bims-mascan 2020-04-19 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2020–04–19
27 papers selected by
Giovanny Rodríguez Blanco, The Beatson Institute for Cancer Research

PI(3,4)P2 Signaling in Cancer and Metabolism.
Leucine and branched chain amino acid metabolism contribute to the growth of bone sarcomas by regulating AMPK and mTORC1 signaling.
Molecular principles of metastasis: a hallmark of cancer revisited.
Dual mass spectrometry as a tool to improve annotation and quantification in targeted plasma lipidomics.
The role of ubiquitination in tumorigenesis and targeted drug discovery.
Decreased Triacylglycerol Content and Elevated Contents of Cell Membrane Lipids in Colorectal Cancer Tissue: A Lipidomic Study.
Computational models applied to metabolomics data hints at the relevance of glutamine metabolism in breast cancer.
Nitrogen Metabolism in Cancer and Immunity.
Dietary lipids fuel GPX4-restricted enteritis resembling Crohn's disease.
The yin and yang functions of extracellular ATP and adenosine in tumor immunity.
Shedding New Light on Cancer Metabolism: A Metabolic Tightrope Between Life and Death.
Metabolomics identified new biomarkers for the precise diagnosis of pancreatic cancer and associated tissue metastasis.
Unraveling the RNA modification code with mass spectrometry.
The emerging molecular mechanism of m6A modulators in tumorigenesis and cancer progression.
Development of a 96-well plate sample preparation method for integrated N- and O-glycomics using porous graphitized carbon liquid chromatography-mass spectrometry.
Progress in Understanding Ferroptosis and Challenges in Its Targeting for Therapeutic Benefit.
Metabolomics and lipidomics profiling in asymptomatic severe intracranial arterial stenosis: results from a population-based study.
Identification of potential metabolite markers for colon cancer and rectal cancer using serum metabolomics.
Liquid Biopsy-Based Biomarkers of Treatment Response and Resistance.
Selective inhibition of cancer cell self-renewal through a Quisinostat-histone H1.0 axis.
Ozonization of tissue sections for MALDI MS imaging of carbon-carbon double bond positional isomers of phospholipids.
Warburg effects on cancer cells survival: the role of sugar starvation in cancer therapy.
Validation of a simplified procedure for convenient and rapid quantification of reduced and oxidized glutathione in human plasma by liquid chromatography tandem mass spectrometry analysis.
Extracellular Vesicle-Mediated Nucleic Acid Transfer And Reprogramming In The Tumor Microenvironment.
The Chemistry and Biology of Ferroptosis.
Unbiased proteomics identifies plasminogen activator inhibitor-1 as a negative regulator of endothelial nitric oxide synthase.
LDL subclass lipidomics in atherogenic dyslipidemia:Effect of statin therapy on bioactive lipids and dense LDL.

Front Oncol. 2020 ;10 360

PI(3,4)P2 Signaling in Cancer and Metabolism.

Luca Gozzelino, Maria Chiara De Santis, Federico Gulluni, Emilio Hirsch, Miriam Martini.

  The phosphatidylinositide 3 kinases (PI3Ks) and their downstream mediators AKT and mammalian target of rapamycin (mTOR) are central regulators of glycolysis, cancer metabolism, and cancer cell proliferation. At the molecular level, PI3K signaling involves the generation of the second messenger lipids phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P3] and phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2]. There is increasing evidence that PI(3,4)P2 is not only the waste product for the removal of PI(3,4,5)P3 but can also act as a signaling molecule. The selective cellular functions for PI(3,4)P2 independent of PI(3,4,5)P3 have been recently described, including clathrin-mediated endocytosis and mTOR regulation. However, the specific spatiotemporal dynamics and signaling role of PI3K minor lipid messenger PI(3,4)P2 are not well-understood. This review aims at highlighting the biological functions of this lipid downstream of phosphoinositide kinases and phosphatases and its implication in cancer metabolism.

Keywords:  AKT; INPP4; PI3K; PTEN; cancer biology; cancer metabolism; phosphatases; phosphoinositide

DOI:  https://doi.org/10.3389/fonc.2020.00360
Biochem J. 2020 Apr 16. pii: BCJ20190754. [Epub ahead of print]

Leucine and branched chain amino acid metabolism contribute to the growth of bone sarcomas by regulating AMPK and mTORC1 signaling.

Shailer B Martin, William S Reiche, Nicholas A Fifelski, Alexander J Schultz, Spencer J Stanford, Alexander A Martin, Danielle L Nack, Bernard Radlwimmer, Michael P Boyer, Elitsa Ananieva.

  Osteosarcoma and chondrosarcoma are sarcomas of the bone and the cartilage that are primarily treated by surgical intervention combined with high toxicity chemotherapy. In search of alternative metabolic approaches to address the challenges in treating bone sarcomas, we assessed the growth dependence of these cancers on leucine, one of the branched chain amino acids (BCAAs), and BCAA metabolism. Tumor biopsies from bone sarcoma patients revealed differential expression of BCAA metabolic enzymes. The cytosolic branched chain aminotransferase (BCATc) that is commonly overexpressed in cancer cells, was downregulated in chondrosarcoma (SW1353) in contrast to osteosarcoma (143B) cells that expressed both BCATc and its mitochondrial isoform BCATm. Treating SW1353cells with gabapentin, a selective inhibitor of BCATc, further revealed that these cells failed to respond to gabapentin. Application of the structural analog of leucine, N-acetyl-leucine amide (NALA) to disrupt leucine uptake, indicated that all bone sarcoma cells used leucine to support their energy metabolism and biosynthetic demands. This was evident from the increased activity of the energy sensor AMP-activated protein kinase (AMPK), downregulation of complex 1 of the mammalian target of rapamycin (mTORC1), and reduced cell viability in response to NALA. The observed changes were most profound in the 143B cells, which appeared highly dependent on cytosolic and mitochondrial BCAA metabolism. This study thus demonstrates that bone sarcomas rely on leucine and BCAA metabolism for energy and growth; however, the differential expression of BCAA enzymes and the presence of other carbon sources may dictate how efficiently these cancer cells take advantage of BCAA metabolism.

