Historical and contemporary stable isotope tracer approaches to studying mammalian protein metabolism

Numbers of Exchangeable Hydrogens from LC-MS Data of Heavy Water Metabolically Labeled Samples

Labeling with deuterium oxide (D2O) has emerged as one of the preferred approaches for measuring the synthesis of individual proteins in vivo. In these experiments, the synthesis rates of proteins are determined by modeling mass shifts in peptides during the labeling period. This modeling depends on a theoretical maximum enrichment determined by the number of labeling sites (NEH) of each amino acid in the peptide sequence. Currently, NEH is determined from one set of published values. However, it has been demonstrated that NEH can differ between species and potentially tissues. The goal of this work was to determine the number of NEH for each amino acid within a given experiment to capture the conditions unique to that experiment. We used four methods to compute the NEH values. To test these approaches, we used two publicly available data sets. In a de novo approach, we compute NEH values and the label enrichment from the abundances of three mass isotopomers. The other three methods use the complete isotope profiles and body water enrichment in deuterium as an input parameter. They determine the NEH values by (1) minimizing the residual sum of squares, (2) from the mole percent excess of labeling, and (3) the time course profile of the depletion of the relative isotope abundance of monoisotope. In the test samples, the method using residual sum of squares performed the best. The methods are implemented in a tool for determining the NEH for each amino acid within a given experiment to use in the determination of protein synthesis rates using D2O.

Enabling population protein dynamics through Bayesian modeling

MOTIVATION

The knowledge of protein dynamics, or turnover, in patients provides invaluable information related to certain diseases, drug efficacy, or biological processes. A great corpus of experimental and computational methods has been developed, including by us, in the case of human patients followed in vivo. Moving one step further, we propose a novel modeling approach to capture population protein dynamics using Bayesian methods.

RESULTS

Using two datasets, we demonstrate that models inspired by population pharmacokinetics can accurately capture protein turnover within a cohort and account for inter-individual variability. Such models pave the way for comparative studies searching for altered dynamics or biomarkers in diseases.

AVAILABILITY AND IMPLEMENTATION

R code and preprocessed data are available from zenodo.org. Raw data are available from panoramaweb.org.

Modeling the Simultaneous Dynamics of Proteins in Blood Plasma and the Cerebrospinal Fluid in Human In Vivo

The analysis of protein dynamics or turnover in patients has the potential to reveal altered protein recycling, such as in Alzheimer's disease, and to provide informative data regarding drug efficacy or certain biological processes. The observed protein dynamics in a solid tissue or a fluid is the net result of not only protein synthesis and degradation but also transport across biological compartments. We report an accurate 3-biological compartment model able to simultaneously account for the protein dynamics observed in blood plasma and the cerebrospinal fluid (CSF) including a hidden central nervous system (CNS) compartment. We successfully applied this model to 69 proteins of a single individual displaying similar or very different dynamics in plasma and CSF. This study puts a strong emphasis on the methods and tools needed to develop this type of model. We believe that it will be useful to any researcher dealing with protein dynamics data modeling.

Metabolomic and proteomic applications to exercise biomedicine

Objectives

'OMICs encapsulates study of scaled data acquisition, at the levels of DNA, RNA, protein, and metabolite species. The broad objectives of OMICs in biomedical exercise research are multifarious, but commonly relate to biomarker development and understanding features of exercise adaptation in health, ageing and metabolic diseases.

Methods

This field is one of exponential technical (i.e., depth of feature coverage) and scientific (i.e., in health, metabolic conditions and ageing, multi-OMICs) progress adopting targeted and untargeted approaches.

Results

Key findings in exercise biomedicine have led to the identification of OMIC features linking to heritability or adaptive responses to exercise e.g., the forging of GWAS/proteome/metabolome links to cardiovascular fitness and metabolic health adaptations. The recent addition of stable isotope tracing to proteomics ('dynamic proteomics') and metabolomics ('fluxomics') represents the next phase of state-of-the-art in 'OMICS.

Conclusions

These methods overcome limitations associated with point-in-time 'OMICs and can be achieved using substrate-specific tracers or deuterium oxide (D2O), depending on the question; these methods could help identify how individual protein turnover and metabolite flux may explain exercise responses. We contend application of these methods will shed new light in translational exercise biomedicine.

Understanding HDL Metabolism and Biology Through In Vivo Tracer Kinetics

HDL (high-density lipoprotein), owing to its high protein content and small size, is the densest circulating lipoprotein. In contrast to lipid-laden VLDL (very-low-density lipoprotein) and LDL (low-density lipoprotein) that promote atherosclerosis, HDL is hypothesized to mitigate atherosclerosis via reverse cholesterol transport, a process that entails the uptake and clearance of excess cholesterol from peripheral tissues. This process is mediated by APOA1 (apolipoprotein A-I), the primary structural protein of HDL, as well as by the activities of additional HDL proteins. Tracer-dependent kinetic studies are an invaluable tool to study HDL-mediated reverse cholesterol transport and overall HDL metabolism in humans when a cardiovascular disease therapy is investigated. Unfortunately, HDL cholesterol-raising therapies have not been successful at reducing cardiovascular events suggesting an incomplete picture of HDL biology. However, as HDL tracer studies have evolved from radioactive isotope- to stable isotope-based strategies that in turn are reliant on mass spectrometry technologies, the complexity of the HDL proteome and its metabolism can be more readily addressed. In this review, we outline the motivations, timelines, advantages, and disadvantages of the various tracer kinetics strategies. We also feature the metabolic properties of select HDL proteins known to regulate reverse cholesterol transport, which in turn underscore that HDL lipoproteins comprise a heterogeneous particle population whose distinct protein constituents and kinetics likely determine its function and potential contribution to cholesterol clearance.

Metabolic pathway analysis using stable isotopes in patients with cancer

Metabolic reprogramming is central to malignant transformation and cancer cell growth. How tumours use nutrients and the relative rates of reprogrammed pathways are areas of intense investigation. Tumour metabolism is determined by a complex and incompletely defined combination of factors intrinsic and extrinsic to cancer cells. This complexity increases the value of assessing cancer metabolism in disease-relevant microenvironments, including in patients with cancer. Stable-isotope tracing is an informative, versatile method for probing tumour metabolism in vivo. It has been used extensively in preclinical models of cancer and, with increasing frequency, in patients with cancer. In this Review, we describe approaches for using in vivo isotope tracing to define fuel preferences and pathway engagement in tumours, along with some of the principles that have emerged from this work. Stable-isotope infusions reported so far have revealed that in humans, tumours use a diverse set of nutrients to supply central metabolic pathways, including the tricarboxylic acid cycle and amino acid synthesis. Emerging data suggest that some activities detected by stable-isotope tracing correlate with poor clinical outcomes and may drive cancer progression. We also discuss current challenges in isotope tracing, including comparisons of in vivo and in vitro models, and opportunities for future discovery in tumour metabolism.

Stable isotope and trace element analyses with non-linear machine-learning data analysis improved coffee origin classification and marker selection

BACKGROUND

This study investigated the geographical origin classification of green coffee beans from continental to country and regional levels. An innovative approach combined stable isotope and trace element analyses with non-linear machine learning data analysis to improve coffee origin classification and marker selection. Specialty green coffee beans sourced from three continents, eight countries, and 22 regions were analyzed by measuring five isotope ratios (δ¹³ C, δ¹⁵ N, δ¹⁸ O, δ² H, and δ³⁴ S) and 41 trace elements. Partial least squares discriminant analysis (PLS-DA) was applied to the integrated dataset for origin classification.

