, approaches are needed that decrease (or eliminate) animal testing while increasing predictivity. Efforts in many countries have focused on a toxicological pathway-based vision for human health assessments relying on in vitro systems and predictive models,1 vision equally applicable to ecological risk assessment.2 A pathway-based analysis of chemical effects opens numerous opportunities to apply nontraditional approaches for understanding the risks of chemical exposure. Conservation of molecular initiating and key events leading to adverse outcomes of regulatory concern provide a defensible framework for extrapolating chemical effects across species, even if the specific adverse outcomes differ between them.3.

Network biology in development of monoclonal antibody therapeutics

Monoclonal antibodies (mAbs) are large glycoproteins that recognize and remove/neutralize a specific target. Inflammation and inflammatory diseases are often treated with mAb-based therapeutics. Mathematical modeling is widely used in development of mAbs. Bioinformatics and structural modeling is used for humanization of mAbs and PK/PD modeling is extensively used in preclinical and clinical development. The objective of this commentary is to introduce systems biology-based modeling that can accelerate and improve development of mAbs.

Environmental side effects of pharmaceutical cocktails: what we know and what we should know

Cocktails of pharmaceuticals are released in the environment after human consumption and due to the incomplete removal at the wastewater treatment plants. Pharmaceuticals are considered as contaminants of emerging concern and, a plethora of journal articles addressing their possible adverse effects have been published during the past 20 years. The emphasis during the early years of research within this field, was on the assessment of acute effects of pharmaceuticals applied singly, leading to results regarding their environmental risk, potentially not realistic or relevant to the actual environmental conditions. Only recently has the focus been shifted to chronic exposure and to the assessment of cocktail effects. To this end, this review provides an up-to-date compilation of 57 environmental and human toxicology studies published during 2000-2014 dealing with the adverse effects of pharmaceutical mixtures. The main challenges regarding the design of experiments and the analysis of the results regarding the effects of pharmaceutical mixtures to different biological systems are presented and discussed herein. The gaps of knowledge are critically reviewed highlighting specific future research needs and perspectives.

Endocrinology: advances through omics and related technologies

The rapid development of new omics technologies to measure changes at genetic, transcriptomic, proteomic, and metabolomics levels together with the evolution of methods to analyze and integrate the data at a systems level are revolutionizing the study of biological processes. Here we discuss how new approaches using omics technologies have expanded our knowledge especially in nontraditional models. Our increasing knowledge of these interactions and evolutionary pathway conservation facilitates the use of nontraditional species, both invertebrate and vertebrate, as new model species for biological and endocrinology research. The increasing availability of technology to create organisms overexpressing key genes in endocrine function allows manipulation of complex regulatory networks such as growth hormone (GH) in transgenic fish where disregulation of GH production to produce larger fish has also permitted exploration of the role that GH plays in testis development, suggesting that it does so through interactions with insulin-like growth factors. The availability of omics tools to monitor changes at nearly any level in any organism, manipulate gene expression and behavior, and integrate data across biological levels, provides novel opportunities to explore endocrine function across many species and understand the complex roles that key genes play in different aspects of the endocrine function.

Interspecies Differences in Reaction to a Biodegradable Subcutaneous Tissue Filler

Soft tissue filler products have become very popular in recent years, with ever-increasing medical and aesthetic indications. While generally considered safe, the number of reported complications with tissue fillers is growing. Nevertheless, there is no specific animal model that is considered as the gold standard for assessing safety or efficacy of tissue fillers, and there are very little data on interspecies differences in reaction to these products. Here, we report on interspecies differences in reaction to a subcutaneous injectable co-polyester, composed of castor oil and citric acid. Comparison of the histopathological local tissue changes following 1-month postimplantation, indicated that in rats the reaction consisted of cavities, surrounded by relatively thin fibrotic enveloping capsule. In contrast, an unexpected severe inflammatory granulomatous reaction was noticed in Sinclair minipigs. To our knowledge, this is the first report on significant interspecies differences in sensitivity to tissue fillers. It emphasizes the importance of using the appropriate animal model for performing preclinical biocompatibility assays for biodegradable polymers, tissue fillers, and implanted medical devices in general. It also makes the Sinclair minipig subject for scrutiny as an animal model in future biocompatibility studies.

