Individual Metabolic Phenotype Research Articles

Global 13C tracing and metabolic flux analysis of intact human liver tissue ex vivo.

Liver metabolism is central to human physiology and influences the pathogenesis of common metabolic diseases. Yet, our understanding of human liver metabolism remains incomplete, with much of current knowledge based on animal or cell culture models that do not fully recapitulate human physiology. Here, we perform in-depth measurement of metabolism in intact human liver tissue ex vivo using global 13C tracing, non-targeted mass spectrometry and model-based metabolic flux analysis. Isotope tracing allowed qualitative assessment of a wide range of metabolic pathways within a single experiment, confirming well-known features of liver metabolism but also revealing unexpected metabolic activities such as de novo creatine synthesis and branched-chain amino acid transamination, where human liver appears to differ from rodent models. Glucose production ex vivo correlated with donor plasma glucose, suggesting that cultured liver tissue retains individual metabolic phenotypes, and could be suppressed by postprandial levels of nutrients and insulin, and also by pharmacological inhibition of glycogen utilization. Isotope tracing ex vivo allows measuring human liver metabolism with great depth and resolution in an experimentally tractable system.

Intermittent fasting modulates human gut microbiota diversity in a phenotype-dependent manner: a systematic review.

Cumulative evidence suggests that intermittent fasting (IF) has beneficial effects on human metabolic health. It has been indicated that its impact on the gut microbiota may mediate these beneficial effects. As a result, we hypothesized that IF may impact the human gut microbiota. A systematic review was carried out according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) protocol using the PubMed, Scopus, and CINAHL databases. We registered our systematic review protocol in PROSPERO under registration number CRD42021270050. Human intervention studies published until April 30, 2023, were included. The quality of the included studies was assessed using National Institutes of Health (NIH) quality assessment study tools for intervention studies. The search in the database returned 166 studies, of which 13 matched all criteria for the final qualitative analysis. The body of evidence suggests that IF modulates human gut microbiota alpha and beta diversity in lean (relatively healthy) and relatively healthy overweight/obese individuals but not in individuals with metabolic syndrome. Furthermore, IF also alters human gut microbiota composition in all phenotypes. Of interest, the gut microbiota taxa or microbial metabolites after an IF intervention are associated with metabolic markers. According to this review, IF influences the diversity and taxonomic levels of the human gut microbiota. Individual metabolic phenotypes may alter the effect of IF on the diversity and taxonomic levels of the gut microbiota.

SAT445 Exposure To Perfluoroalkyl Substances At Preconception In Association With Metabolic Phenotype In Women From Singapore

Abstract Disclosure: N.J. Cohen: None. M. Yao: None. V. Midya: None. S. India-Aldana: None. S.S. Andra: None. S. Narasimhan: None. A.K. Meher: None. M. Arora: None. J.K. Chan: None. S.Y. Chan: None. Y. Kway: None. N. Michael: None. S.A. Sadanathan: None. J.G. Eriksson: None. S.S. Velan: None. T.K. Hian: None. Y. Oulhote: None. J. Huang: None. D. Valvi: None. Background and Aim: Exposure to perfluoroalkyl substances (PFAS) may result in adverse metabolic health outcomes, but few studies have focused on preconception PFAS exposures and metabolic dysregulation which could impact pregnancy. We assessed cross-sectional and prospective associations between preconception PFAS concentrations and glucose regulation, insulin sensitivity, and magnetic resonance imaging (MRI) based adiposity measures in a Singaporean cohort of women who were actively attempting to conceive. Methods: Our analyses included 384 participants from the Singapore Preconception Study of Long-Term Maternal and Child Outcomes (S-PRESTO), from which 126 underwent abdominal MRI at preconception. 15 different PFAS in preconception plasma samples were measured, and metabolic measures were cross-sectionally assessed at preconception (waist-to-height ratio [WHtR], 2-hour oral glucose tolerance test [OGTT] indices, and MRI-based measures of abdominal adiposity and liver fat), and prospectively at 24-28 weeks of gestation (2-hour OGTT indices). We used linear regression models to assess associations between individual PFAS and metabolic phenotype at preconception and pregnancy. In addition, we used Bayesian weighted quantile sum (BWQS) regression to assess the joint associations of the PFAS mixture with study outcomes. Results: We observed negative associations between perfluorononanoic acid (PFNA) concentrations and visceral adipose tissue (VAT; log2-transformed) volume (β per doubling of PFNA=-0.12 cm3, 95% CI -0.24, 0.00) and log2-transformed liver fat percentage (β=-0.28%, 95% CI -0.52, -0.04). Inverse associations were observed between the individual PFAS and most mid-pregnancy OGTT indices and insulin resistance, but were not statistically significant. Associations were not statistically significant for all preconception OGTT indices. Conclusions: We did not find strong evidence for an association between preconception PFAS concentrations and prenatal metabolic outcomes in young women in Singapore. Cross-sectional analyses indicated reduced adiposity in VAT volume and liver fat percentage with increasing PFAS concentration, which requires further investigation in prospective, more diverse, and larger studies. Presentation: Saturday, June 17, 2023

