bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2019‒08‒11
fourteen papers selected by
Giovanny Rodriguez Blanco
The Beatson Institute for Cancer Research


  1. Int J Mol Sci. 2019 Aug 08. pii: E3873. [Epub ahead of print]20(16):
    Licha D, Vidali S, Aminzadeh-Gohari S, Alka O, Breitkreuz L, Kohlbacher O, Reischl RJ, Feichtinger RG, Kofler B, Huber CG.
      The application of ketogenic diet (KD) (high fat/low carbohydrate/adequate protein) as an auxiliary cancer therapy is a field of growing attention. KD provides sufficient energy supply for healthy cells, while possibly impairing energy production in highly glycolytic tumor cells. Moreover, KD regulates insulin and tumor related growth factors (like insulin growth factor-1, IGF-1). In order to provide molecular evidence for the proposed additional inhibition of tumor growth when combining chemotherapy with KD, we applied untargeted quantitative metabolome analysis on a spontaneous breast cancer xenograft mouse model, using MDA-MB-468 cells. Healthy mice and mice bearing breast cancer xenografts and receiving cyclophosphamide chemotherapy were compared after treatment with control diet and KD. Metabolomic profiling was performed on plasma samples, applying high-performance liquid chromatography coupled to tandem mass spectrometry. Statistical analysis revealed metabolic fingerprints comprising numerous significantly regulated features in the group of mice bearing breast cancer. This fingerprint disappeared after treatment with KD, resulting in recovery to the metabolic status observed in healthy mice receiving control diet. Moreover, amino acid metabolism as well as fatty acid transport were found to be affected by both the tumor and the applied KD. Our results provide clear evidence of a significant molecular effect of adjuvant KD in the context of tumor growth inhibition and suggest additional mechanisms of tumor suppression beyond the proposed constrain in energy supply of tumor cells.
    Keywords:  HPLC-MS; breast cancer; hydrophilic liquid interaction chromatography; ketogenic diet; reversed phase chromatography; untargeted metabolomics; xenograft
    DOI:  https://doi.org/10.3390/ijms20163873
  2. EMBO Rep. 2019 Aug 05. e48115
    Zhang Y, Li C, Hu C, Wu Q, Cai Y, Xing S, Lu H, Wang L, Huang , Sun L, Li T, He X, Zhong X, Wang J, Gao P, Smith ZJ, Jia W, Zhang H.
      Lin28 plays an important role in promoting tumor development, whereas its exact functions and underlying mechanisms are largely unknown. Here, we show that both human homologs of Lin28 accelerate de novo fatty acid synthesis and promote the conversion from saturated to unsaturated fatty acids via the regulation of SREBP-1. By directly binding to the mRNAs of both SREBP-1 and SCAP, Lin28A/B enhance the translation and maturation of SREBP-1, and protect cancer cells from lipotoxicity. Lin28A/B-stimulated tumor growth is abrogated by SREBP-1 inhibition and by the impairment of the RNA binding properties of Lin28A/B, respectively. Collectively, our findings uncover that post-transcriptional regulation by Lin28A/B enhances de novo fatty acid synthesis and metabolic conversion of saturated and unsaturated fatty acids via SREBP-1, which is critical for cancer progression.
    Keywords:  Lin28; SREBP cleavage-activating protein; SREBP-1; de novo fatty acid synthesis; lipotoxicity; saturated and unsaturated fatty acids
    DOI:  https://doi.org/10.15252/embr.201948115
  3. Amino Acids. 2019 Aug 06.
    Gessner A, Mieth M, Auge D, Chafai A, Müller F, Fromm MF, Maas R.
      Cardiovascular disease (CVD) and chronic kidney disease (CKD) constitute substantial burdens for public health. The identification and validation of risk markers for CVD and CKD in epidemiological studies requires frequent adaption of existing analytical methods as well as development of new methods. In this study, an analytical procedure to simultaneously quantify ten endogenous biomarkers for CVD and CKD is described. An easy-to-handle sample preparation requiring only 20 µL of human plasma is followed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). The method was successfully validated according to established guidelines meeting required criteria for accuracy, precision, recovery, linearity, selectivity, and limits of quantification. The scalability of the method for application in larger cohorts was assessed using a set of plasma samples from healthy volunteers (n = 391) providing first reference values for the recently established biomarker Nɛ-acetyllysine (Nɛ-AcLys). Other biomarkers analyzed were creatinine, β-aminoisobutyric acid (β-AIB), carnitine, 1-methylnicotinamide (1-MNA), citrulline, symmetric dimethylarginine (SDMA), asymmetric dimethylarginine (ADMA), homoarginine (hArg), and ornithine. All obtained results are within reference values specified elsewhere. Overall, these results demonstrate the suitability of the method for simultaneous quantification of ten endogenous biomarkers for CVD and CKD in plasma samples from larger cohorts and allow validation of Nɛ-AcLys as a biomarker in large cohorts.
