Combination of LC-MS- and GC-MS-based metabolomics to study the effect of ozonated autohemotherapy on human blood

Probiotic Lactobacillus plantarum 299v supplementation in patients with major depression in a double-blind, randomized, placebo-controlled trial: A metabolomics study

BACKGROUND

Understanding the multifactorial nature of major depressive disorder (MDD) is crucial for tailoring treatments. However, the complex interplay of various factors underlying the development and progression of MDD poses significant challenges. Our previous study demonstrated improvements in cognitive functions in MDD patients undergoing treatment with selective serotonin reuptake inhibitors (SSRIs) supplemented with Lactobacillus plantarum 299v (LP299v).

METHODS

To elucidate the biochemical mechanisms underlying cognitive functions improvements, we explored underlying metabolic changes. We employed multi-platform metabolomics, including LC-QTOF-MS and CE-TOF-MS profiling, alongside chiral LC-QqQ-MS analysis for amino acids.

RESULTS

Supplementation of SSRI treatment with LP299v intensified the reduction of long-chain acylcarnitines, potentially indicating improved mitochondrial function. LP299v supplementation reduced N-acyl taurines more than four times compared to the placebo, suggesting a substantial impact on restoring biochemical balance. The LP299v-supplemented group showed increased levels of oxidized glycerophosphocholine (oxPC). Additionally, LP299v supplementation led to higher levels of sphingomyelins, L-histidine, D-valine, and p-cresol.

LIMITATIONS

This exploratory study suggests potential metabolic pathways influenced by LP299v supplementation. However, the need for further research hinders the ability to draw definitive conclusions.

CONCLUSIONS

Observed metabolic changes were linked to mitochondrial dysfunction, inflammation, oxidative stress, and gut microbiota disruption. Despite the subtle nature of this alterations, our research successfully detected these differences and connected them to the metabolic disruptions associated with MDD. Our findings emphasise the intricate relationship between metabolism, gut microbiota, and mental health prompting further research into the mechanisms of action of probiotics in MDD treatment.

Basic accuracy of a 1D NOESY with presaturation method using standard solutions of amino and maleic acids

1D NOESY with presaturation (NOESY-presat) is the most popular water suppression method. When D2O solutions of L-phenylalanine or L-valine were measured using NOESY, the absolute concentration biases increased with longer mixing and evolution times, reaching a maximum of 54% with respect to the preparation values. At mixing and evolution times of 0 ms and 0 µs, respectively, the absolute concentration biases were reduced to less than 3%. The remaining biases were caused by the off-resonance effect, which was prevented by setting the frequency offset to an intermediate value between the analyte and internal standard 3-(trimethylsilyl)-1-propanesulfonic acid-d6 (DSS-d6) signals. Nevertheless, NOESY-presat gave maximum absolute biases of 26% and 11% for glycine and maleic acid concentrations, respectively, in three H2O/D2O (90/10 vol%) solutions. The proposed NOESY-dual-presat method reduced the absolute biases to below 4%. However, water suppression was insufficient but was improved by setting the frequency offset to the same as the presaturation offset with the H2O signal, although the absolute biases rose to 5 to 13%. Quantitative analyses using NOESY-presat and NOESY-dual-presat require careful consideration of the off-resonance effect.

The Impact of Mechanical Cues on the Metabolomic and Transcriptomic Profiles of Human Dermal Fibroblasts Cultured in Ultrashort Self-Assembling Peptide 3D Scaffolds

Cells' interactions with their microenvironment influence their morphological features and regulate crucial cellular functions including proliferation, differentiation, metabolism, and gene expression. Most biological data available are based on in vitro two-dimensional (2D) cellular models, which fail to recapitulate the three-dimensional (3D) in vivo systems. This can be attributed to the lack of cell-matrix interaction and the limitless access to nutrients and oxygen, in contrast to in vivo systems. Despite the emergence of a plethora of 3D matrices to address this challenge, there are few reports offering a proper characterization of these matrices or studying how the cell-matrix interaction influences cellular metabolism in correlation with gene expression. In this study, two tetrameric ultrashort self-assembling peptide sequences, FFIK and FIIK, were used to create in vitro 3D models using well-described human dermal fibroblast cells. The peptide sequences are derived from naturally occurring amino acids that are capable of self-assembling into stable hydrogels without UV or chemical cross-linking. Our results showed that 2D cultured fibroblasts exhibited distinct metabolic and transcriptomic profiles compared to 3D cultured cells. The observed changes in the metabolomic and transcriptomic profiles were closely interconnected and influenced several important metabolic pathways including the TCA cycle, glycolysis, MAPK signaling cascades, and hemostasis. Data provided here may lead to clearer insights into the influence of the surrounding microenvironment on human dermal fibroblast metabolic patterns and molecular mechanisms, underscoring the importance of utilizing efficient 3D in vitro models to study such complex mechanisms.

The Biological and Molecular Action of Ozone and Its Derivatives: State-of-the-Art, Enhanced Scenarios, and Quality Insights

The ultimate objective of this review is to encourage a multi-disciplinary and integrated methodological approach that, starting from the recognition of some current uncertainties, helps to deepen the molecular bases of ozone treatment effects on human and animal well-being and to optimize their performance in terms of reproducibility of results, quality, and safety. In fact, the common therapeutic treatments are normally documented by healthcare professionals' prescriptions. The same applies to medicinal gases (whose uses are based on their pharmacological effects) that are intended for patients for treatment, diagnostic, or preventive purposes and that have been produced and inspected in accordance with good manufacturing practices and pharmacopoeia monographs. On the contrary, it is the responsibility of healthcare professionals, who thoughtfully choose to use ozone as a medicinal product, to achieve the following objectives: (i) to understand the molecular basis of the mechanism of action; (ii) to adjust the treatment according to the clinical responses obtained in accordance with the principles of precision medicine and personalized therapy; (iii) to ensure all quality standards.

