bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2020‒03‒22
sixteen papers selected by
Giovanny Rodriguez Blanco
The Beatson Institute for Cancer Research


  1. Metabolites. 2020 Mar 12. pii: E103. [Epub ahead of print]10(3):
    Rathod R, Gajera B, Nazir K, Wallenius J, Velagapudi V.
      The tricarboxylic acid (TCA) cycle is a central part of carbon and energy metabolism, also connecting to glycolysis, amino acid, and lipid metabolism. The quantitation of the TCA cycle intermediate within one method is lucrative due to the interest in central carbon metabolism profiling in cells and tissues. In addition, TCA cycle intermediates in serum have been discovered to correspond as biomarkers to various underlying pathological conditions. In this work, an Liquid Chromatography-Mass Spectrometry/Mass Spectrometry-based quantification method is developed and validated, which takes advantage of fast, specific, sensitive, and cost-efficient precipitation extraction. Chromatographic separation is achieved while using Atlantis dC18 2.1 mm × 100 mm, particle size 3-μm of Waters column with a gradient elution mobile phase while using formic acid in water (0.1% v/v) and acetonitrile. Linearity was clearly seen over a calibration range of: 6.25 to 6400 ng/mL (r2 > 0.980) for malic acid; 11.72 to 12,000 ng/mL (r2 > 0.980) for cis-aconitic acid and L-aspartic acid; 29.30 to 30,000 ng/mL (r2 > 0.980) for isocitric acid, l-serine, and l-glutamic acid; 122.07 to 125,000 ng/mL (r2 > 0.980) for citric acid, glycine, oxo-glutaric acid, l-alanine, and l-glutamine; 527.34 to 540,000 ng/mL (r2 > 0.980) for l-lactic acid; 976.56 to 1,000,000 ng/mL (r2 > 0.980) for d-glucose; 23.44 to 24,000 ng/mL (r2 > 0.980) for fumaric acid and succinic acid; and, 244.14 to 250,000 ng/mL (r2 > 0.980) for pyruvic acid. Validation was carried out, as per European Medicines Agency (EMA) "guidelines on bioanalytical method validation", for linearity, precision, accuracy, limit of detection (LOD), limit of quantification (LLOQ), recovery, matrix effect, and stability. The recoveries from serum and tissue were 79-119% and 77-223%, respectively. Using this method, we measured TCA intermediates in serum, plasma (NIST 1950 SRM), and in mouse liver samples. The concentration found in NIST SRM 1950 (n = 6) of glycine (246.4 µmol/L), l-alanine (302.4 µmol/L), and serine (92.9 µmol/L).
    Keywords:  bioanalytical method validation; chromatography; mass spectrometry; metabolites; tricarboxylic acid (TCA) cycle
    DOI:  https://doi.org/10.3390/metabo10030103
  2. Cell Metab. 2020 Mar 16. pii: S1550-4131(20)30114-5. [Epub ahead of print]
    Yang L, Garcia Canaveras JC, Chen Z, Wang L, Liang L, Jang C, Mayr JA, Zhang Z, Ghergurovich JM, Zhan L, Joshi S, Hu Z, McReynolds MR, Su X, White E, Morscher RJ, Rabinowitz JD.
      NADH provides electrons for aerobic ATP production. In cells deprived of oxygen or with impaired electron transport chain activity, NADH accumulation can be toxic. To minimize such toxicity, elevated NADH inhibits the classical NADH-producing pathways: glucose, glutamine, and fat oxidation. Here, through deuterium-tracing studies in cultured cells and mice, we show that folate-dependent serine catabolism also produces substantial NADH. Strikingly, when respiration is impaired, serine catabolism through methylene tetrahydrofolate dehydrogenase (MTHFD2) becomes a major NADH source. In cells whose respiration is slowed by hypoxia, metformin, or genetic lesions, mitochondrial serine catabolism inhibition partially normalizes NADH levels and facilitates cell growth. In mice with engineered mitochondrial complex I deficiency (NDUSF4-/-), serine's contribution to NADH is elevated, and progression of spasticity is modestly slowed by pharmacological blockade of serine degradation. Thus, when respiration is impaired, serine catabolism contributes to toxic NADH accumulation.
