Single-cell mass spectrometry reveals small molecules that affect cell fates in the 16-cell embryo

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 112; no. 21; pp. 6545 - 6550
• Main Authors: Onjiko, Rosemary M., Moody, Sally A., Nemes, Peter
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 26.05.2015; National Acad Sciences
• Subjects: Animals; Biological Sciences; Blastomeres - cytology; Blastomeres - metabolism; Cell Size; Cells; Cytoplasm; Electrophoresis, Capillary - methods; Embryo, Nonmammalian - cytology; Embryo, Nonmammalian - metabolism; Female; Frogs; Genotype & phenotype; Male; Metabolic Networks and Pathways; Metabolites; Metabolome; Molecules; Physical Sciences; Single-Cell Analysis - methods; Spectrometry, Mass, Electrospray Ionization - methods; Xenopus laevis - embryology; Xenopus laevis - metabolism; Xenopus; embryo development; mass spectrometry; single cell; metabolomics
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1423682112

Spatial and temporal changes in molecular expression are essential to embryonic development, and their characterization is critical to understand mechanisms by which cells acquire different phenotypes. Although technological advances have made it possible to quantify expression of large molecules during embryogenesis, little information is available on metabolites, the ultimate indicator of physiological activity of the cell. Here, we demonstrate that single-cell capillary electrophoresis-electrospray ionization mass spectrometry is able to test whether differential expression of the genome translates to the domain of metabolites between single embryonic cells. Dissection of three different cell types with distinct tissue fates from 16-cell embryos of the South African clawed frog ( Xenopus laevis ) and microextraction of their metabolomes enabled the identification of 40 metabolites that anchored interconnected central metabolic networks. Relative quantitation revealed that several metabolites were differentially active between the cell types in the wild-type, unperturbed embryos. Altering postfertilization cytoplasmic movements that perturb dorsal development confirmed that these three cells have characteristic small-molecular activity already at cleavage stages as a result of cell type and not differences in pigmentation, yolk content, cell size, or position in the embryo. Changing the metabolite concentration caused changes in cell movements at gastrulation that also altered the tissue fates of these cells, demonstrating that the metabolome affects cell phenotypes in the embryo. Significance Spatiotemporal characterization of molecular expression during embryonic development is critical for understanding how cells become different and give rise to distinct tissues and organs. Technological advances enabled the measurement of RNAs and proteins in single cells of embryos, but there is very little information on small molecules, metabolites, that are the ultimate indication of the physiological state. To fill this knowledge gap, we developed and used a single-cell technology to find that embryonic cells that give rise to different tissues have characteristically different metabolic signatures that are not simply a reflection of cell pigmentation, yolk content, size, or position in the embryo, but also affect cell fate. This approach is likely to provide new mechanistic insights into early embryo development.