bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2023–12–31
eight papers selected by
Giovanny Rodriguez Blanco, University of Edinburgh
  1. Simple Routes to Stable Isotope-Coded Native Glycans.
  2. Peroxisome proliferator-activated receptors: A key link between lipid metabolism and cancer progression.
  3. Targeted Mass Spectrometry Analyses of Somatic Mutations in Colorectal Cancer Specimens Using Differential Ion Mobility.
  4. Advances in proteomics methods for the analysis of exhaled breath condensate.
  5. Phosphoprotein dynamics of interacting T cells and tumor cells by HySic.
  6. Characterization of the In Vivo Deuteration of Native Phospholipids by Mass Spectrometry Yields Guidelines for Their Regiospecific Customization.
  7. Cyclin D1 extensively reprograms metabolism to support biosynthetic pathways in hepatocytes.
  8. Detection of Protein Tyrosine Phosphatase Interacting Partners by Mass Spectrometry.
  1. Anal Chem. 2023 Dec 28.
    Simple Routes to Stable Isotope-Coded Native Glycans.
    Johannes Helm, Clemens Grünwald-Gruber, Jonathan Urteil, Martin Pabst, Friedrich Altmann.
      Understanding the biological role of protein-linked glycans requires the reliable identification of glycans. Isomer separation and characterization often entail mass spectrometric detection preceded by high-performance chromatography on porous graphitic carbon. To this end, stable isotope-labeled glycans have emerged as powerful tools for retention time normalization. Hitherto, such standards were obtained by chemoenzymatic or purely enzymatic methods, which introduce, e.g., 13C-containing N-acetyl groups or galactose into native glycans. Glycan release with anhydrous hydrazine opens another route for heavy isotope introduction via concomitant de-N-acetylation. Here, we describe that de-N-acetylation can also be achieved with hydrazine hydrate, which is a more affordable and less hazardous reagent. Despite the slower reaction rate, complete conversion is achievable in 72 h at 100 °C for glycans with biantennary glycans with or without sialic acids. Shorter incubation times allow for the isolation of intermediate products with a defined degree of free amino groups, facilitating introduction of different numbers of heavy isotopes. Mass encoded glycans obtained by this versatile approach can serve a broad range of applications, e.g., as internal standards for isomer-specific studies of N-glycans, O-glycans, and human milk oligosaccharide by LC-MS on either porous graphitic carbon or─following permethylation─on reversed phase.
    DOI:  https://doi.org/10.1021/acs.analchem.3c03446
  2. Clin Nutr. 2023 Dec 09. pii: S0261-5614(23)00427-2. [Epub ahead of print]43(2): 332-345
    Peroxisome proliferator-activated receptors: A key link between lipid metabolism and cancer progression.
    Yunkuo Li, Yujie Pan, Xiaodong Zhao, Shouwang Wu, Faping Li, Yuxiong Wang, Bin Liu, Yanghe Zhang, Xin Gao, Yishu Wang, Honglan Zhou.
      Lipids represent the essential components of membranes, serve as fuels for high-energy processes, and play crucial roles in signaling and cellular function. One of the key hallmarks of cancer is the reprogramming of metabolic pathways, especially abnormal lipid metabolism. Alterations in lipid uptake, lipid desaturation, de novo lipogenesis, lipid droplets, and fatty acid oxidation in cancer cells all contribute to cell survival in a changing microenvironment by regulating feedforward oncogenic signals, key oncogenic functions, oxidative and other stresses, immune responses, or intercellular communication. Peroxisome proliferator-activated receptors (PPARs) are transcription factors activated by fatty acids and act as core lipid sensors involved in the regulation of lipid homeostasis and cell fate. In addition to regulating whole-body energy homeostasis in physiological states, PPARs play a key role in lipid metabolism in cancer, which is receiving increasing research attention, especially the fundamental molecular mechanisms and cancer therapies targeting PPARs. In this review, we discuss how cancer cells alter metabolic patterns and regulate lipid metabolism to promote their own survival and progression through PPARs. Finally, we discuss potential therapeutic strategies for targeting PPARs in cancer based on recent studies from the last five years.
    Keywords:  Anticancer therapy; Cancer; Metabolic reprogramming; PPAR
    DOI:  https://doi.org/10.1016/j.clnu.2023.12.005
  3. J Proteome Res. 2023 Dec 28.
    Targeted Mass Spectrometry Analyses of Somatic Mutations in Colorectal Cancer Specimens Using Differential Ion Mobility.
    Zhaoguan Wu, Éric Bonneil, Michael Belford, Cornelia Boeser, Jean-Jacques Dunyach, Pierre Thibault.