    Keywords:  MTHFD2; NAD; NADH; SHMT2; complex I inhibitor; hypoxia; methylene tetrahydrofolate dehydrogenase; mitochondrial disease; redox; respiration inhibition; serine catabolism; serine hydroxymethyltransferase
    DOI:  https://doi.org/10.1016/j.cmet.2020.02.017
  3. Nat Commun. 2020 Mar 17. 11(1): 1320
    Kodama M, Oshikawa K, Shimizu H, Yoshioka S, Takahashi M, Izumi Y, Bamba T, Tateishi C, Tomonaga T, Matsumoto M, Nakayama KI.
      Glucose metabolism is remodeled in cancer, but the global pattern of cancer-specific metabolic changes remains unclear. Here we show, using the comprehensive measurement of metabolic enzymes by large-scale targeted proteomics, that the metabolism both carbon and nitrogen is altered during the malignant progression of cancer. The fate of glutamine nitrogen is shifted from the anaplerotic pathway into the TCA cycle to nucleotide biosynthesis, with this shift being controlled by glutaminase (GLS1) and phosphoribosyl pyrophosphate amidotransferase (PPAT). Interventions to reduce the PPAT/GLS1 ratio suppresses tumor growth of many types of cancer. A meta-analysis reveals that PPAT shows the strongest correlation with malignancy among all metabolic enzymes, in particular in neuroendocrine cancer including small cell lung cancer (SCLC). PPAT depletion suppresses the growth of SCLC lines. A shift in glutamine fate may thus be required for malignant progression of cancer, with modulation of nitrogen metabolism being a potential approach to SCLC treatment.
    DOI:  https://doi.org/10.1038/s41467-020-15136-9
  4. Metabolites. 2020 Mar 12. pii: E101. [Epub ahead of print]10(3):
    Koelmel JP, Li X, Stow SM, Sartain MJ, Murali A, Kemperman R, Tsugawa H, Takahashi M, Vasiliou V, Bowden JA, Yost RA, Garrett TJ, Kitagawa N.
      Lipidomics has great promise in various applications; however, a major bottleneck in lipidomics is the accurate and comprehensive annotation of high-resolution tandem mass spectral data. While the number of available lipidomics software has drastically increased over the past five years, the reduction of false positives and the realization of obtaining structurally accurate annotations remains a significant challenge. We introduce Lipid Annotator, which is a user-friendly software for lipidomic analysis of data collected by liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS). We validate annotation accuracy against lipid standards and other lipidomics software. Lipid Annotator was integrated into a workflow applying an iterative exclusion MS/MS acquisition strategy to National Institute of Standards and Technology (NIST) SRM 1950 Metabolites in Frozen Human Plasma using reverse phase LC-HRMS/MS. Lipid Annotator, LipidMatch, and MS-DIAL produced consensus annotations at the level of lipid class for 98% and 96% of features detected in positive and negative mode, respectively. Lipid Annotator provides percentages of fatty acyl constituent species and employs scoring algorithms based on probability theory, which is less subjective than the tolerance and weighted match scores commonly used by available software. Lipid Annotator enables analysis of large sample cohorts and improves data-processing throughput as compared to previous lipidomics software.
    Keywords:  automation; ion mobility; lipid annotation; lipidomics; liquid chromatography; metabolomics; software; tandem mass spectrometry; time-of-flight
    DOI:  https://doi.org/10.3390/metabo10030101
  5. Front Oncol. 2020 ;10 239
    Nazemi M, Rainero E.
      The extracellular matrix (ECM) is a complex network of secreted proteins which provides support for tissues and organs. Additionally, the ECM controls a plethora of cell functions, including cell polarity, migration, proliferation, and oncogenic transformation. One of the hallmarks of cancer is altered cell metabolism, which is currently being exploited to develop anti-cancer therapies. Several pieces of evidence indicate that the tumor microenvironment and the ECM impinge on tumor cell metabolism. Therefore, it is essential to understand the contribution of the complex 3D microenvironment in controlling metabolic plasticity and responsiveness to therapies targeting cell metabolism. In this mini-review, we will describe how the tumor microenvironment and cancer-associated fibroblasts dictate cancer cell metabolism, resulting in increased tumor progression. Moreover, we will define the cross-talk between nutrient signaling and the trafficking of the ECM receptors of the integrin family. Finally, we will present recent data highlighting the contribution of nutrient scavenging from the microenvironment to support cancer cells growth under nutrient starvation conditions.