Keywords:  BCAAs; BCATc; BCATm; Leucine; chondrosarcoma; osteosarcoma

DOI:  https://doi.org/10.1042/BCJ20190754
Signal Transduct Target Ther. 2020 Mar 12. 5(1): 28

Molecular principles of metastasis: a hallmark of cancer revisited.

Jawad Fares, Mohamad Y Fares, Hussein H Khachfe, Hamza A Salhab, Youssef Fares.

Metastasis is the hallmark of cancer that is responsible for the greatest number of cancer-related deaths. Yet, it remains poorly understood. The continuous evolution of cancer biology research and the emergence of new paradigms in the study of metastasis have revealed some of the molecular underpinnings of this dissemination process. The invading tumor cell, on its way to the target site, interacts with other proteins and cells. Recognition of these interactions improved the understanding of some of the biological principles of the metastatic cell that govern its mobility and plasticity. Communication with the tumor microenvironment allows invading cancer cells to overcome stromal challenges, settle, and colonize. These characteristics of cancer cells are driven by genetic and epigenetic modifications within the tumor cell itself and its microenvironment. Establishing the biological mechanisms of the metastatic process is crucial in finding open therapeutic windows for successful interventions. In this review, the authors explore the recent advancements in the field of metastasis and highlight the latest insights that contribute to shaping this hallmark of cancer.

DOI: https://doi.org/10.1038/s41392-020-0134-x
Metabolomics. 2020 Apr 17. 16(5): 53

Dual mass spectrometry as a tool to improve annotation and quantification in targeted plasma lipidomics.

Liang Gao, Amaury Cazenave-Gassiot, Bo Burla, Markus R Wenk, Federico Torta.

   INTRODUCTION: High quality data, based on reliable quantification and clear identification of the reported lipid species, are required for the clinical translation of human plasma lipidomic studies.
OBJECTIVE: Lipid quantification can be efficiently performed on triple quadrupole (QqQ) mass spectrometers in targeted multiple reaction monitoring (MRM) mode. However, a series of issues can be encountered when aiming at unambiguous identification and accurate quantification, including (i) resolving peaks of polyunsaturated species, (ii) discriminating between plasmanyl-, plasmenyl- and odd chain species and (iii) resolving the isotopic overlap between co-eluting lipid species.
METHODS: As a practical tool to improve the quality of targeted lipidomics studies, we applied a Dual MS platform by simultaneously coupling a reversed-phase liquid chromatography separation to a QqQ and a quadrupole-time of flight (Q-ToF) mass spectrometers. In one single experiment, this platform allows to correctly identify, by high-resolution MS and MS/MS, the peaks that are quantified by MRM.
RESULTS: As proof of concept, we applied the platform on glycerophosphocholines (GPCs) and sphingomyelins (SMs), which are highly abundant in human plasma and play crucial roles in various physiological functions. Our results demonstrated that Dual MS could provide a higher level of confidence in the identification and quantification of GPCs and SMs in human plasma. The same approach can also be applied to improve the study of other lipid classes and expanded for the identification of novel lipid molecular species.
CONCLUSIONS: This methodology might have a great potential to achieve a better specificity in the quantification of lipids by targeted lipidomics in high-throughput studies.

Keywords:  Glycerophosphocholine; Identification; Lipidomics; Liquid chromatography; Plasma; Quantification; Sphingomyelin; Tandem mass spectrometry

DOI:  https://doi.org/10.1007/s11306-020-01677-z
Signal Transduct Target Ther. 2020 Feb 29. 5(1): 11

The role of ubiquitination in tumorigenesis and targeted drug discovery.

Lu Deng, Tong Meng, Lei Chen, Wenyi Wei, Ping Wang.

Ubiquitination, an important type of protein posttranslational modification (PTM), plays a crucial role in controlling substrate degradation and subsequently mediates the "quantity" and "quality" of various proteins, serving to ensure cell homeostasis and guarantee life activities. The regulation of ubiquitination is multifaceted and works not only at the transcriptional and posttranslational levels (phosphorylation, acetylation, methylation, etc.) but also at the protein level (activators or repressors). When regulatory mechanisms are aberrant, the altered biological processes may subsequently induce serious human diseases, especially various types of cancer. In tumorigenesis, the altered biological processes involve tumor metabolism, the immunological tumor microenvironment (TME), cancer stem cell (CSC) stemness and so on. With regard to tumor metabolism, the ubiquitination of some key proteins such as RagA, mTOR, PTEN, AKT, c-Myc and P53 significantly regulates the activity of the mTORC1, AMPK and PTEN-AKT signaling pathways. In addition, ubiquitination in the TLR, RLR and STING-dependent signaling pathways also modulates the TME. Moreover, the ubiquitination of core stem cell regulator triplets (Nanog, Oct4 and Sox2) and members of the Wnt and Hippo-YAP signaling pathways participates in the maintenance of CSC stemness. Based on the altered components, including the proteasome, E3 ligases, E1, E2 and deubiquitinases (DUBs), many molecular targeted drugs have been developed to combat cancer. Among them, small molecule inhibitors targeting the proteasome, such as bortezomib, carfilzomib, oprozomib and ixazomib, have achieved tangible success. In addition, MLN7243 and MLN4924 (targeting the E1 enzyme), Leucettamol A and CC0651 (targeting the E2 enzyme), nutlin and MI-219 (targeting the E3 enzyme), and compounds G5 and F6 (targeting DUB activity) have also shown potential in preclinical cancer treatment. In this review, we summarize the latest progress in understanding the substrates for ubiquitination and their special functions in tumor metabolism regulation, TME modulation and CSC stemness maintenance. Moreover, potential therapeutic targets for cancer are reviewed, as are the therapeutic effects of targeted drugs.