      Identification of K-Ras and B-Raf mutations in colorectal cancer (CRC) is essential to predict patients' response to anti-EGFR therapy and formulate appropriate therapeutic strategies to improve prognosis and survival. Here, we combined parallel reaction monitoring (PRM) with high-field asymmetric waveform ion mobility (FAIMS) to enhance mass spectrometry sensitivity and improve the identification of low-abundance K-Ras and B-Raf mutations in biological samples without immunoaffinity enrichment. In targeted LC-MS/MS analyses, FAIMS reduced the occurrence of interfering ions and enhanced precursor ion purity, resulting in a 3-fold improvement in the detection limit for K-Ras and B-Raf mutated peptides. In addition, the ion mobility separation of isomeric peptides using FAIMS facilitated the unambiguous identification of K-Ras G12D and G13D peptides. The application of targeted LC-MS/MS analyses using FAIMS is demonstrated for the detection and quantitation of B-Raf V600E, K-Ras G12D, G13D, and G12V in CRC cell lines and primary specimens.
    Keywords:  BRAF; KRAS; colorectal cancer mutations; high-field asymmetric waveform ion mobility (FAIMS); mass spectrometry; parallel reaction monitoring (PRM)
    DOI:  https://doi.org/10.1021/acs.jproteome.3c00444
  4. Mass Spectrom Rev. 2023 Dec 27.
    Advances in proteomics methods for the analysis of exhaled breath condensate.
    Edwin J Yoo, Julie S Kim, Stephanie Stransky, Simon Spivack, Simone Sidoli.
      The analysis of exhaled breath condensate (EBC) demonstrates a promising avenue of minimally invasive biopsies for diagnostics. EBC is obtained by cooling exhaled air and collecting the condensation to be utilized for downstream analysis using various analytical methods. The aqueous phase of breath contains a large variety of miscible small compounds including polar electrolytes, amino acids, cytokines, chemokines, peptides, small proteins, metabolites, nucleic acids, and lipids/eicosanoids-however, these analytes are typically present at minuscule levels in EBC, posing a considerable technical challenge. Along with recent improvements in devices for breath collection, the sensitivity and resolution of liquid chromatography coupled to online mass spectrometry-based proteomics has attained subfemtomole sensitivity, vastly enhancing the quality of EBC sample analysis. As a result, proteomics analysis of EBC has been expanding the field of breath biomarker research. We present an au courant overview of the achievements in proteomics of EBC, the advancement of EBC collection devices, and the current and future applications for EBC biomarker analysis.
    Keywords:  clinical; exhaled breath condensate; liquid chromatography; mass spectrometry; proteomics
    DOI:  https://doi.org/10.1002/mas.21871
  5. Cell Rep. 2023 Dec 26. pii: S2211-1247(23)01610-8. [Epub ahead of print]43(1): 113598
    Phosphoprotein dynamics of interacting T cells and tumor cells by HySic.
    Sofía Ibáñez-Molero, Joannes T M Pruijs, Alisha Atmopawiro, Fujia Wang, Alexandra M Terry, Maarten Altelaar, Daniel S Peeper, Kelly E Stecker.
      Functional interactions between cytotoxic T cells and tumor cells are central to anti-cancer immunity. However, our understanding of the proteins involved is limited. Here, we present HySic (hybrid quantification of stable isotope labeling by amino acids in cell culture [SILAC]-labeled interacting cells) as a method to quantify protein and phosphorylation dynamics between and within physically interacting cells. Using co-cultured T cells and tumor cells, we directly measure the proteome and phosphoproteome of engaged cells without the need for physical separation. We identify proteins whose abundance or activation status changes upon T cell:tumor cell interaction and validate our method with established signal transduction pathways including interferon γ (IFNγ) and tumor necrosis factor (TNF). Furthermore, we identify the RHO/RAC/PAK1 signaling pathway to be activated upon cell engagement and show that pharmacologic inhibition of PAK1 sensitizes tumor cells to T cell killing. Thus, HySic is a simple method to study rapid protein signaling dynamics in physically interacting cells that is easily extended to other biological systems.
    Keywords:  CP: Cancer; CP: Immunology; T cell; cancer; cell-cell interaction; immunology; phosphoproteomics; proteomics
    DOI:  https://doi.org/10.1016/j.celrep.2023.113598
  6. Anal Chem. 2023 Dec 27.
    Characterization of the In Vivo Deuteration of Native Phospholipids by Mass Spectrometry Yields Guidelines for Their Regiospecific Customization.
    Matthew J Keller, Qiu Zhang, Shuo Qian, Brian C Sanders, Hugh M O'Neill, Robert L Hettich.
