bims-metlip Biomed News
on Methods and protocols in metabolomics and lipidomics
Issue of 2019‒10‒20
23 papers selected by
Sofia Costa
Cold Spring Harbor Laboratory

  1. Anal Chem. 2019 Oct 18.
      In untargeted metabolomics, conventional data preprocessing software (e.g., XCMS, MZmine 2, MS-DIAL) are used extensively due to their high efficiency in metabolic feature extraction. However, these programs present limitations in recognizing low-abundance metabolic features, thus hindering complete metabolome coverage from the analysis. In this work, we explored the possibility of enhancing the metabolome coverage of data-dependent liquid chromatography-tandem mass spectrometry (LC-MS/MS) results by rescuing metabolic features that are missed by conventional software. To achieve this goal, we first categorized the metabolic features into four confidence levels based on their chromatographic peak shapes and the presence of corresponding MS/MS spectra. We then assessed the false positives and quantitative accuracy of the metabolic features that contain MS/MS spectra but are not recognized by conventional software. Our results indicate that these missed features contain valid and important metabolic information and should be integrated into the conventional metabolomics results. Thus, we developed a data-preprocessing pipeline to extract low-abundance metabolic features and integrate them with the results from conventional programs. This integrated feature extraction strategy was tested on a set of fecal metabolomic data retrieved from mice who have undergone normal diet vs. high-fat diet treatments. In our test dataset, the integrated feature extraction approach increased the number of significant features being extracted by 24.4% and identified five additional metabolites bearing critical biological meanings. Our results show that this integrated feature extraction strategy remarkably improves the metabolome coverage beyond that of conventional data preprocessing, therefore facilitating the confirmation of metabolites of interest and accomplishment of a higher success rate in de novo metabolite identification.
  2. J Pharm Biomed Anal. 2019 Oct 03. pii: S0731-7085(19)31365-2. [Epub ahead of print]178 112902
      Nucleoside reverse transcriptase inhibitors (NRTIs) are prodrugs that require intracellular phosphorylation to active triphosphate nucleotide metabolites (NMs) for their pharmacological activity. However, monitoring these pharmacologically active NMs is challenging due to their instability, high hydrophilicity, and their low concentrations in blood and tissues. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is the gold standard technique for the quantification of NRTIs and their phosphorylated NMs. In this review, an overview of the publications describing the quantitative analysis of intracellular and total tissue concentration of NMs is presented. The focus of this review is the comparison of the different approaches and challenges associated with sample collection, tissue homogenization, cell lysis, cell counting, analyte extraction, sample storage conditions, and LC-MS analysis. Quantification methods of NMs via LC-MS can be categorized into direct and indirect methods. In the direct LC-MS methods, chromatographic retention of the NMs is accomplished by ion-exchange (IEX), ion-pairing (IP), hydrophilic interaction (HILIC), porous graphitic carbon (PGC) chromatography, or capillary electrophoresis (CE). In indirect methods, parent nucleosides are 1st generated from the dephosphorylation of NMs during sample preparation and are then quantified by reverse phase LC-MS as surrogates for their corresponding NMs. Both approaches have advantages and disadvantages associated with them, which are discussed in this review.
    Keywords:  Direct quantification; Indirect quantification; LC–MS/MS; Nucleoside analogs; Nucleotide metabolites
  3. J Pharm Biomed Anal. 2019 Oct 04. pii: S0731-7085(19)31855-2. [Epub ahead of print]178 112912
      Cortisol (CRT), the main glucocorticoid in humans, plays a crucial role in many physiological processes, therefore, the measurement of its serum level is of great clinical significance. Matrix-assisted laser desorption/ionization-tandem mass spectrometry (MALDI-MS/MS) might be an effective approach for the quantification of CRT in serum due to its attractive properties, i.e., high specificity, ease of use, ruggedness and rapid analysis. In this study, we developed a method to quantify the serum CRT by MALDI-MS/MS. This method employed the derivatization using a Girard-type reagent, 1-(hydrazinocarbonylmethyl)isoquinolinium chloride, which compensated for the lack of sensitivity. This method enabled the reproducible quantification of the serum CRT using a 20-μL sample (intra- and inter-assay relative standard deviations, 7.4% or lower), and the measurable range was 25-500 ng/mL. The serum CRT concentrations determined by the newly-developed MALDI-MS/MS method agreed well with those by liquid chromatography/electrospray ionization-MS/MS or electrochemiluminescence immunoassay. The MALDI-MS/MS method was used for the analysis of peripheral venous serum samples of healthy subjects and adrenal venous serum samples of patients with primary aldosteronism, and satisfactory results were obtained.
