Jeroen L. A. Pennings

Transcriptomics-based identification of developmental toxicants through their interference with cardiomyocyte differentiation of embryonic stem cells.

The embryonic stem cell test (EST) predicts developmental toxicity based on the inhibition of cardiomyocyte differentiation of embryonic stem cells (ESC). The subjective endpoint, the long culture duration together with the undefined applicability domain and related predictivity need further improvement to facilitate implementation of the EST into regulatory strategies. These aspects may be improved by studying gene expression changes in the ESC differentiation cultures and their modulation by compound exposure using transcriptomics. Here, we tested the developmental toxicants monobutyl phthalate and 6-aminonicotinamide. ESC were allowed to differentiated, and cardiomyocyte differentiation was assessed after 10 days of culture. RNA of solvent controls was collected after 0, 24, 48, 72 and 96 h of exposure, and RNA of developmental-toxicant-exposed cultures was collected after 24 and 96 h. Samples were hybridized to DNA microarrays, and 1355 genes were found differentially expressed among the unexposed experimental groups. These regulated genes were involved in differentiation-related processes, and Principal Component Analysis (PCA) based on these genes showed that the unexposed experimental groups appeared in chronological order in the PCA, which can therefore be regarded as a continuous representation of the differentiation track. The developmental-toxicant-exposed cultures appeared to deviate significantly from this differentiation track, which confirms the compound-modulating effects on the differentiation process. The incorporation of transcriptomics in the EST is expected to provide a more informative and improved endpoint in the EST as compared with morphology, allowing early detection of differentiation modulation. Furthermore, this approach may improve the definition of the applicability domain and predictivity of the EST.

Host Transcription Profiles upon Primary Respiratory Syncytial Virus Infection

ABSTRACT Respiratory syncytial virus (RSV) is a common cause of severe lower respiratory tract infection in children. Severe RSV disease is related to an inappropriate immune response to RSV resulting in enhanced lung pathology which is influenced by host genetic factors. To gain insight into the early pathways of the pathogenesis of and immune response to RSV infection, we determined the transcription profiles of lungs and lymph nodes on days 1 and 3 after infection of mice. Primary RSV infection resulted in a rapid but transient innate, proinflammatory response, as exemplified by the induction of a large number of type I interferon-regulated genes and chemokine genes, genes involved in inflammation, and genes involved in antigen processing. Interestingly, this response is much stronger on day 1 than on day 3 after infection, indicating that the strong transcriptional response in the lung precedes the peak of viral replication. Surprisingly, the set of down-regulated genes was small and none of these genes displayed strong down-regulation. Responses in the lung-draining lymph nodes were much less prominent than lung responses and are suggestive of NK cell activation. Our data indicate that at time points prior to the peak of viral replication and influx of inflammatory cells, the local lung response, measured at the transcriptional level, has already dampened down. The processes and pathways induced shortly after RSV infection can now be used for the selection of candidate genes for human genetic studies of children with severe RSV infection.

Exploring the zebrafish embryo as an alternative model for the evaluation of liver toxicity by histopathology and expression profiling

The whole zebrafish embryo model (ZFE) has proven its applicability in developmental toxicity testing. Since functional hepatocytes are already present from 36 h post fertilization onwards, whole ZFE have been proposed as an attractive alternative to mammalian in vivo models in hepatotoxicity testing. The goal of the present study is to further underpin the applicability of whole ZFE for hepatotoxicity testing by combining histopathology and next-generation sequencing-based gene expression profiling. To this aim, whole ZFE and adult zebrafish were exposed to a set of hepatotoxic reference compounds. Histopathology revealed compound and life-stage-specific effects indicative of toxic injury in livers of whole ZFE and adult zebrafish. Next-generation sequencing (NGS) was used to compare transcript profiles in pooled individual RNA samples of whole ZFE and livers of adult zebrafish. This revealed that hepatotoxicity-associated expression can be detected beyond the overall transcription noise in the whole embryo. In situ hybridization verified liver specificity of selected highly expressed markers in whole ZFE. Finally, cyclosporine A (CsA) was used as an illustrative case to support applicability of ZFE in hepatotoxicity testing by comparing CsA-induced gene expression between ZFE, in vivo mouse liver and HepaRG cells on the levels of single genes, pathways and transcription factors. While there was no clear overlap on single gene level between the whole ZFE and in vivo mouse liver, strong similarities were observed between whole ZFE and in vivo mouse liver in regulated pathways related to hepatotoxicity, as well as in relevant overrepresented transcription factors. In conclusion, both the use of NGS of pooled RNA extracts analysis combined with histopathology and traditional microarray in single case showed the potential to detect liver-related genes and processes within the transcriptome of a whole zebrafish embryo. This supports the applicability of the whole ZFE model for compound-induced hepatotoxicity screening.

