bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2019‒10‒13
seventeen papers selected by
Giovanny Rodriguez Blanco
The Beatson Institute for Cancer Research


  1. Nat Metab. 2019 Sep;1(9): 861-867
    Diehl FF, Lewis CA, Fiske BP, Vander Heiden MG.
      The de novo serine synthesis pathway is upregulated in many cancers. However, even cancer cells with increased serine synthesis take up large amounts of serine from the environment1 and we confirm that exogenous serine is needed for maximal proliferation of these cells. Here we show that even when enzymes in the serine synthesis pathway are genetically upregulated, the demand for oxidized NAD+ constrains serine synthesis, rendering serine-deprived cells sensitive to conditions that decrease the cellular NAD+/NADH ratio. Further, purine depletion is a major consequence of reduced intracellular serine availability, particularly when NAD+ regeneration is impaired. Thus, cells rely on exogenous serine consumption to maintain purine biosynthesis. In support of this explanation, providing exogenous purine nucleobases, or increasing NAD+ availability to facilitate de novo serine and purine synthesis, both rescue maximal proliferation even in the absence of extracellular serine. Together, these data indicate that NAD+ is an endogenous limitation for cancer cells to synthesize the serine needed for purine production to support rapid proliferation.
    DOI:  https://doi.org/10.1038/s42255-019-0108-x
  2. Precis Clin Med. 2019 Sep;2(3): 183-191
    Chen M, Huang J.
      Cancer cells undergo metabolic reprogramming to support cell proliferation, growth, and dissemination. Alterations in lipid metabolism, and specifically the uptake and synthesis of fatty acids (FAs), comprise one well-documented aspect of this reprogramming. Recent studies have revealed an expanded range of roles played by FA in promoting the aggressiveness of cancer while simultaneously identifying new potential targets for cancer therapy. This article provides a brief review of these advances in our understanding of FA metabolism in cancer, highlighting both recent discoveries and the inherent challenges caused by the metabolic plasticity of cancer cells in targeting lipid metabolism for cancer therapy.
    Keywords:  cancer; fatty acid metabolism; lipid metabolism; metabolic plasticity
    DOI:  https://doi.org/10.1093/pcmedi/pbz017
  3. Cells. 2019 Oct 09. pii: E1225. [Epub ahead of print]8(10):
    Rodríguez-Enríquez S, Marín-Hernández Á, Gallardo-Pérez JC, Pacheco-Velázquez SC, Belmont-Díaz JA, Robledo-Cadena DX, Vargas-Navarro JL, Corona de la Peña NA, Saavedra E, Moreno-Sánchez R.
      Cancer development, growth, and metastasis are highly regulated by several transcription regulators (TRs), namely transcription factors, oncogenes, tumor-suppressor genes, and protein kinases. Although TR roles in these events have been well characterized, their functions in regulating other important cancer cell processes, such as metabolism, have not been systematically examined. In this review, we describe, analyze, and strive to reconstruct the regulatory networks of several TRs acting in the energy metabolism pathways, glycolysis (and its main branching reactions), and oxidative phosphorylation of nonmetastatic and metastatic cancer cells. Moreover, we propose which possible gene targets might allow these TRs to facilitate the modulation of each energy metabolism pathway, depending on the tumor microenvironment.
    Keywords:  cancer transcriptional regulators; energy metabolism regulation; glycolysis; oncogenes; oxidative phosphorylation; transcriptional factors
    DOI:  https://doi.org/10.3390/cells8101225
  4. Mol Cell. 2019 Sep 24. pii: S1097-2765(19)30693-8. [Epub ahead of print]
    Riscal R, Skuli N, Simon MC.
