bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2019‒05‒19
forty-two papers selected by
Giovanny Rodriguez Blanco
The Beatson Institute for Cancer Research


  1. Clin Chem. 2019 May 17. pii: clinchem.2018.299651. [Epub ahead of print]
    Subramaniam S, Jeet V, Clements JA, Gunter JH, Batra J.
      BACKGROUND: Metabolic reprogramming is a hallmark of cancer. MicroRNAs (miRNAs) have been found to regulate cancer metabolism by regulating genes involved in metabolic pathways. Understanding this layer of complexity could lead to the development of novel therapeutic approaches.CONTENT: miRNAs are noncoding RNAs that have been implicated as master regulators of gene expression. Studies have revealed the role of miRNAs in the metabolic reprogramming of tumor cells, with several miRNAs both positively and negatively regulating multiple metabolic genes. The tricarboxylic acid (TCA) cycle, aerobic glycolysis, de novo fatty acid synthesis, and altered autophagy allow tumor cells to survive under adverse conditions. In addition, major signaling molecules, hypoxia-inducible factor, phosphatidylinositol-3 kinase/protein kinase B/mammalian target of rapamycin/phosphatase and tensin homolog, and insulin signaling pathways facilitate metabolic adaptation in tumor cells and are all regulated by miRNAs. Accumulating evidence suggests that miRNA mimics or inhibitors could be used to modulate the activity of miRNAs that drive tumor progression via altering their metabolism. Currently, several clinical trials investigating the role of miRNA-based therapy for cancer have been launched that may lead to novel therapeutic interventions in the future.
    SUMMARY: In this review, we summarize cancer-related metabolic pathways, including glycolysis, TCA cycle, pentose phosphate pathway, fatty acid metabolism, amino acid metabolism, and other metabolism-related oncogenic signaling pathways, and their regulation by miRNAs that are known to lead to tumorigenesis. Further, we discuss the current state of miRNA therapeutics in the clinic and their future potential.
    DOI:  https://doi.org/10.1373/clinchem.2018.299651
  2. J Oleo Sci. 2019 May 16.
    Stark KD.
      Assessing dietary intake is critical for understanding the relationship between diet and health. Fatty acid blood biomarkers have been particularly useful in determining dietary intakes and assessing the risk of chronic disease. However, fatty acid analysis involves the removal of fatty acids from their complex lipid structures resulting in a loss of potentially useful biological information. "Lipidomics" involves the use of mass spectrometry to identify lipids in their native form. Lipidomic approaches present challenges as an alternative to fatty acid analysis. This includes different types of lipidomic approaches and a lack of consensus on the lipids reported in different studies. Distinguishing between macrolipidomic approaches to characterize highly abundant lipids and microlipidomic approaches examining low abundant bioactive lipids and the use of brutto, medio, genio, and infinio to describe the level of information of lipidomic data can provide clarity to the field. Using lipidomic measurements for understanding docosahexaenoic acid metabolism during pregnancy will also be examined.
    Keywords:  biomarkers; dietary intake; fatty acids; lipidomics; omega-3 polyunsaturated fatty acids
    DOI:  https://doi.org/10.5650/jos.ess19042
  3. Cancers (Basel). 2019 May 16. pii: E686. [Epub ahead of print]11(5):
    Loras A, Suárez-Cabrera C, Martínez-Bisbal MC, Quintás G, Paramio JM, Martínez-Máñez R, Gil S, Ruiz-Cerdá JL.
      Metabolism reprogramming is considered a hallmark of cancer. The study of bladder cancer (BC) metabolism could be the key to developing new strategies for diagnosis and therapy. This work aimed to identify tissue and urinary metabolic signatures as biomarkers of BC and get further insight into BC tumor biology through the study of gene-metabolite networks and the integration of metabolomics and transcriptomics data. BC and control tissue samples (n = 44) from the same patients were analyzed by High-Resolution Magic Angle Spinning Nuclear Magnetic Resonance and microarrays techniques. Besides, urinary profiling study (n = 35) was performed in the same patients to identify a metabolomic profile, linked with BC tissue hallmarks, as a potential non-invasive approach for BC diagnosis. The metabolic profile allowed for the classification of BC tissue samples with a sensitivity and specificity of 100%. The most discriminant metabolites for BC tissue samples reflected alterations in amino acids, glutathione, and taurine metabolic pathways. Transcriptomic data supported metabolomic results and revealed a predominant downregulation of metabolic genes belonging to phosphorylative oxidation, tricarboxylic acid cycle, and amino acid metabolism. The urinary profiling study showed a relation with taurine and other amino acids perturbed pathways observed in BC tissue samples, and classified BC from non-tumor urine samples with good sensitivities (91%) and specificities (77%). This urinary profile could be used as a non-invasive tool for BC diagnosis and follow-up.
    Keywords:  bladder cancer; cancer biomarkers; cancer metabolic reprogramming; metabolic pathways; metabolomics; transcriptomics; tumor metabolome
    DOI:  https://doi.org/10.3390/cancers11050686
  4. Am J Chin Med. 2019 May 15. 1-15
    Zhang WS, Pan A, Yang L, Cai YY, Liu BL, Li P, Qi LW, Li J, Liu Q.
      American ginseng and Asian ginseng, which occupy prominent positions in the list of best-selling natural products in the West and East, are suitable for different indications in the traditional pharmacological uses. Currently, the effects of American ginseng and Asian ginseng in the protection against metabolic dysfunction and the differences between them are still unknown. Herein, an untargeted metabolomics based on liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS) was determined. The serum metabolomics and dynamic feces metabolomics revealed significant metabolic distinction between American ginseng and Asian ginseng in diet-induced obese (DIO) mice. The results show that American ginseng and Asian ginseng alleviate glucose and lipid metabolism disorder in DIO mice. A total of 45 differential metabolites were confirmed between the drug-naïve and American ginseng group, and 32 metabolites were confirmed between the drug-naïve and Asian ginseng group. Metabolic pathways analysis shows that these two ginsengs treatment dynamic rectifies metabolic disorder in DIO mice mainly via regulating linoleic acids metabolism, cysteine and methionine metabolism and biosynthesis of unsaturated fatty acid. Moreover, American ginseng's specific function in monitoring the carnitines and taurine/hypotaurine metabolism might make it more effective in meliorating lipids metabolism disorder than Asian ginseng.
    Keywords:  American Ginseng; Asian Ginseng; Carnitines; Metabolism Disorder; Metabolomics; Taurine Metabolism
    DOI:  https://doi.org/10.1142/S0192415X19500411
  5. Clin Chim Acta. 2019 May 08. pii: S0009-8981(19)31849-2. [Epub ahead of print]
    Smon A, Cuk V, Brecelj J, Murko S, Groselj U, Tansek MZ, Battelino T, Lampret BR.
      OBJECTIVES: Precise quantification of amino acids (AAs) is mandatory for successful diagnosis and monitoring of patients with metabolic diseases. We compared ion-exchange chromatography (IEC) and liquid chromatography with tandem mass spectrometry (LC-MS/MS), the two methods most commonly used in clinical laboratories for the quantification of AAs in physiological samples.DESIGN & METHODS: 123 apparently healthy children were selected for the study. The plasma samples for LC-MS/MS were prepared accordingly to the aTRAQ Kit for Physiological Fluids on Sciex 3200 Qtrap, for IEC according to the protocol from Pickering laboratories on the AA analyzer Pinnacle PCX. Results were interpreted using the Pearson correlation coefficient and the percent difference Bland-Altman test.