Proteome profiling of mouse embryonic stem cells to define markers for cell differentiation and embryotoxicity

In search for alternative methods for developmental toxicity testing, we investigated whether embryonic stem cell (ESC) differentiation and its modulation by toxic exposure could be monitored by proteome profiling. We compared the proteomes of mouse ESC, differentiating ESC (DIF) and differentiating ESC exposed to the embryotoxicant monobutyl phthalate (MBP). Experiments were performed in duplicates for each cell culture and the proteins extracted from the cells were separated by one-dimensional SDS-PAGE. The identified proteins were quantified using a label-free quantitative method based on counting the observed peptides as an index of protein abundance. Fifty-seven proteins were upregulated in DIF relative to ESC, whereas 42 proteins were downregulated. Most of the upregulated proteins could be correlated with cardiomyocyte functionality. In contrast, the downregulated proteins were principally pluripotency markers, chaperones and ribosomal proteins. Higher expression levels of enzymes involved in DNA mismatch repair (MSH6) and in methylation reactions (MAT2A, AHCY) were also detected in the ESC, suggesting that these processes are more active in the ESC. In addition, the detection of gluthatione S-transferase alpha 4 (GSTA4) and Park7 DJ-1 protein (antioxidant) in ESC indicates that these cells have potential detoxification mechanisms. Furthermore, MBP affected the expression of 33 proteins, including MYH6, a cardiomyocyte-specific protein, which was significantly downregulated. MBP also affected the expression levels of chaperones, metabolic enzymes and chromatin modulating proteins, suggesting that MBP alters the differentiation process. Western blot analysis of MYH6 and HSPB1 confirmed the proteomic data. In addition, a favorable correlation was observed between protein expression and published changes in the expression of related genes at the transcriptomics level. Together, the results reveal potential protein markers that may be used as endpoints in an ESC based animal free alternative test for embryotoxicity though further studies are required for confirmation.

Discriminating classes of developmental toxicants using gene expression profiling in the embryonic stem cell test

The embryonic stem cell test (EST) has been shown to be a promising in vitro method for the prediction of developmental toxicity. In our previous studies, we demonstrated that the implementation of gene expression analysis in the EST may further improve the identification of developmental toxicants. In the present study, we investigated if gene expression profiling could be used to discriminate compound classes with distinct modes of action (MoA) using the EST protocol. Gene expression data of our previous study were used and were analyzed of embryonic stem cell (ESC) differentiation cultures exposed to six compounds belonging to two classes with distinct MoA, namely phthalates and triazoles. We used three approaches to study class-characteristic gene regulation that may be useful for discrimination of compound classes. First, at the individual gene level, gene signatures characteristic for each class were identified that successfully discriminated both classes using principal component analysis. Second, at the functional level, enriched gene ontology (GO) biological processes showed their usefulness for class discrimination via hierarchical clustering. Third, two previously identified gene sets, which we designed to predict developmental toxicity, appeared successful in separating phthalate from triazole compounds. In summary, we established the possibility to discriminate between compound classes in the EST system using three different specific transcriptomics-based approaches. Differential gene expression information specific for the class of compound under study may be employed to optimize prioritization of compounds within that class for further testing.

In vitro immunotoxicity of bis(tri-n-butyltin)oxide (TBTO) studied by toxicogenomics

The biocide and environmental pollutant bis(tri-n-butyltin)oxide (TBTO) causes thymus atrophy in rodents. Whether the depletion of thymic lymphocytes by tributyltin compounds may be the result of inhibition of cell proliferation or induction of apoptosis is subject of debate. We examined gene expression profiles in primary rat thymocytes exposed to TBTO in vitro at dose levels of 0, 0.1, 0.3, 0.5, and 1.0microM. By measuring cell viability and apoptosis, exposure conditions were selected that would provide information on changes in gene expression preceding or accompanying functional effects of TBTO. Several processes related to TBTO-induced toxicity were detected at the transcriptome level. Effects on lipid metabolisms appeared to be the first indication of disruption of cellular function. Many transcriptional effects of TBTO at higher dose levels were related to apoptotic processes, which corresponded to present or subsequent thymocyte apoptosis observed phenotypically. The gene expression profile was, however, not unambiguous since expression of apoptosis-related genes was both increased and decreased. Stimulation of glucocorticoid receptor signaling appeared to be a relevant underlying mechanism of action. These findings suggest that TBTO exerts its toxic effects on the thymus primarily by affecting apoptotic processes, but the possibility is discussed that this may in fact represent an early effect that precedes inhibition of cell proliferation. At the highest dose level tested, TBTO additionally repressed mitochondrial function and immune cell activation. Our in vitro toxicogenomics approach thus identified several cellular and molecular targets of TBTO that may mediate the toxicity towards thymocytes and thereby its immunosuppressive effects.