The Role of Metabolic Phenotype in the Capacity to Balance Competing Energetic Demands.

AbstractGiven the critical role of metabolism in the life history of all organisms, there is particular interest in understanding the relationship between individual metabolic phenotypes and the capacity to partition energy into competing life history traits. Such relationships could be predictive of individual phenotypic performances throughout life. Here, we were specifically interested in whether an individual fish's metabolic phenotype can shape its propensity to feed following a significant stressor (2-min exhaustive exercise challenge). Such a relationship would provide insight into previous intraspecific observations linking high metabolism with faster growth. Using a teleost fish, the barramundi (Lates calcarifer), we predicted that individuals with high standard metabolic rates (SMRs) and maximal metabolic rates (MMRs) would be faster to recover and resume feeding after exercise. Contrary to our prediction, neither SMR nor MMR was correlated with latency to feed after exercise (food was offered at 0.5, 1.5, 3, and 18 h after exercise). Only time after exercise and individual fish ID were significant predictors of latency to feed. Measurements of MMR from the same individuals (three measurements spaced 8-12 d apart) revealed a moderate degree of repeatability (). We propose that interindividual differences in biochemical and endocrine processes may be more influential than whole-organism metabolic phenotype in mediating feeding latency after exercise.

Neonatal phenylalanine wash-out in phenylketonuria.

Phenylketonuria (PKU) is the most common inborn error of amino acids metabolism. PKU management aims to keep as soon as possible blood phenylalanine (Phe), a non-acutely neurotoxic metabolite, within safe ranges through a dietary Phe restriction tailored to individual dietary Phe tolerance. Information on initial neonatal management of PKU, when Phe tolerance is still unknown, is scanty.We reviewed the metabolic data from 304 patients with PAH deficiency detected at newborn screening within the last 37years. In keeping with the general neonatal management of intoxication-type inborn errors of metabolism, initial management consisted in a Phe wash-out through the exclusive administration of normocaloric Phe-free formulas until normalization of blood Phe.Based on genotype and Phe tolerance assessed at follow-up, 55 patients had classic PKU (18%), 50 mild PKU (17%), and 199 non-PKU hyperphenylalaninemia (HPA) (65%). The duration of Phe wash-out amounted to 7 ± 2days in classic PKU, 4 ± 2days in mild PKU, and < 24h in non-PKU HPA (p < 0.001). After the wash-out, dietary Phe re-introduction and its upwardly titration allowed the assessment of individual metabolic phenotype. During the first 6years of life, Phe tolerance was stable in classic PKU (~ 200mg/day) but increased in milder forms, allowing unrestricted diet in non-PKU HPA.Neonatal Phe wash-out in PKU ensures the earliest correction of HPA. This metabolic reset also facilitates the prompt definition of individual Phe tolerance, allowing anticipation of dietary personalization and optimization of longitudinal metabolic control.

The Use of the Methadone/Metabolite Ratio (MMR) to Identify an Individual Metabolic Phenotype and Assess Risks of Poor Response and Adverse Effects: Towards Scientific Methadone Dosing.

