Precise Lipidomics Decipher Circulating Ceramide and Sphingomyelin Cycle Associated with the Progression of Rheumatoid Arthritis

Rheumatoid arthritis (RA) is a long-term autoimmune condition that causes joint and surrounding tissue inflammation. Lipid mediators are involved in inflammation and deterioration of the joints. Despite attempts to discover effective drug targets to intervene with lipid metabolism in the disease, progress has been limited. In this study, precise lipidomic technology was employed to quantify a broad range of serum ceramides and sphingomyelin (SM) in a large cohort, revealing an association between the accumulation of circulating ceramides and disturbed ceramide/SM cycles during the progression of RA. In our investigation, we discovered that eight ceramides exhibited a positive correlation with the activity of RA, thereby enhancing the accuracy of RA diagnosis, particularly in patients with serum antibody-negative RA. Furthermore, the enzyme SM phosphodiesterase 3 (SMPD3) was found to disrupt the circulating SM cycle and accelerate the progression of RA. The activity of SMPD3 can be inhibited by methotrexate, resulting in decreased metabolic conversion of SM to ceramide. These findings suggest that targeting the SM cycle may provide a new therapeutic option for RA.

Rapid, sensitive, and high-throughput quantification of broad serological ceramides by using isotope dilution liquid chromatography-negative ion electrospray tandem mass spectrometry

Ceramides are important intermediates in the metabolism of sphingolipids. High-throughput liquid chromatography-mass spectrometry has been used extensively for monitoring the levels of serological ceramides, but is still limited by inadequate coverage or lack of sensitivity. Herein, a rapid, sensitive, and high-throughput isotope dilution liquid chromatography-negative ion electrospray tandem mass spectrometry (IDLC-nESI-MS/MS) method was developed and verified for accurate quantification of 41 ceramides, involving ceramides with C16-20 sphingosine, dihydro-ceramide, and dehydro-ceramide. This method was validated with excellent linearity (R² > 0.99) and good recovery in the range of 90-110%. Intra- and inter-day imprecision were below 5.57% and 7.83% respectively. The improved high-throughput quantitative method developed in this study may aid in the accurate characterization of ceramides for understanding ceramide biology and application in disease diagnosis.

The adenosine analog prodrug ATV006 is orally bioavailable and has preclinical efficacy against parental SARS-CoV-2 and variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus driving the ongoing coronavirus disease 2019 (COVID-19) pandemic, continues to rapidly evolve. Due to the limited efficacy of vaccination in prevention of SARS-CoV-2 transmission and continuous emergence of variants of concern (VOC), orally bioavailable and broadly efficacious antiviral drugs are urgently needed. Previously we showed that the parent nucleoside of remdesivir, GS-441524, possesses potent anti-SARS-CoV-2 activity. Herein, we report that esterification of the 5′-hydroxyl moieties of GS-441524 markedly improved antiviral potency. This 5′-hydroxyl-isobutyryl prodrug, ATV006, demonstrated excellent oral bioavailability in rats and cynomolgus monkeys and exhibited potent antiviral efficacy against different SARS-CoV-2 VOCs in vitro and in three mouse models. Oral administration of ATV006 reduced viral loads and alleviated lung damage when administered prophylactically and therapeutically to K18-hACE2 mice challenged with the Delta variant of SARS-CoV-2. These data indicate that ATV006 represents a promising oral antiviral drug candidate for SARS-CoV-2.

Serum metabolomic and lipidomic profiling identifies diagnostic biomarkers for seropositive and seronegative rheumatoid arthritis patients

BACKGROUND

Diagnosing seronegative rheumatoid arthritis (RA) can be challenging due to complex diagnostic criteria. We sought to discover diagnostic biomarkers for seronegative RA cases by studying metabolomic and lipidomic changes in RA patient serum.

METHODS

We performed comprehensive metabolomic and lipidomic profiling in serum of 225 RA patients and 100 normal controls. These samples were divided into a discovery set (n = 243) and a validation set (n = 82). A machine-learning-based multivariate classification model was constructed using distinctive metabolites and lipids signals.

RESULTS

Twenty-six metabolites and lipids were identified from the discovery cohort to construct a RA diagnosis model. The model was subsequently tested on a validation set and achieved accuracy of 90.2%, with sensitivity of 89.7% and specificity of 90.6%. Both seropositive and seronegative patients were identified using this model. A co-occurrence network using serum omics profiles was built and parsed into six modules, showing significant association between the inflammation and immune activity markers and aberrant metabolism of energy metabolism, lipids metabolism and amino acid metabolism. Acyl carnitines (20:3), aspartyl-phenylalanine, pipecolic acid, phosphatidylethanolamine PE (18:1) and lysophosphatidylethanolamine LPE (20:3) were positively correlated with the RA disease activity, while histidine and phosphatidic acid PA (28:0) were negatively correlated with the RA disease activity.

