bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2020‒06‒28
eighteen papers selected by
Giovanny Rodriguez Blanco
The Beatson Institute for Cancer Research


  1. Cancer Metab. 2020 ;8 11
    Tousignant KD, Rockstroh A, Poad BLJ, Talebi A, Young RSE, Taherian Fard A, Gupta R, Zang T, Wang C, Lehman ML, Swinnen JV, Blanksby SJ, Nelson CC, Sadowski MC.
      Background: Metabolic reprograming, non-mutational epigenetic changes, increased cell plasticity, and multidrug tolerance are early hallmarks of therapy resistance in cancer. In this temporary, therapy-tolerant state, cancer cells are highly sensitive to ferroptosis, a form of regulated cell death that is caused by oxidative stress through excess levels of iron-dependent peroxidation of polyunsaturated fatty acids (PUFA). However, mechanisms underpinning therapy-induced ferroptosis hypersensitivity remain to be elucidated.Methods: We used quantitative single-cell imaging of fluorescent metabolic probes, transcriptomics, proteomics, and lipidomics to perform a longitudinal analysis of the adaptive response to androgen receptor-targeted therapies (androgen deprivation and enzalutamide) in prostate cancer (PCa).
    Results: We discovered that cessation of cell proliferation and a robust reduction in bioenergetic processes were associated with multidrug tolerance and a strong accumulation of lipids. The gain in lipid biomass was fueled by enhanced lipid uptake through cargo non-selective (macropinocytosis, tunneling nanotubes) and cargo-selective mechanisms (lipid transporters), whereas de novo lipid synthesis was strongly reduced. Enzalutamide induced extensive lipid remodeling of all major phospholipid classes at the expense of storage lipids, leading to increased desaturation and acyl chain length of membrane lipids. The rise in membrane PUFA levels enhanced membrane fluidity and lipid peroxidation, causing hypersensitivity to glutathione peroxidase (GPX4) inhibition and ferroptosis. Combination treatments against AR and fatty acid desaturation, lipase activities, or growth medium supplementation with antioxidants or PUFAs altered GPX4 dependence.
    Conclusions: Our work provides mechanistic insight into processes of lipid metabolism that underpin the acquisition of therapy-induced GPX4 dependence and ferroptosis hypersensitivity to standard of care therapies in PCa. It demonstrates novel strategies to suppress the therapy-tolerant state that may have potential to delay and combat resistance to androgen receptor-targeted therapies, a currently unmet clinical challenge of advanced PCa. Since enhanced GPX4 dependence is an adaptive phenotype shared by several types of cancer in response to different therapies, our work might have universal implications for our understanding of metabolic events that underpin resistance to cancer therapies.
    Keywords:  Ferroptosis; GPX4; Lipid remodeling; Lipid uptake; Metabolic reprograming; Multidrug tolerance; Prostate cancer; Therapy resistance
    DOI:  https://doi.org/10.1186/s40170-020-00217-6
  2. Cell Rep. 2020 Jun 23. pii: S2211-1247(20)30787-7. [Epub ahead of print]31(12): 107806
    Triki M, Rinaldi G, Planque M, Broekaert D, Winkelkotte AM, Maier CR, Janaki Raman S, Vandekeere A, Van Elsen J, Orth MF, Grünewald TGP, Schulze A, Fendt SM.
      Cancer cells display an increased plasticity in their lipid metabolism, which includes the conversion of palmitate to sapienate via the enzyme fatty acid desaturase 2 (FADS2). We find that FADS2 expression correlates with mammalian target of rapamycin (mTOR) signaling and sterol regulatory element-binding protein 1 (SREBP-1) activity across multiple cancer types and is prognostic in some cancer types. Accordingly, activating mTOR signaling by deleting tuberous sclerosis complex 2 (Tsc2) or overexpression of SREBP-1/2 is sufficient to increase FADS2 mRNA expression and sapienate metabolism in mouse embryonic fibroblasts (MEFs) and U87 glioblastoma cells, respectively. Conversely, inhibiting mTOR signaling decreases FADS2 expression and sapienate biosynthesis in MEFs with Tsc2 deletion, HUH7 hepatocellular carcinoma cells, and orthotopic HUH7 liver xenografts. In conclusion, we show that mTOR signaling and SREBP activity are sufficient to activate sapienate metabolism by increasing FADS2 expression. Consequently, targeting mTOR signaling can reduce sapienate metabolism in vivo.