    Keywords:  Cortisol; Derivatization; Girard-type reagent; Matrix assisted laser desorption/ionization-tandem mass spectrometry; Quantification
  4. Ther Drug Monit. 2019 Oct 14.
      BACKGROUND: The enantiomeric pharmacokinetics and metabolism of tramadol and its metabolites have not fully been understood. This study aimed to develop a reversed-phase mode liquid chromatography coupled to tandem mass spectrometry method for the enantiomeric quantitation of tramadol and its metabolites in human plasma, and to evaluate the stereoselective demethylation.METHODS: Racemic tramadol and its metabolites in plasma specimens were separated using a chiral selector coated with cellulose tris(3,5-dimethylphenylcarbamate) on silica gel under reversed-phase mode. The mass spectrometer ran in the positive ion multiple reaction monitoring mode. This method was performed to quantify plasma samples from 20 cancer patients treated with oral tramadol. The stereoselective demethylation was evaluated using recombinant cytochrome P450 (CYP) enzymes.
    RESULTS: The calibration curves of (+)- and (-)-tramadol, (+)- and (-)-O-desmethyltramadol (ODT), and (+)- and (-)-N-desmethyltramadol (NDT) were linear over the plasma concentration ranges of 6.25-800, 1.25-160, and 3.13-400 ng/mL for the respective enantiomers. In the present method, the intra- and inter-day accuracies and imprecisions were 94.2-108.3% and 0.5-6.0% for all analytes. The plasma concentrations of (+)-tramadol and NDT were higher than those of (-)-enantiomers. In contrast, no differences were observed between the plasma concentrations of (+)- and (-)-ODT. In the demethylation assay, the O-demethylations of tramadol and NDT by CYP2D6 were (-)-form-selective.
    CONCLUSIONS: The present method can be useful in the enantiomeric evaluation of tramadol and its metabolites in human plasma. Although CYP2D6 contributed to the stereoselective demethylation of tramadol, remarkable differences between (+)- and (-)-ODT were not observed in the plasma of the cancer patients.
  5. J Chromatogr A. 2019 Oct 04. pii: S0021-9673(19)31005-2. [Epub ahead of print] 460597
      The incorporation of ion mobility (IM) into LC-MS analysis has been demonstrated to result in the generation of superior quality MS and MS/MS spectral data as well as providing enhanced resolution in the IM dimension based on lipid class. Here a sub 4 min microbore LC-ion mobility-accurate mass MS (LC-IM-MS) method has been developed for the rapid, profiling of lipids in biological fluids. The method was scaled directly from a conventional, 12  min, LC-MS analysis maintaining the chromatographic performance and lipid separation observed in the longer methodology giving a 75% saving in mobile phase consumption and analysis time. Because of the additional dimension of separation provided by IM, improvements in mass spectral quality from the increased resolution of co-eluting species were also seen when compared to the same separation without IM, thus aiding the identification of target lipids. When applied to human plasma samples some 5037 (positive ESI) and 2020 (negative ESI) mass/retention time features were detected following adduct deconvolution and, of these, 3727 and 800 of those present in the pooled plasma QC samples had a CV of below 30% for positive and negative ESI modes respectively. The method was applied to the analysis of a pilot set of commercially sourced breast cancer plasma samples enabling the differentiation of samples from healthy controls and patients based on their lipid phenotypes. Analysis of the resulting data showed that phosphatidylcholines, triglycerides and diglycerides exhibited lower expression and phosphatidylserine showed increased expression in the breast cancer samples compared to those of healthy subjects. The coefficients of variation, determined by reference to the QC data, for all of the features identified as potential markers of disease, were 6% or less.
