Metabolomics of developing zebrafish embryos using gas chromatography- and liquid chromatography-mass spectrometry

Zebrafish embryogenesis is a rapid process driven by a myriad of gene products and small molecules. As previous studies have detailed the relevant transcriptional and proteomics changes, here we assess the metabolomic changes that occur at different stages of embryogenesis (4, 8, 12, 24 and 48 hours post fertilization). Metabolite levels were detected using GC-MS and LC-MS, following which multivariate analysis (OPLS-DA) was applied to identify metabolites that were differentially regulated throughout embryogenesis. From the two robust OPLS-DA models that were generated (Q(2)(cum) = 0.940 and Q(2)(cum) = 0.894), a total of 60 detected metabolites (20 from GC-MS, 40 from LC-MS) were identified and found to be important in discriminating between developmental stages. Hierarchical clustering analysis was applied to the dataset and metabolite classes such as amino acids and lipids were shown to be differentially regulated. Biologically relevant transcriptomic and proteomic data were associated with metabolites to provide a more holistic systems perspective of embryogenesis. In summary, the metabolic profiles of different developmental stages highlight the dynamic changes occurring during embryogenesis. These data could serve as a basis for future toxicological or developmental studies.