bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2021‒02‒28
fourteen papers selected by
Giovanny Rodriguez Blanco
University of Edinburgh
  1. Targeted Profiling of Short-, Medium-, and Long-Chain Fatty Acyl-Coenzyme As in Biological Samples by Phosphate Methylation Coupled to Liquid Chromatography-Tandem Mass Spectrometry.
  2. Nanoparticle assisted cation adduction and fragmentation of small metabolites.
  3. Multi-Omic Single-Shot Technology for Integrated Proteome and Lipidome Analysis.
  4. A unique subset of glycolytic tumour-propagating cells drives squamous cell carcinoma.
  5. Recent technical progress in sample preparation and liquid-phase separation-mass spectrometry for proteomic analysis of mass-limited samples.
  6. Novel Strategy for Mining and Identification of Acylcarnitines Using Data-Independent-Acquisition-Based Retention Time Prediction Modeling and Pseudo-Characteristic Fragmentation Ion Matching.
  7. PhosR enables processing and functional analysis of phosphoproteomic data.
  8. PDK4 dictates metabolic resistance to ferroptosis by suppressing pyruvate oxidation and fatty acid synthesis.
  9. BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers.
  10. Lipid and glucose metabolism in white adipocytes: pathways, dysfunction and therapeutics.
  11. An overview of open tubular liquid chromatography with a focus on the coupling with mass spectrometry for the analysis of small molecules.
  12. Optimised data-independent acquisition strategy recaptures the classification of early-stage hepatocellular carcinoma based on data-dependent acquisition.
  13. Fragmentation study of tryptophan-derived metabolites induced by electrospray ionization mass spectrometry for highly sensitive analysis.
  14. Spatial Proteomics: A Gateway to Understanding Cell Biology.
  1. Anal Chem. 2021 Feb 23.
    Targeted Profiling of Short-, Medium-, and Long-Chain Fatty Acyl-Coenzyme As in Biological Samples by Phosphate Methylation Coupled to Liquid Chromatography-Tandem Mass Spectrometry.
    Peng Li, Meinrad Gawaz, Madhumita Chatterjee, Michael Lämmerhofer.
      Fatty acyl-coenzyme As (acyl-CoAs) are of central importance in lipid metabolism pathways. Short-chain acyl-CoAs are usually part of metabolomics, and medium- to (very) long-chain acyl-CoAs are focus of lipidomics studies. However, owing to the specific complex and amphiphilic nature contributed by fatty acyl chains and hydrophilic CoA moiety, lipidomic analysis of acyl-CoAs is still challenging, especially in terms of sample preparation and chromatographic coverage. In this work, we propose a derivatization strategy of acyl-CoAs based on phosphate methylation. After derivatization, full coverage (from free CoA to C25:0-CoA) and good peak shape in liquid chromatography were achieved. At the same time, analyte loss due to the high affinity of phosphate groups to glass and metallic surfaces was resolved, which is beneficial for routine analysis in large-scale lipidomics studies. A sample preparation method based on mixed-mode SPE was developed to optimize extraction recoveries and allow optimal integration of the derivatization process in the analytical workflow. LC-MS/MS was performed with targeted data acquisition by SRM transitions, which were constructed based on similar fragmentation rules observed for all methylated acyl-CoAs. To achieve accurate quantification, uniformly 13C-labeled metabolite extract from yeast cells was taken as internal standards. Odd-chain and stable isotope-labeled acyl-CoAs were used as surrogate calibrants in the same matrix. LOQs were between 16.9 nM (short-chain acyl-CoAs) and 4.2 nM (very-long-chain acyl-CoAs). This method was validated in cultured cells and was applied in HeLa cells and human platelets of coronary artery disease patients. It revealed distinct acyl-CoA profiles in HeLa cells and platelets. The results showed that this method can effectively detect acyl-CoAs in biological samples. Considering their central importance in many de novo lipid biosynthesis and remodeling processes, this targeted method offers a valid foundation for future lipidomics analysis of acyl-CoA profiles in biological samples, particularly those concerning metabolic syndrome.
    DOI:  https://doi.org/10.1021/acs.analchem.1c00664
  2. Angew Chem Int Ed Engl. 2021 Feb 24.
    Nanoparticle assisted cation adduction and fragmentation of small metabolites.
    Kun Qian, Shiyu Sun, Wanshan Liu, Jing Yang, Hang Wang.