    Keywords:  Cancer; Ion mobility spectrometry; Lipidomics; Liquid chromatography; Mass spectrometry
  6. Mass Spectrom Rev. 2019 Oct 15.
      Metabolomics is a dynamically evolving field, with a major application in identifying biomarkers for drug development and personalized medicine. Numerous metabolomic studies have identified endogenous metabolites that, in principle, are eligible for translation to clinical practice. However, few metabolomic-derived biomarker candidates have been qualified by regulatory bodies for clinical applications. Such interruption in the biomarker qualification process can be largely attributed to various reasons including inappropriate study design and inadequate data to support the clinical utility of the biomarkers. In addition, the lack of robust assays for the routine quantification of candidate biomarkers has been suggested as a potential bottleneck in the biomarker qualification process. In fact, the nature of the endogenous metabolites precludes the application of the current validation guidelines for bioanalytical methods. As a result, there have been individual efforts in modifying existing guidelines and/or developing alternative approaches to facilitate method validation. In this review, three main challenges for method development and validation for endogenous metabolites are discussed, namely matrix effects evaluation, alternative analyte-free matrices, and the choice of internal standards (ISs). Some studies have modified the equations described by the European Medicines Agency for the evaluation of matrix effects. However, alternative strategies were also described; for instance, calibration curves can be generated in solvents and in biological samples and the slopes can be compared through ratios, relative standard deviation, or a modified Stufour suggested approaches while quantifying mainly endogenous metabolitesdent t-test. ISs, on the contrary, are diverse; in which seven different possible types, used in metabolomics-based studies, were identified in the literature. Each type has its advantages and limitations; however, isotope-labeled ISs and ISs created through isotope derivatization show superior performance. Finally, alternative matrices have been described and tested during method development and validation for the quantification of endogenous entities. These alternatives are discussed in detail, highlighting their advantages and shortcomings. The goal of this review is to compare, apprise, and debate current knowledge and practices in order to aid researchers and clinical scientists in developing robust assays needed during the qualification process of candidate metabolite biomarkers.
    Keywords:  LC-MS/MS; blank matrix; endogenous biomarkers; internal standards; metabolomics; validation
  7. Anal Chim Acta. 2019 Dec 11. pii: S0003-2670(19)30987-0. [Epub ahead of print]1088 99-106
      Mass spectrometry-based stable isotope labeling provides the advantages of multiplexing capability and accurate quantification but requires tailored bioinformatics tools for data analysis. Despite the rapid advancements in analytical methodology, it is often challenging to analyze stable isotope labeling-based metabolomics data, particularly for isobaric labeling using MS/MS reporter ions for quantification. We report Metandem, a novel online software tool for isobaric labeling-based metabolomics, freely available at Metandem provides a comprehensive data analysis pipeline integrating feature extraction, metabolite quantification, metabolite identification, batch processing of multiple data files, online parameter optimization for custom datasets, data normalization, and statistical analysis. Systematic evaluation of the Metandem tool was demonstrated on UPLC-MS/MS, nanoLC-MS/MS, CE-MS/MS and MALDI-MS platforms, via duplex, 4-plex, 10-plex, and 12-plex isobaric labeling experiments and the application to various biological samples.
    Keywords:  DiLeu; Isobaric labeling; Metabolomics; Metandem; Software; Stable isotope labeling
  8. J Pharm Biomed Anal. 2019 Oct 05. pii: S0731-7085(19)31185-9. [Epub ahead of print]178 112908
      The need of a continuous productivity increases in medicinal chemistry laboratories of the pharmaceutical industry motivated the development, over the years, of new software solutions to enable Open-Access in many analytical techniques such as NMR or LC, among others, to characterize and assess the purity of new molecules. These approaches have been widely spread in LC with low resolution MS systems, but similar automated platforms have been rather less explored with high resolution MS. In this work, an improved Automated Open-Access methodology on an UHPLC with DAD coupled to ESI and quadrupole time-of-flight MS system is described. Detailed reports from standard UHPLC-MS runs containing chromatograms and different spectra (MS with different fragmentation) are automatically sent to the chemists. High resolution MS data is typically achieved within ± 1 mDa mass accuracy regardless of sample concentration. Upon training, chemists log-in samples into the system by selecting appropriate methods, being able to interpret the results by themselves in 95% of the cases. The instrument is working unattended, except for a limited number of samples (5%) which require more complex experiments. To the best of our knowledge, this is the first time a completely automated Open-Access LC-HRMS approach has been implemented for medicinal chemists of a pharmaceutical industry.
