bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2022‒01‒16
twenty-six papers selected by
Giovanny Rodriguez Blanco
University of Edinburgh
  1. Cancer metabolism and intervention therapy.
  2. Achieving Absolute Molar Lipid Concentrations: A Phospholipidomics Cross-Validation Study.
  3. Aberrant lipid metabolism in cancer cells and tumor microenvironment: the player rather than bystander in cancer progression and metastasis.
  4. Glutamine-Derived Aspartate Biosynthesis in Cancer Cells: Role of Mitochondrial Transporters and New Therapeutic Perspectives.
  5. A Fast and Selective Approach for Profiling Vicinal Diols Using Liquid Chromatography-Post Column Derivatization-Double Precursor Ion Scanning Mass Spectrometry.
  6. Lipidomic profiling of human serum enables detection of pancreatic cancer.
  7. Restriction of extracellular lipids renders pancreatic cancer dependent on autophagy.
  8. Tip-tip filtration ameliorates single-phase extraction methods for plasma large-scale lipidomics analysis.
  9. Integrating in vitro metabolomics with a 96-well high-throughput screening platform.
  10. THEM6-mediated reprogramming of lipid metabolism supports treatment resistance in prostate cancer.
  11. The role of m6A RNA methylation in cancer metabolism.
  12. Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry.
  13. Ferroptosis: a promising target for cancer immunotherapy.
  14. Ferroptosis inducers for prostate cancer therapy.
  15. An expanding repertoire of protein acylations.
  16. Lipid Metabolism in Cancer: The Role of Acylglycerolphosphate Acyltransferases (AGPATs).
  17. Amino Acid Metabolism in Cancer Drug Resistance.
  18. The role of lipid metabolism in shaping the expansion and the function of regulatory T cells.
  19. Folate Transport and One-Carbon Metabolism in Targeted Therapies of Epithelial Ovarian Cancer.
  20. Fatty Acid Metabolism in Myeloid-Derived Suppressor Cells and Tumor-Associated Macrophages: Key Factor in Cancer Immune Evasion.
  21. PKCβII phosphorylates ACSL4 to amplify lipid peroxidation to induce ferroptosis.
  22. Oxylipin metabolism is controlled by mitochondrial β-oxidation during bacterial inflammation.
  23. Quantitative Proteomics Using Isobaric Labeling: A Practical Guide.
  24. Atlas of exercise metabolism reveals time-dependent signatures of metabolic homeostasis.
  25. Proteomic and metabolomic profiling of urine uncovers immune responses in patients with COVID-19.
  26. Untargeted Metabolomics Analysis of the Serum Metabolic Signature of Childhood Obesity.
  1. Mol Biomed. 2021 Feb 20. 2(1): 5
    Cancer metabolism and intervention therapy.
    Huakan Zhao, Yongsheng Li.
      Metabolic reprogramming with heterogeneity is a hallmark of cancer and is at the basis of malignant behaviors. It supports the proliferation and metastasis of tumor cells according to the low nutrition and hypoxic microenvironment. Tumor cells frantically grab energy sources (such as glucose, fatty acids, and glutamine) from different pathways to produce a variety of biomass to meet their material needs via enhanced synthetic pathways, including aerobic glycolysis, glutaminolysis, fatty acid synthesis (FAS), and pentose phosphate pathway (PPP). To survive from stress conditions (e.g., metastasis, irradiation, or chemotherapy), tumor cells have to reprogram their metabolism from biomass production towards the generation of abundant adenosine triphosphate (ATP) and antioxidants. In addition, cancer cells remodel the microenvironment through metabolites, promoting an immunosuppressive microenvironment. Herein, we discuss how the metabolism is reprogrammed in cancer cells and how the tumor microenvironment is educated via the metabolic products. We also highlight potential metabolic targets for cancer therapies.
    Keywords:  Cancer; Heterogeneity; Metabolic reprogramming; Targeted therapy; Tumor microenvironment
    DOI:  https://doi.org/10.1186/s43556-020-00012-1
  2. Anal Chem. 2022 Jan 13.
    Achieving Absolute Molar Lipid Concentrations: A Phospholipidomics Cross-Validation Study.
    Harald Schoeny, Evelyn Rampler, Dinh Binh Chu, Anna Schoeberl, Luis Galvez, Markus Blaukopf, Paul Kosma, Gunda Koellensperger.
      Standardization is essential in lipidomics and part of a huge community effort. However, with the still ongoing lack of reference materials, benchmarking quantification is hampered. Here, we propose traceable lipid class quantification as an important layer for the validation of quantitative lipidomics workflows. 31P nuclear magnetic resonance (NMR) and inductively coupled plasma (ICP)-mass spectrometry (MS) can use certified species-unspecific standards to validate shotgun or liquid chromatography (LC)-MS-based lipidomics approaches. We further introduce a novel lipid class quantification strategy based on lipid class separation and mass spectrometry using an all ion fragmentation (AIF) approach. Class-specific fragments, measured over a mass range typical for the lipid classes, are integrated to assess the lipid class concentration. The concept proved particularly interesting as low absolute limits of detection in the fmol range were achieved and LC-MS platforms are widely used in the field of lipidomics, while the accessibility of NMR and ICP-MS is limited. Using completely independent calibration strategies, the introduced validation scheme comprised the quantitative assessment of the complete phospholipid sub-ome, next to the individual lipid classes. Komagataella phaffii served as a prime example, showcasing mass balances and supporting the value of benchmarks for quantification at the lipid species level.
    DOI:  https://doi.org/10.1021/acs.analchem.1c03743
  3. J Cancer. 2021 ;12(24): 7498-7506
    Aberrant lipid metabolism in cancer cells and tumor microenvironment: the player rather than bystander in cancer progression and metastasis.
