NMR-based metabolomic analysis of plasma from elderly patients with CVD before and after using contrast media

Contrast-induced acute kidney injury (CI-AKI) is a growingly common kidney problem caused by medical procedures involving contrast media (CM), especially in older patients with existing health issues. It is crucial to pinpoint potential biomarkers for the early detection of CI-AKI. Previously, we observed that iodixanol affects glucose, choline, and glutathione metabolism in endothelial cells under laboratory conditions. In this study, we used 1H NMR-based metabolomics to examine the metabolic changes in the blood plasma of elderly patients with cardiovascular disease (CVD) before and after receiving iodixanol. We identified altered metabolites in plasma 24 and 48 h after iodixanol injection compared to levels before injection. Notably, metabolites such as glucose, unsaturated fatty acids (UFA), low-density lipoprotein (LDL)/very low-density lipoprotein (VLDL), pyruvate, choline, and glycine showed potential as biomarkers at 24 h post-injection compared to levels before injection. Similarly, glucose, pyruvate, lactate, choline, and glycine in plasma could serve as potential biomarkers at 48 h post-injection. Iodixanol notably affected pathways related to glycolysis, fatty acid breakdown, and amino acid metabolism according to our metabolic pathway analysis. The altered levels of specific metabolites in plasma could be indicative of CM-induced kidney injury. Overall, this research aids in understanding the physiological mechanisms involved and in identifying early biomarkers and prevention strategies for CI-AKI.

NMR Metabolite Profiling for the Characterization of Vessalico Garlic Ecotype and Bioactivity against Xanthomonas campestris pv. campestris

The Italian garlic ecotype "Vessalico" possesses distinct characteristics compared to its French parent cultivars Messidor and Messidrôme, used for sowing, as well as other ecotypes in neighboring regions. However, due to the lack of a standardized seed supply method and cultivation protocol among farmers in the Vessalico area, a need to identify garlic products that align with the Vessalico ecotype arises. In this study, an NMR-based approach followed by multivariate analysis to analyze the chemical composition of Vessalico garlic sourced from 17 different farms, along with its two French parent cultivars, was employed. Self-organizing maps allowed to identify a homogeneous subset of representative samples of the Vessalico ecotype. Through the OPLS-DA model, the most discriminant metabolites based on values of VIP (Variable Influence on Projections) were selected. Among them, S-allylcysteine emerged as a potential marker for distinguishing the Vessalico garlic from the French parent cultivars by NMR screening. Additionally, to promote sustainable agricultural practices, the potential of Vessalico garlic extracts and its main components as agrochemicals against Xanthomonas campestris pv. campestris, responsible for black rot disease, was explored. The crude extract exhibited a MIC of 125 μg/mL, and allicin demonstrated the highest activity among the tested compounds (MIC value of 31.25 μg/mL).

Circulatory Metabolite Ratios as Indicators of Lifestyle Risk Factors Based on a Greek NAFLD Case-Control Study

An ensemble of confounding factors, such as an unhealthy diet, obesity, physical inactivity, and smoking, have been linked to a lifestyle that increases one's susceptibility to chronic diseases and early mortality. The circulatory metabolome may provide a rational means of pinpointing the advent of metabolite variations that reflect an adherence to a lifestyle and are associated with the occurrence of chronic diseases. Data related to four major modifiable lifestyle factors, including adherence to the Mediterranean diet (estimated on MedDietScore), body mass index (BMI), smoking, and physical activity level (PAL), were used to create the lifestyle risk score (LS). The LS was further categorized into four groups, where a higher score group indicates a less healthy lifestyle. Drawing on this, we analyzed 223 NMR serum spectra, 89 MASLD patients and 134 controls; these were coupled to chemometrics to identify "key" features and understand the biological processes involved in specific lifestyles. The unsupervised analysis verified that lifestyle was the factor influencing the samples' differentiation, while the supervised analysis highlighted metabolic signatures. Τhe metabolic ratios of alanine/formic acid and leucine/formic acid, with AUROC > 0.8, may constitute discriminant indexes of lifestyle. On these grounds, this research contributed to understanding the impact of lifestyle on the circulatory metabolome and highlighted "prudent lifestyle" biomarkers.

Towards objective measurements of habitual dietary intake patterns: comparing NMR metabolomics and food frequency questionnaire data in a population-based cohort

BACKGROUND

Low-quality, non-diverse diet is a main risk factor for premature death. Accurate measurement of habitual diet is challenging and there is a need for validated objective methods. Blood metabolite patterns reflect direct or enzymatically diet-induced metabolites. Here, we aimed to evaluate associations between blood metabolite patterns and a priori and data-driven food intake patterns.

METHODS

1, 895 participants in the Northern Sweden Health and Disease Study, a population-based prospective cohort study, were included. Fasting plasma samples were analyzed with 1H Nuclear Magnetic Resonance. Food intake data from a 64-item validated food frequency questionnaire were summarized into a priori Healthy Diet Score (HDS), relative Mediterranean Diet Score (rMDS) and a set of plant-based diet indices (PDI) as well as data driven clusters from latent class analyses (LCA). Orthogonal projections to latent structures (OPLS) were used to explore clustering patterns of metabolites and their relation to reported dietary intake patterns.

RESULTS

Age, sex, body mass index, education and year of study participation had significant influence on OPLS metabolite models. OPLS models for healthful PDI and LCA-clusters were not significant, whereas for HDS, rMDS, PDI and unhealthful PDI significant models were obtained (CV-ANOVA p < 0.001). Still, model statistics were weak and the ability of the models to correctly classify participants into highest and lowest quartiles of rMDS, PDI and unhealthful PDI was poor (50%/78%, 42%/75% and 59%/70%, respectively).

CONCLUSION

Associations between blood metabolite patterns and a priori as well as data-driven food intake patterns were poor. NMR metabolomics may not be sufficiently sensitive to small metabolites that distinguish between complex dietary intake patterns, like lipids.

Metabolites, ions, and the mechanisms behind seasonal cold hardening of Pyrochroa coccinea (Pyrochroidae) larvae

The larvae of the black headed cardinal beetle Pyrochroa coccinea, overwinters under the bark of dead logs in northern European dioecious forests, and are thus exposed to temperatures below the melting point of their bodily fluids. Here we explore the mechanisms behind their seasonal cold hardening by characterising field samples collected monthly throughout the year. Both the lower lethal temperature and supercooling point dropped as much as 10℃ in the second half of November, reaching values around -15℃ by the beginning of December. This change was accompanied by a 320 mosmol/kg increase in hemolymph osmolality, which is a doubling compared to the summer levels. We used NMR metabolomics to identify and measure the absolute concentrations of the responsible cryoprotective C-H containing metabolites in the hemolymph. The largest increase was found to be in either glucose or trehalose, with an average total increase of 120 mM. Proline, alanine, and choline concentrations were found to increase by around 10 mM each. Contrarily, phosphocholine and phosphoethanolamine were halved, resulting in a total decrease of around 50 mM. These measurements were complemented with ion exchange chromatography measurements. This allowed us to account for all the osmotic pressure in the summer hemolymph, and the measured concentration changes explained as much as 40 % of the observed osmolality increase upon cold hardening. Preliminary results indicate that the remainder may be explained by non-colligative protein contributions.

Primary Human M2 Macrophage Subtypes Are Distinguishable by Aqueous Metabolite Profiles

The complexity of macrophage (MΦ) plasticity and polarization states, which include classically activated pro-inflammatory (M1) and alternatively activated anti-inflammatory (M2) MΦ phenotypes, is becoming increasingly appreciated. Within the M2 MΦ polarization state, M2a, M2b, M2c, and M2d MΦ subcategories have been defined based on their expression of specific cell surface receptors, secreted cytokines, and specialized immune effector functions. The importance of immunometabolic networks in mediating the function and regulation of MΦ immune responses is also being increasingly recognized, although the exact mechanisms and extent of metabolic modulation of MΦ subtype phenotypes and functions remain incompletely understood. In this study, proton (1H) nuclear magnetic resonance (NMR) metabolomics was employed to determine the polar metabolomes of M2 MΦ subtypes and to investigate the relationship between aqueous metabolite profiles and M2 MΦ functional phenotypes. Results from this study demonstrate that M2a MΦs are most distinct from M2b, M2c, and M2d MΦ subtypes, and that M2b MΦs display several metabolic traits associated with an M1-like MΦ phenotype. The significance of metabolome differences for metabolites implicated in glycolysis, the tricarboxylic acid (TCA) cycle, phospholipid metabolism, and creatine-phosphocreatine cycling is discussed. Altogether, this study provides biochemical insights into the role of metabolism in mediating the specialized effector functions of distinct M2 MΦ subtypes and supports the concept of a continuum of macrophage activation states rather than two well-separated and functionally distinct M1/M2 MΦ classes, as originally proposed within a classical M1/M2 MΦ framework.