RESULTS

Origins were predicted well at the country level and showed promise at the regional level, with discriminating marker selection at all levels. However, PLS-DA predicted origin poorly at the continental and Central American regional levels. Non-linear machine learning techniques improved predictions and enabled the identification of a higher number of origin markers, and those that were identified were more relevant. The best predictive accuracy was found using ensemble decision trees, random forest and extreme gradient boost, with accuracies of up to 0.94 and 0.89 for continental and Central American regional models, respectively.

CONCLUSION

The potential for advanced machine learning models to improve origin classification and the identification of relevant origin markers was demonstrated. The decision-tree-based models were superior with their embedded variable identification features and visual interpretation. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Advances of stable isotope technology in food safety analysis and nutrient metabolism research

Food quality, safety, and the regulatory metabolism of food nutrients in cells are primary factors in determining human health. However, residues of undesirable or hazardous compounds in food products and dysregulation in the nutrient metabolism inevitably occur occasionally. For years, chromatography-mass spectrometry technology has been recognized as an essential research tool in food analysis and nutrient metabolism research, and it is more accurate and robust when coupled with stable isotopes. In this study, we summarize the applications of stable isotope technology in the quantification of contaminant residues (pesticides, veterinary drugs, mycotoxins, polycyclic aromatic hydrocarbons, and other hazardous compounds) in foods and in the nutrients (glucose, lipids, amino acids and proteins) metabolism research. The aim of this review was to serve as a reference for providing effective analysis techniques for protecting food quality and human health, and to pave the way for the broader application of stable isotope technology.

Quantifying label enrichment from two mass isotopomers increases proteome coverage for in vivo protein turnover using heavy water metabolic labeling

Heavy water metabolic labeling followed by liquid chromatography coupled with mass spectrometry is a powerful high throughput technique for measuring the turnover rates of individual proteins in vivo. The turnover rate is obtained from the exponential decay modeling of the depletion of the monoisotopic relative isotope abundance. We provide theoretical formulas for the time course dynamics of six mass isotopomers and use the formulas to introduce a method that utilizes partial isotope profiles, only two mass isotopomers, to compute protein turnover rate. The use of partial isotope profiles alleviates the interferences from co-eluting contaminants in complex proteome mixtures and improves the accuracy of the estimation of label enrichment. In five different datasets, the technique consistently doubles the number of peptides with high goodness-of-fit characteristics of the turnover rate model. We also introduce a software tool, d2ome+, which automates the protein turnover estimation from partial isotope profiles.

Measurement of protein in vivo turnover rate with metabolic labeling using LC-MS

Understanding the protein dynamics of a drug target is important for pharmaceutical research because it provides insight into drug design, target engagement, pharmacodynamics and drug efficacy. Nonradioactive isotope labeling has been the method of choice for protein turnover measurement thanks to the advancement of high-resolution mass spectrometry. While the changes in proteome in cell cultures can be monitored precisely, as the culture media can be completely replaced with ² H-, ¹⁵ N- or ¹³ C-labeled essential amino acids, quantifying rates of protein synthesis in vivo is more challenging. The amount of isotope tracer that can be administered into the body is relatively small compared with the existing protein, thus requiring more sensitive detection, and the precursor-product labeling relationship is more complicated to interpret. The purpose of this review is to provide an overview of the principles of in vivo protein turnover studies using deuterium water (² H₂ O) with an emphasis on targeted protein analysis by hybrid LC-MS assay platforms. The pursuit of these opportunities will facilitate drug discovery and research in preclinical and clinical stages.

Advancements in Pulsed Stable Isotope-Resolved Metabolomics

The understanding of biochemical processes of metabolism is gained through the measurement of the concentration of intermediates and the rate of metabolite conversion. However, the measurement of metabolite concentrations does not give a full representation of this dynamic system. To understand the kinetics of metabolism, the system must be described and quantified in terms of metabolite flow as a function of time. In order to measure the metabolite flow, or more precisely the metabolic flux through a biological system, substrates of the cell are labelled with stable isotopes. The usage of these substrates by the cell leads to the incorporation of the isotopes into downstream intermediates.The most important metabolic pathways are encompassed in the central carbon metabolism (CCM). According to the Kyoto Encyclopedia of Genes and Genomes (KEGG), the central carbon metabolism "is the most basic aspect of life". It includes all metabolites and enzymatic reactions within: glycolysis and gluconeogenesis, pentose phosphate pathway (PPP), tricarboxylic acid (TCA) cycle, oxidative phosphorylation (OXPHOS), amino acids and nucleotide metabolic pathways. Some molecules are at the crossroad of metabolic pathways, interconnecting diverse metabolic and therefore functional outcomes. Labelling these nodal metabolites and analysing their isotopic composition allows the precise determination of the metabolic flow within the biochemical networks that they are in.Application of stable isotope labelled substrates allows the measurement of metabolic flux through a biochemical pathway. The rapid turnover of metabolites in pathways requires pulse-feeding cells with a labelled substrate. This method allows for the determination of different cell states. For example, the action of a drug from immediate impact until the compensatory response of the metabolic system (cell, organs, organisms). Pulsed labelling is an elegant way to analyse the action of small molecules and drugs and enables the analysis of regulatory metabolic processes in short time scales.

Atoms for Nutrition: IAEA's Contribution to Tackling Malnutrition

Nuclear techniques, including stable isotope techniques, provide great potential for understanding nutrition and human health with better accuracy and precision compared with other routine techniques. The International Atomic Energy Agency (IAEA) has been at the forefront for more than 25 y to offer guidance and support on the use of nuclear techniques. This article demonstrates how the IAEA has enabled its Member States to contribute to good health and well-being in their countries and to assess progress toward achieving global nutrition and health targets to combat malnutrition in all its forms. Support is provided in several ways including research, capacity building, education, and training as well as the provision of guidance materials. The nuclear techniques help to objectively measure nutritional and health-related outcomes such as body composition, energy expenditure, nutrient uptake, and body stores and assess breastfeeding practices as well as environmental interactions. These techniques are continuously improved to make nutritional assessments more affordable and less invasive with wide use in field settings. New research areas are emerging to assess diet quality with changing food systems and to explore stable isotope-assisted metabolomics to address key questions on nutrient metabolism. Through a deeper understanding of mechanisms, nuclear techniques can contribute to eradicating malnutrition worldwide.

Maternal Nutrition Affects Nitrogen Isotopic Signature in Blood Plasma of Beef Cattle Dams and Their Offspring

This study evaluated the effects of gestational supplementation strategy on nitrogen isotopic signature in blood plasma of beef cows and their progeny. The study comprised 15 pregnant Nellore cows divided into three different supplementation protocols: NP) non-programmed group; PP) cows receiving protein−energy supplement in the last third of pregnancy; and FP) cows receiving protein−energy supplement throughout the gestational period. Blood plasma from cows was sampled at the beginning of gestation, in the prepartum, and postpartum periods as well as from their calves at 30 and 180 days of age, for the analysis of stable isotope ratios 15 N/14 N. At pre- and postpartum periods, cows fed PP and FP presented greater abundance of δ15 N compared to NP (p < 0.05) at pre- and postpartum. All three groups showed significant differences (p < 0.05) in the postpartum period. The δ15 N values of calves at 30 days of age differed between the NP group and PP and FP groups (p < 0.05), with no difference (p > 0.05) at 180 days of age. The different gestational supplementation strategies influenced isotopic fractionation of nutrients of cows and their calves after birth, indicating effects on nutritional metabolism and cumulative behavior on isotope abundance related to consumption during gestation.

