NMR-based Stable Isotope Resolved Metabolomics in systems biochemistry

Abstract

Metabolism is the basic activity of live cells, and monitoring the metabolic state provides a dynamic picture of the cells or tissues, and how they respond to external changes, for in disease or treatment with drugs. NMR is an extremely versatile analytical tool that can be applied to a wide range of biochemical problems. Despite its modest sensitivity its versatility make it an ideal tool for analyzing biochemical dynamics both in vitro and in vivo, especially when coupled with its isotope editing capabilities, from which isotope distributions can be readily determined. These are critical for any analyses of flux in live organisms. This review focuses on the utility of NMR spectroscopy in metabolomics, with an emphasis on NMR applications in stable isotope-enriched tracer research for elucidating biochemical pathways and networks with examples from nucleotide biochemistry. The knowledge gained from this area of research provides a ready link to genomic, epigenomic, transcriptomic, and proteomic information to achieve systems biochemical understanding of living cells and organisms.

Pancreatic β-cells respond to fuel pressure with an early metabolic switch

“…Fully 13 C labelled glucose can for instance be used as a metabolic tracer to probe the NAD + -dependent oxidation of glucose to pyruvate in glycolysis. The metabolic transformations of the tracer lead to distinct labeling patterns in metabolic intermediates 11 . In this way, metabolic fluxes can be measured from temporal profiles of metabolite concentration changes.…”

Recent Advances in Targeted and Untargeted Metabolomics by NMR and MS/NMR Methods

“…The analysis of metabolite profiles of common biofluids, such as urine and serum, provides diagnostic and prognostic information about diseases, dietary patterns, and drug toxicity [ 11 , 12 , 13 ]. Stable isotope labeling of metabolites followed by the analysis of positional enrichments reveals activity of alternative metabolic pathways contributing to certain biochemical reactions, such as in healthy versus cancer cells [ 14 , 15 , 16 ].…”

Resolving Metabolic Heterogeneity in Experimental Models of the Tumor Microenvironment from a Stable Isotope Resolved Metabolomics Perspective

“…Human macrophages were isolated as described above were induced to form spheroids in 6-well plates in organoid medium and were treated with 10 mM 13 C 6 -glucose for 24 h before harvesting and immediate extraction for polar, non-polar and protein fractions using our CH 3 CN/H 2 O/CHCl 3 solvent partitioning method [223,224]. After lyophilization and reconstitution, polar metabolites were identified and quantified by IC-FTMS and NMR according to our untargeted workflow that can resolve multiple tracer atoms (e.g., 2 H, 13 C, and 15 N) in the same metabolite [91,92,170,[225][226][227][228]. For co-cultures, macrophages were mixed with an equal number of A549 cells and induced to form spheroids and incubated for 24 h with medium containing 10 mM 2 H 7 -glucose + 70 µM 15 N 2 tryptophan + 2 mM 13 C 5 glutamine.…”