DOI: https://doi.org/10.1038/s41392-020-0107-0
J Clin Med. 2020 Apr 12. pii: E1095. [Epub ahead of print]9(4):

Decreased Triacylglycerol Content and Elevated Contents of Cell Membrane Lipids in Colorectal Cancer Tissue: A Lipidomic Study.

Adriana Mika, Alicja Pakiet, Aleksandra Czumaj, Zbigniew Kaczynski, Ivan Liakh, Jarek Kobiela, Adrian Perdyan, Krystian Adrych, Wojciech Makarewicz, Tomasz Sledzinski.

  Recent evidence suggests that lipid composition in cancer tissues may undergo multiple alterations. However, no comprehensive analysis of various lipid groups in colorectal cancer (CRC) tissue has been conducted thus far. To address the problem in question, we determined the contents of triacylglycerols (TG), an energetic substrate, various lipids necessary for cell membrane formation, among them phospholipids (phosphatidylcholine, phosphatidylethanolamine), sphingolipids (sphingomyelin) and cholesterol (free, esterified and total), and fatty acids included in complex lipids. 1H-nuclear magnetic resonance (1H-NMR) and gas chromatography-mass spectrometry (GC-MS) were used to analyze the lipid composition of colon cancer tissue and normal large intestinal mucosa from 25 patients. Compared with normal tissue, cancer tissues had significantly lower TG content, along with elevated levels of phospholipids, sphingomyelin, and cholesterol. Moreover, the content of oleic acid, the main component of TG, was decreased in cancer tissues, whereas the levels of saturated fatty acids and polyunsaturated fatty acids (PUFAs), which are principal components of polar lipids, were elevated. These lipidome rearrangements were associated with the overexpression of genes associated with fatty acid oxidation, and the synthesis of phospholipids and cholesterol. These findings suggest that reprogramming of lipid metabolism might occur in CRC tissue, with a shift towards increased utilization of TG for energy production and enhanced synthesis of membrane lipids, necessary for the rapid proliferation of cancer cells.

Keywords:  cancer cell proliferation; cell membrane; colorectal cancer; lipid oxidation; lipids; nuclear magnetic resonance; polyunsaturated fatty acids

DOI:  https://doi.org/10.3390/jcm9041095
BMC Cancer. 2020 Apr 15. 20(1): 307

Computational models applied to metabolomics data hints at the relevance of glutamine metabolism in breast cancer.

Lucía Trilla-Fuertes, Angelo Gámez-Pozo, Elena López-Camacho, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Rocío López-Vacas, Jorge M Arevalillo, Mariana Díaz-Almirón, Hilario Navarro, Paloma Maín, Enrique Espinosa, Pilar Zamora, Juan Ángel Fresno Vara.

   BACKGROUND: Metabolomics has a great potential in the development of new biomarkers in cancer and it has experiment recent technical advances.
METHODS: In this study, metabolomics and gene expression data from 67 localized (stage I to IIIB) breast cancer tumor samples were analyzed, using (1) probabilistic graphical models to define associations using quantitative data without other a priori information; and (2) Flux Balance Analysis and flux activities to characterize differences in metabolic pathways.
RESULTS: On the one hand, both analyses highlighted the importance of glutamine in breast cancer. Moreover, cell experiments showed that treating breast cancer cells with drugs targeting glutamine metabolism significantly affects cell viability. On the other hand, these computational methods suggested some hypotheses and have demonstrated their utility in the analysis of metabolomics data and in associating metabolomics with patient's clinical outcome.
CONCLUSIONS: Computational analyses applied to metabolomics data suggested that glutamine metabolism is a relevant process in breast cancer. Cell experiments confirmed this hypothesis. In addition, these computational analyses allow associating metabolomics data with patient prognosis.

Keywords:  Breast cancer; Computational analyses; Glutamine metabolism; Metabolomics

DOI:  https://doi.org/10.1186/s12885-020-06764-x
Trends Cell Biol. 2020 May;pii: S0962-8924(20)30040-4. [Epub ahead of print]30(5): 408-424

Nitrogen Metabolism in Cancer and Immunity.

Kiran Kurmi, Marcia C Haigis.

  As one of the fundamental requirements for cell growth and proliferation, nitrogen acquisition and utilization must be tightly regulated. Nitrogen can be generated from amino acids (AAs) and utilized for biosynthetic processes through transamination and deamination reactions. Importantly, limitations of nitrogen availability in cells can disrupt the synthesis of proteins, nucleic acids, and other important nitrogen-containing compounds. Rewiring cellular metabolism to support anabolic processes is a feature common to both cancer and proliferating immune cells. In this review, we discuss how nitrogen is utilized in biosynthetic pathways and highlight different metabolic and oncogenic programs that alter the flow of nitrogen to sustain biomass production and growth, an important emerging feature of cancer and immune cell proliferation.

Keywords:  T cells; ammonia; cancer cells; nitrogen metabolism; non-essential amino acids; transaminases; tumor microenvironment

DOI:  https://doi.org/10.1016/j.tcb.2020.02.005
Nat Commun. 2020 Apr 14. 11(1): 1775

Dietary lipids fuel GPX4-restricted enteritis resembling Crohn's disease.

Lisa Mayr, Felix Grabherr, Julian Schwärzler, Isabelle Reitmeier, Felix Sommer, Thomas Gehmacher, Lukas Niederreiter, Gui-Wei He, Barbara Ruder, Kai T R Kunz, Piotr Tymoszuk, Richard Hilbe, David Haschka, Clemens Feistritzer, Romana R Gerner, Barbara Enrich, Nicole Przysiecki, Markus Seifert, Markus A Keller, Georg Oberhuber, Susanne Sprung, Qitao Ran, Robert Koch, Maria Effenberger, Ivan Tancevski, Heinz Zoller, Alexander R Moschen, Günter Weiss, Christoph Becker, Philip Rosenstiel, Arthur Kaser, Herbert Tilg, Timon E Adolph.

