bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2020–06–14
24 papers selected by
Giovanny Rodríguez Blanco, The Beatson Institute for Cancer Research
  1. The Molecular Link from Diet to Cancer Cell Metabolism.
  2. NMR and MS-based Stable Isotope-Resolved Metabolomics and Applications in Cancer Metabolism.
  3. Correlation of plasma metabolites with glucose and lipid fluxes in human insulin resistance.
  4. Restriction of essential amino acids dictates the systemic metabolic response to dietary protein dilution.
  5. Metabolic reprogramming related to whole-chromosome instability in models for Hürthle cell carcinoma.
  6. The branched-chain amino acids valine and leucine have differential effects on hepatic lipid metabolism.
  7. MetaboKit: a comprehensive data extraction tool for untargeted metabolomics.
  8. Antineoplastic Agents Targeting Sphingolipid Pathways.
  9. QSRR Automator: A Tool for Automating Retention Time Prediction in Lipidomics and Metabolomics.
  10. First total syntheses of novel non-enzymatic polyunsaturated fatty acid metabolites and their identification in edible oils.
  11. Toll-Like Receptors Induce Signal-Specific Reprogramming of the Macrophage Lipidome.
  12. COVID-19 infection results in alterations of the kynurenine pathway and fatty acid metabolism that correlate with IL-6 levels and renal status.
  13. Adenylate Kinase and Metabolic Signaling in Cancer Cells.
  14. GLOBAL AND TARGETED PROFILING OF GTP-BINDING PROTEINS IN BIOLOGICAL SAMPLES BY MASS SPECTROMETRY.
  15. The potential for metabolomics in the study and treatment of major depressive disorder and related conditions.
  16. Local Mitochondrial ATP Production Regulates Endothelial Fatty Acid Uptake and Transport.
  17. Metabolic Reprogramming and Epithelial-Mesenchymal Plasticity: Opportunities and Challenges for Cancer Therapy.
  18. Fast Quantification without Conventional Chromatography, the Growing Power of Mass Spectrometry.
  19. The Regulatory Role of Key Metabolites in the Control of Cell Signaling.
  20. Measuring Bioenergetic Signatures of Peripheral Nerve Segments by Extracellular Flux Analysis.
  21. Fatty Acid and Carnitine Metabolism Are Dysregulated in Systemic Sclerosis Patients.
  22. Histone Methylation Connects DNA Repair to Metabolism in Cancer Cells.
  23. A Novel Function of Sphingosine Kinase 2 in the Metabolism of Sphinga-4,14-Diene Lipids.
  24. Absolute quantitative analysis of intact and oxidized amino acids by LC-MS without prior derivatization.
  1. Mol Cell. 2020 Jun 02. pii: S1097-2765(20)30319-1. [Epub ahead of print]
    The Molecular Link from Diet to Cancer Cell Metabolism.
    Shree Bose, Annamarie E Allen, Jason W Locasale.
      Malignant cells remodel their metabolism to meet the demands of uncontrolled cell proliferation. These demands lead to differential requirements in energy, biosynthetic precursors, and signaling intermediates. Both genetic programs arising from oncogenic events and transcriptional programs and epigenomic events are important in providing the necessary metabolic network activity. Accumulating evidence has established that environmental factors play a major role in shaping cancer cell metabolism. For metabolism, diet and nutrition are the major environmental aspects and have emerged as key components in determining cancer cell metabolism. In this review, we discuss these emerging concepts in cancer metabolism and how diet and nutrition influence cancer cell metabolism.
    DOI:  https://doi.org/10.1016/j.molcel.2020.05.018
  2. Trends Analyt Chem. 2019 Nov;pii: 115322. [Epub ahead of print]120
    NMR and MS-based Stable Isotope-Resolved Metabolomics and Applications in Cancer Metabolism.
    Andrew N Lane, Richard M Higashi, Teresa W-M Fan.
      There is considerable interest in defining metabolic reprogramming in human diseases, which is recognized as a hallmark of human cancer. Although radiotracers have a long history in specific metabolic studies, stable isotope-enriched precursors coupled with modern high resolution mass spectrometry and NMR spectroscopy have enabled systematic mapping of metabolic networks and fluxes in cells, tissues and living organisms including humans. These analytical platforms are high in information content, are complementary and cross-validating in terms of compound identification, quantification, and isotope labeling pattern analysis of a large number of metabolites simultaneously. Furthermore, new developments in chemoselective derivatization and in vivo spectroscopy enable tracking of labile/low abundance metabolites and metabolic kinetics in real-time. Here we review developments in Stable Isotope Resolved Metabolomics (SIRM) and recent applications in cancer metabolism using a wide variety of stable isotope tracers that probe both broad and specific aspects of cancer metabolism required for proliferation and survival.
    Keywords:  NMR; SIRM; cancer metabolism; mass spectrometry; model systems
    DOI:  https://doi.org/10.1016/j.trac.2018.11.020
  3. Obes Sci Pract. 2020 Jun;6(3): 340-349
    Correlation of plasma metabolites with glucose and lipid fluxes in human insulin resistance.
    Annick V Hartstra, Pieter F de Groot, Diogo Mendes Bastos, Evgeni Levin, Mireille J Serlie, Maarten R Soeters, Ceyda T Pekmez, Lars O Dragsted, Mariette T Ackermans, Albert K Groen, Max Nieuwdorp.