    Xiujing Yu, Shuyi Mi, Jun Ye, Guochun Lou.
      As the primary cause of cancer-induced fatality and morbidity, cancer metastasis has been a hard nut to crack. Existing studies indicate that lipid metabolism reprogramming occurring in cancer cells and surrounding cells in TME also endows the aggressive and spreading properties with malignant cells. In this review we describe the lipid metabolic reprogramming of cancer cells at different steps along the metastatic process, we also summarize the altered lipid metabolism of non-cancer cells in TME during tumor metastasis. Additionally, we reveal both intrinsic and extrinsic factors which influence the cellular lipid metabolism reprogramming.
    Keywords:  cancer metastasis; extrinsic factors; intrinsic factors; lipid metabolism remodeling; tumor microenvironment
    DOI:  https://doi.org/10.7150/jca.64833
  4. Cancers (Basel). 2022 Jan 04. pii: 245. [Epub ahead of print]14(1):
    Glutamine-Derived Aspartate Biosynthesis in Cancer Cells: Role of Mitochondrial Transporters and New Therapeutic Perspectives.
    Ruggiero Gorgoglione, Valeria Impedovo, Christopher L Riley, Deborah Fratantonio, Stefano Tiziani, Luigi Palmieri, Vincenza Dolce, Giuseppe Fiermonte.
      Aspartate has a central role in cancer cell metabolism. Aspartate cytosolic availability is crucial for protein and nucleotide biosynthesis as well as for redox homeostasis. Since tumor cells display poor aspartate uptake from the external environment, most of the cellular pool of aspartate derives from mitochondrial catabolism of glutamine. At least four transporters are involved in this metabolic pathway: the glutamine (SLC1A5_var), the aspartate/glutamate (AGC), the aspartate/phosphate (uncoupling protein 2, UCP2), and the glutamate (GC) carriers, the last three belonging to the mitochondrial carrier family (MCF). The loss of one of these transporters causes a paucity of cytosolic aspartate and an arrest of cell proliferation in many different cancer types. The aim of this review is to clarify why different cancers have varying dependencies on metabolite transporters to support cytosolic glutamine-derived aspartate availability. Dissecting the precise metabolic routes that glutamine undergoes in specific tumor types is of upmost importance as it promises to unveil the best metabolic target for therapeutic intervention.
    Keywords:  SLC1A5_var; UCP2; aspartate; aspartate/glutamate carrier; cancer; glutamate carrier; glutamine metabolism; mitochondrial carriers
    DOI:  https://doi.org/10.3390/cancers14010245
  5. Molecules. 2022 Jan 03. pii: 283. [Epub ahead of print]27(1):
    A Fast and Selective Approach for Profiling Vicinal Diols Using Liquid Chromatography-Post Column Derivatization-Double Precursor Ion Scanning Mass Spectrometry.
    Debin Wan, Christophe Morisseau, Bruce D Hammock, Jun Yang.
      Vicinal diols are important signaling metabolites of various inflammatory diseases, and some of them are potential biomarkers for some diseases. Utilizing the rapid reaction between diol and 6-bromo-3-pyridinylboronic acid (BPBA), a selective and sensitive approach was established to profile these vicinal diols using liquid chromatography-post column derivatization coupled with double precursor ion scan-mass spectrometry (LC-PCD-DPIS-MS). After derivatization, all BPBA-vicinal-diol esters gave a pair of characteristic isotope ions resulting from 79Br and 81Br. The unique isotope pattern generated two characteristic fragment ions of m/z 200 and 202. Compared to a traditional offline derivatization technique, the new LC-PCD-DPIS-MS method retained the capacity of LC separation. In addition, it is more sensitive and selective than a full scan MS method. As an application, an in vitro study of the metabolism of epoxy fatty acids by human soluble epoxide hydrolase was tested. These vicinal-diol metabolites of individual regioisomers from different types of polyunsaturated fatty acids were easily identified. The limit of detection (LOD) reached as low as 25 nM. The newly developed LC-PCD-DPIS-MS method shows significant advantages in improving the selectivity and therefore can be employed as a powerful tool for profiling vicinal-diol compounds from biological matrices.
    Keywords:  double precursor ion scan; epoxide hydrolase; online post-column derivatization; vicinal diols
    DOI:  https://doi.org/10.3390/molecules27010283
  6. Nat Commun. 2022 Jan 10. 13(1): 124
    Lipidomic profiling of human serum enables detection of pancreatic cancer.
    Denise Wolrab, Robert Jirásko, Eva Cífková, Marcus Höring, Ding Mei, Michaela Chocholoušková, Ondřej Peterka, Jakub Idkowiak, Tereza Hrnčiarová, Ladislav Kuchař, Robert Ahrends, Radana Brumarová, David Friedecký, Gabriel Vivo-Truyols, Pavel Škrha, Jan Škrha, Radek Kučera, Bohuslav Melichar, Gerhard Liebisch, Ralph Burkhardt, Markus R Wenk, Amaury Cazenave-Gassiot, Petr Karásek, Ivo Novotný, Kristína Greplová, Roman Hrstka, Michal Holčapek.
      Pancreatic cancer has the worst prognosis among all cancers. Cancer screening of body fluids may improve the survival time prognosis of patients, who are often diagnosed too late at an incurable stage. Several studies report the dysregulation of lipid metabolism in tumor cells, suggesting that changes in the blood lipidome may accompany tumor growth. Here we show that the comprehensive mass spectrometric determination of a wide range of serum lipids reveals statistically significant differences between pancreatic cancer patients and healthy controls, as visualized by multivariate data analysis. Three phases of biomarker discovery research (discovery, qualification, and verification) are applied for 830 samples in total, which shows the dysregulation of some very long chain sphingomyelins, ceramides, and (lyso)phosphatidylcholines. The sensitivity and specificity to diagnose pancreatic cancer are over 90%, which outperforms CA 19-9, especially at an early stage, and is comparable to established diagnostic imaging methods. Furthermore, selected lipid species indicate a potential as prognostic biomarkers.