    Keywords:  cancer associated fibroblasts; cell metabolism; extracellular matrix; nutrient scavenging; nutrient signaling
    DOI:  https://doi.org/10.3389/fonc.2020.00239
  6. Biochem Biophys Res Commun. 2020 Mar 11. pii: S0006-291X(20)30475-7. [Epub ahead of print]
    Wang L, Dong E, Fang L, Luo M, Tang C, Li J.
      Evidences suggest that dietary docosahexaenoic acid (DHA) supplementation may have pleiotropic beneficial effects on health. However, the underlying mechanisms and crucial targets that are involved in achieving these benefits remain to be clarified. In this study, we employed biochemical analysis and liquid chromatography-mass spectrometry (LC-MS) based untargeted metabolomics coupled with multivariate statistical analysis to identify potential metabolic targets of DHA in adult rats at 48 h post-feeding. Blood biochemical analysis showed a significant decrease in triglyceride level of DHA diet group, the untargeted metabolomic analysis revealed that some metabolites were significantly different between the DHA diet group and the basal diet group, including fatty acids (16:0, 18:1, 20:5n3, 22:2n6 and 24:0), diglyceride (20:0/18:2n6, 18:3n6/22:6n3, 20:4n3/20:4n3, and 22:0/24:0), PIP2 (18:2/20:3), phytol, lysoSM (d18:1), 12-hydroxyheptadecatrienoic acid, dihydrocorticosterone and N1-acetylspermine, which are mainly involved in fat mobilization and triglyceride hydrolysis, arachidonic acid, steroid hormone, and polyamine metabolism. To our knowledge, this is the first report that links the metabolic effects of DHA with arachidonic acid, steroid, and polyamine metabolism. Our finding suggests that the beneficial effects of DHA, may not directly require its own metabolic derivatives, but could be achieved by metabolic regulation.
    Keywords:  Docosahexaenoic acid; LC-MS; Metabolic target; Metabolomics
    DOI:  https://doi.org/10.1016/j.bbrc.2020.02.167
  7. Mol Metab. 2020 Jan 09. pii: S2212-8778(20)30005-3. [Epub ahead of print]34 174-186
    Sengupta D, Cassel T, Teng KY, Aljuhani M, Chowdhary VK, Hu P, Zhang X, Fan TW, Ghoshal K.
      OBJECTIVE: It is well established that the liver-specific miR-122, a bona fide tumor suppressor, plays a critical role in lipid homeostasis. However, its role, if any, in amino acid metabolism has not been explored. Since glutamine (Gln) is a critical energy and anaplerotic source for mammalian cells, we assessed Gln metabolism in control wild type (WT) mice and miR-122 knockout (KO) mice by stable isotope resolved metabolomics (SIRM) studies.METHODS: Six-to eight-week-old WT and KO mice and 12- to 15-month-old liver tumor-bearing mice were injected with [U-13C5,15N2]-L-Gln, and polar metabolites from the liver tissues were analyzed by nuclear magnetic resonance (NMR) imaging and ion chromatography-mass spectrometry (IC-MS). Gln-metabolism was also assessed in a Gln-dependent hepatocellular carcinoma (HCC) cell line (EC4). Expressions of glutaminases (Gls and Gls2) were analyzed in mouse livers and human primary HCC samples.