    RESULTS: The Spearman correlation coefficients of the 14 AAs that we evaluated varied from 0.67 in Tau to 0.89 in Leu and Thr. The mean differences in measurements (IEC compared to LC-MS/MS) of 11 AAs complied with our acceptance criterion of <15%, the differences of Ser and Tyr were higher (19.5% and -19.0%, respectively), and the measured concentrations of Cit were much lower in LC-MS/MS than IEC (31% difference).
    CONCLUSION: The two methods are sufficiently comparable enough for most AAs and the reference values for individual AAs did not have to be refined, with the exception of citrulline. For the monitoring of patients on therapy (e.g. patients with phenylketonuria), it is still advisable to always use the same analytical method for the quantification of AAs.
    Keywords:  Amino acid analyzer; Amino acids; Dietary management; Inborn errors of metabolism; Tandem mass spectrometry
    DOI:  https://doi.org/10.1016/j.cca.2019.05.007
  6. Cell Rep. 2019 May 14. pii: S2211-1247(19)30487-5. [Epub ahead of print]27(7): 2063-2074.e5
    Qiu J, Villa M, Sanin DE, Buck MD, O'Sullivan D, Ching R, Matsushita M, Grzes KM, Winkler F, Chang CH, Curtis JD, Kyle RL, Van Teijlingen Bakker N, Corrado M, Haessler F, Alfei F, Edwards-Hicks J, Maggi LB, Zehn D, Egawa T, Bengsch B, Klein Geltink RI, Jenuwein T, Pearce EJ, Pearce EL.
      Competition for nutrients like glucose can metabolically restrict T cells and contribute to their hyporesponsiveness during cancer. Metabolic adaptation to the surrounding microenvironment is therefore key for maintaining appropriate cell function. For instance, cancer cells use acetate as a substrate alternative to glucose to fuel metabolism and growth. Here, we show that acetate rescues effector function in glucose-restricted CD8+ T cells. Mechanistically, acetate promotes histone acetylation and chromatin accessibility and enhances IFN-γ gene transcription and cytokine production in an acetyl-CoA synthetase (ACSS)-dependent manner. Ex vivo acetate treatment increases IFN-γ production by exhausted T cells, whereas reducing ACSS expression in T cells impairs IFN-γ production by tumor-infiltrating lymphocytes and tumor clearance. Thus, hyporesponsive T cells can be epigenetically remodeled and reactivated by acetate, suggesting that pathways regulating the use of substrates alternative to glucose could be therapeutically targeted to promote T cell function during cancer.
    Keywords:  T cell exhaustion; T cell hyporesponsiveness; T cells; acetate; acetyl-CoA synthetase; chromatin remodeling; effector functions; tumor immunity; tumor-infiltrating lymphocytes
    DOI:  https://doi.org/10.1016/j.celrep.2019.04.022
  7. Metabolomics. 2019 May 13. 15(5): 78
    Mock A, Rapp C, Warta R, Abdollahi A, Jäger D, Sakowitz O, Brors B, von Deimling A, Jungk C, Unterberg A, Herold-Mende C.
      INTRODUCTION: Translational cancer research has seen an increasing interest in metabolomic profiling to decipher tumor phenotypes. However, the impact of post-surgical freezing delays on mass spectrometric metabolomic measurements of the cancer tissue remains elusive.OBJECTIVES: To evaluate the impact of post-surgical freezing delays on cancer tissue metabolomics and to investigate changes per metabolite and per metabolic pathway.
    METHODS: We performed untargeted metabolomics on three cortically located and bulk-resected glioblastoma tissues that were sequentially frozen as duplicates at up to six different time delays (0-180 min, 34 samples).
    RESULTS: Statistical modelling revealed that 10% of the metabolome (59 of 597 metabolites) changed significantly after a 3 h delay. While carbohydrates and energy metabolites decreased, peptides and lipids increased. After a 2 h delay, these metabolites had changed by as much as 50-100%. We present the first list of metabolites in glioblastoma tissues that are sensitive to post-surgical freezing delays and offer the opportunity to define individualized fold change thresholds for future comparative metabolomic studies.
    CONCLUSION: More researchers should take these pre-analytical factors into consideration when analyzing metabolomic data. We present a strategy for how to work with metabolites that are sensitive to freezing delays.
    Keywords:  MetaboDiff; Metabolome; Quenching; Snap-frozen
    DOI:  https://doi.org/10.1007/s11306-019-1541-2
  8. Methods Mol Biol. 2019 ;1983 79-106
    Lindahl AJ, Lawton AJ, Baeza J, Dowell JA, Denu JM.
      Posttranslational modifications of proteins control many complex biological processes, including genome expression, chromatin dynamics, metabolism, and cell division through a language of chemical modifications. Improvements in mass spectrometry-based proteomics have demonstrated protein acetylation is a widespread and dynamic modification in the cell; however, many questions remain on the regulation and downstream effects, and an assessment of the overall acetylation stoichiometry is needed. In this chapter, we describe the determination of acetylation stoichiometry using data-independent acquisition mass spectrometry to expand the number of acetylation sites quantified. However, the increased depth of data-independent acquisition is limited by the spectral library used to deconvolute fragmentation spectra. We describe a powerful approach of subcellular fractionation in conjunction with offline prefractionation to increase the depth of the spectral library. This deep interrogation of subcellular compartments provides essential insights into the compartment-specific regulation and downstream functions of protein acetylation.
    Keywords:  Acetylation; Chromatin; Mass spectrometry; Mitochondria; Posttranslational modification; Protein acetylation; Proteomics; Stoichiometry
    DOI:  https://doi.org/10.1007/978-1-4939-9434-2_6
  9. Clin Chim Acta. 2019 May 13. pii: S0009-8981(19)31862-5. [Epub ahead of print]
    Peng MZ, Cai YN, Shao YX, Zhao L, Jiang MY, Lin YT, Yin X, Sheng HY, Liu L.
      Urea cycle disorders (UCD) are inborn errors of ammonia detoxification in which early diagnosis and treatment are critical to prevent metabolic emergencies. Unfortunately, the diagnosis was often and pronounced delayed. To improve diagnosis, we developed herein a liquid chromatography-tandem mass spectrometry method to investigate the disturbance of amino acid profile caused by UCD. The method enabled absolute quantification of 48 amino acids (AAs) within 20 min. Only 2.5 μL plasma was required for the analysis. The lower limits of quantification for most AAs were 0.01 μmol/L. Method accuracies ranged from 89.9% to 113.4%. The within- and between-run coefficients of variation were 0.8-7.7% and 2.6-14.5%, respectively. With this method, age-specific reference values were established for 42 AAs by analyzing 150 samples from normal controls, and patients with different subtypes of UCD were successfully distinguished. The data of patients revealed that UCD not only disturbed the metabolism of urea cycle AAs and induced accumulation of ammonia detoxification AAs, but also interfered the metabolism of some nervous system related AAs, such as pipecolic acid and N-acetylaspartic acid. This data may provide new insight into pathogenesis for UCD.
    Keywords:  Amino acids; Homocitrulline; LC-MS/MS; Ornithine transcarbamylase deficiency; Urea cycle disorders
    DOI:  https://doi.org/10.1016/j.cca.2019.05.011
  10. Cell Syst. 2019 May 03. pii: S2405-4712(19)30115-2. [Epub ahead of print]
    Yang P, Humphrey SJ, Cinghu S, Pathania R, Oldfield AJ, Kumar D, Perera D, Yang JYH, James DE, Mann M, Jothi R.
