bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2020‒05‒31
thirteen papers selected by
Giovanny Rodriguez Blanco
The Beatson Institute for Cancer Research


  1. Cancers (Basel). 2020 May 27. pii: E1371. [Epub ahead of print]12(6):
    Fritsche-Guenther R, Gloaguen Y, Kirchner M, Mertins P, Tunn PU, Kirwan JA.
      Osteosarcoma (OS) is a primary malignant bone tumor and OS metastases are mostly found in the lung. The limited understanding of the biology of metastatic processes in OS limits the ability for effective treatment. Alterations to the metabolome and its transformation during metastasis aids the understanding of the mechanism and provides information on treatment and prognosis. The current study intended to identify metabolic alterations during OS progression by using a targeted gas chromatography mass spectrometry approach. Using a female OS cell line model, malignant and metastatic cells increased their energy metabolism compared to benign OS cells. The metastatic cell line showed a faster metabolic flux compared to the malignant cell line, leading to reduced metabolite pools. However, inhibiting both glycolysis and glutaminolysis resulted in a reduced proliferation. In contrast, malignant but non-metastatic OS cells showed a resistance to glycolytic inhibition but a strong dependency on glutamine as an energy source. Our in vivo metabolic approach hinted at a potential sex-dependent metabolic alteration in OS patients with lung metastases (LM), although this will require validation with larger sample sizes. In line with the in vitro results, we found that female LM patients showed a decreased central carbon metabolism compared to metastases from male patients.
    Keywords:  GC-MS; flux analysis; glucose; glutamine, sex and gender; osteosarcoma
    DOI:  https://doi.org/10.3390/cancers12061371
  2. J Pathol. 2020 May 27.
    Wallace PW, Conrad C, Brückmann S, Pang Y, Caleiras E, Murakami M, Korpershoek E, Zhuang Z, Rapizzi E, Kroiss M, Gudziol V, J L M Timmers H, Mannelli M, Pietzsch J, Beuschlein F, Pacak K, Robledo M, Klink B, Peitzsch M, Gill AJ, Tischler AS, de Krijger RR, Papathomas T, Aust D, Eisenhofer G, Richter S.
      Phaeochromocytomas and paragangliomas (PPGL) are rare neuroendocrine tumours with a hereditary background in over one third of patients. Mutations in succinate dehydrogenase (SDH) genes increase the risk for PPGLs and several other tumours. Mutations in subunit B (SDHB) in particular are a risk factor for metastatic disease, further highlighting the importance of identifying SDH mutations for patient management. Genetic variants of unknown significance, where implications for the patient and family members are unclear, are a problem for interpretation. For such cases, reliable methods for evaluating protein functionality are required. Immunohistochemistry for SDHB (SDHB-IHC) is the method of choice but does not assess functionality at the enzymatic level. Liquid chromatography mass spectrometry-based measurements of metabolite precursors and products of enzymatic reactions provides an alternative method. Here, we compare SDHB-IHC with metabolite profiling in 189 tumours from 187 PPGL patients. Besides evaluating succinate:fumarate ratios (SFR), machine learning algorithms were developed to establish predictive models for interpreting metabolite data. Metabolite profiling showed higher diagnostic specificity compared to SDHB-IHC (99.2% versus 92.5%, p = 0.021), whereas sensitivity was comparable. Application of machine learning algorithms to metabolite profiles improved predictive ability over that of the SFR, in particular for hard-to-interpret cases of head and neck paragangliomas (AUC 0.9821 versus 0.9613, p = 0.044). Importantly, the combination of metabolite profiling with SDHB-IHC has complementary utility, as SDHB-IHC correctly classified all but one of the false-negatives from metabolite profiling strategies while metabolite profiling correctly classified all but one of the false-negatives/positives from SDHB-IHC. From 186 tumours with confirmed status of SDHx variant pathogenicity, the combination of the two methods resulted in 185 correct predictions, highlighting the benefits of both strategies for patient management. This article is protected by copyright. All rights reserved.
    Keywords:  Krebs cycle metabolites; LC-MS/MS; diagnostics; linear discriminant analysis; mass spectrometry; metabolite profiling; multi-observer; prediction models; succinate to fumarate ratio; variants of unknown significance
    DOI:  https://doi.org/10.1002/path.5472
  3. Thorax. 2020 May 28. pii: thoraxjnl-2019-214241. [Epub ahead of print]
    Bottolo L, Miller S, Johnson SR.