The increased incidence of inflammatory bowel disease (IBD) has become a global phenomenon that could be related to adoption of a Western life-style. Westernization of dietary habits is partly characterized by enrichment with the ω-6 polyunsaturated fatty acid (PUFA) arachidonic acid (AA), which entails risk for developing IBD. Glutathione peroxidase 4 (GPX4) protects against lipid peroxidation (LPO) and cell death termed ferroptosis. We report that small intestinal epithelial cells (IECs) in Crohn's disease (CD) exhibit impaired GPX4 activity and signs of LPO. PUFAs and specifically AA trigger a cytokine response of IECs which is restricted by GPX4. While GPX4 does not control AA metabolism, cytokine production is governed by similar mechanisms as ferroptosis. A PUFA-enriched Western diet triggers focal granuloma-like neutrophilic enteritis in mice that lack one allele of Gpx4 in IECs. Our study identifies dietary PUFAs as a trigger of GPX4-restricted mucosal inflammation phenocopying aspects of human CD.

DOI: https://doi.org/10.1038/s41467-020-15646-6
Cancer Cell Int. 2020 ;20 110

The yin and yang functions of extracellular ATP and adenosine in tumor immunity.

Li-Li Feng, Yi-Qing Cai, Ming-Chen Zhu, Li-Jie Xing, Xin Wang.

  Extracellular adenosine triphosphate (eATP) and its main metabolite adenosine (ADO) constitute an intrinsic part of immunological network in tumor immunity. The concentrations of eATP and ADO in tumor microenvironment (TME) are controlled by ectonucleotidases, such as CD39 and CD73, the major ecto-enzymes expressed on immune cells, endothelial cells and cancer cells. Once accumulated in TME, eATP boosts antitumor immune responses, while ADO attenuates immunity against tumors. eATP and ADO, like yin and yang, represent two opposite aspects from immune-activating to immune-suppressive signals. Here we reviewed the functions of eATP and ADO in tumor immunity and attempt to block eATP hydrolysis, ADO formation and their contradictory effects in tumor models, allowing the induction of effective anti-tumor immune responses in TME. These attempts documented that therapeutic approaches targeting eATP/ADO metabolism and function may be effective methods in cancer therapy.

Keywords:  Adenosine; CD39; CD73; Extracellular adenosine triphosphate; Tumor immunity

DOI:  https://doi.org/10.1186/s12935-020-01195-x
Front Oncol. 2020 ;10 409

Shedding New Light on Cancer Metabolism: A Metabolic Tightrope Between Life and Death.

Matthias Läsche, Günter Emons, Carsten Gründker.

  Since the earliest findings of Otto Warburg, who discovered the first metabolic differences between lactate production of cancer cells and non-malignant tissues in the 1920s, much time has passed. He explained the increased lactate levels with dysfunctional mitochondria and aerobic glycolysis despite adequate oxygenation. Meanwhile, we came to know that mitochondria remain instead functional in cancer cells; hence, metabolic drift, rather than being linked to dysfunctional mitochondria, was found to be an active act of direct response of cancer cells to cell proliferation and survival signals. This metabolic drift begins with the use of sugars and the full oxidative phosphorylation via the mitochondrial respiratory chain to form CO2, and it then leads to the formation of lactic acid via partial oxidation. In addition to oncogene-driven metabolic reprogramming, the oncometabolites themselves alter cell signaling and are responsible for differentiation and metastasis of cancer cells. The aberrant metabolism is now considered a major characteristic of cancer within the past 15 years. However, the proliferating anabolic growth of a tumor and its spread to distal sites of the body is not explainable by altered glucose metabolism alone. Since a tumor consists of malignant cells and its tumor microenvironment, it was important for us to understand the bilateral interactions between the primary tumor and its microenvironment and the processes underlying its successful metastasis. We here describe the main metabolic pathways and their implications in tumor progression and metastasis. We also portray that metabolic flexibility determines the fate of the cancer cell and ultimately the patient. This flexibility must be taken into account when deciding on a therapy, since singular cancer therapies only shift the metabolism to a different alternative path and create resistance to the medication used. As with Otto Warburg in his days, we primarily focused on the metabolism of mitochondria when dealing with this scientific question.

Keywords:  cancer; metabolism; metastasis; microenvironment; therapy

DOI:  https://doi.org/10.3389/fonc.2020.00409
Pharmacol Res. 2020 Apr 08. pii: S1043-6618(20)31113-0. [Epub ahead of print] 104805

Metabolomics identified new biomarkers for the precise diagnosis of pancreatic cancer and associated tissue metastasis.

Xialin Luo, Jingjing Liu, Huaizhi Wang, Haitao Lu.

  Pancreatic cancer (PC) is one of the most aggressive malignancies with high mortality due to a complex and latent pathogenesis leading to the severe lack of early diagnosis methods. To improve clinical diagnosis and enhance therapeutic outcome, we employed the newly developed precision-targeted metabolomics method to identify and validate metabolite biomarkers from the plasma samples of patients with pancreatic cancer that can sensitively and efficiently diagnose the onsite progression of the disease. Many differential metabolites have the capacity to markedly distinguish patients with pancreatic cancer (n = 60) from healthy controls (n = 60). To further enhance the specificity and selectivity of metabolite biomarkers, a dozen tumor tissues from PC patients and paired normal tissues were used to clinically validate the biomarker performance. We eventually verified five new metabolite biomarkers in plasma (creatine, inosine, beta-sitosterol, sphinganine and glycocholic acid), which can be used to readily diagnose pancreatic cancer in a clinical setting. Excitingly, we proposed a panel biomarker by integrating these five individual metabolites into one pattern, demonstrating much higher accuracy and specificity to precisely diagnose pancreatic cancer than conventional biomarkers (CA125, CA19-9, CA242 and CEA); moreover, this plasma panel biomarker used for PC diagnosis is also quite convenient to implement in clinical practice. Using the same metabolomics method, we characterized succinic acid and gluconic acid as having a great capability to monitor the progression and metastasis of pancreatic cancer at different stages. Taken together, this metabolomics method was used to identify and validate metabolite biomarkers that can precisely and sensitively diagnose the onsite progression and metastasis of pancreatic cancer in a clinical setting. Furthermore, such effort should leave clinicians with the correct time frame to facilitate early and efficient therapeutic interventions, which could largely improve the five-year survival rate of PC patients by significantly lowering clinical mortality.