Seeds from Italy and In Vitro Antioxidant and Antifungal Activity

The metabolite fingerprinting of four Italian commercial bean seed cultivars, i.e., Phaseolus Cannellino (PCANN), Controne (PCON), Vellutina (PVEL), and Occhio Nero (PON), were investigated by Nuclear Magnetic Resonance (NMR) spectroscopy and multivariate data analysis. The hydroalcoholic and organic extract analysis disclosed more than 32 metabolites from various classes, i.e., carbohydrates, amino acids, organic acids, nucleosides, alkaloids, and fatty acids. PVEL, PCON, and PCANN varieties displayed similar chemical profiles, albeit with somewhat different quantitative results. The PON metabolite composition was slightly different from the others; it lacked GABA and pipecolic acid, featured a higher percentage of malic acid than the other samples, and showed quantitative variations of several metabolites. The lipophilic extracts from all four cultivars demonstrated the presence of omega-3 and omega-6 unsaturated fatty acids. After the determination of the total phenolic, flavonoids, and condensed tannins content, in vitro antioxidant activity was then assessed using the DPPH scavenging activity, the ABTS scavenging assay, and ferric-reducing antioxidant power (FRAP). Compared to non-dark seeds (PCON, PCANN), brown seeds (PVEL, PON) featured a higher antioxidant capacity. Lastly, only PON extract showed in vitro antifungal activity against the sclerotia growth of S. rolfsii, by inhibiting halo growth by 75%.

Effects of fat loss and low energy availability on the serum cardiometabolic profile of physique athletes

Low energy availability (LEA) is a health concern for athletes, although it may paradoxically lead to improved cardiometabolic health in the general population. We investigated the associations between LEA, body composition, and serum cardiometabolic profile in 23 physique athletes (DIET) and 21 controls (CONT) during a 5-month pre-competition diet (MID), followed by 1 week of increased energy availability (COMP) and a 5-month weight regain period (POST). Quantification of 250 serum metabolome variables was conducted by NMR spectroscopy, body composition by dual-energy x-ray absorptiometry, dietary intake by food diaries, and exercise levels by training logs. Body fat percentage decreased from 19.5 ± 7.0% to 8.3 ± 5.3% (p < 0.001) in DIET through increased exercise levels and decreased energy intake, while CONT maintained those constant. In MID, DIET had increased (FDR < 0.01) HDL cholesterol, HDL particle size and number, and decreased (FDR < 0.05) VLDL lipids, serum triglycerides, and low-grade inflammation (glycoprotein acetyls) compared to baseline and CONT. The changes were associated with reduced android fat mass (-78 ± 13%) and energy intake (-28 ± 10%). In COMP, most of the metabolic changes found in MID persisted, except for altered triglycerides in all lipoprotein classes. After weight regain in POST, serum metabolome, body composition, energy intake, and exercise levels had reverted to baseline levels. In conclusion, fat loss and LEA may have beneficial yet transient effects on the serum cardiometabolic profile of lean individuals. Especially the HDL lipidome and lipoprotein triglycerides offer potential novel biomarkers for detecting LEA in athletes.

Technical Report: A Comprehensive Comparison between Different Quantification Versions of Nightingale Health's 1H-NMR Metabolomics Platform

1H-NMR metabolomics data is increasingly used to track health and disease. Nightingale Health, a major supplier of 1H-NMR metabolomics, has recently updated the quantification strategy to further align with clinical standards. Such updates, however, might influence backward replicability, particularly affecting studies with repeated measures. Using data from BBMRI-NL consortium (~28,000 samples from 28 cohorts), we compared Nightingale data, originally released in 2014 and 2016, with a re-quantified version released in 2020, of which both versions were based on the same NMR spectra. Apart from two discontinued and twenty-three new analytes, we generally observe a high concordance between quantification versions with 73 out of 222 (33%) analytes showing a mean ρ > 0.9 across all cohorts. Conversely, five analytes consistently showed lower Spearman's correlations (ρ < 0.7) between versions, namely acetoacetate, LDL-L, saturated fatty acids, S-HDL-C, and sphingomyelins. Furthermore, previously trained multi-analyte scores, such as MetaboAge or MetaboHealth, might be particularly sensitive to platform changes. Whereas MetaboHealth replicated well, the MetaboAge score had to be retrained due to use of discontinued analytes. Notably, both scores in the re-quantified data recapitulated mortality associations observed previously. Concluding, we urge caution in utilizing different platform versions to avoid mixing analytes, having different units, or simply being discontinued.

HDL-Related Parameters and COVID-19 Mortality: The Importance of HDL Function

COVID-19, caused by the SARS-CoV-2 coronavirus, emerged as a global pandemic in late 2019, resulting in significant global public health challenges. The emerging evidence suggests that diminished high-density lipoprotein (HDL) cholesterol levels are associated with the severity of COVID-19, beyond inflammation and oxidative stress. Here, we used nuclear magnetic resonance spectroscopy to compare the lipoprotein and metabolic profiles of COVID-19-infected patients with non-COVID-19 pneumonia. We compared the control group and the COVID-19 group using inflammatory markers to ensure that the differences in lipoprotein levels were due to COVID-19 infection. Our analyses revealed supramolecular phospholipid composite (SPC), phenylalanine, and HDL-related parameters as key discriminators between COVID-19-positive and non-COVID-19 pneumonia patients. More specifically, the levels of HDL parameters, including apolipoprotein A-I (ApoA-I), ApoA-II, HDL cholesterol, and HDL phospholipids, were significantly different. These findings underscore the potential impact of HDL-related factors in patients with COVID-19. Significantly, among the HDL-related metrics, the cholesterol efflux capacity (CEC) displayed the strongest negative association with COVID-19 mortality. CEC is a measure of how well HDL removes cholesterol from cells, which may affect the way SARS-CoV-2 enters cells. In summary, this study validates previously established markers of COVID-19 infection and further highlights the potential significance of HDL functionality in the context of COVID-19 mortality.

Metabolomic Profiling of Second-Trimester Amniotic Fluid for Predicting Preterm Delivery: Insights from NMR Analysis

Preterm delivery (PTD) is a notable pregnancy complication, affecting one out of every ten births. This study set out to investigate whether analyzing the metabolic composition of amniotic fluid (AF) collected from pregnant women during the second trimester of pregnancy could offer valuable insights into prematurity. The research employed 1H-NMR metabolomics to examine AF samples obtained from 17 women who gave birth prematurely (between 29+0 and 36+5 weeks of gestation) and 43 women who delivered at full term. The application of multivariate analysis revealed metabolites (dimethylglycine, glucose, myo-inositol, and succinate) that can serve as possible biomarkers for the prognosis and early diagnosis of preterm delivery. Additionally, pathway analysis unveiled the most critical metabolic pathways relevant to our research hypothesis. In summary, these findings suggest that the metabolic composition of AF in the second trimester can be a potential indicator for identifying biomarkers associated with the risk of PTD.

Serum metabolomic profiling unveils distinct sex-related metabolic patterns in NAFLD

Objective

Obesity poses an increased risk for the onset of Nonalcoholic fatty liver disease (NAFLD). The influence of other factors, such as sex in the incidence and severity of this liver disease has not yet been fully elucidated. Thus, we aimed to identify the NAFLD serum metabolic signatures associated with sex in normal, overweight and obese patients and to associate the metabolite fluctuations across the increasing liver steatosis stages.

Methods and results

Using nuclear magnetic resonance (NMR) serum samples of 210 NAFLD cases and control individuals diagnosed with liver U/S, our untargeted metabolomics enquiry provided a sex distinct metabolic bouquet. Increased levels of alanine, histidine and tyrosine are associated with severity of NAFLD in both men and women. Moreover, higher serum concentrations of valine, aspartic acid and mannose were positively associated with the progression of NAFLD among the male subjects, while a negative association was observed with the levels of creatine, phosphorylcholine and acetic acid. On the other hand, glucose was positively associated with the progression of NAFLD among the female subjects, while levels of threonine were negatively related. Fluctuations in ketone bodies acetoacetate and acetone were also observed among the female subjects probing a significant reduction in the circulatory levels of the former in NAFLD cases. A complex glycine response to hepatic steatosis of the female subjects deserves further investigation.

Conclusion

Results of this study aspire to address the paucity of data on sex differences regarding NAFLD pathogenesis. Targeted circulatory metabolome measurements could be used as diagnostic markers for the distinct stages of NAFLD in each sex and eventually aid in the development of novel sex-related therapeutic options.

Peripheral Blood Serum NMR Metabolomics Is a Powerful Tool to Discriminate Benign and Malignant Ovarian Tumors

Ovarian cancer is the major cause of death from gynecological cancer and the third most common gynecological malignancy worldwide. Despite a slight improvement in the overall survival of ovarian carcinoma patients in recent decades, the cure rate has not improved. This is mainly due to late diagnosis and resistance to therapy. It is therefore urgent to develop effective methods for early detection and prognosis. We hypothesized that, besides being able to distinguish serum samples of patients with ovarian cancer from those of patients with benign ovarian tumors, 1H-NMR metabolomics analysis might be able to predict the malignant potential of tumors. For this, serum 1H-NMR metabolomics analyses were performed, including patients with malignant, benign and borderline ovarian tumors. The serum metabolic profiles were analyzed by multivariate statistical analysis, including principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) methods. A metabolic profile associated with ovarian malignant tumors was defined, in which lactate, 3-hydroxybutyrate and acetone were increased and acetate, histidine, valine and methanol were decreased. Our data support the use of 1H-NMR metabolomics analysis as a screening method for ovarian cancer detection and might be useful for predicting the malignant potential of borderline tumors.