    Keywords:  Automation; Drug Discovery; Open-access high resolution mass spectrometry; Open-access liquid chromatography
  9. Clin Chem Lab Med. 2019 Oct 17. pii: /j/cclm.ahead-of-print/cclm-2019-0604/cclm-2019-0604.xml. [Epub ahead of print]
      Background Quantification of plasma amino acids is key to the diagnosis of inherited defects of amino acid synthesis, catabolism and transport, many of which present as clinical emergencies. The utility of this test is limited by the long analysis time and subsequent inability of laboratories to provide results in real-time. Traditionally, analysis has been performed by ion exchange chromatography (IEC) but recently there has been a move towards liquid chromatography tandem mass spectrometry (LC-MS/MS) which provides the potential for faster analysis. However, the necessity to derivatise the sample and/or utilise an ion-pair reagent, combined with lack of commercially available stable isotope internal standards (IS) has prevented laboratories fully exploiting the benefits of this methodology. We describe an underivatised LC-MS/MS method enabling patient results to be reported with an improved turnaround time (<1 h). Methods Methanolic IS was added to plasma (10 μL) to precipitate protein. Following centrifugation amino acids were analysed by LC-MS/MS using selected reaction monitoring (SRM) for each analyte and corresponding IS. Results Patient samples (n = 57) and external quality assessment (EQA) material (n = 11) were analysed and results compared with IEC. Comparable accuracy and precision were obtained with 15-min analysis time. Conclusions This method enables the analysis of a clinically comprehensive amino acid profile without the need for derivatisation/ion-pair reagents and benefitting from improved analytical quantitation through multipoint calibration and use of stable isotope IS. The analysis time is fast in comparison to IEC, improves efficiency of laboratory workflow and enables stat analysis of clinically urgent samples.
    Keywords:  amino acids; liquid chromatography tandem mass spectrometry (LC-MS/MS); plasma; tandem mass spectrometry
  10. Anal Chim Acta. 2019 Dec 16. pii: S0003-2670(19)31145-6. [Epub ahead of print]1089 100-107
      Steroid hormones, structural derivatives of cyclopentanoperhydrophenanthrene, play important roles in modulation of many physiological processes. Comprehensive characterization of steroid hormones is valuable for understanding the process of human life activities and even disease diagnosis. Hitherto systematical characterization of steroid hormones has been rarely investigated. Here, we presented an integrated method for human urine analysis based on ultra-high performance liquid chromatography-high resolution mass spectrometry in data-dependent acquisition mode with the following parallel reaction monitoring mode. To process the data acquired by two scan modes, a comparative study of standards' fragmentation behaviors and diagnostic product ions (DPIs) were firstly conducted to facilitate the characterization of steroid hormones. The fragmentation behaviors, DPIs, elemental composition and double-bond equivalent were then simultaneously utilized for systematical characterization of steroid hormones in human urine. Consequently, fragmentation pathways and DPIs for all types of steroid hormones were comprehensively interpreted. It is interesting to find that dehydration is not restricted in the form of hydroxyl groups loss, elimination of the carbonyl oxygen could also generate dehydrated ions. Ultimately, a total of 80 and 107 steroidal hormones were characterized or tentatively identified in human urine of male and female, respectively. The proposed method is expected to provide valuable insights for chemical characterization in complex matrixes.
    Keywords:  Data-dependent acquisition; Diagnostic product ions; Parallel reaction monitoring; Steroid hormones; Urine
  11. Anal Chem. 2019 Oct 15.
      LC-MS-based untargeted metabolomics have been proved to be an extremely promising technique to discover biomarkers and explore the mechanisms underlying diseases, which, however, heavily relies on sample pretreatment for metabolite extraction. In the present study, a systematic and pragmatic evaluation of eight protocols employing conventional metabolites extraction strategies, protein precipitation (PPT) and liquid-liquid extraction (LLE), with and without proteinase K (PK) incubation was performed simultaneously using human plasma and a mixture of thirty nine endogenous metabolites standards. These protocols were as follows: 1) PPT with methanol, 2) PPT with acetonitrile, 3) PPT with 2-propanol, 4) two-step LLE of CH2Cl2-MeOH followed by MeOH-H2O, 5) PK incubation combining two-step LLE of CH2Cl2-MeOH followed by MeOH-H2O, 6) two-step LLE of CHCl3-MeOH followed by MeOH-H2O, 7) PK incubation combining two-step LLE of CHCl3-MeOH followed by MeOH-H2O, 8) PK incubation combining MeOH-EtOH PPT. The results suggested that two-step LLE produced broader metabolome coverage than protein precipitation, and the addition of proteinase K enhanced the extraction performance further. Taken together, PK incubation combining two-step LLE of CHCl3-MeOH followed by MeOH-H2O was determined to be the most suitable extraction method due to its broad metabolome coverage, high reproducibility and satisfactory recovery. Next, the developed optimal sample preparation method was applied successfully to profile the plasma metabolome of colorectal adenoma and uncover its potential mechanism for significant differential changes in linoleic acid and phospholipid metabolism.