       Objective: Insulin resistance develops prior to the onset of overt type 2 diabetes, making its early detection vital. Direct accurate evaluation is currently only possible with complex examinations like the stable isotope-based hyperinsulinemic euglycemic clamp (HIEC). Metabolomic profiling enables the detection of thousands of plasma metabolites, providing a tool to identify novel biomarkers in human obesity.
    Design: Liquid chromatography mass spectrometry-based untargeted plasma metabolomics was applied in 60 participants with obesity with a large range of peripheral insulin sensitivity as determined via a two-step HIEC with stable isotopes [6,6-2H2]glucose and [1,1,2,3,3-2H5]glycerol. This additionally enabled measuring insulin-regulated lipolysis, which combined with metabolomics, to the knowledge of this research group, has not been reported on before.
    Results: Several plasma metabolites were identified that significantly correlated with glucose and lipid fluxes, led by plasma (gamma-glutamyl)citrulline, followed by betaine, beta-cryptoxanthin, fructosyllysine, octanylcarnitine, sphingomyelin (d18:0/18:0, d19:0/17:0) and thyroxine. Subsequent machine learning analysis showed that a panel of these metabolites derived from a number of metabolic pathways may be used to predict insulin resistance, dominated by non-essential amino acid citrulline and its metabolite gamma-glutamylcitrulline.
    Conclusion: This approach revealed a number of plasma metabolites that correlated reasonably well with glycemic and lipolytic flux parameters, measured using gold standard techniques. These metabolites may be used to predict the rate of glucose disposal in humans with obesity to a similar extend as HOMA, thus providing potential novel biomarkers for insulin resistance.
    Keywords:  citrulline; human insulin resistance; plasma metabolites; stable isotope hyperinsulinemic clamp
    DOI:  https://doi.org/10.1002/osp4.402
  4. Nat Commun. 2020 Jun 09. 11(1): 2894
    Restriction of essential amino acids dictates the systemic metabolic response to dietary protein dilution.
    Yann W Yap, Patricia M Rusu, Andrea Y Chan, Barbara C Fam, Andreas Jungmann, Samantha M Solon-Biet, Christopher K Barlow, Darren J Creek, Cheng Huang, Ralf B Schittenhelm, Bruce Morgan, Dieter Schmoll, Bente Kiens, Matthew D W Piper, Mathias Heikenwälder, Stephen J Simpson, Stefan Bröer, Sofianos Andrikopoulos, Oliver J Müller, Adam J Rose.
      Dietary protein dilution (DPD) promotes metabolic-remodelling and -health but the precise nutritional components driving this response remain elusive. Here, by mimicking amino acid (AA) supply from a casein-based diet, we demonstrate that restriction of dietary essential AA (EAA), but not non-EAA, drives the systemic metabolic response to total AA deprivation; independent from dietary carbohydrate supply. Furthermore, systemic deprivation of threonine and tryptophan, independent of total AA supply, are both adequate and necessary to confer the systemic metabolic response to both diet, and genetic AA-transport loss, driven AA restriction. Dietary threonine restriction (DTR) retards the development of obesity-associated metabolic dysfunction. Liver-derived fibroblast growth factor 21 is required for the metabolic remodelling with DTR. Strikingly, hepatocyte-selective establishment of threonine biosynthetic capacity reverses the systemic metabolic response to DTR. Taken together, our studies of mice demonstrate that the restriction of EAA are sufficient and necessary to confer the systemic metabolic effects of DPD.
    DOI:  https://doi.org/10.1038/s41467-020-16568-z
  5. Sci Rep. 2020 Jun 12. 10(1): 9578
    Metabolic reprogramming related to whole-chromosome instability in models for Hürthle cell carcinoma.
    Ruben D Addie, Sarantos Kostidis, Willem E Corver, Jan Oosting, Sepideh Aminzadeh-Gohari, René G Feichtinger, Barbara Kofler, Mehtap Derya Aydemirli, Martin Giera, Hans Morreau.
      Hürthle cell carcinoma (HCC) is a recurrent subtype of non-medullary thyroid cancer. HCC is characterized by profound whole-chromosome instability (w-CIN), resulting in a near-homozygous genome (NHG), a phenomenon recently attributed to reactive oxygen species (ROS) generated during mitosis by malfunctioning mitochondria. We studied shared metabolic traits during standard and glucose-depleted cell culture in thyroid cancer cell lines (TCCLs), with or without a NHG, using quantitative analysis of extra and intracellular metabolites and ROS production following inhibition of complex III with antimycin A. We found that the XTC.UC1 and FTC-236 cell lines (both NHG) are functionally impaired in complex I and produce significantly more superoxide radicals than SW579 and BHP 2-7 (non-NHG) after challenge with antimycin A. FTC-236 showed the lowest levels of glutathione and SOD2. XTC.UC1 and FTC-236 both exhibited reduced glycolytic activity and utilization of alternative sources to meet energy demands. Both cell lines also shared low levels of α-ketoglutarate and high levels of creatine, phosphocreatine, uridine diphosphate-N-acetylglucosamine, pyruvate and acetylcarnitine. Furthermore, the metabolism of XTC.UC1 was skewed towards the de novo synthesis of aspartate, an effect that persisted even in glucose-free media, pointing to reductive carboxylation. Our data suggests that metabolic reprogramming and a subtle balance between ROS generation and scavenging/conversion of intermediates may be involved in ROS-induced w-CIN in HCC and possibly also in rare cases of follicular thyroid cancer showing a NHG.