CONCLUSIONS

A panel of 26 serum markers were selected from omics profiles to build a machine-learning-based prediction model that could aid in diagnosing seronegative RA patients. Potential markers were also identified in stratifying RA cases based on disease activity.

Machine Learning for Investigation on Endocrine-Disrupting Chemicals with Gestational Age and Delivery Time in a Longitudinal Cohort

Endocrine-disrupting chemicals (EDCs) are widespread environmental chemicals that are often considered as risk factors with weak activity on the hormone-dependent process of pregnancy. However, the adverse effects of EDCs in the body of pregnant women were underestimated. The interaction between dynamic concentration of EDCs and endogenous hormones (EHs) on gestational age and delivery time remains unclear. To define a temporal interaction between the EDCs and EHs during pregnancy, comprehensive, unbiased, and quantitative analyses of 33 EDCs and 14 EHs were performed for a longitudinal cohort with 2317 pregnant women. We developed a machine learning model with the dynamic concentration information of EDCs and EHs to predict gestational age with high accuracy in the longitudinal cohort of pregnant women. The optimal combination of EHs and EDCs can identify when labor occurs (time to delivery within two and four weeks, AUROC of 0.82). Our results revealed that the bisphenols and phthalates are more potent than partial EHs for gestational age or delivery time. This study represents the use of machine learning methods for quantitative analysis of pregnancy-related EDCs and EHs for understanding the EDCs' mixture effect on pregnancy with potential clinical utilities.

Pericardial adipose tissue-derived leptin promotes myocardial apoptosis in high fat diet-induced obese rats through JAK2/ROS/NKA signaling pathway

Background

Pathophysiologic mechanisms underlying cardiac structural and functional changes in obesity are complex and linked to adipocytokines released from pericardial adipose tissue (PAT) and cardiomyocyte apoptosis. Although leptin is involved in various pathological conditions, its role in paracrine action of pericardial adipose tissue on myocardial apoptosis remains unknown.

Purpose

This study was designed to investigate the role of PAT-derived leptin on myocardial apoptosis in high fat diet-induced obese rats.

Methods and results

Hearts were isolated from lean or high fat diet-induced obese Wistar rats for myocardial remodeling studies. Obese rats had abnormal myocardial structure, diastolic dysfunction, greatly elevated cardiac apoptosis and increased oxidative stress level. Enzyme-linked immunosorbent assay (ELISA) detected significantly higher than circulating leptin level in PAT of obese, but not lean rats. Western blot and immunohistochemical analyses demonstrated increased leptin receptor density in obese heart. H9c2 rat cardiomyoblasts after exposed to PAT-conditioned medium of obese rats exhibited pronounced reactive oxygen species (ROS)-mediated apoptosis, which was partially reversed by leptin antagonist. Moreover, leptin derived from PAT of obese rats inhibited Na+/K+-ATPase activity of H9c2 cells through stimulating ROS, thereby activating calcium-dependent apoptosis. Pretreatment with specific inhibitors revealed that JAK2/STAT3 and PI3K/Akt signaling pathways was involved in the leptin-induced myocardial apoptosis.

Conclusion

PAT-derived leptin induces myocardial apoptosis in high fat diet-induced obese rats via activating JAK2/STAT3/ROS signaling pathway and inhibiting its downstream Na+/K+-ATPase activity.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): Nature Science Foundation of ChinaKey Projects of Shaanxi Science and Technology Research and Development Plan

CPVA: a web-based metabolomic tool for chromatographic peak visualization and annotation

MOTIVATION

Liquid chromatography-mass spectrometry-based non-targeted metabolomics is routinely performed to qualitatively and quantitatively analyze a tremendous amount of metabolite signals in complex biological samples. However, false-positive peaks in the datasets are commonly detected as metabolite signals by using many popular software, resulting in non-reliable measurement.

RESULTS

To reduce false-positive calling, we developed an interactive web tool, termed CPVA, for visualization and accurate annotation of the detected peaks in non-targeted metabolomics data. We used a chromatogram-centric strategy to unfold the characteristics of chromatographic peaks through visualization of peak morphology metrics, with additional functions to annotate adducts, isotopes and contaminants. CPVA is a free, user-friendly tool to help users to identify peak background noises and contaminants, resulting in decrease of false-positive or redundant peak calling, thereby improving the data quality of non-targeted metabolomics studies.