    DOI:  https://doi.org/10.1038/s41467-021-27765-9
  7. J Exp Clin Cancer Res. 2022 Jan 08. 41(1): 16
    Restriction of extracellular lipids renders pancreatic cancer dependent on autophagy.
    Maria Saliakoura, Matteo Rossi Sebastiano, Ioanna Nikdima, Chiara Pozzato, Georgia Konstantinidou.
      BACKGROUND: KRAS is the predominant oncogene mutated in pancreatic ductal adenocarcinoma (PDAC), the fourth cause of cancer-related deaths worldwide. Mutant KRAS-driven tumors are metabolically programmed to support their growth and survival, which can be used to identify metabolic vulnerabilities. In the present study, we aimed to understand the role of extracellularly derived fatty acids in KRAS-driven pancreatic cancer.METHODS: To assess the dependence of PDAC cells on extracellular fatty acids we employed delipidated serum or RNAi-mediated suppression of ACSL3 (to inhibit the activation and cellular retention of extracellular fatty acids) followed by cell proliferation assays, qPCR, apoptosis assays, immunoblots and fluorescence microscopy experiments. To assess autophagy in vivo, we employed the KrasG12D/+;p53flox/flox;Pdx1-CreERT2 (KPC) mice crossed with Acsl3 knockout mice, and to assess the efficacy of the combination therapy of ACSL3 and autophagy inhibition we used xenografted human cancer cell-derived tumors in immunocompromised mice.
    RESULTS: Here we show that depletion of extracellularly derived lipids either by serum lipid restriction or suppression of ACSL3, triggers autophagy, a process that protects PDAC cells from the reduction of bioenergetic intermediates. Combined extracellular lipid deprivation and autophagy inhibition exhibits anti-proliferative and pro-apoptotic effects against PDAC cell lines in vitro and promotes suppression of xenografted human pancreatic cancer cell-derived tumors in mice. Therefore, we propose lipid deprivation and autophagy blockade as a potential co-targeting strategy for PDAC treatment.
    CONCLUSIONS: Our work unravels a central role of extracellular lipid supply in ensuring fatty acid provision in cancer cells, unmasking a previously unappreciated metabolic vulnerability of PDAC cells.
    Keywords:  Combination therapy; Extracellular lipids; Lipid metabolism; Pancreatic cancer; Tumor metabolic vulnerabilities
    DOI:  https://doi.org/10.1186/s13046-021-02231-y
  8. J Chromatogr B Analyt Technol Biomed Life Sci. 2022 Jan 06. pii: S1570-0232(22)00003-4. [Epub ahead of print]1189 123099
    Tip-tip filtration ameliorates single-phase extraction methods for plasma large-scale lipidomics analysis.
    Camillo Morano, Gabriella Roda, Rita Paroni, Michele Dei Cas.
      We evaluated the performance of three different single-phase extraction methods to be used before untargeted lipidomics analysis by Liquid Chromatography High-Resolution Mass Spectrometry. Lipids were extracted from a pool of healthy human donors' plasma in triplicates and run in both positive and negative ESI. The most satisfactory results were attained using methanol/chloroform (2:1, v/v) mixture. Eventually, we evaluated whether a filtration of the samples could be beneficial to yield cleaner and more mass-friendly extracts. Instead of using syringes, we set up a method we called tip-tip filtration, which requires the usage of a filtrating pipette tip. This way of purification led to superior results than the solvent extraction method alone. This additional procedure not only increased reproducibility but also allowed the same lipid coverage. In addition, it permitted to spare time and money, as tip-tip filtration is not particularly expensive nor time-consuming and hopefully it may be useful to increase analytical column lifetime.
    Keywords:  Lipid extraction; Mass spectrometry; Sample pre-treatment; Untargeted lipidomics
    DOI:  https://doi.org/10.1016/j.jchromb.2022.123099
  9. Metabolomics. 2022 Jan 09. 18(1): 11
    Integrating in vitro metabolomics with a 96-well high-throughput screening platform.
    Julia M Malinowska, Taina Palosaari, Jukka Sund, Donatella Carpi, Mounir Bouhifd, Ralf J M Weber, Maurice Whelan, Mark R Viant.
      INTRODUCTION: High-throughput screening (HTS) is emerging as an approach to support decision-making in chemical safety assessments. In parallel, in vitro metabolomics is a promising approach that can help accelerate the transition from animal models to high-throughput cell-based models in toxicity testing.OBJECTIVE: In this study we establish and evaluate a high-throughput metabolomics workflow that is compatible with a 96-well HTS platform employing 50,000 hepatocytes of HepaRG per well.
    METHODS: Low biomass cell samples were extracted for metabolomics analyses using a newly established semi-automated protocol, and the intracellular metabolites were analysed using a high-resolution spectral-stitching nanoelectrospray direct infusion mass spectrometry (nESI-DIMS) method that was modified for low sample biomass.
    RESULTS: The method was assessed with respect to sensitivity and repeatability of the entire workflow from cell culturing and sampling to measurement of the metabolic phenotype, demonstrating sufficient sensitivity (> 3000 features in hepatocyte extracts) and intra- and inter-plate repeatability for polar nESI-DIMS assays (median relative standard deviation < 30%). The assays were employed for a proof-of-principle toxicological study with a model toxicant, cadmium chloride, revealing changes in the metabolome across five sampling times in the 48-h exposure period. To allow the option for lipidomics analyses, the solvent system was extended by establishing separate extraction methods for polar metabolites and lipids.
