bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2019–08–04
thirteen papers selected by
Giovanny Rodríguez Blanco, The Beatson Institute for Cancer Research
  1. Untangling the Metabolic Reprogramming in Brain Cancer: Discovering Key Molecular Players Using Mass Spectrometry.
  2. Hepatocarcinoma Discrimination by Ratiometric Lipid Profiles Using Tip-Contact Sampling/Ionization Mass Spectrometry.
  3. Dietary methionine influences therapy in mouse cancer models and alters human metabolism.
  4. Alteration of intracellular metabolome in osteosarcoma stem cells revealed by liquid chromatography-tandem mass spectrometry.
  5. Targeting of lipid metabolism with a metabolic inhibitor cocktail eradicates peritoneal metastases in ovarian cancer cells.
  6. Quantitative Profiling of Oncometabolites in Frozen and Formalin-Fixed Paraffin-Embedded Tissue Specimens by Liquid Chromatography Coupled with Tandem Mass Spectrometry.
  7. Linking in silico MS/MS spectra with chemistry data to improve identification of unknowns.
  8. Should we consider subcellular compartmentalization of metabolites, and if so, how do we measure them?
  9. The Role of Sodium Hydrogen Exchanger 1 in Dysregulation of Proton Dynamics and Reprogramming of Cancer Metabolism as a Sequalae.
  10. MALDI Mass Spectrometry Imaging of Early- and Late-Stage Serous Ovarian Cancer Tissue Reveals Stage-Specific N-Glycans.
  11. Evaluating the Role of RARβ Signaling on Cellular Metabolism in Melanoma Using the Seahorse XF Analyzer.
  12. 12-Lipoxygenase Regulates Cold Adaptation and Glucose Metabolism by Producing the Omega-3 Lipid 12-HEPE from Brown Fat.
  13. Preparation of the Low Molecular Weight Serum Proteome for Mass Spectrometry Analysis.
  1. Curr Top Med Chem. 2019 Jul 29.
    Untangling the Metabolic Reprogramming in Brain Cancer: Discovering Key Molecular Players Using Mass Spectrometry.
    Anatoly Sorokin, Vsevolod Shurkhay, Stanislav Pekov, Evgeny Zhvansky, Daniil Ivanov, Eugene E Kulikov, Igor Popov, Alexander Potapov, Eugene Nikolaev.
      Cells metabolism alteration is the new hallmark of cancer as well as the way for carcinogenesis investigation. It is well known that malignant cells switch to aerobic glycolysis pathway occurring also in healthy proliferating cells. Recently, it was shown that in malignant cells, intracellular fatty acids synthesis replace dietary fatty acids which change cancer cells lipid composition noticeably. These alterations in energy metabolism and structural lipid production explain the high proliferation rate of malignant tissues. However, metabolic reprogramming affects not only lipid metabolism but many of the metabolic pathways in the cell. 2-hydroxyglutarate was considered as cancer cell biomarker and its presence is associated with oxidative stress influencing the mitochondria functions. Among the variety of metabolites detection methods, mass spectrometry highlights as the most effective method for simultaneous identification and quantification of the metabolites. As the metabolic reprogramming is tightly connected with epigenetics and signaling modifications, the evaluation of metabolites alterations in cells is a promising approach to investigate the carcinogenesis which is necessary for improving current diagnostic capabilities and therapeutics capabilities. In this paper we overview recent studies on metabolic alteration and oncometabolites, especially concerning brain cancer and mass spectrometry approaches which are now in use for metabolic pathways investigations.
    Keywords:  brain cancer; lipids; mass spectrometry; metabolic reprogramming; metabolism; oncometabolites
    DOI:  https://doi.org/10.2174/1568026619666190729154543
  2. Anal Chem. 2019 Jul 31.
    Hepatocarcinoma Discrimination by Ratiometric Lipid Profiles Using Tip-Contact Sampling/Ionization Mass Spectrometry.
    Xiaoming Chen, Jiaqi Gao, Tao Wang, Xinrong Jiang, Jiang Chen, Xiao Liang, Jianmin Wu.