  12. J Chromatogr A. 2019 Oct 04. pii: S0021-9673(19)30975-6. [Epub ahead of print] 460581
      The present research is focused on the object to improve identification capability in liquid chromatography (LC), by creating a system as similar as possible to gas chromatography (GC), where the combination/complementarity of Linear Retention Index (LRI) and Electron Ionization Mass Spectrometry (EI-MS) data makes the identification process easy, automatic and reliable. Conversely, in LC the untargeted characterization of real-world samples is still a challenge, due to the not repeatable and poorly informative nature of typical atmospheric pressure ionization mass spectrometry, normally hyphenated to LC. In the last decades the miniaturization of LC instrumentation together with the considerable progresses in MS vacuum pump capability has made the LC-EI-MS hyphenation more feasible. In the present work, a prototypal nanoLC-EI-MS system was used for the determination of typically LC-amenable compunds, such as coumarins, furocoumarins and polymethoxyflavones in citrus essential oils. All the compounds provided high quality EI-MS spectra, evaluated by the comparison with thousands of spectra present in commercial EI-MS libraries. Spectral similarities major than 80% were achieved. Furthermore, an LRI system, based on the use of an alkyl aryl ketone homologue reference series, was proposed as additional filter to achieve a univocal identification. Then, a novel dual-filter LRI/EI-MS library was built and resulted very helpful in the case of isomeric compounds characterized by identical EI-MS spectrum, but different retention behaviour. The very low inter-day variability attained for each LRI value, together with the satisfactory chromatographic resolution of the developed method, led to a 100% reliability of the identification process based on LRI.
    Keywords:  Citrus essential oils; Electron ionization mass spectrometry; Heterocyclic oxygenated compounds; Linear retention index; Nano LC; Reliable identification
  13. BMC Bioinformatics. 2019 Oct 17. 20(1): 501
      BACKGROUND: Identifying differentially abundant features between different experimental groups is a common goal for many metabolomics and proteomics studies. However, analyzing data from mass spectrometry (MS) is difficult because the data may not be normally distributed and there is often a large fraction of zero values. Although several statistical methods have been proposed, they either require the data normality assumption or are inefficient.RESULTS: We propose a new semi-parametric differential abundance analysis (SDA) method for metabolomics and proteomics data from MS. The method considers a two-part model, a logistic regression for the zero proportion and a semi-parametric log-linear model for the possibly non-normally distributed non-zero values, to characterize data from each feature. A kernel-smoothed likelihood method is developed to estimate model coefficients and a likelihood ratio test is constructed for differential abundant analysis. The method has been implemented into an R package, SDAMS, which is available at .
    CONCLUSION: By introducing the two-part semi-parametric model, SDA is able to handle both non-normally distributed data and large fraction of zero values in a MS dataset. It also allows for adjustment of covariates. Simulations and real data analyses demonstrate that SDA outperforms existing methods.
    Keywords:  Differential abundance analysis; Kernel smoothing; Metabolomics; Proteomics; Semi-parametric log-linear model
  14. Methods Enzymol. 2019 ;pii: S0076-6879(19)30277-0. [Epub ahead of print]626 407-428
      Lipids exert key structural, metabolic, and signaling functions in cells. Lipid diversity found in cells and tissues is regulated principally by metabolic enzymes whose activity is modulated posttranslationally to shape head group and fatty acyl composition of membrane lipids. Methodologies capable of monitoring in vivo changes in the lipidome are needed to assign substrate specificity of metabolic enzymes, which represents a key step toward understanding structure-function of lipids in living systems. The resulting lipid annotations also serve as important biomarkers for understanding mode of action for pharmacological agents targeting metabolic enzymes in cells and animal models. In this chapter, we describe a general metabolomics workflow to complement (chemo)proteomic efforts to modulate lipid pathways for basic science and translational applications.