Vinpocetine mitigates DMH-induce pre-neoplastic colon damage in rats through inhibition of pro-inflammatory cytokines

Colorectal cancer (CRC) is currently recognized as the third most prevalent cancer worldwide. Vinpocetine is a synthetic derivative of the vinca alkaloid vincamine. It has been found effective in ameliorating the growth and progression of cancerous cells. However, its pharmacological effect on colon damage remains elusive. Hence, in this study, we have shown the role of vinpocetine in DMH-induced colon carcinogenesis. At first, male albino Wistar rats were administered with DMH consistently for four weeks to induce pre-neoplastic colon damage. Afterward, animals were treated with vinpocetine (4.2 and 8.4 mg/kg/day p.o.) for 15 days. Serum samples were collected to assess the physiological parameters, including ELISA and NMR metabolomics. Colon from all the groups was collected and processed separately for histopathology and western blot analysis. Vinpocetine attenuated the altered plasma parameters; lipid profile and showed anti-proliferative action as evidenced by suppressed COX-2 stimulation and decreased levels of IL-1β, IL-2, IL-6, and IL-10. Vinpocetine is significantly effective in preventing CRC which may be associated with its anti-inflammatory and antioxidant potential. Accordingly, vinpocetine could serve as a potential anticancer agent for CRC treatment and thus be considered for future clinical and therapeutic research.

Prediction of Pathologic Change Development in the Pancreas Associated with Diabetes Mellitus Assessed by NMR Metabolomics

Nuclear magnetic resonance (NMR) metabolomics was used for identification of metabolic changes in pancreatic cancer (PC) blood plasma samples when compared to healthy controls or diabetes mellitus patients. An increased number of PC samples enabled a subdivision of the group according to individual PC stages and the construction of predictive models for finer classification of at-risk individuals recruited from patients with recently diagnosed diabetes mellitus. High-performance values of orthogonal partial least squares (OPLS) discriminant analysis were found for discrimination between individual PC stages and both control groups. The discrimination between early and metastatic stages was achieved with only 71.5% accuracy. A predictive model based on discriminant analyses between individual PC stages and the diabetes mellitus group identified 12 individuals out of 59 as at-risk of development of pathological changes in the pancreas, and four of them were classified as at moderate risk.

Influence of protein source (cricket, pea, whey) on amino acid bioavailability and activation of the mTORC1 signaling pathway after resistance exercise in healthy young males

PURPOSE

New dietary proteins are currently introduced to replace traditional animal protein sources. However, not much is known about their bioaccessibility and ability to stimulate muscle protein synthesis compared to the traditional protein sources. We aimed to compare effects of ingesting a protein bolus (0.25 g/kg fat free mass) of either cricket (insect), pea, or whey protein on circulating amino acid levels and activation of the mTORC1 signaling pathway in the skeletal muscle at rest and after exercise.

METHODS

In a randomized parallel controlled trial, young males (n = 50) performed a one-legged resistance exercise followed by ingestion of one of the three protein sources. Blood samples were collected before and in the following 4 h after exercise. Muscle biopsies were obtained at baseline and after 3 h from the non-exercised and exercised leg.

RESULTS

Analysis of blood serum showed a significantly higher concentration of amino acids after ingestion of whey protein compared to cricket and pea protein. No difference between protein sources in activation of the mTORC1 signaling pathway was observed either at rest or after exercise.

CONCLUSION

Amino acid blood concentration after protein ingestion was higher for whey than pea and cricket protein, whereas activation of mTORC1 signaling pathway at rest and after exercise did not differ between protein sources.

TRIAL REGISTRATION NUMBER

Clinicaltrials.org ID NCT04633694.

Polygenic risk in Type III hyperlipidaemia and risk of cardiovascular disease: An epidemiological study in UK Biobank and Oxford Biobank

BACKGROUND

Type III hyperlipidaemia (T3HL) is characterised by equimolar increases in plasma triglycerides (TG) and cholesterol in <10% of APOE22 carriers conveying high cardiovascular disease (CVD) risk. We investigate the role of a weighted triglyceride-raising polygenic score (TG.PS) precipitating T3HL.

METHODS

The TG.PS (restricted to genome-wide significance and weighted by published independent effect estimates) was applied to the Oxford Biobank (OBB, n = 6952) and the UK Biobank (UKB, n = 460,037), to analyse effects on plasma lipid phenotypes. Fasting plasma lipid, lipoprotein biochemistry and NMR lipoprotein profiles were analysed in OBB. CVD prevalence/incidence was examined in UKB.

RESULTS

One TG.PS standard-deviation (SD) was associated with 13.0% (95% confidence-interval 12.0-14.0%) greater TG in OBB and 15.2% (15.0-15.4%) in UKB. APOE22 carriers had 19.0% (1.0-39.0%) greater TG in UKB. Males were more susceptible to TG.PS effects (4.0% (2.0-6.0%) greater TG with 1 TG.PS SD in OBB, 1.6% (1.3-1.9%) in UKB) than females. There was no interaction between APOE22 and TG.PS, BMI, sex or age on TG. APOE22 carriers had lower apolipoprotein B (apoB) (OBB; -0.35 (-0.29 to -0.40)g/L, UKB; -0.41 (-0.405 to -0.42)g/L). NMR lipoprotein lipid concentrations were discordant to conventional biochemistry in APOE22 carriers. In APOE22 compared with APOE33, CVD was no more prevalent in similarly hypertriglyceridaemic participants (OR 0.97 95%CI 0.76-1.25), but was less prevalent in normolipidaemia (OR 0.81, 95%CI 0.69-0.95); no differences were observed in CVD incidence.

CONCLUSIONS

TG.PS confers an additive risk for developing T3HL, that is of comparable effect size to conventional risk factors. The protective effect of APOE22 for prevalent CVD is consistent with lower apoB in APOE22 carriers.

Association between NMR metabolomic signatures of healthy lifestyle and incident coronary artery disease

AIMS

To identify metabolites associated with a healthy lifestyle and explore the possible mechanisms of lifestyle in coronary artery disease (CAD).

METHODS AND RESULTS

The nuclear magnetic resonance metabolomics platform was applied to perform metabolomic profiling of baseline plasma samples from a randomly selected subset of 121 733 UK Biobank participants. Cox proportional hazards models with covariate adjustments were used to investigate the associations between validated lifestyle-associated metabolites and incident CAD and to estimate the accuracy of the inclusion of metabolites to predict CAD compared with traditional prediction models. The discriminatory ability of each model was evaluated using Harrell's C statistic, integrated discrimination improvement (IDI), and continuous net reclassification improvement (NRI) indexes. During a median of 8.6 years of follow-up, 5513 incident CAD cases were documented. Among the 111 lifestyle-associated metabolites, 65 were significantly associated with incident CAD after multivariate adjustment (Bonferroni P < 3.11 × 10-04). The addition of these metabolites to classic risk prediction models [Framingham Risk Score (FRS) using lipids; FRS using body mass index] improved CAD prediction accuracy as assessed by the C statistic (increasing to 0.739 [95% CI, 0.731-0.747] and 0.752 [95% CI, 0.746-0.758]), respectively; continuous NRI (0.274 [0.227-0.325] and 0.266 [0.223-0.317]) and IDI (0.003 [0.002-0.004] and 0.003 [0.002-0.004]).

CONCLUSION

Healthy lifestyle-associated metabolites are associated with the incidence of CAD and may help improve the prediction of CAD risk. The use of metabolite information combined with the FRS model warrants further investigation before clinical implementation.

Metabolic Reprogramming of Breast Tumor-Educated Macrophages Revealed by NMR Metabolomics

The metabolic crosstalk between tumor cells and tumor-associated macrophages (TAMs) has emerged as a critical contributor to tumor development and progression. In breast cancer (BC), the abundance of immune-suppressive TAMs positively correlates with poor prognosis. However, little is known about how TAMs reprogram their metabolism in the BC microenvironment. In this work, we have assessed the metabolic and phenotypic impact of incubating THP-1-derived macrophages in conditioned media (CM) from two BC cell lines cultured in normoxia/hypoxia: MDA-MB-231 cells (highly metastatic, triple-negative BC), and MCF-7 cells (less aggressive, luminal BC). The resulting tumor-educated macrophages (TEM) displayed prominent differences in their metabolic activity and composition, compared to control cells (M0), as assessed by exo- and endometabolomics. In particular, TEM turned to the utilization of extracellular pyruvate, alanine, and branched chain keto acids (BCKA), while exhibiting alterations in metabolites associated with several intracellular pathways, including polyamines catabolism (MDA-TEM), collagen degradation (mainly MCF-TEM), adenosine accumulation (mainly MDA-TEM) and lipid metabolism. Interestingly, following a second-stage incubation in fresh RPMI medium, TEM still displayed several metabolic differences compared to M0, indicating persistent reprogramming. Overall, this work provided new insights into the metabolic plasticity of TEM, revealing potentially important nutritional exchanges and immunoregulatory metabolites in the BC TME.