    Keywords:  FADS2; SCD1; SREBP; cancer; fatty acid metabolism; glioblastoma; hepatocellular carcinoma; mTOR; palmitate; palmitoleate; sapienate
    DOI:  https://doi.org/10.1016/j.celrep.2020.107806
  3. Sci Rep. 2020 Jun 24. 10(1): 10250
    Gonsalves WI, Broniowska K, Jessen E, Petterson XM, Bush AG, Gransee J, Lacy MQ, Hitosugi T, Kumar SK.
      Oncogenic drivers of progression of monoclonal gammopathy of undetermined significance (MGUS) to multiple myeloma (MM) such as c-MYC have downstream effects on intracellular metabolic pathways of clonal plasma cells (PCs). Thus, extracellular environments such as the bone marrow (BM) plasma likely have unique metabolite profiles that differ from patients with MGUS compared to MM. This study utilized an untargeted metabolite and targeted complex lipid profiling of BM plasma to identify significant differences in the relative metabolite levels between patients with MGUS and MM from an exploratory cohort. This was followed by verification of some of the metabolite differences of interest by targeted quantification of the metabolites using isotopic internal standards in the exploratory cohort as well as an independent validation cohort. Significant differences were noted in the amino acid profiles such as decreased branch chain amino acids (BCAAs) and increased catabolism of tryptophan to the active kynurenine metabolite 3-hydroxy-kynurenine between patients with MGUS and MM. A decrease in the total levels of complex lipids such as phosphatidylethanolamines (PE), lactosylceramides (LCER) and phosphatidylinositols (PI) were also detected in the BM plasma samples from MM compared to MGUS patients. Thus, metabolite and complex lipid profiling of the BM plasma identifies differences in levels of metabolites and lipids between patients with MGUS and MM. This may provide insight into the possible differences of the intracellular metabolic pathways of their clonal PCs.
    DOI:  https://doi.org/10.1038/s41598-020-67105-3
  4. Cancer Discov. 2020 Jun 22. pii: CD-19-1228. [Epub ahead of print]
    Ngo B, Kim E, Osorio-Vasquez V, Doll S, Bustraan S, Liang RJ, Luengo A, Davidson SM, Ali A, Ferraro GB, Fischer GM, Eskandari R, Kang DS, Ni J, Plasger A, Rajasekhar VK, Kastenhuber ER, Bacha S, Sriram RK, Stein BD, Bakhoum SF, Snuderl M, Cotzia P, Healey JH, Mainolfi N, Suri V, Friedman A, Manfredi M, Sabatini DM, Jones DR, Yu M, Zhao JJ, Jain RK, Keshari KR, Davies MA, Vander Heiden MG, Hernando E, Mann M, Cantley LC, Pacold ME.
      A hallmark of metastasis is the adaptation of tumor cells to new environments. Metabolic constraints imposed by the serine and glycine-limited brain environment restrict metastatic tumor growth. How brain metastases overcome these growth-prohibitive conditions is poorly understood. Here, we demonstrate that 3-phosphoglycerate dehydrogenase (PHGDH), which catalyzes the rate-limiting step of glucose-derived serine synthesis, is a major determinant of brain metastasis in multiple human cancer types and preclinical models. Enhanced serine synthesis proved important for nucleotide production and cell proliferation in highly aggressive brain metastatic cells. In vivo, genetic suppression and pharmacological inhibition of PHGDH attenuated brain metastasis, but not extracranial tumor growth, and improved overall survival in mice. These results reveal that extracellular amino acid availability determines serine synthesis pathway dependence, and suggests that PHGDH inhibitors may be useful in the treatment of brain metastasis.
    DOI:  https://doi.org/10.1158/2159-8290.CD-19-1228
  5. J Am Soc Mass Spectrom. 2020 Jun 22.
    Elahee Doomun SN, Nie S, Loke S, Kowalski GM, Beech PL, Callahan DL.