Qualitative and Quantitative Mass Spectrometry in Salivary Metabolomics and Proteomics

The metabolomics and proteomics analysis of saliva, an excellent biofluid that is a rich source of biological compounds, allows for the safe and frequent screening of drugs, their metabolites, and molecular biomarkers of various diseases. One of the most frequently used analytical methods in saliva analysis is liquid chromatography coupled with mass spectrometry (LC-MS) and tandem mass spectrometry. The low ionisation efficiency of some compounds and a complex matrix makes their identification by MS difficult. Furthermore, quantitative analysis by LC-MS frequently cannot be performed without isotopically labelled standards, which usually have to be specially synthesised. This review presented reports on qualitative and quantitative approaches in salivary metabolomics and proteomics. The purpose of this manuscript was to present the challenges, advances, and future prospects of mass spectrometry, both in the analysis of salivary metabolites and proteins. The presented review should appeal to those interested in the recent advances and trends in qualitative and quantitative mass spectrometry in salivary metabolomics and proteomics, which may facilitate a diagnostic accuracy, the evaluation of treatment efficacy, the early diagnosis of disease, and a forensic investigation of some unapproved drugs for any medical or dietary administration.

Cellular Lactate Spectroscopy Using 1.5 Tesla Clinical Apparatus

Cellular lactate is a key cellular metabolite and marker of anaerobic glycolysis. Cellular lactate uptake, release, production from glucose and glycogen, and interconversion with pyruvate are important determinants of cellular energy. It is known that lactate is present in the spectrum of neoplasms and low malignancy (without necrotic lesions). Also, the appearance of lactate signals is associated with anaerobic glucose, mitochondrial dysfunction, and other inflammatory responses. The aim of this study was the detection of lactate in cell cultures with the use of proton magnetic resonance (¹H MRS) and a 1.5 Tesla clinical apparatus (MR OPTIMA 360), characterized as a medium-field system. In this study, selected metabolites, together with cellular lactate, were identified with the use of an appropriate protocol and management algorithm. This paper describes the results obtained for cancer cell cultures. This medium-field system has proven the possibility of detecting small molecules, such as lactate, with clinical instruments. ¹H MRS performed using clinical MR apparatus is a useful tool for clinical analysis.

Lysophosphatidylcholine: Potential Target for the Treatment of Chronic Pain

The bioactive lipid lysophosphatidylcholine (LPC), a major phospholipid component of oxidized low-density lipoprotein (Ox-LDL), originates from the cleavage of phosphatidylcholine by phospholipase A2 (PLA2) and is catabolized to other substances by different enzymatic pathways. LPC exerts pleiotropic effects mediated by its receptors, G protein-coupled signaling receptors, Toll-like receptors, and ion channels to activate several second messengers. Lysophosphatidylcholine (LPC) is increasingly considered a key marker/factor positively in pathological states, especially inflammation and atherosclerosis development. Current studies have indicated that the injury of nervous tissues promotes oxidative stress and lipid peroxidation, as well as excessive accumulation of LPC, enhancing the membrane hyperexcitability to induce chronic pain, which may be recognized as one of the hallmarks of chronic pain. However, findings from lipidomic studies of LPC have been lacking in the context of chronic pain. In this review, we focus in some detail on LPC sources, biochemical pathways, and the signal-transduction system. Moreover, we outline the detection methods of LPC for accurate analysis of each individual LPC species and reveal the pathophysiological implication of LPC in chronic pain, which makes it an interesting target for biomarkers and the development of medicine regarding chronic pain.

UPLC-MS/MS method for the determination of the herb composition of Tangshen formula and the in vivo pharmacokinetics of its metabolites in rat plasma

INTRODUCTION

Tangshen formula (TSF) is a traditional Chinese medicine composed of seven medicinal herbs including Astragalus membranaceus, Rehmannia glutinosa Libosch, Citrus aurantium L., etc. which is used to treat diabetic nephropathy III, IV qi and yin deficiency and stasis syndrome. Most of the studies on TSF are pharmacological and pharmacodynamic experiments. There are few basic studies on its chemical substances, and the effective constituents are not clear.

OBJECTIVE

To analyse the main chemical components of TSF and the absorbed components in rat plasma following oral administration based on liquid chromatography tandem mass spectrometry (LC-MS/MS). Moreover, providing a rapid and valid analytical strategy for simultaneous determination of six components in rat plasma and use it in pharmacokinetic studies.

RESULTS

A total of 132 components were identified in TSF, and 44 components were identified in rat plasma after oral TSF, 35 of which were prototype components and nine were metabolic components. A sensitive and reliable LC-MS/MS method was developed for simultaneous determination of six components in rat plasma. The intra-day and inter-day precision relative standard deviation (RSD) was lower than 15%; the accuracy of low, medium and high concentrations ranged from 80% to 120%. The recovery met the requirements and the RSD of the recoveries was less than 15%.

CONCLUSION

A total of 132 components were identified in TSF. The LC-MS/MS quantitative method for the simultaneous determination of morroniside, loganin, notoginsenoside R₁ , ginsenoside Re, ginsenoside Rb₁ and astragaloside IV in rat plasma was established for the first time. The pharmacokinetic parameters are clarified, which can guide the clinical medication of TSF.

Fluxomics - New Metabolomics Approaches to Monitor Metabolic Pathways

Fluxomics is an innovative -omics research field that measures the rates of all intracellular fluxes in the central metabolism of biological systems. Fluxomics gathers data from multiple different -omics fields, portraying the whole picture of molecular interactions. Recently, fluxomics has become one of the most relevant approaches to investigate metabolic phenotypes. Metabolic flux using 13C-labeled molecules is increasingly used to monitor metabolic pathways, to probe the corresponding gene-RNA and protein-metabolite interaction networks in actual time. Thus, fluxomics reveals the functioning of multi-molecular metabolic pathways and is increasingly applied in biotechnology and pharmacology. Here, we describe the main fluxomics approaches and experimental platforms. Moreover, we summarize recent fluxomic results in different biological systems.

Ozonation of Whole Blood Results in an Increased Release of Microparticles from Blood Cells

Autohemotherapy with ozonated blood is used in the treatment of a broad spectrum of clinical disorders. Ozone demonstrates strong oxidizing properties and causes damage to cell membranes. The impact of whole-blood ozonation on the release of microparticles from blood and endothelial cells and the concentration of selected markers in the hemostatic system (APTT, PT, D-dimer, fibrinogen) were investigated. Venous blood, obtained from 19 healthy men, was split into four equal parts and treated with air, 15 µg/mL ozone, or 30 µg/mL ozone, or left untreated. The number and types of microparticles released were determined using flow cytometry on the basis of surface antigen expression: erythrocyte-derived microparticles (CD235⁺), platelet-derived microparticles (CD42⁺), leukocyte-derived microparticles (CD45⁺), and endothelial-derived microparticles (CD144⁺). The study is the first to demonstrate that ozone induces a statistically significant increase in the number of microparticles derived from blood and endothelial cells. Although statistically significant, the changes in some coagulation factors were somewhat mild and did not exceed normal values.