AVAILABILITY AND IMPLEMENTATION

The CPVA is freely available at http://cpva.eastus.cloudapp.azure.com. Source code and installation instructions are available on GitHub: https://github.com/13479776/cpva.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Combinatory Data-Independent Acquisition and Parallel Reaction Monitoring Method for Deep Profiling of Gangliosides

Ganglioside is an important class of lipid species involved in intercellular signaling and various diseases, especially for neurodegenerative diseases. Systematic ganglioside profiling is challenging because of their naturally low abundance and highly diverse species. Herein, a new data-independent acquisition and parallel reaction monitoring (DIA/PRM) method with superior sensitivity was developed. The untargeted DIA acquisition consecutively records all the precursor ion and fragment ions at the same time, while the targeted PRM analysis with versatile higher collisional dissociation generates full MS/MS spectra for structure elucidation and verification. As compared with traditional data-dependent acquisition (DDA), the DIA/PRM method unbiasedly detected the majority of abundant ganglioside species and as low as 50 pg of ganglioside in an untargeted manner. Gangliosides in four kinds of biological samples including the mouse brain, mouse plasma, HeLa cell, and human colon cancer tissue were systematically identified, and low-abundance ganglioside species were further extended on the basis of linear chromatography retention rules of the most frequently detected ganglioside species. A total of 383 ganglioside features were defined with 329 of them derived from 32 ganglioside species. Taking advantage of the high-resolution MS analysis, rare ganglioside species were further elucidated according to their characteristic fragment ions and neutral losses. In total, 18 gangliosides with a ceramide carbon number from 20 to 25 and modified gangliosides, including 18 acetylated, 8 diacetylated, 1 phosphorylated, 36 N-glycolyneuraminic acid (NeuGc)-containing, and 7 di-NeuGc-containing gangliosides, were newly identified. The developed DIA/PRM method therefore generated a rich ganglioside resource for further functional exploration and is a unique alternative for DDA analysis for global ganglioside profiling in various biological systems.

The health concern of polychlorinated biphenyls (PCBs) in a notorious e-waste recycling site

Polychlorinated biphenyls (PCBs) remain a relatively high level in e-waste recycling regions 3 decades after ban on use. Illegal recycling activities cunningly moved under the environmental law enforcement. Here, we analyzed PCBs in soils and plants from Guiyu, China (one of the world's largest recycling areas) to understand the relationship between PCBs pollution and the transition of recycling activities (locations and techniques). High concentrations of PCBs were found in soil and plant samples from emerging recycling sites, up to 234 ng g^-1 and 236 ng g^-1 (dry weight), respectively. The recycling activities, specifically the open burning process, would obviously aggravate the PCB pollution levels in its environment. The calculated values of estimated daily intake and hazard ratios of PCBs in dietary routes showed that health risks should be taken seriously.

Study of metabolic disorders associated with BDE-47 exposure in Drosophila model by MS-based metabolomics

Epidemiological and animal studies have revealed a possible linkage between 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) exposure and neurodegenerative disease such as Parkinson's disease (PD). However, whether or how BDE-47 would affect the PD progression remains unclear. Here, we carried out a metabolomics study based on liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectrometry (GC-MS) to investigate the possible contribution of BDE-47 exposure to PD progression in Drosophila (fly) model. Transgenic PD flies were exposed to BDE-47 through diet for 30 days. Global metabolomic analysis identified 48 altered metabolites after the exposure. These metabolites were mainly involved in tryptophan metabolism, phenylalanine metabolism, purine metabolism, and alanine, aspartate and glutamate metabolism. Further, by quantifying metabolites of interest using LC-MS/MS, we confirmed that the formation of neuro-protector kynurenic acid was slowed down while the formation of neurotoxin 3-hydroxy-kynurenine was speeded up on the 20^th exposure day. Moreover, the levels of SAM/SAH (an index of methylation potential) and GSH/GSSG (an indicator of oxidative stress) were found to decrease on the 30^th exposure day. Our results suggest that BDE-47 could induce imbalance of kynurenine metabolism and methylation potential, and oxidative stress, which might further accelerate PD progression.

Study of BDE-47 induced Parkinson's disease-like metabolic changes in C57BL/6 mice by integrated metabolomic, lipidomic and proteomic analysis

As the predominant congener of polybrominated diphenyl ethers (PBDEs) detected in human serum, 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) has been reported to induce neurotoxicity. However, the possible linkage between BDE-47 and typical neurodegenerative diseases such as Parkinson's disease (PD) is still unclear. Here we carried out omics studies using liquid chromatography-orbitrap mass spectrometry (LC-orbitrap MS) to depict the BDE-47 induced metabolic changes in C57BJ/L mice to explore the possible contribution of BDE-47 exposure to PD pathology. BDE-47 dissolved in corn oil was orally administered to mice for 30 consecutive days. Results of metabolomics and lipidomics studies of PD-related brain regions revealed significant metabolite changes in pathways involved in oxidative stress and neurotransmitter production. Moreover, isobaric tags for relative and absolute quantitation (iTRAQ) proteomics study of the striatum, which is the part of brain that is most intensively studied in PD pathogenesis, revealed that BDE-47 could induce neurotransmitter system disturbance, abnormal phosphorylation, mitochondrial dysfunction and oxidative stress. Overall, this study depicts the possible contribution of BDE-47 exposure to PD pathology and highlights the powerfulness of omics platforms to deepen the mechanistic understanding of environmental pollutant-caused toxicity.