      BACKGROUND: Lymphangioleiomyomatosis (LAM) is a rare multisystem disease almost exclusively affecting women which causes loss of lung function, lymphatic abnormalities and angiomyolipomas. LAM occurs sporadically and in people with tuberous sclerosis complex (TSC). Loss of TSC gene function leads to dysregulated mechanistic target of rapamycin (mTOR) signalling. As mTOR is a regulator of lipid and nucleotide synthesis, we hypothesised that the serum metabolome would be altered in LAM and related to disease severity and activity.METHODS: Ultrahigh performance liquid chromatography-tandem mass spectroscopy was used to examine the serum metabolome of 79 closely phenotyped women with LAM, including 29 receiving treatment with an mTOR inhibitor and 43 healthy control women.
    RESULTS: Sphingolipid, fatty acid and phospholipid metabolites were associated with FEV1 in women with LAM (eg, behenoyl sphingomyelin adjusted (adj.) p=8.10 × 10-3). Those with higher disease-burden scores had abnormalities in fatty acid, phospholipid and lysolipids. Rate of loss of FEV1 was associated with differences in acyl-carnitine, acyl-glycines, acyl-glutamine, fatty acids, endocanbinoids and sphingolipids (eg, myristoleoylcarnitine adj. p=0.07). In TSC-LAM, rapamycin affected modules of interrelated metabolites which comprised linoleic acid, the tricarboxylic acid cycle, aminoacyl-tRNA biosynthesis, cysteine, methionine, arginine and proline metabolism. Metabolomic pathway analysis within modules reiterated the importance of glycerophospholipid metabolites (adj. p=0.047).
    CONCLUSIONS: Women with LAM have altered lipid metabolism. The associations between these metabolites, multiple markers of disease activity and their potential biological roles in cell survival and signalling, suggest that lipid species may be both disease-relevant biomarkers and potential therapeutic targets for LAM.
    Keywords:  rare lung diseases
    DOI:  https://doi.org/10.1136/thoraxjnl-2019-214241
  4. Int J Mol Sci. 2020 May 25. pii: E3731. [Epub ahead of print]21(10):
    Ripoll C, Roldan M, Contreras-Montoya R, Diaz-Mochon JJ, Martin M, Ruedas-Rama MJ, Orte A.
      The main role of mitochondria, as pivotal organelles for cellular metabolism, is the production of energy (ATP) through an oxidative phosphorylation system. During this process, the electron transport chain creates a proton gradient that drives the synthesis of ATP. One of the main features of tumoral cells is their altered metabolism, providing alternative routes to enhance proliferation and survival. Hence, it is of utmost importance to understand the relationship between mitochondrial pH, tumoral metabolism, and cancer. In this manuscript, we develop a highly specific nanosensor to accurately measure the intramitochondrial pH using fluorescence lifetime imaging microscopy (FLIM). Importantly, we have applied this nanosensor to establish differences that may be hallmarks of different metabolic pathways in breast cancer cell models, leading to the characterization of different metabophenotypes.
    Keywords:  FLIM microscopy; cancer metabolism; intracellular sensors; nanosensing; tumoral metabolism
    DOI:  https://doi.org/10.3390/ijms21103731
  5. Front Oncol. 2020 ;10 723
    Daher B, Vučetić M, Pouysségur J.
      Cancer cells are characterized as highly proliferative at the expense of enhancement of metabolic rate. Consequently, cancer cells rely on antioxidant defenses to overcome the associated increased production of reactive oxygen species (ROS). The reliance of tumor metabolism on amino acids, especially amino acid transport systems, has been extensively studied over the past decade. Although cysteine is the least abundant amino acid in the cell, evidences described it as one of the most important amino acid for cell survival and growth. Regarding its multi-functionality as a nutrient, protein folding, and major component for redox balance due to its involvement in glutathione synthesis, disruption of cysteine homeostasis appears to be promising strategy for induction of cancer cell death. Ten years ago, ferroptosis, a new form of non-apoptotic cell death, has been described as a result of cysteine insufficiency leading to a collapse of intracellular glutathione level. In the present review, we summarized the metabolic networks involving the amino acid cysteine in cancer and ferroptosis and we focused on describing the recently discovered glutathione-independent pathway, a potential player in cancer ferroptosis resistance. Then, we discuss the implication of cysteine as key player in ferroptosis as a precursor for glutathione first, but also as metabolic precursor in glutathione-independent ferroptosis axis.
    Keywords:  cysteine; ferroptosis; glutathione; lipid peroxides; tumor-resistance; xCT transporter
    DOI:  https://doi.org/10.3389/fonc.2020.00723
  6. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi. 2020 Apr 20. 38(4): 246-250
    Peng FD, Wang YJ, Zhang B, Gao HL, Tang AH, Qian QJ, Ding CG.
