Omics in Zebrafish Teratogenesis

Metabolomic Fingerprint Assay in Zebrafish Embryos

In order for new drugs to enter the market, extensive studies are needed to examine toxic effects. Among others, teratogenicity studies are of paramount importance. Of even higher importance is to gain knowledge on the biological responses that take place upon drug exposure, so as to have a better understanding of the molecular mechanisms that govern developmental changes. Metabolomics is the research field that studies the changes in the chemical composition of metabolites contained within cells. Conducting metabolomics studies results in valuable information. Zebrafish is a vertebrate model organism that bridges in vivo assays and in vivo studies. In this chapter, we propose a metabolomic fingerprint assay for the study of metabolic changes in zebrafish embryos upon exposure to various drugs. The metabolome of zebrafish is extracted, and the 1H-NMR spectrum is recorded. Using open-access metabolomic databases, a list of tentative metabolites is retrieved. The presence of the tentative metabolites is further confirmed by UHPLC-HRMS. Ultimately, after a metabolic pathway analysis, the metabolic network is revealed and useful conclusions can be drawn.

Recent research advances on non-linear phenomena in various biosystems

All biological phenomena can be classified as open, dissipative and non-linear. Moreover, the most typical phenomena are associated with non-linearity, dissipation and openness in biological systems. In this review article, four research topics on non-linear biosystems are described to show the examples from various biological systems. First, membrane dynamics of a lipid bilayer for the cell membrane is described. Since the cell membrane separates the inside of the cell from the outside, self-organizing systems that form spatial patterns on membranes often depend on non-linear dynamics. Second, various data banks based on recent genomics analysis supply the data including vast functional proteins from many organisms and their variable species. Since the proteins existing in nature are only a very small part of the space represented by amino acid sequence, success of mutagenesis-based molecular evolution approach crucially depends on preparing a library with high enrichment of functional proteins. Third, photosynthetic organisms depend on ambient light, the regular and irregular changes of which have a significant impact on photosynthetic processes. The light-driven process proceeds through many redox couples in the cyanobacteria constituting chain of redox reactions. Forth topics focuses on a vertebrate model, the zebrafish, which can help to understand, predict and control the chaos of complex biological systems. In particular, during early developmental stages, developmental differentiation occurs dynamically from a fertilized egg to divided and mature cells. These exciting fields of complexity, chaos, and non-linear science have experienced impressive growth in recent decades. Finally, future directions for non-liner biosystems are presented.

Identification of proteome markers for drug-induced liver injury in zebrafish embryos

The zebrafish embryo (ZFE) is a promising alternative non-rodent model in toxicology, and initial studies suggested its applicability in detecting hepatic responses related to drug-induced liver injury (DILI). Here, we hypothesize that detailed analysis of underlying mechanisms of hepatotoxicity in ZFE contributes to the improved identification of hepatotoxic properties of compounds and to the reduction of rodents used for hepatotoxicity assessment. ZFEs were exposed to nine reference hepatotoxicants, targeted at induction of steatosis, cholestasis, and necrosis, and effects compared with negative controls. Protein profiles of the individual compounds were generated using LC-MS/MS. We identified differentially expressed proteins and pathways, but as these showed considerable overlap, phenotype-specific responses could not be distinguished. This led us to identify a set of common hepatotoxicity marker proteins. At the pathway level, these were mainly associated with cellular adaptive stress-responses, whereas single proteins could be linked to common hepatotoxicity-associated processes. Applying several stringency criteria to our proteomics data as well as information from other data sources resulted in a set of potential robust protein markers, notably Igf2bp1, Cox5ba, Ahnak, Itih3b.2, Psma6b, Srsf3a, Ces2b, Ces2a, Tdo2b, and Anxa1c, for the detection of adverse responses.

Sediment toxicity assessment using zebrafish (Danio rerio) as a model system: Historical review, research gaps and trends

Sediment is an important compartment in aquatic environments and acts as a sink for environmental pollutants. Sediment toxicity tests have been suggested as critical components in environmental risk assessment. Since the zebrafish (Danio rerio) has been indicated as an emerging model system in ecotoxicological tests, a scientometric and systematic review was performed to evaluate the use of zebrafish as an experimental model system in sediment toxicity assessment. A total of 97 papers were systematically analyzed and summarized. The historical and geographical distributions were evaluated and the data concerning the experimental design, type of sediment toxicity tests and approach (predictive or retrospective), pollutants and stressors, zebrafish developmental stages and biomarkers responses were summarized and discussed. The use of zebrafish to assess the sediment toxicity started in 1996, using mainly a retrospective approach. After this, research showed an increasing trend, especially after 2014-2015. Zebrafish exposed to pollutant-bound sediments showed bioaccumulation and several toxic effects, such as molecular, biochemical, morphological, physiological and behavioral changes. Zebrafish is a suitable model system to assess the toxicity of freshwater, estuarine and marine sediments, and sediment spiked in the laboratory. The pollutant-bound sediment toxicity in zebrafish seems to be overall dependent on physical and chemical properties of pollutants, experimental design, environmental factor, developmental stages and presence of organic natural matter. Overall, results showed that the zebrafish embryos and larvae are suitable model systems to assess the sediment-associated pollutant toxicity.

