bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2022–02–13
fourteen papers selected by
Giovanny Rodríguez Blanco, University of Edinburgh
  1. Targeting fuel pocket of cancer cell metabolism: A focus on glutaminolysis.
  2. Maximizing MS/MS Acquisition for Lipidomics Using Capillary Separation and Orbitrap Tribrid Mass Spectrometer.
  3. A protocol for investigating lipidomic dysregulation and discovering lipid biomarkers from human serums.
  4. Personalized Medicine for Prostate Cancer: Is Targeting Metabolism a Reality?
  5. Expression of gamma-glutamyltransferase 1 in glioblastoma cells confers resistance to cystine deprivation-induced ferroptosis.
  6. Comparative metabolomics with Metaboseek reveals functions of a conserved fat metabolism pathway in C. elegans.
  7. Cancer-cell-derived GABA promotes β-catenin-mediated tumour growth and immunosuppression.
  8. The hallmarks of cancer metabolism: Still emerging.
  9. Infrared Photoactivation Boosts Reporter Ion Yield in Isobaric Tagging.
  10. The altered lipidome of hepatocellular carcinoma.
  11. Lactate rewires lipid metabolism and sustains a metabolic-epigenetic axis in prostate cancer.
  12. Spatially resolved isotope tracing reveals tissue metabolic activity.
  13. A Practitioner's Dilemma Mass Spectrometry-Based Annotation and Identification of Human Plasma and Urinary Polyphenol Metabolites.
  14. SMAP is a pipeline for sample matching in proteogenomics.
  1. Biochem Pharmacol. 2022 Feb 04. pii: S0006-2952(22)00037-5. [Epub ahead of print] 114943
    Targeting fuel pocket of cancer cell metabolism: A focus on glutaminolysis.
    Shagun Sharma, Navneet Agnihotri, Sandeep Kumar.
      Advances in cell metabolism over the past few decades have demonstrated glutamine as an essential nutrient for cancer cell survival and proliferation. Glutamine offers a remarkable capacity to fuel diverse metabolic pathways in cancer cells including the Krebs cycle, maintenance of redox homeostasis, and synthesis of cellular building blocks such as nucleic acids, fatty acids, glutathione, and other amino acids. The increase in glutaminolysis has further been linked to the accumulation of oncometabolites such as 2HG (2-Hydroxyglutarate), succinate, fumarate, etc., thereby contributing to tumorigenesis via regulating epigenetic modification of imprinted genes. Therefore, therapeutic targeting of glutaminolysis in cancer cells is worth exploring for possible treatment strategies for cancer management. In this review, we have discussed the detailed mechanism of glutamine uptake, transport, and its instrumental role in rewiring the metabolic adaptation of cancer cells in the tumor microenvironment under nutrient deprivation and hypoxia. Furthermore, we have attempted to provide an updated therapeutic intervention of glutamine metabolism as a treatment strategy for cancer management.
    Keywords:  Cancer Cell Metabolism; Glutamine; Glutaminolysis; Tumor Microenvironment, Chemotherapy
    DOI:  https://doi.org/10.1016/j.bcp.2022.114943
  2. Anal Chem. 2022 Feb 09.
    Maximizing MS/MS Acquisition for Lipidomics Using Capillary Separation and Orbitrap Tribrid Mass Spectrometer.
    Yuchen He, Dain R Brademan, Paul D Hutchins, Katherine A Overmyer, Joshua J Coon.
      Liquid chromatography-mass spectrometry (LC-MS) is a typical strategy for lipidomics analysis. Although capillary LC-MS is a common analytical technique for proteomics analysis, its application to lipidomics has been limited. In this study, we aim at improving lipid identifications achieved in a single LC-MS analysis by a 3-fold approach: capillary LC and nanoelectrospray for enhanced ionization, ion trap for higher sensitivity tandem MS, and parallelization of mass analyzers for increased speed of acquisition on an Orbitrap hybrid system. By applying the methods to a complex lipid mixture of human plasma, we identified and performed relative quantification on over 1500 lipids within a 60 min capillary LC-MS analysis.
    DOI:  https://doi.org/10.1021/acs.analchem.1c05552
  3. STAR Protoc. 2022 Mar 18. 3(1): 101125
    A protocol for investigating lipidomic dysregulation and discovering lipid biomarkers from human serums.