      The analysis of 13C labelled lipids by mass spectrometry is challenging due to the complexity from labelling the large number of carbon atoms in lipids. To further add to the complexity, different adducts can be produced during electrospray ionisation and in-source fragmentation which can create complex overlapping isotope patterns that can only be resolved using high resolution mass spectrometry. Co-elution of lipids even after chromatographic separation also adds to the potential for overlapping mass spectra. Here, we describe a procedure that enables full 13C labelled patterns to be resolved in complex microalgal lipid extracts as well a procedure that provides structural labelling information. Mass resolving powers of 240,000 full width half maximum (FWHM) and fast targeted MS/MS allowed the differentiation of isotopologues, adducts and unresolved lipid species after chromatographic separation. This enabled the percentage of 13C enrichment to be calculated for each individual lipid species over a time series in the microalgal lipidome. The application of tandem mass spectrometry (MS/MS) also allowed the degree of labelling within the head-group vs acyl chains to be determined, further adding to the detail of information collected. This information is particularly useful for studying lipid synthesis and re-modelling processes and can be extended to other biological systems.
    DOI:  https://doi.org/10.1021/jasms.0c00192
  6. Am J Respir Crit Care Med. 2020 Jun 22.
    Gardner AI, Haq IJ, Simpson AJ, Becker KA, Gallagher J, Saint-Criq V, Verdon B, Mavin E, Trigg A, Gray MA, Koulman A, McDonnell MJ, Fisher AJ, Kramer EL, Clancy JP, Ward C, Schuchman EH, Gulbins E, Brodlie M.
      Rationale: In cystic fibrosis the major cause of morbidity and mortality is lung disease characterized by inflammation and infection. The influence of sphingolipid metabolism is poorly understood with a lack of studies using human airway model systems. Objectives: To investigate sphingolipid metabolism in cystic fibrosis and the effects of treatment with recombinant human acid ceramidase on inflammation and infection. Methods: Sphingolipids were measured using mass spectrometry in fully-differentiated cultures of primary human airway epithelial cells and co-cultures with Pseudomonas aeruginosa. In situ activity assays, Western blotting and quantitative polymerase chain reaction were used to investigate function and expression of ceramidase and sphingomyelinase. Effects of treatment with recombinant human acid ceramidase on sphingolipid profile and inflammatory mediator production were assessed in cell cultures and murine models. Measurements and Main Results: Ceramide is increased in cystic fibrosis airway epithelium due to differential function of enzymes regulating sphingolipid metabolism. Sphingosine, a metabolite of ceramide with antimicrobial properties, is not upregulated in response to Pseudomonas aeruginosa by cystic fibrosis airway epithelia. Tumor necrosis factor receptor 1 is increased in the apical membrane of cystic fibrosis epithelia and activates NF-κB signaling, generating inflammation. Treatment with recombinant human acid ceramidase, to decrease ceramide, reduced both inflammatory mediator production and susceptibility to infection. Conclusions: Sphingolipid metabolism is altered in airway epithelial cells cultured from people with cystic fibrosis. Treatment with recombinant acid ceramidase ameliorates the two pivotal features of cystic fibrosis lung disease, inflammation and infection, and thus represents a therapeutic approach worthy of further exploration. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/).
    Keywords:  Ceramide; Lung; Sphingolipid; Sphingosine
    DOI:  https://doi.org/10.1164/rccm.202001-0180OC
  7. Stud Health Technol Inform. 2020 Jun 23. 271 39-48
    Krettler CA, Hartler J, Thallinger GG.
      Changes in lipid homeostasis can lead to a plethora of diseases, raising the importance of reliable identification and measurement of lipids enabled by bioinformatics tools. However, due to the enormous diversity of lipids, most contemporary tools cover only a marginal range of lipid classes. To reduce such a shortcoming, this work extends the lipid species covered by Lipid Data Analyzer (LDA) to galactolipids and oxidized lipids. Appropriate mass lists were generated for MS1 identifications and the proprietary decision rule sets were extended for MS2 identifications of the novel lipid classes. Furthermore, LDA was extended to enable identification of oxidatively modified fatty acyl chains. With these extensions, LDA can reliably identify the most important galactolipids as well as oxidatively modified versions of the 22 previously implemented lipid classes. Comparison with other up to date lipidomics tools show that LDA has a better coverage of the newly implemented lipid species. The extended version of LDA provides researchers with a powerful platform to elucidate diseases caused by perturbations in the oxidized lipidome. LDA is freely available from https://genome.tugraz.at/lda.
