Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

PubMed
NCBI: db=pubmed; Term=metabolomics
Updated: 1 hour 45 min ago

Breast cancer risk in relation to plasma metabolites among Hispanic and African American women.

Sun, 17/02/2019 - 12:31
Breast cancer risk in relation to plasma metabolites among Hispanic and African American women. Breast Cancer Res Treat. 2019 Feb 15;: Authors: Zhao H, Shen J, Moore SC, Ye Y, Wu X, Zanetti KA, Esteva FJ, Tripathy D, Chow WH Abstract PURPOSE: The metabolic etiology of breast cancer has been explored in the past several years using metabolomics. However, most of these studies only included non-Hispanic White individuals. METHODS: To fill this gap, we performed a two-step (discovery and validation) metabolomics profiling in plasma samples from 358 breast cancer patients and 138 healthy controls. All study subjects were either Hispanics or non-Hispanic African Americans. RESULTS: A panel of 14 identified metabolites significantly differed between breast cancer cases and healthy controls in both the discovery and validation sets. Most of these identified metabolites were lipids. In the pathway analysis, citrate cycle (TCA cycle), arginine and proline metabolism, and linoleic acid metabolism pathways were observed, and they significantly differed between breast cancer cases and healthy controls in both sets. From those 14 metabolites, we selected 9 non-correlated metabolites to generate a metabolic risk score. Increased metabolites risk score was associated with a 1.87- and 1.63-fold increased risk of breast cancer in the discovery and validation sets, respectively (Odds ratio (OR) 1.87, 95% Confidence interval (CI) 1.50, 2.32; OR 1.63, 95% CI 1.36, 1.95). CONCLUSIONS: In summary, our study identified metabolic profiles and pathways that significantly differed between breast cancer cases and healthy controls in Hispanic or non-Hispanic African American women. The results from our study might provide new insights on the metabolic etiology of breast cancer. PMID: 30771047 [PubMed - as supplied by publisher]

Identification Potential Plasma Biomarkers and Metabolic Dysfunction for Unstable Angina Pectoris and Its Complication based on Global Metabolomics.

Sun, 17/02/2019 - 12:31
Related Articles Identification Potential Plasma Biomarkers and Metabolic Dysfunction for Unstable Angina Pectoris and Its Complication based on Global Metabolomics. Biosci Rep. 2019 Feb 15;: Authors: Wang J, Xu W, Zhao H, Chen J, Zhu B, Li X, Deng D, Wang J, Liu J, Yu Y, Xiao H, Wang W Abstract Unstable angina pectoris (UA) is one of the most dangerous clinical symptoms of acute coronary syndrome due to the risk of myocardial ischemia, which can lead to high morbidity and mortality worldwide. Though there are many advantages in understanding the pathophysiology of UA, the identification of biomarkers for the diagnosis, prognosis, and treatment of UA remains a challenge in the clinic. A global metabolomics research based on ultra performance liquid chromatography (UPLC) combined with time of flight mass spectrometry (Q-TOF/MS) was performed to discover the metabolic profile of health controls, UA patients, and UA patients with diabetes mellitus (DM), and screen for potential biomarkers. Twenty-seven potential biomarkers were determined using pattern recognition. These biomarkers, which include free fatty acids, amino acids, lysoPE and lysoPC species, and organic acids, can benefit the clinical diagnosis of UA. Pathway analysis indicated that arginine and proline metabolism, glycerophospholipid metabolism, and purine metabolism were affected in the UA patients, uniquely. Additionally, alterations in the metabolic signatures between UA and UA complicated diabetes mellitus (DM) were also explored. As a result, six differential metabolites with an area under the curve (AUC) of more than 0.85 were identified as biomarkers for the diagnosis of UA and UA complicated with DM. Pathway analysis implied tryptophan metabolism was a key metabolic pathway in UA patients with DM, which provides new insights into the pathological study and drug discovery of UA. PMID: 30770400 [PubMed - as supplied by publisher]

Metabolomics Approaches for the Diagnosis and Understanding of Kidney Diseases.