      Mass spectrometry (MS) promises small metabolite profiling as tool of the future and calls for comprehensive understanding of key procedures to enhance its capability. Herein, we studied cation adduction and fragmentation of small metabolites combining theoretical and experimental approaches, via nanoparticle assisted laser desorption/ionization (LDI)-MS and MS/MS. We calculated the energies of adduction conformers and atomic bond orders, to establish the rules of cation-metabolite affinity and multiple cation adductions in charge transfer. Further, we demonstrated the reaction paths of adducted ions and mapped the potential energy surfaces, to characterize the loss of given groups during fragmentation. Finally, we successfully controlled metabolite fragmentation by selected and multiple adductions, to enhance the atomic/fragment coverage as defined for metabolite identification toward profiling. Considering the success of MS in analysis of large biomolecules as honored by Nobel Prize in 2002, our work may have an impact and guide to advanced analysis of small metabolites.
    Keywords:  Mass spectrometry; Nanoparticles; cation adduction; fragmentation; metabolites
    DOI:  https://doi.org/10.1002/anie.202100734
  3. Anal Chem. 2021 Feb 22.
    Multi-Omic Single-Shot Technology for Integrated Proteome and Lipidome Analysis.
    Yuchen He, Edrees H Rashan, Vanessa Linke, Evgenia Shishkova, Alexander S Hebert, Adam Jochem, Michael S Westphall, David J Pagliarini, Katherine A Overmyer, Joshua J Coon.
      Mass spectrometry (MS) serves as the centerpiece technology for proteome, lipidome, and metabolome analysis. To gain a better understanding of the multifaceted networks of myriad regulatory layers in complex organisms, integration of different multiomic layers is increasingly performed, including joint extraction methods of diverse biomolecular classes and comprehensive data analyses of different omics. Despite the versatility of MS systems, fractured methodology drives nearly all MS laboratories to specialize in analysis of a single ome at the exclusion of the others. Although liquid chromatography-mass spectrometry (LC-MS) analysis is similar for different biomolecular classes, the integration on the instrument level is lagging behind. The recent advancements in high flow proteomics enable us to take a first step towards integration of protein and lipid analysis. Here, we describe a technology to achieve broad and deep coverage of multiple molecular classes simultaneously through multi-omic single-shot technology (MOST), requiring only one column, one LC-MS instrument, and a simplified workflow. MOST achieved great robustness and reproducibility. Its application to a Saccharomyces cerevisiae study consisting of 20 conditions revealed 2842 protein groups and 325 lipids and potential molecular relationships.
    DOI:  https://doi.org/10.1021/acs.analchem.0c04764
  4. Nat Metab. 2021 Feb;3(2): 182-195
    A unique subset of glycolytic tumour-propagating cells drives squamous cell carcinoma.
    Jee-Eun Choi, Carlos Sebastian, Christina M Ferrer, Caroline A Lewis, Moshe Sade-Feldman, Thomas LaSalle, Anna Gonye, Begona G C Lopez, Walid M Abdelmoula, Michael S Regan, Murat Cetinbas, Gloria Pascual, Gregory R Wojtkiewicz, Giorgia G Silveira, Ruben Boon, Kenneth N Ross, Itay Tirosh, Srinivas V Saladi, Leif W Ellisen, Ruslan I Sadreyev, Salvador Aznar Benitah, Nathalie Y R Agar, Nir Hacohen, Raul Mostoslavsky.
      Head and neck squamous cell carcinoma (SCC) remains among the most aggressive human cancers. Tumour progression and aggressiveness in SCC are largely driven by tumour-propagating cells (TPCs). Aerobic glycolysis, also known as the Warburg effect, is a characteristic of many cancers; however, whether this adaptation is functionally important in SCC, and at which stage, remains poorly understood. Here, we show that the NAD+-dependent histone deacetylase sirtuin 6 is a robust tumour suppressor in SCC, acting as a modulator of glycolysis in these tumours. Remarkably, rather than a late adaptation, we find enhanced glycolysis specifically in TPCs. More importantly, using single-cell RNA sequencing of TPCs, we identify a subset of TPCs with higher glycolysis and enhanced pentose phosphate pathway and glutathione metabolism, characteristics that are strongly associated with a better antioxidant response. Together, our studies uncover enhanced glycolysis as a main driver in SCC, and, more importantly, identify a subset of TPCs as the cell of origin for the Warburg effect, defining metabolism as a key feature of intra-tumour heterogeneity.
    DOI:  https://doi.org/10.1038/s42255-021-00350-6
  5. Anal Methods. 2021 Feb 25.
    Recent technical progress in sample preparation and liquid-phase separation-mass spectrometry for proteomic analysis of mass-limited samples.