    Keywords:  bioinformatics; cheminformatics; galactolipids; lipidomics; mass spectrometry; oxidized lipids
    DOI:  https://doi.org/10.3233/SHTI200072
  8. Lipids. 2020 Jun 25.
    Newell M, Patel D, Goruk S, Field CJ.
      To better understand how docosahexaenoic acid (DHA) improves the effects of doxorubicin (DOX), we examined DHA ± DOX on changes in whole cell and lipid raft phospholipids (PL) of MDA-MB-231 and MCF-7 breast cancer cells. We sought to confirm whether the relative changes in PL DHA content of MDA-MB-231 cells could be extended to PL from MDA-MB-231 tumors grown in mice fed a DHA supplemented diet ±DOX. Treatment with DHA did not change PL composition yet DOX increased the proportion of phosphatidylserine in MCF-7 cell lipid rafts by two-fold (p < 0.001). Regardless of DOX, the relative percent incorporation of DHA was higher in MDA-MB-231 cells compared to MCF-7 cells in phosphatidylserine, phosphatidylethanolamine, and phosphatidylcholine (whole cell and lipid rafts); and higher in phosphatidylethanolamine vs. phosphatidylcholine (4.4-fold in MCF-7 and 6-fold in MDA-MB-231 cells respectively). DHA treatment increased eicosapentaenoic acid and docosapentaenoic acid in MDA-MB-231 cells but not MCF-7 cells. Increased DHA content in MDA-MB-231 cells, MCF-7 cells, and MDA-MB-231 tumors in all PL moieties (except sphingomyelin) corresponded with reduced arachidonic acid (p < 0.05). Feeding mice 2.8% (w/w of fat) DHA ± DOX increased tumor necrotic regions (p < 0.05). This study established differential incorporation of DHA into whole cell and lipid rafts between human breast cancer cell lines. However, within each cell line, this incorporation was not altered by DOX confirming that DOX does not change membrane lipid composition. Furthermore, our findings indicate that membrane changes observed in vitro are translatable to in vivo changes and that DHA + DOX could contribute to the anticancer effects through increased necrosis.
    Keywords:  Analytical Techniques; Cancer; Docosahexaenoic acid; Fatty acid analysis; Nutrition; Phospholipid analysis; Physiology; Specific lipids; n-3 Fatty acids
    DOI:  https://doi.org/10.1002/lipd.12252
  9. Cells. 2020 Jun 20. pii: E1505. [Epub ahead of print]9(6):
    Battaglia AM, Chirillo R, Aversa I, Sacco A, Costanzo F, Biamonte F.
      Ferroptosis is a new type of oxidative regulated cell death (RCD) driven by iron-dependent lipid peroxidation. As major sites of iron utilization and master regulators of oxidative metabolism, mitochondria are the main source of reactive oxygen species (ROS) and, thus, play a role in this type of RCD. Ferroptosis is, indeed, associated with severe damage in mitochondrial morphology, bioenergetics, and metabolism. Furthermore, dysregulation of mitochondrial metabolism is considered a biochemical feature of neurodegenerative diseases linked to ferroptosis. Whether mitochondrial dysfunction can, per se, initiate ferroptosis and whether mitochondrial function in ferroptosis is context-dependent are still under debate. Cancer cells accumulate high levels of iron and ROS to promote their metabolic activity and growth. Of note, cancer cell metabolic rewiring is often associated with acquired sensitivity to ferroptosis. This strongly suggests that ferroptosis may act as an adaptive response to metabolic imbalance and, thus, may constitute a new promising way to eradicate malignant cells. Here, we review the current literature on the role of mitochondria in ferroptosis, and we discuss opportunities to potentially use mitochondria-mediated ferroptosis as a new strategy for cancer therapy.
    Keywords:  ROS; cancer; cell death; ferroptosis; iron; mitochondria
    DOI:  https://doi.org/10.3390/cells9061505
  10. Nat Commun. 2020 Jun 23. 11(1): 3169
    Xiong N, Gao X, Zhao H, Cai F, Zhang FC, Yuan Y, Liu W, He F, Zacharias LG, Lin H, Vu HS, Xing C, Yao DX, Chen F, Luo B, Sun W, DeBerardinis RJ, Xu H, Ge WP.