      Objective: To explore the non-target metabonomics of serum in worker's pneumoconiosis (CWP) patients with latent tuberculosis and the biomarkers of latent tuberculosis infection of pneumoconiosis. Methods: In December 2018, 39 CWP inpatients from a hospital in Beijing were taken as subjects. The subjects were screened for latent tuberculosis using the in vitro release test of mycobacterium tuberculosis-interferon (IGRAs) test. According to the screening results, 21 positive patients with latent tuberculosis infection were selected as the latent tuberculosis group of pneumoconiosis. While 18 negative patients with CWP alone were selected as the pneumoconiosis group. Polarity components of metabolites were analyzed by UPLC-QTOF/MS. The data was processed with Progenesis QI software for multidimensional statistical analysis. Identification of structure of differential metabolites were matched through accurate mass and secondary mass spectrum. Searching the Human Metabolome Database (HMDB) , differential metabolites were imported into MetaboAnalyst 4.0 to analyze the metabolic pathways. Results: All 42 differential metabolites were screened out. Excepted for exogenous metabolites, 14 endogenous differential metabolites were identified. Compared with the pneumoconiosis group, 6 metabolites including PC [18∶4 (6Z, 9Z, 12Z, 15Z) /P-18∶1 (11Z) ], 3-Oxododecanoyl-CoA in the latent tuberculosis group were up-regulated, while 8 metabolites including the Stearoyl-CoA, (2S) -Pristanoyl-CoA were down-regulated. These results might be related to lipid, fatty acid and arachidonic acid metabolism pathways. Conclusion: There are significant differences in serum metabonomics between the patients with latent tuberculosis of pneumoconiosis and the patients with ordinary pneumoconiosis, which provide a reference for the study of biomarkers for the diagnosis of latent tuberculosis infection of pneumoconiosis.
    Keywords:  Latent tuberculosis; Metabolomics; Pneumoconiosis; Ultra performance liquid chromatography tandem quadrupole time of flight mass spectrometry (UPLC-QTOF/MS)
    DOI:  https://doi.org/10.3760/cma.j.cn121094-20190613-00239
  7. Arch Biochem Biophys. 2020 May 24. pii: S0003-9861(20)30440-9. [Epub ahead of print] 108431
    Guerra IMS, Ferreira HB, Neves B, Melo T, Diogo LM, Domingues MR, Moreira ASP.
      Phenylketonuria (PKU) is the most prevalent inborn error of amino acid metabolism. The disease is due to the deficiency of phenylalanine (Phe) hydroxylase activity, which causes the accumulation of Phe. Early diagnosis through neonatal screening is essential for early treatment implementation, avoiding cognitive impairment and other irreversible sequelae. Treatment is based on Phe restriction in the diet that should be maintained throughout life. High dietary restrictions can lead to imbalances in specific nutrients, notably lipids. Previous studies in PKU patients revealed changes in levels of plasma/serum lipoprotein lipids, as well as in fatty acid profile of plasma and red blood cells. Most studies showed a decrease in important polyunsaturated fatty acids, namely DHA (22:6n-3), AA (20:4n-6) and EPA (20:5n-6). Increased oxidative stress and subsequent lipid peroxidation have also been observed in PKU. Despite the evidences that the lipid profile is changed in PKU patients, more studies are needed to understand in detail how lipidome is affected. As highlighted in this review, mass spectrometry-based lipidomics is a promising approach to evaluate the effect of the diet restrictions on lipid metabolism in PKU patients, monitor their outcome, namely concerning the risk for other chronic diseases, and find possible prognosis biomarkers.
    Keywords:  Inborn errors of metabolism; Lipid changes; Lipidomics; Mass spectrometry; Oxidative stress; Phenylketonuria
    DOI:  https://doi.org/10.1016/j.abb.2020.108431
  8. Anal Chem. 2020 May 29.
    Chen D, Han W, Tao H, Li L, Li L.
      Blood metabolomics has been widely used for discovering potential metabolite biomarkers of various diseases. In this study, we report our investigation of the effects of freeze-thaw cycles (FTCs) of human serum samples on quantitative metabolomics using a differential chemical isotope labeling (CIL) LC-MS method. A total of 99 serum samples collected from healthy individuals (47 females and 52 males) were subjected to 5 FTCs, followed by 12C-/13C-dansylation labeling LC-MS analysis. A total of 2790 peak pairs or metabolites were relatively quantified among the 495 comparative samples, including 150 positively identified metabolites, 235 high-confident putatively identified metabolites and 1949 mass-matched metabolites from database searches. Multivariate analysis of the metabolome data showed a clustering of the 3rd-5th FTC samples in contrast to the separation of the 1st and 2nd FTC samples, indicating that the extent of FTC-induced metabolome changes became smaller after the third cycle. The changing patterns among the FTC-effected metabolites were found to be complex. Using sex as a biological factor for grouping, we observed a clear separation of males and females when the samples were subjected to the same number of FTCs. However, when the male- and female-samples with different numbers of FTCs were compared, the number of significant metabolites found in male-female comparison increased dramatically, indicating that FTC effects could lead to a large number of false positives in biomarker discovery. Finally, we proposed a method of detecting the FTC effects by re-analyzing the original samples after subjecting them an additional FTC.