    Keywords:  Cardiovascular disease; Chronic kidney disease; Human plasma; LC–MS/MS; N ɛ-acetyllysine
    DOI:  https://doi.org/10.1007/s00726-019-02765-8
  4. J Chromatogr A. 2019 Jul 31. pii: S0021-9673(19)30797-6. [Epub ahead of print] 460413
    Willacey CCW, Naaktgeboren M, Lucumi Moreno E, Wegrzyn AB, van der Es D, Karu N, Fleming RMT, Harms AC, Hankemeier T.
      Recent advances in metabolomics have enabled larger proportions of the human metabolome to be analyzed quantitatively. However, this usually requires the use of several chromatographic methods coupled to mass spectrometry to cover the wide range of polarity, acidity/basicity and concentration of metabolites. Chemical derivatization allows in principle a wide coverage in a single method, as it affects both the separation and the detection of metabolites: it increases retention, stabilizes the analytes and improves the sensitivity of the analytes. The majority of quantitative derivatization techniques for LC-MS in metabolomics react with amines, phenols and thiols; however, there are unfortunately very few methods that can target carboxylic acids at the same time, which contribute to a large proportion of the human metabolome. Here, we describe a derivatization technique which simultaneously labels carboxylic acids, thiols and amines using the reagent dimethylaminophenacyl bromide (DmPABr). We further improve the quantitation by employing isotope-coded derivatization (ICD), which uses internal standards derivatized with an isotopically-labelled reagent (DmPABr-D6). We demonstrate the ability to measure and quantify 64 central carbon and energy-related metabolites including amino acids, N-acetylated amino acids, metabolites from the TCA cycle and pyruvate metabolism, acylcarnitines and medium-/long-chain fatty acids. To demonstrate the applicability of the analytical approach, we analyzed urine and SUIT-2 cells utilizing a 15-minute single UPLC-MS/MS method in positive ionization mode. SUIT-2 cells exposed to rotenone showed definitive changes in 28 out of the 64 metabolites, including metabolites from all 7 classes mentioned. By realizing the full potential of DmPABr to derivatize and quantify amines and thiols in addition to carboxylic acids, we extended the coverage of the metabolome, producing a strong platform that can be further applied to a variety of biological studies.
    Keywords:  Derivatization; Dimethylaminophenacyl bromide; LC–MS; N-Acetylated amino acids; TCA cycle; Urine
    DOI:  https://doi.org/10.1016/j.chroma.2019.460413
  5. Nutrients. 2019 Aug 03. pii: E1795. [Epub ahead of print]11(8):
    Franko A, Hartwig S, Kotzka J, Ruoß M, Nüssler AK, Königsrainer A, Häring HU, Lehr S, Peter A.
      The liver plays a pivotal role in whole-body carbohydrate, lipid, and protein metabolism. One of the key regulators of glucose and lipid metabolism are hepatokines, which are found among the liver secreted proteins, defined as liver secretome. To elucidate the composition of the human liver secretome and identify hepatokines in primary human hepatocytes (PHH), we conducted comprehensive protein profiling on conditioned medium (CM) of PHH. Secretome profiling using liquid chromatography-electrospray ionization tandem mass spectrometry (LC-MS/MS) identified 691 potential hepatokines in PHH. Subsequently, pathway analysis assigned these proteins to acute phase response, coagulation, and complement system pathways. The secretome of PHH was compared to the secreted proteins of the liver hepatoma cell line HepG2. Although the secretome of PHH and HepG2 cells show a high overlap, the HepG2 secretome rather mirrors the fetal liver with some cancer characteristics. Collectively, our study represents one of the most comprehensive secretome profiling approaches for PHH, allowing new insights into the composition of the secretome derived from primary human material, and points out strength and weakness of using HepG2 cell secretome as a model for the analysis of the human liver secretome.