      Understanding tumor metabolism holds the promise of new insights into cancer biology, diagnosis and treatment. To assess human cancer metabolism, here we report a method to collect intra-operative samples of blood from an artery directly upstream and a vein directly downstream of a brain tumor, as well as samples from dorsal pedal veins of the same patients. After performing targeted metabolomic analysis, we characterize the metabolites consumed and produced by gliomas in vivo by comparing the arterial supply and venous drainage. N-acetylornithine, D-glucose, putrescine, and L-acetylcarnitine are consumed in relatively large amounts by gliomas. Conversely, L-glutamine, agmatine, and uridine 5-monophosphate are produced in relatively large amounts by gliomas. Further we verify that D-2-hydroxyglutarate (D-2HG) is high in venous plasma from patients with isocitrate dehydrogenases1 (IDH1) mutations. Through these paired comparisons, we can exclude the interpatient variation that is present in plasma samples usually taken from the cubital vein.
    DOI:  https://doi.org/10.1038/s41467-020-16810-8
  11. Aging (Albany NY). 2020 Jun 24. 12
    Wilkinson DJ, Rodriguez-Blanco G, Dunn WB, Phillips BE, Williams JP, Greenhaff PL, Smith K, Gallagher IJ, Atherton PJ.
      Ageing compromises skeletal muscle mass and function through poorly defined molecular aetiology. Here we have used untargeted metabolomics using UHPLC-MS to profile muscle tissue from young (n=10, 25±4y), middle aged (n=18, 50±4y) and older (n=18, 70±3y) men and women (50:50). Random Forest was used to prioritise metabolite features most informative in stratifying older age, with potential biological context examined using the prize-collecting Steiner forest algorithm embedded in the PIUMet software, to identify metabolic pathways likely perturbed in ageing. This approach was able to filter a large dataset of several thousand metabolites down to subnetworks of age important metabolites. Identified networks included the common age-associated metabolites such as androgens, (poly)amines/amino acids and lipid metabolites, in addition to some potentially novel ageing related markers such as dihydrothymine and imidazolone-5-proprionic acid. The present study reveals that this approach is a potentially useful tool to identify processes underlying human tissue ageing, and could therefore be utilised in future studies to investigate the links between age predictive metabolites and common biomarkers linked to health and disease across age.
    Keywords:  aging; markers; metabolomics; muscle
    DOI:  https://doi.org/10.18632/aging.103513
  12. Nat Commun. 2020 Jun 26. 11(1): 3244
    Kleinpenning F, Steigenberger B, Wu W, Heck AJR.
      Bioorthogonal chemistry introduces affinity-labels into biomolecules with minimal disruption to the original system and is widely applicable in a range of contexts. In proteomics, immobilized metal affinity chromatography (IMAC) enables enrichment of phosphopeptides with extreme sensitivity and selectivity. Here, we adapt and combine these superb assets in a new enrichment strategy using phosphonate-handles, which we term PhosID. In this approach, click-able phosphonate-handles are introduced into proteins via 1,3-dipolar Huisgen-cycloaddition to azido-homo-alanine (AHA) and IMAC is then used to enrich exclusively for phosphonate-labeled peptides. In interferon-gamma (IFNγ) stimulated cells, PhosID enabled the identification of a large number of IFN responsive newly synthesized proteins (NSPs) whereby we monitored the differential synthesis of these proteins over time. Collectively, these data validate the excellent performance of PhosID with efficient analysis and quantification of hundreds of NSPs by single LC-MS/MS runs. We envision PhosID as an attractive and alternative tool for studying stimuli-sensitive proteome subsets.
    DOI:  https://doi.org/10.1038/s41467-020-17010-0
  13. Mass Spectrom Rev. 2020 Jun 26.
    Sutton JM, Kim J, El Zahar NM, Bartlett MG.
      Since 2016, eight new oligonucleotide therapies have been approved which has led to increased interest in oligonucleotide analysis. There is a particular need for powerful bioanalytical tools to study the metabolism and biotransformation of these molecules. This review provides the background on the biological basis of these molecules as currently used in therapies. The article also reviews the current state of analytical methodology including state of the art sample preparation techniques, liquid chromatography-mass spectrometry methods, and the current limits of detection/quantitation. Finally, the article summarizes the challenges in oligonucleotide bioanalysis and provides future perspectives for this emerging field. © 2020 John Wiley & Sons Ltd. Mass Spec Rev 1-25, 2020.