Metabolomics as a Potential Chemotaxonomical Tool: Application on the Selected Euphorbia Species Growing Wild in Serbia

Chemotaxonomy presents various challenges that need to be overcome in order to obtain valid and reliable results. Individual genetic and environmental variations can give a false picture and lead to wrong conclusions. Applying a holistic approach, based on multivariate data analysis, these challenges can be overcome. Thus, a metabolomics approach has to be optimized depending on the subject of research. We used ¹H NMR-based metabolomics as a potential chemotaxonomic tool on the selected Euphorbia species growing wild in Serbia. Principal components analysis (PCA), soft independent modeling by class analogy (SIMCA) and Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) were used to analyze obtained NMR data in order to reveal chemotaxonomic biomarkers. The standard protocol for plant metabolomics was optimized aiming to extract more specific metabolites, which are characteristic for the Euphorbia genus. The obtained models were validated, which revealed that variables unique for each species were associated with certain classes of molecules according to literature data. In E. salicifolia, acacetin-7-O-glycoside (not found before in the species) was detected, and the structure of the aglycone part was solved based on 2D NMR data. In the presented paper, we have shown that metabolomics can be successfully used in Euphorbia chemotaxonomy.

Prospective Metabolomic Studies in Precision Medicine: The AKRIBEA Project

For a long time, conventional medicine has analysed biomolecules to diagnose diseases. Yet, this approach has proven valid only for a limited number of metabolites and often through a bijective relationship with the disease (i.e. glucose relationship with diabetes), ultimately offering incomplete diagnostic value. Nowadays, precision medicine emerges as an option to improve the prevention and/or treatment of numerous pathologies, focusing on the molecular mechanisms, acting in a patient-specific dimension, and leveraging multiple contributing factors such as genetic, environmental, or lifestyle. Metabolomics grasps the required subcellular complexity while being sensitive to all these factors, which results in a most suitable technique for precision medicine. The aim of this chapter is to describe how NMR-based metabolomics can be integrated in the design of a precision medicine strategy, using the Precision Medicine Initiative of the Basque Country (the AKRIBEA project) as a case study. To that end, we will illustrate the procedures to be followed when conducting an NMR-based metabolomics study with a large cohort of individuals, emphasizing the critical points. The chapter will conclude with the discussion of some relevant biomedical applications.

Shifting-corrected regularized regression for 1H NMR metabolomics identification and quantification

The process of identifying and quantifying metabolites in complex mixtures plays a critical role in metabolomics studies to obtain an informative interpretation of underlying biological processes. Manual approaches are time-consuming and heavily reliant on the knowledge and assessment of nuclear magnetic resonance (NMR) experts. We propose a shifting-corrected regularized regression method, which identifies and quantifies metabolites in a mixture automatically. A detailed algorithm is also proposed to implement the proposed method. Using a novel weight function, the proposed method is able to detect and correct peak shifting errors caused by fluctuations in experimental procedures. Simulation studies show that the proposed method performs better with regard to the identification and quantification of metabolites in a complex mixture. We also demonstrate real data applications of our method using experimental and biological NMR mixtures.

Problems, principles and progress in computational annotation of NMR metabolomics data

BACKGROUND

Compound identification remains a critical bottleneck in the process of exploiting Nuclear Magnetic Resonance (NMR) metabolomics data, especially for ¹H 1-dimensional (¹H 1D) data. As databases of reference compound spectra have grown, workflows have evolved to rely heavily on their search functions to facilitate this process by generating lists of potential metabolites found in complex mixture data, facilitating annotation and identification. However, approaches for validating and communicating annotations are most often guided by expert knowledge, and therefore are highly variable despite repeated efforts to align practices and define community standards.

AIM OF REVIEW

This review is aimed at broadening the application of automated annotation tools by discussing the key ideas of spectral matching and beginning to describe a set of terms to classify this information, thus advancing standards for communicating annotation confidence. Additionally, we hope that this review will facilitate the growing collaboration between chemical data scientists, software developers and the NMR metabolomics community aiding development of long-term software solutions.

KEY SCIENTIFIC CONCEPTS OF REVIEW

We begin with a brief discussion of the typical untargeted NMR identification workflow. We differentiate between annotation (hypothesis generation, filtering), and identification (hypothesis testing, verification), and note the utility of different NMR data features for annotation. We then touch on three parts of annotation: (1) generation of queries, (2) matching queries to reference data, and (3) scoring and confidence estimation of potential matches for verification. In doing so, we highlight existing approaches to automated and semi-automated annotation from the perspective of the structural information they utilize, as well as how this information can be represented computationally.

The plasma amino acid response to blended protein beverages: a randomised crossover trial

Soya-dairy protein blends can extend post-exercise muscle synthesis in young people more than whey protein control. Older adults differ metabolically from young people, and their ability to absorb amino acids from dietary protein is important for muscle function. The objective was to determine how protein source affects postprandial plasma amino acid response and/or metabolomic profile in older adults via a single-blind randomised crossover trial (n 16, males 50-70 years), using three nutritionally equivalent meal replacement drinks containing 30 g protein, from a 1:1 (mass ratio) soya:dairy blend, a 1:2 soya:dairy blend or whey protein. The outcome measures were plasma amino acid concentrations at 0-300 min postprandially and urine metabolomic fingerprint. Soya:dairy drinks gave similar amino acid response in plasma over time and similar urinary metabolite fingerprints. However, there were significant differences in plasma amino acid concentrations and AUC values for the soya:dairy drinks v. the whey protein drink. AUC for Leu, Trp and Lys was lower and AUC for Phe and Pro was higher for the soya:dairy drinks. Differences partly reflected the amino acid profiles of the drinks, but overall plasma amino acid response patterns were qualitatively unchanged. Plasma amino acid differences between the whey protein drink and the soya:dairy blends were reflected in urine metabolite patterns. In conclusion, postprandial plasma amino acid responses were broadly similar, irrespective of protein source (and soya:dairy ratio). There were significant differences for some plasma amino acid concentrations, reflecting different amino acid profiles of the protein source and influencing urine metabolite fingerprints.

Yogurt Benefits Bone Mineralization in Ovariectomized Rats with Concomitant Modulation of the Gut Microbiome

SCOPE

Evidence supports that gut-modulating foods potentially can suppress bone loss in postmenopausal women. This study aims to investigate the effect of milk calcium-enriched milk, yogurt, and yogurt-inulin combination on the gut-bone association.

METHODS AND RESULTS

A 6-week intervention study is conducted in ovariectomized rats. Four pastes containing milk calcium-fortified milk (M-Ca), milk calcium-fortified yogurt (Y-Ca), inulin-fortified Y-Ca (Y-I-Ca), or an isoconcentration of calcium carbonate (Ca-N), and a calcium-deficient paste are provided. M-Ca does not influence bone mineral density and content (BMD and BMC), femur mechanical strength, or femoral microstructure compared to Ca-N, but Y-Ca increases spine BMD. The serum metabolome reveals that Y-Ca modulated glycine-related pathways with reduced glycine, serine, and threonine. No additive effects of yogurt and inulin are found on bone parameters. Correlation analysis shows that increased lactobacilli and reduced Clostridiaceae members in Y-Ca is associated with an increased spine BMD. Increases in Bifidobacterium pseudolongum, Turicibacter, Blautia, and Allobaculum and gut short-chain fatty acids in Y-I-Ca are not reflected in bone parameters.

CONCLUSION

Yogurt as calcium vehicle contributes to increased spine BMD concomitant with changes in the gut microbiome and glycine-related pathways, while adding inulin to yogurt does not affect bone mineralization in ovariectomized rats.

Hippocampal metabolic recovery as a manifestation of the protective effect of ischemic preconditioning in rats

The ever-present risk of brain ischemic events in humans and its full prevention make the detailed studies of an organism's response to ischemia at different levels essential to understanding the mechanism of the injury as well as protection. We used the four-vessel occlusion as an animal model of forebrain ischemia to investigate its impact on the metabolic alterations in both the hippocampus and the blood plasma to see changes on the systemic level. By inducing sublethal ischemic stimuli, we focused on the endogenous phenomena known as ischemic tolerance. NMR spectroscopy was used to analyze relative metabolite levels in tissue extracts from rats' hippocampus and blood plasma in three various ischemic/reperfusion times: 3 h, 24 h, and 72 h. Hippocampal tissues were characterized by postischemically decreased glutamate and GABA (4-aminobutyrate) tissue content balanced with increased glutamine level, with most pronounced changes at 3 h reperfusion time. Glutamate (as well as glutamine) levels recovered towards the control levels on the third day, as if the glutamate re-synthesis would be firstly preferred before GABA. These results are indicating the higher feasibility of re-establishing of glutamatergic transmission three days after an ischemic event, in contrast to GABA-ergic. Tissue levels of N-acetylaspartate (NAA), as well as choline, were decreased without the tendency to recover three days after the ischemic event. Metabolomic analysis of blood plasma revealed that ischemically preconditioned rats, contrary to the non-preconditioned animals, did not show hyperglycemic conditions. Ischemically induced semi-ketotic state, manifested in increased plasma ketone bodies 3-hydroxybutyrate and acetoacetate, seems to be programmed to support the brain tissue revitalization after the ischemic event. These and other metabolites changes found in blood plasma as well as in the hippocampus were observed to a lower extent or recovered faster in preconditioned animals. Some metabolomic changes in hippocampal tissue extract were so strong that even single metabolites were able to differentiate between ischemic, ischemically preconditioned, and control brain tissues.