13C tracer analysis suggests extensive recycling of endogenous CO2 in vivo

Background

¹³C tracer analysis is increasingly used to monitor cellular metabolism in vivo and in intact cells, but data interpretation is still the key element to unveil the complexity of metabolic activities. The distinct ¹³C labeling patterns (e.g., M + 1 species in vivo but not in vitro) of metabolites from [U-¹³C]-glucose or [U-¹³C]-glutamine tracing in vivo and in vitro have been previously reported by multiple groups. However, the reason for the difference in the M + 1 species between in vivo and in vitro experiments remains poorly understood.

Methods

We have performed [U-¹³C]-glucose and [U-¹³C]-glutamine tracing in sarcoma-bearing mice (in vivo) and in cancer cell lines (in vitro). ¹³C enrichment of metabolites in cultured cells and tissues was determined by LC coupled with high-resolution mass spectrometry (LC-HRMS). All p-values are obtained from the Student’s t-test two-tailed using GraphPad Prism 8 unless otherwise noted.

Results

We observed distinct enrichment patterns of tricarboxylic acid cycle intermediates in vivo and in vitro. As expected, citrate M + 2 or M + 4 was the dominant mass isotopologue in vitro. However, citrate M + 1 was unexpectedly the dominant isotopologue in mice receiving [U-¹³C]-glucose or [U-¹³C]-glutamine infusion, but not in cultured cells. Our results are consistent with a model where the difference in M + 1 species is due to the different sources of CO₂ in vivo and in vitro, which was largely overlooked in the past. In addition, a time course study shows the generation of high abundance citrate M + 1 in plasma of mice as early as few minutes after [U-¹³C]-glucose infusion.

Conclusions

Altogether, our results show that recycling of endogenous CO₂ is substantial in vivo. The production and recycling of ¹³CO₂ from the decarboxylation of [U-¹³C]-glucose or [U-¹³C]-glutamine is negligible in vitro partially due to dilution by the exogenous HCO₃⁻/CO₂ source, but in vivo incorporation of endogenous ¹³CO₂ into M + 1 metabolites is substantial and should be considered. These findings provide a new paradigm to understand carbon atom transformations in vivo and should be taken into account when developing mathematical models to better reflect carbon flux.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40170-022-00287-8.

Provenances, preponderances, and distribution of humic acids and organic pollutants in hydro-geosphere: The co-existence, interaction and isotopic biomarkers in the riverine ecosystem

This paper aims to critically review the importance of geochemical fingerprinting and tracing using biomarkers and stable isotopes in the riverine ecosystem and depicts that isotopic ratios of δ¹³C, δ¹⁵N, and δ³⁴S can be used for tracing pollution sources. Stable isotopes like carbon, hydrogen, nitrogen, oxygen, and sulfur are being used for this purpose, and their isotopic signatures are primarily used to distinguish close sources of organic matter through dual isotopes. The present review is articulated to bridge the critical research gaps of the previous and contemporary documented literature on the genesis and transport of OM between freshwater and marine systems. This review comprehensively provides methods and techniques in geochemical tracing and discusses the future directions to address the challenges of the current methods to enhance the knowledge about the source identification of organic matter in the riverine environment. Tracer geochemistry emphasizes the implications of elemental abundances and isotope ratio variations in geologic substances to track natural earth processes, anthropogenic contaminants, and geochemical signatures in the hydrologic system. The principal constituent of organic matter comprises humic substances like humic acid, fulvic acid, and humin, and these comprise 50-75% of the sediments and DOC in natural waters. Their structural and functional characterization is required to elucidate the transport and fate of organic matter, which are often influenced by several paleoenvironmental factors.

Dynamic Methods for Childhood Hypoglycemia Phenotyping: A Narrative Review

Hypoglycemia results from an imbalance between glucose entering the blood compartment and glucose demand, caused by a defect in the mechanisms regulating postprandial glucose homeostasis. Hypoglycemia represents one of the most common metabolic emergencies in childhood, potentially leading to serious neurologic sequelae, including death. Therefore, appropriate investigation of its specific etiology is paramount to provide adequate diagnosis, specific therapy and prevent its recurrence. In the absence of critical samples for biochemical studies, etiological assessment of children with hypoglycemia may include dynamic methods, such as in vivo functional tests, and continuous glucose monitoring. By providing detailed information on actual glucose fluxes in vivo, proof-of-concept studies have illustrated the potential (clinical) application of dynamic stable isotope techniques to define biochemical and clinical phenotypes of inherited metabolic diseases associated with hypoglycemia. According to the textbooks, individuals with glycogen storage disease type I (GSD I) display the most severe hypoglycemia/fasting intolerance. In this review, three dynamic methods are discussed which may be considered during both diagnostic work-up and monitoring of children with hypoglycemia: 1) functional in vivo tests; 2) in vivo metabolic profiling by continuous glucose monitoring (CGM); 3) stable isotope techniques. Future applications and benefits of dynamic methods in children with hypoglycemia are also discussed.

Isotope Labels Combined with Solution NMR Spectroscopy Make Visible the Invisible Conformations of Small-to-Large RNAs

RNA is central to the proper function of cellular processes important for life on earth and implicated in various medical dysfunctions. Yet, RNA structural biology lags significantly behind that of proteins, limiting mechanistic understanding of RNA chemical biology. Fortunately, solution NMR spectroscopy can probe the structural dynamics of RNA in solution at atomic resolution, opening the door to their functional understanding. However, NMR analysis of RNA, with only four unique ribonucleotide building blocks, suffers from spectral crowding and broad linewidths, especially as RNAs grow in size. One effective strategy to overcome these challenges is to introduce NMR-active stable isotopes into RNA. However, traditional uniform labeling methods introduce scalar and dipolar couplings that complicate the implementation and analysis of NMR measurements. This challenge can be circumvented with selective isotope labeling. In this review, we outline the development of labeling technologies and their application to study biologically relevant RNAs and their complexes ranging in size from 5 to 300 kDa by NMR spectroscopy.

Protein turnover models for LC-MS data of heavy water metabolic labeling

Protein turnover is vital for cellular functioning and is often associated with the pathophysiology of a variety of diseases. Metabolic labeling with heavy water followed by liquid chromatography coupled to mass spectrometry is a powerful tool to study in vivo protein turnover in high throughput and large scale. Heavy water is a cost-effective and easy to use labeling agent. It labels all nonessential amino acids. Due to its toxicity in high concentrations (20% or higher), small enrichments (8% or smaller) of heavy water are used with most organisms. The low concentration results in incomplete labeling of peptides/proteins. Therefore, the data processing is more challenging and requires accurate quantification of labeled and unlabeled forms of a peptide from overlapping mass isotopomer distributions. The work describes the bioinformatics aspects of the analysis of heavy water labeled mass spectral data, available software tools and current challenges and opportunities.

The effects of elective abdominal surgery on protein turnover: A meta-analysis of stable isotope techniques to investigate postoperative catabolism

BACKGROUND & AIMS

Elective surgery induces skeletal muscle wasting driven by an imbalance between muscle protein synthesis and breakdown. From examination of diverse stable isotope tracer techniques, the dynamic processes driving this imbalance are unclear. This meta-analysis aimed to elucidate the mechanistic driver(s) of postoperative protein catabolism through stable isotope assessment of protein turnover before and after abdominal surgery.

METHODS

Meta-analysis was performed of randomized controlled trials and cohort studies in patients undergoing elective abdominal surgery that contained measurements of whole-body or skeletal muscle protein turnover using stable isotope tracer methodologies pre- and postoperatively. Postoperative changes in protein synthesis and breakdown were assessed through subgroup analysis of tracer methodology and perioperative care.