    RESULTS: The results showed that loss of miR-122 promoted glutaminolysis but suppressed gluconeogenesis in mouse livers as evident from the buildup of 13C- and/or 15N-Glu and decrease in glucose-6-phosphate (G6P) levels, respectively, in KO livers. Enhanced glutaminolysis is consistent with the upregulation of expressions of Gls (kidney-type glutaminase) and Slc1a5, a neutral amino acid transporter in KO livers. Both Gls and Slc1a5 were confirmed as direct miR-122 targets by the respective 3'-UTR-driven luciferase assays. Importantly, expressions of Gls and Slc1a5 as well as glutaminase activity were suppressed in a Gln-dependent HCC (EC4) cell line transfected with miR-122 mimic that resulted in decreased 13C-Gln, 13C-á-ketoglutarate, 13C-isocitrate, and 13C-citrate levels. In contrast, 13C-phosphoenolpyruvate and 13C-G6P levels were elevated in cells expressing ectopic miR-122, suggesting enhanced gluconeogenesis. Finally, The Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) database analysis showed that expression of GLS is negatively correlated with miR-122 in primary human HCCs, and the upregulation of GLS RNA is associated with higher tumor grade. More importantly, patients with higher expressions of GLS or SLC1A5 in tumors exhibited poor survival compared with those expressing lower levels of these proteins.
    CONCLUSIONS: Collectively, these results show that miR-122 modulates Gln metabolism both in vitro and in vivo, implicating the therapeutic potential of miR-122 in HCCs that exhibit relatively high GLS levels.
    Keywords:  Gluconeogenesis; Glutaminase; Glutaminolysis; Krebs cycle; SIRM; Slc1a5; miR-122; miRNA-122
    DOI:  https://doi.org/10.1016/j.molmet.2020.01.003
  8. Chem Biol Interact. 2020 Mar 11. pii: S0009-2797(19)31320-1. [Epub ahead of print] 109058
    Barron K, Jeffries KA, Krupenko NI.
      Epidemiological evidence underscores alcohol consumption as a strong risk factor for multiple cancer types, with liver cancer being most commonly associated with alcohol intake. While mechanisms linking alcohol consumption to malignant tumors development are not fully understood, the likely players in ethanol-induced carcinogenesis are genotoxic stress caused by formation of acetaldehyde, increased oxidative stress and altered nutrient metabolism, including the impairment of methyl transfer reactions. Alterations of sphingolipid metabolism and associated signaling pathways are another potential link between ethanol and cancer development. In particular, ceramides are involved in the regulation of cellular proliferation, differentiation, senescence and apoptosis and are known to function as important regulators of malignant transformation as well as tumor progression. However, to date, the cross-talk between ceramides and alcohol in cancer disease is largely an open question and only limited data are available on this subject. Most studies linking ceramide to cancer considered liver steatosis as the underlying mechanism, which is not surprising taking into consideration that ceramide pathways are an integral part of the overall lipid metabolism. This review summarizes the latest studies pointing to ceramide as important mediator of cancer-promoting effects of chronic alcohol consumption and underscores the necessity of understanding the role of sphingolipids and lipid signaling in response to alcohol in order to prevent and/or successfully manage diseases caused by alcohol.
    Keywords:  Alcohol consumption; Cancer; Ceramide; Sphingolipids; p53
    DOI:  https://doi.org/10.1016/j.cbi.2020.109058
  9. Int J Biol Sci. 2020 ;16(7): 1194-1206
    Lin W, Zhou Q, Wang CQ, Zhu L, Bi C, Zhang S, Wang X, Jin H.
      Metabolic reprogramming is a hallmark of cancer. Mammalian genome is characterized by pervasive transcription, generating abundant non-coding RNAs (ncRNAs). Long non-coding RNAs (lncRNAs) are freshly discovered functional ncRNAs exerting extensive regulatory impact through diverse mechanisms. Emerging studies have revealed widespread roles of lncRNAs in the regulation of various cellular activities, including metabolic pathways. In this review, we summarize the latest advances regarding the regulatory roles of lncRNAs in cancer metabolism, particularly their roles in mitochondrial function, glucose, glutamine, and lipid metabolism. Moreover, we discuss the clinical application and challenges of targeting lncRNAs in cancer metabolism. Understanding the complex and special behavior of lncRNAs will allow a better depiction of cancer metabolic networks and permit the development of lncRNA-based clinical therapies by targeting cancer metabolism.