Variations of phthalate exposure and metabolism over three trimesters

Maternal exposure to phthalates may cause some adverse health effects on both mother and fetus, but variations of phthalate exposure and metabolism during pregnancy have not been thoroughly characterized. A total of 946 participants were selected from a cohort study conducted in Wuhan between 2014 and 2015 through which they had provided a complete set of urine samples at three trimesters. Eight phthalate metabolites were analyzed in 2838 urine samples. Based on urinary concentrations, various parameters (i.e. phthalate metabolite concentrations, ratios of metabolites of bis(2-ethylhexyl) phthalate (DEHP) in DEHP, and percentages of individual metabolites in total phthalates) were compared over three visits. We observed that levels of phthalate metabolites showed a U-shaped trend across three trimesters. The significant variations in the ratios of DEHP metabolites indicated that the efficiency in metabolizing DEHP declined during pregnancy and less recent exposure occurred in mid-pregnancy. The changes of percentages of individual compound in total phthalates suggested the inconsistent pattern over trimesters. This longitudinal study found that the exposure pattern, exposure timing and metabolic susceptibility varied by trimesters, which suggests that urine samples should be collected at multiple time points and mothers should be especially careful in the early pregnancy.

Mass spectrometry-based metabolomics: Targeting the crosstalk between gut microbiota and brain in neurodegenerative disorders

Metabolomics seeks to take a "snapshot" in a time of the levels, activities, regulation and interactions of all small molecule metabolites in response to a biological system with genetic or environmental changes. The emerging development in mass spectrometry technologies has shown promise in the discovery and quantitation of neuroactive small molecule metabolites associated with gut microbiota and brain. Significant progress has been made recently in the characterization of intermediate role of small molecule metabolites linked to neural development and neurodegenerative disorder, showing its potential in understanding the crosstalk between gut microbiota and the host brain. More evidence reveals that small molecule metabolites may play a critical role in mediating microbial effects on neurotransmission and disease development. Mass spectrometry-based metabolomics is uniquely suitable for obtaining the metabolic signals in bidirectional communication between gut microbiota and brain. In this review, we summarized major mass spectrometry technologies including liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, and imaging mass spectrometry for metabolomics studies of neurodegenerative disorders. We also reviewed the recent advances in the identification of new metabolites by mass spectrometry and metabolic pathways involved in the connection of intestinal microbiota and brain. These metabolic pathways allowed the microbiota to impact the regular function of the brain, which can in turn affect the composition of microbiota via the neurotransmitter substances. The dysfunctional interaction of this crosstalk connects neurodegenerative diseases, including Parkinson's disease, Alzheimer's disease and Huntington's disease. The mass spectrometry-based metabolomics analysis provides information for targeting dysfunctional pathways of small molecule metabolites in the development of the neurodegenerative diseases, which may be valuable for the investigation of underlying mechanism of therapeutic strategies.

Large-Scale Longitudinal Metabolomics Study Reveals Different Trimester-Specific Alterations of Metabolites in Relation to Gestational Diabetes Mellitus

Despite the increasing research attention paid to gestational diabetes mellitus (GDM) due to its high prevalence, limited knowledge is available about its pathogenesis. In this study, 428 serum samples were collected from 107 pregnant women suffering from GDM and 107 matched healthy controls. The nontargeted metabolomics data of maternal serum samples from the first (T1, n = 214) and second trimesters (T2, n = 214) were acquired by using ultrahigh performance liquid chromatography coupled with Orbitrap mass spectrometry (MS). A total of 93 differential metabolites were identified on the basis of the accurate mass and MS/MS fragmentation. After false discovery rate correction, the levels of 31 metabolites in GDM group were significantly altered in the first trimester. The differential metabolites were mainly attributed to purine metabolism, fatty acid β-oxidation, urea cycle, and tricarboxylic acid cycle pathways. The fold changes across pregnancy (T2/T1) of six amino acids (serine, proline, leucine/isoleucine, glutamic acid, tyrosine, and ornithine), a lysophosphatidylcholine (LysoPC(20:4)), and uric acid in GDM group were significantly different from those in the control groups, suggesting that these 8 metabolites might have contributed to the occurrence and progression of GDM. The findings revealed that the amino acid metabolism, lipid metabolism, and other pathways might be disturbed prior to GDM onset and during the period from the first to the second trimester of pregnancy.

PCI-GC-MS-MS approach for identification of non-amino organic acid and amino acid profiles

Alkyl chloroformate have been wildly used for the fast derivatization of metabolites with amino and/or carboxyl groups, coupling of powerful separation and detection systems, such as GC-MS, which allows the comprehensive analysis of non-amino organic acids and amino acids. The reagents involving n-alkyl chloroformate and n-alcohol are generally employed for providing symmetric labeling terminal alkyl chain with the same length. Here, we developed an asymmetric labeling strategy and positive chemical ionization gas chromatography-tandem mass spectrometry (PCI-GC-MS-MS) approach for determination of non-amino organic acids and amino acids, as well as the short chain fatty acids. Carboxylic and amino groups could be selectively labelled by propyl and ethyl groups, respectively. The specific neutral loss of C₃H₈O (60Da), C₃H₅O₂ (74Da) and C₄H₈O₂ (88Da) were useful in the selective identification for qualitative analysis of organic acids and amino acid derivatives. PCI-GC-MS-MS using multiple reaction monitoring (MRM) was applied for semi-quantification of typical non-amino organic acids and amino acids. This method exhibited a wide range of linear range, good regression coefficient (R²) and repeatability. The relative standard deviation (RSD) of targeted metabolites showed excellent intra- and inter-day precision (<5%). Our method provided a qualitative and semi-quantitative PCI-GC-MS-MS, coupled with alkyl chloroformate derivatization.