Significant genetic variability of metabolism confounds reliable clinical use of methadone because physicians have no way of identifying individual patient metabolism. The methadone/metabolite ratio (MMR), the numerical ratio of serum methadone to its inactive metabolite ethylidine-dimethyl-diphenypyrrolidine (EDDP), represents the net expression of the genes controlling metabolism. The MMR has been adapted to four established pharmacogenetic metabolic categories: ultra-rapid (URM), extensive (EM, normal), intermediate (IM), and ultra-slow (USM). This study reports on the analysis of 1700 paired peak and trough serum samples for methadone and EDDP. The MMR data were stratified by metabolic category. The reliability of these categories and the relationship of the MMR to 2 other laboratory assessments, a peak/trough ratio (PTR) and a methadone half-life, was tested. Additionally, peak and trough serum levels were analyzed by MMR category. Each category of MMR identified significantly different mean serum levels (peak and trough), peak/trough ratios, and half-lives. When serum levels were analyzed, evidence of subtherapeutic serum levels were found, predominantly in the URM and EM categories. Seventeen percent of peak serum levels were greater than 1000 ng (a level indicating potential toxicity) with a range up to 2384 ng, predominantly in the IM and USM categories. The MMR measures an individual's phenotype for methadone metabolism. The data suggested underdosing in the URM category, as well as evidence of excessive dosing in IM and USM categories. The MMR provides a guide to safe and effective dosing, an alternative to the pharmacokinetically 'blind' dosing algorithms currently in use.

Energy sources identify metabolic phenotypes in pancreatic cancer.

Metabolic reprogramming is one of the emerging hallmarks of cancers. As a highly malignant tumor, pancreatic ductal adenocarcinoma (PDA) is not only a metabolic disease but also a heterogeneous disease. Heterogeneity induces PDA dependence on distinct nutritive substrates, thereby inducing different metabolic phenotypes. We stratified PDA into four phenotypes with distinct types of energy metabolism, including a Warburg phenotype, a reverse Warburg phenotype, a glutaminolysis phenotype, and a lipid-dependent phenotype. The four phenotypes possess distinct metabolic features and reprogram their metabolic pathways to adapt to stress. The metabolic type present in PDA should prompt differential imaging and serologic metabolite detection for diagnosis and prognosis. The targeting of an individual metabolic phenotype with corresponding metabolic inhibitors is considered a promising therapeutic approach and, in combination with chemotherapy, is expected to be a novel strategy for PDA treatment.

Longitudinal Investigation into Genetics in the Conservation of Metabolic Phenotypes in Danish and Chinese Twins.

Longitudinal twin studies on long term conservation of individual metabolic phenotypes can help to explore the genetic and environmental basis in maintaining metabolic homeostasis and metabolic health. We performed a longitudinal twin study on 12 metabolic phenotypes from Danish twins followed up for 12 years and Chinese twins traced for 7 years. The study covered a relatively large sample of 502 pairs of Danish adult twins with a mean age at intake of 38 years and a total of 181 Chinese adult twin pairs with a mean baseline age of 39.5 years. Bivariate twin models were fitted to the longitudinal measurements taken at two time points (at baseline and follow-up) to estimate the genetic and environmental contributions to phenotype variation and correlation at and between the two time points. High genetic components in the regulation of intra-individual phenotype correlation or stability over time were estimated in both Danish (h2>0.75 except fasting blood glucose) and Chinese (h2>0.72 except blood pressure) twins; moderate to high genetic contribution to phenotype variation at the two time points were also estimated except for the low genetic regulation on glucose in Danish and on blood pressure in Chinese twins. Meanwhile the bivariate twin models estimated shared environmental contributions to the variance and covariance in fasting blood glucose in Danish twins, and in systolic and diastolic blood pressure, low and high density lipoprotein cholesterol in Chinese twins. Overall, our longitudinal twin study on long-term stability of metabolic phenotypes in Danish and Chinese twins identified a common pattern of high genetic control over phenotype conservation, and at the same time revealed population-specific patterns of genetic and common environmental regulation on the variance as well as covariance of glucose and blood pressure.

Entropy-Based Network Representation of the Individual Metabolic Phenotype.

We approach here the problem of defining and estimating the nature of the metabolite-metabolite association network underlying the human individual metabolic phenotype in healthy subjects. We retrieved significant associations using an entropy-based approach and a multiplex network formalism. We defined a significantly over-represented network formed by biologically interpretable metabolite modules. The entropy of the individual metabolic phenotype is also introduced and discussed.

Individual Human Metabolic Phenotype Analyzed by (1)H NMR of Saliva Samples.