    Zhichang Yang, Liangliang Sun.
      Mass spectrometry (MS)-based proteomics has enabled the identification and quantification of thousands of proteins from complex proteomes in a single experiment. However, its performance for mass-limited proteome samples (e.g., single cells and tissue samples from laser capture microdissection) is still not satisfying. The development of novel proteomic methodologies with better overall sensitivity is vital. During the last several years, substantial technical progress has been achieved for the preparation and liquid-phase separation-MS characterization of mass-limited proteome samples. In this review, we summarize recent technological progress of sample preparation, liquid chromatography (LC)-MS, capillary zone electrophoresis (CZE)-MS and MS instrumentation for bottom-up proteomics of trace biological samples, highlight some exciting applications of the novel techniques for single-cell proteomics, and provide a very brief perspective about the field at the end.
    DOI:  https://doi.org/10.1039/d1ay00171j
  6. J Proteome Res. 2021 Feb 24.
    Novel Strategy for Mining and Identification of Acylcarnitines Using Data-Independent-Acquisition-Based Retention Time Prediction Modeling and Pseudo-Characteristic Fragmentation Ion Matching.
    Chao Feng, Liming Xue, Dasheng Lu, Yu'e Jin, Xinlei Qiu, Frank J Gonzalez, Guoquan Wang, Zhijun Zhou.
      It is a challenging work to screen, identify, and quantify acylcarnitines in complex biological samples. A method, based on the retention time (RT) prediction and data-independent acquisition strategies, was proposed for the large-scale identification of acylcarnitines using liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS). Relative cumulative eluotropic strength was introduced as a novel descriptor in building a linear prediction model, which not only solves the problem that acylcarnitines with long carbon chains cannot be well predicted in traditional models but also proves its robustness and transferability across instruments in two data sets that were acquired in distinct chromatography conditions. The accessibility of both predictive RT and MS2 spectra of suspect features effectively reduced about 30% false-positive results, and consequently, 150 and 186 acylcarnitines were identified in the rat liver and human plasma (NIST SRM 1950), respectively. This method provides a new approach in large-scale analysis of acylcarnitine in lipidomic studies and can also be extended to the analysis of other lipids.
    Keywords:  acylcarnitines; data independence acquisition; eluotropic strength; metabolomics; retention time prediction
    DOI:  https://doi.org/10.1021/acs.jproteome.0c00810
  7. Cell Rep. 2021 Feb 23. pii: S2211-1247(21)00084-X. [Epub ahead of print]34(8): 108771
    PhosR enables processing and functional analysis of phosphoproteomic data.
    Hani Jieun Kim, Taiyun Kim, Nolan J Hoffman, Di Xiao, David E James, Sean J Humphrey, Pengyi Yang.
      Mass spectrometry (MS)-based phosphoproteomics has revolutionized our ability to profile phosphorylation-based signaling in cells and tissues on a global scale. To infer the action of kinases and signaling pathways in phosphoproteomic experiments, we present PhosR, a set of tools and methodologies implemented in a suite of R packages facilitating comprehensive analysis of phosphoproteomic data. By applying PhosR to both published and new phosphoproteomic datasets, we demonstrate capabilities in data imputation and normalization by using a set of "stably phosphorylated sites" and in functional analysis for inferring active kinases and signaling pathways. In particular, we introduce a "signalome" construction method for identifying a collection of signaling modules to summarize and visualize the interaction of kinases and their collective actions on signal transduction. Together, our data and findings demonstrate the utility of PhosR in processing and generating biological knowledge from MS-based phosphoproteomic data.
    Keywords:  batch correction; imputation; kinase-substrate prediction; mass spectrometry; normalisation; phosphoproteomics; signalling networks; signalomes; stably phosphorylated sites
    DOI:  https://doi.org/10.1016/j.celrep.2021.108771
  8. Cell Rep. 2021 Feb 23. pii: S2211-1247(21)00080-2. [Epub ahead of print]34(8): 108767
    PDK4 dictates metabolic resistance to ferroptosis by suppressing pyruvate oxidation and fatty acid synthesis.
    Xinxin Song, Jiao Liu, Feimei Kuang, Xin Chen, Herbert J Zeh, Rui Kang, Guido Kroemer, Yangchun Xie, Daolin Tang.
