bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2019‒10‒20
twenty papers selected by
Giovanny Rodriguez Blanco
The Beatson Institute for Cancer Research


  1. Cell Metab. 2019 Oct 03. pii: S1550-4131(19)30512-1. [Epub ahead of print]
    Zhu J, Berisa M, Schwörer S, Qin W, Cross JR, Thompson CB.
      Cysteine acts both as a building unit for protein translation and as the limiting substrate for glutathione synthesis to support the cellular antioxidant system. In addition to transporter-mediated uptake, cellular cysteine can also be synthesized from methionine through the transsulfuration pathway. Here, we investigate the regulation of transsulfuration and its role in sustaining cell proliferation upon extracellular cysteine limitation, a condition reported to occur in human tumors as they grow in size. We observed constitutive expression of transsulfuration enzymes in a subset of cancer cell lines, while in other cells, these enzymes are induced following cysteine deprivation. We show that both constitutive and inducible transsulfuration activities contribute to the cellular cysteine pool and redox homeostasis. The rate of transsulfuration is determined by the cellular capacity to conduct methylation reactions that convert S-adenosylmethionine to S-adenosylhomocysteine. Finally, our results demonstrate that transsulfuration-mediated cysteine synthesis is critical in promoting tumor growth in vivo.
    Keywords:  cancer; cysteine; glutathione; metabolism; methylation; redox homeostasis; transsulfuration; xCT
    DOI:  https://doi.org/10.1016/j.cmet.2019.09.009
  2. Cancer Res. 2019 Oct 15. 79(20): 5149-5150
    Carbone M, Melino G.
      Better therapies are urgently needed for ovarian cancer, which is associated with an overall median survival of less than 5 years from diagnosis. In this issue of Cancer Research, Tesfay and colleagues show that stearoyl CoA desaturase (SCD1) is expressed at high levels in different isotypes of ovarian cancer and that SCD1 protects ovarian cancer cells from cell death. Pharmaceutical inhibition of SCD1 induces apoptosis and ferroptosis in vitro and in vivo Combination therapies of SCD1 inhibitors and ferroptosis inducers significantly decrease ovarian tumor masses in mice. This novel therapy may prove useful to treat women with ovarian cancer.See related article by Tesfay et al., p. 5355.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-19-2453
  3. Methods Enzymol. 2019 ;pii: S0076-6879(19)30293-9. [Epub ahead of print]626 1-21
    Trefely S, Doan MT, Snyder NW.
      Dynamic interplay between cellular metabolism and histone acetylation is a key mechanism underlying metabolic control of epigenetics. In particular, the central metabolite acetyl-coenzyme A (acetyl-CoA) acts as the acetyl-donor for histone acetylation in both an enzymatic and non-enzymatic manner. Since members of the family of histone acetyl transferases (HATs) that catalyze the acetylation of histone tails possess a Michaelis constant (Km) within the range of physiological cellular acetyl-CoA concentrations, changing concentrations of acetyl-CoA can restrict or promote enzymatic histone acetylation. Likewise, non-enzymatic histone acetylation occurs at physiological concentrations. These concepts implicate acetyl-CoA as a rheostat for nutrient availability acting, in part, by controlling histone acetylation. Histone acetylation is an important epigenetic modification that controls gene expression and acetyl-CoA dependent changes in both histone acetylation and gene expression have been shown in yeast and mammalian systems. However, quantifying the metabolic conditions required to achieve specific changes in histone acetylation is a major challenge. The relationship between acetyl-CoA and histone acetylation may be influenced by a variety of factors including sub-cellular location of metabolites and enzymes, relative quantities of metabolites, and substrate availability/preference. A diversity of substrates can contribute the two-carbon acyl-chain to acetyl-CoA, a number of pathways can create or degrade acetyl-CoA, and only a handful of potential mechanisms for the crosstalk between metabolism and histone acetylation have been explored. The centrality of acetyl-CoA in intermediary metabolism means that acetyl-CoA levels may change, or be resistant to change, in unexpected ways. Thus, quantification of relevant metabolites is critical evidence in understanding how the nutrient rheostat is set in normal and pathological contexts. Coupling metabolite quantitation with isotope tracing to examine fate of specific metabolites is critical to the crosstalk between metabolism and histone acetylation, including but not limited to acetyl-CoA provides necessary context. This chapter provides guidance on experimental design of quantification with isotope dilution and/or tracing of acetyl-CoA within a targeted or highly multiplexed multi-analyte workflow.