      Deregulated cell proliferation is an established feature of cancer, and altered tumor metabolism has witnessed renewed interest over the past decade, including the study of how cancer cells rewire metabolic pathways to renew energy sources and "building blocks" that sustain cell division. Microenvironmental oxygen, glucose, and glutamine are regarded as principal nutrients fueling tumor growth. However, hostile tumor microenvironments render O2/nutrient supplies chronically insufficient for increased proliferation rates, forcing cancer cells to develop strategies for opportunistic modes of nutrient acquisition. Recent work shows that cancer cells overcome this nutrient scarcity by scavenging other substrates, such as proteins and lipids, or utilizing adaptive metabolic pathways. As such, reprogramming lipid metabolism plays important roles in providing energy, macromolecules for membrane synthesis, and lipid-mediated signaling during cancer progression. In this review, we highlight more recently appreciated roles for lipids, particularly cholesterol and its derivatives, in cancer cell metabolism within intrinsically harsh tumor microenvironments.
    Keywords:  bile acids; cancer; cholesterol; lipids; metabolism; oxysterols
    DOI:  https://doi.org/10.1016/j.molcel.2019.09.008
  5. Metabolites. 2019 Oct 09. pii: E219. [Epub ahead of print]9(10):
    Wandy J, Davies V, J J van der Hooft J, Weidt S, Daly R, Rogers S.
      Liquid chromatography (LC) coupled to tandem mass spectrometry (MS/MS) is widely used in identifying small molecules in untargeted metabolomics. Various strategies exist to acquire MS/MS fragmentation spectra; however, the development of new acquisition strategies is hampered by the lack of simulators that let researchers prototype, compare, and optimize strategies before validations on real machines. We introduce Virtual Metabolomics Mass Spectrometer (ViMMS), a metabolomics LC-MS/MS simulator framework that allows for scan-level control of the MS2 acquisition process in silico. ViMMS can generate new LC-MS/MS data based on empirical data or virtually re-run a previous LC-MS/MS analysis using pre-existing data to allow the testing of different fragmentation strategies. To demonstrate its utility, we show how ViMMS can be used to optimize N for Top-N data-dependent acquisition (DDA) acquisition, giving results comparable to modifying N on the mass spectrometer. We expect that ViMMS will save method development time by allowing for offline evaluation of novel fragmentation strategies and optimization of the fragmentation strategy for a particular experiment.
    Keywords:  data-dependent acquisition (DDA); fragmentation (MS/MS); in silico; liquid chromatography–mass spectrometry (LC/MS); simulator
    DOI:  https://doi.org/10.3390/metabo9100219
  6. Metabolites. 2019 Oct 04. pii: E216. [Epub ahead of print]9(10):
    Sousa J, Westhoff P, Methling K, Lalk M.
      Pyruvate is a key intermediate of diverse metabolic pathways of central carbon metabolism. In addition to being the end product of glycolysis, pyruvate is an essential carbon distribution point to oxidative metabolism, amino acid and fatty acid syntheses, and overflow metabolite production. Hence, a tight regulation of pyruvate kinase (Pyk) activity is of great importance. This study aimed to analyze targeted metabolites from several pathways and possible changes in Bacillus subtilis lacking Pyk. Wild type and Δpyk cells were cultivated in chemically defined medium with glucose and pyruvate as carbon sources, and the extracted metabolites were analyzed by 1H-NMR, GC-MS, HPLC-MS, and LC-MS/MS. The results showed that the perturbation created in the pyruvate node drove an adaptation to new conditions by altering the nutritional compounds' consumption. In Δpyk, pyruvate, which is subject to glucose-dependent carbon catabolite repression, did not comply with the hierarchy in carbon source utilization. Other metabolic alterations were observed such as the higher secretion of the overflow metabolites acetoin and 2,3-butanediol by Δpyk. Our results help to elucidate the regulatory transport of glucose and pyruvate in B. subtilis and possible metabolic reroute to alternative pathways in the absence of Pyk.
    Keywords:  Bacillus subtilis; carbon catabolite repression; metabolomics; overflow metabolites; pyruvate; pyruvate kinase
    DOI:  https://doi.org/10.3390/metabo9100216
  7. Methods Mol Biol. 2019 ;2049 233-245
    Chaleckis R, Ohashi K, Meister I, Naz S, Wheelock CE.