    CONCLUSIONS: Experimental, analytical and informatics workflows reported here met pre-defined criteria in terms of sensitivity, repeatability and ability to detect metabolome changes induced by a toxicant and are ready for application in metabolomics-driven toxicity testing to complement HTS assays.
    Keywords:  Chemical risk assessment; Direct infusion mass spectrometry; HepaRG; High-throughput screening; In vitro metabolomics; Toxicology
    DOI:  https://doi.org/10.1007/s11306-021-01867-3
  10. EMBO Mol Med. 2022 Jan 11. e14764
    THEM6-mediated reprogramming of lipid metabolism supports treatment resistance in prostate cancer.
    Arnaud Blomme, Coralie Peter, Ernest Mui, Giovanny Rodriguez Blanco, Ning An, Louise M Mason, Lauren E Jamieson, Grace H McGregor, Sergio Lilla, Chara Ntala, Rachana Patel, Marc Thiry, Sonia H Y Kung, Marine Leclercq, Catriona A Ford, Linda K Rushworth, David J McGarry, Susan Mason, Peter Repiscak, Colin Nixon, Mark J Salji, Elke Markert, Gillian M MacKay, Jurre J Kamphorst, Duncan Graham, Karen Faulds, Ladan Fazli, Martin E Gleave, Edward Avezov, Joanne Edwards, Huabing Yin, David Sumpton, Karen Blyth, Pierre Close, Daniel J Murphy, Sara Zanivan, Hing Y Leung.
      Despite the clinical benefit of androgen-deprivation therapy (ADT), the majority of patients with advanced prostate cancer (PCa) ultimately develop lethal castration-resistant prostate cancer (CRPC). In this study, we identified thioesterase superfamily member 6 (THEM6) as a marker of ADT resistance in PCa. THEM6 deletion reduces in vivo tumour growth and restores castration sensitivity in orthograft models of CRPC. Mechanistically, we show that the ER membrane-associated protein THEM6 regulates intracellular levels of ether lipids and is essential to trigger the induction of the ER stress response (UPR). Consequently, THEM6 loss in CRPC cells significantly alters ER function, reducing de novo sterol biosynthesis and preventing lipid-mediated activation of ATF4. Finally, we demonstrate that high THEM6 expression is associated with poor survival and correlates with high levels of UPR activation in PCa patients. Altogether, our results highlight THEM6 as a novel driver of therapy resistance in PCa as well as a promising target for the treatment of CRPC.
    Keywords:  ATF4; ER stress; lipid metabolism; prostate cancer; therapy resistance
    DOI:  https://doi.org/10.15252/emmm.202114764
  11. Mol Cancer. 2022 Jan 12. 21(1): 14
    The role of m6A RNA methylation in cancer metabolism.
    Yuanyuan An, Hua Duan.
      Metabolic reprogramming is one of the main characteristics of malignant tumors, which is due to the flexible changes of cell metabolism that can meet the needs of cell growth and maintain the homeostasis of tissue environments. Cancer cells can obtain metabolic adaptation through a variety of endogenous and exogenous signaling pathways, which can not only promote the growth of malignant cancer cells, but also start the transformation process of cells to adapt to tumor microenvironment. Studies show that m6A RNA methylation is widely involved in the metabolic recombination of tumor cells. In eukaryotes, m6A methylation is the most abundant modification in mRNA, which is involved in almost all the RNA cycle stages, including regulation the transcription, maturation, translation, degradation and stability of mRNA. M6A RNA methylation can be involved in the regulation of physiological and pathological processes, including cancer. In this review, we discuss the role of m6A RNA methylation modification plays in tumor metabolism-related molecules and pathways, aiming to show the importance of targeting m6A in regulating tumor metabolism.
    Keywords:  Cancer; Metabolism reprogramming; The m6A
    DOI:  https://doi.org/10.1186/s12943-022-01500-4
  12. Nat Commun. 2022 Jan 10. 13(1): 37
    Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry.
    Sofani Tafesse Gebreyesus, Asad Ali Siyal, Reta Birhanu Kitata, Eric Sheng-Wen Chen, Bayarmaa Enkhbayar, Takashi Angata, Kuo-I Lin, Yu-Ju Chen, Hsiung-Lin Tu.
      Single-cell proteomics can reveal cellular phenotypic heterogeneity and cell-specific functional networks underlying biological processes. Here, we present a streamlined workflow combining microfluidic chips for all-in-one proteomic sample preparation and data-independent acquisition (DIA) mass spectrometry (MS) for proteomic analysis down to the single-cell level. The proteomics chips enable multiplexed and automated cell isolation/counting/imaging and sample processing in a single device. Combining chip-based sample handling with DIA-MS using project-specific mass spectral libraries, we profile on average ~1,500 protein groups across 20 single mammalian cells. Applying the chip-DIA workflow to profile the proteomes of adherent and non-adherent malignant cells, we cover a dynamic range of 5 orders of magnitude with good reproducibility and <16% missing values between runs. Taken together, the chip-DIA workflow offers all-in-one cell characterization, analytical sensitivity and robustness, and the option to add additional functionalities in the future, thus providing a basis for advanced single-cell proteomics applications.
    DOI:  https://doi.org/10.1038/s41467-021-27778-4
  13. Am J Cancer Res. 2021 ;11(12): 5856-5863
    Ferroptosis: a promising target for cancer immunotherapy.
    Lin-Lin Sun, Dong-Li Linghu, Mien-Chie Hung.
