In-cell NMR: from metabolites to macromolecules.

In-cell NMR of macromolecules has gained momentum over the last ten years as an approach that might bridge the branches of cell biology and structural biology. In this review, we put it in the context of earlier efforts that aimed to characterize by NMR the cellular environment of live cells and their intracellular metabolites. Although technical aspects distinguish these earlier in vivo NMR studies and the more recent in cell NMR efforts to characterize macromolecules in a cellular environment, we believe that both share major concerns ranging from sensitivity and line broadening to cell viability. Approaches to overcome the limitations in one subfield thereby can serve the other one and vice versa. The relevance in biomedical sciences might stretch from the direct following of drug metabolism in the cell to the observation of target binding, and thereby encompasses in-cell NMR both of metabolites and macromolecules. We underline the efforts of the field to move to novel biological insights by some selected examples.

High mTORC1 activity drives glycolysis addiction and sensitivity to G6PD inhibition in acute myeloid leukemia cells.

Alterations in metabolic activities are cancer hallmarks that offer a wide range of new therapeutic opportunities. Here we decipher the interplay between mTORC1 activity and glucose metabolism in acute myeloid leukemia (AML). We show that mTORC1 signaling that is constantly overactivated in AML cells promotes glycolysis and leads to glucose addiction. The level of mTORC1 activity determines the sensitivity of AML cells to glycolysis inhibition as switch-off mTORC1 activity leads to glucose-independent cell survival that is sustained by an increase in mitochondrial oxidative phosphorylation. Metabolic analysis identified the pentose phosphate pathway (PPP) as an important pro-survival pathway for glucose metabolism in AML cells with high mTORC1 activity and provided a clear rational for targeting glucose-6-phosphate dehydrogenase (G6PD) in AML. Indeed, our analysis of the cancer genome atlas AML database pinpointed G6PD as a new biomarker in AML, as its overexpression correlated with an adverse prognosis in this cohort. Targeting the PPP using the G6PD inhibitor 6-aminonicotinamide induces in vitro and in vivo cytotoxicity against AML cells and synergistically sensitizes leukemic cells to chemotherapy. Our results demonstrate that high mTORC1 activity creates a specific vulnerability to G6PD inhibition that may work as a new AML therapy.

Mitochondrial energetic and AKT status mediate metabolic effects and apoptosis of metformin in human leukemic cells.

Previous reports demonstrate that metformin, an anti-diabetic drug, can decrease the risk of cancer and inhibit cancer cell growth. However, its mechanism in cancer cells is still unknown. Metformin significantly blocks cell cycle and inhibits cell proliferation and colony formation of leukemic cells. However, the apoptotic response to metformin varies. Furthermore, daily treatment with metformin induces apoptosis and reduces tumor growth in vivo. While metformin induces early and transient activation of AMPK, inhibition of AMPKα1/2 does not abrogate anti-proliferative or pro-apoptotic effects of metformin. Metformin decreases electron transport chain complex I activity, oxygen consumption and mitochondrial ATP synthesis, while stimulating glycolysis for ATP and lactate production, pentose phosphate pathway for purine biosynthesis, fatty acid metabolism, as well as anaplerotic and mitochondrial gene expression. Importantly, leukemic cells with high basal AKT phosphorylation, glucose consumption or glycolysis exhibit a markedly reduced induction of the Pasteur effect in response to metformin and are resistant to metformin-induced apoptosis. Accordingly, glucose starvation or treatment with deoxyglucose or an AKT inhibitor induces sensitivity to metformin. Overall, metformin elicits reprogramming of intermediary metabolism leading to inhibition of cell proliferation in all leukemic cells and apoptosis only in leukemic cells responding to metformin with AKT phosphorylation and a strong Pasteur effect.

Functional genomics of the muscle response to restraint and transport in chickens.