      Liquid chromatography-mass spectrometry (LC-MS) based nontargeted metabolomics has been applied to a wide range of biological samples and can provide information on thousands of compounds. However, reliable identification of the compounds remains a challenge affecting result interpretation. In this protocol, we describe comparable yeast cell and whole blood metabolome sample preparation for extracting similar compound groups, and we present a LC-MS method using the all ion fragmentation (AIF) approach for the purposes of increasing accuracy in metabolite annotation. Our method enables database-dependent targeted as well as nontargeted metabolomics analysis from the same data acquisition, while simultaneously improving the accuracy in metabolite identification to increase the quality of the resulting biological information.
    Keywords:  All ion fragmentation (AIF); Liquid chromatography–mass spectrometry (LC-MS); Metabolite annotation; Metabolomics
    DOI:  https://doi.org/10.1007/978-1-4939-9736-7_14
  8. Molecules. 2019 Oct 08. pii: E3615. [Epub ahead of print]24(19):
    Rampler E, Egger D, Schoeny H, Rusz M, Pacheco MP, Marino G, Kasper C, Naegele T, Koellensperger G.
      The molecular study of fat cell development in the human body is essential for our understanding of obesity and related diseases. Mesenchymal stem/stromal cells (MSC) are the ideal source to study fat formation as they are the progenitors of adipocytes. In this work, we used human MSCs, received from surgery waste, and differentiated them into fat adipocytes. The combination of several layers of information coming from lipidomics, metabolomics and proteomics enabled network analysis of the biochemical pathways in adipogenesis. Simultaneous analysis of metabolites, lipids, and proteins in cell culture is challenging due to the compound's chemical difference, so most studies involve separate analysis with unimolecular strategies. In this study, we employed a multimolecular approach using a two-phase extraction to monitor the crosstalk between lipid metabolism and protein-based signaling in a single sample (~105 cells). We developed an innovative analytical workflow including standardization with in-house produced 13C isotopically labeled compounds, hyphenated high-end mass spectrometry (high-resolution Orbitrap MS), and chromatography (HILIC, RP) for simultaneous untargeted screening and targeted quantification. Metabolite and lipid concentrations ranged over three to four orders of magnitude and were detected down to the low fmol (absolute on column) level. Biological validation and data interpretation of the multiomics workflow was performed based on proteomics network reconstruction, metabolic modelling (MetaboAnalyst 4.0), and pathway analysis (OmicsNet). Comparing MSCs and adipocytes, we observed significant regulation of different metabolites and lipids such as triglycerides, gangliosides, and carnitine with 113 fully reprogrammed pathways. The observed changes are in accordance with literature findings dealing with adipogenic differentiation of MSC. These results are a proof of principle for the power of multimolecular extraction combined with orthogonal LC-MS assays and network construction. Considering the analytical and biological validation performed in this study, we conclude that the proposed multiomics workflow is ideally suited for comprehensive follow-up studies on adipogenesis and is fit for purpose for different applications with a high potential to understand the complex pathophysiology of diseases.
    Keywords:  LC-MS; fat differentiation; lipidomics; mathematical modelling; mesenchymal stem cells; metabolomics; multiomics; network analysis; proteomics; stromal cells
    DOI:  https://doi.org/10.3390/molecules24193615
  9. J Proteome Res. 2019 Oct 07.
    Bichmann L, Nelde A, Ghosh M, Heumos L, Mohr C, Peltzer A, Kuchenbecker L, Sachsenberg T, Walz JS, Stevanović S, Rammensee HG, Kohlbacher O.