    DOI:  https://doi.org/10.1038/s41598-020-66599-1
  6. FASEB J. 2020 Jun 07.
    The branched-chain amino acids valine and leucine have differential effects on hepatic lipid metabolism.
    Christopher A Bishop, Matthias B Schulze, Susanne Klaus, Karolin Weitkunat.
      Dairy intake, as a source of branched-chain amino acids (BCAA), has been linked to a lower incidence of type-2-diabetes and increased circulating odd-chain fatty acids (OCFA). To understand this connection, we aimed to investigate differences in BCAA metabolism of leucine and valine, a possible source of OCFA, and their role in hepatic metabolism. Male mice were fed a high-fat diet supplemented with leucine and valine for 1 week and phenotypically characterized with a focus on lipid metabolism. Mouse primary hepatocytes were treated with the BCAA or a Pparα activator WY-14643 to systematically examine direct hepatic effects and their mechanisms. Here, we show that only valine supplementation was able to increase hepatic and circulating OCFA levels via two pathways; a PPARα-dependent induction of α-oxidation and an increased supply of propionyl-CoA for de novo lipogenesis. Meanwhile, we were able to confirm leucine-mediated effects on the inhibition of food intake and transport of fatty acids, as well as induction of S6 ribosomal protein phosphorylation. Taken together, these data illustrate differential roles of the BCAA in lipid metabolism and provide preliminary evidence that exclusively valine contributes to the endogenous formation of OCFA which is important for a better understanding of these metabolites in metabolic health.
    Keywords:  OCFA; fatty acid metabolism; leucine; liver; valine
    DOI:  https://doi.org/10.1096/fj.202000195R
  7. Mol Omics. 2020 Jun 10.
    MetaboKit: a comprehensive data extraction tool for untargeted metabolomics.
    Pradeep Narayanaswamy, Guoshou Teo, Jin Rong Ow, Adam Lau, Philipp Kaldis, Stephen Tate, Hyungwon Choi.
      We have developed MetaboKit, a comprehensive software package for compound identification and relative quantification in mass spectrometry-based untargeted metabolomics analysis. In data dependent acquisition (DDA) analysis, MetaboKit constructs a customized spectral library with compound identities from reference spectral libraries, adducts, dimers, in-source fragments (ISF), MS/MS fragmentation spectra, and more importantly the retention time information unique to the chromatography system used in the experiment. Using the customized library, the software performs targeted peak integration for precursor ions in DDA analysis and for precursor and product ions in data independent acquisition (DIA) analysis. With its stringent identification algorithm requiring matches by both MS and MS/MS data, MetaboKit provides identification results with significantly greater specificity than the competing software packages without loss in sensitivity. The proposed MS/MS-based screening of ISFs also reduces the chance of unverifiable identification of ISFs considerably. MetaboKit's quantification module produced peak area values highly correlated with known concentrations in a DIA analysis of the metabolite standards at both MS1 and MS2 levels. Moreover, the analysis of Cdk1Liv-/- mouse livers showed that MetaboKit can identify a wide range of lipid species and their ISFs, and quantitatively reconstitute the well-characterized fatty liver phenotype in these mice. In DIA data, the MS1-level and MS2-level peak area data produced similar fold change estimates in the differential abundance analysis, and the MS2-level peak area data allowed for quantitative comparisons in compounds whose precursor ion chromatogram was too noisy for peak integration.
    DOI:  https://doi.org/10.1039/d0mo00030b
  8. Front Oncol. 2020 ;10 833
    Antineoplastic Agents Targeting Sphingolipid Pathways.
    Alexander Kroll, Hwang Eui Cho, Min H Kang.
      Emerging studies in the enigmatic area of bioactive lipids have made many exciting new discoveries in recent years. Once thought to play a strictly structural role in cellular function, it has since been determined that sphingolipids and their metabolites perform a vast variety of cellular functions beyond what was previously believed. Of utmost importance is their role in cellular signaling, for it is now well understood that select sphingolipids serve as bioactive molecules that play critical roles in both cancer cell death and survival, as well as other cellular responses such as chronic inflammation, protection from intestinal pathogens, and intrinsic protection from intestinal contents, each of which are associated with oncogenesis. Importantly, it has been demonstrated time and time again that many different tumors display dysregulation of sphingolipid metabolism, and the exact profile of said dysregulation has been proven to be useful in determining not only the presence of a tumor, but also the susceptibility to various chemotherapeutic drugs, as well as the metastasizing characteristics of the malignancies. Since these discoveries surfaced it has become apparent that the understanding of sphingolipid metabolism and profile will likely become of great importance in the clinic for both chemotherapy and diagnostics of cancer. The goal of this paper is to provide a comprehensive review of the current state of chemotherapeutic agents that target sphingolipid metabolism that are undergoing clinical trials. Additionally, we will formulate questions involving the use of sphingolipid metabolism as chemotherapeutic targets in need of further research.