Keywords:  Clinical Applications; Molecular Diagnosis; New Metabolite Biomarkers; Pancreatic Cancer; Serum Metabolomics; Tissue Metastasis

DOI:  https://doi.org/10.1016/j.phrs.2020.104805
Mol Omics. 2020 Apr 14.

Unraveling the RNA modification code with mass spectrometry.

Richard Lauman, Benjamin A Garcia.

The discovery and analysis of modifications on proteins and nucleic acids has provided functional information that has rapidly accelerated the field of epigenetics. While protein post-translational modifications (PTMs), especially on histones, have been highlighted as critical components of epigenetics, the post-transcriptional modification of RNA has been a subject of more recently emergent interest. Multiple RNA modifications have been known to be present in tRNA and rRNA since the 1960s, but the exploration of mRNA, small RNA, and inducible tRNA modifications remains nascent. Sequencing-based methods have been essential to the field by creating the first epitranscriptome maps of m6A, m5C, hm5C, pseudouridine, and inosine; however, these methods possess significant limitations. Here, we discuss the past, present, and future of the application of mass spectrometry (MS) to the study of RNA modifications.

DOI: https://doi.org/10.1039/c8mo00247a
Biomed Pharmacother. 2020 Apr 13. pii: S0753-3322(20)30290-0. [Epub ahead of print]127 110098

The emerging molecular mechanism of m6A modulators in tumorigenesis and cancer progression.

Shuiping Liu, Qiujie Li, Ke Chen, Qin Zhang, Guohua Li, Lvjia Zhuo, Bingtao Zhai, Xinbing Sui, Xiaotong Hu, Tian Xie.

  N6-methyladenosine (m6A) is the most abundant RNA modification; m6A modifications are installed by methyltransferases, removed by demethylases and recognized by reader proteins. M6A plays crucial roles in a variety of biological processes by regulating target RNA translation, splicing, nuclear export, and decay. Since the establishment of methylated RNA immunoprecipitation-sequencing methodology, over three hundred articles about m6A modulators, including "writers", "erasers" and "readers", have been reported in the last four years. In addition, an increasing number of molecular mechanisms underlying m6A RNA methylation in human cancers have been comprehensively clarified. The recently emerged molecular mechanisms of m6A modulators in cancer cell proliferation, cell cycle progression, migration and invasion, apoptosis, and autophagy remain to be summarized. Hence, this review specifically summarizes these recent advances in the understanding of m6A molecular mechanisms in tumorigenesis and cancer progression. In addition, we discuss the prospect of using an m6A methylation modulator as a new diagnostic biomarker and therapeutic target for human cancers.

Keywords:  Cancer progression; Cancer therapy; Diagnostic biomarker; M(6)A modification; Tumorigenesis

DOI:  https://doi.org/10.1016/j.biopha.2020.110098
Mol Omics. 2020 Apr 13.

Development of a 96-well plate sample preparation method for integrated N- and O-glycomics using porous graphitized carbon liquid chromatography-mass spectrometry.

Tao Zhang, Katarina Madunić, Stephanie Holst, Jing Zhang, Chunsheng Jin, Peter Ten Dijke, Niclas G Karlsson, Kathrin Stavenhagen, Manfred Wuhrer.

Changes in glycosylation signatures of cells have been associated with pathological processes in cancer as well as infectious and autoimmune diseases. The current protocols for comprehensive analysis of N-glycomics and O-glycomics derived from cells and tissues often require a large amount of biological material. They also only allow the processing of very limited numbers of samples at a time. Here we established a workflow for sequential release of N-glycans and O-glycans based on PVDF membrane immobilization in 96-well format from 5 × 105 cells. Released glycans are reduced, desalted, purified, and reconstituted, all in 96-well format plates, without additional staining or derivatization. Glycans are then analyzed with porous graphitized carbon nano-liquid chromatography coupled to tandem mass spectrometry using negative-mode electrospray ionization, enabling the chromatographic resolution and structural elucidation of glycan species including many compositional isomers. The approach was demonstrated using glycoprotein standards and further applied to analyze the glycosylation of the murine mammary gland NMuMG cell line. The developed protocol allows the analysis of N- and O-glycans from relatively large numbers of samples in a less time consuming way with high repeatability. Inter- and intraday repeatability of the fetuin N-glycan analysis showed two median intraday coefficients of variations (CVs) of 7.6% and 8.0%, and a median interday CV of 9.8%. Median CVs of 7.9% and 8.7% for the main peaks of N- and O-glycans released from the NMuMG cell line indicate a very good repeatability. The method is applicable to purified glycoproteins as well as to biofluids and cell- or tissue-based samples.

DOI: https://doi.org/10.1039/c9mo00180h
Cell Chem Biol. 2020 Apr 16. pii: S2451-9456(20)30112-4. [Epub ahead of print]27(4): 463-471

Progress in Understanding Ferroptosis and Challenges in Its Targeting for Therapeutic Benefit.

Yilong Zou, Stuart L Schreiber.

Ferroptosis is an iron-dependent cell-death modality driven by oxidative phospholipid damage. In contrast to apoptosis, which enables organisms to eliminate targeted cells purposefully at specific times, ferroptosis appears to be a vulnerability of cells that otherwise use high levels of polyunsaturated lipids to their advantage. Cells in this high polyunsaturated lipid state generally have safeguards that mitigate ferroptotic risk. Since its recognition, ferroptosis has been implicated in degenerative diseases in tissues including kidney and brain, and is a targetable vulnerability in multiple cancers-each likely characterized by the high polyunsaturated lipid state with insufficient or overwhelmed ferroptotic safeguards. In this Perspective, we present progress toward defining the essential roles and key mediators of lipid peroxidation and ferroptosis in disease contexts. Moreover, we discuss gaps in our understanding of ferroptosis and list key challenges that have thus far limited the full potential of targeting ferroptosis for improving human health.