    Keywords:  Acetyl-coenzyme A; Acetylation; Liquid chromatography mass spectrometry; Metabolism
    DOI:  https://doi.org/10.1016/bs.mie.2019.07.013
  4. Anal Chim Acta. 2019 Dec 11. pii: S0003-2670(19)30987-0. [Epub ahead of print]1088 99-106
    Hao L, Zhu Y, Wei P, Johnson J, Buchberger A, Frost D, Kao WJ, Li L.
      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 http://metandem.com/web/. 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
    DOI:  https://doi.org/10.1016/j.aca.2019.08.046
  5. Methods Enzymol. 2019 ;pii: S0076-6879(19)30307-6. [Epub ahead of print]626 41-65
    Kreuzer J, Edwards A, Haas W.
      Post-translational modifications (PTMs) of proteins increase a biological system's repertoire of regulatory tools to control cellular mechanisms. Protein phosphorylation is the most studied PTM and known to be dysregulated in many diseases, including cancer, and protein kinases are among the most important drug targets. Many proteins across the eukaryotic proteome are phosphorylated, and more than 50,000 unique protein phosphorylation sites have been identified in a single human cell line. Understanding the vast biological networks directed by protein phosphorylation requires deep quantitative mapping of the phosphoproteome across many samples. Multiplexed proteomics using isobaric labeling reagents to barcode proteome samples for simultaneous quantification has greatly increased the throughput of mass spectrometry-based proteomics and enabled the number of analyses required to understand complex biological systems. We are presenting a detailed protocol to use multiplexed proteomics for mapping phosphoproteomes in samples from cell culture experiments and in tissue samples. The protocol includes phosphopeptide enrichment with TiO2 and phosphotyrosine antibody technology. We are using tandem mass tag (TMT) reagents for barcoding the samples allowing parallel quantification of up to 11 samples. The mass spectrometry method is based on the MultiNotch MS3 method to generate quantitative data of high accuracy and reproducibility. Tandem mass spectrometry (MS2) based on regular collision-induced dissociation (CID) and higher-energy collisional dissociation (HCD) is used to maximize the number of quantified phosphopeptides. The protocol typically enables the quantification of more than 20,000 unique phosphoforms (unique patterns of peptide phosphorylations) from proteome samples of human origin requiring less than 8h of mass spectrometry time per sample.
    Keywords:  Isobaric labels; Multiplexing; Phosphoproteomics; Quantitative proteomics; TMT
    DOI:  https://doi.org/10.1016/bs.mie.2019.07.027
  6. Nat Methods. 2019 Oct 14.
    Thiele C, Wunderling K, Leyendecker P.
      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.
    DOI:  https://doi.org/10.1038/s41592-019-0593-6
  7. Cell Prolif. 2019 Oct 19. e12702
    Oppermann H, Birkemeyer C, Meixensberger J, Gaunitz F.
      OBJECTIVES: Carnosine (β-alanyl-l-histidine) is a naturally occurring dipeptide that selectively inhibits cancer cell growth, possibly by influencing glucose metabolism. As its precise mode of action and its primary targets are unknown, we analysed carnosine's effect on metabolites and pathways in glioblastoma cells.MATERIALS AND METHODS: Glioblastoma cells, U87, T98G and LN229, were treated with carnosine, and metabolites were analysed by gas chromatography coupled with mass spectrometry. Furthermore, mitochondrial ATP production was determined by extracellular flux analysis and reaction products of carnosine were investigated using mass spectrometry.
    RESULTS: Carnosine decreased the intracellular abundance of several metabolites indicating a reduced activity of the pentose phosphate pathway, the malate-aspartate shuttle and the glycerol phosphate shuttle. Mitochondrial respiration was reduced in U87 and T98G but not in LN229 cells, independent of whether glucose or pyruvate was used as substrate. Finally, we demonstrate non-enzymatic reaction of carnosine with dihydroxyacetone phosphate and glyceraldehyde-3-phosphate. However, glycolytic flux from glucose to l-lactate appeared not to be affected by the reaction of carnosine with the metabolites.