Matrix-assisted laser desorption/ionization mass spectrometry imaging of cell cultures for the lipidomic analysis of potential lipid markers in human breast cancer invasion

RATIONALE

Breast cancer is the leading cause of cancer death among women worldwide. Identification of lipid targets that play a role in breast cancer invasion may advance our understanding of the rapid progression of cancer and may lead to the development of new biomarkers for the disease.

METHODS

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) was applied for the lipidomic profiling of two poorly invasive and two highly invasive breast cancer cell lines to identify the differentially accumulated lipids related to the invasive phenotype. The four cell lines were individually grown on indium tin oxide (ITO)-coated glass slides, analyzed as cell cultures. The raster width and matrix for detection were optimized to improve detection sensitivity.

RESULTS

Optimized MSI measurements were performed directly on the cell culture with 9-aminoacridine as matrix, resulting in 215 endogenous compounds detected in positive ion mode and 267 endogenous compounds in negative ion mode in all the four cell lines, representing the largest group of analytes that have been analyzed from cells by a single MSI study. In highly invasive cell lines, 31 lipids including phosphatidylglycerol (PG) and phosphatidic acids were found upregulated and eight lipids including sphingomyelin (SM) downregulated in negative ion mode. The products of de novo fatty acid synthesis incorporated into membrane phospholipids, like oleic-acid-containing PG, may be involved in mitochondrial dysfunction and thus affect the invasion of breast cancer cells. The deficiency of SM may be related to the disruption of apoptosis in highly invasive cancer cells.

CONCLUSIONS

This work uncovered more analytes in cells by MSI than previous reports, providing a better visualization and novel insights to advance our understanding of the relationship between rapid progression of breast cancer and lipid metabolism. The most altered lipids may aid the discovery of diagnostic markers and therapeutic targets of breast cancer.

Cardioprotection against experimental myocardial ischemic injury using cornin

Phosphorylated-cyclic adenosine monophosphate response element-binding protein (Phospho-CREB) has an important role in the pathogenesis of myocardial ischemia. We isolated the iridoid glycoside cornin from the fruit of Verbena officinalis L, investigated its effects against myocardial ischemia and reperfusion (I/R) injury in vivo, and elucidated its potential mechanism in vitro. Effects of cornin on cell viability, as well as expression of phospho-CREB and phospho-Akt in hypoxic H9c2 cells in vitro, and myocardial I/R injury in vivo, were investigated. Cornin attenuated hypoxia-induced cytotoxicity significantly in H9c2 cells in a concentration-dependent manner. Treatment of H9c2 cells with cornin (10 µM) blocked the reduction of expression of phospho-CREB and phospho-Akt in a hypoxic condition. Treatment of rats with cornin (30 mg/kg, iv) protected them from myocardial I/R injury as indicated by a decrease in infarct volume, improvement in hemodynamics, and reduction of severity of myocardial damage. Cornin treatment also attenuated the reduction of expression of phospho-CREB and phospho-Akt in ischemic myocardial tissue. These data suggest that cornin exerts protective effects due to an increase in expression of phospho-CREB and phospho-Akt.

Comprehensive urinary metabolomic profiling and identification of potential noninvasive marker for idiopathic Parkinson's disease

Urine metabolic phenotyping has been associated with the development of Parkinson’s disease (PD). However, few studies using a comprehensive metabolomics approach have investigated the correlation between changes in the urinary markers and the progression of clinical symptoms in PD. A comprehensive metabolomic study with robust quality control procedures was performed using gas chromatography - mass spectrometry (GC - MS) and liquid chromatography - mass spectrometry (LC - MS) to characterize the urinary metabolic phenotypes of idiopathic PD patients at three stages (early, middle and advanced) and normal control subjects, with the aim of discovering potential urinary metabolite markers for the diagnosis of idiopathic PD. Both GC-MS and LC-MS metabolic profiles of idiopathic PD patients differed significantly from those of normal control subjects. 18 differentially expressed metabolites were identified as constituting a unique metabolic marker associated with the progression of idiopathic PD. Related metabolic pathway variations were observed in branched chain amino acid metabolism, glycine derivation, steroid hormone biosynthesis, tryptophan metabolism, and phenylalanine metabolism. Comprehensive, successive metabolomic profiling revealed changes in the urinary markers associated with progression of idiopathic PD. This profiling relies on noninvasive sampling, and is complementary to existing clinical modalities.

