bims-mascan 2021-04-11 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2021–04–11
twenty-one papers selected by
Giovanny Rodriguez Blanco, University of Edinburgh

Immune-regulated IDO1-dependent tryptophan metabolism is source of one-carbon units for pancreatic cancer and stellate cells.
Metabolomics Signatures of Aging: Recent Advances.
Cell Metabolism and DNA Repair Pathways: Implications for Cancer Therapy.
Robust and Comprehensive Targeted Metabolomics Method for Quantification of 50 Different Primary, Secondary, and Sulfated Bile Acids in Multiple Biological Species (Human, Monkey, Rabbit, Dog, and Rat) and Matrices (Plasma and Urine) Using Liquid Chromatography High Resolution Mass Spectrometry (LC-HRMS) Analysis.
Oxylipin biosynthesis reinforces cellular senescence and allows detection of senolysis.
Serum lipid profiling analysis and potential marker discovery for ovarian cancer based on liquid chromatography-Mass spectrometry.
Spectral prediction features as a solution for the search space size problem in proteogenomics.
Untargeted Stable Isotope Probing of the Gut Microbiota Metabolome Using 13C-Labeled Dietary Fibers.
Hypoxia drives murine neutrophil protein scavenging to maintain central carbon metabolism.
Breast Cancer Brain Metastases Rely on FASN-Mediated Lipid Biosynthesis.
Direct Analysis from Phase-Separated Liquid Samples using ADE-OPI-MS: Applicability to High-Throughput Screening for Inhibitors of Diacylglycerol Acyltransferase 2.
Metabotype analysis of Mthfd1l-null mouse embryos using desorption electrospray ionization mass spectrometry imaging.
An Integrative Proteomics and Metabolomics Analysis Reveals Metabolic Phenotype in Mice with Cardiac-specific Deletion of Natriuretic Peptide Receptor A.
Coordination of asparagine uptake and asparagine synthetase expression modulates CD8+ T cell activation.
Genome Scale-Differential Flux Analysis reveals deregulation of lung cell metabolism on SARS-CoV-2 infection.
Towards low false discovery rate estimation for protein-protein interactions detected by chemical cross-linking.
UHPLC-MS/HRMS method for the quantitation of pyrithione metabolites in human urine.
mzRAPP - A tool for reliability assessment of data pre-processing in non-targeted metabolomics.
There is detectable variation in the lipidomic profile between stable and progressive patients with idiopathic pulmonary fibrosis (IPF).
The Application of Mass Spectrometry in Drug Metabolism and Pharmacokinetics.
Anticancer potential of small molecule inhibitors of fatty acid amide hydrolase and monoacylglycerol lipase - A mini-review.

Mol Cell. 2021 Apr 04. pii: S1097-2765(21)00214-8. [Epub ahead of print]

Immune-regulated IDO1-dependent tryptophan metabolism is source of one-carbon units for pancreatic cancer and stellate cells.

Alice Clare Newman, Mattia Falcone, Alejandro Huerta Uribe, Tong Zhang, Dimitris Athineos, Matthias Pietzke, Alexei Vazquez, Karen Blyth, Oliver David Kenneth Maddocks.

  Cancer cells adapt their metabolism to support elevated energetic and anabolic demands of proliferation. Folate-dependent one-carbon metabolism is a critical metabolic process underpinning cellular proliferation supplying carbons for the synthesis of nucleotides incorporated into DNA and RNA. Recent research has focused on the nutrients that supply one-carbons to the folate cycle, particularly serine. Tryptophan is a theoretical source of one-carbon units through metabolism by IDO1, an enzyme intensively investigated in the context of tumor immune evasion. Using in vitro and in vivo pancreatic cancer models, we show that IDO1 expression is highly context dependent, influenced by attachment-independent growth and the canonical activator IFNγ. In IDO1-expressing cancer cells, tryptophan is a bona fide one-carbon donor for purine nucleotide synthesis in vitro and in vivo. Furthermore, we show that cancer cells release tryptophan-derived formate, which can be used by pancreatic stellate cells to support purine nucleotide synthesis.