    DOI:  https://doi.org/10.1021/acs.analchem.0c01610
  9. Nat Metab. 2020 Mar;2(3): 270-277
    Ding CC, Rose J, Sun T, Wu J, Chen PH, Lin CC, Yang WH, Chen KY, Lee H, Xu E, Tian S, Akinwuntan J, Zhao J, Guan Z, Zhou P, Chi JT.
      Critical to the bacterial stringent response is the rapid relocation of resources from proliferation toward stress survival through the respective accumulation and degradation of (p)ppGpp by RelA and SpoT homologues. While mammalian genomes encode MESH1, a homologue of the bacterial (p)ppGpp hydrolase SpoT, neither (p)ppGpp nor its synthetase has been identified in mammalian cells. Here, we show that human MESH1 is an efficient cytosolic NADPH phosphatase that facilitates ferroptosis. Visualization of the MESH1-NADPH crystal structure revealed a bona fide affinity for the NADPH substrate. Ferroptosis-inducing erastin or cystine deprivation elevates MESH1, whose overexpression depletes NADPH and sensitizes cells to ferroptosis, whereas MESH1 depletion promotes ferroptosis survival by sustaining the levels of NADPH and GSH and by reducing lipid peroxidation. The ferroptotic protection by MESH1 depletion is ablated by suppression of the cytosolic NAD(H) kinase, NADK, but not its mitochondrial counterpart NADK2. Collectively, these data shed light on the importance of cytosolic NADPH levels and their regulation under ferroptosis-inducing conditions in mammalian cells.
    DOI:  https://doi.org/10.1038/s42255-020-0181-1
  10. Pharmacol Res. 2020 May 25. pii: S1043-6618(20)31227-5. [Epub ahead of print] 104919
    Qiu Y, Cao Y, Cao W, Jia Y, Lu N.
      Ferroptosis is a new kind of regulated cell death that is characterized by highly iron-dependent lipid peroxidation. Ferroptosis involves various biology processes, such as iron metabolism, lipid metabolism, oxidative stress and biosynthesis of nicotinamide adenine dinucleotide phosphate (NADPH), glutathione (GSH) and coenzyme Q10 (CoQ10). A growing body of evidence suggests that ferroptosis is associated with cancer and neurodegenerative diseases (Alzheimer's disease, Parkinson's disease and Huntington's disease). This finding has helped develop a novel cytoprotective strategy to protect cells in neurodegenerative, blood and heart diseases by inhibiting ferroptosis. Meanwhile, the selective induction of ferroptosis has been adopted as a potential treatment strategy in some kinds of cancer. This review aims to summarize the mechanism of ferroptosis regulation and relevance to pathological physiology.
    Keywords:  Deferasirox (PubChem CID: 214348); Deferoxamine (PubChem CID: 2973); Erastin (PubChem CID: 11214940); Ferrostatin-1 (PubChem CID: 4068248); Lapatinib (PubChem CID: 208908); RAS-selective lethal 3 (PubChem CID: 1750826); Sorafenib (PubChem CID: 216239); cancer; cell death; ferroptosis; iron metabolism; lipid peroxidation; reactive oxygen species
    DOI:  https://doi.org/10.1016/j.phrs.2020.104919
  11. Dev Cell. 2020 May 22. pii: S1534-5807(20)30357-9. [Epub ahead of print]
    Stegen S, Rinaldi G, Loopmans S, Stockmans I, Moermans K, Thienpont B, Fendt SM, Carmeliet P, Carmeliet G.