Saliva is an important physiological fluid that contains a complex mixture of analytes that may produce a characteristic individual signature. In recent years, it has been demonstrated that urine possesses a clear signature of the individual metabolic phenotype. Here NMR-based metabolomics was employed to analyze saliva from 23 healthy volunteers. About six saliva samples were collected daily from each individual for 10 consecutive days: 7 days in a real-life situation (days 1-7, Phase I) and 3 days (days 8-10, Phase II) under a standardized diet plus a physical exercise program at day 10. The result is the first demonstration of the existence of an individual metabolic phenotype in saliva. A systematic comparative analysis with urine samples from the same collection scheme demonstrates that the individual phenotype in saliva is slightly weaker than that in urine but less influenced by diet.

Allostasis and Resilience of the Human Individual Metabolic Phenotype

The urine metabotype of 12 individuals was followed over a period of 8-10 years, which provided the longest longitudinal study of metabolic phenotypes to date. More than 2000 NMR metabolic profiles were analyzed. The majority of subjects have a stable metabotype. Subjects who were exposed to important pathophysiological stressful conditions had a significant metabotype drift. When the stress conditions ceased, the original metabotypes were regained, while an irreversible stressful condition resulted in a permanent metabotype change. These results suggest that each individual occupies a well-defined region in the broad metabolic space, within which a limited degree of allostasis is permitted. The insurgence of significant stressful conditions causes a shift of the metabotype to another distinct region. The spontaneous return to the original metabolic region when the stressful conditions are removed suggests that the original metabotype has some degree of resilience. In this picture, precision medicine should aim at reinforcing the patient's metabolic resilience, that is, his or her ability to revert to his or her specific metabotype rather than to a generic healthy one.

Hypothesis: the sound of the individual metabolic phenotype? Acoustic detection of NMR experiments.

We present here an innovative hypothesis and report preliminary evidence that the sound of NMR signals could provide an alternative to the current representation of the individual metabolic fingerprint and supply equally significant information. The NMR spectra of the urine samples provided by four healthy donors were converted into audio signals that were analyzed in two audio experiments by listeners with both musical and non-musical training. The listeners were first asked to cluster the audio signals of two donors on the basis of perceived similarity and then to classify unknown samples after having listened to a set of reference signals. In the clustering experiment, the probability of obtaining the same results by pure chance was 7.04% and 0.05% for non-musicians and musicians, respectively. In the classification experiment, musicians scored 84% accuracy which compared favorably with the 100% accuracy attained by sophisticated pattern recognition methods. The results were further validated and confirmed by analyzing the NMR metabolic profiles belonging to two other different donors. These findings support our hypothesis that the uniqueness of the metabolic phenotype is preserved even when reproduced as audio signal and warrants further consideration and testing in larger study samples.

Nutrimetabonomics: nutritional applications of metabolic profiling.

An individual's metabolic phenotype, and ultimately health, is significantly influenced by complex interactions between their genes and the diet. Studying these associations and their downstream biochemical consequences has proven extremely challenging using traditional hypothesis-led strategies. Metabonomics, a systems biology approach, allows the global metabolic response of biological systems to stimuli to be characterised. Through the application of this approach to nutritional-based research, nutrimetabonomics, the biochemical response to dietary inputs is being investigated at greater levels of resolution. This has allowed novel insights to be gained regarding intricate diet-gene interactions and their consequences for health and disease. In this review, we present some of the latest research exploring how nutrimetabonomics can assist in the elucidation of novel biomarkers of dietary behaviour and provide new perspectives on diet-health relationships. The use of this approach to study the metabolic interplay between the gut microbiota and the host is also explored.