Sun, 17/02/2019 - 12:31
Related Articles Metabolomics Approaches for the Diagnosis and Understanding of Kidney Diseases. Metabolites. 2019 Feb 14;9(2): Authors: Abbiss H, Maker GL, Trengove RD Abstract Diseases of the kidney are difficult to diagnose and treat. This review summarises the definition, cause, epidemiology and treatment of some of these diseases including chronic kidney disease, diabetic nephropathy, acute kidney injury, kidney cancer, kidney transplantation and polycystic kidney diseases. Numerous studies have adopted a metabolomics approach to uncover new small molecule biomarkers of kidney diseases to improve specificity and sensitivity of diagnosis and to uncover biochemical mechanisms that may elucidate the cause and progression of these diseases. This work includes a description of mass spectrometry-based metabolomics approaches, including some of the currently available tools, and emphasises findings from metabolomics studies of kidney diseases. We have included a varied selection of studies (disease, model, sample number, analytical platform) and focused on metabolites which were commonly reported as discriminating features between kidney disease and a control. These metabolites are likely to be robust indicators of kidney disease processes, and therefore potential biomarkers, warranting further investigation. PMID: 30769897 [PubMed]

Identification of Key Aroma Compounds in Type I Sourdough-Based Chinese Steamed Bread: Application of Untargeted Metabolomics Analysisp.

Sun, 17/02/2019 - 12:31
Related Articles Identification of Key Aroma Compounds in Type I Sourdough-Based Chinese Steamed Bread: Application of Untargeted Metabolomics Analysisp. Int J Mol Sci. 2019 Feb 14;20(4): Authors: Yan B, Sadiq FA, Cai Y, Fan D, Zhang H, Zhao J, Chen W Abstract Untargeted metabolomics is a valuable tool to analyze metabolite profiles or aroma fingerprints of different food products. However, less attention has been paid to determining the aroma characteristics of Chinese steamed breads (CSBs) by using this approach. The aim of this work was to evaluate the key aroma compounds and their potential generation pathway in Chinese steamed bread produced with type I sourdough by a metabolomics approach. Based on the aroma characteristics analysis, CSBs produced with type I sourdough and baker's yeast were clearly distinguishable by principal component analysis (PCA) scores plot. A total of 13 compounds in sourdough-based steamed breads were given the status of discriminant markers through the untargeted metabolomics analysis. According to the odor activity values (OAVs) of discriminant aroma markers, ethyl acetate (fruity), ethyl lactate (caramel-like), hexyl acetate (fruity), (E)-2-nonenal (fatty) and 2-pentylfuran (fruity) were validated as the key volatile compounds in the breads produced with type I sourdough as compared to the baker's yeast leavened steamed bread. The metabolite analysis in proofed dough indicated that esters are mainly generated by the reaction between acid and alcohol during steaming, and aldehydes are derived from the oxidation of palmitoleic acid and linoleic acid during proofing and steaming. PMID: 30769815 [PubMed - in process]

Greek Graviera Cheese Assessment through Elemental Metabolomics-Implications for Authentication, Safety and Nutrition.

Sun, 17/02/2019 - 12:31
Related Articles Greek Graviera Cheese Assessment through Elemental Metabolomics-Implications for Authentication, Safety and Nutrition. Molecules. 2019 Feb 14;24(4): Authors: Danezis G, Theodorou C, Massouras T, Zoidis E, Hadjigeorgiou I, Georgiou CA Abstract This study presents the comprehensive elemental profile of Greek Graviera (Gruyère) cheeses. In total, 105 samples from nine different geographic regions produced from sheep, goat and cow milk and their mixtures were assessed. Elemental signatures of 61 elements were investigated for determination of geographic origin and milk type. Regional and milk type classification through Linear Discriminant Analysis was successful for almost all cases, while a less optimistic cross validation exercise presented lower classification rates. That points to further research using a much larger sample set, increasing confidence for cheese authentication utilizing also bioinformatics tools under development. This is the first study reporting signatures of 61 elements in dairy products including all sixteen rare earth elements and all seven precious metals. Safety and quality were assessed regarding toxic and nutritive elements. According to both EU and USA regulations and directives, Graviera is a nutritional source for trace and macro elements with low levels of toxic elements. PMID: 30769769 [PubMed - in process]

A strategy for validating concentrations of oxylipin standards for external calibration.

Sat, 16/02/2019 - 12:22
A strategy for validating concentrations of oxylipin standards for external calibration. Prostaglandins Other Lipid Mediat. 2019 Feb 12;: Authors: Hartung NM, Mainka M, Kampschulte N, Ostermann AI, Schebb NH Abstract Quantitative analysis of oxylipins by means of chromatography/mass spectrometry is based on (external) calibration with standard compounds. Therefore, the quality of analytical standards is of fundamental importance for accurate results. Recently launched certified standards with an assured concentration within a narrow range are useful tools for this purpose. However, such standards are only available for a few compounds. Based on the exemplary comparison of certified with none certified standards we suggest a tiered approach to validate and control the concentrations when preparing an external calibration based on non-certified oxylipin standards. Concentrations are evaluated by means of liquid chromatography negative electrospray ionization mass spectrometry (LC-ESI(-)-MS) in selected ion monitoring mode and UV spectroscopy (235 nm). Based on the suggested approach, more than 50% of the standards in our calibration mix could be validated. Though most of the non-certified standards are of good quality several oxylipin concentrations differ considerably demonstrating that a quality control strategy as suggested here is a mandatory prerequisite for quantitative oxylipin metabolomics. PMID: 30769102 [PubMed - as supplied by publisher]

Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors.