      Personalized multi-peptide vaccines are currently discussed intensively for tumor immunotherapy. In order to identify epitopes - short, immunogenic peptides - suitable for eliciting a tumor-specific immune response, human leukocyte antigen (HLA)-presented peptides are isolated by immunoaffinity purification from cancer tissue samples and analyzed by liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS). Here, we present MHCquant, a fully automated, portable computational pipeline able to process LC-MS/MS data automatically and generate annotated, FDR-controlled lists of (neo-)epitopes with associated relative quantification information. We could show that MHCquant achieves higher sensitivity than established methods. While obtaining the highest number of unique peptides, the rate of predicted MHC binders remains still comparable to other tools. Re-processing of the data from a previously published study resulted in the identification of several neoepitopes not detected by previously applied methods. MHCquant integrates tailor-made pipeline components with existing open-source software into a coherent processing workflow. Container-based virtualization permits execution of this workflow without complex software installation, execution on cluster/cloud infrastructures, and full reproducibility of the results. Integration with the data analysis workbench KNIME enables easy mining of large-scale immunopeptidomics data sets. MHCquant is available as open-source software along with accompanying documentation on our website at https://www.openms.de/mhcquant/.
    DOI:  https://doi.org/10.1021/acs.jproteome.9b00313
  10. Angew Chem Int Ed Engl. 2019 Oct 07.
    Wei Z, Xie Z, Kuvelkar R, Shah V, Bateman K, McLaren DG, Cooks RG.
      A multiplexed system based on inductive nanoelectrospray mass spectrometry (nESI-MS) has been developed for high-throughput screening (HTS) bioassays. This system combines inductive nESI and field amplification micro-electrophoresis to achieve a "dip-and-go" sample loading and purification strategy that enables nESI-MS based HTS assays in 96-well microtiter plates. The combination of inductive nESI and micro-electrophoresis makes it possible to perform efficient in situ separations and clean-up of biological samples. The sensitivity of the system is such that quantitative analysis of peptides from 1-10,000 nM can be performed in a biological matrix. A prototype of the automation system has been developed to handle 12 samples (one row of a microtiter plate) at a time. The sample loading and electrophoretic clean-up of biosamples can be done in parallel within 20 s followed by MS analysis at a rate of 1.3 to 3.5 s/sample. The system was used successfully for the quantitative analysis of BACE1-catalyzed peptide hydrolysis, a prototypical HTS assay of relevance to drug discovery. IC 50 values for this system were in agreement with LC-MS but recorded in times more than an order of magnitude shorter.
    Keywords:  enzyme inhibition; field amplification; inductive nanoelectrospray; micro electrophoresis; pharmacokinetics
    DOI:  https://doi.org/10.1002/anie.201909047
  11. Br J Cancer. 2019 Oct 07.
    Lima AR, Pinto J, Azevedo AI, Barros-Silva D, Jerónimo C, Henrique R, de Lourdes Bastos M, Guedes de Pinho P, Carvalho M.
      BACKGROUND: The lack of sensitive and specific biomarkers for the early detection of prostate cancer (PCa) is a major hurdle to improve patient management.METHODS: A metabolomics approach based on GC-MS was used to investigate the performance of volatile organic compounds (VOCs) in general and, more specifically, volatile carbonyl compounds (VCCs) present in urine as potential markers for PCa detection.
    RESULTS: Results showed that PCa patients (n = 40) can be differentiated from cancer-free subjects (n = 42) based on their urinary volatile profile in both VOCs and VCCs models, unveiling significant differences in the levels of several metabolites. The models constructed were further validated using an external validation set (n = 18 PCa and n = 18 controls) to evaluate sensitivity, specificity and accuracy of the urinary volatile profile to discriminate PCa from controls. The VOCs model disclosed 78% sensitivity, 94% specificity and 86% accuracy, whereas the VCCs model achieved the same sensitivity, a specificity of 100% and an accuracy of 89%. Our findings unveil a panel of 6 volatile compounds significantly altered in PCa patients' urine samples that was able to identify PCa, with a sensitivity of 89%, specificity of 83%, and accuracy of 86%.
    CONCLUSIONS: It is disclosed a biomarker panel with potential to be used as a non-invasive diagnostic tool for PCa.