Keywords:  IDO1; IFNγ; PDAC; cancer immunology; cancer metabolism; epacadostat; formate; immunometabolism; immunotherapy; one-carbon metabolism; pancreas; serine; stellate cells; tryptophan; tumor microenvironment

DOI:  https://doi.org/10.1016/j.molcel.2021.03.019
Aging Dis. 2021 Apr;12(2): 646-661

Metabolomics Signatures of Aging: Recent Advances.

Sunil S Adav, Yulan Wang.

  Metabolomics is the latest state-of-the-art omics technology that provides a comprehensive quantitative profile of metabolites. The metabolites are the cellular end products of metabolic reactions that explain the ultimate response to genomic, transcriptomic, proteomic, or environmental changes. Aging is a natural inevitable process characterized by a time-dependent decline of various physiological and metabolic functions and are dominated collectively by genetics, proteomics, metabolomics, environmental factors, diet, and lifestyle. The precise mechanism of the aging process is unclear, but the metabolomics has the potential to add significant insight by providing a detailed metabolite profile and altered metabolomic functions with age. Although the application of metabolomics to aging research is still relatively new, extensive attempts have been made to understand the biology of aging through a quantitative metabolite profile. This review summarises recent developments and up-to-date information on metabolomics studies in aging research with a major emphasis on aging biomarkers in less invasive biofluids. The importance of an integrative approach that combines multi-omics data to understand the complex aging process is discussed. Despite various innovations in metabolomics and metabolite associated with redox homeostasis, central energy pathways, lipid metabolism, and amino acid, a major challenge remains to provide conclusive aging biomarkers.

Keywords:  aging; amino acids; lipids; mass spectrometry; metabolites; metabolomics

DOI:  https://doi.org/10.14336/AD.2020.0909
Front Cell Dev Biol. 2021 ;9 633305

Cell Metabolism and DNA Repair Pathways: Implications for Cancer Therapy.

Thais Sobanski, Maddison Rose, Amila Suraweera, Kenneth O'Byrne, Derek J Richard, Emma Bolderson.

  DNA repair and metabolic pathways are vital to maintain cellular homeostasis in normal human cells. Both of these pathways, however, undergo extensive changes during tumorigenesis, including modifications that promote rapid growth, genetic heterogeneity, and survival. While these two areas of research have remained relatively distinct, there is growing evidence that the pathways are interdependent and intrinsically linked. Therapeutic interventions that target metabolism or DNA repair systems have entered clinical practice in recent years, highlighting the potential of targeting these pathways in cancer. Further exploration of the links between metabolic and DNA repair pathways may open new therapeutic avenues in the future. Here, we discuss the dependence of DNA repair processes upon cellular metabolism; including the production of nucleotides required for repair, the necessity of metabolic pathways for the chromatin remodeling required for DNA repair, and the ways in which metabolism itself can induce and prevent DNA damage. We will also discuss the roles of metabolic proteins in DNA repair and, conversely, how DNA repair proteins can impact upon cell metabolism. Finally, we will discuss how further research may open therapeutic avenues in the treatment of cancer.

Keywords:  DNA repair; cell metabolism; glycolysis; homologous recombination; non-homologous end-joining; tumor metabolic reprogramming; warburg effect

DOI:  https://doi.org/10.3389/fcell.2021.633305
J Am Soc Mass Spectrom. 2021 Apr 07.

Robust and Comprehensive Targeted Metabolomics Method for Quantification of 50 Different Primary, Secondary, and Sulfated Bile Acids in Multiple Biological Species (Human, Monkey, Rabbit, Dog, and Rat) and Matrices (Plasma and Urine) Using Liquid Chromatography High Resolution Mass Spectrometry (LC-HRMS) Analysis.

Dewakar Sangaraju, Yao Shi, Michael Van Parys, Adam Ray, Abigail Walker, Rachel Caminiti, Dennis Milanowski, Allan Jaochico, Brian Dean, Xiaorong Liang.