    Keywords:  Cancer; Long non-coding RNA; Metabolism
    DOI:  https://doi.org/10.7150/ijbs.40769
  10. Methods Enzymol. 2020 ;pii: S0076-6879(19)30317-9. [Epub ahead of print]636 93-108
    Astarita G, Dhungana S, Shrestha B, Laiakis EC.
      Tumors are characterized by metabolic dysregulation, reprogramming, and the presence of metabolites, which can act both as energy mediators and signaling messengers. Measuring the concentration and composition of metabolites in the tumor microenvironment can help to better understand the tumor pathology and might improve therapeutic treatments. Metabolomics can provide a description of the physiological and pathological status, as well as help to identify biomarkers of the disease. Additionally, mass spectrometry-based tissue imaging techniques can show the spatial distribution of metabolites. In this chapter we present protocols for the extraction and analysis of metabolites and lipids, with emphasis on liquid chromatography-mass spectrometry and mass spectrometry imaging.
    Keywords:  Lipid; Lipidomics; Metabolite; Metabolomics; Targeted; Tissue imaging; Untargeted
    DOI:  https://doi.org/10.1016/bs.mie.2019.07.037
  11. Proteomics. 2020 Mar 20. e1900141
    Hentschel A, Ahrends R.
      Targeted data acquisition using nano-LC coupled mass spectrometry is an emerging approach when there is need to quantify proteins with high accuracy, sensitivity and reproducibility. Nevertheless, creating assays meeting all those criteria still remains a laborious task, especially when investigating low abundant proteins and small concentration changes. In this work we develop a targeted data acquisition workflow reducing time and effort to target and investigate key players of metabolic pathways during the process of adipocyte differentiation. This leads to accurate and sensitive quantification of proteins involved in the synthesis of fatty acids, glycerolipids, glycerophospholipids sphingolipids, the production of energy and reduction equivalents. Additionally low abundant signaling molecules part of the PPARγ and insulin signaling pathway with approximately 400 for the insulin receptor substrate and 1100 copies/cell for PPARγ were determined. This article is protected by copyright. All rights reserved.
    Keywords:  Absolute quantification; adipogenesis; metabolic pathways; targeted proteomics
    DOI:  https://doi.org/10.1002/pmic.201900141
  12. J Cancer. 2020 ;11(7): 1761-1767
    Yang J, Wang L, Jia R.
      Despite extensive research in the cancer field, cancer remains one of the most prevalent diseases. There is an urgent need to identify specific targets that are safe and effective for the treatment of cancer. In recent years, cancer metabolism has come into the spotlight in cancer research. Lipid metabolism, especially cholesterol metabolism, plays a critical role in membrane synthesis as well as lipid signaling in cancer. This review focuses on the contribution of the de novo cholesterol synthesis pathway to tumorigenesis, cancer progression and metastasis. In conclusion, cholesterol metabolism could be an effective target for novel anticancer treatment.
    Keywords:  cancer progress; de novo cholesterol synthesis; metabolic reprogramming
    DOI:  https://doi.org/10.7150/jca.38598
  13. Signal Transduct Target Ther. 2020 ;5 28
    Fares J, Fares MY, Khachfe HH, Salhab HA, Fares Y.
      Metastasis is the hallmark of cancer that is responsible for the greatest number of cancer-related deaths. Yet, it remains poorly understood. The continuous evolution of cancer biology research and the emergence of new paradigms in the study of metastasis have revealed some of the molecular underpinnings of this dissemination process. The invading tumor cell, on its way to the target site, interacts with other proteins and cells. Recognition of these interactions improved the understanding of some of the biological principles of the metastatic cell that govern its mobility and plasticity. Communication with the tumor microenvironment allows invading cancer cells to overcome stromal challenges, settle, and colonize. These characteristics of cancer cells are driven by genetic and epigenetic modifications within the tumor cell itself and its microenvironment. Establishing the biological mechanisms of the metastatic process is crucial in finding open therapeutic windows for successful interventions. In this review, the authors explore the recent advancements in the field of metastasis and highlight the latest insights that contribute to shaping this hallmark of cancer.