      Pluripotency is highly dynamic and progresses through a continuum of pluripotent stem cell states. The two states that bookend the pluripotency continuum, naive and primed, are well characterized, but our understanding of the intermediate states and transitions between them remains incomplete. Here, we dissect the dynamics of pluripotent state transitions underlying pre- to post-implantation epiblast differentiation. Through comprehensive mapping of the proteome, phosphoproteome, transcriptome, and epigenome of embryonic stem cells transitioning from naive to primed pluripotency, we find that rapid, acute, and widespread changes to the phosphoproteome precede ordered changes to the epigenome, transcriptome, and proteome. Reconstruction of the kinase-substrate networks reveals signaling cascades, dynamics, and crosstalk. Distinct waves of global proteomic changes mark discrete phases of pluripotency, with cell-state-specific surface markers tracking pluripotent state transitions. Our data provide new insights into multi-layered control of the phased progression of pluripotency and a foundation for modeling mechanisms regulating pluripotent state transitions (www.stemcellatlas.org).
    Keywords:  EpiLC; MAPK/ERK; embryonic development; embryonic stem cells; epiblast; formative pluripotency; mTOR; pluripotency; protein phosphorylation; signaling
    DOI:  https://doi.org/10.1016/j.cels.2019.03.012
  11. Nat Commun. 2019 05 13. 10(1): 2137
    Lageveen-Kammeijer GSM, de Haan N, Mohaupt P, Wagt S, Filius M, Nouta J, Falck D, Wuhrer M.
      The in-depth, high-sensitivity characterization of the glycome from complex biological samples, such as biofluids and tissues, is of utmost importance in basic biological research and biomarker discovery. Major challenges often arise from the vast structural diversity of glycans in combination with limited sample amounts. Here, we present a method for the highly sensitive characterization of released N-glycans by combining a capillary electrophoresis-electrospray ionization-mass spectrometry (CE-ESI-MS) approach with linkage-specific derivatization of sialic acids and uniform cationic reducing end labelling of all glycans. This method allows the analysis of glycans at the attomole level, provides information on sialic acid isomers and enables the in-depth characterization of complex samples, even when available in minute amounts.
    DOI:  https://doi.org/10.1038/s41467-019-09910-7
  12. J Proteome Res. 2019 May 16.
    Shao C, Lu W, Wan N, Wu M, Bao Q, Tian Y, Lu G, Wang N, Hao H, Ye H.
      Metronomic chemotherapy, a relatively new dosing paradigm for anti-cancer therapy, is an alternative to traditional chemotherapy that uses maximal tolerated dose (MTD). Although these two dosing regimens both lead to tumor cell death, how cell metabolism is differentially affected during apoptosis remains elusive. Herein, we employed metabolomics to monitor the metabolic profiles of MCF-7 cells in response to the two dosing regimens that mimic MTD and MN treatments using a model chemotherapeutic drug, Doxorubicin (Dox), and correlated the changes of metabolic genes examined by PCR array to integratively describe the reprogrammed metabolic patterns. We found glycolysis, amino acid and nucleotide synthesis-associated metabolic pathways were activated in response to the MN treatment, whereas these pathways were pronouncedly inhibited in response to the MTD treatment. Direct supplementation of key metabolites and pharmacological modulation of targeted metabolic enzymes can both regulate cell fates. Subsequently, we tested the combined use of MN dosing with targeted metabolic intervention using a normal cell line, and found the combined treatment hardly affected its apoptotic rate. Our in vitro findings using MCF-7 and MCF-10A cells thus suggest the promising perspective of combining MN dosing of chemotherapeutic agents with metabolic modulation to selectively kill cancer cells rather than normal cells.
    DOI:  https://doi.org/10.1021/acs.jproteome.9b00138
  13. Proteomics. 2019 May 17. e1900068
    Kim T, Chen IR, Parker BL, Humphrey SJ, Crossett B, Cordwell SJ, Yang P, Yang JYH.
      The increasing role played by liquid chromatography-mass spectrometry (LC-MS)-based proteomics in biological discovery has led to a growing need for quality control on the LC-MS systems. While numerous quality control tools have been developed to track the performance of LC-MS systems based on a pre-defined set of performance factors (e.g. mass error, retention time), the precise influence and contribution of the performance factors and their generalization property to different biological samples are not as well characterized. Here, we developed a web-based application (QCMAP) for interactive diagnosis and prediction of the performance of LC-MS systems across different biological sample types. Leveraging on a standardized HeLa cell sample run as QC within a multi-user facility, we trained predictive models on a panel of commonly used performance factors to pinpoint the precise conditions to a (un)satisfactory performance in three LC-MS systems. We demonstrated that the learned model can be applied to predict LC-MS system performance for brain samples generated from an independent study. By compiling these predictive models into our web-application, QCMAP allows users to benchmark the performance of their LC-MS systems using their own samples and identify key factors for instrument optimization. QCMAP is freely available from: http://shiny.maths.usyd.edu.au/QCMAP/. This article is protected by copyright. All rights reserved.
    Keywords:  LC-MS; interactive web-tool; performance diagnosis; prediction; proteomics
    DOI:  https://doi.org/10.1002/pmic.201900068
  14. Metabolites. 2019 May 15. pii: E98. [Epub ahead of print]9(5):
    Pannkuk EL, Laiakis EC, Girgis M, Dowd SE, Dhungana S, Nishita D, Bujold K, Bakke J, Gahagen J, Authier S, Chang PY, Fornace AJ.
      Whole body exposure to ionizing radiation damages tissues leading to physical symptoms which contribute to acute radiation syndrome. Radiation biodosimetry aims to determine characteristic early biomarkers indicative of radiation exposure and is necessary for effective triage after an unanticipated radiological incident. Radiation metabolomics can address this aim by assessing metabolic perturbations following exposure. Gas chromatography-mass spectrometry (GC-MS) is a standardized platform ideal for compound identification. We performed GC time-of-flight MS for the global profiling of nonhuman primate urine and serum samples up to 60 d after a single 4 Gy γ-ray total body exposure. Multivariate statistical analysis showed higher group separation in urine vs. serum. We identified biofluid markers involved in amino acid, lipid, purine, and serotonin metabolism, some of which may indicate host microbiome dysbiosis. Sex differences were observed for amino acid fold changes in serum samples. Additionally, we explored mitochondrial dysfunction by tricarboxylic acid intermediate analysis in the first week with a GC tandem quadrupole MS platform. By adding this temporal component to our previous work exploring dose effects at 7 d, we observed the highest fold changes occurring at 3 d, returning closer to basal levels by 7 d. These results emphasize the utility of both MS-based metabolomics for biodosimetry and complementary analytical platforms for increased metabolome coverage.
    Keywords:  GC-MS; acute radiation syndrome; biodosimetry; ionizing radiation; mass spectrometry; metabolomics; nonhuman primates
    DOI:  https://doi.org/10.3390/metabo9050098
  15. Cancers (Basel). 2019 May 15. pii: E675. [Epub ahead of print]11(5):
    Choi BH, Coloff JL.
      Far beyond simply being 11 of the 20 amino acids needed for protein synthesis, non-essential amino acids play numerous important roles in tumor metabolism. These diverse functions include providing precursors for the biosynthesis of macromolecules, controlling redox status and antioxidant systems, and serving as substrates for post-translational and epigenetic modifications. This functional diversity has sparked great interest in targeting non-essential amino acid metabolism for cancer therapy and has motivated the development of several therapies that are either already used in the clinic or are currently in clinical trials. In this review, we will discuss the important roles that each of the 11 non-essential amino acids play in cancer, how their metabolic pathways are linked, and how researchers are working to overcome the unique challenges of targeting non-essential amino acid metabolism for cancer therapy.
    Keywords:  arginine; asparagine; aspartate; cancer; cysteine; glutamate; glutamine; glycine; proline; serine
    DOI:  https://doi.org/10.3390/cancers11050675
  16. J Biol Chem. 2019 May 16. pii: jbc.RA118.006074. [Epub ahead of print]
    Ghosh S, Wicks SE, Vandanmagsar B, Mendoza TM, Bayless DS, Salbaum JM, Dearth SP, Campagna SR, Mynatt RL, Noland RC.