      Ferroptosis is a recently recognized type of programmed cell death and emerges to play an important role in cancer biology and therapies. This unique form of cell death, characterized by iron-dependent lipid peroxidation, is exquisitely regulated by the cellular metabolic networks such as lipid, iron and amino acid metabolism. The sensitivity to ferroptosis varies among different tumors. Recent evidence reveals that triple-negative breast cancer (TNBC), a highly aggressive disease with limited effective targeted therapies is particularly vulnerable to ferroptosis inducers, suggesting this new form of non-apoptotic cell death as an attractive target for the treatment of the "difficult-to-treat" tumor. Intriguingly, ferroptosis has recently been implicated to be involved in T cell-mediated anti-tumor immunity and affect the efficacy of cancer immunotherapy. Better understanding of this ferroptotic cell death will shed light on the discovery of novel combination therapeutic strategies for cancer treatment. Herein, we provide an overview of the key hallmarks of ferroptosis, use TNBC as a model to characterize the regulation of ferroptosis in cancer, and highlight ferroptosis-modulating combination therapeutic strategies in the context of cancer immunotherapy.
    Keywords:  Ferroptosis; cancer immunotherapy; triple-negative breast cancer
  14. Curr Med Chem. 2022 Jan 11.
    Ferroptosis inducers for prostate cancer therapy.
    Nadia Zaffaroni, Giovanni Luca Beretta.
      Lipid peroxidation-driven iron-dependent ferroptosis is a regulated cell death mechanism implicated in numerous disease, such as neurological diseases, kidney injury, ischemia, and tumors, including prostate cancer. The cellular mechanisms of ferrosptosis are strongly associated with iron, reactive oxygen species and aminoacid metabolic pathways. Several compounds, namely ferroptosis inducers, impact on these pathways and trigger ferroptosis by i) inhibiting Xc- transporter system, ii) impairing GPX4 functions and iii) oxidizing iron and polyunsaturated phospholipids. Preclinical studies showed that in combination with conventional anticancer drugs, ferroptosis inducers are effective in prostate cancer and in combating the progression towards the castration resistant disease. This review overviews the mechanisms implicated in ferroptosis and discusses the findings achieved in prostate cancer.
    Keywords:  GPX4; Prostate cancer; ROS; ferroptosis; lipid peroxidation
    DOI:  https://doi.org/10.2174/0929867329666220111120924
  15. Mol Cell Proteomics. 2022 Jan 06. pii: S1535-9476(22)00001-9. [Epub ahead of print] 100193
    An expanding repertoire of protein acylations.
    Yuxuan Xu, Zhenyu Shi, Li Bao.
      Protein post-translational modifications (PTMs) play key roles in multiple cellular processes by allowing rapid reprogramming of individual protein functions. Acylation, one of the most important PTMs, is involved in different physiological activities including cell differentiation and energy metabolism. In recent years, the progression in technologies, especially the antibodies against acylation and the highly sensitive and effective mass spectrometry (MS)-based proteomics, as well as optimized functional studies, greatly deepen our understanding of protein acylation. In this review, we give a general overview of the twelve main protein acylations (formylation, acetylation, propionylation, butyrylation, malonylation, succinylation, glutarylation, palmitoylation, myristoylation, benzoylation, crotonylation and 2-hydroxyisobutyrylation), including their substrates (histones and non-histone proteins), regulatory enzymes (writers, readers and erasers), biological functions (transcriptional regulation, metabolic regulation, subcellular targeting, protein-membrane interactions, protein stability and folding), and related diseases (cancer, diabetes, heart disease, neurodegenerative disease and viral infection), to present a complete picture of protein acylations and highlight their functional significance in future research.
    DOI:  https://doi.org/10.1016/j.mcpro.2022.100193
  16. Cancers (Basel). 2022 Jan 04. pii: 228. [Epub ahead of print]14(1):
    Lipid Metabolism in Cancer: The Role of Acylglycerolphosphate Acyltransferases (AGPATs).
    Angeliki Karagiota, Georgia Chachami, Efrosyni Paraskeva.
      Altered lipid metabolism is an emerging hallmark of aggressive tumors, as rapidly proliferating cancer cells reprogram fatty acid (FA) uptake, synthesis, storage, and usage to meet their increased energy demands. Central to these adaptive changes, is the conversion of excess FA to neutral triacylglycerides (TAG) and their storage in lipid droplets (LDs). Acylglycerolphosphate acyltransferases (AGPATs), also known as lysophosphatidic acid acyltransferases (LPAATs), are a family of five enzymes that catalyze the conversion of lysophosphatidic acid (LPA) to phosphatidic acid (PA), the second step of the TAG biosynthesis pathway. PA, apart from its role as an intermediate in TAG synthesis, is also a precursor of glycerophospholipids and a cell signaling molecule. Although the different AGPAT isoforms catalyze the same reaction, they appear to have unique non-overlapping roles possibly determined by their distinct tissue expression and substrate specificity. This is best exemplified by the role of AGPAT2 in the development of type 1 congenital generalized lipodystrophy (CGL) and is also manifested by recent studies highlighting the involvement of AGPATs in the physiology and pathology of various tissues and organs. Importantly, AGPAT isoform expression has been shown to enhance proliferation and chemoresistance of cancer cells and correlates with increased risk of tumor development or aggressive phenotypes of several types of tumors.
    Keywords:  AGPAT; LPAAT; cancer; lipids; metabolism; phosphatidic acid
    DOI:  https://doi.org/10.3390/cancers14010228
  17. Cells. 2022 Jan 02. pii: 140. [Epub ahead of print]11(1):
    Amino Acid Metabolism in Cancer Drug Resistance.
    Hee-Chan Yoo, Jung-Min Han.