Ozone and its derivatives in veterinary medicine: A careful appraisal

The therapeutic use of ozone and its derivatives in the veterinary medicine it is still in an emergent stage. Gaseous ozone chemical instability makes necessary its extemporaneous preparation and the accordance about ozone treatments with the highest quality standards in publications is of paramount importance. Moreover, the numerous method of administration in different animal species, the prevalence of case reports, the deficiency of consistent evaluation of the outcomes, as well as the lack of standardization of the treatment operating procedures represents an open question for its spreading and official approval. The keywords "ozone", "ozonated", "ozonation" "ozonized", "ozonization", "oxygen-ozone therapy", "veterinary", "pets", "animal" were used to perform a literature review using PubMed, Cochrane, Google Scholar, Zotero databases with the temporal restriction for published manuscripts starting from 2010. All the researches were critically evaluated, regardless of the impact factor, if any, of the journals in which they were presented. The deepening of the mechanisms of action of this bio-oxidative therapy can open new horizons on its use. The distinctive condition to achieve such a scenario is an improved knowledge of the qualitative/quantitative characteristics of ozone and its derivatives. All with the aim of taking nothing away to the cited original research papers, but of improving the promising therapeutic implications of ozone therapy in veterinary medicine as a standardization stimulus about this therapeutic resource with multiple application specificities.

Evaluation of Biological Mechanisms of Eucommiae Folium in Hypertensive Kidney Injury by Integration of Untargeted Metabolomics and Network Pharmacology

Hypertensive kidney injury (Hki) is one of the most common complications of hypertension. Early prevention and treatment of renal injury in patients with hypertension is great significance. The study, which used an integrated ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS) analysis, network pharmacology approach, and plasma metabolomics, aimed to discover the active ingredients and therapeutic mechanisms of Eucommiae folium (Ef) in treating Hki. The chemical components of Ef were analyzed by UPLC-quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS), and the "compound-target-disease" network was constructed by screening the closely related drug targets from the drug-target database, then the signaling pathways related to Hki were analyzed. Finally, the enzyme-linked immunosorbent assay (ELISA) and real-time quantitative reverse-transcription polymerase chain reaction were used to test and verify the key targets in the common pathways of metabolomics and network pharmacology. The results indicated that Eucommiae folium might play an excellent role in treating Hki, likely through regulating the vascular endothelial growth factor signaling pathway, hypoxia inducible factor 1 (HIF-1) signaling pathway, and glycerophospholipid metabolism pathway, which were validated by increasing levels of nitric oxide, endothelial nitric oxide synthase and reducing levels of endothelin 1, angiotensin II, renin, cyclic guanosine monophosphate, blood urea nitrogen, and serum creatinine, as well as the reduced gene expression of Ache, Ddah2, Egfr, Lcat, Pla2g2a, Stat3 and Vegfa. The study systematically explored the protective mechanisms of Ef against Hki and also provided the practical treatment strategies of Hki from the Chinese herb.

Expert consensus of Chinese Association for the Study of Pain on the application of ozone therapy in pain medicine

This consensus was compiled by first-line clinical experts in the field of pain medicine and was organized by the Chinese Association for the Study of Pain. To reach this consensus, we consulted a wide range of opinions and conducted in-depth discussions on the mechanism, indications, contraindications, operational specifications and adverse reactions of ozone iatrotechnique in the treatment of pain disorders. We also referred to related previous preclinical and clinical studies published in recent years worldwide. The purpose of this consensus is to standardize the rational application of ozone iatrotechnique in pain treatment, to improve its efficacy and safety and to reduce and prevent adverse reactions and complications in this process.

A network pharmacology-integrated metabolomics strategy for clarifying the action mechanisms of Schisandrae Chinensis Fructus for treating drug-induced liver injury by acetaminophen

Schisandrae Chinensis Fructus (SCF) was a Traditional Chinese Medicine (TCM) for protecting liver. However, underlying therapeutic mechanisms of SCF for drug-induced liver injury (DILI) by acetaminophen (APAP) are still unclear. This study aims to discover the potential regulation mechanisms of SCF in the treatment of DILI by APAP using the integrated network pharmacology, plasma metabolomics profiling with UPLC-Q-TOF-MS approach. The key targets in the shared pathways of network pharmacology and metabolomics were screened and experimentally validated by Quantitative Real-time PCR analysis. The results showed that SCF could exert excellent effects on DILI by APAP probably through regulating ErbB signaling pathway and Arachidonic acid metabolism pathway, which was reflected by the reduced gene expression of TNF-α, IL-6, IL-1β, COX-2 and EGFR, as well as the increased gene expression of Nrf2, HO-1, MDM2, MAPK8, SRC, PLD1, CYP2E1, CYP1A2, CYP3A1. This study systematically explored the pharmacological mechanisms of SCF in the treatment of DILI, meanwhile, metabolomics combine with network pharmacology approach might be a useful strategy for early diagnosis of DILI by APAP.

A humoral solution: Autologous blood products and tissue repair

Autologous blood-derived products (ABP) are the focus of growing scientific interest and are investigated and used for multiple medical indications. ABPs hold promise thanks to their availability, ease of preparation, and low risk of adverse allogenic reaction, hypersensitivity, and contamination. Compositional analysis of ABPs reveals a diverse mixture of cellular components, cytokines and growth factors that play roles in healing processes such as tissue proliferation and angiogenesis, modulation of the local environment through chemotaxis and regulation of inflammation and the extracellular matrix, as well as several immunomodulatory actions. Thus, the administration of ABP induces supraphysiological levels of components necessary for orchestrating reparative efforts in currently difficult-to-treat medical conditions. In this article, we review the variety of autologous blood-derived products, their composition, current clinical uses, regulatory climate, and mechanisms of action.