      Although induction of ferroptosis, an iron-dependent form of non-apoptotic cell death, has emerged as an anticancer strategy, the metabolic basis of ferroptotic death remains poorly elucidated. Here, we show that glucose determines the sensitivity of human pancreatic ductal carcinoma cells to ferroptosis induced by pharmacologically inhibiting system xc-. Mechanistically, SLC2A1-mediated glucose uptake promotes glycolysis and, thus, facilitates pyruvate oxidation, fuels the tricyclic acid cycle, and stimulates fatty acid synthesis, which finally facilitates lipid peroxidation-dependent ferroptotic death. Screening of a small interfering RNA (siRNA) library targeting metabolic enzymes leads to identification of pyruvate dehydrogenase kinase 4 (PDK4) as the top gene responsible for ferroptosis resistance. PDK4 inhibits ferroptosis by blocking pyruvate dehydrogenase-dependent pyruvate oxidation. Inhibiting PDK4 enhances the anticancer activity of system xc- inhibitors in vitro and in suitable preclinical mouse models (e.g., a high-fat diet diabetes model). These findings reveal metabolic reprogramming as a potential target for overcoming ferroptosis resistance.
    Keywords:  PDK4; cancer; fatty acid; ferroptosis; glucose; glycolysis; metabolism; pyruvate oxidation; resistance; therapy
    DOI:  https://doi.org/10.1016/j.celrep.2021.108767
  9. J Proteome Res. 2021 Feb 24.
    BioContainers Registry: Searching Bioinformatics and Proteomics Tools, Packages, and Containers.
    Jingwen Bai, Chakradhar Bandla, Jiaxin Guo, Roberto Vera Alvarez, Mingze Bai, Juan Antonio Vizcaíno, Pablo Moreno, Björn Grüning, Olivier Sallou, Yasset Perez-Riverol.
      BioContainers is an open-source project that aims to create, store, and distribute bioinformatics software containers and packages. The BioContainers community has developed a set of guidelines to standardize software containers including the metadata, versions, licenses, and software dependencies. BioContainers supports multiple packaging and container technologies such as Conda, Docker, and Singularity. The BioContainers provide over 9000 bioinformatics tools, including more than 200 proteomics and mass spectrometry tools. Here we introduce the BioContainers Registry and Restful API to make containerized bioinformatics tools more findable, accessible, interoperable, and reusable (FAIR). The BioContainers Registry provides a fast and convenient way to find and retrieve bioinformatics tool packages and containers. By doing so, it will increase the use of bioinformatics packages and containers while promoting replicability and reproducibility in research.
    Keywords:  BioContainers; cloud; computational proteomics; high-performance computing; large-scale data analysis
    DOI:  https://doi.org/10.1021/acs.jproteome.0c00904
  10. Nat Rev Endocrinol. 2021 Feb 24.
    Lipid and glucose metabolism in white adipocytes: pathways, dysfunction and therapeutics.
    Pauline Morigny, Jeremie Boucher, Peter Arner, Dominique Langin.
      In mammals, the white adipocyte is a cell type that is specialized for storage of energy (in the form of triacylglycerols) and for energy mobilization (as fatty acids). White adipocyte metabolism confers an essential role to adipose tissue in whole-body homeostasis. Dysfunction in white adipocyte metabolism is a cardinal event in the development of insulin resistance and associated disorders. This Review focuses on our current understanding of lipid and glucose metabolic pathways in the white adipocyte. We survey recent advances in humans on the importance of adipocyte hypertrophy and on the in vivo turnover of adipocytes and stored lipids. At the molecular level, the identification of novel regulators and of the interplay between metabolic pathways explains the fine-tuning between the anabolic and catabolic fates of fatty acids and glucose in different physiological states. We also examine the metabolic alterations involved in the genesis of obesity-associated metabolic disorders, lipodystrophic states, cancers and cancer-associated cachexia. New challenges include defining the heterogeneity of white adipocytes in different anatomical locations throughout the lifespan and investigating the importance of rhythmic processes. Targeting white fat metabolism offers opportunities for improved patient stratification and a wide, yet unexploited, range of therapeutic opportunities.
    DOI:  https://doi.org/10.1038/s41574-021-00471-8
  11. J Chromatogr A. 2021 Feb 12. pii: S0021-9673(21)00113-8. [Epub ahead of print]1641 461989
    An overview of open tubular liquid chromatography with a focus on the coupling with mass spectrometry for the analysis of small molecules.
    Deyber Arley Vargas Medina, Natalia Gabrielly Pereira Dos Santos, Juliana Soares da Silva Burato, João Victor Basolli Borsatto, Fernando Mauro Lanças.