Sat, 16/02/2019 - 12:22
Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors. Elife. 2019 Feb 15;8: Authors: Shapiguzov A, Vainonen JP, Hunter K, Tossavainen H, Tiwari A, Järvi S, Hellman M, Aarabi F, Alseekh S, Wybouw B, Van Der Kelen K, Nikkanen L, Krasensky-Wrzaczek J, Sipari N, Keinänen M, Tyystjärvi E, Rintamäki E, De Rybel B, Salojärvi J, van Breusegem F, Fernie AR, Brosché M, Permi P, Aro EM, Wrzaczek M, Kangasjarvi J Abstract Reactive oxygen species (ROS)-dependent signaling pathways from chloroplasts and mitochondria merge at the nuclear protein RADICAL-INDUCED CELL DEATH1 (RCD1). RCD1 interacts in vivo and suppresses the activity of the transcription factors ANAC013 and ANAC017, which mediate a ROS-related retrograde signal originating from mitochondrial complex III. Inactivation of RCD1 leads to increased expression of mitochondrial dysfunction stimulon (MDS) genes regulated by ANAC013 and ANAC017. Accumulating MDS gene products, including alternative oxidases (AOXs), affect redox status of the chloroplasts, leading to changes in chloroplast ROS processing and increased protection of photosynthetic apparatus. ROS alter the abundance, thiol redox state and oligomerization of the RCD1 protein in vivo, providing feedback control on its function. RCD1-dependent regulation is linked to chloroplast signaling by 3'-phosphoadenosine 5'-phosphate (PAP). Thus, RCD1 integrates organellar signaling from chloroplasts and mitochondria to establish transcriptional control over the metabolic processes in both organelles. PMID: 30767893 [PubMed - as supplied by publisher]

Role of metabolomics in identification of biomarkers related to food intake.

Sat, 16/02/2019 - 12:22
Role of metabolomics in identification of biomarkers related to food intake. Proc Nutr Soc. 2019 Feb 15;:1-8 Authors: Collins C, McNamara AE, Brennan L Abstract Dietary assessment methods including FFQ and food diaries are associated with many measurement errors including energy under-reporting and incorrect estimation of portion sizes. Such errors can lead to inconsistent results especially when investigating the relationship between food intake and disease causation. To improve the classification of a person's dietary intake and therefore clarify proposed links between diet and disease, reliable and accurate dietary assessment methods are essential. Dietary biomarkers have emerged as a complementary approach to the traditional methods, and in recent years, metabolomics has developed as a key technology for the identification of new dietary biomarkers. The objective of this review is to give an overview of the approaches used for the identification of biomarkers and potential use of the biomarkers. Over the years, a number of strategies have emerged for the discovery of dietary biomarkers including acute and medium term interventions and cross-sectional/cohort study approaches. Examples of the different approaches will be presented. Concomitant with the focus on single biomarkers of specific foods, there is an interest in the development of biomarker signatures for the identification of dietary patterns. In the present review, we present an overview of the techniques used in food intake biomarker discover, including the experimental approaches used and challenges faced in the field. While significant progress has been achieved in the field of dietary biomarkers in recent years, a number of challenges remain. Addressing these challenges will be key to ensure success in implementing use of dietary biomarkers. PMID: 30767789 [PubMed - as supplied by publisher]

Metabolomic diagnostics and human digital image.

Sat, 16/02/2019 - 12:22
Metabolomic diagnostics and human digital image. Per Med. 2019 Feb 15;: Authors: Balashova EE, Lokhov PG, Ponomarenko EA, Markin SS, Lisitsa AV, Archakov AI Abstract The existing clinical laboratory practice has limitations in terms of specificity and sensitivity of diagnosis, making the introduction of new methods in medicine more topical. Application of 'omics' technologies, especially metabolomics, allows overcoming these limitations. The composition of blood metabolites reflects the physical state of an organism at the molecular level. The analysis of blood metabolome can serve as effective means of diagnosis, implementation of which in healthcare is timely and relevant. This paper demonstrates the versatility of metabolomic diagnostics, its applicability to various diseases. We discussed the standard of human digital image, which includes the metabolomic data sufficient to make an accurate assessment of general health and carry out precision diagnostics of a wide range of diseases. PMID: 30767631 [PubMed - as supplied by publisher]

Metabolic responses to potassium availability and waterlogging reshape respiration and carbon use efficiency in oil palm.