RESULTS

Surgery elicited no overall change in protein synthesis [standardized mean difference (SMD) -0.47, 95% confidence interval (CI): -1.32, 0.39, p = 0.25]. However, subgroup analysis revealed significant suppressions via direct-incorporation methodology [SMD -1.53, 95%CI: -2.89, -0.17, p = 0.03] within skeletal muscle. Changes of this nature were not present among arterio-venous [SMD 0.61, 95%CI: -1.48, 2.70, p = 0.58] or end-product [SMD -0.09, 95%CI: -0.81, 0.64, p = 0.82] whole-body measures. Surgery resulted in no overall change in protein breakdown [SMD 0.63, 95%CI: -0.06, 1.32, p = 0.07]. Yet, separation by tracer methodology illustrated significant increases in urinary end-products (urea/ammonia) [SMD 0.70, 95%CI: 0.38, 1.02, p < 0.001] that were not present among arterio-venous measures [SMD 0.67, 95%CI: -1.05, 2.38, p = 0.45].

CONCLUSIONS

Elective abdominal surgery elicits suppressions in skeletal muscle protein synthesis that are not reflected on a whole-body level. Lack of uniform changes across whole-body tracer techniques are likely due to contribution from tissues other than skeletal muscle.

Multiple Infusion Start Time Mass Spectrometry Imaging of Dynamic SIL-Glutathione Biosynthesis Using Infrared Matrix-Assisted Laser Desorption Electrospray Ionization

Due to the high association of glutathione metabolism perturbation with a variety of disease states, there is a dire need for analytical techniques to study glutathione kinetics. Additionally, the elucidation of microenvironmental effects on changes in glutathione metabolism would significantly improve our understanding of the role of glutathione in disease. We therefore present a study combining a multiple infusion start time protocol, stable isotope labeling technology, infrared matrix-assisted laser desorption electrospray ionization, and high-resolution accurate mass-mass spectrometry imaging to study spatial changes in glutathione kinetics across in sectioned mouse liver tissues. After injecting a mouse with the isotopologues [2-¹³C,¹⁵N]-glycine, [1,2-¹³C₂]-glycine, and [1,2-¹³C₂,¹⁵N]-glycine at three different time points, we were able to fully resolve and spatially map their metabolism into three isotopologues of glutathione and calculate their isotopic enrichment in glutathione. We created a tool in the open-source mass spectrometry imaging software MSiReader to accurately compute the percent isotope enrichment (PIE) of these labels in glutathione and visualize them in heat-maps of the tissue sections. In areas of high flux, we found that each label enriched an approximate median of 1.6%, 1.8%, and 1.5%, respectively, of the glutathione product pool measured in each voxel. This method may be adapted to study the heterogeneity of glutathione flux in diseased versus healthy tissues.

Recent advances in measuring and understanding the regulation of exercise-mediated protein degradation in skeletal muscle

Skeletal muscle protein turnover plays a crucial role in controlling muscle mass and protein quality control, including sarcomeric (structural and contractile) proteins. Protein turnover is a dynamic and continual process of protein synthesis and degradation. The ubiquitin proteasome system (UPS) is a key degradative system for protein degradation and protein quality control in skeletal muscle. UPS-mediated protein quality control is known to be impaired in aging and diseases. Exercise is a well-recognized, nonpharmacological approach to promote muscle protein turnover rates. Over the past decades, we have acquired substantial knowledge of molecular mechanisms of muscle protein synthesis after exercise. However, there have been considerable gaps in the mechanisms of how muscle protein degradation is regulated at the molecular level. The main challenge to understand muscle protein degradation is due in part to the lack of solid stable isotope tracer methodology to measure muscle protein degradation rate. Understanding the mechanisms of UPS with the concomitant measurement of protein degradation rate in skeletal muscle will help identify novel therapeutic strategies to ameliorate impaired protein turnover and protein quality control in aging and diseases. Thus, the goal of this present review was to highlight how recent advances in the field may help improve our understanding of exercise-mediated protein degradation. We discuss 1) the emerging roles of protein phosphorylation and ubiquitylation modifications in regulating proteasome-mediated protein degradation after exercise and 2) methodological advances to measure in vivo myofibrillar protein degradation rate using stable isotope tracer methods.

Resistance Exercise, Aging, Disuse, and Muscle Protein Metabolism

Skeletal muscle is the organ of locomotion, its optimal function is critical for athletic performance, and is also important for health due to its contribution to resting metabolic rate and as a site for glucose uptake and storage. Numerous endogenous and exogenous factors influence muscle mass. Much of what is currently known regarding muscle protein turnover is owed to the development and use of stable isotope tracers. Skeletal muscle mass is determined by the meal- and contraction-induced alterations of muscle protein synthesis and muscle protein breakdown. Increased loading as resistance training is the most potent nonpharmacological strategy by which skeletal muscle mass can be increased. Conversely, aging (sarcopenia) and muscle disuse lead to the development of anabolic resistance and contribute to the loss of skeletal muscle mass. Nascent omics-based technologies have significantly improved our understanding surrounding the regulation of skeletal muscle mass at the gene, transcript, and protein levels. Despite significant advances surrounding the mechanistic intricacies that underpin changes in skeletal muscle mass, these processes are complex, and more work is certainly needed. In this article, we provide an overview of the importance of skeletal muscle, describe the influence that resistance training, aging, and disuse exert on muscle protein turnover and the molecular regulatory processes that contribute to changes in muscle protein abundance. © 2021 American Physiological Society. Compr Physiol 11:2249-2278, 2021.

Stable Isotope Abundance and Fractionation in Human Diseases

The natural abundance of heavy stable isotopes (¹³C, ¹⁵N, ¹⁸O, etc.) is now of considerable importance in many research fields, including human physiology. In fact, it varies between tissues and metabolites due to isotope effects in biological processes, that is, isotope discriminations between heavy and light isotopic forms during enzyme or transporter activity. The metabolic deregulation associated with many diseases leads to alterations in metabolic fluxes, resulting in changes in isotope abundance that can be identified easily with current isotope ratio technologies. In this review, we summarize the current knowledge on changes in natural isotope composition in samples (including various tissues, hair, plasma, saliva) found in patients compared to controls, caused by human diseases. We discuss the metabolic origin of such isotope fractionations and highlight the potential of using isotopes at natural abundance for medical diagnosis and/or prognostic.

A collagen extraction and deuterium oxide stable isotope tracer method for the quantification of bone collagen synthesis rates in vivo

The development of safe and practical strategies to prevent weakening of bone tissue is vital, yet attempts to achieve this have been hindered by a lack of understanding of the short-term (days-weeks) physiology of bone collagen turnover. To address this, we have developed a method to quantify bone collagen synthesis in vivo, using deuterium oxide (D₂ O) tracer incorporation techniques combined with gas chromatography pyrolysis isotope-ratio mass spectrometry (GC-pyrolysis-IRMS). Forty-six male and female rats from a selectively bred model ingested D₂ O for 3 weeks. Femur diaphyses (FEM), tibia proximal (T-PRO), and distal (T-DIS) epiphyses-metaphyses and tibia mid-shaft diaphyses (T-MID) were obtained from all rats after necropsy. After demineralisation, collagen proteins were isolated and hydrolysed and collagen fractional synthetic rates (FSRs) determined by incorporation of deuterium into protein-bound alanine via GC-pyrolysis-IRMS. The collagen FSR for the FEM (0.131 ± 0.078%/day; 95% CI [0.106-0.156]) was greater than the FSR at T-MID (0.055 ± 0.049%/day; 95% CI [0.040-0.070]; p < 0.001). The T-PRO site had the highest FSR (0.203 ± 0.123%/day; 95% CI [0.166-0.241]) and T-DIS the lowest (0.027 ± 0.015%/day; 95% CI [0.022-0.031]). The three tibial sites exhibited different FSRs (p < 0.001). Herein, we have developed a sensitive method to quantify in vivo bone collagen synthesis and identified site-specific rates of synthesis, which could be applicable to studies of human bone collagen turnover.