Bile acids (BAs) are biomolecules synthesized in the liver from cholesterol and are constituents of bile. The in-vivo BA pool includes more than 50 known diverse BAs which are unconjugated, amino acid conjugated, sulfated, and glucuronidated metabolites. Hemostasis of bile acids is known to be highly regulated and an interplay between liver metabolism, gut microbiome function, intestinal absorption, and enterohepatic recirculation. Interruption of BA homeostasis has been attributed to several metabolic diseases and drug induced liver injury (DILI), and their use as potential biomarkers is increasingly becoming important. Speciated quantitative and comprehensive profiling of BAs in various biomatrices from humans and preclinical animal species are important to understand their significance and biological function. Consequently, a versatile one single bioanalytical method for BAs is required to accommodate quantitation in a broad range of biomatrices from human and preclinical animal species. Here we report a versatile, comprehensive, and high throughput liquid chromatography-high resolution mass spectrometry (LC-HRMS) targeted metabolomics method for quantitative analysis of 50 different BAs in multiple matrices including human serum, plasma, and urine and plasma and urine of preclinical animal species (rat, rabbit, dog, and monkey). The method has been sufficiently qualified for accuracy, precision, robustness, and ruggedness and addresses the issue of nonspecific binding of bile acids to plastic for urine samples. Application of this method includes comparison for BA analysis between matched plasma and serum samples, human and animal species differences in BA pools, data analysis, and visualization of complex BA data using BA indices or ratios to understand BA biology, metabolism, and transport.

DOI: https://doi.org/10.1021/jasms.0c00435
Cell Metab. 2021 Mar 31. pii: S1550-4131(21)00115-7. [Epub ahead of print]

Oxylipin biosynthesis reinforces cellular senescence and allows detection of senolysis.

Christopher D Wiley, Rishi Sharma, Sonnet S Davis, Jose Alberto Lopez-Dominguez, Kylie P Mitchell, Samantha Wiley, Fatouma Alimirah, Dong Eun Kim, Therese Payne, Andrew Rosko, Eliezer Aimontche, Sharvari M Deshpande, Francesco Neri, Chisaka Kuehnemann, Marco Demaria, Arvind Ramanathan, Judith Campisi.

  Cellular senescence is a stress or damage response that causes a permanent proliferative arrest and secretion of numerous factors with potent biological activities. This senescence-associated secretory phenotype (SASP) has been characterized largely for secreted proteins that participate in embryogenesis, wound healing, inflammation, and many age-related pathologies. By contrast, lipid components of the SASP are understudied. We show that senescent cells activate the biosynthesis of several oxylipins that promote segments of the SASP and reinforce the proliferative arrest. Notably, senescent cells synthesize and accumulate an unstudied intracellular prostaglandin, 1a,1b-dihomo-15-deoxy-delta-12,14-prostaglandin J2. Released 15-deoxy-delta-12,14-prostaglandin J2 is a biomarker of senolysis in culture and in vivo. This and other prostaglandin D2-related lipids promote the senescence arrest and SASP by activating RAS signaling. These data identify an important aspect of cellular senescence and a method to detect senolysis.

Keywords:  15d-PGJ2; RAS; SASP; aging; biomarker; cellular senescence; dihomo-prostaglandin; eicosanoid; lipids; mass spectrometry; metabolomics; oxylipin; prostaglandin; senescence

DOI:  https://doi.org/10.1016/j.cmet.2021.03.008
J Pharm Biomed Anal. 2021 Mar 26. pii: S0731-7085(21)00160-6. [Epub ahead of print]199 114048

Serum lipid profiling analysis and potential marker discovery for ovarian cancer based on liquid chromatography-Mass spectrometry.

Yuting Wang, Yisheng Wang, Chen Chen, Fang Ren, Rui Cao, Yuefei Wang, Pin Han, Xiaoyan Zhang, Congjian Xu, Xinyu Liu, Guowang Xu.