In the present study, we used global approaches (proteomics, transcriptomics, and metabolomics) to assess the molecular basis of the muscle response to stress in chickens. A restraint test, combined with transport for 2 h (RT test) was chosen as the potentially stressful situation. Chickens (6 wk old) were either nontreated (control chickens) or submitted to the RT test (treated chickens). The RT test induced a 6-fold increase in corticosterone concentrations, suggesting hypothalamic-pituitary-adrenal axis activation. The RT test decreased the relative abundance of several hexose phosphates [glucose-1-P (G1P), glucose-6-P (G6P), fructose-6-P (F6P), and mannose-6-P (M6P)] in thigh muscle. In addition, 55 transcripts, among which 39 corresponded to unique annotated genes, were significantly up- (12 genes) or downregulated (27 genes) by treatment. Similarly, 45 proteic spots, among which 29 corresponded to unique annotated proteins, were overexpressed (11 proteins), underexpressed (14 proteins), or only expressed in treated chickens. Integrative analysis of differentially expressed genes and proteins showed that most transcripts and proteins belong to 2 networks whose genes were mainly related with cytoskeleton structure or carbohydrate metabolism. Whereas the decrease in energetic metabolites suggested an activation of glycogenolysis and glycolysis in response to the RT test, the reduced expression of genes and proteins involved in these pathways suggested the opposite. We hypothesized that the prolonged RT test resulted in a repression of glycogenolysis and glycolysis in thigh muscle of chickens. The down-expression of genes and proteins involved in the formation of fiber stress after the RT test suggests a reinforcement of myofibrils in response to stress.

Relevance and isotopic assessment of hexose-6-phosphate recycling in micro-organisms.

Some pathways of hexose-6-phosphate recycling--those involving a breakdown of the hexose skeleton--through carbohydrate metabolism of micro-organisms were analyzed for both metabolic and isotopic effects. Two modes of recycling were proposed based on the degree of alteration of the hexose molecule through the catabolic part of the cycle. Simulated operation of most of these pathways resulted in increased synthesis of hexose-6-phosphate and NADPH, and reduced the NADH and moreover the ATP synthesis within the carbohydrate metabolism. A basic model for the quantitative assessment by means of isotopic studies of the processes of hexose-6-phosphate recycling is presented. The model was initially designed for the study of micro-organisms producing polysaccharides, but it can be extended to other situations.

Cyclic organization of the carbohydrate metabolism in Sinorhizobium meliloti.

The pathways of polysaccharide biosynthesis were investigated in cells of Sinorhizobium meliloti (strain Su47) using a stable isotope approach. The isotopic labeling of the periplasmic beta-1,2-glucans synthesized from glucose labeled at various positions evidenced the involvement of catabolic pathways, namely the pentose-phosphate and Entner-Doudoroff pathways, into the early steps of polysaccharide synthesis. The exopolysaccharides produced at the same time had a labeling pattern similar to that of the beta-glucans, indicating similar early steps for both polysaccharides. The results emphasized a cyclic organization of the carbohydrate metabolism in S. meliloti, in which the carbons of the initial hexose were allowed to re-enter the catabolic pathways many times. The metabolic incidences of such metabolic topology are discussed.

Mechanism of gluconate synthesis in Rhizobium meliloti by using in vivo NMR.

The dehydrogenation of [1-(13)C]- and [2-(13)C]glucose into gluconate was monitored by NMR spectroscopy in living cell suspensions of two Rhizobium meliloti strains. The synthesis of gluconate was accompanied, in the cellular environment, by the formation of two gluconolactones, a gamma-lactone being detected in addition to the expected delta-lactone. These lactones--as well as the gluconate--could be further metabolized by the cells. The delta-lactone was utilized faster than the gamma-lactone. The presence--in significant amounts--and the relative stability of the lactones raise the question of their possible physiological significance.

Glucose and glutamine metabolism in C6 glioma cells studied by carbon 13 NMR.