      Open tubular liquid chromatography (OT-LC) can provide superior chromatographic performance and more favorable mass spectrometry (MS) detection conditions. These features could provide enhanced sensitivity when coupled with electrospray ionization sources (ESI-) and lead to unprecedented detection capabilities if interfaced with a highly structural informative electron ionization (EI) source. In the past, the exploitation of OT columns in liquid chromatography evolved slowly. However, the recent instrumental developments in capillary/nanoLC-MS created new opportunities in developing and applying OT-LC-MS. Currently, the analytical advantages of OT-LC-MS are mainly exploited in the fields of proteomics and biosciences analysis. Nevertheless, under the right conditions, OT-LC-MS can also offer superior chromatographic performance and enhanced sensitivity in analyzing small molecules. This review will provide an overview of the latest developments in OT-LC-MS, focusing on the wide variety of employed separation mechanisms, innovative stationary phases, emerging column fabrication technologies, and new OT formats. In the same way, the OT-LC's opportunities and shortcomings coupled to both ESI and EI will be discussed, highlighting the complementary character of those two ionization modes to expand the LC's detection boundaries in the performance of targeted and untargeted studies.
    Keywords:  electron ionization; mass spectrometry; nano-electrospray ionization; nano-liquid chromatography; open tubular column; open tubular liquid chromatography
    DOI:  https://doi.org/10.1016/j.chroma.2021.461989
  12. J Proteomics. 2021 Feb 17. pii: S1874-3919(21)00051-8. [Epub ahead of print] 104152
    Optimised data-independent acquisition strategy recaptures the classification of early-stage hepatocellular carcinoma based on data-dependent acquisition.
    Shuang Weng, Mingchao Wang, Yingyi Zhao, Wantao Ying, Xiaohong Qian.
      Proteomics is increasingly used for exploring disease biomarkers and therapeutic targets. The data-independent acquisition (DIA) method collects all peptide signals in a sample, and provides a convenient way to archive disease-related molecular features for further exploration. In this study, we first established a high-coverage human hepatocellular carcinoma (HCC) spectral library containing 9393 protein groups, 119,903 peptides. Furthermore, we optimised the DIA method with respect to four key parameters: settings for mass spectrometry acquisition, gradient length, amount of sample loading, and length of analytical column. More than 6000 proteins from HepG2 cells could be stably quantified using the optimised one-shot DIA approach with a 2 h gradient time. One-shot DIA identified a similar number of proteins as did multi-fraction data-dependent acquisition (DDA) from the same group of HCC samples, but at a quarter of the total acquisition time. DIA data could recapture the classification results obtained from DDA data, thus paving the way for large-scale, multi-centre proteomics analysis of clinical samples. SIGNIFICANCE: The organ-specific spectral library for HCC and the optimised 2 h DIA approach met the urgent demands for large-scale quantitative proteomics analysis of HCC clinical samples. Compared with multi-fraction-DDA, the optimised one-shot DIA could reach a similar identification while consuming shorter acquisition time, thus making it possible to analyse thousands of clinical samples.
    Keywords:  Classification; Data dependent acquisition; Data independent acquisition; Hepatocellular carcinoma
    DOI:  https://doi.org/10.1016/j.jprot.2021.104152
  13. Analyst. 2021 Feb 23.
    Fragmentation study of tryptophan-derived metabolites induced by electrospray ionization mass spectrometry for highly sensitive analysis.
    Daiki Asakawa, Hajime Mizuno, Eiji Sugiyama, Kenichiro Todoroki.
      Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is interfaced with electrospray ionization (ESI), which generally produces intact gas-phase ions of biomolecules. However, ESI induces the fragmentation of tryptophan-derived metabolites, which are known to act as neurotransmitters and psychoactive drugs. Tryptophan-derived metabolites undergo N-Cα bond dissociation during ESI, producing a fragment ion with a spiro[cyclopropane-indolium] backbone. Fragmentation is suppressed by the presence of an α-carboxyl group and the modification of amino groups. In particular, tryptamine and serotonin, which lack such functional groups, produce more intense fragment-ion signals than protonated molecules. The multiple reaction monitoring (MRM)-based quantitative analysis of tryptamine and serotonin used the fragment ions produced from in-source collision-induced dissociation as the precursor ions, which improved the signal-to-noise ratio of the resulting spectra. The present method allows for the quantitative analysis of tryptamine and serotonin with high sensitivity.
    DOI:  https://doi.org/10.1039/d0an02069a
  14. Proteomics. 2020 Dec;20(23): e1900328
    Spatial Proteomics: A Gateway to Understanding Cell Biology.
    Georg H H Borner.
      
    DOI:  https://doi.org/10.1002/pmic.201900328
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