  Low early diagnosis rate and unclear pathogenesis are the primary reasons for the high mortality of epithelial ovarian cancer (EOC). Lipidomics is a powerful tool for marker discovery and mechanism explanation. Hence, a ultra high-performance liquid chromatography-mass spectrometry based non-targeted lipidomics analysis was performed to acquire lipid profiling of 153 serum samples including healthy control (HC, n = 50), benign ovarian tumor (BOT, n = 41), and EOC (n = 62) to reveal lipid disturbance, then differential lipids were verified in another sample set including 187 sera. Significant lipid disturbance occurred in BOT and EOC, fatty acid, lyso-phosphatidylcholine, and lyso-phosphatidylethanolamine were observed to be increased in BOT and EOC subjects, while phosphatidylcoline, ether phosphatidylcoline (PC-O), ether phosphatidylethanolamine (PE-O), and sphingomyelin significantly decreased. Compared with BOT, PC-Os and PE-Os presented a greater reduction in EOC, and serum ceramide increased only in EOC. Moreover, potential markers consisting of 4 lipids were defined and validated for EOC diagnosis. High areas under the curve (0.854∼0.865 and 0.903∼0.923 for distinguishing EOC and early EOC from non-cancer, respectively) as well as good specificity and sensitivity were obtained. This study not only revealed the characteristics of lipid metabolism in EOC, but also provided a potential marker pattern for aiding EOC diagnosis.

Keywords:  Lipidomics; Liquid chromatography – mass spectrometry; Marker discovery; Ovarian cancer

DOI:  https://doi.org/10.1016/j.jpba.2021.114048
Mol Cell Proteomics. 2021 Apr 03. pii: S1535-9476(21)00049-9. [Epub ahead of print] 100076

Spectral prediction features as a solution for the search space size problem in proteogenomics.

Steven Verbruggen, Siegfried Gessulat, Ralf Gabriels, Anna Matsaroki, Hendrik Van de Voorde, Bernhard Kuster, Sven Degroeve, Lennart Martens, Wim Van Criekinge, Mathias Wilhelm, Gerben Menschaert.

  Proteogenomics approaches often struggle with the distinction between true and false peptide-to-spectrum matches as the database size enlarges. However, features extracted from tandem mass spectrometry intensity predictors can enhance the peptide identification rate and can provide extra confidence for peptide-to-spectrum matching in a proteogenomics context. To that end, features from the spectral intensity pattern predictors MS2PIP and Prosit were combined with the canonical scores from MaxQuant in the Percolator post-processing tool for protein sequence databases constructed out of ribosome profiling and nanopore RNA-seq analyses. The presented results provide evidence that this approach enhances both the identification rate as well as the validation stringency in a proteogenomic setting.

Keywords:  MS(2)PIP; PROTEOFORMER; Percolator; Prosit; RNA-seq; deep learning; intensity features; machine learning; nanopore sequencing; proteoform; proteogenomics; random forest; ribosome profiling; spectrum predictor

DOI:  https://doi.org/10.1016/j.mcpro.2021.100076
J Proteome Res. 2021 Apr 08.

Untargeted Stable Isotope Probing of the Gut Microbiota Metabolome Using 13C-Labeled Dietary Fibers.

Pan Deng, Taylor Valentino, Michael D Flythe, Hunter N B Moseley, Jacqueline R Leachman, Andrew J Morris, Bernhard Hennig.

  The gut microbiome generates numerous metabolites that exert local effects and enter the circulation to affect the functions of many organs. Despite extensive sequencing-based characterization of the gut microbiome, there remains a lack of understanding of microbial metabolism. Here, we developed an untargeted stable isotope-resolved metabolomics (SIRM) approach for the holistic study of gut microbial metabolites. Viable microbial cells were extracted from fresh mice feces and incubated anaerobically with 13C-labeled dietary fibers including inulin or cellulose. High-resolution mass spectrometry was used to monitor 13C enrichment in metabolites associated with glycolysis, the Krebs cycle, the pentose phosphate pathway, nucleotide synthesis, and pyruvate catabolism in both microbial cells and the culture medium. We observed the differential use of inulin and cellulose as substrates for biosynthesis of essential and non-essential amino acids, neurotransmitters, vitamin B5, and other coenzymes. Specifically, the use of inulin for these biosynthetic pathways was markedly more efficient than the use of cellulose, reflecting distinct metabolic pathways of dietary fibers in the gut microbiome, which could be related with host effects. This technology facilitates deeper and holistic insights into the metabolic function of the gut microbiome (Metabolomic Workbench Study ID: ST001651).

Keywords:  dietary fiber; inulin; metabolite; metabolomics; microbiome; stable isotope

DOI:  https://doi.org/10.1021/acs.jproteome.1c00124
J Clin Invest. 2021 Apr 06. pii: 134073. [Epub ahead of print]

Hypoxia drives murine neutrophil protein scavenging to maintain central carbon metabolism.