      Precise diagnosis at the molecular level is essential for the improvement of surgery and treatment. High-throughput and spatial-resolved mass spectrometric (MS) methods for in situ detection of metabolites on tissue samples can reveal the dysregulation of metabolism in abnormal tissue and help identification of tumor. We here report a nondestructive MS method named as tip-contact sampling/ionization (TCSI)-MS technology which can quickly acquire lipidomic information from liver tissue and thereby realize tumor identification. Using this technology, fatty acids and lipids at the liver tissue surface can be rapidly imprinted onto a silicon nanowire tip attached with reduced graphene oxide (rGO) and sensitively detected by on-chip MS. With proper data pretreatment and statistical analysis, the clinical primary hepatocellular carcinoma (HCC) tissues can be discriminated from the nontumor parts. In addition, we found that a panel of adjacent dual peaks' ratio can be used to build a prediction model in artificial neural networks (ANN), resulting in high accuracy (91.7-98.3%) for tumor discrimination. Ratiometric TCSI-MS imaging using a selected dual peaks' ratio can greatly enhance the spatial resolution of tumor margin. The feature ratiometric data of lipid molecules may guide the study of metabolism pathways involved in hepatocarcinoma and ultimately become new metabolic biomarkers in clinical diagnosis. The present work demonstrated that the TCSI-MS technology may pave a novel way for surgery guidance and precision diagnosis in tissue biopsy.
    DOI:  https://doi.org/10.1021/acs.analchem.9b02623
  3. Nature. 2019 Jul 31.
    Dietary methionine influences therapy in mouse cancer models and alters human metabolism.
    Xia Gao, Sydney M Sanderson, Ziwei Dai, Michael A Reid, Daniel E Cooper, Min Lu, John P Richie, Amy Ciccarella, Ana Calcagnotto, Peter G Mikhael, Samantha J Mentch, Juan Liu, Gene Ables, David G Kirsch, David S Hsu, Sailendra N Nichenametla, Jason W Locasale.
      Nutrition exerts considerable effects on health, and dietary interventions are commonly used to treat diseases of metabolic aetiology. Although cancer has a substantial metabolic component1, the principles that define whether nutrition may be used to influence outcomes of cancer are unclear2. Nevertheless, it is established that targeting metabolic pathways with pharmacological agents or radiation can sometimes lead to controlled therapeutic outcomes. By contrast, whether specific dietary interventions can influence the metabolic pathways that are targeted in standard cancer therapies is not known. Here we show that dietary restriction of the essential amino acid methionine-the reduction of which has anti-ageing and anti-obesogenic properties-influences cancer outcome, through controlled and reproducible changes to one-carbon metabolism. This pathway metabolizes methionine and is the target of a variety of cancer interventions that involve chemotherapy and radiation. Methionine restriction produced therapeutic responses in two patient-derived xenograft models of chemotherapy-resistant RAS-driven colorectal cancer, and in a mouse model of autochthonous soft-tissue sarcoma driven by a G12D mutation in KRAS and knockout of p53 (KrasG12D/+;Trp53-/-) that is resistant to radiation. Metabolomics revealed that the therapeutic mechanisms operate via tumour-cell-autonomous effects on flux through one-carbon metabolism that affects redox and nucleotide metabolism-and thus interact with the antimetabolite or radiation intervention. In a controlled and tolerated feeding study in humans, methionine restriction resulted in effects on systemic metabolism that were similar to those obtained in mice. These findings provide evidence that a targeted dietary manipulation can specifically affect tumour-cell metabolism to mediate broad aspects of cancer outcome.
    DOI:  https://doi.org/10.1038/s41586-019-1437-3
  4. Talanta. 2019 Nov 01. pii: S0039-9140(19)30582-X. [Epub ahead of print]204 6-12
    Alteration of intracellular metabolome in osteosarcoma stem cells revealed by liquid chromatography-tandem mass spectrometry.
    Zhihui Zhong, Sifeng Mao, Haifeng Lin, Haifang Li, Jianhua Lin, Jin-Ming Lin.