    Keywords:  HepG2 cells; hepatokines; mass spectrometry; primary human hepatocytes; proteomics
    DOI:  https://doi.org/10.3390/nu11081795
  6. Sci Transl Med. 2019 Aug 07. pii: eaau4972. [Epub ahead of print]11(504):
    Wang X, Yang K, Wu Q, Kim LJY, Morton AR, Gimple RC, Prager BC, Shi Y, Zhou W, Bhargava S, Zhu Z, Jiang L, Tao W, Qiu Z, Zhao L, Zhang G, Li X, Agnihotri S, Mischel PS, Mack SC, Bao S, Rich JN.
      Glioblastoma stem cells (GSCs) reprogram glucose metabolism by hijacking high-affinity glucose uptake to survive in a nutritionally dynamic microenvironment. Here, we trace metabolic aberrations in GSCs to link core genetic mutations in glioblastoma to dependency on de novo pyrimidine synthesis. Targeting the pyrimidine synthetic rate-limiting step enzyme carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, dihydroorotase (CAD) or the critical downstream enzyme dihydroorotate dehydrogenase (DHODH) inhibited GSC survival, self-renewal, and in vivo tumor initiation through the depletion of the pyrimidine nucleotide supply in rodent models. Mutations in EGFR or PTEN generated distinct CAD phosphorylation patterns to activate carbon influx through pyrimidine synthesis. Simultaneous abrogation of tumor-specific driver mutations and DHODH activity with clinically approved inhibitors demonstrated sustained inhibition of metabolic activity of pyrimidine synthesis and GSC tumorigenic capacity in vitro. Higher expression of pyrimidine synthesis genes portends poor prognosis of patients with glioblastoma. Collectively, our results demonstrate a therapeutic approach of precision medicine through targeting the nexus between driver mutations and metabolic reprogramming in cancer stem cells.
    DOI:  https://doi.org/10.1126/scitranslmed.aau4972
  7. Biochim Biophys Acta Mol Cell Biol Lipids. 2019 Jul 31. pii: S1388-1981(19)30135-0. [Epub ahead of print]
    Kuwata H, Nakatani E, Shimbara-Matsubayashi S, Ishikawa F, Shibanuma M, Sasaki Y, Yoda E, Nakatani Y, Hara S.
      Long-chain acyl-coenzyme A synthetases (ACSLs) are a family of enzymes that convert free long-chain fatty acids into their acyl-coenzyme A (CoA) forms. ACSL4, belonging to the ACSL family, shows a preferential use of arachidonic acid (AA) as its substrate and plays a role in the remodeling of AA-containing phospholipids by incorporating free AA. However, little is known about the roles of ACSL4 in inflammatory responses. Here, we assessed the roles of ACSL4 on the effector functions of bone marrow-derived macrophages (BMDMs) obtained from mice lacking ACSL4. Liquid chromatography-tandem mass spectrometry analysis revealed that various highly unsaturated fatty acid (HUFA)-derived fatty acyl-CoA species were markedly decreased in the BMDMs obtained from ACSL4-deficient mice compared with those in the BMDMs obtained from wild-type mice. BMDMs from ACSL4-deficient mice also showed a reduced incorporation of HUFA into phosphatidylcholines. The stimulation of BMDMs with lipopolysaccharide (LPS) elicited the release of prostaglandins (PGs), such as PGE2, PGD2 and PGF2α, and the production of these mediators was significantly enhanced by ACSL4 deficiency. In contrast, neither the LPS-induced release of cytokines, such as IL-6 and IL-10, nor the endocytosis of zymosan or dextran was affected by ACSL4 deficiency. These results suggest that ACSL4 has a crucial role in the maintenance of HUFA composition of certain phospholipid species and in the incorporation of free AA into the phospholipids in LPS-stimulated macrophages. ACSL4 dysfunction may facilitate inflammatory responses by an enhanced eicosanoid storm.
    Keywords:  Acyl-CoA; Eicosanoid; Glycerophospholipid; Long-chain acyl-CoA synthetase 4; Phagocytosis; Polyunsaturated fatty acid
    DOI:  https://doi.org/10.1016/j.bbalip.2019.07.013
  8. Proteomics. 2019 Aug 08. e1800285
    Pergande MR, Serna-Perez F, Mohsin SB, Hanek J, Cologna SM.