      Mitochondrial lipid overload in skeletal muscle contributes to insulin resistance and strategies limiting this lipid pressure improve glucose homeostasis; however, comprehensive cellular adaptations that occur in response to such an intervention have not been reported. Herein mice with skeletal muscle-specific deletion of carnitine palmitoyltransferase 1b (Cpt1bM-/-), which limits mitochondrial lipid entry, were fed a moderate fat (25%) diet and samples were subjected to a multi-modal analysis merging transcriptomics, proteomics, and non-targeted metabolomics to characterize the coordinated multi-level cellular responses that occur when mitochondrial lipid burden is mitigated. Limiting mitochondrial fat entry predictably improves glucose homeostasis; however, remodeling of glucose metabolism pathways pale in comparison to adaptations in amino acid and lipid metabolism pathways, shifts in nucleotide metabolites, and biogenesis of mitochondria and peroxisomes. Despite impaired fat utilization, Cpt1bM-/- mice have increased acetyl-CoA (14-fold) and NADH (2-fold), indicating metabolic shifts yield sufficient precursors to meet energy demand; however, this doesn't translate to enhance energy status as Cpt1bM-/- mice have low ATP and high AMP levels, signifying energy deficit. Comparative analysis of transcriptomic data with disease-associated gene-sets not only predicted reduced risk of glucose metabolism disorders, but were also consistent with lower risk for hepatic steatosis, cardiac hypertrophy, and premature death. Collectively these results suggest induction of metabolic inefficiency under conditions of energy surfeit likely contribute to improvements in metabolic health when mitochondrial lipid burden is mitigated. Moreover, the breadth of disease states to which mechanisms induced by muscle-specific Cpt1b inhibition may mediate health benefits could be more extensive than previously predicted.
    Keywords:  fatty acid metabolism; genomics; glucose metabolism; lipid oxidation; metabolomics; mitochondria; peroxisome; proteomics; skeletal muscle metabolism; systems biology
    DOI:  https://doi.org/10.1074/jbc.RA118.006074
  17. Mol Cell Proteomics. 2019 May 14. pii: mcp.TIR118.001209. [Epub ahead of print]
    Brademan DR, Riley NM, Kwiecien NW, Coon JJ.
      Here we present IPSA, an innovative web-based spectrum annotator that visualizes and characterizes peptide tandem mass spectra. A tool for the scientific community, IPSA can visualize peptides collected using a wide variety of experimental and instrumental configurations. Annotated spectra are customizable via a selection of interactive features and can be exported as editable scalable vector graphics to aid in the production of publication-quality figures. Single spectra can be analyzed through provided web forms, while data for multiple peptide spectral matches can be uploaded using the Proteomics Standards Initiative file formats mzTab, mzIdentML, and mzML. Alternatively, peptide identifications and spectral data can be provided using generic file formats.  IPSA provides supports for annotating spectra collecting using negative-mode ionization and facilitates the characterization of experimental MS/MS performance through the optional export of fragment ion statistics from one to many peptide spectral matches. This resource is made freely accessible at http://interactivepeptidespectralannotator.com, while the source code and user guides are available at https://github.com/coongroup/IPSA for private hosting or custom implementations.
    Keywords:  Bioinformatics; Bioinformatics software; Data evaluation; Mass Spectrometry; Peptides*; Quality control and metrics; Tandem Mass Spectrometry
    DOI:  https://doi.org/10.1074/mcp.TIR118.001209
  18. Br J Cancer. 2019 May 16.
    Munir R, Lisec J, Swinnen JV, Zaidi N.
      Cancer cells are often exposed to a metabolically challenging environment with scarce availability of oxygen and nutrients. This metabolic stress leads to changes in the balance between the endogenous synthesis and exogenous uptake of fatty acids, which are needed by cells for membrane biogenesis, energy production and protein modification. Alterations in lipid metabolism and, consequently, lipid composition have important therapeutic implications, as they affect the survival, membrane dynamics and therapy response of cancer cells. In this article, we provide an overview of recent insights into the regulation of lipid metabolism in cancer cells under metabolic stress and discuss how this metabolic adaptation helps cancer cells thrive in a harsh tumour microenvironment.
    DOI:  https://doi.org/10.1038/s41416-019-0451-4
  19. Stat Appl Genet Mol Biol. 2019 May 11. pii: /j/sagmb.2019.18.issue-3/sagmb-2018-0039/sagmb-2018-0039.xml. [Epub ahead of print]18(3):
    Liang Y, Kelemen A, Kelemen A.
      Reproducibility of disease signatures and clinical biomarkers in multi-omics disease analysis has been a key challenge due to a multitude of factors. The heterogeneity of the limited sample, various biological factors such as environmental confounders, and the inherent experimental and technical noises, compounded with the inadequacy of statistical tools, can lead to the misinterpretation of results, and subsequently very different biology. In this paper, we investigate the biomarker reproducibility issues, potentially caused by differences of statistical methods with varied distribution assumptions or marker selection criteria using Mass Spectrometry proteomic ovarian tumor data. We examine the relationship between effect sizes, p values, Cauchy p values, False Discovery Rate p values, and the rank fractions of identified proteins out of thousands in the limited heterogeneous sample. We compared the markers identified from statistical single features selection approaches with machine learning wrapper methods. The results reveal marked differences when selecting the protein markers from varied methods with potential selection biases and false discoveries, which may be due to the small effects, different distribution assumptions, and p value type criteria versus prediction accuracies. The alternative solutions and other related issues are discussed in supporting the reproducibility of findings for clinical actionable outcomes.
    Keywords:  false discovery rate; mass spectrometry; ovarian cancer; p value; proteomics; reproducibility
    DOI:  https://doi.org/10.1515/sagmb-2018-0039
  20. Metabolomics. 2019 May 13. 15(5): 77
    Zhang T, Xu J, Liu Y, Liu J.
      INTRODUCTION: Dermatomyositis (DM) is a rare autoimmune myopathy characterized by skin lesions, proximal muscle weakness and muscle inflammation. The pathogenesis of DM is unclear, and identification of reliable biomarkers for early diagnosis of DM is critical for design of a specific therapy for this disease.OBJECTIVES: To find and identify potential serum biomarkers in DM patients.
    METHODS: We performed an untargeted metabolomic approach using UHPLC-MS/MS. The blood serum metabolomic profiles of 26 DM patients and 26 healthy controls were collected. Multivariate analysis of the metabolomic profile was applied to differentiate DM patients and controls and to find potential biomarkers.
    RESULTS: A significantly disturbed metabolic profile of DM patients was observed. Pathway analysis showed that aminoacyl-tRNA biosynthesis, phenylalanine, tyrosine and tryptophan biosynthesis, and nitrogen metabolism are the most prominently altered pathways in DM. Receiver operating characteristic curve indicated that glutamine, methionine, isoleucine, tryptophan, glutamic acid, indole, protocatechuic acid, and phenylalanine were potential biomarkers for DM diagnosis in terms of both sensitivity and specificity.
    CONCLUSIONS: Our study provides new insight into underlying mechanisms of DM, and we suggest that we should pay more attention to these metabolic pathways in the prevention and treatment of DM.
    Keywords:  Biomarker; Dermatomyositis; LC–MS; Metabolic pathways; Metabolomics
    DOI:  https://doi.org/10.1007/s11306-019-1539-9
  21. Cancer Metab. 2019 ;7 5
    Rosso M, Lapyckyj L, Besso MJ, Monge M, Reventós J, Canals F, Quevedo Cuenca JO, Matos ML, Vazquez-Levin MH.