      Cancer stem cells (CSCs) are the origin of many malignant tumours, including osteosarcoma that mainly affects adolescents and is accompanied by a poor prognosis. However, little is known about the intrinsic biological information of osteosarcoma stem cells, particularly for the metabolomics features. Hence, an ultra-high performance liquid chromatography coupled with tandem Q-Exactive Orbitrap mass spectrometer (UHPLC-QE-MS)-based metabolomics approach was developed to investigate the metabolism changes in the human osteosarcoma (HOS) cell line in order to understand its possible mechanism. HMDB, METLIN and m/z Cloud databases were used to identify the metabolic markers. Additionally, the compounds were further identified using standards of the metabolites. Comparing HOS-CSCs with non-CSCs, 154 different metabolites were identified in both the positive and negative modes. Based on the clearly distinct metabolites, the changed metabolic pathways were analysed using MetaboAnalyst. The top five altered pathways included alanine, aspartate and glutamate metabolism; arginine and proline metabolism; glutathione metabolism; cysteine and methionine metabolism; and the citrate cycle (TCA cycle). The downregulation of the TCA cycle and elevation of oxidized glutathione levels suggested a decline of mitochondrial metabolism, while most of the amino acid metabolisms were upregulated. Further biological experiments including an analysis of mitochondrial activity confirmed the above hypotheses that were deduced from metabolomics results. These findings not only enhance our understanding of the altered metabolome in osteosarcoma stem cells but also demonstrate the great potential of such a metabolomics method based on UHPLC-QE-MS in large-scale cell studies.
    Keywords:  Cancer stem cell; Metabolomics; Mitochondria; Osteosarcoma; UHPLC-QE-MS
    DOI:  https://doi.org/10.1016/j.talanta.2019.05.088
  5. Commun Biol. 2019 ;2 281
    Targeting of lipid metabolism with a metabolic inhibitor cocktail eradicates peritoneal metastases in ovarian cancer cells.
    Rain R Chen, Mingo M H Yung, Yang Xuan, Shijie Zhan, Leanne L Leung, Rachel R Liang, Thomas H Y Leung, Huijuan Yang, Dakang Xu, Rakesh Sharma, Karen K L Chan, Siew-Fei Ngu, Hextan Y S Ngan, David W Chan.
      Ovarian cancer is an intra-abdominal tumor in which the presence of ascites facilitates metastatic dissemination, and associated with poor prognosis. However, the significance of metabolic alterations in ovarian cancer cells in the ascites microenvironment remains unclear. Here we show ovarian cancer cells exhibited increased aggressiveness in ascites microenvironment via reprogramming of lipid metabolism. High lipid metabolic activities are found in ovarian cancer cells when cultured in the ascites microenvironment, indicating a metabolic shift from aerobic glycolysis to β-oxidation and lipogenesis. The reduced AMP-activated protein kinase (AMPK) activity due to the feedback effect of high energy production led to the activation of its downstream signaling, which in turn, enhanced the cancer growth. The combined treatment of low toxic AMPK activators, the transforming growth factor beta-activated kinase 1 (TAK1) and fatty acid synthase (FASN) inhibitors synergistically impair oncogenic augmentation of ovarian cancer. Collectively, targeting lipid metabolism signaling axis impede ovarian cancer peritoneal metastases.
    Keywords:  Cancer metabolism
    DOI:  https://doi.org/10.1038/s42003-019-0508-1
  6. Sci Rep. 2019 Aug 02. 9(1): 11238
    Quantitative Profiling of Oncometabolites in Frozen and Formalin-Fixed Paraffin-Embedded Tissue Specimens by Liquid Chromatography Coupled with Tandem Mass Spectrometry.
    Xun Bao, Jianmei Wu, Brian Shuch, Patricia LoRusso, Ranjit S Bindra, Jing Li.
      Given the implications of oncometabolites [succinate, fumarate, and 2-hydroxyglutarate (2HG)] in cancer pathogenesis and therapeutics, quantitative determination of their tissue levels has significant diagnostic, prognostic, and therapeutic values. Here, we developed and validated a multiplex liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) platform that allows simultaneous determination of oncometabolites (including succinate, fumarate and total 2HG) and other tricarboxylic acid cycle metabolites (α-ketoglutarate, malic acid, and glutamate) in frozen and FFPE tissues specimens. In addition, by employing chiral derivatization in the sample preparation, the platform enabled separation and determination of 2HG enantiomers (D- and L-2HG) in frozen and FFPE tissues. Isotope-labeled internal standard method was used for the quantitation. Linear calibration curve ranges in aqueous solution were 0.02-10, 0.2-100, 0.002-10, and 0.002-5 µM for succinate, fumarate, total 2HG, and D/L-2HG, respectively. Intra- and inter-day precision and accuracy for individual oncometabolites were within the generally accepted criteria for bioanalytical method validation (<15%). The recovery of spiked individual oncometabolites from pooled homogenate of FFPE or frozen tissue ranged 86-112%. Method validation indicated the technical feasibility, reliability and reproducibility of the platform. Oncometabolites were notably lost during the routine FFPE process. The ratios of succinate to glutamate, fumarate to α-ketoglutarate, 2HG to glutamate, and D-2HG to L-2HG were reliable surrogate measurements for the detection of altered levels of oncometabolites in FFPE specimens. Our study laid a foundation for the utility of archival FFPE specimens for oncometabolite profiling as a valid technique in clinical research and routine medical care.