Non-targeted metabolomics and lipidomics LC-MS data from maternal plasma of 180 healthy pregnant women

Background

Metabolomics has the potential to be a powerful and sensitive approach for investigating the low molecular weight metabolite profiles present in maternal fluids and their role in pregnancy.

Findings

In this Data Note, LC–MS metabolome, lipidome and carnitine profiling data were collected from 180 healthy pregnant women, representing six time points spanning all three trimesters, and providing sufficient coverage to model the progression of normal pregnancy.

Conclusions

As a relatively large scale, real-world dataset with robust numbers of quality control samples, the data are expected to prove useful for algorithm optimization and development, with the potential to augment studies into abnormal pregnancy. All data and ISA-TAB format enriched metadata are available for download in the MetaboLights and GigaScience databases.

Electronic supplementary material

The online version of this article (doi:10.1186/s13742-015-0054-9) contains supplementary material, which is available to authorized users.

Discrimination of sepsis stage metabolic profiles with an LC/MS-MS-based metabolomics approach

Background

To identify metabolic biomarkers that can be used to differentiate sepsis from systemic inflammatory response syndrome (SIRS), assess severity and predict outcomes.

Methods

65 patients were involved in this study, including 35 patients with sepsis, 15 patients with SIRS and 15 normal patients. Small metabolites that were present in patient serum samples were measured by liquid chromatography mass spectrometry techniques and analysed using multivariate statistical methods.

Results

The metabolic profiling of normal patients and patients with SIRS or sepsis was markedly different. A significant decrease in the levels of lactitol dehydrate and S-phenyl-d-cysteine and an increase in the levels of S-(3-methylbutanoyl)-dihydrolipoamide-E and N-nonanoyl glycine were observed in patients with sepsis in comparison to patients with SIRS (p<0.05). Patients with severe sepsis and septic shock displayed lower levels of glyceryl-phosphoryl-ethanolamine, Ne, Ne dimethyllysine, phenylacetamide and d-cysteine (p<0.05) in their sera. The profiles of patients with sepsis 48 h before death illustrated an obvious state of metabolic disorder, such that S-(3-methylbutanoyl)-dihydrolipoamide-E, phosphatidylglycerol (22:2 (13Z, 16Z)/0:0), glycerophosphocholine and S-succinyl glutathione were significantly decreased (p<0.05). The receiver operating characteristic curve of the differential expression of these metabolites was also performed.

Conclusions

The body produces significant evidence of metabolic disorder during SIRS or sepsis. Seven metabolites may potentially be used to diagnose sepsis.

Trial registration number

ClinicalTrial.gov identifier NCT01649440.

LC-MS-based urinary metabolite signatures in idiopathic Parkinson's disease

Increasing evidence has shown that abnormal metabolic phenotypes in body fluids reflect the pathogenesis and pathophysiology of Parkinson's disease (PD). These body fluids include urine; however, the relationship between, specifically, urinary metabolic phenotypes and PD is not fully understood. In this study, urinary metabolites from a total of 401 clinical urine samples collected from 106 idiopathic PD patients and 104 normal control subjects were profiled by using high-performance liquid chromatography coupled to high-resolution mass spectrometry. Our study revealed significant correlation between clinical phenotype and urinary metabolite profile. Metabolic profiles of idiopathic PD patients differed significantly and consistently from normal controls, with related metabolic pathway variations observed in steroidogenesis, fatty acid beta-oxidation, histidine metabolism, phenylalanine metabolism, tryptophan metabolism, nucleotide metabolism, and tyrosine metabolism. In the fruit fly Drosophila melanogaster, the alteration of the kynurenine pathway in tryptophan metabolism corresponded with pathogenic changes in the alpha-synuclein overexpressed Drosophila model of PD. The results suggest that LC-MS-based urinary metabolomic profiling can reveal the metabolite signatures and related variations in metabolic pathways that characterize PD. Consistent PD-related changes across species may provide the basis for understanding metabolic regulation of PD at the molecular level.

Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

As an economic crop, pepper satisfies people's spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded ∼0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of ∼81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs.

Pregnancy-induced metabolic phenotype variations in maternal plasma

Metabolic variations occur during normal pregnancy to provide the growing fetus with a supply of nutrients required for its development and to ensure the health of the woman during gestation. Mass spectrometry-based metabolomics was employed to study the metabolic phenotype variations in the maternal plasma that are induced by pregnancy in each of its three trimesters. Nontargeted metabolomics analysis showed that pregnancy significantly altered the profile of metabolites in maternal plasma. The levels of six metabolites were found to change significantly throughout pregnancy, with related metabolic pathway variations observed in biopterin metabolism, phospholipid metabolism, amino acid derivatives, and fatty acid oxidation. In particular, there was a pronounced elevation of dihydrobiopterin (BH₂), a compound produced in the synthesis of dopa, dopamine, norepinephrine, and epinephrine, in the second trimester, whereas it was markedly decreased in the third trimester. The turnover of BH₂ and tryptophan catabolites indicated that the fluctuations of neurotransmitters throughout pregnancy might reveal the metabolic adaption in the maternal body for the growth of the fetus. Furthermore, 11 lipid classes and 41 carnitine species were also determined and this showed variations in the presence of long-chain acylcarnitines and lysophospholipids in later pregnancy, suggesting changes of acylcarnitines and lysophospholipids to meet the energy demands in pregnant women. To our knowledge, this work is the first report of dynamic metabolic signatures and proposed related metabolic pathways in the maternal plasma for normal pregnancies and provided the basis for time-dependent metabolic trajectory against which disease-related disorders may be contrasted.