Milk Metabolomics Reveals Potential Biomarkers for Early Prediction of Pregnancy in Buffaloes Having Undergone Artificial Insemination

This study aimed to identify potential biomarkers for early pregnancy diagnosis in buffaloes subjected to artificial insemination (AI). The study was carried out on 10 pregnant and 10 non-pregnant buffaloes that were synchronized by Ovsynch-Timed Artificial Insemination Program and have undergone the first AI. Furthermore, milk samples were individually collected ten days before AI (the start of the synchronization treatment), on the day of AI, day 7 and 18 after AI, and were analyzed by LC-MS. Statistical analysis was carried out by using Mass Profile Professional (Agilent Technologies, Santa Clara, CA, USA). Metabolomic analysis revealed the presence of several metabolites differentially expressed between pregnant and non-pregnant buffaloes. Among these, a total of five metabolites were identified by comparison with an online database and a standard compound as acetylcarnitine (3-Acetoxy-4-(trimethylammonio)butanoate), arginine-succinic acid hydrate, 5'-O-{[3-({4-[(3aminopropyl)amino]butyl}amino)propyl]carbamoyl}-2'-deoxyadenosine, N-(1-Hydroxy-2-hexadecanyl)pentadecanamide, and N-[2,3-Bis(dodecyloxy)propyl]-L-lysinamide). Interestingly, acetylcarnitine was dominant in milk samples collected from non-pregnant buffaloes. The results obtained from milk metabolic profile and hierarchical clustering analysis revealed significant differences between pregnant and non-pregnant buffaloes, as well as in the metabolite expression. Overall, the findings indicate the potential of milk metabolomics as a powerful tool to identify biomarkers of early pregnancy in buffalo undergoing AI.

Metabolomic Signature of Early Vascular Aging (EVA) in Hypertension

Arterial stiffening is a hallmark of early vascular aging (EVA) syndrome and an independent predictor of cardiovascular morbidity and mortality. In this case-control study we sought to identify plasma metabolites associated with EVA syndrome in the setting of hypertension. An untargeted metabolomic approach was used to identify plasma metabolites in an age-, BMI-, and sex-matched groups of EVA (n = 79) and non-EVA (n = 73) individuals with hypertension. After raw data processing and filtration, 497 putative compounds were characterized, out of which 4 were identified as lysophosphaditylcholines (LPCs) [LPC (18:2), LPC (16:0), LPC (18:0), and LPC (18:1)]. A main finding of this study shows that identified LPCs were independently associated with EVA status. Although LPCs have been shown previously to be positively associated with inflammation and atherosclerosis, we observed that hypertensive individuals characterized by 4 down-regulated LPCs had 3.8 times higher risk of EVA compared to those with higher LPC levels (OR = 3.8, 95% CI 1.7–8.5, P < 0.001). Our results provide new insights into a metabolomic phenotype of vascular aging and warrants further investigation of negative association of LPCs with EVA status. This study suggests that LPCs are potential candidates to be considered for further evaluation and validation as predictors of EVA in patients with hypertension.

NMR Spectroscopy for Metabolomics Research

Over the past two decades, nuclear magnetic resonance (NMR) has emerged as one of the three principal analytical techniques used in metabolomics (the other two being gas chromatography coupled to mass spectrometry (GC-MS) and liquid chromatography coupled with single-stage mass spectrometry (LC-MS)). The relative ease of sample preparation, the ability to quantify metabolite levels, the high level of experimental reproducibility, and the inherently nondestructive nature of NMR spectroscopy have made it the preferred platform for long-term or large-scale clinical metabolomic studies. These advantages, however, are often outweighed by the fact that most other analytical techniques, including both LC-MS and GC-MS, are inherently more sensitive than NMR, with lower limits of detection typically being 10 to 100 times better. This review is intended to introduce readers to the field of NMR-based metabolomics and to highlight both the advantages and disadvantages of NMR spectroscopy for metabolomic studies. It will also explore some of the unique strengths of NMR-based metabolomics, particularly with regard to isotope selection/detection, mixture deconvolution via 2D spectroscopy, automation, and the ability to noninvasively analyze native tissue specimens. Finally, this review will highlight a number of emerging NMR techniques and technologies that are being used to strengthen its utility and overcome its inherent limitations in metabolomic applications.

Application of ozone therapy in interventional medicine

Ozone therapy has been gradually accepted by doctors in various fields because it has been safe, convenient, and inexpensive since the twentieth century. It has been used in the treatment of various diseases with satisfactory results, especially in the application of interventional surgery. For lumbar disc herniation, knee osteoarthritis, tissue ischemia-reperfusion after revascularization, stroke, and cancer, ozone therapy can improve the efficacy of interventional surgery and reduce postoperative acute and chronic complications. Prospects of ozone therapy in interventional therapy and the underlying mechanisms of efficacy need further exploration.

New plasma preparation approach to enrich metabolome coverage in untargeted metabolomics: plasma protein bound hydrophobic metabolite release with proteinase K

Plasma untargeted metabolomics is a common method for evaluation of the mechanisms underlying human pathologies and identification of novel biomarkers. The plasma proteins provide the environment for transport of hydrophobic metabolites. The current sample preparation protocol relies on the immediate precipitation of proteins and thus leads to co-precipitation of a significant fraction of hydrophobic metabolites. Here we present a new simple procedure that overcomes the co-precipitation problem and improves metabolome coverage. Introducing an additional step preceding the protein precipitation, namely limited digestion with proteinase K, allows release of associated metabolites through the relaxation of the native proteins tertiary structure. The modified protocol allows clear detection of hydrophobic metabolites including fatty acids and phospholipids. Considering the potential involvement of the hydrophobic metabolites in human cardiovascular and cancer diseases, the method may constitute a novel approach in plasma untargeted metabolomics.

Integrated Metabolomics and Network Pharmacology Approach to Explain Possible Action Mechanisms of Xin-Sheng-Hua Granule for Treating Anemia

As a well-known traditional Chinese medicine (TCM) prescription, Xin-Sheng-Hua Granule (XSHG) has been applied in China for more than 30 years to treat postpartum diseases, especially anemia. However, underlying therapeutic mechanisms of XSHG for anemia were still unclear. In this study, plasma metabolomics profiling with UHPLC-QTOF/MS and multivariate data method was firstly analyzed to discover the potential regulation mechanisms of XSHG on anemia rats induced by bleeding from the orbit. Afterward, the compound-target-pathway network of XSHG was constructed by the use of network pharmacology, thus anemia-relevant signaling pathways were dissected. Finally, the crucial targets in the shared pathways of metabolomics and network pharmacology were experimentally validated by ELISA and Western Blot analysis. The results showed that XSHG could exert excellent effects on anemia probably through regulating coenzyme A biosynthesis, sphingolipids metabolism and HIF-1α pathways, which was reflected by the increased levels of EPOR, F2, COASY, as well as the reduced protein expression of HIF-1α, SPHK1, and S1PR1. Our work successfully explained the polypharmcological mechanisms underlying the efficiency of XSHG on treating anemia, and meanwhile, it probed into the potential treatment strategies for anemia from TCM prescription.