      Despite the numerous investigations on resistance mechanisms, drug resistance in cancer therapies still limits favorable outcomes in cancer patients. The complexities of the inherent characteristics of tumors, such as tumor heterogeneity and the complicated interaction within the tumor microenvironment, still hinder efforts to overcome drug resistance in cancer cells, requiring innovative approaches. In this review, we describe recent studies offering evidence for the essential roles of amino acid metabolism in driving drug resistance in cancer cells. Amino acids support cancer cells in counteracting therapies by maintaining redox homeostasis, sustaining biosynthetic processes, regulating epigenetic modification, and providing metabolic intermediates for energy generation. In addition, amino acid metabolism impacts anticancer immune responses, creating an immunosuppressive or immunoeffective microenvironment. A comprehensive understanding of amino acid metabolism as it relates to therapeutic resistance mechanisms will improve anticancer therapeutic strategies.
    Keywords:  amino acids; cancer; drug resistance; immune response
    DOI:  https://doi.org/10.3390/cells11010140
  18. Clin Exp Immunol. 2021 Dec 15. pii: uxab033. [Epub ahead of print]
    The role of lipid metabolism in shaping the expansion and the function of regulatory T cells.
    Alessandra Pinzon Grimaldos, Simone Bini, Ilenia Pacella, Alessandra Rossi, Alessia Di Costanzo, Ilenia Minicocci, Laura D'Erasmo, Marcello Arca, Silvia Piconese.
      Metabolic inflammation, defined as a chronic low-grade inflammation, is implicated in numerous metabolic diseases. In recent years, the role of regulatory T cells (Tregs) as key controllers of metabolic inflammation has emerged, but our comprehension on how different metabolic pathways influence Treg functions needs a deeper understanding. Here we focus on how circulating and intracellular lipid metabolism, in particular cholesterol metabolism, regulates Treg homeostasis, expansion, and functions. Cholesterol is carried through the bloodstream by circulating lipoproteins (chylomicrons, very low-density lipoproteins, low-density lipoproteins). Tregs are equipped with a wide array of metabolic sensors able to perceive and respond to changes in the lipid environment through the activation of different intracellular pathways thus conferring to these cells a crucial metabolic and functional plasticity. Nevertheless, altered cholesterol transport, as observed in genetic dyslipidemias and atherosclerosis, impairs Treg proliferation and function through defective cellular metabolism. The intracellular pathway devoted to the cholesterol synthesis is the mevalonate pathway and several studies have shown that this pathway is essential for Treg stability and suppressive activity. High cholesterol concentrations in the extracellular environment may induce massive accumulation of cholesterol inside the cell thus impairing nutrients sensors and inhibiting the mevalonate pathway. This review summarizes the current knowledge regarding the role of circulating and cellular cholesterol metabolism in the regulation of Treg metabolism and functions. In particular, we will discuss how different pathological conditions affecting cholesterol transport may affect cellular metabolism in Tregs.
    Keywords:  Treg; atherosclerosis; cholesterol; dyslipidemia; lipoproteins
    DOI:  https://doi.org/10.1093/cei/uxab033
  19. Cancers (Basel). 2021 Dec 31. pii: 191. [Epub ahead of print]14(1):
    Folate Transport and One-Carbon Metabolism in Targeted Therapies of Epithelial Ovarian Cancer.
    Adrianne Wallace-Povirk, Zhanjun Hou, Md Junayed Nayeen, Aleem Gangjee, Larry H Matherly.
      New therapies are urgently needed for epithelial ovarian cancer (EOC), the most lethal gynecologic malignancy. To identify new approaches for targeting EOC, metabolic vulnerabilities must be discovered and strategies for the selective delivery of therapeutic agents must be established. Folate receptor (FR) α and the proton-coupled folate transporter (PCFT) are expressed in the majority of EOCs. FRβ is expressed on tumor-associated macrophages, a major infiltrating immune population in EOC. One-carbon (C1) metabolism is partitioned between the cytosol and mitochondria and is important for the synthesis of nucleotides, amino acids, glutathione, and other critical metabolites. Novel inhibitors are being developed with the potential for therapeutic targeting of tumors via FRs and the PCFT, as well as for inhibiting C1 metabolism. In this review, we summarize these exciting new developments in targeted therapies for both tumors and the tumor microenvironment in EOC.
    Keywords:  epithelial ovarian cancer; folate; folate receptor; folate transport; one-carbon metabolism; proton-coupled folate transporter; tumor microenvironment
    DOI:  https://doi.org/10.3390/cancers14010191
  20. Cancers (Basel). 2022 Jan 04. pii: 250. [Epub ahead of print]14(1):
    Fatty Acid Metabolism in Myeloid-Derived Suppressor Cells and Tumor-Associated Macrophages: Key Factor in Cancer Immune Evasion.
    Sophiya Siddiqui, Rainer Glauben.
      The tumor microenvironment (TME) comprises various cell types, soluble factors, viz, metabolites or cytokines, which together play in promoting tumor metastasis. Tumor infiltrating immune cells play an important role against cancer, and metabolic switching in immune cells has been shown to affect activation, differentiation, and polarization from tumor suppressive into immune suppressive phenotypes. Macrophages represent one of the major immune infiltrates into TME. Blood monocyte-derived macrophages and myeloid derived suppressor cells (MDSCs) infiltrating into the TME potentiate hostile tumor progression by polarizing into immunosuppressive tumor-associated macrophages (TAMs). Recent studies in the field of immunometabolism focus on metabolic reprogramming at the TME in polarizing tumor-associated macrophages (TAMs). Lipid droplets (LD), detected in almost every eukaryotic cell type, represent the major source for intra-cellular fatty acids. Previously, LDs were mainly described as storage sites for fatty acids. However, LDs are now recognized to play an integral role in cellular signaling and consequently in inflammation and metabolism-mediated phenotypical changes in immune cells. In recent years, the role of LD dependent metabolism in macrophage functionality and phenotype has been being investigated. In this review article, we discuss fatty acids stored in LDs, their role in modulating metabolism of tumor-infiltrating immune cells and, therefore, in shaping the cancer progression.