The Diurnal Blood Metabolome and Effects of Vitamin D Supplementation: A Randomised Crossover Trial in Postmenopausal Women

A way to maintain an adequate vitamin D status is through supplementation. Demonstration of blood-metabolome rhythmicity of vitamin D3 post-dosing effects is lacking in the pharmaco-metabonomics area. Thus, the overall aim of this study was to investigate the diurnal changes in the blood metabolome and how these are affected by vitamin D3 supplementation. The study was conducted as a crossover study, and the treatment included 200 µg (8000 IU) of vitamin D3 as compared with placebo with a washout period of at least 10 days. The participants were postmenopausal women aged 60−80 years (N = 29) with vitamin D insufficiency (serum 25-hydroxyvitamin D < 50 nmol/L) but otherwise healthy. During the intervention day, blood samples were taken at 0 h, 2 h, 4 h, 6 h, 8 h, 10 h, 12 h, and 24 h, and plasma was analysed by proton nuclear magnetic resonance (NMR) spectroscopy as a metabolomics approach. In general, diurnal effects were identified for the majority of the 20 quantified metabolites, and hierarchical cluster analysis revealed a change in the overall plasma metabolome around 12 AM (6 h after intervention), suggesting that the diurnal rhythm is reflected in two diurnal plasma metabolomes; a morning metabolome (8−12 AM) and an afternoon/evening metabolome (2−8 PM). Overall, the effect of vitamin D supplementation on the blood metabolome was minor, with no effect on the diurnal rhythm. However, a significant effect of the vitamin D supplementation on plasma acetone levels was identified. Collectively, our findings reveal an influence of diurnal rhythm on the plasma metabolome, while vitamin D supplementation appears to have minor influence on fluctuations in the plasma metabolome.

Fluctuations in Metabolites and Bone Markers Across the Menstrual Cycle in Eumenorrheic Women and Oral Contraceptive Users

CONTEXT

Little is known about changes in circulating metabolites during the menstrual cycle and how use of oral contraceptives (OCs) affects these changes.

OBJECTIVES

To study fluctuations in circulating metabolite and bone marker levels during the menstrual/pill cycle in eumenorrheic women and OC users.

METHODS

Plasma samples were collected from 28 eumenorrheic women and 10 OC users at 7 to 9 time points across a menstrual/pill cycle. Longitudinal and cross-sectional analyses were performed to examine the cycle- and OC-induced variations in the plasma metabolite and bone turnover marker levels.

RESULTS

In eumenorrheic women, plasma levels of alanine, glutamine, threonine, and tyrosine varied significantly across the menstrual cycle, and all dropped to the lowest level around day 21 of the menstrual cycle. These amino acid concentrations were negatively correlated with fluctuations in progesterone and/or estrogen levels. A between-group analysis showed that plasma levels of alanine, glutamine, glycine, proline, and tyrosine were lower in OC users than in nonusers. Concomitantly, plasma C-terminal telopeptide of type I collagen (CTX) and N-terminal propeptide of type I procollagen (PINP) levels were lower in OC users. Intriguingly, when all data were pooled, variations in CTX and PINP levels were positively correlated with fluctuations in proline and glycine concentrations (r > 0.5 or 0.3 < r < 0.5, P < 0.05).

CONCLUSIONS

The menstrual cycle and the use of OCs alter plasma levels of metabolites and bone turnover markers in young women. While the impact of these findings remains to be established, the lower glycine level among OC users and the accompanying lower CTX level supports that the use of OCs lowers collagen turnover in young women and may thereby have long-term implications for bone health among OC users.

Uncontrolled Thyroid during Pregnancy Alters the Circulative and Exerted Metabolome

Normal levels of thyroid hormones (THs) are essential for a normal pregnancy outcome, fetal growth and the normal function of the central nervous system. Hypothyroidism, a common endocrine disorder during pregnancy, is a significant metabolic factor leading to cognitive impairments. It is essential to investigate whether patients with thyroid dysfunction may present an altered circulative and excreted metabolic profile, even after receiving treatment with thyroxine supplements. NMR metabolomics was employed to analyze 90 serum and corresponding colostrum samples. Parallel analyses of the two biological specimens provided a snapshot of the maternal metabolism through the excretive and circulating characteristics of mothers. The metabolomics data were analyzed by performing multivariate statistical, biomarker and pathway analyses. Our results highlight the impact of hypothyroidism on metabolites’ composition during pregnancy and lactation. Thyroid disorder causing metabolite fluctuations may lead to impaired lipid and glucose metabolic pathways as well as aberrant prenatal neurodevelopment, thus posing a background for the occurrence of metabolic syndrome or neurogenerative diseases later in life. This risk applies to not only untreated but also hypothyroid women under replacement therapy since our findings in both biofluids framed a different metabolic phenotype for the latter group, thus emphasizing the need to monitor women adequately after treatment initiation.

Berberis lycium fruit extract and its phytoconstituents berberine and rutin mitigate collagen-CFA-induced arthritis (CIA) via improving GSK3β/STAT/Akt/MAPKs/NF-κB signaling axis mediated oxi-inflammation and joint articular damage in murine model

Rheumatoid arthritis (RA), a chronic auto-immune disease, is often result of persistent and misdirectional inflammation and cannot be effectually resolved by single-target selective drugs. Present study attempted to uncover anti-arthritic efficacy and governing molecular mechanism of BLFE and its phytoconstituents berberine and rutin, with focus on dysregulated oxi-inflammation and structural integrity during articular damage using Collagen II-CFA-induced RA mice model. NMR-based phytometabolomic analysis revealed presence of phenolics and alkaloids such as berberine and rutin. BLFE, rutin and berberine remarkably mitigated Collagen II-CFA-induced disease severity index, articular damage, immune cells influx and pannus formation. An effective decrease in levels of TNF-α, IL-6, IL-1β, IFN-γ, IL-13, IL-17, MMPs, RORγt, Ob-cadherin, Cox-2, iNOS and enhancement in IL-10, IL-4 and IL-5, BMP-6/7 was observed in BLFE, rutin and berberine treatments. Molecular mechanistic analysis demonstrated reduction in expression of p-STAT-1/3, p-PI3K, p-Akt, p-JNK, p-p38, p-IκB, p-NF-κB and β-catenin via BLFE, rutin and berberine. Furthermore, reduced activation of p-ERK and p-GSK3β and enhanced splenic Tregs was only noticed in BLFE and berberine. Thus, the signifying presence of these phytoconstituents could contribute to the above-mentioned findings. These findings imply that BLFE could be beneficial for assuaging deleterious aspects of RA mediated via perturbed inflammation.

Uneven metabolic and lipidomic profiles in recovered COVID-19 patients as investigated by plasma NMR metabolomics

COVID-19 is a systemic infectious disease that may affect many organs, accompanied by a measurable metabolic dysregulation. The disease is also associated with significant mortality, particularly among the elderly, patients with comorbidities, and solid organ transplant recipients. Yet, the largest segment of the patient population is asymptomatic, and most other patients develop mild to moderate symptoms after SARS-CoV-2 infection. Here, we have used NMR metabolomics to characterize plasma samples from a cohort of the abovementioned group of COVID-19 patients (n = 69), between 3 and 10 months after diagnosis, and compared them with a set of reference samples from individuals never infected by the virus (n = 71). Our results indicate that half of the patient population show abnormal metabolism including porphyrin levels and altered lipoprotein profiles six months after the infection, while the other half show little molecular record of the disease. Remarkably, most of these patients are asymptomatic or mild COVID-19 patients, and we hypothesize that this is due to a metabolic reflection of the immune response stress.

Dynamic Associations of Milk Components With the Infant Gut Microbiome and Fecal Metabolites in a Mother-Infant Model by Microbiome, NMR Metabolomic, and Time-Series Clustering Analyses

Background: The gut microbiome and fecal metabolites of breastfed infants changes during lactation, and are influenced by breast milk components. This study aimed to investigate dynamic associations of milk components with the infant gut microbiome and fecal metabolites throughout the lactation period in a mother–infant model.

Methods: One month after delivery, breast milk and subsequent infant feces were collected in a pair for 5 months from a mother and an exclusively breastfed infant. Composition of the fecal microbiome was determined with 16S rRNA sequencing. Low-molecular-weight metabolites, including human milk oligosaccharides (HMOs), and antibacterial proteins were measured in feces and milk using ¹H NMR metabolomics and enzyme-linked immunosorbent assays. The association of milk bioactive components with the infant gut microbiome and fecal metabolites was determined with Python clustering and correlation analyses.