    CONCLUSIONS: Carnosine reacts non-enzymatically with glycolytic intermediates reducing the activity of the pentose phosphate pathway which is required for cell proliferation. Although the activity of the malate-aspartate and the glycerol phosphate shuttle appear to be affected, reduced mitochondrial ATP production under the influence of the dipeptide is cell-specific and appears to be independent of the effect on the shuttles.
    Keywords:  carnosine; glioblastoma; metabolomics; pentose phosphate pathway
    DOI:  https://doi.org/10.1111/cpr.12702
  8. Methods Enzymol. 2019 ;pii: S0076-6879(19)30316-7. [Epub ahead of print]626 475-498
    Lund PJ, Lehman SM, Garcia BA.
      Since protein activity is often regulated by posttranslational modifications, the qualitative and quantitative analysis of modification sites is critical for understanding the regulation of biological pathways that control cell function and phenotype. Methylation constitutes one of the many types of posttranslational modifications that target lysine residues. Although lysine methylation is perhaps most commonly associated with histone proteins and the epigenetic regulation of processes involving chromatin, methylation has also been observed as an important regulatory modification on other proteins, which has spurred the development of methods to profile lysine methylation sites more globally. As with many posttranslational modifications, tandem mass spectrometry represents an ideal platform for the high-throughput analysis of lysine methylation due to its high sensitivity and resolving power. The following protocol outlines a general method to assay lysine methylation across the proteome using SILAC and quantitative proteomics. First, cells are labeled by SILAC to allow for relative quantitation across different experimental conditions, such as cells with or without ectopic expression of a methyltransferase. Next, cells are lysed and proteins are digested into peptides. Methylated peptides are then enriched by immunoprecipitation with pan-specific antibodies against methylated lysine. Finally, the enriched peptides are analyzed by LC-MS/MS to identify methylated peptides and their modification sites and to compare the relative abundance of methylation events between different conditions. This approach should yield detection of a couple hundred lysine methylation sites, and those showing differential abundance may then be prioritized for further study.
    Keywords:  Affinity purification; Lysine methylation; Mass spectrometry; Posttranslational modifications; SILAC
    DOI:  https://doi.org/10.1016/bs.mie.2019.07.036
  9. Dis Model Mech. 2019 Oct 18. pii: dmm.040741. [Epub ahead of print]
    Itzhak DN, Sacco F, Nagaraj N, Tyanova S, Mann M, Murgia M.
      The unfolded protein response (UPR) involves extensive proteome remodeling in many cellular compartments. So far, a comprehensive analysis has been missing due to technological limitations. Here we employ Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC)-based proteomics to quantify over 6200 proteins at increasing concentrations of tunicamycin in HeLa cells. We further compare the effects of tunicamycin (5 ug/ml) to those of thapsigargin (1 µM) and DTT (2mM), both activating the UPR through different mechanisms. The systematic quantification of the proteome-wide expression changes following proteostatic stress is a resource for the scientific community, which enables the discovery of novel players involved in the pathophysiology of the broad range of disorders linked to proteostasis. We identified 38 proteins not previously linked to the UPR, whose expression increases, of which 15 likely remediate ER stress, and the remainder may contribute to pathological outcomes. Unexpectedly, there are few strongly downregulated proteins, despite expression of the pro-apoptotic transcription factor CHOP, suggesting that IRE1-dependent mRNA decay (RIDD) has a limited contribution to ER-stress mediated cell death in our system.
    Keywords:  Endoplasmic Reticulum stress; Proteomics; SILAC; Tunicamycin; Unfolded Protein Response
    DOI:  https://doi.org/10.1242/dmm.040741
  10. J Biol Chem. 2019 Oct 18. pii: jbc.AW119.008146. [Epub ahead of print]
    Thompson CB, Bielska AA.
      How cells utilize nutrients to produce the ATP needed for bioenergetic homeostasis has been well characterized. What is less well studied is how resting cells metabolically shift from an ATP-producing catabolic metabolism to a metabolism that supports anabolic growth. In metazoan organisms, the discovery of growth factors and the ability of their receptors to induce new transcription and translation led to the hypothesis that the bioenergetic and synthetic demands of cell growth were primarily met through the replacement of nutrients consumed during net macromolecular synthesis, a demand-based system of nutrient uptake. Recent data have challenged this hypothesis. Instead there is increasing evidence that cellular nutrient uptake is a push system. Growth factor signaling has been linked to direct stimulation of nutrient uptake. The ability of growth factor signaling to increase the uptake of glucose, lipids, and amino acids to levels that exceed a cell's bioenergetic and synthetic needs has been documented in a wide variety of settings. In some tissues, this leads to the storage of the excess nutrients in the form of glycogen or fat. In others, the excess is secreted as lactate and certain non-essential amino acids. When growth factor signaling stimulates nutrient uptake to levels that exceed a cell's bioenergetic needs, adaptive changes in intermediate metabolism lead to the production of anabolic precursors that fuel the net synthesis of protein, lipids, and nucleic acids. Through the increased production of these precursors, growth factor signaling provides a supply side stimulation of cell growth and proliferation.