    Keywords:  immunosuppression; lipid droplet (LD); metabolic reprogramming; myeloid derived suppressor cells (MDSCs); tumor microenvironment (TME); tumor-associated macrophages (TAMs)
    DOI:  https://doi.org/10.3390/cancers14010250
  21. Nat Cell Biol. 2022 Jan;24(1): 88-98
    PKCβII phosphorylates ACSL4 to amplify lipid peroxidation to induce ferroptosis.
    Hai-Liang Zhang, Bing-Xin Hu, Zhi-Ling Li, Tian Du, Jia-Lu Shan, Zhi-Peng Ye, Xiao-Dan Peng, Xuan Li, Yun Huang, Xian-Ying Zhu, Yu-Hong Chen, Gong-Kan Feng, Dajun Yang, Rong Deng, Xiao-Feng Zhu.
      The accumulation of lipid peroxides is recognized as a determinant of the occurrence of ferroptosis. However, the sensors and amplifying process of lipid peroxidation linked to ferroptosis remain obscure. Here we identify PKCβII as a critical contributor of ferroptosis through independent genome-wide CRISPR-Cas9 and kinase inhibitor library screening. Our results show that PKCβII senses the initial lipid peroxides and amplifies lipid peroxidation linked to ferroptosis through phosphorylation and activation of ACSL4. Lipidomics analysis shows that activated ACSL4 catalyses polyunsaturated fatty acid-containing lipid biosynthesis and promotes the accumulation of lipid peroxidation products, leading to ferroptosis. Attenuation of the PKCβII-ACSL4 pathway effectively blocks ferroptosis in vitro and impairs ferroptosis-associated cancer immunotherapy in vivo. Our results identify PKCβII as a sensor of lipid peroxidation, and the lipid peroxidation-PKCβII-ACSL4 positive-feedback axis may provide potential targets for ferroptosis-associated disease treatment.
    DOI:  https://doi.org/10.1038/s41556-021-00818-3
  22. Nat Commun. 2022 Jan 10. 13(1): 139
    Oxylipin metabolism is controlled by mitochondrial β-oxidation during bacterial inflammation.
    Mariya Misheva, Konstantinos Kotzamanis, Luke C Davies, Victoria J Tyrrell, Patricia R S Rodrigues, Gloria A Benavides, Christine Hinz, Robert C Murphy, Paul Kennedy, Philip R Taylor, Marcela Rosas, Simon A Jones, James E McLaren, Sumukh Deshpande, Robert Andrews, Nils Helge Schebb, Magdalena A Czubala, Mark Gurney, Maceler Aldrovandi, Sven W Meckelmann, Peter Ghazal, Victor Darley-Usmar, Daniel A White, Valerie B O'Donnell.
      Oxylipins are potent biological mediators requiring strict control, but how they are removed en masse during infection and inflammation is unknown. Here we show that lipopolysaccharide (LPS) dynamically enhances oxylipin removal via mitochondrial β-oxidation. Specifically, genetic or pharmacological targeting of carnitine palmitoyl transferase 1 (CPT1), a mitochondrial importer of fatty acids, reveal that many oxylipins are removed by this protein during inflammation in vitro and in vivo. Using stable isotope-tracing lipidomics, we find secretion-reuptake recycling for 12-HETE and its intermediate metabolites. Meanwhile, oxylipin β-oxidation is uncoupled from oxidative phosphorylation, thus not contributing to energy generation. Testing for genetic control checkpoints, transcriptional interrogation of human neonatal sepsis finds upregulation of many genes involved in mitochondrial removal of long-chain fatty acyls, such as ACSL1,3,4, ACADVL, CPT1B, CPT2 and HADHB. Also, ACSL1/Acsl1 upregulation is consistently observed following the treatment of human/murine macrophages with LPS and IFN-γ. Last, dampening oxylipin levels by β-oxidation is suggested to impact on their regulation of leukocyte functions. In summary, we propose mitochondrial β-oxidation as a regulatory metabolic checkpoint for oxylipins during inflammation.
    DOI:  https://doi.org/10.1038/s41467-021-27766-8
  23. Genomics Proteomics Bioinformatics. 2022 Jan 07. pii: S1672-0229(22)00001-8. [Epub ahead of print]
    Quantitative Proteomics Using Isobaric Labeling: A Practical Guide.
    Xiulan Chen, Yaping Sun, Tingting Zhang, Lian Shu, Peter Roepstorff, Fuquan Yang.
      In the past decade, relative proteomic quantification using isobaric labeling technology has developed into a key tool for comparing the expression of proteins in biological samples. Although its multiplexing capacity and flexibility make this a valuable technology for addressing various biological questions, its quantitative accuracy and precision still pose significant challenges to the reliability of its quantification results. Here, we give a detailed overview of the different kinds of isobaric mass tags and the advantages and disadvantages of the isobaric labeling method. We also discuss which precautions should be taken at each step of the isobaric labeling workflow, to obtain reliable quantification results in large-scale quantitative proteomics experiments. In the last section, we discuss the broad applications of the isobaric labeling technology in biological and clinical studies, with an emphasis on thermal proteome profiling and proteogenomics.
    Keywords:  Isobaric labeling; Mass spectrometry; Quantitative proteomics; TMT; iTRAQ
    DOI:  https://doi.org/10.1016/j.gpb.2021.08.012
  24. Cell Metab. 2022 Jan 10. pii: S1550-4131(21)00635-5. [Epub ahead of print]
    Atlas of exercise metabolism reveals time-dependent signatures of metabolic homeostasis.