    DOI:  https://doi.org/10.1038/s41598-019-47669-5
  7. Sci Data. 2019 Aug 02. 6(1): 141
    Linking in silico MS/MS spectra with chemistry data to improve identification of unknowns.
    Andrew D McEachran, Ilya Balabin, Tommy Cathey, Thomas R Transue, Hussein Al-Ghoul, Chris Grulke, Jon R Sobus, Antony J Williams.
      Confident identification of unknown chemicals in high resolution mass spectrometry (HRMS) screening studies requires cohesive workflows and complementary data, tools, and software. Chemistry databases, screening libraries, and chemical metadata have become fixtures in identification workflows. To increase confidence in compound identifications, the use of structural fragmentation data collected via tandem mass spectrometry (MS/MS or MS2) is vital. However, the availability of empirically collected MS/MS data for identification of unknowns is limited. Researchers have therefore turned to in silico generation of MS/MS data for use in HRMS-based screening studies. This paper describes the generation en masse of predicted MS/MS spectra for the entirety of the US EPA's DSSTox database using competitive fragmentation modelling and a freely available open source tool, CFM-ID. The generated dataset comprises predicted MS/MS spectra for ~700,000 structures, and mappings between predicted spectra, structures, associated substances, and chemical metadata. Together, these resources facilitate improved compound identifications in HRMS screening studies. These data are accessible via an SQL database, a comma-separated export file (.csv), and EPA's CompTox Chemicals Dashboard.
    DOI:  https://doi.org/10.1038/s41597-019-0145-z
  8. Curr Opin Clin Nutr Metab Care. 2019 Sep;22(5): 347-354
    Should we consider subcellular compartmentalization of metabolites, and if so, how do we measure them?
    Kathryn E Wellen, Nathaniel W Snyder.
       PURPOSE OF REVIEW: To examine the consequences of metabolism compartmentalized at the subcellular level, provide prototypical examples of compartmentalized metabolism, and describe methods to examine compartmentalized metabolism.
    RECENT FINDINGS: Progress in metabolomics and isotope tracing has underscored the importance of subcellular compartments of metabolism. The discovery of biological effects of metabolites as bioenergetic intermediates, anabolic building blocks, signaling mediators, and effectors in posttranslation modifications of proteins and nucleic acids have highlighted the role of compartmentalization in determining metabolic fate. Recent advances in both direct and indirect methods to quantify compartmentalized metabolism have improved upon historical approaches. Genetically encoded metabolite sensors, chemical probes, immunoaffinity purification, and compartment-resolved metabolic modeling have all been recently applied to study compartmentalization.
    SUMMARY: Accurate measurement of metabolites in distinct subcellular compartments is important for understanding and pharmacologically targeting metabolic pathways in diverse disease contexts, including cancer, diabetes, heart failure, obesity, and regulation of the immune system. Direct and indirect approaches to quantify compartmentalized metabolism are advancing rapidly. Yet, major challenges remain in the generalizability, rigor, and interpretation of data from the available methods to quantify compartmentalized metabolism.
    DOI:  https://doi.org/10.1097/MCO.0000000000000580
  9. Int J Mol Sci. 2019 Jul 28. pii: E3694. [Epub ahead of print]20(15):
    The Role of Sodium Hydrogen Exchanger 1 in Dysregulation of Proton Dynamics and Reprogramming of Cancer Metabolism as a Sequalae.