Long term conservation of human metabolic phenotypes and link to heritability

Changes in an individual’s human metabolic phenotype (metabotype) over time can be indicative of disorder-related modifications. Studies covering several months to a few years have shown that metabolic profiles are often specific for an individual. This “metabolic individuality” and detected changes may contribute to personalized approaches in human health care. However, it is not clear whether such individual metabotypes persist over longer time periods. Here we investigate the conservation of metabotypes characterized by 212 different metabolites of 818 participants from the Cooperative Health Research in the Region of Augsburg; Germany population, taken within a 7-year time interval. For replication, we used paired samples from 83 non-related individuals from the TwinsUK study. Results indicated that over 40 % of all study participants could be uniquely identified after 7 years based on their metabolic profiles alone. Moreover, 95 % of the study participants showed a high degree of metabotype conservation (>70 %) whereas the remaining 5 % displayed major changes in their metabolic profiles over time. These latter individuals were likely to have undergone important biochemical changes between the two time points. We further show that metabolite conservation was positively associated with heritability (rank correlation 0.74), although there were some notable exceptions. Our results suggest that monitoring changes in metabotypes over several years can trace changes in health status and may provide indications for disease onset. Moreover, our study findings provide a general reference for metabotype conservation over longer time periods that can be used in biomarker discovery studies.Electronic supplementary materialThe online version of this article (doi:10.1007/s11306-014-0629-y) contains supplementary material, which is available to authorized users.

Human Breath Analysis May Support the Existence of Individual Metabolic Phenotypes

The metabolic phenotype varies widely due to external factors such as diet and gut microbiome composition, among others. Despite these temporal fluctuations, urine metabolite profiling studies have suggested that there are highly individual phenotypes that persist over extended periods of time. This hypothesis was tested by analyzing the exhaled breath of a group of subjects during nine days by mass spectrometry. Consistent with previous metabolomic studies based on urine, we conclude that individual signatures of breath composition exist. The confirmation of the existence of stable and specific breathprints may contribute to strengthen the inclusion of breath as a biofluid of choice in metabolomic studies. In addition, the fact that the method is rapid and totally non-invasive, yet individualized profiles can be tracked, makes it an appealing approach.

Nutrigenetics, Nutrigenomics, and the Future of Dietary Advice

Our individual metabolic phenotype is the result of the interaction between nutrients and DNA to modify gene expression. This is a combination of epigenetic interactions whereby nutrients modify the structure of DNA to affect gene expression as well as individual genetic variation that alters our response to diet. Our metabolic phenotype is influenced by developmental plasticity, imprinting in early life and interactions with environmental factors over time. Unlike the human genome which is relatively fixed and stable throughout the body, the human metabolic phenotype is far more complex and dynamic, varying over time and among cells and varying greatly from person to person. Dietary recommendations are often generalized and intended to avert chronic illnesses such as diabetes and cardiovascular disease. In a climate where we are striving for personalisation of healthcare maybe we need a simpler approach; one that embraces genetic variation yet focuses on the optimum nutritional benefit of dietary components.

Metabolic profiling detects early effects of environmental and lifestyle exposure to cadmium in a human population

BackgroundThe 'exposome' represents the accumulation of all environmental exposures across a lifetime. Top-down strategies are required to assess something this comprehensive, and could transform our understanding of how environmental factors affect human health. Metabolic profiling (metabonomics/metabolomics) defines an individual's metabolic phenotype, which is influenced by genotype, diet, lifestyle, health and xenobiotic exposure, and could also reveal intermediate biomarkers for disease risk that reflect adaptive response to exposure. We investigated changes in metabolism in volunteers living near a point source of environmental pollution: a closed zinc smelter with associated elevated levels of environmental cadmium.MethodsHigh-resolution 1H NMR spectroscopy (metabonomics) was used to acquire urinary metabolic profiles from 178 human volunteers. The spectral data were subjected to multivariate and univariate analysis to identify metabolites that were correlated with lifestyle or biological factors. Urinary levels of 8-oxo-deoxyguanosine were also measured, using mass spectrometry, as a marker of systemic oxidative stress.ResultsSix urinary metabolites, either associated with mitochondrial metabolism (citrate, 3-hydroxyisovalerate, 4-deoxy-erythronic acid) or one-carbon metabolism (dimethylglycine, creatinine, creatine), were associated with cadmium exposure. In particular, citrate levels retained a significant correlation to urinary cadmium and smoking status after controlling for age and sex. Oxidative stress (as determined by urinary 8-oxo-deoxyguanosine levels) was elevated in individuals with high cadmium exposure, supporting the hypothesis that heavy metal accumulation was causing mitochondrial dysfunction.ConclusionsThis study shows evidence that an NMR-based metabolic profiling study in an uncontrolled human population is capable of identifying intermediate biomarkers of response to toxicants at true environmental concentrations, paving the way for exposome research.