      Niemann-Pick Disease, type C1 (NPC1) is a fatal, autosomal recessive, neurodegenerative disorder caused by mutations in the NPC1 gene. As a result of the genetic defect, there is accumulation of unesterified cholesterol and sphingolipids in the late endosomal/lysosomal system causing both visceral and neurological defects. These manifest clinically as hepatosplenomegaly, liver dysfunction, and neurodegeneration. While significant progress has been made to better understand NPC1, the downstream effects of cholesterol storage and the major mechanisms that drive these pathologies remains less understood. In this study, we sought to investigate free fatty acid levels in Npc1-/- mice with focus on the polyunsaturated ω-3 and ω-6 fatty acids. Since fatty acids are the main constituents of numerous lipids species, we also performed a discovery based lipidomic study of liver tissue in Npc1-/- mice. To this end, we report alterations in fatty acid synthesis, including the ω-3 and 6 fatty acids. Further, we report alterations in enzymes that regulate the synthesis of ω-3 and 6 fatty acid synthesis. Analysis of the liver lipidome revealed alterations in both storage and membrane lipids including cardiolipins, fatty acids, phosphatidylcholamines, phosphatidylglycerols, phosphatidylethanolamines, sphingomyelins, and triacylglycerols in Npc1-/- mice at a late stage of disease progression. This article is protected by copyright. All rights reserved.
    Keywords:  GC-MS; LC-MS; Niemann-Pick; fatty acids; lipidomics; mass spectrometry; type C
    DOI:  https://doi.org/10.1002/pmic.201800285
  9. Anal Chem. 2019 Aug 05.
    Lita A, Kuzmin AN, Pliss A, Baev A, Rzhevskii A, Gilbert M, Larion M, Prasad PN.
      Detailed studies of lipids in biological systems including their role in cellular structure, metabolism and disease development, comprise an increasingly prominent discipline called lipidomics. However, the conventional lipidomics tools, such as mass spectrometry, cannot investigate lipidomes until they are extracted, and thus cannot be used neither for probing the lipids distribution, nor for studying in live cells. Furthermore, conventional techniques rely on the lipid extraction from relatively large samples, which averages the data across the cellular populations and masks essential cell-to-cell variations. Further advancement of the discipline of lipidomics critically depends on the capability of high-resolution lipid profiling in live cells and, potentially, in single organelles. Here we report micro-Raman assay designed for single organelle lipidomics. We demonstrate how Raman microscopy can be used to measure the local intracellular biochemical composition and lipidome hallmarks - lipids concentration and unsaturation level, cis/trans isomers ratio, as well sphingolipids and cholesterol levels in live cells, with a submicron resolution, which is sufficient for profiling of subcellular structures. These lipidome data were generated by a newly developed Biomolecular Component Analysis software, which provides a shared platform for data analysis among different research groups. We outline a robust, reliable and user-friendly protocol for quantitative analysis of lipid profiles in subcellular structures. This method expands the capabilities of Raman-based lipidomics towards the analysis of single organelles within either live or fixed cells, thus allowing an unprecedented measure of organellar lipid heterogeneity, and opening new quantitative ways to study the phenotypic variability in normal and diseased cells.
    DOI:  https://doi.org/10.1021/acs.analchem.9b02663
  10. Biologicals. 2019 Aug 07. pii: S1045-1056(19)30078-8. [Epub ahead of print]
    Sun Z, Ji Q, Evans AR, Lewis MJ, Mo J, Hu P.
      Monitoring cell culture metabolites, including media components and cellular byproducts, during bio manufacturing is critical for gaining insights into cell growth, productivity and product quality. Historically, cell culture metabolite analysis was a complicated process requiring several orthogonal methods to cover the large number of metabolites with diverse properties over wide concentration ranges. These off-line analyses are time consuming and not suitable for real time bioreactor monitoring. In this study, we present a high-throughput LC-MS method with a 17-min cycle time that is capable of simultaneously monitoring 93 cell culture metabolites, including amino acids, nucleic acids, vitamins, sugars and others. This method has high precision and accuracy and has been successfully applied to the daily profiling of bioreactors and raw material qualification. Information obtained in these studies has been used to identify limiting amino acids during production, which guided adjustments to the feed strategy that prevented the potential misincorporation of amino acids. This type of metabolite profiling can be further utilized to build predictive process models for adaptive feedback control and pave the road for continuous manufacturing and real-time release testing.
    Keywords:  Cell culture; LC-MS; Mass spectrometry; Metabolite analysis; Multiple reaction monitoring (MRM); Sequence variant
    DOI:  https://doi.org/10.1016/j.biologicals.2019.07.003
  11. Mass Spectrom Rev. 2019 Aug 07.
    Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL.
      Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
    Keywords:  FF; FFPE; LC-MS; proteome; protocols; sample preparation; tissue
    DOI:  https://doi.org/10.1002/mas.21598
  12. J Natl Cancer Inst. 2019 Aug 10. pii: djz155. [Epub ahead of print]
    Lin Y, Liao K, Miao Y, Qian Z, Fang Z, Yang X, Nie Q, Jiang G, Liu J, Yu Y, Wan J, Zhang X, Hu Y, Jiang J, Qiu Y.
      BACKGROUND: Isocitrate dehydrogenase (IDH)-wild-type (WT) glioblastoma (GBM) accounts for 90% of all GBMs, while only 27% of IDH-WT-GBMs have p53 mutations. However, the tumor surveillance function of WT-p53 in GBM is subverted by mechanisms that are not fully understood.METHODS: We investigated the proteolytic inactivation of WT-p53 by asparaginyl endopeptidase (AEP) and its effects on GBM progression in cancer cells, murine models, and patients' specimens using biochemical and functional assays. The sera of healthy donors (n = 48) and GBM patients (n = 20) were examined by enzyme-linked immunosorbent assay. Furthermore, effects of AEP inhibitors on GBM progression were evaluated in murine models (n = 6-8 per group). The statistical significance between groups was determined using two-tailed Student t tests.
    RESULTS: We demonstrate that AEP binds to and directly cleaves WT-p53, resulting in the inhibition of WT-p53-mediated tumor suppressor function in both tumor cells and stromal cells via extracellular vesicle communication. High expression of uncleavable p53-N311A-mutant rescue AEP-induced tumorigenesis, proliferation, and anti-apoptotic abilities. Knockdown or pharmacological inhibition of AEP reduced tumorigenesis and prolonged survival in murine models. However, overexpression of AEP promoted tumorigenesis and shortened the survival time. Moreover, high AEP levels in GBM tissues were associated with a poor prognosis of GBM patients (n = 83; HR = 3.94 (95%CI=1.87-8.28), p<.001). A correlation was found between high plasma AEP levels and a larger tumor size in GBM patients (r = 0.6, p=.03), which decreased dramatically after surgery.
    CONCLUSION: Our results indicate that AEP promotes GBM progression via inactivation of WT-p53 and may serve as a prognostic and therapeutic target for GBM.
    DOI:  https://doi.org/10.1093/jnci/djz155
  13. Cell Death Dis. 2019 Aug 08. 10(8): 596
    Zgheib R, Battaglia-Hsu SF, Hergalant S, Quéré M, Alberto JM, Chéry C, Rouyer P, Gauchotte G, Guéant JL, Namour F.
      Methionine dependency of tumor growth, although not well-understood, is detectable by 11C-methionine positron emission tomography and may contribute to the aggressivity of glioblastomas (GBM) and meningiomas. Cytosolic folate cycle is required for methionine synthesis. Its dysregulation may influence cell reprogramming towards pluripotency. We evaluated methionine-dependent growth of monolayer (ML) cells and stem cell-like tumor spheres (TS) derived from 4 GBM (U251, U87, LN299, T98G) and 1 meningioma (IOMM-LEE) cell lines. Our data showed that for all cell lines studied, exogenous methionine is required for TS formation but not for ML cells proliferation. Furthermore, for GBM cell lines, regardless of the addition of folate cycle substrates (folic acid and formate), the level of 3 folate isoforms, 5-methytetrahydrofolate, 5,10-methenyltetrahydrofolate, and 10-formyltetrahydrofolate, were all downregulated in TS relative to ML cells. Unlike GBM cell lines, in IOMM-LEE cells, 5-methyltetrahydrofolate was actually more elevated in TS than ML, and only 5,10-methenyltetrahydrofolate and 10-formyltetrahydrofolate were downregulated. The functional significance of this variation in folate cycle repression was revealed by the finding that Folic Acid and 5-methyltetrahydrofolate promote the growth of U251 TS but not IOMM-LEE TS. Transcriptome-wide sequencing of U251 cells revealed that DHFR, SHMT1, and MTHFD1 were downregulated in TS vs ML, in concordance with the low activity cytosolic folate cycle observed in U251 TS. In conclusion, we found that a repressed cytosolic folate cycle underlies the methionine dependency of GBM and meningioma cell lines and that 5-methyltetrahydrofolate is a key metabolic switch for glioblastoma TS formation. The finding that folic acid facilitates TS formation, although requiring further validation in diseased human tissues, incites to investigate whether excessive folate intake could promote cancer stem cells formation in GBM patients.
    DOI:  https://doi.org/10.1038/s41419-019-1836-2