      Background: Breast cancer (BC) is the most common female cancer and the leading cause of cancer death in women worldwide. Alterations in epithelial cadherin (E-cadherin) expression and functions are associated to BC, but the underlying molecular mechanisms have not been fully elucidated. We have previously reported a novel human E-cadherin splice variant (E-cadherin variant) mRNA. Stable transfectants in MCF-7 human BC cells (MCF7Ecadvar) depicted fibroblast-like cell morphology, E-cadherin wild-type downregulation, and other molecular changes characteristic of the epithelial-to-mesenchymal transition process, reduced cell-cell adhesion, and increased cell migration and invasion. In this study, a two-dimensional differential gel electrophoresis (2D-DIGE) combined with mass spectrometry (MS) protein identification and bioinformatics analyses were done to characterize biological processes and canonical pathways affected by E-cadherin variant expression.Results: By 2D-DIGE and MS analysis, 50 proteins were found differentially expressed (≥ Δ1.5) in MCF7Ecadvar compared to control cells. Validation of transcript expression was done in the ten most overexpressed and underexpressed proteins. Bioinformatics analyses revealed that 39 of the 50 proteins identified had been previously associated to BC. Moreover, metabolic processes were the most affected, and glycolysis the canonical pathway most altered. The lactate dehydrogenase B (LDHB) was the highest overexpressed protein, and transcript levels were higher in MCF7Ecadvar than in control cells. In agreement with these findings, MCF7Ecadvar conditioned media had lower glucose and higher lactate levels than control cells. MCF7Ecadvar cell treatment with 5 mM of the glycolytic inhibitor 2-deoxy-glucose led to decreased cell viability, and modulation of LDHB expression in MCF7Ecadvar cells with a specific small interfering RNA resulted in decreased cell proliferation. Finally, a positive association between expression levels of the E-cadherin variant and LDHB transcripts was demonstrated in 21 human breast tumor tissues, and breast tumor samples with higher Ki67 expression showed higher LDHB mRNA levels.
    Conclusions: Results from this investigation contributed to further characterize molecular changes associated to the novel E-cadherin splice variant expression in BC cells. They also revealed an association between expression of the novel variant and changes related to BC progression and aggressiveness, in particular those associated to cell metabolism.
    Keywords:  2D-DIGE; Alternative splicing; Breast cancer; Epithelial cadherin; Epithelial to mesenchymal transition; Glycolysis; Lactate dehydrogenase B; Mass spectrometry; Proteomic analysis
    DOI:  https://doi.org/10.1186/s40170-019-0196-9
  22. Prostaglandins Other Lipid Mediat. 2019 May 11. pii: S1098-8823(18)30086-8. [Epub ahead of print] 106337
    Watson JE, Kim JS, Das A.
      Cannabinoid receptor activation is involved in homeostatic regulation of the body. These receptors are activated by cannabinoids, that include the active constituents of Cannabis sativa as well as endocannabinoids (eCBs). The eCBs are endogenously synthesized from the omega-6 and omega-3 polyunsaturated fatty acids (PUFAs). The consumption of omega-3 fatty acids shifts the balance towards a higher proportion of omega-3 eCBs, whose physiological functions warrants further investigation. Herein, we review the discovery of omega-3 fatty acid derived eCBs that are generated from long chain omega-3 PUFAs - docosahexaenoyl ethanolamide (DHA-EA or synaptamide), docosahexanoyl-glycerol (DHG), eicosapentaenoyl ethanolamide (EPA-EA), eicosapentanoylglycerol (EPG). Furthermore, we outline the lesser known omega-3 eCB-like molecules that arise from the conjugation of the omega-3 fatty acids with neurotransmitters serotonin and dopamine - DHA-serotonin (DHA-5HT), EPA-serotonin (EPA-5HT), DHA-dopamine (DHA-DA) and EPA-dopamine (EPA-DA). Additionally, we describe the role of these omega-3 eCBs and their derivatives in different disease states such as pain, inflammation and cancer. Moreover, we detail the formation and potential physiological roles of the oxidative metabolites that arise from the metabolism of omega-3 eCBs by eicosanoid synthesizing enzymes - cyclooxygenase (COX), lipoxygenase (LOX) and cytochrome P450 epoxygenase (CYP450). In summary, we outline the novel findings regarding a growing class of signaling molecules, omega-3 eCBs, that can control the physiological and pathophysiological processes in the body.
    Keywords:  Endocannabinoids; cancer; inflammation; metabolism; omega-3 fatty acids
    DOI:  https://doi.org/10.1016/j.prostaglandins.2019.106337
  23. J Proteome Res. 2019 May 13.
    Huffman RG, Chen AT, Specht H, Slavov N.
      The performance of ultrasensitive LC-MS/MS methods, such as Single-Cell Proteomics by Mass Spectrometry (SCoPE-MS), depends on multiple interdependent parameters. This interdependence makes it challenging to specifically pinpoint sources of problems in the LC-MS/MS methods and approaches for resolving them. For example, low signal at MS2 level can be due to poor LC separation, ionization, apex targeting, ion transfer, or ion detection. We sought to specifically diagnose such problems by interactively visualizing data from all levels of bottom-up LC-MS/MS analysis. Many search engines, such as MaxQuant, already provide such data, and we developed an open source platform for their interactive visualization and analysis: Data-driven Optimization of MS (DO-MS). We found that in many cases DO-MS not only specifically diagnosed problems but also enabled us to rationally optimize them. For example, by using DO-MS to optimize the sampling of the elution peak apices, we increased ion accumulation times and apex sampling, which resulted in 370 % more efficient delivery of ions for MS2 analysis. DO-MS is easy to install and use, and its GUI allows for interactive data subsetting and high-quality figure generation. The modular design of DO-MS facilitates customization and expansion. DO-MS is available for download from GitHub: https://github.com/SlavovLab/DO-MS.
    DOI:  https://doi.org/10.1021/acs.jproteome.9b00039
  24. Methods Mol Biol. 2019 ;1983 3-16
    Schilling B, Meyer JG, Wei L, Ott M, Verdin E.
      The dynamic nature of protein posttranslational modification (PTM) allows cells to rapidly respond to changes in their environment, such as nutrition, stress, or signaling. Lysine residues are targets for several types of modifications, including methylation, ubiquitination, and various acylation groups, especially acetylation. Currently, one of the best methods for identification and quantification of protein acetylation is immunoaffinity enrichment in combination with high-resolution mass spectrometry. As we are using a relatively novel and comprehensive mass spectrometric approach, data-independent acquisition (DIA), this protocol provides high-throughput, accurate, and reproducible label-free PTM quantification. Here we describe detailed protocols to process relatively small amounts of mouse liver tissue that integrate isolation of proteins, proteolytic digestion into peptides, immunoaffinity enrichment of acetylated peptides, identification of acetylation sites, and comprehensive quantification of relative abundance changes for thousands of identified lysine acetylation sites.
    Keywords:  Acetylation; Data-independent acquisition; Mass spectrometry; Posttranslational modifications; Quantification
    DOI:  https://doi.org/10.1007/978-1-4939-9434-2_1
  25. Xenobiotica. 2019 May 16. 1-27
    Zhou X, Li Z, Wang X, Jiang G, Shan C, Liu S.