Sat, 16/02/2019 - 12:22
Related Articles Metabolic responses to potassium availability and waterlogging reshape respiration and carbon use efficiency in oil palm. New Phytol. 2019 Feb 15;: Authors: Cui J, Davanture M, Zivy M, Lamade E, Tcherkez G Abstract Oil palm is by far the major oil-producing crop at the global scale, with ≈62 Mt oil produced each year. This species is a strong potassium (K)-demanding species cultivated in regions where soil K availability is generally low and waterlogging due to tropical heavy rains can limit further nutrient absorption. However, the metabolic effects of K and waterlogging have never been assessed precisely. Here, we examined the metabolic response of oil palm saplings in the greenhouse under controlled conditions (nutrient composition with low or high K availability, with or without waterlogging), using gas exchange, metabolomics and proteomics analyses. Our results show that both low K and waterlogging have a detrimental effect on photosynthesis but stimulate leaf respiration, with differential accumulation of typical metabolic intermediates and enzymes of the Krebs cycle and alternative catabolic pathways. In addition, we found a strong relationship between metabolic composition, the rate of leaf dark respiration, and cumulated respiratory loss. Advert environmental conditions (here, low K and waterlogging) thus have an enormous impact on respiration in oil palm. Leaf metabolome and proteome appear to be good predictors of carbon balance, and open avenues for cultivation biomonitoring using functional genomics technologies. This article is protected by copyright. All rights reserved. PMID: 30767245 [PubMed - as supplied by publisher]

Pharmacometabolomic prediction of individual differences of gastrointestinal toxicity complicating myelosuppression in rats induced by irinotecan.

Sat, 16/02/2019 - 12:22
Related Articles Pharmacometabolomic prediction of individual differences of gastrointestinal toxicity complicating myelosuppression in rats induced by irinotecan. Acta Pharm Sin B. 2019 Jan;9(1):157-166 Authors: Gao Y, Li W, Chen J, Wang X, Lv Y, Huang Y, Zhang Z, Xu F Abstract Pharmacometabolomics has been already successfully used in toxicity prediction for one specific adverse effect. However in clinical practice, two or more different toxicities are always accompanied with each other, which puts forward new challenges for pharmacometabolomics. Gastrointestinal toxicity and myelosuppression are two major adverse effects induced by Irinotecan (CPT-11), and often show large individual differences. In the current study, a pharmacometabolomic study was performed to screen the exclusive biomarkers in predose serums which could predict late-onset diarrhea and myelosuppression of CPT-11 simultaneously. The severity and sensitivity differences in gastrointestinal toxicity and myelosuppression were judged by delayed-onset diarrhea symptoms, histopathology examination, relative cytokines and blood cell counts. Mass spectrometry-based non-targeted and targeted metabolomics were conducted in sequence to dissect metabolite signatures in predose serums. Eventually, two groups of metabolites were screened out as predictors for individual differences in late-onset diarrhea and myelosuppression using binary logistic regression, respectively. This result was compared with existing predictors and validated by another independent external validation set. Our study indicates the prediction of toxicity could be possible upon predose metabolic profile. Pharmacometabolomics can be a potentially useful tool for complicating toxicity prediction. Our findings also provide a new insight into CPT-11 precision medicine. PMID: 30766787 [PubMed]

Distinct Metabolic Endotype Mirroring Acute Respiratory Distress Syndrome (ARDS) Subphenotype and its Heterogeneous Biology.