    Keywords:  Analytical chemistry; Chemical biology; Fats; Lipidomics; Lipids; Mass spectrometry; Metabolomics; Orbitrap
  15. J Pharm Biomed Anal. 2019 Oct 07. pii: S0731-7085(19)30955-0. [Epub ahead of print]178 112914
      In-tube solid phase microextraction (IT-SPME) coupled on-line to capillary liquid chromatography with diode array detection provides a simple and fast analytical methodology for the simultaneous quantitation of caffeine and its three primary metabolites (theobromine, paraxanthine and theophylline) in micro samples of serum, saliva and urine matrices. The sample amount required for one analysis was only 2.5 μL of saliva, 6.25 μL of serum or 40 μL of urine, a requirement for its implementation in a hospital laboratory for preterm newborns, where sample availability is a major problem. In standard conditions, 25 μL of diluted saliva or serum (or 100 μL of urine) were processed by IT-SPME in 30 cm of commercially available capillary GC column coated with ZB-FFAP (100% nitroterephthalic modified polyethylene glycol). The retained compounds were desorbed from the IT-SPME capillary by the mobile phase (a gradient mixture of water and methanol) and the separation was carried out in a C18 column (150 mm × 0.5 mm i.d., 5 μm particle size). Analytes eluted before 14 min, at a flow rate of 15 μL min-1, and were detected by absorbance at 275 nm. The calibration graphs presented good linearity (R2 > 0.99), without the presence of matrix effect, and recoveries between 84 and 112% were obtained. Limits of detection (S/N = 3) were 0.1 μg·mL-1 in serum and 0.5 μg·mL-1 in saliva and urine samples, for all compounds, and the intra- and inter-day variation coefficients (n = 3) were between 3 and 17%. Analytical figures of merit were similar to those proposed by other methodologies, but using lower sample volume and a faster and simpler sample treatment and analysis. Paired samples of serum and saliva from preterm newborns treated with caffeine at the pediatric intensive care unit were analyzed by the method, with statistically equivalent results for caffeine concentrations.
    Keywords:  Biological samples; Capillary liquid chromatography; In-tube solid-phase microextraction; Trimethylxanthines
  16. J Chromatogr B Analyt Technol Biomed Life Sci. 2019 Oct 10. pii: S1570-0232(19)30596-3. [Epub ahead of print]1129 121821
      Here we show the determination of different polyamines (putrescine, cadaverine, spermidine) and related compounds (gamma-aminobutyric acid and l-ornithine) in saliva samples. These compounds are known to be biomarkers for several diseases. We have optimised an in situ derivatization process using ethyl chloroformate, an automated microextraction by packed sorbent and the determination of the corresponding products using a programmed temperature vaporizer coupled to a gas chromatograph - mass spectrometer. After finding that saliva matrix has an effect on the analysis, quantitation was performed using the one-point standard additions method and normalization to IS. This allows the detection of the analytes in the range of µg/L within a matrix obtained by a non-invasive procedure. The method has been successfully validated and it has been used in the determination of these compounds in six saliva samples finding that putrescine and cadaverine present the highest concentrations in the subject diagnosed with rheumatoid arthritis. For ornithine and spermidine, the highest concentrations were found for male subjects, especially heavy smokers. All concentrations found for the compounds were in good agreement with data found in bibliography.
    Keywords:  Ethyl chloroformate; Gas chromatography; MEPS; Mass spectrometry; Polyamines; Saliva samples
  17. iScience. 2019 Sep 27. pii: S2589-0042(19)30375-X. [Epub ahead of print]20 359-372
      Monoamine neurotransmitters are released by specialized neurons regulating behavioral, motor, and cognitive functions. Although the localization of monoaminergic neurons in the brain is well known, the distribution and kinetics of monoamines remain unclear. Here, we generated a murine brain atlas of serotonin (5-HT), dopamine (DA), and norepinephrine (NE) levels using mass spectrometry imaging (MSI). We found several nuclei rich in both 5-HT and a catecholamine (DA or NE) and identified the paraventricular nucleus of the thalamus (PVT), where 5-HT and NE are co-localized. The analysis of 5-HT fluctuations in response to acute tryptophan depletion and infusion of isotope-labeled tryptophan in vivo revealed a close kinetic association between the raphe nuclei, PVT, and amygdala but not the other nuclei. Our findings imply the existence of a highly dynamic 5-HT-mediated raphe to PVT pathway that likely plays a role in the brain monoamine system.