      Correct functioning of chondrocytes is crucial for long bone growth and fracture repair. These cells are highly anabolic but survive and function in an avascular environment, implying specific metabolic requirements that are, however, poorly characterized. Here, we show that chondrocyte identity and function are closely linked with glutamine metabolism in a feedforward process. The master chondrogenic transcription factor SOX9 stimulates glutamine metabolism by increasing glutamine consumption and levels of glutaminase 1 (GLS1), a rate-controlling enzyme in this pathway. Consecutively, GLS1 action is critical for chondrocyte properties and function via a tripartite mechanism. First, glutamine controls chondrogenic gene expression epigenetically through glutamate dehydrogenase-dependent acetyl-CoA synthesis, necessary for histone acetylation. Second, transaminase-mediated aspartate synthesis supports chondrocyte proliferation and matrix synthesis. Third, glutamine-derived glutathione synthesis avoids harmful reactive oxygen species accumulation and allows chondrocyte survival in the avascular growth plate. Collectively, our study identifies glutamine as a metabolic regulator of cartilage fitness during bone development.
    Keywords:  GLS1; GLUD1; GOT2; biosynthesis; chondrocyte; endochondral ossification; glutamine metabolism; histone acetylation; redox homeostasis; survival
    DOI:  https://doi.org/10.1016/j.devcel.2020.05.001
  12. Life Sci. 2020 May 20. pii: S0024-3205(20)30567-1. [Epub ahead of print] 117818
    Wang Z, Yang X, Kai J, Wang F, Wang Z, Shao J, Tan S, Chen A, Zhang F, Wang S, Zhang Z, Zheng S.
      Activation of hepatic stellate cells (HSCs) is a central event in the pathogenesis of liver fibrosis and is characterized by the disappearance of lipid droplets. Although the exogenous supplementation of lipid droplet content can effectively reverse the activation of HSCs, the underlying molecular mechanisms are largely unknown. In our current study, we sought to investigate the role of lncRNA-H19 in the process of lipid droplets disappearance and to further examine the underlying molecular mechanisms. We found that the lncRNA-H19 level was increased in CCl4-induced fibrotic liver, which activated HSCs. Further research showed that hypoxia inducible factor-1α (HIF-1α) significantly increased lncRNA-H19 expression by binding to the lncRNA-H19 promoter at two hypoxia response element (HRE) sites located at 492-499 and 515-522 bp. Importantly, lncRNA-H19 knockdown markedly inhibited HSC activation and alleviated liver fibrosis, indicating that lncRNA-H19 may be a potential target for anti-fibrosis therapeutic approaches. Moreover, lncRNA-H19 knockdown could reverse the lipid droplet phenotype of activated HSCs, inhibiting the phosphorylated AMPK-mediated lipid oxidation signaling pathway. The AMPK agonist AICAR promoted AMPK phosphorylation and abrogated lipid droplets restoration in HSCs transfected with the lncRNA-H19 knockdown plasmid. Experimental molecular analysis showed that lncRNA-H19 triggered AMPKα to interact with LKB1 and resulted in AMPKα phosphorylation, which accelerating lipid droplets degradation and lipid oxidation. Taken together, our results highlighted the role of lncRNA-H19 in the metabolism of lipid droplets in HSC, and revealed a new molecular target for alleviating liver fibrosis.
    Keywords:  AMP-activated protein kinase; Hepatic stellate cells; Lipid droplet; Liver fibrosis; LncRNA-H19
    DOI:  https://doi.org/10.1016/j.lfs.2020.117818
  13. Hepatology. 2020 May 27.
    Hall Z, Chiarugi D, Charidemou E, Leslie J, Scott E, Pelligrinet L, Allison M, Mocciaro G, Anstee QM, Evan GI, Hoare M, Vidal-Puig A, Oakley F, Vacca M, Griffin JL.
      BACKGROUND & AIMS: Hepatocytes undergo profound metabolic rewiring when primed to proliferate during compensatory regeneration and in hepatocellular carcinoma (HCC). However, the metabolic control of these processes is not fully understood. In order to capture the metabolic signature of proliferating hepatocytes, we applied state-of-the-art systems biology approaches to models of liver regeneration, pharmacologically- and genetically-activated cell proliferation, and HCC.APPROACH & RESULTS: Integrating metabolomics, lipidomics and transcriptomics, we link changes in the lipidome of proliferating hepatocytes to altered metabolic pathways including lipogenesis, fatty acid desaturation, and generation of phosphatidylcholine (PC). We confirm this altered lipid signature in human HCC and show a positive correlation of monounsaturated-PC with hallmarks of cell proliferation and hepatic carcinogenesis.
    CONCLUSION: Overall, we demonstrate that specific lipid metabolic pathways are coherently altered when hepatocytes switch to proliferation. These represent a source of targets for the development of new therapeutic strategies and prognostic biomarkers of HCC.
    Keywords:  HCC; cancer metabolism; liver regeneration; mass spectrometry imaging; phosphatidylcholine
    DOI:  https://doi.org/10.1002/hep.31391