    Moran Chen, Yanhong Hao, Suming Chen.
      Lipids play important roles in various human diseases. Disease-associated lipid dysregulation and biomarkers could provide molecular clues for diagnosis, pathogenesis, and therapy. This protocol provides a step-by-step workflow to investigate lipid dysregulation and discover biomarkers in human serum samples by liquid chromatography-mass spectrometry (LC-MS)-based lipidomics and machine learning analysis. The workflow includes project design, serum collection, sample preparation, data acquisition, data processing, and machine learning analysis. For complete details on the use and execution of this profile, please refer to Hao et al. (2021).
    Keywords:  Bioinformatics; Biotechnology and bioengineering; Clinical Protocol; Health Sciences; Mass Spectrometry; Metabolism
    DOI:  https://doi.org/10.1016/j.xpro.2022.101125
  4. Front Oncol. 2021 ;11 778761
    Personalized Medicine for Prostate Cancer: Is Targeting Metabolism a Reality?
    Gio Fidelito, Matthew J Watt, Renea A Taylor.
      Prostate cancer invokes major shifts in gene transcription and metabolic signaling to mediate alterations in nutrient acquisition and metabolic substrate selection when compared to normal tissues. Exploiting such metabolic reprogramming is proposed to enable the development of targeted therapies for prostate cancer, yet there are several challenges to overcome before this becomes a reality. Herein, we outline the role of several nutrients known to contribute to prostate tumorigenesis, including fatty acids, glucose, lactate and glutamine, and discuss the major factors contributing to variability in prostate cancer metabolism, including cellular heterogeneity, genetic drivers and mutations, as well as complexity in the tumor microenvironment. The review draws from original studies employing immortalized prostate cancer cells, as well as more complex experimental models, including animals and humans, that more accurately reflect the complexity of the in vivo tumor microenvironment. In synthesizing this information, we consider the feasibility and potential limitations of implementing metabolic therapies for prostate cancer management.
    Keywords:  lipid metabolism; metabolic heterogeneity; metabolic targeting; metabolism; obesity; patient-derived xenograft; prostate neoplasia
    DOI:  https://doi.org/10.3389/fonc.2021.778761
  5. J Biol Chem. 2022 Feb 08. pii: S0021-9258(22)00143-0. [Epub ahead of print] 101703
    Expression of gamma-glutamyltransferase 1 in glioblastoma cells confers resistance to cystine deprivation-induced ferroptosis.
    Kazuki Hayashima, Hironori Katoh.
      Ferroptosis is an iron-dependent mode of cell death caused by excessive oxidative damage to lipids. Lipid peroxidation is normally suppressed by glutathione peroxidase 4, which requires reduced glutathione. Cystine is a major resource for glutathione synthesis, especially in cancer cells. Therefore, cystine deprivation or inhibition of cystine uptake promotes ferroptosis in cancer cells. However, the roles of other molecules involved in cysteine deprivation-induced ferroptosis are unexplored. We report here that the expression of gamma-glutamyltransferase 1 (GGT1), an enzyme that cleaves extracellular glutathione, determines the sensitivity of glioblastoma cells to cystine deprivation-induced ferroptosis at high cell density. In glioblastoma cells expressing GGT1, pharmacological inhibition or deletion of GGT1 suppressed the cell density-induced increase in intracellular glutathione levels and cell viability under cystine deprivation, which were restored by the addition of cysteinylglycine, the GGT product of glutathione cleavage. On the other hand, cystine deprivation induced glutathione depletion and ferroptosis in GGT1-deficient glioblastoma cells even at a high cell density. Exogenous expression of GGT1 in GGT1-deficient glioblastoma cells inhibited cystine deprivation-induced glutathione depletion and ferroptosis at a high cell density. This suggests that GGT1 plays an important role in glioblastoma cell survival under cystine-limited, high-cell density conditions. We conclude that combining GGT inhibitors with ferroptosis inducers may provide an effective therapeutic approach for treating glioblastoma.
    Keywords:  amino acid; cell death; cell metabolism; cell surface enzyme; glioblastoma; glutathione
    DOI:  https://doi.org/10.1016/j.jbc.2022.101703
  6. Nat Commun. 2022 Feb 10. 13(1): 782
    Comparative metabolomics with Metaboseek reveals functions of a conserved fat metabolism pathway in C. elegans.