Untargeted Metabolomics Provides Insight into the Mechanisms Underlying Resistant Hypertension

BACKGROUND

Resistant hypertension (RH) affects about 15-20% of treated hypertensive patients worldwide. RH increases the risk of cardiovascular events such as myocardial infarction and stroke by 50%. The pathological mechanisms underlying resistance to treatment are still poorly understood.

OBJECTIVE

The main goal of this pilot study was to determine and compare plasma metabolomic profiles in resistant and non-resistant hypertensive patients.

METHODS

We applied untargeted metabolomic profiling in plasma samples collected from 69 subjects with RH and 81 subjects with controlled hypertension. To confirm patients' compliance to antihypertensive treatment, levels of selected drugs and their metabolites were determined in plasma samples with the LC-ESI-TOF/MS technique.

RESULTS

The results showed no statistically significant differences in the administration of antihypertensive drug in the compared groups. We identified 19 up-regulated and 13 downregulated metabolites in the RH.

CONCLUSION

The metabolites altered in RH are linked to oxidative stress and inflammation, endothelium dysfunction, vasoconstriction and cell proliferation. Our results may generate new hypothesis about RH development and progression.

Discriminant biomarkers of acute respiratory distress syndrome associated to H1N1 influenza identified by metabolomics HPLC-QTOF-MS/MS platform

Acute respiratory distress syndrome (ARDS) is a serious complication of influenza A (H1N1) virus infection. Its pathogenesis is unknown and biomarkers are lacking. Untargeted metabolomics allows the analysis of the whole metabolome in a biological compartment, identifying patterns associated with specific conditions. We hypothesized that LC-MS could help identify discriminant metabolites able to define the metabolic alterations occurring in patients with influenza A (H1N1) virus infection that developed ARDS. Serum samples from patients diagnosed with 2009 influenza A (H1N1) virus infection with (n = 25) or without (n = 32) ARDS were obtained on the day of hospital admission and analyzed by LC-MS/MS. Metabolite identification was determined by MS/MS analysis and analysis of standards. The specificity of the patterns identified was confirmed in patients without 2009 influenza A(H1N1) virus pneumonia (15 without and 17 with ARDS). Twenty-three candidate biomarkers were found to be significantly different between the two groups, including lysophospholipids and sphingolipids related to inflammation; bile acids, tryptophan metabolites, and thyroxine, related to the metabolism of the gut microflora. Confirmation results demonstrated the specificity of major alterations occurring in ARDS patients with influenza A (H1N1) virus infection.

Serum metabolic fingerprinting after exposure of rats to quinolinic acid

Quinolinic acid (QUIN), one of the end metabolites in the kynurenine pathway, plays an important role in the pathogenesis of several diseases. Serum QUIN concentration rises in patients with renal dysfunction, liver cirrhosis, and many other inflammatory diseases. In the present study, osmotic minipumps containing QUIN (0.3 and 1mg/day) were implanted intraperitoneally into rats for 28days. Then, the physiological and toxicological variables were evaluated and LC-QTOF-MS serum metabolic fingerprinting was performed. QUIN significantly decreased the serum concentrations of several amino acids (phenylalanine, valine, tyrosine, and tryptophan), pantothenic acid, branched chain C4 acylcarnitine, total cholesterol, and glucose; increased the serum concentrations of amides (pentadecanoic amide, palmitic amide, oleamide, and stearamide), polyamines (spermine and spermidine), sphingosine, and deoxy-prostaglandin; caused alterations in phospholipids. This is the first report of comprehensive metabolites analysis after chronic intraperitoneal administration of QUIN. Further studies could develop new therapeutics for patients with disorders accompanied by increased serum level of QUIN.

PLS-Based and Regularization-Based Methods for the Selection of Relevant Variables in Non-targeted Metabolomics Data

Non-targeted metabolomics constitutes a part of the systems biology and aims at determining numerous metabolites in complex biological samples. Datasets obtained in the non-targeted metabolomics studies are high-dimensional due to sensitivity of mass spectrometry-based detection methods as well as complexity of biological matrices. Therefore, a proper selection of variables which contribute into group classification is a crucial step, especially in metabolomics studies which are focused on searching for disease biomarker candidates. In the present study, three different statistical approaches were tested using two metabolomics datasets (RH and PH study). The orthogonal projections to latent structures-discriminant analysis (OPLS-DA) without and with multiple testing correction as well as the least absolute shrinkage and selection operator (LASSO) with bootstrapping, were tested and compared. For the RH study, OPLS-DA model built without multiple testing correction selected 46 and 218 variables based on the VIP criteria using Pareto and UV scaling, respectively. For the PH study, 217 and 320 variables were selected based on the VIP criteria using Pareto and UV scaling, respectively. In the RH study, OPLS-DA model built after correcting for multiple testing, selected 4 and 19 variables as in terms of Pareto and UV scaling, respectively. For the PH study, 14 and 18 variables were selected based on the VIP criteria in terms of Pareto and UV scaling, respectively. In the RH and PH study, the LASSO selected 14 and 4 variables with reproducibility between 99.3 and 100%, respectively. In the light of PLS-based models, the larger the search space the higher the probability of developing models that fit the training data well with simultaneous poor predictive performance on the validation set. The LASSO offers potential improvements over standard linear regression due to the presence of the constrain, which promotes sparse solutions. This paper is the first one to date utilizing the LASSO penalized logistic regression in untargeted metabolomics studies.

Insulin resistance in prepubertal obese children correlates with sex-dependent early onset metabolomic alterations

Background:

Insulin resistance (IR) is usually the first metabolic alteration diagnosed in obese children and the key risk factor for development of comorbidities. The factors determining whether or not IR develops as a result of excess body mass index (BMI) are still not completely understood.