Principles of stable isotope research - with special reference to protein metabolism

The key to understanding the mechanisms regulating disease stems from the ability to accurately quantify the dynamic nature of the metabolism underlying the physiological and pathological changes occurring as a result of the disease. Stable isotope tracer technologies have been at the forefront of this for almost 80 years now, and through a combination of both intense theoretical and technological development over these decades, it is now possible to utilise stable isotope tracers to investigate the complexities of in vivo human metabolism from a whole body perspective, down to the regulation of sub-nanometer cellular components (i.e organelles, nucleotides and individual proteins). This review therefore aims to highlight; 1) the advances made in these stable isotope tracer approaches - with special reference given to their role in understanding the nutritional regulation of protein metabolism, 2) some considerations required for the appropriate application of these stable isotope techniques to study protein metabolism, 3) and finally how new stable isotopes approaches and instrument/technical developments will help to deliver greater clinical insight in the near future.

18Oxygen Substituted Nucleosides Combined with Proton Beam Therapy: Therapeutic Transmutation In Vitro

Purpose

Proton therapy precisely delivers radiation to cancers to cause damaging strand breaks to cellular DNA, kill malignant cells, and stop tumor growth. Therapeutic protons also generate short-lived activated nuclei of carbon, oxygen, and nitrogen atoms in patients as a result of atomic transmutations that are imaged by positron emission tomography (PET). We hypothesized that the transition of ¹⁸O to ¹⁸F in an ¹⁸O-substituted nucleoside irradiated with therapeutic protons may result in the potential for combined diagnosis and treatment for cancer with proton therapy.

Materials and Methods

Reported here is a feasibility study with a therapeutic proton beam used to irradiate H₂¹⁸O to a dose of 10 Gy produced by an 85 MeV pristine Bragg peak. PET imaging initiated >45 minutes later showed an ¹⁸F decay signal with T_1/2 of ∼111 minutes.

Results

The ¹⁸O to ¹⁸F transmutation effect on cell survival was tested by exposing SQ20B squamous carcinoma cells to physiologic ¹⁸O-thymidine concentrations of 5 μM for 48 hours followed by 1- to 9-Gy graded doses of proton radiation given 24 hours later. Survival analyses show radiation sensitization with a dose modification factor (DMF) of 1.2.

Conclusions

These data support the idea of therapeutic transmutation in vitro as a biochemical consequence of proton activation of ¹⁸O to ¹⁸F in substituted thymidine enabling proton radiation enhancement in a cancer cell. ¹⁸O-substituted molecules that incorporate into cancer targets may hold promise for improving the therapeutic window of protons and can be evaluated further for postproton therapy PET imaging.

Comparing Stable Isotope Enrichment by Gas Chromatography with Time-of-Flight, Quadrupole Time-of-Flight, and Quadrupole Mass Spectrometry

Stable isotope tracers are applied for in vivo and in vitro studies to reveal the activity of enzymes and intracellular metabolic pathways. Most often, such tracers are used with gas chromatography coupled to mass spectrometry (GC-MS) owing to its ease of operation and reproducible mass spectral databases. Differences in isotope tracer performance of the classic GC-quadrupole MS instrument and newer time-of-flight instruments are not well studied. Here, we used three commercially available instruments for the analysis of identical samples from a stable isotope labeling study that used [U-13C6] d-glucose to investigate the metabolism of the bacterium Rothia mucilaginosa with respect to 29 amino acids and hydroxyl acids involved in primary metabolism. The prokaryote R. mucilaginosa belongs to the family of Micrococcaceae and is present and metabolically active in the airways and sputum of cystic fibrosis patients. Overall, all three GC-MS instruments (low-resolution GC-SQ MS, low-resolution GC-TOF MS, and high-resolution GC-QTOF MS) can be used to perform stable isotope tracing studies for glycolytic intermediates, tricarboxylic acid (TCA) metabolites, and amino acids, yielding similar biological results, with high-resolution GC-QTOF MS offering additional capabilities to identify the chemical structures of unknown compounds that might show significant isotope enrichments in biological studies.

Comprehensive assessment of post-prandial protein handling by the application of intrinsically labelled protein in vivo in human subjects

All human tissues are in a constant state of remodelling, regulated by the balance between tissue protein synthesis and breakdown rates. It has been well-established that protein ingestion stimulates skeletal muscle and whole-body protein synthesis. Stable isotope-labelled amino acid methodologies are commonly applied to assess the various aspects of protein metabolism in vivo in human subjects. However, to achieve a more comprehensive assessment of post-prandial protein handling in vivo in human subjects, intravenous stable isotope-labelled amino acid infusions can be combined with the ingestion of intrinsically labelled protein and the collection of blood and muscle tissue samples. The combined application of ingesting intrinsically labelled protein with continuous intravenous stable isotope-labelled amino acid infusion allows the simultaneous assessment of protein digestion and amino acid absorption kinetics (e.g. release of dietary protein-derived amino acids into the circulation), whole-body protein metabolism (whole-body protein synthesis, breakdown and oxidation rates and net protein balance) and skeletal muscle metabolism (muscle protein fractional synthesis rates and dietary protein-derived amino acid incorporation into muscle protein). The purpose of this review is to provide an overview of the various aspects of post-prandial protein handling and metabolism with a focus on insights obtained from studies that have applied intrinsically labelled protein under a variety of conditions in different populations.

Tendon Extracellular Matrix Assembly, Maintenance and Dysregulation Throughout Life

In his Lissner Award medal lecture in 2000, Stephen Cowin asked the question: "How is a tissue built?" It is not a new question, but it remains as relevant today as it did when it was asked 20 years ago. In fact, research on the organization and development of tissue structure has been a primary focus of tendon and ligament research for over two centuries. The tendon extracellular matrix (ECM) is critical to overall tissue function; it gives the tissue its unique mechanical properties, exhibiting complex non-linear responses, viscoelasticity and flow mechanisms, excellent energy storage and fatigue resistance. This matrix also creates a unique microenvironment for resident cells, allowing cells to maintain their phenotype and translate mechanical and chemical signals into biological responses. Importantly, this architecture is constantly remodeled by local cell populations in response to changing biochemical (systemic and local disease or injury) and mechanical (exercise, disuse, and overuse) stimuli. Here, we review the current understanding of matrix remodeling throughout life, focusing on formation and assembly during the postnatal period, maintenance and homeostasis during adulthood, and changes to homeostasis in natural aging. We also discuss advances in model systems and novel tools for studying collagen and non-collagenous matrix remodeling throughout life, and finally conclude by identifying key questions that have yet to be answered.

Proteome Turnover in the Spotlight: Approaches, Applications, and Perspectives

In all cells, proteins are continuously synthesized and degraded to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein turnover. At a steady state, protein turnover is constant to maintain protein homeostasis, but in dynamic responses, proteins change their rates of synthesis and degradation to adjust their proteomes to internal or external stimuli. Thus, probing the kinetics and dynamics of protein turnover lends insight into how cells regulate essential processes such as growth, differentiation, and stress response. Here, we outline historical and current approaches to measuring the kinetics of protein turnover on a proteome-wide scale in both steady-state and dynamic systems, with an emphasis on metabolic tracing using stable isotope-labeled amino acids. We highlight important considerations for designing proteome turnover experiments, key biological findings regarding the conserved principles of proteome turnover regulation, and future perspectives for both technological and biological investigation.