    DOI:  https://doi.org/10.1038/s41416-019-0585-4
  12. Cancers (Basel). 2019 Oct 06. pii: E1497. [Epub ahead of print]11(10):
    Kim DJ, Cho EJ, Yu KS, Jang IJ, Yoon JH, Park T, Cho JY.
      The established biomarker for hepatocellular carcinoma (HCC), serum α-fetoprotein (AFP), has suboptimal performance in early disease stages. This study aimed to develop a metabolite panel to differentiate early-stage HCC from cirrhosis. Cross-sectional metabolomic analyses of serum samples were performed for 53 and 47 patients with early HCC and cirrhosis, respectively, and 50 matched healthy controls. Results were validated in 82 and 80 patients with early HCC and cirrhosis, respectively. To retain a broad spectrum of metabolites, technically distinct analyses (global metabolomic profiling using gas chromatography time-of-flight mass spectrometry and targeted analyses using liquid chromatography with tandem mass spectrometry) were employed. Multivariate analyses classified distinct metabolites; logistic regression was employed to construct a prediction model for HCC diagnosis. Five metabolites (methionine, proline, ornithine, pimelylcarnitine, and octanoylcarnitine) were selected in a panel. The panel distinguished HCC from cirrhosis and normal controls, with an area under the receiver operating curve (AUC) of 0.82; this was significantly better than that of AFP (AUC: 0.75). During validation, the panel demonstrated significantly better predictability (AUC: 0.94) than did AFP (AUC: 0.78). Defects in ammonia recycling, the urea cycle, and amino acid metabolism, demonstrated on enrichment pathway analysis, may reliably distinguish HCC from cirrhosis. Compared with AFP alone, the metabolite panel substantially improved early-stage HCC detection.
    Keywords:  biomarker; cirrhosis; hepatocellular carcinoma; metabolomics
    DOI:  https://doi.org/10.3390/cancers11101497
  13. Trends Analyt Chem. 2018 Oct;107 21-30
    Zhang Y, Wu X, Andy Tao W.
      Extracellular vesicles (EVs) are a diverse population of complex membrane-encapsulated vesicles released by a variety of cell types and exist in most of body fluids. Continuously growing number of reports revealed that EVs participate in multiple biological processes, such as intercellular communication, immune regulation, and dissemination of cancer cells. Accordingly, recent attention has been given to the characterization of extracellular vesicles and their components. This review focuses on state-of-the-art proteomic technologies to analyze proteomes of EVs, especially their post-translational modifications (PTMs). With their strong biological relevance and the relatively noninvasive accessibility from body fluids, the promising potential and early applications of EV proteome and its PTMs as attracting biomarker sources are also evaluated.
    Keywords:  Extracellular vesicles; Mass Spectrometry; Post-translational modifications; Proteomics
    DOI:  https://doi.org/10.1016/j.trac.2018.07.014
  14. Annu Rev Cell Dev Biol. 2019 Oct 06. 35 85-109
    Balla T, Kim YJ, Alvarez-Prats A, Pemberton J.
      Phospholipids are synthesized primarily within the endoplasmic reticulum and are subsequently distributed to various subcellular membranes to maintain the unique lipid composition of specific organelles. As a result, in most cases, the steady-state localization of membrane phospholipids does not match their site of synthesis. This raises the question of how diverse lipid species reach their final membrane destinations and what molecular processes provide the energy to maintain the lipid gradients that exist between various membrane compartments. Recent studies have highlighted the role of inositol phospholipids in the nonvesicular transport of lipids at membrane contact sites. This review attempts to summarize our current understanding of these complex lipid dynamics and highlights their implications for defining future research directions.
    Keywords:  endoplasmic reticulum; lipid metabolism; lipid transfer protein; membrane contact sites; nonvesicular lipid transport
    DOI:  https://doi.org/10.1146/annurev-cellbio-100818-125251
  15. Histopathology. 2019 Oct 09.
    Masisi BK, El Ansari R, Alfarsi L, Rakha EA, Green AR, Craze ML.