Sat, 16/02/2019 - 12:22
Related Articles Distinct Metabolic Endotype Mirroring Acute Respiratory Distress Syndrome (ARDS) Subphenotype and its Heterogeneous Biology. Sci Rep. 2019 Feb 14;9(1):2108 Authors: Viswan A, Ghosh P, Gupta D, Azim A, Sinha N Abstract Predisposing aetiologies in Acute Respiratory Distress Syndrome (ARDS), perpetuates to heterogeneous clinical course hampering therapeutic response. Therefore, physiological variables need to be identified by stratifying ARDS subphenotypes and endotype, to target ARDS heterogeneity. The present study is stimulated by the fact that the ARDS heterogeneity arises from diverse pathophysiological changes leading to distinct ARDS endotypes characterized by perturbed biological mechanism which can be exploited in terms of metabolic profile by metabolomics. Biological endotypes using (n = 464 patients and controls), mBALF and serum samples were identified by high - resolution NMR spectroscopy from two clinically diagnosed ARDS subtypes grouped under mild, moderate and severe ARDS as subphenotype1and pulmonary and extra - pulmonary ARDS as subphenotype2. The identified mBALF endotypes (isoleucine, leucine, valine, lysine/arginine, tyrosine, threonine) and serum endotypes (proline, glutamate, phenylalanine, valine) in both subphenotypes by statistical analysis were tested for their reproducibility and robustness. By combining metabolic endotypes with clinical based mortality score (APACHE and SOFA) added to their predictive performance as ARDS mortality predictors. Thus, a comprehensive set of mBALF endotypes representing compartmentalized lung milieu and serological endotypes representing systemic markers of ARDS subtypes were validated. The interlinked biological pathway of these disease specific endotype further elucidated their role as candidate biomarker in governing ARDS heterogeneous biology. PMID: 30765824 [PubMed - in process]

Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development.

Sat, 16/02/2019 - 12:22
Related Articles Identification and profiling of narrow-leafed lupin (Lupinus angustifolius) microRNAs during seed development. BMC Genomics. 2019 Feb 14;20(1):135 Authors: DeBoer K, Melser S, Sperschneider J, Kamphuis LG, Garg G, Gao LL, Frick K, Singh KB Abstract BACKGROUND: Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin (Lupinus angustifolius) remains unknown. RESULTS: By conducting a genome- and transcriptome-wide survey we identified 7 Dicer-like and 16 Argonaute narrow-leafed lupin genes, which were highly homologous to their legume counterparts. We identified 43 conserved miRNAs belonging to 16 families, and 13 novel narrow-leafed lupin-specific miRNAs using high-throughput sequencing of small RNAs from foliar and root and five seed development stages. We observed up-regulation of members of the miRNA families miR167, miR399, miR156, miR319 and miR164 in narrow-leafed lupin seeds, and confirmed expression of miR156, miR166, miR164, miR1507 and miR396 using quantitative RT-PCR during five narrow-leafed lupin seed development stages. We identified potential targets for the conserved and novel miRNAs and were able to validate targets of miR399 and miR159 using 5' RLM-RACE. The conserved miRNAs are predicted to predominately target transcription factors and 93% of the conserved miRNAs originate from intergenic regions. In contrast, only 43% of the novel miRNAs originate from intergenic regions and their predicted targets were more functionally diverse. CONCLUSION: This study provides important insights into the miRNA gene regulatory networks during narrow-leafed lupin seed development. PMID: 30764773 [PubMed - in process]

Glycerol supports growth of the Trypanosoma brucei bloodstream forms in the absence of glucose: Analysis of metabolic adaptations on glycerol-rich conditions.

Sat, 16/02/2019 - 12:22
Related Articles Glycerol supports growth of the Trypanosoma brucei bloodstream forms in the absence of glucose: Analysis of metabolic adaptations on glycerol-rich conditions. PLoS Pathog. 2018 11;14(11):e1007412 Authors: Pineda E, Thonnus M, Mazet M, Mourier A, Cahoreau E, Kulyk H, Dupuy JW, Biran M, Masante C, Allmann S, Rivière L, Rotureau B, Portais JC, Bringaud F Abstract The bloodstream forms of Trypanosoma brucei (BSF), the parasite protist causing sleeping sickness, primarily proliferate in the blood of their mammalian hosts. The skin and adipose tissues were recently identified as additional major sites for parasite development. Glucose was the only carbon source known to be used by bloodstream trypanosomes to feed their central carbon metabolism, however, the metabolic behaviour of extravascular tissue-adapted parasites has not been addressed yet. Since the production of glycerol is an important primary function of adipocytes, we have adapted BSF trypanosomes to a glucose-depleted but glycerol-rich culture medium (CMM_Glyc/GlcNAc) and compared their metabolism and proteome to those of parasites grown in standard glucose-rich conditions (CMM_Glc). BSF were shown to consume 2-folds more oxygen per consumed carbon unit in CMM_Glyc/GlcNAc and were 11.5-times more sensitive to SHAM, a specific inhibitor of the plant-like alternative oxidase (TAO), which is the only mitochondrial terminal oxidase expressed in BSF. This is consistent with (i) the absolute requirement of the mitochondrial respiratory activity to convert glycerol into dihydroxyacetone phosphate, as deduced from the updated metabolic scheme and (ii) with the 1.8-fold increase of the TAO expression level compared to the presence of glucose. Proton NMR analysis of excreted end products from glycerol and glucose metabolism showed that these two carbon sources are metabolised through the same pathways, although the contributions of the acetate and succinate branches are more important in the presence of glycerol than glucose (10.2% versus 3.4% of the excreted end products, respectively). In addition, metabolomic analyses by mass spectrometry showed that, in the absence of glucose, 13C-labelled glycerol was incorporated into hexose phosphates through gluconeogenesis. As expected, RNAi-mediated down-regulation of glycerol kinase expression abolished glycerol metabolism and was lethal for BSF grown in CMM_Glyc/GlcNAc. Interestingly, BSF have adapted their metabolism to grow in CMM_Glyc/GlcNAc by concomitantly increasing their rate of glycerol consumption and decreasing that of glucose. However, the glycerol kinase activity was 7.8-fold lower in CMM_Glyc/GlcNAc, as confirmed by both western blotting and proteomic analyses. This suggests that the huge excess in glycerol kinase that is not absolutely required for glycerol metabolism, might be used for another yet undetermined non-essential function in glucose rich-conditions. Altogether, these data demonstrate that BSF trypanosomes are well-adapted to glycerol-rich conditions that could be encountered by the parasite in extravascular niches, such as the skin and adipose tissues. PMID: 30383867 [PubMed - indexed for MEDLINE]