Partial Isotope Profiles Are Sufficient for Protein Turnover Analysis Using Closed-Form Equations of Mass Isotopomer Dynamics

Metabolic labeling with atom-based heavy isotopes, followed by liquid chromatography coupled with mass spectrometry (LC-MS), has been a powerful technique for studies of proteome and metabolome. In proteomics, the protein turnover of thousands of proteins can be estimated from the gradual incorporation of ²H or ¹⁵N in the diet. Software tools have been developed to automate the estimation of protein turnover. Traditionally, the turnover has been estimated using the time course of the depletion of the normalized abundance of monoisotopes. While the bioinformatic aspects of peak detection and integration, time course modeling, and uncertainty estimation have progressed, mass isotopomer dynamics during label incorporation has only been modeled from approximate approaches or numerical simulations. We derive closed-form equations that describe the dynamics of mass isotopomers during metabolic labeling with an atom-based stable isotope. The derived equations create an alternative method for estimating label incorporation. They also provide opportunities for estimation of precursor-product relationships in species or systems where they are unknown. The equations are useful in bioinformatic tools for analyzing mass spectral data from metabolic labeling.

Measuring Protein Turnover in the Field: Implications for Military Research

Protein turnover reflects the continual synthesis and breakdown of body proteins, and can be measured at a whole-body (i.e. aggregated across all body proteins) or tissue (e.g. skeletal muscle only) level using stable isotope methods. Evaluating protein turnover in free-living environments, such as military training, can help inform protein requirements. We undertook a narrative review of published literature with the aim of reviewing the suitability of, and advancements in, stable isotope methods for measuring protein turnover in field research. The 2 primary approaches for measuring protein turnover are based on precursor- and end-product methods. The precursor method is the gold-standard for measuring acute (over several hours) skeletal muscle protein turnover, whereas the end-product method measures chronic (over several weeks) skeletal muscle protein turnover and provides the opportunity to monitor free-living activities. Both methods require invasive procedures such as the infusion of amino acid tracers and muscle biopsies to assess the uptake of the tracer into tissue. However, the end-product method can also be used to measure acute (over 9-24 h) whole-body protein turnover noninvasively by ingesting 15N-glycine, or equivalent isotope tracers, and collecting urine samples. The end-product method using 15N-glycine is a practical method for measuring whole-body protein turnover in the field over short (24 h) time frames and has been used effectively in recent military field research. Application of this method may improve our understanding of protein kinetics during conditions of high physiological stress in free-living environments such as military training.

Preparation and Application of 13C-Labeled myo-Inositol to Identify New Catabolic Products in Inositol Metabolism in Lactobacillus casei

myo-Inositol (mI) is widely distributed in all domains of life and is important for several cellular functions, including bacterial survival. The enzymes responsible for the bacterial catabolism of mI, encoded in the iol operon, can vary from one organism to another, and these pathways have yet to be fully characterized. We previously identified a new scyllo-inositol dehydrogenase (sIDH) in the iol operon of Lactobacillus casei that can oxidize mI in addition to the natural substrate, scyllo-inositol, but the product of mI oxidation was not determined. Here we report the identification of these metabolites by monitoring the reaction with ¹³C nuclear magnetic resonance. We prepared all six singly ¹³C-labeled mI isotopomers through a biocatalytic approach and used these labeled inositols as substrates for sIDH. The use of all six singly labeled mI isotopomers allowed for metabolite characterization without isolation steps. sIDH oxidation of mI produces 1l-5-myo-inosose preferentially, but also two minor products, 1d-chiro-inosose and 1l-chiro-inosose. Together with previous crystal structure data for sIDH, we were able to rationalize the observed oxidation preference. Our relatively simple procedure for the preparation of isotopically labeled mI standards can have broad applications for the study of mI biotransformations.

Report of a member-led meeting: how stable isotope techniques can enhance human nutrition research

A Nutrition Society member-led meeting was held on 9 January 2020 at The University of Surrey, UK. Sixty people registered for the event, and all were invited to participate, either through chairing a session, presenting a '3 min lightning talk' or by presenting a poster. The meeting consisted of an introduction to the topic by Dr Barbara Fielding, with presentations from eight invited speakers. There were also eight lightning talks and a poster session. The meeting aimed to highlight recent research that has used stable isotope tracer techniques to understand human metabolism. Such studies have irrefutably shaped our current understanding of metabolism and yet remain a mystery to many. The meeting aimed to de-mystify their use in nutrition research.

Contemporary stable isotope tracer approaches: Insights into skeletal muscle metabolism in health and disease

NEW FINDINGS

What is the topic of this review? This review discusses the application of new stable isotope tracer techniques in understanding the control of skeletal muscle mass. What advances does it highlight? This review highlights current advances in stable isotope tracer techniques through their combination with high-throughput proteomics technologies.

ABSTRACT

Beyond its primary locomotory and key structural functions, skeletal muscle provides additional vital roles for maintenance of metabolic health, acting as a storage point for glucose and intramuscular lipids for energy production, alongside being the largest reservoir for amino acids in the body. Therefore, maintenance of muscle mass is key to the promotion of health and well-being across the lifespan and in several disease states. As such, when skeletal muscle is lost, in either clinical (cancer, organ failure etc.) or non-clinical (ageing, inactivity) situations, there are potentially devastating consequences attached, with robust links existing between muscle mass loss and mortality. Great efforts are being made to reverse or slow muscle mass declines in health and disease, through combinations of lifestyle changes and nutritional and/or pharmaceutical intervention. However, despite this comprehensive research effort, the underlying metabolic and molecular mechanisms have yet to be defined properly. However, with the rapid acceleration of analytical developments over recent years, the application of stable isotope tracers to the study of human muscle metabolism is providing unique insights into the mechanisms controlling skeletal muscle loss and allowing more targeted therapeutic strategies to be developed. The aim of this review is to highlight the technical breakthroughs in our understanding of muscle wasting in health and disease and how future directions and developments incorporating 'omics' with stable isotope tracers will allow for a more personalized and stratified therapeutic approach.

Benefits of stable isotope labeling in RNA analysis

RNAs are key players in life as they connect the genetic code (DNA) with all cellular processes dominated by proteins. They contain a variety of chemical modifications and many RNAs fold into complex structures. Here, we review recent progress in the analysis of RNA modification and structure on the basis of stable isotope labeling techniques. Mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy are the key tools and many breakthrough developments were made possible by the analysis of stable isotope labeled RNA. Therefore, we discuss current stable isotope labeling techniques such as metabolic labeling, enzymatic labeling and chemical synthesis. RNA structure analysis by NMR is challenging due to two major problems that become even more salient when the size of the RNA increases, namely chemical shift overlaps and line broadening leading to complete signal loss. Several isotope labeling strategies have been developed to provide solutions to these major issues, such as deuteration, segmental isotope labeling or site-specific labeling. Quantification of modified nucleosides in RNA by MS is only possible through the application of stable isotope labeled internal standards. With nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS), it is now possible to analyze the dynamic processes of post-transcriptional RNA modification and demodification. The trend, in both NMR and MS RNA analytics, is without doubt shifting from the analysis of snapshot moments towards the development and application of tools capable of analyzing the dynamics of RNA structure and modification profiles.