Emily R Watts, Andrew Jm Howden, Tyler Morrison, Pranvera Sadiku, Jens L Hukelmann, Alex von Kriegsheim, Bart Ghesquière, Fiona Murphy, Ananda S Mirchandani, Duncan C Humphries, Robert Grecian, Eilise M Ryan, Patricia Coelho, Giovanny Rodriguez-Blanco, Tracie M Plant, Rebecca S Dickinson, Andrew J Finch, Wesley Vermaelen, Doreen A Cantrell, Moira Kb Whyte, Sarah R Walmsley.

  Limiting dysfunctional neutrophilic inflammation whilst preserving effective immunity requires a better understanding of the processes that dictate neutrophil function in the tissues. Quantitative mass-spectrometry identified how inflammatory murine neutrophils regulated expression of cell surface receptors, signal transduction networks and metabolic machinery to shape neutrophil phenotypes in response to hypoxia. Through the tracing of labelled amino acids into metabolic enzymes, pro-inflammatory mediators and granule proteins we demonstrated that ongoing protein synthesis shapes the neutrophil proteome. To maintain energy supplies in the tissues, neutrophils consumed extracellular proteins to fuel central carbon metabolism. The physiological stresses of hypoxia and hypoglycaemia, characteristic of inflamed tissues, promoted this extra-cellular protein scavenging with activation of the lysosomal compartment further driving exploitation of the protein rich inflammatory milieu. This study provides a comprehensive map of neutrophil proteomes, analysis of which has led to the identification of active catabolic and anabolic pathways which enable neutrophils to sustain synthetic and effector functions in the tissues.

Keywords:  Hypoxia; Inflammation; Metabolism; Neutrophils; Proteomics

DOI:  https://doi.org/10.1172/JCI134073
Cancer Discov. 2021 Apr 09.

Breast Cancer Brain Metastases Rely on FASN-Mediated Lipid Biosynthesis.

Brain metastatic breast tumors depended on lipids produced by fatty acid synthase (FASN) for survival.

DOI: https://doi.org/10.1158/2159-8290.CD-RW2021-051
Anal Chem. 2021 Apr 05.

Direct Analysis from Phase-Separated Liquid Samples using ADE-OPI-MS: Applicability to High-Throughput Screening for Inhibitors of Diacylglycerol Acyltransferase 2.

Xiujuan Wen, Chang Liu, Lucien Ghislain, Kiersten Tovar, Vinit Shah, Steven J Stout, Steven Cifelli, Santhosh Satapati, Gregory O'Donnell, Payal R Sheth, Mary Jo Wildey, Sammy S Datwani, Thomas R Covey, Kevin P Bateman, David G McLaren.

The primary goal of high-throughput screening (HTS) is to rapidly survey a broad collection of compounds, numbering from tens of thousands to millions of members, and identify those that modulate the activity of a therapeutic target of interest. For nearly two decades, mass spectrometry has been used as a label-free, direct-detection method for HTS and is widely acknowledged as being less susceptible to interferences than traditional optical techniques. Despite these advantages, the throughput of conventional MS-based platforms like RapidFire or parallel LC-MS, which typically acquire data at speeds of 6-30 s/sample, can still be limiting for large HTS campaigns. To overcome this bottleneck, the field has recently turned to chromatography-free approaches including MALDI-TOF-MS and acoustic droplet ejection-MS, both of which are capable of throughputs of 1 sample/second or faster. In keeping with these advances, we report here on our own characterization of an acoustic droplet ejection, open port interface (ADE-OPI)-MS system as a platform for HTS using the membrane-associated, lipid metabolizing enzyme diacylglycerol acyltransferase 2 (DGAT2) as a model system. We demonstrate for the first time that the platform is capable of ejecting droplets from phase-separated samples, allowing direct coupling of liquid-liquid extraction with OPI-MS analysis. By applying the platform to screen a 6400-member library, we further demonstrate that the ADE-OPI-MS assay is suitable for HTS and also performs comparably to LC-MS, but with an efficiency gain of >20-fold.