Results: The HMOs in milk did not fluctuate throughout the lactation period. However, they began to disappear in infant feces at the beginning of month 4. Notably, at this time-point, a bifidobacterium species switching (from B. breve to B. longum subsp. infantis) occurred, accompanied by fluctuations in several metabolites including acetate and butyrate in infant feces.

Conclusions: Milk bioactive components, such as HMOs, might play different roles in the exclusively breastfed infants depending on the lactation period.

Multiplex Technologies in COVID-19 Research, Diagnostics, and Prognostics: Battling the Pandemic

Due to continuous technical developments and new insights into the high complexity of infectious diseases such as COVID-19, there is an increasing need for multiplex biomarkers to aid clinical management and support the development of new drugs and vaccines. COVID-19 disease requires rapid diagnosis and stratification to enable the most appropriate treatment course for the best possible outcomes for patients. In addition, these tests should be rapid, specific, and sensitive. They should rule out other potential causes of illness with simultaneous testing for other diseases. Elevated levels of specific biomarkers can be used to establish severity risks of chronic diseases so that patients can be provided the proper medication at the right time. This review describes the state-of-the-art technologies in proteomics, transcriptomics, and metabolomics, for multiplex biomarker approaches in COVID-19 research.

Novel imidazopyrimidines-based molecules induce tetramerization of tumor pyruvate kinase M2 and exhibit potent antiproliferative profile

Discovery of novel and potent lead molecules for the specific therapeutic targets by de novo drug design is still in infancy. Here, we disclose the unprecedented development of imidazopyri(mi)dine-based tumor pyruvate kinase M2 (PKM2) modulators by subsequent link and grow strategy. The most potent modulator 15n acts as a PKM2 activator with an AC₅₀ of 90 nM, with considerable cancer cell-selectivity and membrane-permeability. NMR metabolomics studies also revealed that treatment with 15n results in diminution in lactate concentrations in MCF-7 cells. 15n binds to a previously reported site at PKM2 adjacent to the interface of two monomers. In molecular dynamics (MD) simulation studies, it was observed that 15n stabilizes the PKM2 at the dimeric interface, assisting in the formation of a biologically active tetramer conformation. 15n was also screened on MCF-7 breast cancer cell lines grown on 3-D scaffolds, and the results exhibited better anticancer potential compared to control, paving the way for future clinical studies.

Effect of Dairy Matrix on the Postprandial Blood Metabolome

This study investigated the postprandial plasma metabolome following consumption of four dairy matrices different in texture and structure: cheddar cheese (Cheese), homogenized cheddar cheese (Hom. Cheese), and micellar casein isolate (MCI) with cream (MCI Drink) or a MCI Gel. An acute, randomized, crossover trial in male participants (n = 25) with four test days was conducted. Blood samples were collected during an 8-h postprandial period after consumption of a meal similar in micro- and macronutrients containing one of the four dairy matrices, and the metabolome was analyzed using nuclear magnetic resonance (NMR) spectroscopy. A liquid dairy matrix (MCI Drink) resulted in a faster absorption of amino acids compared to products, representing either a semi-solid (MCI Gel and Hom. Cheese) or solid (Cheese) dairy matrix. For the MCI Gel, plasma concentration of acetic acid and formic acid increased approximately 2 h following consumption, while 3-hydroxybyturate and acetoacetic acid increased approximately 6 h after consumption. The structure and texture of the dairy matrix affected the postprandial absorption of amino acids, as revealed by the plasma metabolome. Our study furthermore pointed at endogenous effects associated with consumption of dairy products containing glucono-δ-lactone.

Metabolite Profiling of Helichrysum italicum Derived Food Supplements by 1H-NMR-Based Metabolomics

Helichrysum italicum is a medicinal plant from the Mediterranean area, widely used in traditional medicine for its anti-inflammatory, antibacterial and antioxidant properties and for its preventive effects on microcirculation diseases. Due to these properties, it finds large applications in cosmetic, food and pharmaceutical fields. Additionally, hydroalcoholic extracts and mother tinctures based on H. italicum represent products with a high commercial value, widely distributed not only in drug stores but also on on-line markets. The different extraction procedures used can greatly affect the fingerprints of the extracts, resulting in a different qualitative or quantitative profile of the chemical constituents responsible for biological activity. The aim of the present study was to characterize the composition of bioactive compounds present in water-ethanol and glycerol extracts of H. italicum derived food supplements. Metabolite profiles of the extracts were obtained by ¹H NMR experiments and data were processed by multivariate statistical analysis to highlight differences in the extracts and to evidence the extracts with the highest concentrations of bioactive metabolites. In detail, this work highlights how derived food supplements of H. italicum obtained using ethanol-water mixtures ranging from 45% to 20% of ethanol represent the products with the highest amount of both primary (amino acids) and secondary metabolites including 3,4-dicaffeoylquinic acid (9), chlorogenic acid (10), 3,5-dicaffeoylquinic acid (11), and kaempferol 3-O-glucopyranoside (12). Moreover, it is evident that the use of an ethanol-water mixture 20:80 is the most suitable method to afford the highest number of phenolic compounds, while food-derived supplements obtained by glycerol extraction are characterized by a high amount of β-glucose and α-glucose and a low content of phenolic compounds.

High-Density Lipoprotein 3 Cholesterol and Primary Open-Angle Glaucoma: Metabolomics and Mendelian Randomization Analyses

PURPOSE

We hypothesized that the effect of blood lipid-related metabolites on primary open-angle glaucoma (POAG) would differ according to specific lipoprotein particles and lipid sub-fractions. We investigated the associations of blood levels of lipoprotein particles and lipid sub-fractions with POAG.

DESIGN

Cross-sectional study.

PARTICIPANTS

Individuals recruited for the baseline visit of the population-based Singapore Epidemiology of Eye Disease study (n = 8503).

METHODS

All participants underwent detailed standardized ocular and systemic examinations. A total of 130 blood lipid-related metabolites were quantified using a nuclear magnetic resonance metabolomics platform. The analyses were conducted in 2 stages. First, we investigated whether and which lipid-related metabolites were directly associated with POAG using regression analyses followed by Bayesian network modeling. Second, we investigated if any causal relationship exists between the identified lipid-related metabolites, if any, and POAG using 2-sample Mendelian randomization (MR) analysis. We performed genome-wide association studies (GWAS) on high-density lipoprotein (HDL) 3 cholesterol (after inverse normal transformation) and used the top variants associated with HLD3 cholesterol as instrumental variables (IVs) in the MR analysis.

MAIN OUTCOME MEASURE

Primary open-angle glaucoma.

RESULTS

Of the participants, 175 (2.1%) had POAG. First, a logistic regression model showed that total HDL3 cholesterol (negatively) and phospholipids in very large HDL (positively) were associated with POAG. Further analyses using a Bayesian network analysis showed that only total HDL3 cholesterol was directly associated with POAG (odds ratio [OR], 0.72 per 1 standard deviation increase in HDL3 cholesterol; 95% confidence interval [CI], 0.61-0.84), independently of age, gender, intraocular pressure (IOP), body mass index (BMI), education level, systolic blood pressure, axial length, and statin medication. Using 5 IVs identified from the GWAS and with the inverse variance weighted MR method, we found that higher levels of HDL3 cholesterol were associated with a decreased odds of POAG (OR, 0.91; 95% CI, 0.84-0.99, P = 0.021). Other MR methods, including weighted median, mode-based estimator, and contamination mixture methods, derived consistent OR estimates. None of the routine lipids (blood total, HDL, or low-density lipoprotein [LDL] cholesterol) were associated with POAG.

CONCLUSIONS

Overall, these results suggest that the relationship between HDL3 cholesterol and POAG might be causal and specific, and that dysregulation of cholesterol transport may play a role in the pathogenesis of POAG.

Digesta and Plasma Metabolomics of Rainbow Trout Strains with Varied Tolerance of Plant-Based Diets Highlights Potential for Non-Lethal Assessments of Enteritis Development

The replacement of fishmeal in aquafeeds is essential to the sustainability of aquaculture. Besides the procurement of alternative protein sources, fish can also be selected for better performance on plant-based alternative diets. Rainbow trout (Oncorhynchus mykiss) is one such species in which the strain ARS-Sel has been selected for higher growth and enhanced utilization when fed soy-based diets. The aim of this study was to compare fish growth and plasma and digesta metabolomes between ARS-Sel and two commercial strains (CS-1 and CS-2), when fed plant-protein (PM) and fishmeal-based (FM) diets, and to correlate them with the onset of enteritis. An NMR-metabolomics approach was taken to assess plasma and digesta metabolite profiles. Diet and strain showed significant effects on fish growth, with the ARS-Sel fish receiving the PM diet reaching the highest final weight at sampling. Multivariate analysis revealed differences between plasma and digesta metabolite profiles of ARS-Sel and CS (CS-1 considered together with CS-2) PM-fed groups in the early stages of enteritis development, which was confirmed by intestinal histology. As reported in previous studies, the ARS-Sel strain performed better than the commercial strains when fed the PM diet. Our findings also suggest that metabolomic profiles of plasma and digesta, samples of which can be obtained through non-lethal methods, offer valuable insight in monitoring the occurrence of enteritis in carnivorous aquaculture species due to plant-based diets.