Detailed Characterization of Monoclonal Antibody Receptor Interaction Using Affinity Liquid Chromatography Hyphenated to Native Mass Spectrometry.

Sat, 16/02/2019 - 12:22
Related Articles Detailed Characterization of Monoclonal Antibody Receptor Interaction Using Affinity Liquid Chromatography Hyphenated to Native Mass Spectrometry. Anal Chem. 2017 05 16;89(10):5404-5412 Authors: Gahoual R, Heidenreich AK, Somsen GW, Bulau P, Reusch D, Wuhrer M, Haberger M Abstract We report on the online coupling of FcRn affinity liquid chromatography (LC) with electrospray ionization mass spectrometry (ESI-MS) in native conditions to study the influence of modifications on the interaction of recombinant mAbs with the immobilized FcRn receptor domain. The analysis conditions were designed to fit the requirements of both affinity LC and ESI-MS. The mobile phase composition was optimized to maintain the proteins studied in native conditions and enable sharp pH changes in order to mimic properly IgGs Fc domain/FcRn receptor interaction. Mobile phase components needed to be sufficiently volatile to achieve native MS analysis. MS data demonstrated the conservation of the pseudonative form of IgGs and allowed identification of the separated variants. Native FcRn affinity LC-ESI-MS was performed on a therapeutic mAb undergoing various oxidation stress. Native MS detection was used to determine the sample oxidation level. Lower retention was observed for mAbs oxidized variants compared to their intact counterparts indicating decreased affinities for the receptor. This methodology proved to be suitable to identify and quantify post-translational modifications at native protein level in order to correlate their influence on the binding to the FcRn receptor. Native FcRn affinity LC-ESI-MS can tremendously reduce the time required to assess the biological relevance of the IgG microheterogeneities thus providing valuable information for biopharmaceutical research and development. PMID: 28398745 [PubMed - indexed for MEDLINE]

Biochemical, physiological and clinical effects of l-methylfolate in schizophrenia: a randomized controlled trial.

Sat, 16/02/2019 - 12:22
Related Articles Biochemical, physiological and clinical effects of l-methylfolate in schizophrenia: a randomized controlled trial. Mol Psychiatry. 2018 02;23(2):316-322 Authors: Roffman JL, Petruzzi LJ, Tanner AS, Brown HE, Eryilmaz H, Ho NF, Giegold M, Silverstein NJ, Bottiglieri T, Manoach DS, Smoller JW, Henderson DC, Goff DC Abstract Folic acid supplementation confers modest benefit in schizophrenia, but its effectiveness is influenced by common genetic variants in the folate pathway that hinder conversion to its active form. We examined physiological and clinical effects of l-methylfolate, the fully reduced and bioactive form of folate, in schizophrenia. In this randomized, double-blind trial, outpatients with schizophrenia (n=55) received l-methylfolate 15 mg or placebo for 12 weeks. Patients were maintained on stable doses of antipsychotic medications. The pre-defined primary outcome was change in plasma methylfolate at 12 weeks. Secondary outcomes included change in symptoms (Positive and Negative Syndrome Scale (PANSS), Scale for Assessment of Negative Symptoms, Calgary Depression Scale for Schizophrenia), cognition (Measurement and Treatment Research to Improve Cognition in Schizophrenia composite) and three complementary magnetic resonance imaging measures (working memory-related activation, resting connectivity, cortical thickness). Primary, mixed model, intent-to-treat analyses covaried for six genetic variants in the folate pathway previously associated with symptom severity and/or response to folate supplementation. Analyses were repeated without covariates to evaluate dependence on genotype. Compared with placebo, l-methylfolate increased plasma methylfolate levels (d=1.00, P=0.0009) and improved PANSS Total (d=0.61, P=0.03) as well as PANSS Negative and General Psychopathology subscales. Although PANSS Total and General Psychopathology changes were influenced by genotype, significant PANSS Negative changes occurred regardless of genotype. No treatment differences were seen in other symptom rating scales or cognitive composite scores. Patients receiving l-methylfolate exhibited convergent changes in ventromedial prefrontal physiology, including increased task-induced deactivation, altered limbic connectivity and increased cortical thickness. In conclusion, l-methylfolate supplementation was associated with salutary physiological changes and selective symptomatic improvement in this study of schizophrenia patients, warranting larger clinical trials. ClinicalTrials.gov, NCT01091506. PMID: 28289280 [PubMed - indexed for MEDLINE]