Objectives:

This study aimed to elucidate the mechanisms underpinning the predisposition toward hyperinsulinemia-related complications in obese children by using a metabolomic strategy that allows a profound interpretation of metabolic profiles potentially affected by IR.

Methods:

Serum from 60 prepubertal obese children (30 girls/30 boys, 50% IR and 50% non-IR in each group, but with similar BMIs) were analyzed by using liquid chromatography–mass spectrometry, gas chromatography–mass spectrometry and capillary electrophoresis–mass spectrometry following an untargeted metabolomics approach. Validation was then performed on a group of 100 additional children with the same characteristics.

Results:

When obese children with and without IR were compared, 47 metabolites out of 818 compounds (P<0.05) obtained after data pre-processing were found to be significantly different. Bile acids exhibit the greatest changes (that is, approximately a 90% increase in IR). The majority of metabolites differing between groups were lysophospholipids (15) and amino acids (17), indicating inflammation and central carbon metabolism as the most altered processes in impaired insulin signaling. Multivariate analysis (OPLS-DA models) showed subtle differences between groups that were magnified when females were analyzed alone.

Conclusions:

Inflammation and central carbon metabolism, together with the contribution of the gut microbiota, are the most altered processes in obese children with impaired insulin signaling in a sex-specific fashion despite their prepubertal status.

Methods used to increase the comprehensive coverage of urinary and plasma metabolomes by MS

Metabolomics, focusing on comprehensive analysis of all the metabolites in a biological system, provides a direct signature of biochemical activity. Using emerging technologies in MS, it is possible to simultaneously and rapidly analyze thousands of metabolites. However, due to the chemical and physical diversity of metabolites, it is difficult to acquire a comprehensive and reliable profiling of the whole metabolome. Here, we summarize the state of the art in metabolomics research, focusing on efforts to provide a more comprehensive metabolome coverage via improvements in two fundamental processes: sample preparation and MS analysis. Additionally, the reliable analysis is also highlighted via the combinations of multiple methods (e.g., targeted and untargeted approaches), and analytical quality control and calibration methods.

Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis

NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to nondestructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Precise metabolite quantification is a prerequisite to move any chemical biomarker or biomarker panel from the lab to the clinic. Among the biofluids commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, and easily obtained, needs little sample preparation, and does not require invasive medical procedures for collection. Furthermore, urine captures and concentrates many "unwanted" or "undesirable" compounds throughout the body, providing a rich source of potentially useful disease biomarkers; however, incredible variation in urine chemical concentrations makes analysis of urine and identification of useful urinary biomarkers by NMR challenging. We discuss a number of the most significant issues regarding NMR-based urinary metabolomics with specific emphasis on metabolite quantification for disease biomarker applications and propose data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, sample preparation, and biomarker assessment.

From sample treatment to biomarker discovery: A tutorial for untargeted metabolomics based on GC-(EI)-Q-MS

This tutorial provides a comprehensive description of the GC-MS-based untargeted metabolomics workflow including: ethical approval requirement, sample collection and storage, equipment maintenance and setup, sample treatment, monitoring of analytical variability, data pre-processing including deconvolution by free software such as AMDIS, data processing, statistical analysis and validation, detection of outliers and biological interpretation of the results. For each stage tricks will be suggested, pitfalls will be highlighted and advice will be provided on how to get the best from this methodology and technique. In addition, a step-by-step procedure and an example of our in-house library have been included in the supplementary material to lead the user through the concepts described herein. As a case study, an interesting example from one of our experiments at CEMBIO Research Centre is described, presenting an example of the use of this ready-to use protocol for identification of a metabolite that was not previously included in Fiehn commercial target library.

Differential Gene Expression and Infection Profiles of Cutaneous and Mucosal Leishmania braziliensis Isolates from the Same Patient

Background

Leishmaniasis is a complex disease in which clinical outcome depends on factors such as parasite species, host genetics and immunity and vector species. In Brazil, Leishmania (Viannia) braziliensis is a major etiological agent of cutaneous (CL) and mucosal leishmaniasis (MCL), a disfiguring form of the disease, which occurs in ~10% of L. braziliensis-infected patients. Thus, clinical isolates from patients with CL and MCL may be a relevant source of information to uncover parasite factors contributing to pathogenesis. In this study, we investigated two pairs of L. (V.) braziliensis isolates from mucosal (LbrM) and cutaneous (LbrC) sites of the same patient to identify factors distinguishing parasites that migrate from those that remain at the primary site of infection.

Methodology/Principal Findings

We observed no major genomic divergences among the clinical isolates by molecular karyotype and genomic sequencing. RT-PCR revealed that the isolates lacked Leishmania RNA virus (LRV). However, the isolates exhibited distinct in vivo pathogenesis in BALB/c mice; the LbrC isolates were more virulent than the LbrM isolates. Metabolomic analysis revealed significantly increased levels of 14 metabolites in LbrC parasites and 31 metabolites in LbrM parasites that were mainly related to inflammation and chemotaxis. A proteome comparative analysis revealed the overexpression of LbrPGF2S (prostaglandin f2-alpha synthase) and HSP70 in both LbrC isolates. Overexpression of LbrPGF2S in LbrC and LbrM promastigotes led to an increase in infected macrophages and the number of amastigotes per cell at 24–48 h post-infection (p.i.).

Conclusions/Significance

Despite sharing high similarity at the genome structure and ploidy levels, the parasites exhibited divergent expressed genomes. The proteome and metabolome results indicated differential profiles between the cutaneous and mucosal isolates, primarily related to inflammation and chemotaxis. BALB/c infection revealed that the cutaneous isolates were more virulent than the mucosal parasites. Furthermore, our data suggest that the LbrPGF2S protein is a candidate to contribute to parasite virulence profiles in the mammalian host.