Current perspectives on the use of alternative species in human health and ecological hazard assessments

BACKGROUND

Traditional animal toxicity tests can be time and resource intensive, thereby limiting the number of chemicals that can be comprehensively tested for potential hazards to humans and/or to the environment.

OBJECTIVE

We compared several types of data to demonstrate how alternative models can be used to inform both human and ecological risk assessment.

METHODS

We reviewed and compared data derived from high throughput in vitro assays to fish reproductive tests for seven chemicals. We investigated whether human-focused assays can be predictive of chemical hazards in the environment. We examined how conserved pathways enable the use of nonmammalian models, such as fathead minnow, zebrafish, and Xenopus laevis, to understand modes of action and to screen for chemical risks to humans.

RESULTS

We examined how dose-dependent responses of zebrafish embryos exposed to flusilazole can be extrapolated, using pathway point of departure data and reverse toxicokinetics, to obtain human oral dose hazard values that are similar to published mammalian chronic toxicity values for the chemical. We also examined how development/safety data for human health can be used to help assess potential risks of pharmaceuticals to nontarget species in the environment.

DISCUSSION

Using several examples, we demonstrate that pathway-based analysis of chemical effects provides new opportunities to use alternative models (nonmammalian species, in vitro tests) to support decision making while reducing animal use and associated costs.

CONCLUSIONS

These analyses and examples demonstrate how alternative models can be used to reduce cost and animal use while being protective of both human and ecological health.

An approach for integrating toxicogenomic data in risk assessment: the dibutyl phthalate case study

An approach for evaluating and integrating genomic data in chemical risk assessment was developed based on the lessons learned from performing a case study for the chemical dibutyl phthalate. A case study prototype approach was first developed in accordance with EPA guidance and recommendations of the scientific community. Dibutyl phthalate (DBP) was selected for the case study exercise. The scoping phase of the dibutyl phthalate case study was conducted by considering the available DBP genomic data, taken together with the entire data set, for whether they could inform various risk assessment aspects, such as toxicodynamics, toxicokinetics, and dose-response. A description of weighing the available dibutyl phthalate data set for utility in risk assessment provides an example for considering genomic data for future chemical assessments. As a result of conducting the scoping process, two questions--Do the DBP toxicogenomic data inform 1) the mechanisms or modes of action?, and 2) the interspecies differences in toxicodynamics?--were selected to focus the case study exercise. Principles of the general approach include considering the genomics data in conjunction with all other data to determine their ability to inform the various qualitative and/or quantitative aspects of risk assessment, and evaluating the relationship between the available genomic and toxicity outcome data with respect to study comparability and phenotypic anchoring. Based on experience from the DBP case study, recommendations and a general approach for integrating genomic data in chemical assessment were developed to advance the broader effort to utilize 21st century data in risk assessment.

Enzyme sequence similarity improves the reaction alignment method for cross-species pathway comparison

Pathway-based information has become an important source of information for both establishing evolutionary relationships and understanding the mode of action of a chemical or pharmaceutical among species. Cross-species comparison of pathways can address two broad questions: comparison in order to inform evolutionary relationships and to extrapolate species differences used in a number of different applications including drug and toxicity testing. Cross-species comparison of metabolic pathways is complex as there are multiple features of a pathway that can be modeled and compared. Among the various methods that have been proposed, reaction alignment has emerged as the most successful at predicting phylogenetic relationships based on NCBI taxonomy. We propose an improvement of the reaction alignment method by accounting for sequence similarity in addition to reaction alignment method. Using nine species, including human and some model organisms and test species, we evaluate the standard and improved comparison methods by analyzing glycolysis and citrate cycle pathways conservation. In addition, we demonstrate how organism comparison can be conducted by accounting for the cumulative information retrieved from nine pathways in central metabolism as well as a more complete study involving 36 pathways common in all nine species. Our results indicate that reaction alignment with enzyme sequence similarity results in a more accurate representation of pathway specific cross-species similarities and differences based on NCBI taxonomy.