The question as to whether glutamine and glucose are both required for optimal growth of glioma cells is studied through the role of these substrates on the metabolism of the cells. C6 rat glioma cells grow only very slowly when glutamine is omitted from the culture medium. The rates of glucose consumption and lactate production on confluent cells in glutamine-free medium were 0.88 +/- 0.09 and 1.06 +/- 0.25 mumol/h/mg protein, respectively. In the presence of 4 mM glutamine, glucose utilization increase to 60% leading to a 45% increase of lactate production. We have studied the kinetics of enrichment of intracellular glutamate at C2, C3 and C4 positions on cells incubated with 5 mM 99% enriched [1-(13)C]glucose in the presence or the absence of glutamine in the incubation medium. The specific enrichments at metabolic steady state of all carbon positions were the same under both conditions, but we observed a significantly reduced rate of 13C incorporation in the presence of glutamine, showing an isotopic dilution of tricarboxylic acid cycle intermediates and indicating the use of this amino acid as an anaplerotic substrate. The fact that no dilution occurred at the level of pyruvate suggests strongly the lack of glutaminolysis in these cells. The main conclusion from this work is that glutamine metabolism in C6 cells appears complementary to that of glucose as far as energy production and carbon sources for the growing of the cells are concerned: glutamine is mainly utilized for anaplerosis as carbon donor to replenish the tricarboxylic acid cycle; it is not a substrate for energy metabolism. In contrast, glucose is poorly anaplerotic and is essentially used as energetic fuel by the C6 cells.

Comparative analysis of 13C-enriched metabolites released in the medium of cerebellar and cortical astrocytes incubated with [1-13C]glucose.

Rat cerebellar and cortical astrocytes cultured for 15 or 35 days were incubated with [1-13C]glucose in the presence or absence of 4 mM exogenous glutamine and the release of 13C-enriched metabolites into cell media was studied by 13C-NMR spectroscopy. In the presence of exogenous glutamine, both cerebellar and cortical astrocytes consumed the amino acid. In contrast, a net production of glutamine occurred in the absence of the amino acid. Simultaneously, a release of 13C-enriched glutamine into cell media was observed and was higher in the presence than in the absence of exogenous glutamine. This demonstrated the occurrence of an isotopic-exchange process which may involve a futile cycle at the level of glutamine synthetase and glutaminase activities. The 13C-enrichment ratio between glutamine carbons C2 and C3 was close to 1 in the presence of exogenous glutamine whereas it was higher than 1 in its absence, indicating that pyruvate carboxylase was more active in the absence of glutamine. In addition to glutamine, alanine was synthesized and exported into the medium of both cerebellar and cortical astrocytes. In contrast, citrate was specifically produced by cortical astrocytes. Slight increases in alanine and glutamine productions were observed for cortical astrocyte cultures between 15 and 35 days, whereas the amino acid production by cerebellar astrocytes increased several-fold after 35 days compared with that at 15 days of culture.

Metabolic flux determination in C6 glioma cells using carbon-13 distribution upon [1-13C]glucose incubation.

A mathematical model of mammalian cell intermediary metabolism is presented. It describes the distribution of the carbon-13 isotope (13C) at the different carbon positions of metabolites in cells fed with 13C-enriched substrates. The model allows the determination of fluxes through different metabolic pathways from 13C- and 1H-NMR spectroscopy and mass spectrometry data. The considered metabolic network includes glycolysis, gluconeogenesis, the citric acid cycle and a number of reactions corresponding to protein or fatty acid metabolism. The model was used for calculating metabolic fluxes in a rat tumor cell line, the C6 glioma, incubated with [1-13C]glucose. After evolution to metabolic and isotopic steady states, the intracellular metabolites were extracted with perchloric acid. The specific enrichments of glutamate, aspartate and alanine carbons were determined from 13C-, 1H-NMR spectroscopy, or mass spectrometry data. Taking into account the rate of glucose consumption and of lactate formation, determined from the evolution of glucose and lactate contents in the cell medium, and knowing the activity of the hexose monophosphate shunt, it was possible to estimate the absolute values of all the considered fluxes. From the analysis the following results were obtained. (a) Glucose accounts for about 78% of the pyruvate and 57% of the CoASAc. (b) A metabolic channelling occurs at the citric acid cycle level; it favours the conversion of carbons 2, 3, 4, and 5 of 2-oxoglutarate into carbons 1, 2, 3, and 4 of oxaloacetate, respectively. The percentage of channelled metabolites amounts to 39%. (c) The pyruvate carboxylase activity and the efflux from the citric acid cycle are estimated to be very low, suggesting a lack of glutamine production in C6 cells. The results emphasize different metabolic characteristics of C6 cells when compared to astrocytes, their normal counterpart.