    Keywords:  bioenergetics; cell growth; cell metabolism; cell proliferation; growth factor
    DOI:  https://doi.org/10.1074/jbc.AW119.008146
  11. J Proteome Res. 2019 Oct 18.
    Khoomrung S, Nookaew I, Sen P, Olafsdottir TA, Persson J, Moritz T, Andersen P, Harandi AM, Nielsen J.
      Alum has been widely used as an adjuvant for human vaccines; however, the impact of Alum on host metabolism remains largely unknown. Herein, we applied mass spectrometry (LCMS)-based metabolic and lipid profiling to monitor the effects of Alum adjuvant on mouse serum at 6, 24, 72 and 168 h post-vaccination. We propose a new strategy termed Subclass Identification and Annotation for Metabolomics (SIAM) for class-wise identification of untargeted metabolomics data generated from high-resolution MS. Using this approach, we identified and validated the levels of several lipids in mouse serum that were significantly altered following Alum administration. These lipids showed a biphasic response even 168 h after vaccination. The majority of the lipids were triglycerides (TAGs), where TAGs with long chain unsaturated fatty acids were decreased at 24 h, and TAGs with short chain fatty acids were decreased at 168 h. To our knowledge, this is the first report on the impact of the human vaccine adjuvant Alum on host metabolome, and may provide new insights into the mechanism of action of Alum.
    DOI:  https://doi.org/10.1021/acs.jproteome.9b00517
  12. Methods. 2019 Oct 09. pii: S1046-2023(19)30136-7. [Epub ahead of print]
    Noberini R, Restellini C, Oliva Savoia E, Bonaldi T.
      Aberrations in histone post-translational modifications (PTMs) have been implicated with the development of numerous pathologies, including cancer. Therefore, profiling histone PTMs in patient samples could provide information useful for the identification of epigenetic biomarkers, as well as the discovery of potential novel targets. While antibody-based methods have been traditionally employed to analyze histone PTM in clinical samples, mass spectrometry (MS) can provide a more comprehensive, unbiased and quantitative view on histones and their PTMs. To combine the power of MS-based methods and the potential offered by histone PTM profiling of clinical samples, we have recently developed a series of methods for the extraction and enrichment of histones from different types of patient samples, including formalin-fixed paraffin-embedded tissues, fresh- and optimal cutting temperature-frozen tissues, and primary cells. Here, we provide a detailed description of these protocols, together with indications on the expected results and the most suitable workflow to be used downstream of each procedure.
    Keywords:  Epigenetics; Formalin-fixed paraffin-embedded tissues; Frozen tissues; Histone post-translational modifications; Mass spectrometry
    DOI:  https://doi.org/10.1016/j.ymeth.2019.10.001
  13. Clin Chem Lab Med. 2019 Oct 17. pii: /j/cclm.ahead-of-print/cclm-2019-0604/cclm-2019-0604.xml. [Epub ahead of print]
    Carling RS, John K, Churchus R, Turner C, Dalton RN.
      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
    DOI:  https://doi.org/10.1515/cclm-2019-0604
  14. Mass Spectrom Rev. 2019 Oct 15.
    Khamis MM, Adamko DJ, El-Aneed A.
      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
    DOI:  https://doi.org/10.1002/mas.21607
  15. World J Stem Cells. 2019 Sep 26. 11(9): 693-704
    Begicevic RR, Arfuso F, Falasca M.
