Metabolic flux analysis: a comprehensive review on sample preparation, analytical techniques, data analysis, computational modelling, and main application areas

Falco, Bruna de; Giannino, Francesco; Cartenì, Fabrizio; Mazzoleni, Stefano; Kim, Dong-Hyun

doi:10.1039/d2ra03326g

Cited by 14 publications

(9 citation statements)

References 170 publications

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“…The mass spectrometry technique is used to detect metabolic tracking from stable isotope tracers [ 23 ]. 13C is the predominant isotope used because of its universal distribution in almost every cellular organic molecule [ 24 ]. In metabolic substrate analysis, M + 0 is an unlabeled molecule, while M + 1, M + 2, M + 3, etc., are different numbers of carbon labeled with 13C [ 25 ].…”

Section: Amino Acid As Energy Source and Tissue Builder In Bonesmentioning

confidence: 99%

Role of Essential Amino Acids in Age-Induced Bone Loss

Shi

Zhang

2022

IJMS

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Age-induced osteoporosis is a global problem. Essential amino acids (EAAs) work as an energy source and a molecular pathway modulator in bone, but their functions have not been systematically reviewed in aging bone. This study aimed to discuss the contribution of EAAs on aging bone from in vitro, in vivo, and human investigations. In aged people with osteoporosis, serum EAAs were detected changing up and down, without a well-established conclusion. The supply of EAAs in aged people either rescued or did not affect bone mineral density (BMD) and bone volume. In most signaling studies, EAAs were proven to increase bone mass. Lysine, threonine, methionine, tryptophan, and isoleucine can increase osteoblast proliferation, activation, and differentiation, and decrease osteoclast activity. Oxidized L-tryptophan promotes bone marrow stem cells (BMSCs) differentiating into osteoblasts. However, the oxidation product of tryptophan called kynurenine increases osteoclast activity, and enhances the differentiation of adipocytes from BMSCs. Taken together, in terms of bone minerals and volume, more views consider EAAs to have a positive effect on aging bone, but the function of EAAs in bone metabolism has not been fully demonstrated and more studies are needed in this area in the future.

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Section: Amino Acid As Energy Source and Tissue Builder In Bonesmentioning

confidence: 99%

Role of Essential Amino Acids in Age-Induced Bone Loss

Shi

Zhang

2022

IJMS

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“…cerevisiae. Since the resulting strains can accumulate different carbon metabolites, including CO 2 fixation products such as pyruvate (see above), they might provide suitable hosts to put related biosensor systems to the test. ,, …”

Section: Identification Of Novel Biosensor Systems and Contextualizat...mentioning

confidence: 99%

“…Since the resulting strains can accumulate different carbon metabolites, including CO 2 fixation products such as pyruvate (see above), they might provide suitable hosts to put related biosensor systems to the test. 10,76,77 Lastly, the nature of reporter genes dictates their applicability and can strongly influence biosensor performance, particularly in the context of living cells. Commonly used reporter proteins include fluorescent proteins, (bacterial) luciferases, and metabolic enzymes such as LacZ (Table 1), and their unique advantages and disadvantages have been discussed earlier.…”

Section: ■ Identification Of Novel Biosensor Systems and Contextualiz...mentioning

confidence: 99%

In Vivo Detection of Low Molecular Weight Platform Chemicals and Environmental Contaminants by Genetically Encoded Biosensors

et al. 2023

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Genetically encoded biosensor systems operating in living cells are versatile, cheap, and transferable tools for the detection and quantification of a broad range of small molecules. This review presents state-of-the-art biosensor designs and assemblies, featuring transcription factor-, riboswitch-, and enzyme-coupled devices, highly engineered fluorescent probes, and emerging two-component systems. Importantly, (bioinformaticassisted) strategies to resolve contextual issues, which cause biosensors to miss performance criteria in vivo, are highlighted. The optimized biosensing circuits can be used to monitor chemicals of low molecular mass (<200 g mol −1 ) and physicochemical properties that challenge conventional chromatographical methods with high sensitivity. Examples herein include but are not limited to formaldehyde, formate, and pyruvate as immediate products from (synthetic) pathways for the fixation of carbon dioxide (CO 2 ), industrially important derivatives like small-and medium-chain fatty acids and biofuels, as well as environmental toxins such as heavy metals or reactive oxygen and nitrogen species. Lastly, this review showcases biosensors capable of assessing the biosynthesis of platform chemicals from renewable resources, the enzymatic degradation of plastic waste, or the bioadsorption of highly toxic chemicals from the environment. These applications offer new biosensor-based manufacturing, recycling, and remediation strategies to tackle current and future environmental and socioeconomic challenges including the wastage of fossil fuels, the emission of greenhouse gases like CO 2 , and the pollution imposed on ecosystems and human health.