    Keywords:  ceramides; lipid biomarkers; sphingolipids; sphingomyelin; sphingosine-1-phosphate
    DOI:  https://doi.org/10.3389/fonc.2020.00833
  9. Metabolites. 2020 Jun 09. pii: E237. [Epub ahead of print]10(6):
    QSRR Automator: A Tool for Automating Retention Time Prediction in Lipidomics and Metabolomics.
    Bradley C Naylor, J Leon Catrow, J Alan Maschek, James E Cox.
      The use of retention time is often critical for the identification of compounds in metabolomic and lipidomic studies. Standards are frequently unavailable for the retention time measurement of many metabolites, thus the ability to predict retention time for these compounds is highly valuable. A number of studies have applied machine learning to predict retention times, but applying a published machine learning model to different lab conditions is difficult. This is due to variation between chromatographic equipment, methods, and columns used for analysis. Recreating a machine learning model is likewise difficult without a dedicated bioinformatician. Herein we present QSRR Automator, a software package to automate retention time prediction model creation and demonstrate its utility by testing data from multiple chromatography columns from previous publications and in-house work. Analysis of these data sets shows similar accuracy to published models, demonstrating the software's utility in metabolomic and lipidomic studies.
    Keywords:  automation; lipidomics; machine learning; metabolomics; retention time prediction
    DOI:  https://doi.org/10.3390/metabo10060237
  10. Chemistry. 2020 Jun 12.
    First total syntheses of novel non-enzymatic polyunsaturated fatty acid metabolites and their identification in edible oils.
    Tereza Pavlickova, Valérie Bultel-Poncé, Alexandre Guy, Amandine Rocher, Guillaume Reversat, Claire Vigor, Thierry Durand, Jean-Marie Galano, Ullrich Jahn, Camille Oger.
      Oxidative stress (OS) is an in-vivo process leading to free radical overproduction, which triggers polyunsaturated fatty acid (PUFA) peroxidation resulting in the formation of racemic non-enzymatic oxygenated metabolites. As potential biomarkers of OS, their in-vivo quantification is of great interest. However, since a large number of isomeric metabolites is formed in parallel, their quantification remains difficult without primary standards. Three new PUFA-metabolites, namely 18-F 3t -Isoprostane (IsoP) from eicosapentaenoic acid (EPA), 20-F 4t -Neuroprostane (NeuroP) from docosahexaenoic acid (DHA) and 20-F 3t -NeuroP from docosapentaenoic acid (DPA n-3 ) were synthesized by two complementary synthetic strategies. The first one relied on a racemic approach to 18( RS )-18-F 3t -IsoP using an oxidative radical anion cyclization as a key step, whereas the second used an enzymatic deracemization of a bicyclo[3.3.0]octene intermediate obtained from cyclooctadiene to pursue an asymmetric synthesis. The synthesized metabolites were applied in targeted lipidomics to prove lipid peroxidation in edible oils of commercial nutraceuticals.
    Keywords:  Isoprostanes; Neuroprostanes; PUFA metabolites; Quantification; total synthesis
    DOI:  https://doi.org/10.1002/chem.202002138
  11. Cell Metab. 2020 May 30. pii: S1550-4131(20)30242-4. [Epub ahead of print]
    Toll-Like Receptors Induce Signal-Specific Reprogramming of the Macrophage Lipidome.
    Wei-Yuan Hsieh, Quan D Zhou, Autumn G York, Kevin J Williams, Philip O Scumpia, Eliza B Kronenberger, Xen Ping Hoi, Baolong Su, Xun Chi, Viet L Bui, Elvira Khialeeva, Amber Kaplan, Young Min Son, Ajit S Divakaruni, Jie Sun, Stephen T Smale, Richard A Flavell, Steven J Bensinger.
      Macrophages reprogram their lipid metabolism in response to activation signals. However, a systems-level understanding of how different pro-inflammatory stimuli reshape the macrophage lipidome is lacking. Here, we use complementary "shotgun" and isotope tracer mass spectrometry approaches to define the changes in lipid biosynthesis, import, and composition of macrophages induced by various Toll-like receptors (TLRs) and inflammatory cytokines. "Shotgun" lipidomics data revealed that different TLRs and cytokines induce macrophages to acquire distinct lipidomes, indicating their specificity in reshaping lipid composition. Mechanistic studies showed that differential reprogramming of lipid composition is mediated by the opposing effects of MyD88- and TRIF-interferon-signaling pathways. Finally, we applied these insights to show that perturbing reprogramming of lipid composition can enhance inflammation and promote host defense to bacterial challenge. These studies provide a framework for understanding how inflammatory stimuli reprogram lipid composition of macrophages while providing a knowledge platform to exploit differential lipidomics to influence immunity.
    Keywords:  MyD88; acetylated-LDL; host defense; inflammation; interferon; lipidomics; macrophages; stable isotope tracer analysis; stearoyl-CoA desaturase; toll-like receptors
    DOI:  https://doi.org/10.1016/j.cmet.2020.05.003
  12. medRxiv. 2020 May 16. pii: 2020.05.14.20102491. [Epub ahead of print]
    COVID-19 infection results in alterations of the kynurenine pathway and fatty acid metabolism that correlate with IL-6 levels and renal status.