    Rosa Angela Cardone, Khalid Omer Alfarouk, Robert L Elliott, Saad Saaed Alqahtani, Samrein B M Ahmed, Ahmed N Aljarbou, Maria Raffaella Greco, Stefania Cannone, Stephan Joel Reshkin.
      Cancer cells have an unusual regulation of hydrogen ion dynamics that are driven by poor vascularity perfusion, regional hypoxia, and increased glycolysis. All these forces synergize/orchestrate together to create extracellular acidity and intracellular alkalinity. Precisely, they lead to extracellular pH (pHe) values as low as 6.2 and intracellular pH values as high as 8. This unique pH gradient (∆pHi to ∆pHe) across the cell membrane increases as the tumor progresses, and is markedly displaced from the electrochemical equilibrium of protons. These unusual pH dynamics influence cancer cell biology, including proliferation, metastasis, and metabolic adaptation. Warburg metabolism with increased glycolysis, even in the presence of Oxygen with the subsequent reduction in Krebs' cycle, is a common feature of most cancers. This metabolic reprogramming confers evolutionary advantages to cancer cells by enhancing their resistance to hypoxia, to chemotherapy or radiotherapy, allowing rapid production of biological building blocks that support cellular proliferation, and shielding against damaging mitochondrial free radicals. In this article, we highlight the interconnected roles of dysregulated pH dynamics in cancer initiation, progression, adaptation, and in determining the programming and re-programming of tumor cell metabolism.
    Keywords:  Na+/H+ exchanger; pH and Warburg metabolism; pH and cancer; proton transport in cancer; tumor metabolic microenvironment
    DOI:  https://doi.org/10.3390/ijms20153694
  10. Proteomics. 2019 Jul 31. e1800482
    MALDI Mass Spectrometry Imaging of Early- and Late-Stage Serous Ovarian Cancer Tissue Reveals Stage-Specific N-Glycans.
    Matthew T Briggs, Mark R Condina, Yin Ying Ho, Arun V Everest-Dass, Parul Mittal, Gurjeet Kaur, Martin K Oehler, Nicolle H Packer, Peter Hoffmann.
      Epithelial ovarian cancer is one of the most fatal gynaecological malignancies in adult women. As studies on protein N-glycosylation have extensively reported aberrant patterns in the ovarian cancer tumour microenvironment, obtaining spatial information will uncover tumour-specific N-glycan alterations in ovarian cancer development and progression. MALDI mass spectrometry imaging (MSI) was employed to investigate N-glycan distribution on formalin-fixed paraffin-embedded (FFPE) ovarian cancer tissue sections from early- and late-stage patients. Tumour-specific N-glycans were identified and structurally characterised by PGC-LC-ESI-MS/MS, and then assigned to high-resolution images obtained from MALDI-MSI. Spatial distribution of 14 N-glycans was obtained by MALDI-MSI and 42 N-glycans (including structural and compositional isomers) identified and structurally characterised by LC-MS. The spatial distribution of oligomannose, complex neutral, bisecting, and sialylated N-glycan families were localised to the tumour regions of late-stage ovarian cancer patients relative to early-stage patients. Potential N-glycan diagnostic markers that emerged include the oligomannose structure, (Hex)6 + (Man)3 (GlcNAc)2 , and the complex neutral structure, (Hex)2 (HexNAc)2 (Deoxyhexose)1 + (Man)3 (GlcNAc)2 . The distribution of these markers was evaluated using a tissue microarray (TMA) of early- and late-stage patients. This article is protected by copyright. All rights reserved.
    Keywords:  FFPE; MALDI; N-glycan; mass spectrometry imaging; ovarian cancer; tissue
    DOI:  https://doi.org/10.1002/pmic.201800482
  11. Methods Mol Biol. 2019 ;2019 171-180
    Evaluating the Role of RARβ Signaling on Cellular Metabolism in Melanoma Using the Seahorse XF Analyzer.
    Christina Dahl, Per Guldberg, Cecilie Abildgaard.