Impacts of Metabolism and Organic Acids on Cell Wall Composition and Pseudomonas aeruginosa Susceptibility to Membrane Active Antimicrobials

Reliable antimicrobial susceptibility testing is essential in informing both clinical antibiotic therapy decisions and the development of new antibiotics. Mammalian cell culture media have been proposed as an alternative to bacteriological media, potentially representing some critical aspects of the infection environment more accurately. Here, we use a combination of NMR metabolomics and electron microscopy to investigate the response of Escherichia coli and Pseudomonas aeruginosa to growth in differing rich media to determine whether and how this determines metabolic strategies, the composition of the cell wall, and consequently susceptibility to membrane active antimicrobials including colistin and tobramycin. The NMR metabolomic approach is first validated by characterizing the expected E. coli acid stress response to fermentation and the accompanying changes in the cell wall composition, when cultured in glucose rich mammalian cell culture media. Glucose is not a major carbon source for P. aeruginosa but is associated with a response to osmotic stress and a modest increase in colistin tolerance. Growth of P. aeruginosa in a range of bacteriological media is supported by consumption of formate, an important electron donor in anaerobic respiration. In mammalian cell culture media, however, the overall metabolic strategy of P. aeruginosa is instead dependent on consumption of glutamine and lactate. Formate doping of mammalian cell culture media does not alter the overall metabolic strategy but is associated with polyamine catabolism, remodelling of both inner and outer membranes, and a modest sensitization of P. aeruginosa PAO1 to colistin. Further, in a panel of P. aeruginosa isolates an increase between 2- and 3-fold in sensitivity to tobramycin is achieved through doping with other organic acids, notably propionate which also similarly enhances the activity of colistin. Organic acids are therefore capable of nonspecifically influencing the potency of membrane active antimicrobials.

Detection of Lung Cancer via Blood Plasma and 1H-NMR Metabolomics: Validation by a Semi-Targeted and Quantitative Approach Using a Protein-Binding Competitor

Metabolite profiling of blood plasma, by proton nuclear magnetic resonance (¹H-NMR) spectroscopy, offers great potential for early cancer diagnosis and unraveling disruptions in cancer metabolism. Despite the essential attempts to standardize pre-analytical and external conditions, such as pH or temperature, the donor-intrinsic plasma protein concentration is highly overlooked. However, this is of utmost importance, since several metabolites bind to these proteins, resulting in an underestimation of signal intensities. This paper describes a novel ¹H-NMR approach to avoid metabolite binding by adding 4 mM trimethylsilyl-2,2,3,3-tetradeuteropropionic acid (TSP) as a strong binding competitor. In addition, it is demonstrated, for the first time, that maleic acid is a reliable internal standard to quantify the human plasma metabolites without the need for protein precipitation. Metabolite spiking is further used to identify the peaks of 62 plasma metabolites and to divide the ¹H-NMR spectrum into 237 well-defined integration regions, representing these 62 metabolites. A supervised multivariate classification model, trained using the intensities of these integration regions (areas under the peaks), was able to differentiate between lung cancer patients and healthy controls in a large patient cohort (n = 160), with a specificity, sensitivity, and area under the curve of 93%, 85%, and 0.95, respectively. The robustness of the classification model is shown by validation in an independent patient cohort (n = 72).

Metabolomic Recovery as a Result of Ischemic Preconditioning Was More Pronounced in Hippocampus than in Cortex That Appeared More Sensitive to Metabolomic Blood Components

The study of an organism's response to ischemia at different levels is essential to understand the mechanism of the injury as well as protection. We used the occlusion of four vessels as an animal model of global cerebral ischemia to investigate metabolic alterations in cerebral cortex, hippocampus, blood plasma, as well as in a remote organ, the heart, in rats undergoing 24 h postischemic reperfusion. By inducing sublethal ischemic stimuli, we focused on endogenous phenomena known as ischemic tolerance that is currently the best known and most effective way of protecting against ischemic injury. NMR spectroscopy was used to analyze relative metabolite levels in homogenates from rats' cerebral cortex, hippocampus, and heart together with deproteinized blood plasma. In individual animals subjected to global cerebral ischemia, relative concentrations of the essential amino acids isoleucine, valine, phenylalanine, and tyrosine in cerebral cortex correlated with those in blood plasma (p < 0.05, or boundary significant p < 0.09). This did not apply for the hippocampus, suggesting a closer relation between ischemic cortex and metabolomic blood components. Hippocampal non-participation on correlation with blood components may emphasize the observed partial or full normalization the post-ischemically altered levels of a number of metabolites in the preconditioned animals. Remarkably, that was observed for cortex to a lesser extent. As a response to the global cerebral ischemia in heart tissue, we observed decreased glutamate and increased 3-hydroxybutyrate. Ischemically induced semi-ketotic state and other changes found in blood plasma partially normalized when ischemic preconditioning was introduced. Some metabolomic changes were so strong that even individual metabolites were able to differentiate between ischemic, ischemically preconditioned, and control brain tissues.

When a Tritrophic Interaction Goes Wrong to the Third Level: Xanthoxylin From Trees Causes the Honeybee Larval Mortality in Colonies Affected by the River Disease

The "River Disease" (RD), a disorder impacting honeybee colonies located close to waterways with abundant riparian vegetation (including Sebastiania schottiana, Euphorbiaceae), kills newly hatched larvae. Forager bees from RD-affected colonies collect honeydew excretions from Epormenis cestri (Hemiptera: Flatidae), a planthopper feeding on trees of S. schottiana. First-instar honeybee larvae fed with this honeydew died. Thus, we postulated that the nectars of RD-affected colonies had a natural toxin coming from either E. cestri or S. schottiana. An untargeted metabolomics characterization of fresh nectars extracts from colonies with and without RD allowed to pinpoint xanthoxylin as one of the chemicals present in higher amounts in nectar from RD-affected colonies than in nectars from healthy colonies. Besides, xanthoxylin was also found in the aerial parts of S. schottiana and the honeydew excreted by E. cestri feeding on this tree. A larva feeding assay where xanthoxylin-enriched diets were offered to 1^st instar larvae showed that larvae died in the same proportion as larvae did when offered enriched diets with nectars from RD-colonies. These findings demonstrate that a xenobiotic can mimic the RD syndrome in honeybee larvae and provide evidence of an interspecific flow of xanthoxylin among three trophic levels. Further, our results give information that can be considered when implementing measures to control this honeybee disease.

Carbon Nanotubes Induce Metabolomic Profile Disturbances in Zebrafish: NMR-Based Metabolomics Platform

The present study aims to investigate the metabolic effects of single-walled carbon nanotubes (SWCNT) on zebrafish (Danio rerio) using ¹H nuclear magnetic resonance (¹H-NMR) spectroscopy. However, there is no significant information available regarding the characterization of organic molecules, and metabolites with SWCNT exposure. Noninvasive biofluid methods have improved our understanding of SWCNT metabolism in zebrafish in recent years. Here, we used targeted metabolomics to quantify a set of metabolites within biological systems. SWCNT at various concentrations was given to zebrafish, and the metabolites were extracted using two immiscible solvent systems, methanol and chloroform. Metabolomics profiling was used in association with univariate and multivariate data analysis to determine metabolomic phenotyping. The metabolites, malate, oxalacetate, phenylaniline, taurine, sn-glycero-3-phosphate, glycine, N-acetyl mate, lactate, ATP, AMP, valine, pyruvate, ADP, serine, niacinamide are significantly impacted. The metabolism of amino acids, energy and nucleotides are influenced by SWCNT which might indicate a disturbance in metabolic reaction networks. In conclusion, using high-throughput analytical methods, we provide a perspective of metabolic impacts and the underlying associated metabolic pathways.

Fibromyalgia and Depression in Women: An 1H-NMR Metabolomic Study

Fibromyalgia is a chronic and systemic syndrome characterized by muscle, bone, and joint pain. It is a gender-specific condition with a 9:1 incidence ratio between women and men. Fibromyalgia is frequently associated with psychic disorders affecting the cognitive and emotional spheres. In the reported work, we compared 31 female fibromyalgia patients to 31 female healthy controls. They were analyzed for biochemical clinical parameters, for autoimmune markers, and were subjected to 1H-NMR metabolomics analysis. To identify a correlation between the metabolomic profile and the psychic condition, a subset of 19 fibromyalgia patients was subjected to HAM-A and HAM-D Hamilton depression tests. Multivariate statistical analysis showed the dysmetabolism of several metabolites involved in energy balance that are associated with systemic inflammatory conditions. The severity of depression worsens dysmetabolic conditions; conversely, glycine and glutamate, known for their critical role as neuromodulators, appear to be potential biomarkers of fibromyalgia and are associated with different severity depression conditions.