[1-13C]glucose metabolism in rat cerebellar granule cells and astrocytes in primary culture. Evaluation of flux parameters by 13C- and 1H-NMR spectroscopy.

The metabolism of [1-13C]glucose in rat cerebellum astrocytes and granule cells was investigated using 13C- and 1H-NMR spectroscopy. Near homogeneous primary cultures of each cell type were incubated with [1-13C]glucose, under the same conditions. Analysing the relative 13C enrichments of metabolites in spectra of cell perchloric acid extracts, on the one hand, the 13C-1H spin-coupling patterns in 1H-NMR spectra of cell medium lactate and the 13C-13C spin-coupling patterns in 13C-NMR spectra of purified cell glutamate, on the other hand, showed significant differences, between the two cell types, in the activity of various metabolic ways. First, the carbon flux through the oxidative branch of the hexose monophosphate shunt, which leads to unenriched lactate, was found higher in granule cells than in astrocytes. Second, although the specific 13C enrichment of lactate was higher in astrocytes than in granule cells, the fraction of 13C-enriched acetyl-CoA entering the citric acid cycle was more than twice as high in granule cells as in astrocytes. Lactate C3 and acetyl-CoA C2 enrichments were very similar in granule cells, whereas acetyl-CoA C2 enrichment was 60% lower than that of lactate C3 in astrocytes. These results can be explained by the fact that granule cells used almost exclusively the exogenous glucose to fuel the citric acid cycle, whereas astrocytes used concomitantly glucose and other carbon sources. Last, in the case of granule cells, glutamate C2 and C3 enrichments were equivalent; the carbon flux through the pyruvate carboxylase route was evaluated to be around 15% of the carbon flux through the citrate synthetase route. In astrocytes, glutamate C2 enrichment was higher than that of C3, which could be explained by a pyruvate carboxylase activity much more active in these cells than in granule cells.

Glutathione, but not glutamine, is detected in 13C-NMR spectra of perchloric acid extracts from C6 glioma cells.

Glutamine, which is expected to be produced by C6 glioma cells, is not detected in both amino-acid analyses and 13C-NMR spectra of perchloric acid extracts of cells incubated for 4 h with [1-13C]glucose in the absence of extracellular glutamine. However, the resonances of a glutamate-linked product are observed in these spectra. The analysis of the pH dependence of chemical shifts from various glutamate-derived compounds shows that the observed resonances came from glutathione. Glutamine and glutathione signals are in close proximity on the frequency scale, leading to possible misinterpretation of the spectra.

Magnetic resonance spectroscopy and metabolism. Applications of proton and 13C NMR to the study of glutamate metabolism in cultured glial cells and human brain in vivo.

Nuclear magnetic resonance (NMR) spectroscopy was used to study the metabolism of cells from the central nervous system both in vitro on perchloric acid extracts obtained either from cultured tumoral cells (C6 rat glioma) or rat astrocytes in primary culture, and in vivo within the human brain. Analysis of carbon 13 NMR spectra of perchloric acid extracts prepared from cultured cells in the presence of NMR [1-13C] glucose as substrate allowed determination of the glutamate and glutamine enrichments in both normal and tumoral cells. Preliminary results indicated large changes in the metabolism of these amino acids (and also of aspartate and alanine) in the C6 cell as compared to its normal counterpart. Localized proton NMR spectra of the human brain in vivo were obtained at 1.5 T, in order to evaluate the content of various metabolites, including glutamate, in peritumoral edema from a selected volume of 2 x 2 x 2 cm3. N-acetyl aspartate, glutamate, phosphocreatine, creatine, choline and inositol derivative resonances were observed in 15 min spectra. N-acetyl-aspartate was found to be at a lower level in contrast to glutamate which was detected at a higher level in the injured area as compared to the contralateral unaffected side.