    Keywords:  Metastasis
    DOI:  https://doi.org/10.1038/s41392-020-0134-x
  14. Cell Death Dis. 2020 Mar 17. 11(3): 192
    Weigand I, Schreiner J, Röhrig F, Sun N, Landwehr LS, Urlaub H, Kendl S, Kiseljak-Vassiliades K, Wierman ME, Angeli JPF, Walch A, Sbiera S, Fassnacht M, Kroiss M.
      Conditions of impaired adrenal function and tissue destruction, such as in Addison's disease, and treatment resistance of adrenocortical carcinoma (ACC) necessitate improved understanding of the pathophysiology of adrenal cell death. Due to relevant oxidative processes in the adrenal cortex, our study investigated the role of ferroptosis, an iron-dependent cell death mechanism and found high adrenocortical expression of glutathione peroxidase 4 (GPX4) and long-chain-fatty-acid CoA ligase 4 (ACSL4) genes, key factors in the initiation of ferroptosis. By applying MALDI mass spectrometry imaging to normal and neoplastic adrenocortical tissue, we detected high abundance of arachidonic and adrenic acid, two long chain polyunsaturated fatty acids which undergo peroxidation during ferroptosis. In three available adrenal cortex cell models (H295R, CU-ACC1 and CU-ACC-2) a high susceptibility to GPX4 inhibition with RSL3 was documented with EC50 values of 5.7 × 10-8, 8.1 × 10-7 and 2.1 × 10-8 M, respectively, while all non-steroidogenic cells were significantly less sensitive. Complete block of GPX4 activity by RSL3 led to ferroptosis which was completely reversed in adrenal cortex cells by inhibition of steroidogenesis with ketoconazole but not by blocking the final step of cortisol synthesis with metyrapone. Mitotane, the only approved drug for ACC did not induce ferroptosis, despite strong induction of lipid peroxidation in ACC cells. Together, this report is the first to demonstrate extraordinary sensitivity of adrenal cortex cells to ferroptosis dependent on their active steroid synthetic pathways. Mitotane does not induce this form of cell death in ACC cells.
    DOI:  https://doi.org/10.1038/s41419-020-2385-4
  15. Int J Mol Sci. 2020 Mar 17. pii: E2061. [Epub ahead of print]21(6):
    Wang Y, Nakajima T, Gonzalez FJ, Tanaka N.
      Peroxisome proliferator-activated receptor (PPAR) α, β/δ, and γ modulate lipid homeostasis. PPARα regulates lipid metabolism in the liver, the organ that largely controls whole-body nutrient/energy homeostasis, and its abnormalities may lead to hepatic steatosis, steatohepatitis, steatofibrosis, and liver cancer. PPARβ/δ promotes fatty acid β-oxidation largely in extrahepatic organs, and PPARγ stores triacylglycerol in adipocytes. Investigations using liver-specific PPAR-disrupted mice have revealed major but distinct contributions of the three PPARs in the liver. This review summarizes the findings of liver-specific PPAR-null mice and discusses the role of PPARs in the liver.
    Keywords:  NAFLD; NASH; PPAR; insulin resistance; liver fibrosis
    DOI:  https://doi.org/10.3390/ijms21062061
  16. Methods Cell Biol. 2020 ;pii: S0091-679X(19)30158-X. [Epub ahead of print]155 321-335
    Montesinos J, Area-Gomez E, Schlame M.
      Mitochondria and their associated membranes actively participate in biosynthesis, trafficking, and degradation of cellular phospholipids. Two crucial lipid biosynthetic activities of mitochondria include (i) the decarboxylation of phosphatidylserine to phosphatidylethanolamine and (ii) the de novo synthesis of cardiolipin. Here we describe protocols to measure these two activities, applying isotope-labeled or exogenous substrates in combination with thin-layer chromatography or mass spectrometry.
    Keywords:  Cardiolipin; MAM; Mitochondria-associated ER membranes; Phosphatidylethanolamine; Phosphatidylserine; Tafazzin
    DOI:  https://doi.org/10.1016/bs.mcb.2019.12.003