Leishmaniasis is a critical public health problem worldwide. The clinical outcome of leishmaniasis depends on the infecting parasite species, host genetics and immune response and insect species. Leishmania braziliensis is a major etiological agent of cutaneous and mucosal leishmaniasis in Brazil. Fewer than 10% of L. braziliensis-infected patients with CL develop the mucosal form (a severe clinical manifestation). The small number of parasites in the mucosae increases the difficulty of obtaining clinical isolates, and parasite samples are frequently derived from individuals with different genetic backgrounds. Therefore, clinical isolates from cutaneous and mucosal sites from the same patient represent unique tools to understand parasite factors that contribute to disease outcome and pathogenesis. In this study, we investigated parasite factors involved in disease progression using two pairs of L. (V.) braziliensis isolates from mucosal (LbrM) and cutaneous (LbrC) sites of the same patient. In conclusion, the murine infection and proteome and metabolome data suggest that the differences between the cutaneous and mucosal isolates are mainly related to inflammation and chemotaxis. Our data also suggest that the LbrPGF2S protein plays a role in parasite virulence in the mammalian host.

A gas chromatography-mass spectrometry based study on urine metabolomics in rats chronically poisoned with hydrogen sulfide

Gas chromatography-mass spectrometry (GS-MS) in combination with multivariate statistical analysis was applied to explore the metabolic variability in urine of chronically hydrogen sulfide- (H2S-) poisoned rats relative to control ones. The changes in endogenous metabolites were studied by partial least squares-discriminate analysis (PLS-DA) and independent-samples t-test. The metabolic patterns of H2S-poisoned group are separated from the control, suggesting that the metabolic profiles of H2S-poisoned rats were markedly different from the controls. Moreover, compared to the control group, the level of alanine, d-ribose, tetradecanoic acid, L-aspartic acid, pentanedioic acid, cholesterol, acetate, and oleic acid in rat urine of the poisoning group decreased, while the level of glycine, d-mannose, arabinofuranose, and propanoic acid increased. These metabolites are related to amino acid metabolism as well as energy and lipid metabolism in vivo. Studying metabolomics using GC-MS allows for a comprehensive overview of the metabolism of the living body. This technique can be employed to decipher the mechanism of chronic H2S poisoning, thus promoting the use of metabolomics in clinical toxicology.

Ozone dosing alters the biological potential and therapeutic outcomes of plasma rich in growth factors

BACKGROUND AND OBJECTIVE

Until now, ozone has been used in a rather empirical way. This in-vitro study investigates, for the first time, whether different ozone treatments of plasma rich in growth factors (PRGF) alter the biological properties and outcomes of this autologous platelet-rich plasma.

MATERIAL AND METHODS

Human plasma rich in growth factors was treated with ozone using one of the following protocols: a continuous-flow method; or a syringe method in which constant volumes of ozone and PRGF were mixed. In both cases, ozone was added before, during and after the addition of calcium chloride. Three ozone concentrations, of the therapeutic range 20, 40 and 80 μg/mL, were tested. Fibrin clot properties, growth factor content and the proliferative effect on primary osteoblasts and gingival fibroblasts were evaluated.

RESULTS

Ozone treatment of PRGF using the continuous flow protocol impaired formation of the fibrin scaffold, drastically reduced the levels of growth factors and significantly decreased the proliferative potential of PRGF on primary osteoblasts and gingival fibroblasts. In contrast, treatment of PRGF with ozone using the syringe method, before, during and after the coagulation process, did not alter the biological outcomes of the autologous therapy.

CONCLUSION

These findings suggest that ozone dose and the way that ozone combines with PRGF may alter the biological potential and therapeutic outcomes of PRGF.

Potential first trimester metabolomic biomarkers of abnormal birth weight in healthy pregnancies

OBJECTIVE

Macrosomia and low birth weight (LBW) can be associated with pregnancy complications and may affect the long-term health of the child. The aim of this study was to evaluate the metabolomic serum profiles of healthy pregnant women to identify early biomarkers of macrosomia and LBW and to understand mechanisms leading to abnormal fetal growth not related to mother's body mass index or presence of gestational diabetes.

METHOD

Serum samples from 770 women were collected between the 12th and 14th gestational week. Delivery samples were divided into three groups according to the infant birth weight as follows: low, <2500 g; normal, 2500-4000 g; and high >4000 g. Samples from women with any complications of pregnancy were excluded. Serum fingerprinting was performed by LC-QTOF-MS.

RESULTS

Lower levels of phospholipids, lysophospholipids, and monoacylglycerols; low vitamin D3 metabolites; and increased bilirubin level were associated with macrosomia. Because most changes involved lipids, as a concept of validation, adipocyte fatty acid-binding protein (A-FABP) levels were measured and found correlated with the studied lipids and birth weight.

CONCLUSION

Serum fingerprinting in early pregnancy can predict the risk of macrosomia. Serum levels of A-FABP and several lipids are promising prognostic markers for macrosomia in healthy pregnancies.

Metabolomics reveals metabolite changes in acute pulmonary embolism

Pulmonary embolism (PE) is a common cardiovascular emergency which can lead to pulmonary hypertension (PH) and right ventricular failure as a consequence of pulmonary arterial bed occlusion. The diagnosis of PE is challenging due to nonspecific clinical presentation, which results in relatively high mortality. Moreover, the pathological factors associated with PE are poorly understood. Metabolomics can provide new highlights which can help in the understanding of the processes and even propose biomarkers for its diagnosis. In order to obtain more information about PE and PH, acute PE was induced in large white pigs and plasma was obtained before and after induction of PE. Metabolic fingerprints from plasma were obtained with LC-QTOF-MS (positive and negative ionization) and GC-Q-MS. Data pretreatment and statistical analysis (uni- and multivariate) were performed in order to compare metabolic fingerprints and to select the metabolites that showed higher loading for the classification (28 from LC and 19 from GC). The metabolites found differentially distributed among groups are mainly related to energy imbalance in hypoxic conditions, such as glycolysis-derived metabolites, ketone bodies, and TCA cycle intermediates, as well as a group of lipidic mediators that could be involved in the transduction of the signals to the cells such as sphingolipids and lysophospholipids, among others. Results presented in this report reveal that combination of LC-MS- and GC-MS-based metabolomics could be a powerful tool for diagnosis and understanding pathophysiological processes due to acute PE.

Combination of ¹H NMR- and GC-MS-based metabonomics to study on the toxicity of Coptidis Rhizome in rats

BACKGROUND

Coptidis Rhizome (CR), widely applied to treat with heat and toxicity, is one of the most commonly used traditional Chinese medicine (TCM), however, an extensive dosage can induce toxicity. Diarrhea is one of the most frequent side effects of CR treatment.

