Tracer-based metabolomics: Concepts and practices

Abstract

Tracer-based metabolomics is a systems biology tool that combines advances in tracer methodology for physiological studies, high throughput "-omics" technologies and constraint based modeling of metabolic networks. It is different from the commonly known metabolomics or metabonomics in that it is a targeted approach based on a metabolic network model in cells. Because of its complexity, it is the least understood among the various "-omics". In this review, the development of concepts and practices of tracer-based metabolomics is traced from the early application of radioactive isotopes in metabolic studies to the recent application of stable isotopes and isotopomer analysis using mass spectrometry; and from the modeling of biochemical reactions using flux analysis to the recent theoretical formulation of the constraint based modeling. How these newer experimental methods and concepts of constraint-based modeling approaches can be applied to metabolic studies is illustrated by examples of studies in determining metabolic responses of cells to pharmacological agents and nutrient environment changes.

Inhibition of Glycogen Phosphorylation Induces Changes in Cellular Proteome and Signaling Pathways in MIA Pancreatic Cancer Cells

“…Loss of P53 regulation is thought to lead to increased glucose uptake and increased pentose cycle activity associated with increased lactate production and cell proliferation of the Warburg effect. The use of a less efficient energy producing pathway in cancer cells in favor of macromolecular synthesis is part of the systems biology of dividing cells to optimization glucose utilization 47 . The principle of systems biology that allows optimization of glucose utilization also predicts that interruption of a metabolic pathway can lead to changes in substrate flow throughout the metabolic network, albeit in a less optimal way for cell proliferation.…”

Strategies for Extending Metabolomics Studies with Stable Isotope Labelling and Fluxomics

“…It was noted that even when care is taken to account for any pre-existing unlabelled precursor at the start of such studies, such forms may further originate from recycling of other metabolic intermediates or environmental fixation and may dilute the labelled tracer along the path of synthesis of downstream products. To overcome this issue, determination of precursor dilution by unlabelled metabolites is necessary, and this can often be achieved by quantitative mass isotopomer distribution analysis [63,64,65]. …”

The Warburg effect: a balance of flux analysis

“…The result is an n-dimensional convex conical solution space. The convex cone can be resolved into a series of two dimensional phenotypic phase planes representing the metabolic phenotype of the metabolic network (Edwards et al, 2002, Lee and Go, 2005, Orth et al, 2010, Paul Lee et al, 2010, Schilling et al, 2000, Schilling and Palsson, 1998). The concept of balance of flux is scalable 3 .…”