    Tiffany Thomas, Davide Stefanoni, Julie A Reisz, Travis Nemkov, Lorenzo Bertolone, Richard O Francis, Krystalyn E Hudson, James C Zimring, Kirk C Hansen, Eldad A Hod, Steven L Spitalnik, Angelo D'Alessandro.
      Previous studies suggest a role for systemic reprogramming of host metabolism during viral pathogenesis to fuel rapidly expanding viral proliferation, for example by providing free amino acids and fatty acids as building blocks. In addition, general alterations in metabolism can provide key understanding of pathogenesis. However, little is known about the specific metabolic effects of SARS-COV-2 infection. The present study evaluated the serum metabolism of COVID-19 patients (n=33), identified by a positive nucleic acid test of a nasopharyngeal swab, as compared to COVID-19-negative control patients (n=16). Targeted and untargeted metabolomics analyses specifically identified alterations in the metabolism of tryptophan into the kynurenine pathway, which is well-known to be involved in regulating inflammation and immunity. Indeed, the observed changes in tryptophan metabolism correlated with serum interleukin-6 (IL-6) levels. Metabolomics analysis also confirmed widespread dysregulation of nitrogen metabolism in infected patients, with decreased circulating levels of most amino acids, except for tryptophan metabolites in the kynurenine pathway, and increased markers of oxidant stress (e.g., methionine sulfoxide, cystine), proteolysis, and kidney dysfunction (e.g., creatine, creatinine, polyamines). Increased circulating levels of glucose and free fatty acids were also observed, consistent with altered carbon homeostasis in COVID-19 patients. Metabolite levels in these pathways correlated with clinical laboratory markers of inflammation and disease severity (i.e., IL-6 and C-reactive protein) and renal function (i.e., blood urea nitrogen). In conclusion, this initial observational study of the metabolic consequences of COVID-19 infection in a clinical cohort identified amino acid metabolism (especially kynurenine and cysteine/taurine) and fatty acid metabolism as correlates of COVID-19, providing mechanistic insights, potential markers of clinical severity, and potential therapeutic targets.
    DOI:  https://doi.org/10.1101/2020.05.14.20102491
  13. Front Oncol. 2020 ;10 660
    Adenylate Kinase and Metabolic Signaling in Cancer Cells.
    Aleksandr Klepinin, Song Zhang, Ljudmila Klepinina, Egle Rebane-Klemm, Andre Terzic, Tuuli Kaambre, Petras Dzeja.
      A hallmark of cancer cells is the ability to rewire their bioenergetics and metabolic signaling circuits to fuel their uncontrolled proliferation and metastasis. Adenylate kinase (AK) is the critical enzyme in the metabolic monitoring of cellular adenine nucleotide homeostasis. It also directs AK→ AMP→ AMPK signaling controlling cell cycle and proliferation, and ATP energy transfer from mitochondria to distribute energy among cellular processes. The significance of AK isoform network in the regulation of a variety of cellular processes, which include cell differentiation and motility, is rapidly growing. Adenylate kinase 2 (AK2) isoform, localized in intermembrane and intra-cristae space, is vital for mitochondria nucleotide exchange and ATP export. AK2 deficiency disrupts cell energetics, causes severe human diseases, and is embryonically lethal in mice, signifying the importance of catalyzed phosphotransfer in cellular energetics. Suppression of AK phosphotransfer and AMP generation in cancer cells and consequently signaling through AMPK could be an important factor in the initiation of cancerous transformation, unleashing uncontrolled cell cycle and growth. Evidence also builds up that shift in AK isoforms is used later by cancer cells for rewiring energy metabolism to support their high proliferation activity and tumor progression. As cell motility is an energy-consuming process, positioning of AK isoforms to increased energy consumption sites could be an essential factor to incline cancer cells to metastases. In this review, we summarize recent advances in studies of the significance of AK isoforms involved in cancer cell metabolism, metabolic signaling, metastatic potential, and a therapeutic target.
    Keywords:  adenylate kinase; cancer; energy metabolism; mitochondria; phosphotransfer
    DOI:  https://doi.org/10.3389/fonc.2020.00660
  14. Mass Spectrom Rev. 2020 Jun 10.
    GLOBAL AND TARGETED PROFILING OF GTP-BINDING PROTEINS IN BIOLOGICAL SAMPLES BY MASS SPECTROMETRY.
    Ming Huang, Yinsheng Wang.
      GTP-binding proteins are among the most important enzyme families that are involved in a plethora of biological processes. However, owing to the enormous diversity of the nucleotide-binding protein family, comprehensive analyses of the expression level, structure, activity, and regulatory mechanisms of GTP-binding proteins remain challenging with the use of conventional approaches. The many advances in mass spectrometry (MS) instrumentation and data acquisition methods, together with a variety of enrichment approaches in sample preparation, render MS a powerful tool for the comprehensive characterizations of the activities and expression levels of various GTP-binding proteins. We review herein the recent developments in the application of MS-based techniques, together with general and widely used affinity enrichment approaches, for the proteome-wide and targeted capture, identification, and quantification of GTP-binding proteins. The working principles, advantages, and limitations of various strategies for profiling the expression level, activity, posttranslational modifications, and interactome of GTP-binding proteins are discussed. It can be envisaged that future applications of MS-based proteomics will lead to a better understanding about the roles of GTP-binding proteins in different biological processes and human diseases. © 2020 John Wiley & Sons Ltd. Mass Spec Rev 00:1-21, 2020.