    Shogo Sato, Kenneth A Dyar, Jonas T Treebak, Sara L Jepsen, Amy M Ehrlich, Stephen P Ashcroft, Kajetan Trost, Thomas Kunzke, Verena M Prade, Lewin Small, Astrid Linde Basse, Milena Schönke, Siwei Chen, Muntaha Samad, Pierre Baldi, Romain Barrès, Axel Walch, Thomas Moritz, Jens J Holst, Dominik Lutter, Juleen R Zierath, Paolo Sassone-Corsi.
      Tissue sensitivity and response to exercise vary according to the time of day and alignment of circadian clocks, but the optimal exercise time to elicit a desired metabolic outcome is not fully defined. To understand how tissues independently and collectively respond to timed exercise, we applied a systems biology approach. We mapped and compared global metabolite responses of seven different mouse tissues and serum after an acute exercise bout performed at different times of the day. Comparative analyses of intra- and inter-tissue metabolite dynamics, including temporal profiling and blood sampling across liver and hindlimb muscles, uncovered an unbiased view of local and systemic metabolic responses to exercise unique to time of day. This comprehensive atlas of exercise metabolism provides clarity and physiological context regarding the production and distribution of canonical and novel time-dependent exerkine metabolites, such as 2-hydroxybutyrate (2-HB), and reveals insight into the health-promoting benefits of exercise on metabolism.
    Keywords:  2-hydroxybutyrate; arteriovenous metabolomics; circadian rhythms; exercise metabolism; exerkines; metabolomics; multitissue analysis
    DOI:  https://doi.org/10.1016/j.cmet.2021.12.016
  25. Cell Rep. 2021 Dec 28. pii: S2211-1247(21)01783-6. [Epub ahead of print] 110271
    Proteomic and metabolomic profiling of urine uncovers immune responses in patients with COVID-19.
    Xiaojie Bi, Wei Liu, Xuan Ding, Shuang Liang, Yufen Zheng, Xiaoli Zhu, Sheng Quan, Xiao Yi, Nan Xiang, Juping Du, Haiyan Lyu, Die Yu, Chao Zhang, Luang Xu, Weigang Ge, Xinke Zhan, Jiale He, Zi Xiong, Shun Zhang, Yanchang Li, Ping Xu, Guangjun Zhu, Donglian Wang, Hongguo Zhu, Shiyong Chen, Jun Li, Haihong Zhao, Yi Zhu, Huafen Liu, Jiaqin Xu, Bo Shen, Tiannan Guo.
      The utility of the urinary proteome in infectious diseases remains unclear. Here, we analyzed the proteome and metabolome of urine and serum samples from patients with COVID-19 and healthy controls. Our data show that urinary proteins effectively classify COVID-19 by severity. We detect 197 cytokines and their receptors in urine, but only 124 in serum using TMT-based proteomics. The decrease in urinary ESCRT complex proteins correlates with active SARS-CoV-2 replication. The downregulation of urinary CXCL14 in severe COVID-19 cases positively correlates with blood lymphocyte counts. Integrative multiomics analysis suggests that innate immune activation and inflammation triggered renal injuries in patients with COVID-19. COVID-19-associated modulation of the urinary proteome offers unique insights into the pathogenesis of this disease. This study demonstrates the added value of including the urinary proteome in a suite of multiomics analytes in evaluating the immune pathobiology and clinical course of COVID-19 and, potentially, other infectious diseases.
    Keywords:  COVID-19; CXCL14; ESCRT super-complex; metabolomics; proteomics; renal injury; serum; urine
    DOI:  https://doi.org/10.1016/j.celrep.2021.110271
  26. Nutrients. 2022 Jan 04. pii: 214. [Epub ahead of print]14(1):
    Untargeted Metabolomics Analysis of the Serum Metabolic Signature of Childhood Obesity.
    Lukasz Szczerbinski, Gladys Wojciechowska, Adam Olichwier, Mark A Taylor, Urszula Puchta, Paulina Konopka, Adam Paszko, Anna Citko, Joanna Goscik, Oliver Fiehn, Sili Fan, Anna Wasilewska, Katarzyna Taranta-Janusz, Adam Kretowski.
      Obesity rates among children are growing rapidly worldwide, placing massive pressure on healthcare systems. Untargeted metabolomics can expand our understanding of the pathogenesis of obesity and elucidate mechanisms related to its symptoms. However, the metabolic signatures of obesity in children have not been thoroughly investigated. Herein, we explored metabolites associated with obesity development in childhood. Untargeted metabolomic profiling was performed on fasting serum samples from 27 obese Caucasian children and adolescents and 15 sex- and age-matched normal-weight children. Three metabolomic assays were combined and yielded 726 unique identified metabolites: gas chromatography-mass spectrometry (GC-MS), hydrophilic interaction liquid chromatography coupled to mass spectrometry (HILIC LC-MS/MS), and lipidomics. Univariate and multivariate analyses showed clear discrimination between the untargeted metabolomes of obese and normal-weight children, with 162 significantly differentially expressed metabolites between groups. Children with obesity had higher concentrations of branch-chained amino acids and various lipid metabolites, including phosphatidylcholines, cholesteryl esters, triglycerides. Thus, an early manifestation of obesity pathogenesis and its metabolic consequences in the serum metabolome are correlated with altered lipid metabolism. Obesity metabolite patterns in the adult population were very similar to the metabolic signature of childhood obesity. Identified metabolites could be potential biomarkers and used to study obesity pathomechanisms.
    Keywords:  childhood obesity; lipidomics; obesity biomarkers; obesity pathogenesis; obesity pathomechanisms; untargeted metabolomics
    DOI:  https://doi.org/10.3390/nu14010214
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