    Maximilian J Helf, Bennett W Fox, Alexander B Artyukhin, Ying K Zhang, Frank C Schroeder.
      Untargeted metabolomics via high-resolution mass spectrometry can reveal more than 100,000 molecular features in a single sample, many of which may represent unidentified metabolites, posing significant challenges to data analysis. We here introduce Metaboseek, an open-source analysis platform designed for untargeted comparative metabolomics and demonstrate its utility by uncovering biosynthetic functions of a conserved fat metabolism pathway, α-oxidation, using C. elegans as a model. Metaboseek integrates modules for molecular feature detection, statistics, molecular formula prediction, and fragmentation analysis, which uncovers more than 200 previously uncharacterized α-oxidation-dependent metabolites in an untargeted comparison of wildtype and α-oxidation-defective hacl-1 mutants. The identified metabolites support the predicted enzymatic function of HACL-1 and reveal that α-oxidation participates in metabolism of endogenous β-methyl-branched fatty acids and food-derived cyclopropane lipids. Our results showcase compound discovery and feature annotation at scale via untargeted comparative metabolomics applied to a conserved primary metabolic pathway and suggest a model for the metabolism of cyclopropane lipids.
    DOI:  https://doi.org/10.1038/s41467-022-28391-9
  7. Nat Cell Biol. 2022 Feb 10.
    Cancer-cell-derived GABA promotes β-catenin-mediated tumour growth and immunosuppression.
    De Huang, Yan Wang, J Will Thompson, Tao Yin, Peter B Alexander, Diyuan Qin, Poorva Mudgal, Haiyang Wu, Yaosi Liang, Lianmei Tan, Christopher Pan, Lifeng Yuan, Ying Wan, Qi-Jing Li, Xiao-Fan Wang.
      Many cancers have an unusual dependence on glutamine. However, most previous studies have focused on the contribution of glutamine to metabolic building blocks and the energy supply. Here, we report that cancer cells with aberrant expression of glutamate decarboxylase 1 (GAD1) rewire glutamine metabolism for the synthesis of γ-aminobutyric acid (GABA)-a prominent neurotransmitter-in non-nervous tissues. An analysis of clinical samples reveals that increased GABA levels predict poor prognosis. Mechanistically, we identify a cancer-intrinsic pathway through which GABA activates the GABAB receptor to inhibit GSK-3β activity, leading to enhanced β-catenin signalling. This GABA-mediated β-catenin activation both stimulates tumour cell proliferation and suppresses CD8+ T cell intratumoural infiltration, such that targeting GAD1 or GABABR in mouse models overcomes resistance to anti-PD-1 immune checkpoint blockade therapy. Our findings uncover a signalling role for tumour-derived GABA beyond its classic function as a neurotransmitter that can be targeted pharmacologically to reverse immunosuppression.
    DOI:  https://doi.org/10.1038/s41556-021-00820-9
  8. Cell Metab. 2022 Feb 01. pii: S1550-4131(22)00022-5. [Epub ahead of print]
    The hallmarks of cancer metabolism: Still emerging.
    Natalya N Pavlova, Jiajun Zhu, Craig B Thompson.
      Metabolism of cancer cells is geared toward biomass production and proliferation. Since the metabolic resources within the local tissue are finite, this can lead to nutrient depletion and accumulation of metabolic waste. To maintain growth in these conditions, cancer cells employ a variety of metabolic adaptations, the nature of which is collectively determined by the physiology of their cell of origin, the identity of transforming lesions, and the tissue in which cancer cells reside. Furthermore, select metabolites not only serve as substrates for energy and biomass generation, but can also regulate gene and protein expression and influence the behavior of non-transformed cells in the tumor vicinity. As they grow and metastasize, tumors can also affect and be affected by the nutrient distribution within the body. In this hallmark update, recent advances are incorporated into a conceptual framework that may help guide further research efforts in exploring cancer cell metabolism.
    DOI:  https://doi.org/10.1016/j.cmet.2022.01.007
  9. Anal Chem. 2022 Feb 10.
    Infrared Photoactivation Boosts Reporter Ion Yield in Isobaric Tagging.
    Kenneth W Lee, Trenton M Peters-Clarke, Keaton L Mertz, Graeme C McAlister, John E P Syka, Michael S Westphall, Joshua J Coon.