Integration of Metabolomics and Transcriptomics Reveals the Therapeutic Mechanism Underlying Paeoniflorin for the Treatment of Allergic Asthma.

Fri, 15/02/2019 - 15:03
Related Articles Integration of Metabolomics and Transcriptomics Reveals the Therapeutic Mechanism Underlying Paeoniflorin for the Treatment of Allergic Asthma. Front Pharmacol. 2018;9:1531 Authors: Shou Q, Jin L, Lang J, Shan Q, Ni Z, Cheng C, Li Q, Fu H, Cao G Abstract Objectives: Asthma is a chronic airway inflammatory disease, which is characterized by airway remodeling, hyperreactivity and shortness of breath. Paeoniflorin is one of the major active ingredients in Chinese peony, which exerts anti-inflammatory and immune-regulatory effects in multiple diseases. However, it remains unclear whether paeoniflorin treatment can suppress allergic asthma. Methods: In this study, we evaluated the effect of paeoniflorin on lung function and airway inflammation in asthmatic mice. These asthmatic Balb/c mice were first sensitized and constructed through ovalbumin (OVA) motivation. Subsequently, we determined the mechanism of action of paeoniflorin in treating allergic asthma through integrated transcriptomic and metabolomic data sets. Results: Our results demonstrated that many genes and metabolites were regulated in the paeoniflorin-treated mice. Moreover, the potential target proteins of paeoniflorin played important roles in fatty acid metabolism, inflammatory response, oxidative stress and local adhesion. Conclusion: Paeoniflorin has a beneficial effect on asthma, which may be achieved through regulating fatty acid metabolism, inflammatory response and the adhesion pathway at system level. PMID: 30761008 [PubMed]

Serum metabolomics model and its metabolic characteristics in patients with different syndromes of dyslipidemia based on nuclear magnetic resonance.

Fri, 15/02/2019 - 12:00
Serum metabolomics model and its metabolic characteristics in patients with different syndromes of dyslipidemia based on nuclear magnetic resonance. J Pharm Biomed Anal. 2019 Feb 04;167:100-113 Authors: Chen J, Ye C, Hu X, Huang C, Yang Z, Li P, Wu A, Xue X, Lin D, Yang H Abstract Dyslipidemia is known as a common clinical disease that affects the health of millions of people around the world. The treatment of dyslipidemia with traditional Chinese medicine (TCM) is generally based on the accurate identification of disease syndromes. TCM syndromes are judged by traditional four-diagnosis method, which is subjective and fuzzy. Additionally, the judgment of TCM syndromes highly depend on doctors' own clinical experience. In this present study, we used nuclear magnetic resonance (NMR)-based serum metabolomics patterns to figure out the metabolic characteristics of different syndromes in patients with dyslipidemia. In total, we enrolled 60 patients with dyslipidemia (30 cases with Spleen and Kidney Yang Deficiency syndrome (SKYD) and 30 cases with Phlegm-Dampness Retention syndrome (PDR)) and 20 healthy controls. Based on NMR technique, the serum metabolomics patterns of patients with different syndromes and healthy controls were analyzed, in the hope of screening the different metabolites among different syndromes and the differential metabolic pathway, as well as exploring the changes of metabolic network among different syndromes of dyslipidemia. The results suggested that the serum metabolomics patterns based on NMR was used to identify serum metabolites in patients with dyslipidemia of SKYD and PDR as well as healthy controls. Besides, it was found that the metabolic patterns of these three groups can be distinguished well and the different metabolites between different syndromes can be screened. From the point of view of metabolites, the metabolic characteristics of the patients with PDR were mainly the accumulation of noxious metabolites, while the metabolic characteristics of the patients with SKYD were mainly the lack of metabolites with protective function. From the point of view of metabolic mode, there were different metabolic patterns in patients with different syndromes of dyslipidemia in liver metabolism, oxidation, inflammatory reaction as well as energy metabolism, which reflects the difference of syndromes from different angles. The differences in metabolic outcomes among patients with different syndromes of dyslipidemia had a close association with to the effects of multiple signaling pathways. This study identified the characteristics of serum metabolic model of patients with different syndromes of dyslipidemia and the potential differential metabolites and characteristic metabolic characteristics of syndromes in order to understand the biological characteristics of patients with dyslipidemia of SKYD and PDR. PMID: 30763881 [PubMed - as supplied by publisher]