Dietary macronutrient composition affects β cell responsiveness but not insulin sensitivity

Altering dietary carbohydrate or fat content may have chronic effects on insulin secretion and sensitivity, which may vary with individual metabolic phenotype. The objective was to evaluate the contribution of tightly controlled diets differing in carbohydrate and fat content for 8 wk to insulin sensitivity and β cell responsiveness and whether effects of diet would vary with race, free-living diet, or insulin response. Healthy overweight men and women (36 European Americans, 33 African Americans) were provided with food for 8 wk and received either a eucaloric standard diet (55% carbohydrate, 27% fat) or a eucaloric reduced-carbohydrate (RedCHO)/higher-fat diet (43% carbohydrate, 39% fat). Insulin sensitivity and β cell responsiveness were assessed at baseline and 8 wk by using a liquid meal tolerance test. Insulin sensitivity did not change with diet (P = 0.1601). Static β cell response to glucose (ФS) was 28.5% lower after the RedCHO/higher-fat diet. Subgroup analyses indicated that lower ФS with the RedCHO/higher-fat diet occurred primarily among African Americans. A significant inverse association was observed for change in glucose area under the curve compared with change in ФS. Consumption of a eucaloric 43% carbohydrate/39% fat diet for 8 wk resulted in down-regulation of β cell responsiveness, which was influenced by baseline phenotypic characteristics. Further study is needed to probe the potential cause-and-effect relation between change in ФS and change in glucose tolerance. This trial is registered at clinicaltrials.gov as NCT00726908.

Secondary electrospray ionization-mass spectrometry: breath study on a control group

A series of fatty acids among other compounds have recently been detected in breath in real time by secondary electrospray ionization mass spectrometry (SESI-MS) (Martínez-Lozano P and Fernández de la Mora J 2008 Anal. Chem. 80 8210). Our main aim in this work was to (1) quantify their abundance in breath calibrating the system with standard vapors and (2) extend the study to a control group for several days, both under fasting conditions and after sucrose intake. For the quantitative study, we fed our system with controlled amounts (∼140–1440 ppt) of fatty acid vapors (i.e. propanoic, butanoic, pentanoic and hexanoic acids). As a result, we found sensitivities ranging between 1 and 2.2 cps/ppt. Estimated concentrations of these particular acids in the breath of a fasting subject were in the order of 100 ppt. These values were in reasonable agreement with those expected from reported typical plasma concentrations and Henry constants. A second set of experiments on three fasting individuals before and after ingesting 15 g of sucrose showed that the concentration of propionic and butanoic acids increased rapidly in breath for two subjects. This response was attributed to bacterial activity in mouth and pharynx. In contrast, a third subject showed no response to the administration of sucrose. In addition, we performed a survey among six fasting subjects comparing nasal and mouth exhalations during 11 days, 4 months apart. The signal intensity was comparable for mouth and nose breath. This observation, in conjunction with the quantitative study, suggests that these compounds are mostly systemic when measured under fasting conditions. We finally used the NIST MS search algorithm to evaluate the possibility of recognizing a breathing subject based on his/her breath signature. The global recognition score was 63% (41 out of 65), while the probability by chance alone was 6 × 10−17. This indicates that (i) there are statistically recognizable differences in individual breath patterns and (ii) the breath pattern for a given subject is relatively stable in time. This is consistent with previous NMR-based studies indicating the existence of stable individual metabolic phenotypes.

Cross-platform analysis of longitudinal data in metabolomics

Metabolic profiling is considered to be a very promising tool for diagnostic purposes, for assessing nutritional status and response to drugs. However, it is also evident that human metabolic profiles have a complex nature, influenced by many external factors. This, together with the understanding of the difficulty to assign people to distinct groups and a general move in clinical science towards personalized medicine, raises the interest to explore individual and variable metabolic features for each individual separately in longitudinal study design. In the current paper we have analyzed a set of metabolic profiles of a selection of six urine samples per person from a set of healthy individuals by (1)H NMR and reversed-phase UPLC-MS. We have demonstrated that the method for recovery of individual metabolic phenotypes can give complementary information to another established method for analysis of longitudinal data--multilevel component analysis. We also show that individual metabolic signatures can be found not only in (1)H NMR data, as has been demonstrated before, but also even more strongly in LC-MS data.