    Keywords:  oligonucleotide mass spectrometry; oligonucleotide metabolite identification; oligonucleotide quantitation; oligonucleotide sample preparation; oligonucleotide therapeutics
    DOI:  https://doi.org/10.1002/mas.21641
  14. Cancers (Basel). 2020 Jun 23. pii: E1668. [Epub ahead of print]12(6):
    Mossenta M, Busato D, Dal Bo M, Toffoli G.
      Hepatocellular carcinoma (HCC) metabolism is redirected to glycolysis to enhance the production of metabolic compounds employed by cancer cells to produce proteins, lipids, and nucleotides in order to maintain a high proliferative rate. This mechanism drives towards uncontrolled growth and causes a further increase in reactive oxygen species (ROS), which could lead to cell death. HCC overcomes the problem generated by ROS increase by increasing the antioxidant machinery, in which key mechanisms involve glutathione, nuclear factor erythroid 2-related factor 2 (Nrf2), and hypoxia-inducible transcription factor (HIF-1α). These mechanisms could represent optimal targets for innovative therapies. The tumor microenvironment (TME) exerts a key role in HCC pathogenesis and progression. Various metabolic machineries modulate the activity of immune cells in the TME. The deregulated metabolic activity of tumor cells could impair antitumor response. Lactic acid-lactate, derived from the anaerobic glycolytic rate of tumor cells, as well as adenosine, derived from the catabolism of ATP, have an immunosuppressive activity. Metabolic reprogramming of the TME via targeted therapies could enhance the treatment efficacy of anti-cancer immunotherapy. This review describes the metabolic pathways mainly involved in the HCC pathogenesis and progression. The potential targets for HCC treatment involved in these pathways are also discussed.
    Keywords:  HCC; anticancer-immunoresponse; glucose metabolism; oxidative stress; tumor microenvironment
    DOI:  https://doi.org/10.3390/cancers12061668
  15. Cancer Biol Med. 2020 May 15. 17(2): 282-292
    Liu Q, Luo Q, Ju Y, Song G.
      Cross-talk between tumor cells and mechanical stress in the tumor microenvironment has been shown to be involved in carcinogenesis. High mechanical stress in tumors can alter the metabolism and behaviors of cancer cells and cause cancer cells to attain cancer stem-like cell properties, thus driving tumor progression and promoting metastasis. The mechanical signal is converted into a biochemical signal that activates tumorigenic signaling pathways through mechanotransduction. Herein, we describe the physical changes occurring during reprogramming of cancer cell metabolism, which regulate cancer stem cell functions and promote tumor progression and aggression. Furthermore, we highlight emerging therapeutic strategies targeting mechanotransduction signaling pathways.
    Keywords:  Cancer stem cell; cell metabolism; mechanical force; tumor progression
    DOI:  https://doi.org/10.20892/j.issn.2095-3941.2019.0437
  16. Cancer Cell Int. 2020 ;20 269
    Wang F, Zhang Z, Li Q, Yu T, Ma C.
      Background: Cancer stem cell (CSC) is identified in osteosarcoma (OS) and considered resistant to chemotherapeutic agents. However, the mechanism of osteosarcoma stem cell (OSC) resistant to chemotherapy remains debatable and vague, and the metabolomics feature of OSC is not clarified.Materials and methods: OSC was isolated by using sphere forming assay and identified. Untargeted LC-MS/MS analysis was performed to reveal the metabolomics feature of OSC and underlying mechanisms of OSC resistant to methotrexate (MTX).
    Results: OSC was efficiently isolated and identified from human OS 143B and MG63 cell lines with enhanced chemo-resistance to MTX. The untargeted LC-MS analysis revealed that OSC showed differential metabolites and perturbed signaling pathways, mainly involved in metabolisms of fatty acid, amino acid, carbohydrate metabolism and nucleic acid. After treated with MTX, metabolomics feature of OSC was mainly involved metabolisms of amino acid, fatty acid, energy and nucleic acid. Moreover, compared with their parental OS cells response to MTX, the differential metabolites and perturbed signaling pathways were mainly involved in metabolism of amino acid, fatty acid and nucleic acid. What's more, Rap1 signaling pathway and Ras signaling pathway were involved in OS cells and their SCs response to MTX.