Development and application of a HILIC UHPLC-MS method for polar fecal metabolome profiling.

Fri, 15/02/2019 - 12:00
Development and application of a HILIC UHPLC-MS method for polar fecal metabolome profiling. J Chromatogr B Analyt Technol Biomed Life Sci. 2019 Feb 04;1109:142-148 Authors: Sillner N, Walker A, Harrieder EM, Schmitt-Kopplin P, Witting M Abstract The fecal metabolome is a complex mixture of endogenous, microbial metabolites, and food derived compounds. Hydrophilic interaction liquid chromatography (HILIC) enables the analysis of polar compounds, which is a valuable alternative to reversed-phase liquid chromatography in the field of metabolomics due to its ability to retain a greater portion of the polar metabolome. The objective of the study was to find the optimal chromatographic solution to perform non-targeted metabolomics of feces by means of HILIC ultra-high-pressure liquid chromatography mass spectrometry (UHPLC-Q-TOF-MS). The performance was systematically investigated analyzing a pooled fecal sample, and mixtures of 150 metabolites from different families, including for example amino acids, amines, indole derivatives, fatty acids and carbohydrates. Three different stationary phases (zwitterionic, amide and unbonded silica) were operated at three pH values (4.6, 6.8 and 9.0), and three salt gradient conditions (5-5, 5-10 and 5-25 mM ammonium acetate). Amide and zwitterionic stationary phases performed similarly at low pH, with highest number of detected standards, which increased by increasing the salt gradient. The amide column showed slightly better performance in terms of separation of isomers and peak widths and remarkably good performance at basic pH, with highest number of metabolite features in the non-targeted analysis. The zwitterionic column operated best in terms of number of detected standards, retention time distribution of standards and metabolite feature across whole chromatographic run. Thus, the zwitterionic column was proven to suit for non-targeted analysis of fecal samples, resulting in good coverage of especially amino acids and carbohydrates. PMID: 30763867 [PubMed - as supplied by publisher]

Progesterone alters the bovine uterine fluid lipidome during the period of elongation.

Fri, 15/02/2019 - 12:00
Progesterone alters the bovine uterine fluid lipidome during the period of elongation. Reproduction. 2019 Feb 01;: Authors: Simintiras C, Sanchez Gomez JM, McDonald M, Lonergan P Abstract Successful bovine pregnancy establishment hinges on conceptus elongation, a key reproductive phenomenon coinciding with the period during which most pregnancies fail. Elongation has yet to be recapitulated in vitro whereas in vivo it is directly driven by uterine secretions and indirectly influenced by prior circulating progesterone levels. To better understand the microenvironment evolved to facilitate this fundamental developmental event, uterine fluid was recovered on Days 12-14 of the estrous cycle - the window of conceptus elongation initiation - from cycling heifers supplemented, or not, with progesterone. Subsequent lipidomic profiling of uterine luminal fluid by advanced high-throughput metabolomics revealed the consistent presence of 75 metabolites, of which 47% were intricately linked to membrane biogenesis, and with seven displaying a day by progesterone interaction (p≤0.05). Eight metabolic pathways were correspondingly enriched according to day and P4 - i.e. comprised metabolites whose concentrations differed between groups (normal vs. high P4) at different times (Days 12 vs. 13 vs. 14). These were inositol, phospholipid, glycerolipid, and primary bile acid metabolism. Moreover, P4 elevated total uterine luminal fluid lipid content on Day 14 (p<0.0001) relative to all other comparisons. The data combined suggest that maternal lipid supply during the elongation-initiation window is primarily geared towards conceptus membrane biogenesis. PMID: 30763281 [PubMed - as supplied by publisher]

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