      Customization of deuterated biomolecules is vital for many advanced biological experiments including neutron scattering. However, because it is challenging to control the proportion and regiospecificity of deuterium incorporation in live systems, often only two or three synthetic lipids are mixed together to form simplistic model membranes. This limits the applicability and biological accuracy of the results generated with these synthetic membranes. Despite some limited prior examination of deuterating Escherichia coli lipids in vivo, this approach has not been widely implemented. Here, an extensive mass spectrometry-based profiling of E. coli phospholipid deuteration states with several different growth media was performed, and a computational method to describe deuterium distributions with a one-number summary is introduced. The deuteration states of 36 lipid species were quantitatively profiled in 15 different growth conditions, and tandem mass spectrometry was used to reveal deuterium localization. Regressions were employed to enable the prediction of lipid deuteration for untested conditions. Small-angle neutron scattering was performed on select deuterated lipid samples, which validated the deuteration states calculated from the mass spectral data. Based on these experiments, guidelines for the design of specifically deuterated phospholipids are described. This unlocks even greater capabilities from neutron-based techniques, enabling experiments that were formerly impossible.
    DOI:  https://doi.org/10.1021/acs.analchem.3c03750
  7. J Biol Chem. 2023 Dec;pii: S0021-9258(23)02435-3. [Epub ahead of print]299(12): 105407
    Cyclin D1 extensively reprograms metabolism to support biosynthetic pathways in hepatocytes.
    Heng Wu, Betsy T Kren, Andrew N Lane, Teresa A Cassel, Richard M Higashi, Teresa W M Fan, George S Scaria, Laurie L Shekels, Mark A Klein, Jeffrey H Albrecht.
      Cell proliferation requires metabolic reprogramming to accommodate biosynthesis of new cell components, and similar alterations occur in cancer cells. However, the mechanisms linking the cell cycle machinery to metabolism are not well defined. Cyclin D1, along with its main partner cyclin-dependent kinase 4 (Cdk4), is a pivotal cell cycle regulator and driver oncogene that is overexpressed in many cancers. Here, we examine hepatocyte proliferation to define novel effects of cyclin D1 on biosynthetic metabolism. Metabolomic studies reveal that cyclin D1 broadly promotes biosynthetic pathways including glycolysis, the pentose phosphate pathway, and the purine and pyrimidine nucleotide synthesis in hepatocytes. Proteomic analyses demonstrate that overexpressed cyclin D1 binds to numerous metabolic enzymes including those involved in glycolysis and pyrimidine synthesis. In the glycolysis pathway, cyclin D1 activates aldolase and GAPDH, and these proteins are phosphorylated by cyclin D1/Cdk4 in vitro. De novo pyrimidine synthesis is particularly dependent on cyclin D1. Cyclin D1/Cdk4 phosphorylates the initial enzyme of this pathway, carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase (CAD), and metabolomic analysis indicates that cyclin D1 depletion markedly reduces the activity of this enzyme. Pharmacologic inhibition of Cdk4 along with the downstream pyrimidine synthesis enzyme dihydroorotate dehydrogenase synergistically inhibits proliferation and survival of hepatocellular carcinoma cells. These studies demonstrate that cyclin D1 promotes a broad network of biosynthetic pathways in hepatocytes, and this model may provide insights into potential metabolic vulnerabilities in cancer cells.
    Keywords:  BAY 2402234; aldolase; anaerobic glycolysis; cell cycle; cyclin D1; glyceraldehyde-3-phosphate dehydrogenase (GAPDH); liver regeneration; palbociclib; pentose phosphate pathway (PPP); purine; pyrimidine
    DOI:  https://doi.org/10.1016/j.jbc.2023.105407
  8. Methods Mol Biol. 2024 ;2743 165-180
    Detection of Protein Tyrosine Phosphatase Interacting Partners by Mass Spectrometry.
    Martina Samiotaki, George Panayotou, Panagiotis Chandris.
      Unraveling interacting partners of protein tyrosine (Tyr) phosphatases is considered a key aspect in resolving the regulation of signaling cascades either in a pathological or in developmental context. Mass spectrometry (MS)-based protein identification has emerged as the major approach in this arena, complemented by the development of novel biochemical methodologies for sample preparation. In this chapter, we highlight two methods that, combined with mass spectrometry, may help the investigator create an interactome map for the phosphatase of interest within a specific biological context.
    Keywords:  APEX2; Interactome; Mass spectrometry; Protein–protein interactions; Proximity labeling; Tyrosine phosphatases
    DOI:  https://doi.org/10.1007/978-1-0716-3569-8_11
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