DOI: https://doi.org/10.1016/j.chembiol.2020.03.015
J Proteome Res. 2020 Apr 16.

Metabolomics and lipidomics profiling in asymptomatic severe intracranial arterial stenosis: results from a population-based study.

Yuan Xue, Xiang Wang, Yuan-Yuan Zhao, Xiao-Tong Ma, Xiao-Kang Ji, Shao-Wei Sang, Sai Shao, Peng Yan, Shan Li, Xiao-Hui Liu, Guang-Bin Wang, Ming Lv, Fu-Zhong Xue, Yi-Feng Du, Qin-Jian Sun.

No data are available on the serum metabolomic and lipidomic profiles of people with asymptomatic intracranial arterial stenosis. We explored the characteristic metabolites of individuals with asymptomatic severe intracranial arterial stenosis (asICAS) using untargeted serum metabolomic and lipidomic analyses based on ultra-high-performance liquid chromatography high-resolution mass spectrometry (UPLC-HRMS). This case-control study included 25 participants with asICAS and 25 age- and sex-matched controls free of asICAS, who were all diagnosed by using magnetic resonance angiography and derived from the same population-based study. Serum metabolomic and lipidomic profiles were determined using UPLC-HRMS, and possible biomarker metabolites were identified. Compared with the control group, the asICAS group showed higher levels of free choline, glycerophosphocholine, uracil, taurine, and four peptide molecules and lower levels of free fatty acids, hydroxydodecanedioic acid, hydroxy valeryl carnitine, hydroxytetradecanedioic acid, and two sphingomyelin molecules. The serum metabolomic and lipidomic profiles for people with asICAS are characterized by abnormal metabolism of sphingomyelin, taurine/hypotaurine, pyrimidine and protein (peptide). The biological changes in asICAS may mainly involve taurine/hypotaurine, glycerophospholipid, and sphingolipid metabolism pathways. Biofunctional analysis indicated that these differential metabolites were correlated with metabolic diseases such as early myocardial injury, heart failure, and diabetes.

DOI: https://doi.org/10.1021/acs.jproteome.9b00644
J Clin Lab Anal. 2020 Apr 13. e23333

Identification of potential metabolite markers for colon cancer and rectal cancer using serum metabolomics.

Jianping Wu, Minyi Wu, Qianxia Wu.

   BACKGROUND: To determine the metabolic characteristics of patients with colon cancer (CC) and rectal cancer (RC) using gas chromatography-mass spectrometry (GC-MS)-based metabolomics.
METHODS: In this study, serum samples were collected from 22 CC patients and 23 RC patients preoperatively and postoperatively and 45 healthy volunteers (HVs), and subjected to metabolomics analysis by GC-MS. Differential metabolites in the preoperative RC and CC samples and HVs were identified as potential biomarkers and evaluated for their utilities by receiver operating characteristic analyses.
RESULTS: The different metabolic markers between CC and RC patients were identified, which may assist in distinguishing the two types of cancers. The area under the curve (AUC) was 0.805 for combination of d-glucose and d-mannose for CC diagnosis, and 0.889 for combination of 2-aminobutanoic acid, 3-hydroxypyridine, d-glucose, d-mannose, isoleucine, l-tryptophan, urea, and uric acid for RC diagnosis. The combinations of metabolite markers showed a better predictability than CEA and CA199 two commonly used protein markers for CRC diagnosis in clinical practice. Combining the metabolite markers with these two protein markers effectively improved the diagnostic accuracy with the AUC reaching 0.936 and 0.937 for CC and RC diagnosis, respectively.
CONCLUSIONS: Metabolic profiles are different in the blood samples between CC and RC patients. The study has established a panel of metabolic markers as a predictive and multiplexing signature for CC and RC diagnosis.

Keywords:  biomarker; colon cancer; diagnosis; metabolomics; rectal cancer

DOI:  https://doi.org/10.1002/jcla.23333
Cancer Cell. 2020 Apr 13. pii: S1535-6108(20)30152-5. [Epub ahead of print]37(4): 485-495

Liquid Biopsy-Based Biomarkers of Treatment Response and Resistance.

Elaine Kilgour, Dominic G Rothwell, Ged Brady, Caroline Dive.

  Predictive biomarkers aid selection of personalized therapy targeted to molecular alterations within an individual's tumor. Patients' responses to targeted therapies are commonly followed by treatment resistance. Here, we survey liquid biopsies as alternatives to tumor biopsies to assess predictive and therapy response biomarkers. We examine the potential of liquid biopsies to meet the challenges of minimal residual disease monitoring after curative intent treatment for earlier detection of disease recurrence. We focus on blood, the most commonly collected minimally invasive clinical sample, and on the two most widely studied assays, circulating tumor DNA and circulating tumor cells.

Keywords:  circulating tumor DNA; circulating tumor cells; liquid biopsy; minimal residual disease monitoring; personalized cancer medicine; predictive biomarkers; sensitivity and specificity; targeted and immunotherapy; treatment resistance; treatment response biomarkers

DOI:  https://doi.org/10.1016/j.ccell.2020.03.012
Nat Commun. 2020 Apr 14. 11(1): 1792

Selective inhibition of cancer cell self-renewal through a Quisinostat-histone H1.0 axis.

Cristina Morales Torres, Mary Y Wu, Sebastijan Hobor, Elanor N Wainwright, Matthew J Martin, Harshil Patel, William Grey, Eva Grönroos, Steven Howell, Joana Carvalho, Ambrosius P Snijders, Michael Bustin, Dominique Bonnet, Paul D Smith, Charles Swanton, Michael Howell, Paola Scaffidi.