    Keywords:  Neuroscience; Spectroscopy; Systems Neuroscience
  18. PLoS Biol. 2019 Oct;17(10): e3000443
      Obesity is associated with changes in the plasma lipids. Although simple lipid quantification is routinely used, plasma lipids are rarely investigated at the level of individual molecules. We aimed at predicting different measures of obesity based on the plasma lipidome in a large population cohort using advanced machine learning modeling. A total of 1,061 participants of the FINRISK 2012 population cohort were randomly chosen, and the levels of 183 plasma lipid species were measured in a novel mass spectrometric shotgun approach. Multiple machine intelligence models were trained to predict obesity estimates, i.e., body mass index (BMI), waist circumference (WC), waist-hip ratio (WHR), and body fat percentage (BFP), and validated in 250 randomly chosen participants of the Malmö Diet and Cancer Cardiovascular Cohort (MDC-CC). Comparison of the different models revealed that the lipidome predicted BFP the best (R2 = 0.73), based on a Lasso model. In this model, the strongest positive and the strongest negative predictor were sphingomyelin molecules, which differ by only 1 double bond, implying the involvement of an unknown desaturase in obesity-related aberrations of lipid metabolism. Moreover, we used this regression to probe the clinically relevant information contained in the plasma lipidome and found that the plasma lipidome also contains information about body fat distribution, because WHR (R2 = 0.65) was predicted more accurately than BMI (R2 = 0.47). These modeling results required full resolution of the lipidome to lipid species level, and the predicting set of biomarkers had to be sufficiently large. The power of the lipidomics association was demonstrated by the finding that the addition of routine clinical laboratory variables, e.g., high-density lipoprotein (HDL)- or low-density lipoprotein (LDL)- cholesterol did not improve the model further. Correlation analyses of the individual lipid species, controlled for age and separated by sex, underscores the multiparametric and lipid species-specific nature of the correlation with the BFP. Lipidomic measurements in combination with machine intelligence modeling contain rich information about body fat amount and distribution beyond traditional clinical assays.
  19. Sci Rep. 2019 Oct 18. 9(1): 15008
      Patient-derived explant (PDE) culture of solid tumors is increasingly being applied to preclinical evaluation of novel therapeutics and for biomarker discovery. In this technique, treatments are added to culture medium and penetrate the tissue via a gelatin sponge scaffold. However, the penetration profile and final concentrations of small molecule drugs achieved have not been determined to date. Here, we determined the extent of absorption of the clinical androgen receptor antagonist, enzalutamide, into prostate PDEs, using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and matrix-assisted laser/desorption ionisation (MALDI) mass spectrometry imaging (MSI). In a cohort of 11 PDE tissues from eight individual patients, LC-MS/MS quantification of PDE homogenates confirmed enzalutamide (10 µM) uptake by all PDEs, which reached maximal average tissue concentration of 0.24-0.50 ng/µg protein after 48 h culture. Time dependent uptake of enzalutamide (50 µM) in PDEs was visualized using MALDI MSI over 24-48 h, with complete penetration throughout tissues evident by 6 h of culture. Drug signal intensity was not homogeneous throughout the tissues but had areas of markedly high signal that corresponded to drug target (androgen receptor)-rich epithelial regions of tissue. In conclusion, application of MS-based drug quantification and visualization in PDEs, and potentially other 3-dimensional model systems, can provide a more robust basis for experimental study design and interpretation of pharmacodynamic data.
  20. Front Genet. 2019 ;10 858
      Pathway analysis is often the first choice for studying the mechanisms underlying a phenotype. However, conventional methods for pathway analysis do not take into account complex protein-protein interaction information, resulting in incomplete conclusions. Previously, numerous approaches that utilize protein-protein interaction information to enhance pathway analysis yielded superior results compared to conventional methods. Hereby, we present pathfindR, another approach exploiting protein-protein interaction information and the first R package for active-subnetwork-oriented pathway enrichment analyses for class comparison omics experiments. Using the list of genes obtained from an omics experiment comparing two groups of samples, pathfindR identifies active subnetworks in a protein-protein interaction network. It then performs pathway enrichment analyses on these identified subnetworks. To further reduce the complexity, it provides functionality for clustering the resulting pathways. Moreover, through a scoring function, the overall activity of each pathway in each sample can be estimated. We illustrate the capabilities of our pathway analysis method on three gene expression datasets and compare our results with those obtained from three popular pathway analysis tools. The results demonstrate that literature-supported disease-related pathways ranked higher in our approach compared to the others. Moreover, pathfindR identified additional pathways relevant to the conditions that were not identified by other tools, including pathways named after the conditions.