Targeted 1H NMR metabolomics and immunological phenotyping of human fresh blood and serum samples discriminate between healthy individuals and inflammatory bowel disease patients treated with anti-TNF

Abstract

Inflammatory bowel disease is a multifactorial etiology, associated with environmental factors that can trigger both debut and relapses. A high level of tumor necrosis factor-α in the gut is the main consequence of immune system imbalance. The aim of treatment is to restore gut homeostasis. In this study, fresh blood and serum samples were used to identify biomarkers and to discriminate between Crohn’s disease and ulcerative colitis patients under remission treated with anti-TNF. Metabolomics based on Nuclear Magnetic Resonance spectroscopy (NMR) was used to detect unique biomarkers for each class of patients. Blood T lymphocyte repertories were characterized, as well as cytokine and transcription factor profiling, to complement the metabolomics data. Higher levels of homoserine-methionine and isobutyrate were identified as biomarkers of Crohn’s disease with ileocolic localization. For ulcerative colitis, lower levels of creatine-creatinine, proline, and tryptophan were found that reflect a deficit in the absorption of essential amino acids in the gut. T lymphocyte phenotyping and its functional profiling revealed that the overall inflammation was lower in Crohn’s disease patients than in those with ulcerative colitis. These results demonstrated that NMR metabolomics could be introduced as a high-throughput evaluation method in routine clinical practice to stratify both types of patients related to their pathology.

Key messages

NMR metabolomics is a non-invasive tool that could be implemented in the normal clinical practice for IBD to assess beneficial effect of the treatment.

NMR metabolomics is a useful tool for precision medicine, in order to sew a specific treatment to a specific group of patients.

Finding predictors of response to IFX would be desirable to select patients affected by IBD.

Immunological status of inflammations correlates with NMR metabolomics biomarkers.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00109-021-02094-y.

The plasma metabolome of Atlantic salmon as studied by 1H NMR spectroscopy using standard operating procedures: effect of aquaculture location and growth stage

INTRODUCTION

Metabolomics applications to the aquaculture research are increasing steadily. The use of standardized proton nuclear magnetic resonance (¹H NMR) spectroscopy can provide the aquaculture industry with an unbiased, reproducible, and high-throughput screening tool, which can help to diagnose nutritional and disease-related metabolic disorders in farmed fish.

OBJECTIVE

Standard operating procedures developed for analysing (human) plasma by ¹H NMR were applied to fingerprint the metabolome in plasma samples collected from Atlantic salmon. The aim was to explore the metabolome of salmon plasma in relation to growth stage and sampling site.

METHODS

A total of 72 salmon were collected from three aquaculture sites in Norway (Lat. 65, 67, and 70 °N) and over two sampling events (December 2017 and November 2018). Plasma drawn from each salmon was measured by ¹H NMR and metabolites were quantified using the SigMa software. The NMR data was analysed by principal component analysis (PCA) and ANOVA-simultaneous component analysis (ASCA).

RESULTS

Important metabolic differences were evidenced, with adult salmon having a much higher content of very low-density lipoproteins and cholesterol in their plasma, while smolts displayed significantly higher levels of propylene glycol. Overall, 24% of the metabolite variation was due to the growth stage, whereas 12% of the metabolite variation was related to the aquaculture site and practice (p < 0.001).

CONCLUSION

This study provides a baseline investigation of the plasma metabolome of the Atlantic salmon and demonstrates how ¹H NMR metabolomics can be used in future investigations for comparing aquaculture practices and their influence on the fish metabolome.

Administration of Bovine Milk Oligosaccharide to Weaning Gnotobiotic Mice Inoculated with a Simplified Infant Type Microbiota

Bovine milk oligosaccharides (BMO) share structural similarity to selected human milk oligosaccharides, which are natural prebiotics for infants. Thus, there is a potential in including BMOs as a prebiotic in infant formula. To examine the in vivo effect of BMO-supplementation on the infant gut microbiota, a BMO-rich diet (2% w/w) was fed to gnotobiotic mice (n = 11) inoculated with an infant type co-culture and compared with gnotobiotic mice receiving a control diet (n = 9). Nuclear magnetic resonance metabolomics in combination with high-throughput 16S rRNA gene amplicon sequencing was used to compare metabolic activity and microbiota composition in different compartments of the lower gastrointestinal tract. BMO components were detected in cecum and colon contents, revealing that BMO was available for the gut bacteria. The gut microbiota was dominated by Enterobacteriaceae and minor abundance of Lactobacilliaceae, while colonization of Bifidobacteriaceae did not succeed. Apart from a lower E. coli population in cecum content and lower formate (in colon) and succinate (in colon and cecum) concentrations, BMO supplementation did not result in significant changes in microbiota composition nor metabolic activity. The present study corroborates the importance of the presence of bifidobacteria for obtaining microbial-derived effects of milk oligosaccharides in the gastrointestinal tract.

NMR-based metabolomics of human cerebrospinal fluid identifies signature of brain death

INTRODUCTION

Brain death (BD) is the irreversible cessation of all functions of the entire brain, including the brainstem. Cerebrospinal fluid (CSF) is a biological liquid that circulates in brain and spine. Metabolomics is able to reveal the response of biological systems to diverse factors in a specific moment or condition. Therefore, the study of this neurological condition through metabolic profiling using high resolution Nuclear Magnetic Resonance (NMR) spectroscopy is important for understanding biochemical events.

OBJECTIVES

The aim of the current study is to identify the metabolomics signature of BD using ¹H-NMR spectroscopy in human CSF.

METHODS

¹H-NMR spectroscopy has been employed for metabolomic untargeted analysis in 46 CSF samples: 22 control and 24 with BD. Spectral data were further subjected to multivariate analysis.

RESULTS

Statistically significant multivariate models separated subject's samples with BD from controls and revealed twenty one discriminatory metabolites. The statistical analysis of control and BD subjects using Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) model resulted in R²X of 0.733 and Q² of 0.635. An elevation in the concentration of statistically discriminant metabolites in BD was observed.

CONCLUSION

This study identifies a metabolic signature associated with BD and the most relevant enriched selected metabolic pathways.

Sex differences in systemic metabolites at four life stages: cohort study with repeated metabolomics

BACKGROUND

Males experience higher rates of coronary heart disease (CHD) than females, but the circulating traits underpinning this difference are poorly understood. We examined sex differences in systemic metabolites measured at four life stages, spanning childhood to middle adulthood.

METHODS

Data were from the Avon Longitudinal Study of Parents and Children (7727 offspring, 49% male; and 6500 parents, 29% male). Proton nuclear magnetic resonance (1H-NMR) spectroscopy from a targeted metabolomics platform was performed on EDTA-plasma or serum samples to quantify 229 systemic metabolites (including lipoprotein-subclass-specific lipids, pre-glycaemic factors, and inflammatory glycoprotein acetyls). Metabolites were measured in the same offspring once in childhood (mean age 8 years), twice in adolescence (16 years and 18 years) and once in early adulthood (25 years), and in their parents once in middle adulthood (50 years). Linear regression models estimated differences in metabolites for males versus females on each occasion (serial cross-sectional associations).

RESULTS

At 8 years, total lipids in very-low-density lipoproteins (VLDL) were lower in males; levels were higher in males at 16 years and higher still by 18 years and 50 years (among parents) for medium-or-larger subclasses. Larger sex differences at older ages were most pronounced for VLDL triglycerides-males had 0.19 standard deviations (SD) (95% CI = 0.12, 0.26) higher at 18 years, 0.50 SD (95% CI = 0.42, 0.57) higher at 25 years, and 0.62 SD (95% CI = 0.55, 0.68) higher at 50 years. Low-density lipoprotein (LDL) cholesterol, apolipoprotein-B, and glycoprotein acetyls were generally lower in males across ages. The direction and magnitude of effects were largely unchanged when adjusting for body mass index measured at the time of metabolite assessment on each occasion.

CONCLUSIONS

Our results suggest that males begin to have higher VLDL triglyceride levels in adolescence, with larger sex differences at older ages. Sex differences in other CHD-relevant metabolites, including LDL cholesterol, show the opposite pattern with age, with higher levels among females. Such life course trends may inform causal analyses with clinical endpoints in specifying traits which underpin higher age-adjusted CHD rates commonly seen among males.

NMR-based leaf metabolic profiling of V. planifolia and three endemic Vanilla species from the Peruvian Amazon

The fruit of Vanilla planifolia is broadly preferred by the agroindustry and gourmet markets due to its refined flavor and aroma. Peruvian Vanilla has been proposed as a possible source for genetic improvement of existing Vanilla cultivars, but, little has been done to facilitate comprehensive studies of these and other Vanilla. Here, a nuclear magnetic resonance (NMR) metabolomic platform was developed to profile for the first time the leaves - organ known to accumulate vanillin putative precursors - of V. planifolia and those of Peruvian V. pompona, V. palmarum, and V. ribeiroi, with the aim to determine metabolic differences among them. Analysis of the NMR spectra allowed the identification of thirty-six metabolites, twenty-five of which were quantified. One-way ANOVA and post-hoc Tukey test revealed that these metabolites changed significantly among species, whilst multivariate-analyses allowed the identification of malic and homocitric acids, together with two vanillin precursors, as relevant metabolic markers for species differentiation.