Advances in stable isotope tracer methodology part 1: hepatic metabolism via isotopomer analysis and postprandial lipolysis modeling

Stable isotope tracers have been used to gain an understanding of integrative animal and human physiology. More commonly studied organ systems include hepatic glucose metabolism, lipolysis from adipose tissue, and whole body protein metabolism. Recent improvements in isotope methodology have included the use of novel physiologic methods/models and mathematical modeling of data during different physiologic states. Here we review some of the latest advancements in this field and highlight future research needs. First we discuss the use of an oral [U-13C3]-glycerol tracer to determine the relative contribution of glycerol carbons to hepatic glucose production after first cycling through the tricarboxylic acid cycle, entry of glycerol into the pentose phosphate pathway or direct conversion of glycerol into the glucose. Second, we describe an adaptation of the established oral minimal model used to define postprandial glucose dynamics to include glycerol dynamics in an oral glucose tolerance test with a [2H5]-glycerol tracer to determine dynamic changes in lipolysis. Simulation results were optimized when parameters describing glycerol flux were determined with a hybrid approach using both tracer-based calculations and constrained parameter optimization. Both of these methodologies can be used to expand our knowledge of not only human physiology, but also the effects of various nutritional strategies and medications on metabolism.

Advances in stable isotope tracer methodology part 2: new thoughts about an “old” method—measurement of whole body protein synthesis and breakdown in the fed state

Whole-body protein turnover (protein synthesis, breakdown, and net balance) model enables quantification of the response to a variety of circumstances, including the response to meal feeding. In the fed state, the whole-body protein turnover model requires taking account of the contribution of absorbed tracee to the observed total appearance of tracee in the peripheral blood (exogenous appearance, RaEXO). There are different approaches to estimating RaEXO. The use of an intrinsically labeled dietary protein is based on the overriding assumption that the appearance in the peripheral circulation of a tracer amino acid incorporated into a dietary protein is exactly proportional to the appearance of absorbed tracee. The bioavailability approach is based on the true ileal digestibility of the dietary protein and the irreversible loss of the tracee in the splanchnic bed via hydroxylation of the tracee (phenylalanine). Finally, RaEXO can be estimated as the increase above the basal rate of appearance of the tracee using traditional tracer dilution methodology. In this paper, we discuss the pros and cons of each approach and conclude that the bioavailability method is the least likely to introduce systematic errors and is therefore the preferable approach.

New advances in stable tracer methods to assess whole-body protein and amino acid metabolism

PURPOSE OF REVIEW

Stable isotope methods have been used for many years to assess whole-body protein and amino acid kinetics in healthy conditions and in response to aging, exercise and (clinically stable) disease states.

RECENT FINDINGS

In recent years, tracer research expanded to the anabolic response to feeding in critical illness and its use during acute metabolic stressors. Furthermore, new isotope approaches and tracer insights have been obtained. In the postabsorptive state, the novel tracer pulse approach has several advantages above the established continuous tracer approach because of the metabolic information that can be obtained, easy applicability, and low tracer costs. The use of bolus versus sip-feeding approaches to assess the anabolic response to a meal is dependent on the research question and its feasibility. Promising new tracer approaches have been developed to measure the anabolic capacity, and protein digestibility and absorption. Advances have been made in the field of mass spectrometry in low enrichment analysis.

SUMMARY

Novel tracer approaches are available that can more readily be used in critical illness and during acute metabolic stressors. Besides the use of tracer application in various clinical conditions, more research is needed on how to incorporate isotopes on an individual level.

Improved Sensitivity for Protein Turnover Quantification by Monitoring Immonium Ion Isotopologue Abundance

We describe an analytical strategy allowing for the direct quantification of stable isotope label incorporation in newly synthesized proteins following administration of the stable isotope tracer deuterium oxide. We present a demonstration of coupling high-resolution mass spectrometry, metabolic stable isotope labeling, and MS/MS-based isotopologue quantification for the measurement of protein turnover. Stable isotope labeling with deuterium oxide, followed by immonium ion isotopologue quantification, is a more sensitive strategy for determining protein fractional synthesis rates compared to peptide centric mass isotopomer distribution analysis approaches when labeling time and/or stable isotope tracer exposure is limited and, as such, offers a great advantage for human studies.

Systems-level analysis of isotopic labeling in untargeted metabolomic data by X13CMS

Identification of previously unreported metabolites (so-called 'unknowns') in untargeted metabolomic data has become an increasingly active area of research. Considerably less attention, however, has been dedicated to identifying unknown metabolic pathways. Yet, for each unknown metabolite structure, there is potentially a yet-to-be-discovered chemical transformation. Elucidating these biochemical connections is essential to advancing our knowledge of cellular metabolism and can be achieved by tracking an isotopically labeled precursor to an unexpected product. In addition to their role in mapping metabolic fates, isotopic labels also provide critical insight into pathway dynamics (i.e., metabolic fluxes) that cannot be obtained from conventional label-free metabolomic analyses. When labeling is compared quantitatively between conditions, for example, isotopic tracers can enable relative pathway activities to be inferred. To discover unexpected chemical transformations or unanticipated differences in metabolic pathway activities, we have developed X13CMS, a platform for analyzing liquid chromatography/mass spectrometry (LC/MS) data at the systems level. After providing cells, animals, or patients with an isotopically enriched metabolite (e.g., 13C, 15N, or 2H), X13CMS identifies compounds that have incorporated the isotopic tracer and reports the extent of labeling for each. The analysis can be performed with a single condition, or isotopic fates can be compared between multiple conditions. The choice of which metabolite to enrich and which isotopic label to use is highly context dependent, but 13C-glucose and 13C-glutamine are often applied because they feed a large number of metabolic pathways. X13CMS is freely available.

SILK studies - capturing the turnover of proteins linked to neurodegenerative diseases

Alzheimer disease (AD) is one of several neurodegenerative diseases characterized by dysregulation, misfolding and accumulation of specific proteins in the CNS. The stable isotope labelling kinetics (SILK) technique is based on generating amino acids labelled with naturally occurring stable (that is, nonradioactive) isotopes of carbon and/or nitrogen. These labelled amino acids can then be incorporated into proteins, enabling rates of protein production and clearance to be determined in vivo and in vitro without the use of radioactive or chemical labels. Over the past decade, SILK studies have been used to determine the turnover of key pathogenic proteins amyloid-β (Aβ), tau and superoxide dismutase 1 (SOD1) in the cerebrospinal fluid of healthy individuals, patients with AD and those with other neurodegenerative diseases. These studies led to the identification of several factors that alter the production and/or clearance of these proteins, including age, sleep and disease-causing genetic mutations. SILK studies have also been used to measure Aβ turnover in blood and within brain tissue. SILK studies offer the potential to elucidate the mechanisms underlying various neurodegenerative disease mechanisms, including neuroinflammation and synaptic dysfunction, and to demonstrate target engagement of novel disease-modifying therapies.

The application of stable-isotope tracers to study human musculoskeletal protein turnover: a tale of bag filling and bag enlargement

The nutritional regulation of protein and amino acid balance in human skeletal muscle carried out by the authors with Mike Rennie is reviewed in the context of a simple physiological model for the regulation of the maintenance and growth of skeletal muscle, the "Bag Theory". Beginning in London in the late 1970s the work has involved the use of stable isotopes to probe muscle protein synthesis and breakdown with two basic experimental models, primed-dose continuous tracer infusions combined with muscle biopsies and arterio-venous (A-V) studies across a limb, most often the leg, allowing both protein synthesis and breakdown as well as net balance to be measured. In this way, over a 30 year period, the way in which amino acids and insulin mediate the anabolic effect of a meal has been elaborated in great detail confirming the original concepts of bag filling within the muscle endomysial "bag", which is limited by the "bag" size unless bag enlargement occurs requiring new collagen synthesis. Finally we briefly review some new developments involving ² H₂ O labelling of muscle proteins.

Getting Our Fingers on the Pulse of Slow-Growing Bacteria in Hard-To-Reach Places

Chronic infections with slow-growing pathogens have plagued humans throughout history. However, assessing the identities and growth rates of bacteria in an infection has remained an elusive goal. Neubauer et al. (J. Bacteriol. 200:e00365-18, 2018, https://doi.org/10.1128/JB.00365-18) combine two cutting-edge approaches to make progress on both fronts: probing specific RNA molecules to assess the identity of actively transcribing microbes and measuring growth rates through incorporation of stable isotope labels. They found that growth rates of pathogens were relatively stable during antibacterial therapy. The article delves into a basic and unanswered question that gets to the heart of understanding infection: what are the microbial growth rates?