    Keywords:  active subnetworks; biological interaction network; enrichment; pathway analysis; tool
  21. Nat Methods. 2019 Oct 14.
      Cellular lipid metabolism is a complex network process comprising dozens of enzymes, multiple organelles and more than a thousand lipid species. Tracing metabolic reactions in this network is a major technological and scientific challenge. Using a click-chemistry mass spectrometry reporter strategy, we have developed a specific, highly sensitive and robust tracing procedure for alkyne-labeled lipids. The method enables sample multiplexing, which improves sample comparison. We demonstrate this by a time-resolved analysis of hepatocyte glycerolipid metabolism with parallel quantitative monitoring of 120 labeled lipid species. The subfemtomole sensitivity enabled a single cell analysis of fatty acid incorporation into neutral and membrane lipids. The results demonstrate the robustness of lipid homeostasis at the single cell level.
  22. Crit Rev Food Sci Nutr. 2019 Oct 17. 1-18
      Biologically active compounds such as carotenoids/isoprenoids, vitamins, steroids, saponins, sugars, long chain fatty acids, and amino acids play a very important role in coordinating functions in living organisms. Determination of those substances is indispensable in advanced biological sciences. Engineered stationary phase in LC for the analysis of biomolecules has become easier with the development of chromatographic science. In general, C18 column is being used for routine analysis but specific columns are being used for specific molecule. Monolithic columns are found to have higher efficiency than normal column. Among recent introduction, triacontyl stationary phases, designed for the separation of carotenoid isomers, are widely used for the estimation of carotenoids. In comparison to conventional C18 phases, C30 phases exhibited superior shape selectivity for the separation of isomers of carotenoids. It is also found useful for better elution and analysis of tocopherols, vitamin K, sterols, and fatty acids. Vitamin K, E, and their isomers are also successfully resoluted and analyzed by using C30 column. Amino bonded phase column is specifically used for better elution of sugars, whereas phenyl columns are suitable for the separation and analysis of curcuminoids and taxol. Like triacontyl stationary phase, pentafluorophenyl columns are also used for the separation and analysis of carotenoids. Similarly, HILIC column are best suited for sugar analysis. All the stationary phases are made possible to resolute and analyze the target biomolecules better, which are the future of liquid chromatography. The present article focuses on the differential interaction between stationary phase and target biomolecules. The applicability of these stationary phases are reported in different matrices.
    Keywords:  Triacontyl; amino stationary phase; carotenoids; curcuminoids; interaction; pentafluorophenyl; phenyl; shape selectivity; sterols; sugars; tocols
  23. Amino Acids. 2019 Oct 15.
      The differentiation therapy is focused on the identification of new agents able to impair the proliferative and metastatic potential of cancer cells through the induction of differentiation. Although several markers of cell differentiation on tumor cells have been identified, their causal relationship with neoplastic competence has not been characterized in sufficient detail to propose their use as new pharmacological targets useful for the design of new differentiation agents. Polyamine level in cancer cells and in body fluids was proposed as potential marker of cell proliferation and differentiation. The main advantage of this marker is the possibility to evaluate the antineoplastic activity of new drugs able to induce cell differentiation and consequently to inhibit tumor growth and metastasis. The presented report shows a simply and highly reproducible reverse-phase high-performance liquid chromatographic (HPLC) method for the determination of ortho-phthalaldehyde (OPA) derivatives of polyamines: putrescine (PUT), cadaverine (CAD), spermidine (SPD) and spermine (SPM). The novelty of this method is the fluorescence response for OPA-derivate of SPM, generally low in other procedures, that has been significantly improved by the use of a fully endcapped packing material with minimal silanol interactions. The limits of detection for PUT, CAD, SPD and SPM were 0.6, 0.7, 0.8, and 0.4 pmol/mL, respectively. The analysis time was ≤ 20 min, and the relative recovery rate was of about 97%. To verify the usefulness of this method, it has been validated in a murine melanoma cell line (B16-F10) treated with two theophylline derivatives (namely 8-chlorotheophylline and 8-bromotheophylline). These two compounds increased the activity of tissue transglutaminase (TG2) and the synthesis of melanin, two recognized markers of melanoma cell differentiation, and significantly reduced the levels of intracellular polyamines.
    Keywords:  Differentiation therapy; Melanoma cells; OPA derivatization; Polyamines