    Conclusion: Sphere-forming assay was able to efficiently isolate OSC from human OS cell lines and the untargeted LC-MS/MS analysis was suggested a sufficient methodology to investigate metabolomics features of OS cells and OSCs. Moreover, the metabolomics features of OSCs response to MTX might reveal a further understanding of chemotherapeutic resistance in OS.
    Keywords:  Cancer stem cell (CSC); Chemo-resistance; Metabolomics; Methotrexate (MTX); Osteosarcoma (OS)
    DOI:  https://doi.org/10.1186/s12935-020-01356-y
  17. Metabolites. 2020 Jun 23. pii: E260. [Epub ahead of print]10(6):
    McEachran AD, Chao A, Al-Ghoul H, Lowe C, Grulke C, Sobus JR, Williams AJ.
      Software applications for high resolution mass spectrometry (HRMS)-based non-targeted analysis (NTA) continue to enhance chemical identification capabilities. Given the variety of available applications, determining the most fit-for-purpose tools and workflows can be difficult. The Critical Assessment of Small Molecule Identification (CASMI) contests were initiated in 2012 to provide a means to evaluate compound identification tools on a standardized set of blinded tandem mass spectrometry (MS/MS) data. Five CASMI contests have resulted in recommendations, publications, and invaluable datasets for practitioners of HRMS-based screening studies. The US Environmental Protection Agency's (EPA) CompTox Chemicals Dashboard is now recognized as a valuable resource for compound identification in NTA studies. However, this application was too new and immature in functionality to participate in the five previous CASMI contests. In this work, we performed compound identification on all five CASMI contest datasets using Dashboard tools and data in order to critically evaluate Dashboard performance relative to that of other applications. CASMI data was accessed via the CASMI webpage and processed for use in our spectral matching and identification workflow. Relative to applications used by former contest participants, our tools, data, and workflow performed well, placing more challenge compounds in the top five of ranked candidates than did the winners of three contest years and tying in a fourth. In addition, we conducted an in-depth review of the CASMI structure sets and made these reviewed sets available via the Dashboard. Our results suggest that Dashboard data and tools would enhance chemical identification capabilities for practitioners of HRMS-based NTA.
    Keywords:  compound database; high-resolution mass spectrometry; mass spectral fragmentation prediction; non-targeted analysis; spectral library
    DOI:  https://doi.org/10.3390/metabo10060260
  18. Nat Protoc. 2020 Jun 24.
    Zheng F, Zhao X, Zeng Z, Wang L, Lv W, Wang Q, Xu G.
      Untargeted methods are typically used in the detection and discovery of small organic compounds in metabolomics research, and ultra-high-performance liquid chromatography-high-resolution mass spectrometry (UHPLC-HRMS) is one of the most commonly used platforms for untargeted metabolomics. Although they are non-biased and have high coverage, untargeted approaches suffer from unsatisfying repeatability and a requirement for complex data processing. Targeted metabolomics based on triple-quadrupole mass spectrometry (TQMS) could be a complementary tool because of its high sensitivity, high specificity and excellent quantification ability. However, it is usually applicable to known compounds: compounds whose identities are known and/or are expected to be present in the analyzed samples. Pseudotargeted metabolomics merges the advantages of untargeted and targeted metabolomics and can act as an alternative to the untargeted method. Here, we describe a detailed protocol of pseudotargeted metabolomics using UHPLC-TQMS. An in-depth, untargeted metabolomics experiment involving multiple UHPLC-HRMS runs with MS at different collision energies (both positive and negative) is performed using a mixture obtained using small amounts of the analyzed samples. XCMS, CAMERA and Multiple Reaction Monitoring (MRM)-Ion Pair Finder are used to find and annotate peaks and choose transitions that will be used to analyze the real samples. A set of internal standards is used to correct for variations in retention time. High coverage and high-performance quantitative analysis can be realized. The entire protocol takes ~5 d to complete and enables the simultaneously semiquantitative analysis of 800-1,300 metabolites.
    DOI:  https://doi.org/10.1038/s41596-020-0341-5