The age-related loss of skeletal muscle mass and function: Measurement and physiology of muscle fibre atrophy and muscle fibre loss in humans

•

Loss of muscle mass with age is due to atrophy and loss of individual muscle fibres.

•

Anabolic resistance is fundamental in age-related fibre atrophy.

•

Fibre loss is associated with denervation and remodelling of motor units.

•

The plasticity of both factors should be considered in future research.

Age-related loss of skeletal muscle mass and function, sarcopenia, is associated with physical frailty and increased risk of morbidity (chronic diseases), in addition to all-cause mortality. The loss of muscle mass occurs incipiently from middle-age (∼1%/year), and in severe instances can lead to a loss of ∼50% by the 8–9th decade of life. This review will focus on muscle deterioration with ageing and highlight the two underpinning mechanisms regulating declines in muscle mass and function: muscle fibre atrophy and muscle fibre loss (hypoplasia) – and their measurement. The mechanisms of muscle fibre atrophy in humans relate to imbalances in muscle protein synthesis (MPS) and breakdown (MPB); however, since there is limited evidence for basal alterations in muscle protein turnover, it would appear that “anabolic resistance” to fundamental environmental cues regulating diurnal muscle homeostasis (namely physical activity and nutrition), underlie age-related catabolic perturbations in muscle proteostasis. While the ‘upstream’ drivers of the desensitization of aged muscle to anabolic stimuli are poorly defined, they most likely relate to impaired efficiency of the conversion of nutritional/exercise stimuli into signalling impacting mRNA translation and proteolysis. Additionally, loss of muscle fibres has been shown in cadaveric studies using anatomical fibre counts, and from iEMG studies demonstrating motor unit loss, albeit with few molecular investigations of this in humans. We suggest that defining countermeasures against sarcopenia requires improved understandings of the co-ordinated regulation of muscle fibre atrophy and fibre loss, which are likely to be inextricably linked.

Pilot Study Examining the Influence of Potassium Bicarbonate Supplementation on Nitrogen Balance and Whole-Body Ammonia and Urea Turnover Following Short-Term Energy Restriction in Older Men

With aging there is a chronic low-grade metabolic-acidosis that may exacerbate negative protein balance during weight loss. The objective of this randomized pilot study was to assess the impact of 90 mmol∙day⁻¹ potassium bicarbonate (KHCO₃) versus a placebo (PLA) on 24-h urinary net acid excretion (NAE), nitrogen balance (NBAL), and whole-body ammonia and urea turnover following short-term diet-induced weight loss. Sixteen (KHCO₃; n = 8, PLA; n = 8) older (64 ± 4 years) overweight (BMI: 28.5 ± 2.1 kg∙day⁻¹) men completed a 35-day controlled feeding study, with a 7-day weight-maintenance phase followed by a 28-day 30% energy-restriction phase. KHCO₃ or PLA supplementation began during energy restriction. NAE, NBAL, and whole-body ammonia and urea turnover (¹⁵N-glycine) were measured at the end of the weight-maintenance and energy-restriction phases. Following energy restriction, NAE was −9.8 ± 27.8 mmol∙day⁻¹ in KHCO₃ and 43.9 ± 27.8 mmol∙day⁻¹ in PLA (p < 0.05). No significant group or time differences were observed in NBAL or ammonia and urea turnover. Ammonia synthesis and breakdown tended (p = 0.09) to be higher in KHCO₃ vs. PLA following energy restriction, and NAE was inversely associated (r = −0.522; p < 0.05) with urea synthesis in all subjects. This pilot study suggests some benefit may exist with KHCO₃ supplementation following energy restriction as lower NAE indicated higher urea synthesis.

Detection of Localized Hepatocellular Amino Acid Kinetics by using Mass Spectrometry Imaging of Stable Isotopes

Mass spectrometry imaging (MSI) simultaneously detects and identifies the spatial distribution of numerous molecules throughout tissues. Currently, MSI is limited to providing a static and ex vivo snapshot of highly dynamic systems in which molecules are constantly synthesized and consumed. Herein, we demonstrate an innovative MSI methodology to study dynamic molecular changes of amino acids within biological tissues by measuring the dilution and conversion of stable isotopes in a mouse model. We evaluate the method specifically on hepatocellular metabolism of the essential amino acid l-phenylalanine, associated with liver diseases. Crucially, the method reveals the localized dynamics of l-phenylalanine metabolism, including its in vivo hydroxylation to l-tyrosine and co-localization with other liver metabolites in a time course of samples from different animals. This method thus enables the dynamics of localized biochemical synthesis to be studied directly from biological tissues.

Using stable isotope techniques in nutrition assessments and tracking of global targets post-2015

Stable isotopes are non-radioactive, safe and are applied for various purposes in human health assessment in trace amounts that minimally disturb normal physiology. The International Atomic Energy Agency supports the use of stable isotope techniques to design and evaluate interventions addressing malnutrition in all its forms with focus on infant and young child feeding; maternal and adolescent nutrition; diet quality; prevention and control of non-communicable diseases; healthy ageing and gut function. These techniques can be used to objectively measure: (1) amount of human milk consumed and whether an infant is exclusively breastfed; (2) body composition in the context of re-feeding programmes for moderate and severe acute malnutrition and as an indicator of the risk for obesity; (3) bioavailability and bioconversion of pro-vitamin A and vitamin A body stores following vitamin A intervention programmes; (4) absorption and retention of iron, zinc and protein; (5) total energy expenditure for validation of physical activity measurement and dietary assessment tools and (6) diagnosis of Helicobacter pylori. Stable isotope techniques will be invaluable in the tracking of global targets on exclusive breast-feeding childhood obesity and anaemia among women. Efforts are underway to make nuclear techniques more affordable, field-friendly and less invasive, and to develop less sophisticated but precise equipment. Advocacy for the wide adoption of the techniques is needed.

Evaluation of Gallium as a Tracer of Exogenous Hemoglobin-Haptoglobin Complexes for Targeted Drug Delivery Applications

Haptoglobin (Hp) is a plasma glycoprotein that generates significant interest in the drug delivery community because of its potential for delivery of antiretroviral medicines with high selectivity to macrophages and monocytes, the latent reservoirs of human immunodeficiency virus. As is the case with other therapies that exploit transport networks for targeted drug delivery, the success of the design and optimization of Hp-based therapies will critically depend on the ability to accurately localize and quantitate Hp-drug conjugates on the varying and unpredictable background of endogenous proteins having identical structure. In this work, we introduce a new strategy for detecting and quantitating exogenous Hp and Hp-based drugs with high sensitivity in complex biological samples using gallium as a tracer of this protein and inductively coupled plasma mass spectrometry (ICP MS) as a method of detection. Metal label is introduced by reconstituting hemoglobin (Hb) with gallium(III)-protoporphyrin IX followed by its complexation with Hp. Formation of the Hp/Hb assembly and its stability are evaluated with native electrospray ionization mass spectrometry. Both stable isotopes of Ga give rise to an abundant signal in ICP MS of a human plasma sample spiked with the metal-labeled Hp/Hb complex. The metal label signal exceeds the spectral interferences' contributions by more than an order of magnitude even with the concentration of the exogenous protein below 10 nM, the level that is more than adequate for the planned pharmacokinetic studies of Hp-based therapeutics. Graphical Abstract ᅟ.