    Keywords:  GTP-binding proteins; activity-based protein profiling; posttranslational modifications; shotgun proteomics; small GTPases; targeted proteomics
    DOI:  https://doi.org/10.1002/mas.21637
  15. Expert Rev Proteomics. 2020 Jun 09. 1-14
    The potential for metabolomics in the study and treatment of major depressive disorder and related conditions.
    Jiajia Duan, Peng Xie.
       INTRODUCTION: Major depressive disorder (MDD) is a common mental disease, associated with a debilitating condition and high prevalence. Although the underlying mechanism of MDD remains to be elucidated, several factors, including social, biological, and psychological factors, have been associated with disease pathogenesis. Metabolomics can provide new insights into the prognosis, treatment response, and related biomarkers associated with MDD at the metabolic level.
    AREAS COVERED: In this review, we investigated the metabolic changes identified in different bio-samples from animal models of depression and MDD patients. Moreover, we summarized the metabolites associated with antidepressant treatment responses. Keywords used for the literature searches were 'depression' [MeSH] and 'metabolomics' [MeSH], in PubMed.
    EXPERT OPINION: Metabolomic evidence in humans has indicated that amino acid metabolism, energy metabolism, and lipid metabolism are the primary metabolic alterations that are observed in the etiology of MDD, and animal models serve as an important theoretical reference in this field. Metabolomics has shed new light on the pathogenic mechanisms and treatment responses during MDD; however, study results are not always consistent. The application of metabolomic results to clinical practice will require the integration of different biological samples and other omics studies, as well as the clinical validation of study findings.
    Keywords:  Major depressive disorder; biomarkers; differential metabolites; metabolomics; treatment response
    DOI:  https://doi.org/10.1080/14789450.2020.1772059
  16. Cell Metab. 2020 Jun 02. pii: S1550-4131(20)30257-6. [Epub ahead of print]
    Local Mitochondrial ATP Production Regulates Endothelial Fatty Acid Uptake and Transport.
    Ayon Ibrahim, Nora Yucel, Boa Kim, Zoltan Arany.
      Most organs use fatty acids (FAs) as a key nutrient, but little is known of how blood-borne FAs traverse the endothelium to reach underlying tissues. We conducted a small-molecule screen and identified niclosamide as a suppressor of endothelial FA uptake and transport. Structure/activity relationship studies demonstrated that niclosamide acts through mitochondrial uncoupling. Inhibitors of oxidative phosphorylation and the ATP/ADP translocase also suppressed FA uptake, pointing principally to ATP production. Decreasing total cellular ATP by blocking glycolysis did not decrease uptake, indicating that specifically mitochondrial ATP is required. Endothelial FA uptake is promoted by fatty acid transport protein 4 (FATP4) via its ATP-dependent acyl-CoA synthetase activity. Confocal microscopy revealed that FATP4 resides in the endoplasmic reticulum (ER), and that endothelial ER is intimately juxtaposed with mitochondria. Together, these data indicate that mitochondrial ATP production, but not total ATP levels, drives endothelial FA uptake and transport via acyl-CoA formation in mitochondrial/ER microdomains.
    Keywords:  ATP; FATP4; endothelial; fatty acid; mitochondria; niclosamide; vectorial acylation
    DOI:  https://doi.org/10.1016/j.cmet.2020.05.018
  17. Front Oncol. 2020 ;10 792
    Metabolic Reprogramming and Epithelial-Mesenchymal Plasticity: Opportunities and Challenges for Cancer Therapy.
    Nai-Yun Sun, Muh-Hwa Yang.
      Metabolic reprogramming and epithelial-mesenchymal plasticity are both hallmarks of the adaptation of cancer cells for tumor growth and progression. For metabolic changes, cancer cells alter metabolism by utilizing glucose, lipids, and amino acids to meet the requirement of rapid proliferation and to endure stressful environments. Dynamic changes between the epithelial and mesenchymal phenotypes through epithelial-mesenchymal transition (EMT) and mesenchymal-epithelial transition (MET) are critical steps for cancer invasion and metastatic colonization. Compared to the extensively studied metabolic reprogramming in tumorigenesis, the metabolic changes in metastasis are relatively unclear. Here, we review metabolic reprogramming, epithelial-mesenchymal plasticity, and their mutual influences on tumor cells. We also review the developing treatments for targeting cancer metabolism and the impact of metabolic targeting on EMT. In summary, understanding the metabolic adaption and phenotypic plasticity will be mandatory for developing new strategies to target metastatic and refractory cancers that are intractable to current treatments.
    Keywords:  aerobic glycolysis; cancer metabolism; drug resistance; epithelial-mesenchymal plasticity; metastasis
    DOI:  https://doi.org/10.3389/fonc.2020.00792
  18. Anal Chem. 2020 Jun 08.
    Fast Quantification without Conventional Chromatography, the Growing Power of Mass Spectrometry.
    George N Gachumi, Randy W Purves, Carsten Hopf, Anas El-Aneed.