      Tumours are known to be a heterogeneous group of cells, which is why they are difficult to eradicate. One possible cause for this is the existence of slow-cycling cancer stem cells (CSCs) endowed with stem cell-like properties of self-renewal, which are responsible for resistance to chemotherapy and radiotherapy. In recent years, the role of lipid metabolism has garnered increasing attention in cancer. Specifically, the key roles of enzymes such as stearoyl-CoA desaturase-1 and 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase in CSCs, have gained particular interest. However, despite accumulating evidence on the role of proteins in controlling lipid metabolism, very little is known about the specific role played by lipid products in CSCs. This review highlights recent findings on the role of lipid metabolism in CSCs, focusing on the specific mechanism by which bioactive lipids regulate the fate of CSCs and their involvement in signal transduction pathways.
    Keywords:  ABC transporters; Bioactive lipids; Cancer stem cells; Lipid metabolism
    DOI:  https://doi.org/10.4252/wjsc.v11.i9.693
  16. Anal Chem. 2019 Oct 18.
    Hu Y, Cai B, Huan T.
      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.
    DOI:  https://doi.org/10.1021/acs.analchem.9b02980
  17. Mol Cell Proteomics. 2019 Oct 18. pii: mcp.TIR119.001669. [Epub ahead of print]
    Szigeti M, Guttman A.
      We introduce an efficient sample preparation workflow to facilitate deep N-glycomics analysis of the human serum by capillary electrophoresis with laser induced fluorescence (CE-LIF) detection and to accommodate the higher sample concentration requirement of electrospray ionization mass spectrometry connected to capillary electrophoresis (CE-ESI-MS). A novel, temperature gradient denaturing protocol was applied on amine functionalized magnetic bead partitioned glycoproteins to circumvent the otherwise prevalent precipitation issue. During this process, the free sugar content of the serum was significantly decreased as well, accommodating enhanced PNGase F mediated release of the N-linked carbohydrates. The liberated oligosaccharides were tagged with aminopyrene-trisulfonate, utilizing a modified evaporative labeling protocol. Processing the samples with this new workflow enabled deep CE-LIF analysis of the human serum N-glycome and provided the appropriate amount of material for CE-ESI-MS analysis in negative ionization mode.
    Keywords:  CE-MS; Electrophoresis; Glycomics; Mass Spectrometry; Separation Technologies; Serum/Plasma*; capillary electrophoresis
    DOI:  https://doi.org/10.1074/mcp.TIR119.001669
  18. PLoS Biol. 2019 Oct;17(10): e3000443
    Gerl MJ, Klose C, Surma MA, Fernandez C, Melander O, Männistö S, Borodulin K, Havulinna AS, Salomaa V, Ikonen E, Cannistraci CV, Simons K.
      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.
    DOI:  https://doi.org/10.1371/journal.pbio.3000443
  19. Prog Lipid Res. 2019 Oct 15. pii: S0163-7827(19)30051-7. [Epub ahead of print] 101008
    Metherel AH, Bazinet RP.
      N-3 polyunsaturated fatty acids (PUFA) and the numerous families of lipid mediators derived from them collectively regulate numerous biological processes. The mechanisms by which n-3 PUFA regulate biological processes begins with an understanding of the n-3 biosynthetic pathway that starts with alpha-linolenic acid (18:3n-3) and is commonly thought to end with the production of docosahexaenoic acid (DHA, 22:6n-3). However, our understanding of this pathway is not as complete as previously believed. In the current review we provide a background of the evidence supporting the pathway as currently understood and provide updates from recent studies challenging three central dogma of n-3 PUFA metabolism. By building on nearly three decades of research primarily in cell culture and oral dosing studies, recent evidence presented focuses on in vivo kinetic modelling and compound-specific isotope abundance studies in rodents and humans that have been instrumental in expanding our knowledge of the pathway. Specifically, we highlight three main updates to the n-3 PUFA biosynthesis pathway: (1) DHA synthesis rates cannot be as low as previously believed, (2) DHA is both a product and a precursor to tetracosahexaenoic acid (24:6n-3) and (3) increases in EPA in response to DHA supplementation are not the result of increased retroconversion.
    Keywords:  Docosahexaenoic acid; Metabolism; Omega-3; Polyunsaturated fatty acid; Retroconversion; Tetracosahexaenoic acid
    DOI:  https://doi.org/10.1016/j.plipres.2019.101008
  20. Bioanalysis. 2019 Oct 16.
    Kellie JF, Sikorski TW, An B, Chen Z, Moghieb AH, Busz MG, Szapacs ME, Angel TE.
      
    Keywords:  biomarkers; drug discovery; mass spectrometry; proteomics
    DOI:  https://doi.org/10.4155/bio-2019-0191