      Isobaric tagging facilitates multiplexed experiments that can determine sequences and relative amounts of peptides in biological samples using tandem mass spectrometry (MSn). Limited reporter ion generation limits quantitative accuracy and precision. As reporter ions are susceptible to unintended fragmentation and scattering by high-energy collisions, we activated peptides with IR photons and prevented successive dissociation of generated reporter ions with ion parking, which altogether boosted reporter ion yield by up to 55%. Even so, unintended co-isolation of contaminating peaks in MS2 experiments distorts reporter ion intensities and can distort quantitative information. MS3 experiments address contamination by generating reporter ions via collisional activation (HCD) of one or more peptide product ions rather than the isolated peptide precursor ion. Because HCD performance is related to m/z, activation of multiple synchronously isolated product ions generates less than optimal reporter ion intensities. In this work, we show that using infrared multiphoton dissociation, which is not dependent on m/z, to generate reporter ions from 10 synchronously isolated peptide product ions results in a 2.4-fold increase in reporter ion intensities, significantly enhancing the sensitivity and dynamic range of quantitation via isobaric tagging.
    DOI:  https://doi.org/10.1021/acs.analchem.1c05398
  10. Semin Cancer Biol. 2022 Feb 04. pii: S1044-579X(22)00025-6. [Epub ahead of print]
    The altered lipidome of hepatocellular carcinoma.
    Shawn Lu Wen Tan, Erez Israeli, Russell E Ericksen, Pierce K H Chow, Weiping Han.
      Alterations in metabolic pathways are a hallmark of cancer. A deeper understanding of the contribution of different metabolites to carcinogenesis is thus vitally important to elucidate mechanisms of tumor initiation and progression to inform therapeutic strategies. Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide and its altered metabolic landscape is beginning to unfold with the advancement of technologies. In particular, characterization of the lipidome of human HCCs has accelerated, and together with biochemical analyses, are revealing recurrent patterns of alterations in glycerophospholipid, sphingolipid, cholesterol and bile acid metabolism. These widespread alterations encompass a myriad of lipid species with numerous roles affecting multiple hallmarks of cancer, including aberrant growth signaling, metastasis, evasion of cell death and immunosuppression. In this review, we summarize the current trends and findings of the altered lipidomic landscape of HCC and discuss their potential biological significance for hepatocarcinogenesis.
    Keywords:  Cancer; Hepatocellular carcinoma; Lipid; Lipidomics; Metabolism
    DOI:  https://doi.org/10.1016/j.semcancer.2022.02.004
  11. Cancer Res. 2022 Feb 08. pii: canres.0914.2021. [Epub ahead of print]
    Lactate rewires lipid metabolism and sustains a metabolic-epigenetic axis in prostate cancer.
    Luigi Ippolito, Giuseppina Comito, Matteo Parri, Marta Iozzo, Assia Duatti, Francesca Virgilio, Nicla Lorito, Marina Bacci, Elisa Pardella, Giada Sandrini, Francesca Bianchini, Roberta Damiano, Lavinia Ferrone, Giancarlo la Marca, Sergio Serni, Pietro Spatafora, Carlo V Catapano, Andrea Morandi, Elisa Giannoni, Paola Chiarugi.
      Lactate is an abundant oncometabolite in the tumor environment. In prostate cancer (PCa), cancer-associated fibroblasts are major contributors of secreted lactate, which can be taken up by cancer cells to sustain mitochondrial metabolism. However, how lactate impacts transcriptional regulation in tumors has yet to be fully elucidated. Here, we describe a mechanism by which CAF-secreted lactate is able to increase the expression of genes involved in lipid metabolism in PCa cells.This regulation enhanced intracellular lipid accumulation in lipid droplets (LD) and provided acetyl moieties for histone acetylation, establishing a regulatory loop between metabolites and epigenetic modification. Inhibition of this loop by targeting the bromodomain and extraterminal (BET) protein family of histone acetylation readers suppressed the expression of perilipin-2 (PLIN2), a crucial component of LDs, disrupting lactate-dependent lipid metabolic rewiring. Inhibition of this CAF-induced metabolic-epigenetic regulatory loop in vivo reduced growth and metastasis of prostate cancer cells, demonstrating its translational relevance as a therapeutic target in PCa. Clinically, PLIN2 expression was elevated in tumors with a higher Gleason grade and in castration resistant prostate cancer compared to primary PCa. Overall, these findings show that lactate has both a metabolic and an epigenetic role in promoting PCa progression.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-21-0914
  12. Nat Methods. 2022 Feb;19(2): 223-230
    Spatially resolved isotope tracing reveals tissue metabolic activity.