      Mass spectrometry (MS) in hyphenated techniques is widely accepted as the gold standard quantitative tool in life sciences. However, MS possesses intrinsic analytical capabilities that allow it to be a stand-alone quantitative technique, particularly with current technological advancements. MS has a great potential for simplifying quantitative analysis without the need for tedious chromatographic separation. Its selectivity relies on multistage MS analysis (MSn), including tandem mass spectrometry (MS/MS), as well as the ever-growing advancements of high-resolution MS instruments. This perspective describes various analytical platforms that utilize MS as a stand-alone quantitative technique namely, flow injection analysis (FIA), matrix assisted laser desorption ionization (MALDI) including MALDI-MS imaging, and ion mobility, particularly high-field asymmetric waveform ion mobility spectrometry (FAIMS). When MS alone is not capable of providing reliable quantitative data, instead of conventional liquid chromatography (LC)-MS, the use of a guard column (i.e., fast chromatography) may be sufficient for quantification. Although the omission of a chromatographic separation simplifies the analytical process, extra procedures may be needed during sample preparation and clean-up to address the issue of matrix effects. The discussion of this manuscript focusses on key parameters underlying the uniqueness of each technique for its application in quantitative analysis without the need for a chromatographic separation. In addition, the potential for each analytical strategy and its challenges are discussed as well as improvements needed to render them as mainstream quantitative analytical tools. Overcoming the hurdles for fully validating a quantitative method will allow MS alone to eventually become an indispensable quantitative tool for clinical and toxicological studies.
    DOI:  https://doi.org/10.1021/acs.analchem.0c00877
  19. Biomolecules. 2020 Jun 05. pii: E862. [Epub ahead of print]10(6):
    The Regulatory Role of Key Metabolites in the Control of Cell Signaling.
    Riccardo Milanesi, Paola Coccetti, Farida Tripodi.
      Robust biological systems are able to adapt to internal and environmental perturbations. This is ensured by a thick crosstalk between metabolism and signal transduction pathways, through which cell cycle progression, cell metabolism and growth are coordinated. Although several reports describe the control of cell signaling on metabolism (mainly through transcriptional regulation and post-translational modifications), much fewer information is available on the role of metabolism in the regulation of signal transduction. Protein-metabolite interactions (PMIs) result in the modification of the protein activity due to a conformational change associated with the binding of a small molecule. An increasing amount of evidences highlight the role of metabolites of the central metabolism in the control of the activity of key signaling proteins in different eukaryotic systems. Here we review the known PMIs between primary metabolites and proteins, through which metabolism affects signal transduction pathways controlled by the conserved kinases Snf1/AMPK, Ras/PKA and TORC1. Interestingly, PMIs influence also the mitochondrial retrograde response (RTG) and calcium signaling, clearly demonstrating that the range of this phenomenon is not limited to signaling pathways related to metabolism.
    Keywords:  RTG; Ras/PKA; Snf1/AMPK/SnRK1; TCA; TORC1; amino acids; calcium; glucose; glycolysis; protein-metabolite interaction
    DOI:  https://doi.org/10.3390/biom10060862
  20. Methods Mol Biol. 2020 ;2143 191-203
    Measuring Bioenergetic Signatures of Peripheral Nerve Segments by Extracellular Flux Analysis.
    Bogdan Beirowski.
      Changes of energy metabolism in axons and their adjacent glia as well as alterations in metabolic axon-glia cross talk are emerging as central mechanistic components underlying axon degeneration. The analysis of extracellular flux with commercial metabolic analyzers greatly facilitates the measurement of key parameters of glycolytic and mitochondrial energy metabolism in cells and tissues. In this chapter, I describe a straightforward method to capture bioenergetic profiles of acutely isolated peripheral nerve segments using the Agilent Seahorse XFe24 platform.
    Keywords:  Axonopathy; Extracellular acidification; Metabolic coupling; Neuropathy; Oligodendrocyte; Oxygen consumption; Schwann cell; Wallerian degeneration
    DOI:  https://doi.org/10.1007/978-1-0716-0585-1_15
  21. Front Immunol. 2020 ;11 822
    Fatty Acid and Carnitine Metabolism Are Dysregulated in Systemic Sclerosis Patients.
    A Ottria, A T Hoekstra, M Zimmermann, M van der Kroef, N Vazirpanah, M Cossu, E Chouri, M Rossato, L Beretta, R G Tieland, C G K Wichers, E Stigter, C Gulersonmez, F Bonte-Mineur, C R Berkers, T R D J Radstake, W Marut.
      Systemic sclerosis (SSc) is a rare chronic disease of unknown pathogenesis characterized by fibrosis of the skin and internal organs, vascular alteration, and dysregulation of the immune system. In order to better understand the immune system and its perturbations leading to diseases, the study of the mechanisms regulating cellular metabolism has gained a widespread interest. Here, we have assessed the metabolic status of plasma and dendritic cells (DCs) in patients with SSc. We identified a dysregulated metabolomic signature in carnitine in circulation (plasma) and intracellularly in DCs of SSc patients. In addition, we confirmed carnitine alteration in the circulation of SSc patients in three independent plasma measurements from two different cohorts and identified dysregulation of fatty acids. We hypothesized that fatty acid and carnitine alterations contribute to potentiation of inflammation in SSc. Incubation of healthy and SSc dendritic cells with etoposide, a carnitine transporter inhibitor, inhibited the production of pro-inflammatory cytokines such as IL-6 through inhibition of fatty acid oxidation. These findings shed light on the altered metabolic status of the immune system in SSc patients and opens up for potential novel avenues to reduce inflammation.