      1. Breast cancer is one of the most common malignancies in women worldwide. Metabolomics has been shown to be a promising strategy to elucidate the underlying pathogenesis of cancer and identify new targets for cancer diagnosis and therapy. Valproic acid (VPA), a histone deacetylase inhibitor, is a potential new drug in tumor therapy. This work used metabolomics to examine the effect of VPA on metabolism in breast cancer cells. 2. Based on UPLC-MS/MS, we identified 3137 differential metabolites in human breast cancer MCF-7 cells and 2472 differential metabolites in human breast cancer MDA-MB-231 cells after VPA treatment. 3. We selected 63 differential metabolites from MCF-7 samples and 61 differential metabolites from MDA-MB-231 cells with the more conspicuous changing trend. Furfural was up-regulated after VPA treatment in both cell lines. In both samples, VPA exerted an effect on the beta-alanine metabolism pathway and the taurine and hypotaurine metabolism pathway. 4. This study identified the effect of VPA on metabolites and metabolic pathways in breast cancer cells, and these findings may contribute to the identification of new targets for breast cancer treatment.
    Keywords:  Breast cancer; Metabolomics; UPLC-MS/MS; Valproic acid
    DOI:  https://doi.org/10.1080/00498254.2019.1618510
  26. J Biol Chem. 2019 May 12. pii: jbc.RA119.008766. [Epub ahead of print]
    Liu GY, Moon SH, Jenkins CM, Sims HF, Guan S, Gross RW.
      Recently, oxidized phospholipid species have emerged as important signaling lipids in activated immune cells and platelets. The canonical pathway for the synthesis of oxidized phospholipids is through the release of arachidonic acid by cytosolic phospholipase A2α (cPLA2α) followed by its enzymatic oxidation, activation of the carboxylate anion by acyl-CoA synthetase(s), and re-esterification to the sn-2 position by sn-2 acyltransferase activity (i.e. the Lands cycle). However, recent studies have demonstrated the unanticipated significance of sn-1 hydrolysis of arachidonoyl-containing choline and ethanolamine glycerophospholipids by other phospholipases to generate the corresponding 2-arachidonoyl-lysolipids. Herein, we identified a pathway for oxidized phospholipid synthesis comprising sequential sn-1 hydrolysis by a phospholipase A1 (e.g. by patatin-like phospholipase domain-containing 8 [PNPLA8]), direct enzymatic oxidation of the resultant 2-arachidonoyl lysophospholipids  and the esterification of oxidized 2-arachidonoyl lysophospholipids by acyl-CoA dependent sn-1 acyltransferase(s). To circumvent ambiguities associated with acyl migration or hydrolysis, we developed a synthesis for optically active (D and L enantiomers) non-hydrolyzable analogues of 2-AA-LPC. sn-1 acyl transferase activity in murine liver microsomes stereospecifically and preferentially utilized the naturally occurring L-enantiomer of the ether analog of lysophosphatidylcholine. Next, we demonstrated the high selectivity of the sn-1 acyl transferase activity for saturated acyl-CoA species. Importantly, we established that 2-15-HETE ether-LPC sn-1 esterification is markedly activated by thrombin treatment of murine platelets to generate oxidized PC. Collectively, these findings demonstrate the enantiomeric specificity and saturated acyl-CoA selectivity of microsomal sn-1 acyltransferase(s) and reveal its participation in a previously uncharacterized pathway for the synthesis of oxidized phospholipids with cell-signaling properties.
    Keywords:  Phospholipase A; acyltransferase; lipid metabolism; lipid peroxidation; lipid synthesis; lipidomics; lysophospholipid; mass spectrometry (MS); oxidized lysophospholipid; oxidized phospholipid; phospholipid; sn-1 acyltransferase; stereoselectivity
    DOI:  https://doi.org/10.1074/jbc.RA119.008766
  27. Cancers (Basel). 2019 May 16. pii: E678. [Epub ahead of print]11(5):
    Combs JA, DeNicola GM.
      The non-essential amino acid cysteine is used within cells for multiple processes that rely on the chemistry of its thiol group. Under physiological conditions, many non-transformed tissues rely on glutathione, circulating cysteine, and the de novo cysteine synthesis (transsulfuration) pathway as sources of intracellular cysteine to support cellular processes. In contrast, many cancers require exogeneous cystine for proliferation and viability. Herein, we review how the cystine transporter, xCT, and exogenous cystine fuel cancer cell proliferation and the mechanisms that regulate xCT expression and activity. Further, we discuss the potential contribution of additional sources of cysteine to the cysteine pool and what is known about the essentiality of these processes in cancer cells. Finally, we discuss whether cyst(e)ine dependency and associated metabolic alterations represent therapeutically targetable metabolic vulnerabilities.
    Keywords:  CBS; CSE; GGT; cystathionine; cysteine; cystine; glutathione; macropinocytosis; transsulfuration; xCT
    DOI:  https://doi.org/10.3390/cancers11050678
  28. Semin Cell Dev Biol. 2019 May 11. pii: S1084-9521(18)30202-7. [Epub ahead of print]
    Schmidt C, Sciacovelli M, Frezza C.
      Cancer is now considered a multifactorial disorder with different aetiologies and outcomes. Yet, all cancers share some common molecular features. Among these, the reprogramming of cellular metabolism has emerged as a key player in tumour initiation and progression. The finding that metabolic enzymes such as fumarate hydratase (FH), succinate dehydrogenase (SDH) and isocitrate dehydrogenase (IDH), when mutated, cause cancer suggested that metabolic dysregulation is not only a consequence of oncogenic transformation, but that it can act as cancer driver. However, the mechanisms underpinning the link between metabolic dysregulation and cancer remain only partially understood. In this review we discuss the role of FH loss in tumorigenesis, focusing on the role of fumarate as a key activator of a variety of oncogenic cascades. We also discuss how these alterations are integrated and converge towards common biological processes. This review highlights the complexity of the signals elicited by FH loss, describes that fumarate can act as a bona fide oncogenic event, and provides a compelling hypothesis of the step wise neoplastic progression after FH loss.
    Keywords:  FH; cancer; fumarate; metabolism; mitochondria
    DOI:  https://doi.org/10.1016/j.semcdb.2019.05.002
  29. Cancer Discov. 2019 May 17.
      The heterodimeric KMT9 complex regulates prostate cancer cell proliferation via H4K12 monomethylation.
    DOI:  https://doi.org/10.1158/2159-8290.CD-RW2019-074
  30. Expert Rev Proteomics. 2019 May 16. 1-8
    Giusti L, Angeloni C, Lucacchini A.
      INTRODUCTION: This review is an update on recent progress in proteomic studies of formalin-fixed paraffin-embedded (FFPE) tissues, which open the opportunity to investigate diseases and research potential biomarkers, particularly when availability of fresh/frozen tissues is low. Areas covered: We described improvement of existing protocols or the new ones regarding deparaffinization and protein extraction of FFPE samples published from 2014 to today. Moreover, the growing interest to use FFPE tissues for mass spectrometry imaging approach is presented together with the search of post-translational modifications. Expert opinion: In the last few years, the number of papers using FFPE tissues in proteomic analysis is growing. The interest to apply proteomic analysis to FFPE tissues lies in the easy accessibility of a great number of samples from archives. Nevertheless, standardization in the approach among the different researchers is not achieved, making essentially incomparable the results obtained. This limit should be overcome.
    Keywords:  Biomarkers; cancer; formalin-fixed paraffin-embedded tissues; fresh/frozen tissues; imaging mass spectrometry; mass spectrometry; proteomics
    DOI:  https://doi.org/10.1080/14789450.2019.1615452
  31. Br J Cancer. 2019 May 16.
    Frantzi M, Gomez Gomez E, Blanca Pedregosa A, Valero Rosa J, Latosinska A, Culig Z, Merseburger AS, Luque RM, Requena Tapia MJ, Mischak H, Carrasco Valiente J.