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“…Immunometabolism explores how changes in the metabolism of immune cells direct and guide their function ( 16 , 17 ). These metabolic alterations can be elucidated by metabolic flux analysis (MFA), a technique for calculating production, consumption, and transformation rates within a biological system ( 18 , 19 ). MFA most commonly relies on balancing fluxes within a stoichiometric network and employing nonlinear regressions.…”

Section: Introductionmentioning

confidence: 99%

13C-Metabolic flux analysis detected a hyperoxemia-induced reduction of tricarboxylic acid cycle metabolism in granulocytes during two models of porcine acute subdural hematoma and hemorrhagic shock

Wolfschmitt,

Vogt,

Hogg

et al. 2024

Front. Immunol.

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IntroductionSupplementation with increased inspired oxygen fractions has been suggested to alleviate the harmful effects of tissue hypoxia during hemorrhagic shock (HS) and traumatic brain injury. However, the utility of therapeutic hyperoxia in critical care is disputed to this day as controversial evidence is available regarding its efficacy. Furthermore, in contrast to its hypoxic counterpart, the effect of hyperoxia on the metabolism of circulating immune cells remains ambiguous. Both stimulating and detrimental effects are possible; the former by providing necessary oxygen supply, the latter by generation of excessive amounts of reactive oxygen species (ROS). To uncover the potential impact of increased oxygen fractions on circulating immune cells during intensive care, we have performed a 13C-metabolic flux analysis (MFA) on PBMCs and granulocytes isolated from two long-term, resuscitated models of combined acute subdural hematoma (ASDH) and HS in pigs with and without cardiovascular comorbidity.MethodsSwine underwent resuscitation after 2 h of ASDH and HS up to a maximum of 48 h after HS. Animals received normoxemia (PaO2 = 80 – 120 mmHg) or targeted hyperoxemia (PaO2 = 200 – 250 mmHg for 24 h after treatment initiation, thereafter PaO2 as in the control group). Blood was drawn at time points T1 = after instrumentation, T2 = 24 h post ASDH and HS, and T3 = 48 h post ASDH and HS. PBMCs and granulocytes were isolated from whole blood to perform electron spin resonance spectroscopy, high resolution respirometry and 13C-MFA. For the latter, we utilized a parallel tracer approach with 1,2-13C2 glucose, U-13C glucose, and U-13C glutamine, which covered essential pathways of glucose and glutamine metabolism and supplied redundant data for robust Bayesian estimation. Gas chromatography-mass spectrometry further provided multiple fragments of metabolites which yielded additional labeling information. We obtained precise estimations of the fluxes, their joint credibility intervals, and their relations, and characterized common metabolic patterns with principal component analysis (PCA).Results13C-MFA indicated a hyperoxia-mediated reduction in tricarboxylic acid (TCA) cycle activity in circulating granulocytes which encompassed fluxes of glutamine uptake, TCA cycle, and oxaloacetate/aspartate supply for biosynthetic processes. We further detected elevated superoxide levels in the swine strain characterized by a hypercholesterolemic phenotype. PCA revealed cell type-specific behavioral patterns of metabolic adaptation in response to ASDH and HS that acted irrespective of swine strains or treatment group.ConclusionIn a model of resuscitated porcine ASDH and HS, we saw that ventilation with increased inspiratory O2 concentrations (PaO2 = 200 – 250 mmHg for 24 h after treatment initiation) did not impact mitochondrial respiration of PBMCs or granulocytes. However, Bayesian 13C-MFA results indicated a reduction in TCA cycle activity in granulocytes compared to cells exposed to normoxemia in the same time period. This change in metabolism did not seem to affect granulocytes’ ability to perform phagocytosis or produce superoxide radicals.

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Metabolic flux analysis: a comprehensive review on sample preparation, analytical techniques, data analysis, computational modelling, and main application areas

Abstract: Metabolic flux analysis (MFA) quantitatively describes cellular fluxes to understand metabolic phenotypes and functional behaviour after environmental and/or genetic perturbations.

Cited by 14 publications

References 170 publications

Role of Essential Amino Acids in Age-Induced Bone Loss

Role of Essential Amino Acids in Age-Induced Bone Loss

In Vivo Detection of Low Molecular Weight Platform Chemicals and Environmental Contaminants by Genetically Encoded Biosensors

13C-Metabolic flux analysis detected a hyperoxemia-induced reduction of tricarboxylic acid cycle metabolism in granulocytes during two models of porcine acute subdural hematoma and hemorrhagic shock

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