    Keywords:  carnitines; dendritic cells; fatty acid oxidation; metabolomics; systemic sclerosis
    DOI:  https://doi.org/10.3389/fimmu.2020.00822
  22. Cancer Discov. 2020 Jun 12.
    Histone Methylation Connects DNA Repair to Metabolism in Cancer Cells.
      Metabolites produced in cancer cells interfered with resolution of DNA double-strand breaks.
    DOI:  https://doi.org/10.1158/2159-8290.CD-RW2020-089
  23. Metabolites. 2020 Jun 08. pii: E236. [Epub ahead of print]10(6):
    A Novel Function of Sphingosine Kinase 2 in the Metabolism of Sphinga-4,14-Diene Lipids.
    Timothy Andrew Couttas, Yepy Hardi Rustam, Huitong Song, Yanfei Qi, Jonathan David Teo, Jinbiao Chen, Gavin Edmund Reid, Anthony Simon Don.
      The number, position, and configuration of double bonds in lipids affect membrane fluidity and the recruitment of signaling proteins. Studies on mammalian sphingolipids have focused on those with a saturated sphinganine or mono-unsaturated sphingosine long chain base. Using high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS), we observed a marked accumulation of lipids containing a di-unsaturated sphingadiene base in the hippocampus of mice lacking the metabolic enzyme sphingosine kinase 2 (SphK2). The double bonds were localized to positions C4-C5 and C14-C15 of sphingadiene using ultraviolet photodissociation-tandem mass spectrometry (UVPD-MS/MS). Phosphorylation of sphingoid bases by sphingosine kinase 1 (SphK1) or SphK2 forms the penultimate step in the lysosomal catabolism of all sphingolipids. Both SphK1 and SphK2 phosphorylated sphinga-4,14-diene as efficiently as sphingosine, however deuterated tracer experiments in an oligodendrocyte cell line demonstrated that ceramides with a sphingosine base are more rapidly metabolized than those with a sphingadiene base. Since SphK2 is the dominant sphingosine kinase in brain, we propose that the accumulation of sphingadiene-based lipids in SphK2-deficient brains results from the slower catabolism of these lipids, combined with a bottleneck in the catabolic pathway created by the absence of SphK2. We have therefore uncovered a previously unappreciated role for SphK2 in lipid quality control.
    Keywords:  SphK2; brain lipids; ceramide; mass spectrometry; sphingadiene; sphingolipids; sphingosine; sphingosine kinase; sphingosine kinase 2
    DOI:  https://doi.org/10.3390/metabo10060236
  24. Redox Biol. 2020 May 28. pii: S2213-2317(20)30580-2. [Epub ahead of print]36 101586
    Absolute quantitative analysis of intact and oxidized amino acids by LC-MS without prior derivatization.
    Luke F Gamon, Chaorui Guo, Jianfei He, Per Hägglund, Clare L Hawkins, Michael J Davies.
      The precise characterization and quantification of oxidative protein damage is a significant challenge due to the low abundance, large variety, and heterogeneity of modifications. Mass spectrometry (MS)-based techniques at the peptide level (proteomics) provide a detailed but limited picture due to incomplete sequence coverage and imperfect enzymatic digestion. This is particularly problematic with oxidatively modified and cross-linked/aggregated proteins. There is a pressing need for methods that can quantify large numbers of modified amino acids, which are often present in low abundance compared to the high background of non-damaged amino acids, in a rapid and reliable fashion. We have developed a protocol using zwitterionic ion-exchange chromatography coupled with LC-MS to simultaneously quantify both parent amino acids and their respective oxidation products. Proteins are hydrolyzed with methanesulfonic acid in the presence of tryptamine and purified by strong cation exchange solid phase extraction. The method was validated for the common amino acids (excluding Gln, Asn, Cys) and the oxidation products 3-chlorotyrosine (3-ClTyr), 3-nitrotyrosine (3-NO2Tyr), di-tyrosine, Nε-(1-carboxymethyl)-l-lysine, o,o'-di-tyrosine, 3,4,-dihydroxyphenylalanine, hydroxy-tryptophan and kynurenine. Linear standard curves were observed over ~3 orders of magnitude dynamic range (2-1000 pmol for parent amino acids, 80 fmol-20 pmol for oxidation products) with limit-of-quantification values as low as 200 fmol (o,o'-di-tyrosine). The validated method was used to quantify Tyr and Trp loss, and formation of 3-NO2Tyr on the isolated protein anastellin treated with peroxynitrous acid, and for 3-ClTyr formation (over a 2 orders of magnitude range) in cell lysates and complex protein mixtures treated with hypochlorous acid.
    Keywords:  3-Chlorotyrosine; 3-Nitrotyrosine; Chlorination; Hypochlorous acid; LC-MS; Methionine sulfoxide; Nitration; Peroxynitrite; Post-translational modifications; Protein oxidation
    DOI:  https://doi.org/10.1016/j.redox.2020.101586
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