      Increased glutamine metabolism (glutaminolysis) is a hallmark of cancer and is recognised as a key metabolic change in cancer cells. As a heterogeneous disease with different morphological and molecular subtypes and response to therapy, breast cancer cells are known to rewire glutamine metabolism to support survival and proliferation. Glutaminase isoenzymes (GLS and GLS2) are key enzymes for glutamine metabolism. Interestingly, GLS and GLS2 display contrasting functions in tumourigenesis. In this review, we explore the role of glutaminase in cancer, primarily focussing on breast cancer, address the role played by oncogenes and tumour suppressor genes in regulating glutaminase, and discuss current therapeutic approaches in targeting glutaminase.
    Keywords:  breast cancer; cancer; glutaminase; glutamine; metabolism; subtypes
    DOI:  https://doi.org/10.1111/his.14014
  16. Talanta. 2020 Jan 15. pii: S0039-9140(19)30889-6. [Epub ahead of print]207 120256
    Zhu B, Li L, Wei H, Zhou W, Zhou W, Li F, Lin P, Sheng J, Wang Q, Yan C, Cheng Y.
      Endogenous metabolites of amino acids and their derivatives in biosamples are frequently highlighted as the most differential metabolites in recent metabolomics studies. The method for the detection of amino acid derivatives such as N-acetyl amino acids and oligopeptides is rarely reported. We developed a rapid, high-throughput, sensitive and reliable quantitative method to simultaneously profile 40 underivatized amino acids and their derivatives including N-acetyl amino acids and oligopeptides in cell lines, based on ultra-high-performance liquid chromatography-electrospray tandem mass spectrometry (UHPLC- MS/MS) by using a hydrophilic interaction liquid chromatography (HILIC) column. The optimized method was successfully validated with satisfactory linearity, sensitivity, accuracy, precision, matrix effects, recovery and stability for all analytes. Only one compound (cysteine-glutathione disulfide) showed relatively low recoveries at three concentration levels (60.8-74.3%). The limit of quantification (LOQ) for most compounds was in the range of 0.6-10 ng/mL (6-100 pg on column). This method was successfully applied to the analysis of amino acids and their derivatives in breast cancer cell samples. Principal component analysis (PCA) and the orthogonal projections to latent structures (OPLS) showed a clear discrimination of the non-tumorigenic breast epithelial cell line MCF-10A from the breast cancer cell line HCC 1806. Characteristic metabolic changes in amino acid metabolism were observed in the breast cancer cell line. This quantified analytical method of 40 endogenous amino acids and their derivatives in cell lines meets the requirement of quantification in specific expanded metabolomics studies with good sensitivity.
    Keywords:  Amino acid; Amino acid derivatives; Cancer cell; HILIC; Target metabolomics; UHPLC-MS/MS
    DOI:  https://doi.org/10.1016/j.talanta.2019.120256
  17. Adv Mater. 2019 Oct 08. e1904197
    Liang C, Zhang X, Yang M, Dong X.
      Ferroptosis is a newly discovered form of regulated cell death that is the nexus between metabolism, redox biology, and human health. Emerging evidence shows the potential of triggering ferroptosis for cancer therapy, particularly for eradicating aggressive malignancies that are resistant to traditional therapies. Recently, there has been a great deal of effort to design and develop anticancer drugs based on ferroptosis induction. Recent advances of ferroptosis-inducing agents at the intersection of chemistry, materials science, and cancer biology are presented. The basis of ferroptosis is summarized first to highlight the feasibility and characteristics of triggering ferroptosis for cancer therapy. A literature review of ferroptosis inducers (including small molecules and nanomaterials) is then presented to delineate their design, action mechanisms, and anticancer applications. Finally, some considerations for research on ferroptosis inducers are spotlighted, followed by a discussion on the challenges and future development directions of this burgeoning field.
    Keywords:  cancer therapy; ferroptosis inducers; iron metabolism; nanomedicine; tumor microenvironment
    DOI:  https://doi.org/10.1002/adma.201904197