Genome-wide transcriptome and antioxidant analyses on gamma-irradiated phases of deinococcus radiodurans R1

Adaptation of D. radiodurans cells to extreme irradiation environments requires dynamic interactions between gene expression and metabolic regulatory networks, but studies typically address only a single layer of regulation during the recovery period after irradiation. Dynamic transcriptome analysis of D. radiodurans cells using strand-specific RNA sequencing (ssRNA-seq), combined with LC-MS based metabolite analysis, allowed an estimate of the immediate expression pattern of genes and antioxidants in response to irradiation. Transcriptome dynamics were examined in cells by ssRNA-seq covering its predicted genes. Of the 144 non-coding RNAs that were annotated, 49 of these were transfer RNAs and 95 were putative novel antisense RNAs. Genes differentially expressed during irradiation and recovery included those involved in DNA repair, degradation of damaged proteins and tricarboxylic acid (TCA) cycle metabolism. The knockout mutant crtB (phytoene synthase gene) was unable to produce carotenoids, and exhibited a decreased survival rate after irradiation, suggesting a role for these pigments in radiation resistance. Network components identified in this study, including repair and metabolic genes and antioxidants, provided new insights into the complex mechanism of radiation resistance in D. radiodurans.

Serum metabolomics reveals lipid metabolism variation between coronary artery disease and congestive heart failure: a pilot study

The aim of this pilot study is to find discriminating signals from the patient's congestive heart failure (HF) caused by coronary artery disease (CAD) through a non-target metabolomics method and test their usefulness in progress of human HF diseases. Multivariate data analysis was used to identify the discriminating signals. Interestingly, 12 metabolites contributing to the complete separation of HF from matched CAD were identified. Metabolic pathways including free fatty acids, sphingolipids and amino acid derivatives were found to be disturbed in HF patients compared with CAD patients. Lipid molecules associated with energy metabolism and signaling pathways may play key roles in the development of failing heart.

Vascular endothelial growth factor gene polymorphisms and colorectal cancer risk: a meta-analysis

Vascular endothelial growth factor (VEGF) is an endothelial cell-specific mitogen involved in a number of pathologic processes, including angiogenesis, tumor growth and metastasis. Polymorphisms of the VEGF gene have been associated with susceptibility to colorectal cancer (CRC). However, the specific association still remains controversial. We made a meta-analysis of the association between VEGF gene polymorphisms and CRC risk. Only eight case-control studies were retrieved, with a total of 2337 CRC patients and 2032 healthy controls. Six VEGF gene polymorphisms were addressed in all studies included, +936C>T (rs3025039), -2578C>A (rs699947), -1154G>A (rs1570360), -634G>C (rs2010963), -460C>T (rs833061), and +405C>G (rs2010963). There was a significant association between -2578C>A polymorphism and susceptibility to CRC in the comparison of C allele carriers (CC + CA) versus AA (odds ratio = 0.77, 95% confidence interval = 0.62-0.96, P = 0.02). No association was found between +936C>T, -1154G>A, -634G>C, -460C>T, and +405C>G with susceptibility to CRC. We conclude that the C allele carrier (CC + CA) of VEGF -2578C>A polymorphism appears to be a protective factor for CRC.

Head movements produced during linear translations in unexpected directions

Passive translation of the body in space elicits a complex combination of directionally-specific torques that are exerted on the neck. The inertial torques that are produced by linear translation are counteracted by linear vestibular and proprioceptive reflexes that maintain head stability. A novel experimental apparatus was used in this study to translate human subjects in a random and unpredictable direction in order to quantify the head's 3-D movement with respect to the direction of translation. Head movements were found to be produced in systematic patterns as a function of stimulus direction. Roll and yaw head movements were produced in proportion to the magnitude of the lateral component of the translation. Pitch head movements were proportionate to the magnitude of the fore-aft component of the translation. One surprising observation was that head movements produced during lateral translations were, on average, 17% smaller than those produced during fore-aft translations. This suggests that linear vestibular reflexes that stabilize the head may be directionally-specific and more active during lateral whole body translations.