    Lin Wang, Xi Xing, Xianfeng Zeng, S RaElle Jackson, Tara TeSlaa, Osama Al-Dalahmah, Laith Z Samarah, Katharine Goodwin, Lifeng Yang, Melanie R McReynolds, Xiaoxuan Li, Jeremy J Wolff, Joshua D Rabinowitz, Shawn M Davidson.
      Isotope tracing has helped to determine the metabolic activities of organs. Methods to probe metabolic heterogeneity within organs are less developed. We couple stable-isotope-labeled nutrient infusion to matrix-assisted laser desorption ionization imaging mass spectrometry (iso-imaging) to quantitate metabolic activity in mammalian tissues in a spatially resolved manner. In the kidney, we visualize gluconeogenic flux and glycolytic flux in the cortex and medulla, respectively. Tricarboxylic acid cycle substrate usage differs across kidney regions; glutamine and citrate are used preferentially in the cortex and fatty acids are used in the medulla. In the brain, we observe spatial gradations in carbon inputs to the tricarboxylic acid cycle and glutamate under a ketogenic diet. In a carbohydrate-rich diet, glucose predominates throughout but in a ketogenic diet, 3-hydroxybutyrate contributes most strongly in the hippocampus and least in the midbrain. Brain nitrogen sources also vary spatially; branched-chain amino acids contribute most in the midbrain, whereas ammonia contributes in the thalamus. Thus, iso-imaging can reveal the spatial organization of metabolic activity.
    DOI:  https://doi.org/10.1038/s41592-021-01378-y
  13. Mol Nutr Food Res. 2022 Feb 10. e2100985
    A Practitioner's Dilemma Mass Spectrometry-Based Annotation and Identification of Human Plasma and Urinary Polyphenol Metabolites.
    Nikolai Kuhnert, Michael N Clifford.
      The practitioner's dilemma in metabolite assignment can be described as follows: For compound and metabolite identification, should we follow strict guidelines using authentic standards only, or should we accept uncertainties in structure assignment of compounds with the certainty of consequential errors. These uncertainties arise due to limitation of software and databases in combination with the complexity of the human body fluid samples. This article is protected by copyright. All rights reserved.
    Keywords:  Compound annotation; data science; mass spectrometry; metabolites; polyphenols
    DOI:  https://doi.org/10.1002/mnfr.202100985
  14. Nat Commun. 2022 Feb 08. 13(1): 744
    SMAP is a pipeline for sample matching in proteogenomics.
    Ling Li, Mingming Niu, Alyssa Erickson, Jie Luo, Kincaid Rowbotham, Kai Guo, He Huang, Yuxin Li, Yi Jiang, Junguk Hur, Chunyu Liu, Junmin Peng, Xusheng Wang.
      The integration of genomics and proteomics data (proteogenomics) holds the promise of furthering the in-depth understanding of human disease. However, sample mix-up is a pervasive problem in proteogenomics because of the complexity of sample processing. Here, we present a pipeline for Sample Matching in Proteogenomics (SMAP) to verify sample identity and ensure data integrity. SMAP infers sample-dependent protein-coding variants from quantitative mass spectrometry (MS), and aligns the MS-based proteomic samples with genomic samples by two discriminant scores. Theoretical analysis with simulated data indicates that SMAP is capable of uniquely matching proteomic and genomic samples when ≥20% genotypes of individual samples are available. When SMAP was applied to a large-scale dataset generated by the PsychENCODE BrainGVEX project, 54 samples (19%) were corrected. The correction was further confirmed by ribosome profiling and chromatin sequencing (ATAC-seq) data from the same set of samples. Our results demonstrate that SMAP is an effective tool for sample verification in a large-scale MS-based proteogenomics study. SMAP is publicly available at https://github.com/UND-Wanglab/SMAP , and a web-based version can be accessed at https://smap.shinyapps.io/smap/ .
    DOI:  https://doi.org/10.1038/s41467-022-28411-8
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