Continuous cancer growth is driven by subsets of self-renewing malignant cells. Targeting of uncontrolled self-renewal through inhibition of stem cell-related signaling pathways has proven challenging. Here, we show that cancer cells can be selectively deprived of self-renewal ability by interfering with their epigenetic state. Re-expression of histone H1.0, a tumor-suppressive factor that inhibits cancer cell self-renewal in many cancer types, can be broadly induced by the clinically well-tolerated compound Quisinostat. Through H1.0, Quisinostat inhibits cancer cell self-renewal and halts tumor maintenance without affecting normal stem cell function. Quisinostat also hinders expansion of cells surviving targeted therapy, independently of the cancer types and the resistance mechanism, and inhibits disease relapse in mouse models of lung cancer. Our results identify H1.0 as a major mediator of Quisinostat's antitumor effect and suggest that sequential administration of targeted therapy and Quisinostat may be a broadly applicable strategy to induce a prolonged response in patients.

DOI: https://doi.org/10.1038/s41467-020-15615-z
Anal Chem. 2020 Apr 14.

Ozonization of tissue sections for MALDI MS imaging of carbon-carbon double bond positional isomers of phospholipids.

Antonín Bednařík, Jan Preisler, Dominika Bezdeková, Markéta Machálková, Michal Hendrych, Jarmila Navratilova, Lucia Knopfová, Eugene Moskovets, Jens Soltwisch, Klaus Dreisewerd.

Visualizing the differential distribution of carbon-carbon double bond (C=C db) positional isomers of unsaturated phospholipids (PL) in tissue sections by use of refined matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) technologies offers a high promise to deeper understand PL metabolism and isomer-specific functions in health and disease. Here we introduce an on-tissue ozonization protocol that enables a particular straightforward derivatization of unsaturated lipids in tissue sections. Collision-induced dissociation (CID) of MALDI-generated ozonide ions (with yields in the several ten percent range) produced the Criegee fragment ion pairs, which are indicative of C=C db position(s). We used our technique for visualizing the differential distribution of 9 and 11 isomers of phosphatidylcholines in mouse brain and in human colon samples with the desorption laser spot size 15 µm emphasizing the potential of the technique to expose local isomer-specific metabolism of PLs.

DOI: https://doi.org/10.1021/acs.analchem.0c00641
Curr Clin Pharmacol. 2020 Apr 13.

Warburg effects on cancer cells survival: the role of sugar starvation in cancer therapy.

Wissam Zam, Imtissal Ahmed, Haneen Yousef.

   BACKGROUND: Cancer is not just one disease; it is a group of diseases either genetic or metabolic due to the malfunction of mitochondria. Thus metabolic pathways are reprogrammed to satisfy tumor cell proliferation and survival requirements.
METHODS: We undertook a structured search of bibliographic databases for peer-reviewed research literature dealing with these metabolic pathways.
RESULTS: It was found that cancer cells prefer fermentation as a source of energy even in the presence of oxygen, this altered metabolism of cancer cells may confer a selective advantage for survival and proliferation according to Warburg effect. Furthermore, some molecules like HIF, PKM2, NADPH and others are essential to the survival of cancer cells into the hypoxic abnormal environment which has limited glucose sources.
CONCLUSION: As cancer cells use glucose for aerobic glycolysis as a preferred substrate for energy yielding metabolism, we discuss in this review the Warburg effect and a strategy of starving cancer from glucose to prevent cancer cell survival and induce apoptosis in various types of cancer which could be the key to future treatment.

Keywords:  Aerobic glycolysis; Warburg effect; apoptosis; cancer cells; glucose starvation; hypoxic environment

DOI:  https://doi.org/10.2174/1574884715666200413121756
Biomed Chromatogr. 2020 Apr 17. e4854

Validation of a simplified procedure for convenient and rapid quantification of reduced and oxidized glutathione in human plasma by liquid chromatography tandem mass spectrometry analysis.

Addison C Enomoto, Erik Schneider, Toni McKinnon, Howard Goldfine, Mark A Levy.

  Endogenous glutathione (GSH) and glutathione disulfide (GSSG) status are highly sensitive to oxidative conditions and have wide applications as surrogate indicators of redox status in vivo. Established methods for GSH and GSSG quantification in whole blood display limited utility in human plasma, where GSH and GSSG levels are ~3-4 orders of magnitude below that observed in whole blood. This study presents simplified sample processing and analytical LC-MS/MS approaches exhibiting the sensitivity and accuracy required to measure GSH and GSSG concentrations in human plasma samples, which after 5-fold dilution to suppress matrix interferences, range from 200-500 nM (GSH) and 5-30 nM (GSSG). The utility of methods reported herein are evidenced by assay performance and validation parameters which indicate notable sensitivity (LLOQs of 4.99 nM (GSH) and 3.65 nM (GSSG)), high assay precision (intra-assay CVs 3.6% and 1.9%, and inter-assay CVs of 7.0% and 2.8% for GSH and GSSG, respectively). These methods also exhibited exceptional recovery of analyte-spiked plasma samples (98.0±7.64% for GSH and 98.5±12.7% for GSSG). Notable sample stability at -80°C was evident for GSH up to 55 weeks and GSSG up to 46 weeks, with average CVs < 15% and <10%, respectively.

Keywords:  GSH; GSSG; clinical analysis; glutathione; sample processing

DOI:  https://doi.org/10.1002/bmc.4854
Cancer Lett. 2020 Apr 11. pii: S0304-3835(20)30186-5. [Epub ahead of print]

Extracellular Vesicle-Mediated Nucleic Acid Transfer And Reprogramming In The Tumor Microenvironment.

Neha N Parayath, Smrithi Padmakumar, Mansoor M Amiji.

  Extracellular vesicles (EVs) have garnered much attention as key mediators of intercellular communication within the tumor microenvironment (TME) as well as at distinct metastatic sites. Nucleic acid molecules are the important components of the EV cargo. Characterizing EVs and strategies for modulating the nucleic acid content to promote anti-tumoral functions has led to the emerging role of EVs as potential novel targets for cancer therapy. Recent approaches of engineering the EVs to reach targeted sites have bought this to the forefront for nucleic acid delivery. In this article, we discuss EV biology with recent methods to analyze their nucleic acid contents. We emphasize the role of EV-mediated nucleic acid transfer in the TME assisting in tumor progression and metastasis and further review the strategies for modulating the nucleic acid content in EV for suppressing tumor growth and immune activation. The article further discusses the recent developments in generating EV mimics as nucleic acid delivery systems.