      BACKGROUND: Prostate cancer progresses slowly when present in low risk forms but can be lethal when it progresses to metastatic disease. A non-invasive test that can detect significant prostate cancer is needed to guide patient management.METHODS: Capillary electrophoresis/mass spectrometry has been employed to identify urinary peptides that may accurately detect significant prostate cancer. Urine samples from 823 patients with PSA (<15 ng/ml) were collected prior to biopsy. A case-control comparison was performed in a training set of 543 patients (nSig = 98; nnon-Sig = 445) and a validation set of 280 patients (nSig = 48, nnon-Sig = 232). Totally, 19 significant peptides were subsequently combined by a support vector machine algorithm.
    RESULTS: Independent validation of the 19-biomarker model in 280 patients resulted in a 90% sensitivity and 59% specificity, with an AUC of 0.81, outperforming PSA (AUC = 0.58) and the ERSPC-3/4 risk calculator (AUC = 0.69) in the validation set.
    CONCLUSIONS: This multi-parametric model holds promise to improve the current diagnosis of significant prostate cancer. This test as a guide to biopsy could help to decrease the number of biopsies and guide intervention. Nevertheless, further prospective validation in an external clinical cohort is required to assess the exact performance characteristics.
    DOI:  https://doi.org/10.1038/s41416-019-0472-z
  32. Alcohol Alcohol. 2019 May 01. 54(3): 225-234
    Voutilainen T, Kärkkäinen O.
      AIMS: The metabolome refers to the functional status of the cell, organ or the whole body. Metabolomic methods measure the metabolome (metabolite profile) which can be used to examine disease progression and treatment responses. Here, our aim was to review metabolomics studies examining effects of alcohol use in humans.METHODS: We performed a literature search using PubMed and Web of Science for reports on changes in the human metabolite profile associated with alcohol use; we found a total of 23 articles published before end of 2018.
    RESULTS: Most studies had investigated plasma, serum or urine samples; only four studies had examined other sample types (liver, faeces and broncho-alveolar lavage fluid). Levels of 51 metabolites were altered in two or more of the reviewed studies. Alcohol use was associated with changes in the levels of lipids and amino acids. In general, levels of fatty acids, phosphatidylcholine diacyls and steroid metabolites tended to increase, whereas those of phosphatidylcholine acyl-alkyls and hydroxysphingomyelins declined. Common alterations in circulatory levels of amino acids included decreased levels of glutamine, and increased levels of tyrosine and alanine.
    CONCLUSIONS: More studies, especially with a longitudinal study design, or using more varied sample materials (e.g. organs or saliva), are needed to clarify alcohol-induced diseases and alterations at a target organ level. Hopefully, this will lead to the discovery of new treatments, improved recognition of individuals at high risk and identification of those subjects who would benefit most from certain treatments.
    DOI:  https://doi.org/10.1093/alcalc/agz030
  33. Methods Mol Biol. 2019 ;1983 17-27
    Agudelo Garcia PA, Gardner M, Freitas MA, Parthun MR.
      Replication-coupled chromatin assembly is a very dynamic process that involves not only the replication fork machinery but also chromatin-related factors such as histones, histone chaperones, histone-modifying enzymes, and chromatin remodelers which ensure not only that the genetic information is properly replicated but also that the epigenetic code is reestablished in the daughter cell. Of the histone modifications associated with chromatin assembly, acetylation is the most abundant. Determining how newly synthesized histones get acetylated and what factors affect this modification is vital to understanding how cells manage to properly duplicate the epigenome. Here we describe a combination of the iPOND, quantitative mass spectrometry, and SILAC methodologies to study the protein composition of newly assembled chromatin and the modification state of the associated histones.
    Keywords:  Acetylation; Histone; Mass spectrometry; Nascent chromatin; SILAC
    DOI:  https://doi.org/10.1007/978-1-4939-9434-2_2
  34. High Throughput. 2019 May 14. pii: E13. [Epub ahead of print]8(2):
    Guo J, Turesky RJ.
      The measurement of DNA adducts, the covalent modifications of DNA upon the exposure to the environmental and dietary genotoxicants and endogenously produced electrophiles, provides molecular evidence for DNA damage. With the recent improvements in the sensitivity and scanning speed of mass spectrometry (MS) instrumentation, particularly high-resolution MS, it is now feasible to screen for the totality of DNA damage in the human genome through DNA adductomics approaches. Several MS platforms have been used in DNA adductomic analysis, each of which has its strengths and limitations. The loss of 2'-deoxyribose from the modified nucleoside upon collision-induced dissociation is the main transition feature utilized in the screening of DNA adducts. Several advanced data-dependent and data-independent scanning techniques originated from proteomics and metabolomics have been tailored for DNA adductomics. The field of DNA adductomics is an emerging technology in human exposure assessment. As the analytical technology matures and bioinformatics tools become available for analysis of the MS data, DNA adductomics can advance our understanding about the role of chemical exposures in DNA damage and disease risk.
    Keywords:  Carcinogens; DNA adducts; adductomics; mass spectrometry
    DOI:  https://doi.org/10.3390/ht8020013
  35. Anal Chim Acta. 2019 Sep 03. pii: S0003-2670(19)30422-2. [Epub ahead of print]1069 89-97
    Liu W, Song Q, Cao Y, Zhao Y, Huo H, Wang Y, Song Y, Li J, Tu P.
      Either widely targeted metabolomics or quantitative proteomics usually requires unique analytical platform. However, cross-platform omics studies entail higher levels of complexity and uncertainty, and result in a significant obstacle for high throughput assay as well. It is thereby urgent to pursue an integrative approach being capable of merging these two omics terms, namely widely targeted bi-omics. As an eligible analytical tool for large-scale targeted metabolomics, reversed phase liquid chromatography-hydrophilic interaction liquid chromatography-tailored selected reaction monitoring (RPLC-HILIC-tailored SRM) was deployed here to further receive the tryptic peptides as the analytes. Comparative evaluation of metabolites and tryptic peptides, 101 ones in total, between HepG2 and SK-Hep1 cells was conducted as a proof-of-concept. All analytes, regardless of metabolites or peptides, exhibited satisfactory chromatographic behaviors on RPLC-HILIC. Quantitative MS parameters, such as SRM transitions and collision energies (CEs), of either tryptic peptides or metabolites were online optimized in a standard compound-independent manner. It was worthwhile to mention that the signal responses of the peptides-of-choice generated by the optimized CEs were significantly superior to those values suggested by Skyline software. Calibration curves of both metabolites and peptides were constructed by serially diluting a so-called universal metabolome standard (UMS) sample. The quasi-content of each peptide or metabolite was gained according to applying those regressive calibration curves. After subjecting the quasi-content dataset into SIMCA-P software, significant differences took place between the two hepatic cell lines, and not only metabolites but tryptic peptides contributed to the discrimination. Above all, RPLC-HILIC-tailored SRM offered a promising choice towards widely targeted bi-omics attributing to the advantage of simultaneous monitoring metabolites and tryptic peptides.
    Keywords:  Quasi-content; Serially coupled reversed phase liquid chromatography and hydrophilic interaction liquid chromatography; Standard compound-free mass spectrometric parameter optimization; Tryptic peptide; Widely targeted bi-omics
    DOI:  https://doi.org/10.1016/j.aca.2019.04.013
  36. Nat Protoc. 2019 May 15.
    Purcell AW, Ramarathinam SH, Ternette N.