      Dysregulation of retinoic acid signaling is implicated in several human cancer types, including melanoma where the gene encoding retinoic acid receptor beta (RARβ) is frequently silenced by promoter hypermethylation. In this chapter, we describe some of the experimental procedures that we have used to characterize the role of RARβ signaling on the regulation of cellular metabolism in melanoma. Central to these studies is the use of the Seahorse XF Analyzer, which allows real-time assessment of the oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) in cultured cells as readouts for oxidative phosphorylation and glycolysis, respectively. The levels of RARβ signaling can be modulated using RARβ agonists (e.g., all-trans retinoic acid) and antagonists (e.g., LE135). The bioenergetic profiles of melanoma cells in response to RARβ modulators and other metabolic modifiers can be the basis for defining new therapeutic strategies.
    Keywords:  Cancer metabolism; Extracellular acidification rate; Glycolytic activity; Melanoma; Metabolic profile; Mitochondrial function; Oxygen consumption rate; Retinoic acid receptor β; Seahorse XF Analyzer; Warburg effect
    DOI:  https://doi.org/10.1007/978-1-4939-9585-1_12
  12. Cell Metab. 2019 Jul 23. pii: S1550-4131(19)30374-2. [Epub ahead of print]
    12-Lipoxygenase Regulates Cold Adaptation and Glucose Metabolism by Producing the Omega-3 Lipid 12-HEPE from Brown Fat.
    Luiz Osório Leiria, Chih-Hao Wang, Matthew D Lynes, Kunyan Yang, Farnaz Shamsi, Mari Sato, Satoru Sugimoto, Emily Y Chen, Valerie Bussberg, Niven R Narain, Brian E Sansbury, Justin Darcy, Tian Lian Huang, Sean D Kodani, Masaji Sakaguchi, Andréa L Rocha, Tim J Schulz, Alexander Bartelt, Gökhan S Hotamisligil, Michael F Hirshman, Klaus van Leyen, Laurie J Goodyear, Matthias Blüher, Aaron M Cypess, Michael A Kiebish, Matthew Spite, Yu-Hua Tseng.
      Distinct oxygenases and their oxylipin products have been shown to participate in thermogenesis by mediating physiological adaptations required to sustain body temperature. Since the role of the lipoxygenase (LOX) family in cold adaptation remains elusive, we aimed to investigate whether, and how, LOX activity is required for cold adaptation and to identify LOX-derived lipid mediators that could serve as putative cold mimetics with therapeutic potential to combat diabetes. By utilizing mass-spectrometry-based lipidomics in mice and humans, we demonstrated that cold and β3-adrenergic stimulation could promote the biosynthesis and release of 12-LOX metabolites from brown adipose tissue (BAT). Moreover, 12-LOX ablation in mouse brown adipocytes impaired glucose uptake and metabolism, resulting in blunted adaptation to the cold in vivo. The cold-induced 12-LOX product 12-HEPE was found to be a batokine that improves glucose metabolism by promoting glucose uptake into adipocytes and skeletal muscle through activation of an insulin-like intracellular signaling pathway.
    Keywords:  12-HEPE; adipocytes; brown adipose tissue; diabetes; eicosapentaenoic acid; fat; lipidomic; lipokine; obesity; thermogenesis
    DOI:  https://doi.org/10.1016/j.cmet.2019.07.001
  13. Methods Mol Biol. 2019 ;2024 95-102
    Preparation of the Low Molecular Weight Serum Proteome for Mass Spectrometry Analysis.
    Timothy D Veenstra.
      The ability to cure or manage many diseases is highly dependent on the ability to correctly diagnose them at the earliest possible stage. Diagnosis relies heavily on biomarkers whether these be visual symptoms or molecules found within samples acquired from the patient. For conditions that lack useful biomarkers, researchers are often faced with the task of sifting through very complex biological samples (i.e., serum, plasma, urine, tissue, cells, etc.) with the hope of discovering a small number of molecules that are exquisitely diagnostic for the condition of interest. One discovery strategy that has been frequently used is to fractionate the biological samples being studied into simpler aliquots that can be more easily characterized using existing technologies. One such fractionation method is to isolate a specific portion based on a specific property (i.e., size, phosphorylation state, charge, etc.) of the proteins within the sample. This method provides a simplified sample that can be characterized at a higher coverage level than the complex sample from which it was derived. This chapter details one of these methods, the extraction and analysis of the low molecular weight proteome of human serum.
    Keywords:  Biomarkers; Low molecular weight proteome; Mass spectrometry; Protein depletion; Serum
    DOI:  https://doi.org/10.1007/978-1-4939-9597-4_5
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