Keywords:  Biogenesis; EV-mimics; Exosomes; Extracellular vesicles; Reprogramming; Tumor Microenvironment

DOI:  https://doi.org/10.1016/j.canlet.2020.04.009
Cell Chem Biol. 2020 Apr 02. pii: S2451-9456(20)30110-0. [Epub ahead of print]

The Chemistry and Biology of Ferroptosis.

Brent R Stockwell, Xuejun Jiang.

  Ferroptosis is a recently described form of cell death driven by iron-dependent lipid peroxidation. This type of cell death was first observed in response to treatment of tumor cells with a small-molecule chemical probe named erastin. Most subsequent advances in understanding the mechanisms governing ferroptosis involved the use of genetic screens and small-molecule probes. We describe herein the utility and limitations of chemical probes that have been used to analyze and perturb ferroptosis, as well as mechanistic studies of ferroptosis that benefitted from the use of these probes and genetic screens. We also suggest probes for ferroptosis and highlight mechanistic questions surrounding this form of cell death that will be a high priority for exploration in the future.

Keywords:  ROS; cancer; cell death; chemical probe; cysteine; ferroptosis; glutathione; iron; lipid peroxidation; metabolism

DOI:  https://doi.org/10.1016/j.chembiol.2020.03.013
Proc Natl Acad Sci U S A. 2020 Apr 16. pii: 201918761. [Epub ahead of print]

Unbiased proteomics identifies plasminogen activator inhibitor-1 as a negative regulator of endothelial nitric oxide synthase.

Victor Garcia, Eon Joo Park, Mauro Siragusa, Florian Frohlich, Mohammad Mahfuzul Haque, Jonathan V Pascale, Katherine R Heberlein, Brant E Isakson, Dennis J Stuehr, William C Sessa.

  Nitric oxide (NO) produced by endothelial nitric oxide synthase (eNOS) is a critical mediator of vascular function. eNOS is tightly regulated at various levels, including transcription, co- and posttranslational modifications, and by various protein-protein interactions. Using stable isotope labeling with amino acids in cell culture (SILAC) and mass spectrometry (MS), we identified several eNOS interactors, including the protein plasminogen activator inhibitor-1 (PAI-1). In cultured human umbilical vein endothelial cells (HUVECs), PAI-1 and eNOS colocalize and proximity ligation assays demonstrate a protein-protein interaction between PAI-1 and eNOS. Knockdown of PAI-1 or eNOS eliminates the proximity ligation assay (PLA) signal in endothelial cells. Overexpression of eNOS and HA-tagged PAI-1 in COS7 cells confirmed the colocalization observations in HUVECs. Furthermore, the source of intracellular PAI-1 interacting with eNOS was shown to be endocytosis derived. The interaction between PAI-1 and eNOS is a direct interaction as supported in experiments with purified proteins. Moreover, PAI-1 directly inhibits eNOS activity, reducing NO synthesis, and the knockdown or antagonism of PAI-1 increases NO bioavailability. Taken together, these findings place PAI-1 as a negative regulator of eNOS and disruptions in eNOS-PAI-1 binding promote increases in NO production and enhance vasodilation in vivo.

Keywords:  PAI-1; eNOS; endothelial cell; fibrosis; vascular function

DOI:  https://doi.org/10.1073/pnas.1918761117
J Lipid Res. 2020 Apr 15. pii: jlr.P119000543. [Epub ahead of print]

LDL subclass lipidomics in atherogenic dyslipidemia:Effect of statin therapy on bioactive lipids and dense LDL.

M John Chapman, Alexina Orsoni, Ricardo Tan, Natalie A Mellett, Anh Nguyen, Paul Robillard, Philippe Giral, Patrice Therond, Peter J Meikle.

  Atherogenic LDL particles are physicochemically and metabolically heterogeneous. Can bioactive lipid cargo differentiate LDL subclasses, and thus potential atherogenicity? What is the effect of statin treatment? Obese, hypertriglyceridemic, hypercholesterolemic males (n=12; Lp(a) <10 mg/dL) received pitavastatin calcium (4mg/day) for 180 days in a single-phase, unblinded study. The lipidomic profiles (23 lipid classes) of five LDL subclasses fractionated from baseline and post-statin plasmas were determined by LC-MS. At baseline and on statin treatment, very small dense LDL (LDL5) was preferentially enriched (up to 3-fold) in specific lysophospholipids (lysophosphatidylcholine (LPC); lysophosphatidylinositol (LPI); lyso-platelet activating factor (LPC(O)); 9,0.2 and 0.14 mol/mol apoB respectively; all p<0.001 versus LDL1-4), suggesting elevated inflammatory potential per particle. In contrast, lysophosphatidylethanolamine was uniformly distributed among LDL subclasses. Statin treatment markedly reduced absolute plasma concentrations of all LDL subclasses (up to 33.5%), including LPC, LPI and LPC(O) contents (up to -52%), consistent with reduction in cardiovascular risk. Despite such reductions, lipotoxic ceramide load per particle in LDL1-5 (1.5 - 3 mol/mol apoB; 3 - 7 mmol/mol phosphatidylcholine) was either conserved or elevated. Bioactive lipids may constitute biomarkers for the cardiometabolic risk associated with specific LDL subclasses in atherogenic dyslipidemia at baseline, and with residual risk on statin therapy.

Keywords:  Atherosclerosis; Ceramides; Cholesterol/Metabolism; Drug therapy/Hypolipidemic drugs; Dyslipidemias; Inflammation; LDL; Lipidomics; Lysophospholipid; Mass spectrometry; atherogenic dsylipidemia; lysophosphatidylcholine; lysophosphatidylinositol; metabolic syndrome; pitavastatin calcium

DOI:  https://doi.org/10.1194/jlr.P119000543