Single-Cell Metabolomics: Analytical and Biological Perspectives

Science  06 Dec 2013:
Vol. 342, Issue 6163, pp.
DOI: 10.1126/science.1243259

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Structured Abstract


In recent years, there has been a surge in the development and application of single-cell genomics, transcriptomics, proteomics, and metabolomics. The metabolome is defined as the full complement of small-molecule metabolites found in a specific cell, organ, or organism. The most interesting potential application of single-cell metabolomics may be in the area of cancer—for example, identification of circulating cancer cells that lead to metastasis. Other fields where single-cell metabolomics is expected to have an impact are systems biology, stem cell research, aging, and the development of drug resistance; more generally, it could be used to discover cells’ chemical strategies for coping with chemical or environmental stress. Relative to other single-cell “-omics” measurements, metabolomics provides a more immediate and dynamic picture of the functionality (i.e., of the phenotype) of a cell, but is arguably also the most difficult to measure. This is because the metabolome can dynamically react to the environment on a very short time scale (seconds or less), because of the large structural diversity and huge dynamic range of metabolites, because it is not possible to amplify metabolites, and because tagging them with fluorescent labels would distort their normal function.

Embedded Image

Single-cell analysis uses a wide variety of imaging and chemical analysis methods to study vastly different cell types and sizes. (A) Closterium acerosum (algal cells, ~300 μm × 40 μm; optical micrograph). (B) Euglena gracilis (algal cells, diameter ~20 μm); Raman image of β-carotene distribution (left) and fluorescence emission from proplastids (right). (C) Baker’s yeast (diameter ~5 μm); optical micrograph. (D) Escherichia coli (diameter ~0.75 μm, length 1 to 3 μm); fluorescence micrograph (image courtesy of M. Heinemann, University of Groningen).


Although deep biological insight based on single-cell metabolomics has not yet been obtained, important steps have been taken toward this goal. Advances in mass spectrometry (MS), MS imaging, capillary electrophoresis, optical spectroscopy, and in the development of fluorescence biosensors now allow the simultaneous determination of hundreds of metabolites in a single cell, with sensitivities in the attomole range. Modern array formats, in particular microfluidic platforms, contribute to our ability to perform such measurements rapidly and with high throughput. Several recent studies show how novel biological insight can be extracted from single-cell metabolomics. Substantial differences in the metabolomes of different snail neurons—for example, in B1 and B2 type neurons—have been found, immediately after isolating them and after overnight culturing. Glycosphingolipids could be labeled with a fluorescent tag, and in lysates of neurons incubated with such conjugates, all metabolic products derived from them were fluorescent and could be identified. Phosphorylation of 3′-deoxy-3′-fluorothymidine in lymphoma cells and solid tumors could be followed after treatment with cancer drugs. The biological effect of treating yeast cells by 2-deoxy-d-glucose (2DG) on the metabolome could be followed. The fact that single-cell measurements exhibited a much larger spread in metabolite concentrations than population measurements was exploited to determine many metabolite-metabolite correlations, which were altered in 2DG-treated yeast cells relative to controls.


The metabolome is an excellent indicator of phenotypic heterogeneity and has been recognized as a key factor in rare-cell survival when populations are subjected to major chemical or environmental challenges. Metabolomics at the single-cell level, however, is only just coming of age. Improvements leading to more complete coverage of the metabolome, better and faster identification of metabolites, and nondestructive measurement are anticipated.


There is currently much interest in broad molecular profiling of single cells; a cell’s metabolome—its full complement of small-molecule metabolites—is a direct indicator of phenotypic diversity of single cells and a nearly immediate readout of how cells react to environmental influences. However, the metabolome is very difficult to measure at the single-cell level because of rapid metabolic dynamics, the structural diversity of the molecules, and the inability to amplify or tag small-molecule metabolites. Measurement techniques including mass spectrometry, capillary electrophoresis, and, to a lesser extent, optical spectroscopy and fluorescence detection have led to impressive advances in single-cell metabolomics. Even though none of these methodologies can currently measure the metabolome of a single cell completely, rapidly, and nondestructively, progress has been sufficient such that the field is witnessing a shift from feasibility studies to investigations that yield new biological insight. Particularly interesting fields of application are cancer biology, stem cell research, and monitoring of xenobiotics and drugs in tissue sections at the single-cell level.

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