Genetic Susceptibility to Drug Teratogenicity: A Systematic Literature Review

Since the 1960s, drugs have been known to cause teratogenic effects in humans. Such teratogenicity has been postulated to be influenced by genetics. The aim of this review was to provide an overview of the current knowledge on genetic susceptibility to drug teratogenicity in humans and reflect on future directions within the field of genetic teratology. We focused on 12 drugs and drug classes with evidence of teratogenic action, as well as 29 drugs and drug classes with conflicting evidence of fetal safety in humans. An extensive literature search was performed in the PubMed and EMBASE databases using terms related to the drugs of interest, congenital anomalies and fetal development abnormalities, and genetic variation and susceptibility. A total of 29 studies were included in the final data extraction. The eligible studies were published between 1999 and 2020 in 10 different countries, and comprised 28 candidate gene and 1 whole-exome sequencing studies. The sample sizes ranged from 20 to 9,774 individuals. Several drugs were investigated, including antidepressants (nine studies), thalidomide (seven studies), antiepileptic drugs (five studies), glucocorticoids (four studies), acetaminophen (two studies), and sex hormones (estrogens, one study; 17-alpha hydroxyprogesterone caproate, one study). The main neonatal phenotypic outcomes included perinatal complications, cardiovascular congenital anomalies, and neurodevelopmental outcomes. The review demonstrated that studies on genetic teratology are generally small, heterogeneous, and exhibit inconsistent results. The most convincing findings were genetic variants in SLC6A4, MTHFR, and NR3C1, which were associated with drug teratogenicity by antidepressants, antiepileptics, and glucocorticoids, respectively. Notably, this review demonstrated the large knowledge gap regarding genetic susceptibility to drug teratogenicity, emphasizing the need for further efforts in the field. Future studies may be improved by increasing the sample size and applying genome-wide approaches to promote the interpretation of results. Such studies could support the clinical implementation of genetic screening to provide safer drug use in pregnant women in need of drugs.

Bitter gourd (Momordica charantia) possess developmental toxicity as revealed by screening the seeds and fruit extracts in zebrafish embryos

Background

Bitter gourd (Momordica charantia) has attracted the focus of researchers owing to its excellent anti-diabetic action. The beneficial effect of Momordica charantia on heart has been reported by in vitro and in vivo studies. However the developmental toxicity or potential risk of M. charantia on fetus heart development is largely unknown. Hence this study was designed to find out the developmental toxicity of M. charantia using zebrafish (Danio rerio) embryos.

Methods

The crude extracts were prepared from fruit and seeds of M. charantia. The Zebrafish embryos were exposed to serial dilution of each of the crude extract. The biologically active fractions were fractionated by C18 column using high pressure liquid chromatography. Fourier-transform infrared spectroscopy and gas chromatography coupled with mass spectrophotometry was done to identify chemical constituents in fruit and seed extract of M. charantia.

Results

The seed extract of M. charantia was lethal with LD₅₀ values of 50 μg/ml to zebrafish embryos and multiple anomalies were observed in zebrafish embryos at sub-lethal concentration. However, the fruit extract was much safe and exposing the zebrafish embryos even to 200 μg/ml did not result any lethality. The fruit extract induced severe cardiac hypertrophy in treated embryos. The time window treatment showed that M. charantia perturbed the cardiac myoblast specification process in treated zebrafish embryos. The Fourier-transform infrared spectroscopy analyses revealed diverse chemical group in the active fruit fraction and five new type of compounds were identified in the crude seeds extract of M. charantia by gas chromatography and mass spectrophotometry.

Conclusion

The teratogenicity of seeds extract and cardiac toxicity by the fruit extract of M. charantia warned that the supplementation made from the fruit and seeds of M. charantia should be used with much care in pregnant diabetic patients to avoid possible damage to developing fetus.

Electronic supplementary material

The online version of this article (10.1186/s12906-019-2599-0) contains supplementary material, which is available to authorized users.