      Peptide antigens bound to molecules encoded by the major histocompatibility complex (MHC) and presented on the cell surface form the targets of T lymphocytes. This critical arm of the adaptive immune system facilitates the eradication of pathogen-infected and cancerous cells, as well as the production of antibodies. Methods to identify these peptide antigens are critical to the development of new vaccines, for which the goal is the generation of effective adaptive immune responses and long-lasting immune memory. Here, we describe a robust protocol for the identification of MHC-bound peptides from cell lines and tissues, using nano-ultra-performance liquid chromatography coupled to high-resolution mass spectrometry (nUPLC-MS/MS) and recent improvements in methods for isolation and characterization of these peptides. The protocol starts with the immunoaffinity capture of naturally processed MHC-peptide complexes. The peptides dissociate from the class I human leukocyte antigens (HLAs) upon acid denaturation. This peptide cargo is then extracted and separated into fractions by HPLC, and the peptides in these fractions are identified using nUPLC-MS/MS. With this protocol, several thousand peptides can be identified from a wide variety of cell types, including cancerous and infected cells and those from tissues, with a turnaround time of 2-3 d.
    DOI:  https://doi.org/10.1038/s41596-019-0133-y
  37. Cancer Discov. 2019 May 17.
      The tumorigenic potential of tumor-initiating cells (TIC) is dependent upon the methionine cycle.
    DOI:  https://doi.org/10.1158/2159-8290.CD-RW2019-073
  38. Free Radic Biol Med. 2019 May 11. pii: S0891-5849(19)30445-9. [Epub ahead of print]
    Gladine C, Ostermann AI, Newman JW, Schebb NH.
      Oxylipins, including the well-known eicosanoids, are potent lipid mediators involved in numerous physiological and pathological processes. Therefore, their quantitative profiling has gained a lot of attention during the last years notably in the active field of health biomarker discovery. Oxylipins include hundreds of structurally and stereochemically distinct lipid species which today are most commonly analyzed by (ultra) high performance liquid chromatography-mass spectrometry based ((U)HPLC-MS) methods. To maximize the utility of oxylipin profiling in clinical research, it is crucial to understand and assess the factors contributing to the analytical and biological variability of oxylipin profiles in humans. In this review, these factors and their impacts are summarized and discussed, providing a framework for recommendations expected to enhance the interlaboratory comparability and biological interpretation of oxylipin profiling in clinical research.
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2019.05.012
  39. J Mass Spectrom. 2019 May 13.
    Damont A, Olivier MF, Warnet A, Lyan B, Pujos-Guillot E, Jamin EL, Debrauwer L, Bernillon S, Junot C, Tabet JC, Fenaille F.
      Nowadays, high-resolution mass spectrometry is widely used for metabolomic studies. Thanks to its high sensitivity, it enables the detection of a large range of metabolites. In metabolomics, the continuous quest for a metabolite identification as complete and accurate as possible has led during the last decade to an ever increasing development of public MS databases (including LC-MS data) concomitantly with bioinformatic tool expansion. To facilitate the annotation process of MS profiles obtained from biological samples, but also to ease data sharing, exchange and exploitation, the standardization and harmonization of the way to describe and annotate mass spectra seemed crucial to us. Indeed, under electrospray (ESI) conditions, a single metabolite does not produce a unique ion corresponding to its protonated or deprotonated form but could lead to a complex mixture of signals. These MS signals result from the existence of different natural isotopologues of the same compound and also to the potential formation of adduct ions, homo and hetero-multimeric ions, fragment ions resulting from "prompt" in-source dissociations. As a joint reflection process within the French Infrastructure for Metabolomics and Fluxomics (MetaboHUB) and with the purpose of developing a robust and exchangeable annotated MS database made from pure reference compounds (chemical standards) analysis, it appeared to us that giving the metabolomics community some clues to standardize and unambiguously annotate each MS feature, was a prerequisite to data entry and further efficient querying of the database. The use of a harmonized notation is also mandatory for inter-laboratory MS data exchange. Additionally, thorough description of the variety of MS signals arising from the analysis of a unique metabolite might provide greater confidence on its annotation.
    Keywords:  Annotation; High-resolution mass spectrometry; MS databases; Mass spectra; Metabolomics
    DOI:  https://doi.org/10.1002/jms.4372
  40. Mol Cell Proteomics. 2019 May 16. pii: mcp.TIR119.001505. [Epub ahead of print]
    Kiweler M, Looso M, Graumann J.
      In the context of publishing data sets acquired by mass spectrometry or works based on such molecular screens, metadata documenting the instrument settings are of central importance to the evaluation and reproduction of results. A single experiment may be linked to hundreds of data acquisitions, which are frequently stored in proprietary file formats. Together with community-, repository-, as well as publisher-specific reporting standards, this state of affairs frequently leads to manual -and thus error prone- metadata extraction and formatting. Data extracted from a single file also often stand in for an entire file set, implying a risk for unreported parameter divergence. In order to support quality control and data reporting, the C# application MARMoSET extracts and reduces publication relevant metadata from Thermo Fischer Scientific RAW files. It is integrated with an R package for easy reporting. The tool is expected to be particularly useful to high throughput environments such as service facilities with large project numbers and/or sizes.
    Keywords:  Bioinformatics; Bioinformatics software; Data standards; Mass Spectrometry; Quality control and metrics
    DOI:  https://doi.org/10.1074/mcp.TIR119.001505
  41. J Nutr. 2019 May 16. pii: nxz048. [Epub ahead of print]
    Malik VS, Guasch-Ferre M, Hu FB, Townsend MK, Zeleznik OA, Eliassen AH, Tworoger SS, Karlson EW, Costenbader KH, Ascherio A, Wilson KM, Mucci LA, Giovannucci EL, Fuchs CS, Bao Y.
      BACKGROUND: Intake of nuts has been inversely associated with risk of type 2 diabetes and cardiovascular disease, partly through inducing a healthy lipid profile. How nut intake may affect lipid metabolites remains unclear.OBJECTIVE: The aim of this study was to identify the plasma lipid metabolites associated with habitual nut consumption in US men and women.
    METHODS: We analyzed cross-sectional data from 1099 participants in the Nurses' Health Study (NHS), NHS II, and Health Professionals Follow-up Study. Metabolic profiling was conducted on plasma by LC-mass spectrometry. Nut intake was estimated from food-frequency questionnaires. We included 144 known lipid metabolites that had CVs ≤25%. Multivariate linear regression was used to assess the associations of nut consumption with individual plasma lipid metabolites.
    RESULTS: We identified 17 lipid metabolites that were significantly associated with nut intake, based on a 1 serving (28 g)/d increment in multivariate models [false discovery rate (FDR) P value <0.05]. Among these species, 8 were positively associated with nut intake [C24:0 sphingomyelin (SM), C36:3 phosphatidylcholine (PC) plasmalogen-A, C36:2 PC plasmalogen, C24:0 ceramide, C36:1 PC plasmalogen, C22:0 SM, C34:1 PC plasmalogen, and C36:2 phosphatidylethanolamine plasmalogen], with changes in relative metabolite level (expressed in number of SDs on the log scale) ranging from 0.36 to 0.46 for 1 serving/d of nuts. The other 9 metabolites were inversely associated with nut intake with changes in relative metabolite level ranging from -0.34 to -0.44. In stratified analysis, 3 metabolites were positively associated with both peanuts and peanut butter (C24:0 SM, C24:0 ceramide, and C22:0 SM), whereas 6 metabolites were inversely associated with other nuts (FDR P value <0.05).
    CONCLUSIONS: A panel of lipid metabolites was associated with intake of nuts, which may provide insight into biological mechanisms underlying associations between nuts and cardiometabolic health. Metabolites that were positively associated with intake of nuts may be helpful in identifying potential biomarkers of nut intake.
    Keywords:  lipid metabolites; lipidomics; metabolites; metabolomics; nuts; peanuts
    DOI:  https://doi.org/10.1093/jn/nxz048