METHODOLOGY/PRINCIPAL FINDINGS

In this study, metabonomics was combined with the multivariate statistical analysis to discover the endogenous metabolites which related to the diarrheal induced by CR. The male Sprague-Dawley rats were dosed with 4.95 g CR/kg weight. Urine samples were collected at day -1 (before treatment), and days 14 and 21 for NMR analysis. Serum and tissues were collected at day 14 for GC-MS analysis and histopathological examination, respectively. The urine and serum metabolic profiles provided clearer distinction between CR-treated group and control group, which was confirmed by body weight change and diarrhea. Through multivariate statistical analysis, 12 marker metabolites from ¹H NMR and 8 ones from GC-MS have been found. Among those metabolites, hippurate, acetate, alanine, glycine and glutamate are likely to break the balance of gut microbiota, whereas, lactate and 2-ketoisovalerate showed association with energy metabolism. Meanwhile, we observed that the CR-induced toxicity will recover when the treatment was stopped.

CONCLUSIONS/SIGNIFICANCE

These results suggest that the main reason for the CR-associated diarrhea might be disturbance in the normal gut microbiota. This metabonomics approach may provide an effective way to study the alteration of gut microbiota, which is expected to find broader application in other drug-induced gastrointestinal reaction assessment.

Histomorphometric evaluation of the effect of systemic and topical ozone on alveolar bone healing following tooth extraction in rats

The aim of this study was to investigate the effects of systemic and topical ozone applications on alveolar bone healing following tooth extraction. One hundred and twelve male Wistar rats were divided into eight groups of 14 rats each; seven groups were experimental (A-G) and one formed the control group (K). The experimental groups were further divided into two sub-groups, with seven rats in each - sacrificed on days 14 and 28 (subgroups 1 and 2). The maxillary right central incisors were extracted under general anaesthesia following the administration of local anaesthesia. After sacrifice, semi-serial histological sections were prepared, and mineralized and trabecular bone and osteoid and osteoblast surfaces were measured. Measurements of the trabecular bone showed statistically higher values in the groups treated with systemic ozone (D(2): 50.01 ± 2.12; E(2): 49.03 ± 3.03; F(2): 48.76 ± 2.61; G(2): 50.24 ± 3.37) than in the groups that underwent topical ozone administration (A(2): 46.01 ± 3.07; B(2): 46.79 ± 3.09; C(2): 47.07 ± 2.12; P = 0.030 (G(2)-A(2), G(2)-B(2), G(2)-C(2))). Within the limitations of the current study, it may be concluded that postoperative long-term systemic ozone application can accelerate alveolar bone healing following extraction. However, additional studies are required to clarify the effects of the different ozone applications on new bone formation.

Fingerprinting-based metabolomic approach with LC-MS to sleep apnea and hypopnea syndrome: a pilot study

Sleep apnea and hypopnea syndrome (SAHS) is a multicomponent disorder, with associated cardiovascular and metabolic alterations, second in order of frequency among respiratory disorders. Sleep apnea is diagnosed with an overnight sleep test called a polysomnogram, which requires having the patient in hospital. In addition, a more clear classification of patients according to mild and severe presentations would be desirable. The aim of the present study was to assess the relative metabolic changes in SAHS to identify new potential biomarkers for diagnosis, able to evaluate disease severity to establish response to therapeutic interventions and outcomes. For this purpose, metabolic fingerprinting represents a valuable strategy to monitor, in a nontargeted manner, the changes that are at the base of the pathophysiological mechanism of SAHS. Plasma samples of 33 SAHS patients were collected after polysomnography and analyzed with LC coupled to MS (LC-QTOF-MS). After data treatment and statistical analysis, signals differentiating nonsevere and severe patients were detected. Putative identification of 14 statistically significant features was obtained and changes that can be related to the episodes of hypoxia/reoxygenation (inflammation) have been highlighted. Among them, the patterns of variation of platelet activating factor and lysophospholipids, together with some compounds related to differential activity of the gut microflora (bile pigments and pipecolic acid) open new lines of research that will benefit our understanding of the alterations, offering new possibilities for adequate monitoring of the stage of the disease.

From numbers to a biological sense: How the strategy chosen for metabolomics data treatment may affect final results. A practical example based on urine fingerprints obtained by LC-MS

Application of high-throughput technologies in metabolomics studies increases the quantity of data obtained, which in turn imposes several problems during data analysis. Correctly and clearly addressed biological question and comprehensive knowledge about data structure and properties are definitely necessary to select proper chemometric tools. However, there is a broad range of chemometric tools available for use with metabolomics data, which makes this choice challenging. Precisely performed data treatment enables valuable extraction of information and its proper interpretation. The effect of an error made at an early stage will be enhanced throughout the later stages, which in combination with other errors made at each step can accumulate and significantly affect the data interpretation. Moreover, adequate application of these tools may help not only to detect, but sometimes also to correct, biological, analytical, or methodological errors, which may affect truthfulness of obtained results. This report presents steps and tools used for LC-MS based metabolomics data extraction, reduction, and visualization. Following such steps as data reprocessing, data pretreatment, data treatment, and data revision, authors want to show how to extract valuable information and how to avoid misinterpretation of results obtained. The purpose of this work was to emphasize problematic characteristics of metabolomics data and the necessity for their attentive and precise treatment. The dataset used to illustrate metabolomics data properties and to illustrate major data treatment challenges was obtained utilizing an animal model of control and diabetic rats, both with and without rosemary treatment. Urine samples were fingerprinted employing LC-QTOF-MS.

Research of medical gases in Poland

Research of medical gases is well established in Poland and has been marked with the foundation of several professional societies. Numerous academic centers including those dealing with hyperbaric and diving medicine conduct studies of medical gases, in vast majority supported with intramural funds. In general, Polish research of medical gases is very much clinical in nature, covering new applications and safety of medical gases in medicine; on the other hand there are several academic centers pursuing preclinical studies, and elaborating basic theories of gas physiology and mathematical modeling of gas exchange. What dominates is research dealing with oxygen and ozone as well as studies of anesthetic gases and their applications. Finally, several research directions involving noble gas, hydrogen and hydrogen sulfide for cell protection, only begin to gain recognition of basic scientists and clinicians. However, further developments require more monetary spending on research and clinical testing as well as formation of new collective bodies for coordinating efforts in this matter.