Current concepts of vestibular nucleus function: transformation of vestibular signals in the vestibular nuclei

The vestibular nerve sends signals to the brain that code the movement and position of the head in space. These signals are used for a variety of functions, including the control of reflex and voluntary movements and the construction of a sense of self-motion. In order to carry out these functions, sensory vestibular signals need to be transformed in a variety of ways. Transformations are thought to occur at an early stage of sensory processing in the brain, and in many cases are apparent in the responses of neurons in the vestibular nuclei that receive direct inputs from the vestibular nerve. Several specific examples of sensory transformation in the vestibular nuclei are presented, and current hypotheses about the mechanisms that are used to produce the transformations are discussed.

Difference between horizontal and vertical optokinetic nystagmus in cats at upright position

The slow-phase velocity (SPV) of optokinetic nystagmus (OKN) and optokinetic after nystagmus (OKAN) in response to a velocity step of surround rotation in the horizontal direction is composed of the rapid and slow components in the cat: a rapid rise, a slow rise to a steady state, a rapid fall, and a slow decline to 0 deg/s. The rapid and slow components are attributed to the direct pathway and velocity storage neuronal mechanisms, respectively. The difference between horizontal and vertical OKN has been reported in the monkey at the upright position, but the slow and rapid components have not been distinguished. The present study compared horizontal OKN-OKAN with vertical OKN-OKAN in the cat at the upright position, distinguishing the rapid and slow components. Constant velocity rotation of a random dot pattern at a velocity of 5 to 160 deg/s was used for optokinetic stimulation.

THE RESULTS

First, the amplitude of the rapid rise was relatively small in all SPV directions and all stimulus velocities investigated, with a slight upward-SPV preference to the downward-SPV (maximum 6.4, 6.0, and 3.4 deg/s in horizontal, upward, and downward SPV directions, respectively). Second, the steady state velocity was large during horizontal OKN (maximum 69.0 deg/s), small during upward-SPV OKN (12.9 deg/s), and missing (SPV is negligibly small and irregular) during downward-SPV OKN, indicating a large directional difference of OKN. Third, the acceleration of the slow rise decreased with the stimulus velocity at higher stimulus velocities >20 deg/s during both horizontal and upward-SPV OKN, suggesting strong nonlinearity in the velocity charge system. Fourth, the decay time course of the OKAN was described by the time constant of the exponential function, and the time constant was longer during horizontal (mean, 8.3 s at a stimulus velocity of 20 deg/s) than during upward-SPV (5.4 s) OKAN, suggesting that the velocity discharge system is relatively linear compared with the velocity charge system. It is concluded that horizontal OKN-OKAN is much larger than vertical OKN-OKAN in the cat at the upright position, and this directional difference is caused mainly by the directional difference in the velocity storage mechanism, but not in the direct pathway mechanism.

Hemolysis of 40% hematocrit, Albunex-supplemented human erythrocytes by pulsed ultrasound: frequency, acoustic pressure and pulse length dependence

The dependence of hemolysis produced by pulsed ultrasound on ultrasound frequency, acoustic pressure and pulse length was explored. Human erythrocytes (40% hematocrit; in Albunex-supplemented autologous plasma) were exposed (60 s) to 20 or 200 microns pulses of ultrasound at frequencies of 1.02, 2.24 or 3.46 MHz and at peak negative pressures [P-] ranging from 0.0 to approximately 3.0 MPa in 0.5 MPa increments. The duty factor was 0.01. At each frequency, hemolysis increased with increasing acoustic pressure and depended weakly on pulse duration. At relatively high acoustic pressures, hemolysis depended strongly on ultrasound frequency; at lower pressures, the frequency dependence was weaker. The potential clinical significance of ultrasonic hemolysis is discussed.

Spontaneous malignant transformation of fibrous dysplasia

OBJECTIVE

To evaluate the clinical and radiological findings in diagnosing spontaneous malignant transformation of fibrous dysplasia.

METHODS

Fifteen cases of sarcomatous transformation proved by operation and pathological examinations were found in a group of 356 patients with fibrous dysplasia, and their radiological manifestations were retrospectively studied. The 15 cases included 8 osteosarcomas, 5 fibrosarcomas and 2 chondrosarcomas. All the 15 patients were known to have long-standing fibrous dysplasia, but no radiation therapy was ever received. Eleven patients had polyostotic fibrous dysplasia and 4 had monostotic type.

RESULTS

Malignant transformation most frequently occurs in the cystic expansive lesion of the long tubular bone. Pains, swelling and late appearance of a bony mass are the main clinical manifestations. The early radiological features of sarcomatous transformation in fibrous dysplasia are moth-eaten or cystic areas of osteolysis located in the involved bone. The cortical destruction and gradual formation of a soft tissue mass that contains tumor-bone are highly suspicious of osteosarcomatous transformation, while ring-like and spotty calcification in the tumor matrix is indicative of chondrosarcoma. Fibrosarcoma usually shows simple osteolytic destruction.

CONCLUSIONS

According to the clinical radiological findings, patients of sarcomatous transformation can be detected in the early stage. These radiological findings may be used as a clue for differentiating various kinds of sarcomatous transformation.