Restricted diet delays accelerated ageing and genomic stress in DNA-repair-deficient mice

Mice deficient in the DNA excision-repair gene Ercc1 (Ercc1∆/−) show numerous accelerated ageing features that limit their lifespan to 4-6 months. They also exhibit a ‘survival response’, which suppresses growth and enhances cellular maintenance. Such a response resembles the anti-ageing response induced by dietary restriction (also known as caloric restriction). Here we report that a dietary restriction of 30% tripled the median and maximal remaining lifespans of these progeroid mice, strongly retarding numerous aspects of accelerated ageing. Mice undergoing dietary restriction retained 50% more neurons and maintained full motor function far beyond the lifespan of mice fed ad libitum. Other DNA-repair-deficient, progeroid Xpg−/− (also known as Ercc5−/−) mice, a model of Cockayne syndrome, responded similarly. The dietary restriction response in Ercc1∆/− mice closely resembled the effects of dietary restriction in wild-type animals. Notably, liver tissue from Ercc1∆/− mice fed ad libitum showed preferential extinction of the expression of long genes, a phenomenon we also observed in several tissues ageing normally. This is consistent with the accumulation of stochastic, transcription-blocking lesions that affect long genes more than short ones. Dietary restriction largely prevented this declining transcriptional output and reduced the number of γH2AX DNA damage foci, indicating that dietary restriction preserves genome function by alleviating DNA damage. Our findings establish the Ercc1∆/− mouse as a powerful model organism for health-sustaining interventions, reveal potential for reducing endogenous DNA damage, facilitate a better understanding of the molecular mechanism of dietary restriction and suggest a role for counterintuitive dietary-restriction-like therapy for human progeroid genome instability syndromes and possibly neurodegeneration in general.

Chronically Alternating Light Cycles Increase Breast Cancer Risk in Mice

Although epidemiological studies in shift workers and flight attendants have associated chronic circadian rhythm disturbance (CRD) with increased breast cancer risk, causal evidence for this association is lacking. Several scenarios have been proposed to contribute to the shift work-cancer connection: (1) internal desynchronization, (2) light at night (resulting in melatonin suppression), (3) sleep disruption, (4) lifestyle disturbances, and (5) decreased vitamin D levels due to lack of sunlight. The confounders inherent in human field studies are less problematic in animal studies, which are therefore a good approach to assess the causal relation between circadian disturbance and cancer. However, the experimental conditions of many of these animal studies were far from the reality of human shift workers. For example, some involved xenografts (addressing tumor growth rather than cancer initiation and/or progression), chemically induced tumor models, or continuous bright light exposure, which can lead to suppression of circadian rhythmicity. Here, we have exposed breast cancer-prone p53(R270H/+)WAPCre conditional mutant mice (in a FVB genetic background) to chronic CRD by subjecting them to a weekly alternating light-dark (LD) cycle throughout their life. Animals exposed to the weekly LD inversions showed a decrease in tumor suppression. In addition, these animals showed an increase in body weight. Importantly, this study provides the first experimental proof that CRD increases breast cancer development. Finally, our data suggest internal desynchronization and sleep disturbance as mechanisms linking shift work with cancer development and obesity.

Identification of a common gene expression response in different lung inflammatory diseases in rodents and macaques.

To identify gene expression responses common to multiple pulmonary diseases we collected microarray data for acute lung inflammation models from 12 studies and used these in a meta-analysis. The data used include exposures to air pollutants; bacterial, viral, and parasitic infections; and allergic asthma models. Hierarchical clustering revealed a cluster of 383 up-regulated genes with a common response. This cluster contained five subsets, each characterized by more specific functions such as inflammatory response, interferon-induced genes, immune signaling, or cell proliferation. Of these subsets, the inflammatory response was common to all models, interferon-induced responses were more pronounced in bacterial and viral models, and a cell division response was more prominent in parasitic and allergic models. A common cluster containing 157 moderately down-regulated genes was associated with the effects of tissue damage. Responses to influenza in macaques were weaker than in mice, reflecting differences in the degree of lung inflammation and/or virus replication. The existence of a common cluster shows that in vivo lung inflammation in response to various pathogens or exposures proceeds through shared molecular mechanisms.

Gene expression pattern in spontaneously hypertensive rats exposed to urban particulate matter (EHC-93).

Epidemiological studies show associations of short-term exposure to particulate matter with morbidity and mortality. Although many studies investigate the health effects of ambient particulate matter, the associated mechanisms, and the causality, they often focus on classical parameters. The objective of the present study was to gain insight into the roles of a wide range of genes in this process. Particular attention has been paid to immediate oxidative stress in the lung. We isolated total lung RNA from spontaneously hypertensive male rats 2–40 h after exposure to reference EHC-93 (10 mg/kg). Our results show that exposure to particulate matter generates a time-dependent pattern of gene expression. From the 8799 genes or expressed sequence tags tested, we see that 132 genes were up- or downregulated shortly after exposure (i.e., 2–6 h), whereas after 15–21 h and 24–40 h, 46 and 56 genes showed altered expression, respectively. Focusing on the earliest point, 99 of the 132 genes were identified as unique. They include genes involved in an oxidative stress response (hemeoxygenase-1, metallothioneins, and thioredoxin reductase), an inflammatory response macrophage inflammatory protein-2, and tumor necrosis factor α), transcription factors belonging to the activating protein-1 family, and genes involved in cardiovascular functions. The present study, although not representing an ambient situation, is used to identify the biological pathways implicated in the initial injury response to PM exposure. Using Affymetrix chips, this study shows time-dependent gene expression, it identifies many genes that can be affected by exposure to particulate matter, and it confirms the involvement of oxidative stress in particulate-matter-related effects.