DOI: https://doi.org/10.1021/acs.analchem.0c04312
Anal Bioanal Chem. 2021 Apr 08.

Metabotype analysis of Mthfd1l-null mouse embryos using desorption electrospray ionization mass spectrometry imaging.

Amanda Vaughn, Rachel J DeHoog, Livia S Eberlin, Dean R Appling.

  Mammalian folate-dependent one-carbon (1C) metabolism provides the building blocks essential during development via amino acid interconversion, methyl-donor production, regeneration of redox factors, and de novo purine and thymidylate synthesis. Folate supplementation prevents many neural tube defects (NTDs) that occur during the embryonic process of neurulation. The mechanism by which folate functions during neurulation is not well understood, and not all NTDs are preventable by folate supplementation. Mthfd1l is a mitochondrial 1C metabolism enzyme that produces formate, a 1C donor that fuels biosynthesis and the methyl cycle in the cytoplasm. Homozygous deletion of the Mthfd1l gene in mice (Mthfd1lz/z) causes embryonic lethality, developmental delay, and folate-resistant NTDs. These mice also have defects in cranial mesenchyme formation. In this work, mass spectrometry imaging was used to obtain ion maps of the cranial mesenchyme that identified the spatial distribution and relative abundance of metabolites in wild-type and Mthfd1lz/z embryos. The relative abundances of purine and thymidylate derivatives, as well as amino acids, were diminished in the cranial mesenchyme of Mthfd1lz/z embryos. Loss of Mthfd1l activity in this region also led to abnormal levels of methionine and dysregulated energy metabolism. These alterations in metabolism suggest possible approaches to preventing NTDs in humans.

Keywords:  DESI; Folate; Imaging mass spectrometry; Metabolomics; Mitochondrial metabolism; Mthfd1l

DOI:  https://doi.org/10.1007/s00216-021-03308-5
Mol Cell Proteomics. 2021 Mar 31. pii: S1535-9476(21)00045-1. [Epub ahead of print] 100072

An Integrative Proteomics and Metabolomics Analysis Reveals Metabolic Phenotype in Mice with Cardiac-specific Deletion of Natriuretic Peptide Receptor A.

Pan Chang, Yan Niu, Xiaomeng Zhang, Jing Zhang, Xihui Wang, Xi Shen, Baoying Chen, Jun Yu.

  Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are important biological markers and cardiac function regulators. Natriuretic peptide receptor A (NPRA) binds to an ANP or BNP ligand and induces transmembrane signal transduction by elevating the intracellular cyclic guanosine monophosphate (cGMP) levels. However, the metabolic phenotype and related mechanisms induced by NPRA deletion remain ambiguous. Here, we constructed myocardial-specific NPRA deletion mice and detected the heart functional and morphological characteristics by histological analysis and explored the altered metabolic pattern and the expression patterns of proteins by liquid chromatography-mass spectrometry (LC-MS)-based omics technology, 20 replicates of two groups for metabolomics and 10 for proteomics. NPRA deficiency unexpectedly did not result in significant cardiac remodelling or dysfunction. However, compared with the matched littermates, NPRA-deficient mice had significant metabolic differences. Metabolomic results showed that the metabolite levels varied in cardiac tissues and plasma. In total, 33 metabolites were identified in cardiac tissues and 54 were identified in plasma. Compared to control mice, NPRA-deficient mice had 20 upregulated and 6 downregulated metabolites in cardiac tissues and 25 upregulated and 23 downregulated metabolites in plasma. Together, NPRA deficiency resulted in increased nucleotide biosynthesis and histidine metabolism only in heart tissues and decreased creatine metabolism only in plasma. Further proteomic analysis identified 136 differentially abundant proteins in cardiac tissues, including 54 proteins with higer anundance and 82 proteins with lower abundance. Among them, Cytochrome c oxidase subunit 7c and 7b (Cox7c, Cox7b), ATP synthase, H+ transporting, mitochondrial Fo complex subunit F2 (ATP5J2), Ubiquinol-cytochrome c reductase, complex III subunit X (Uqcr10) and Myosin Heavy Chain 7 (Myh7) were mainly involved in related metabolic pathways. These results revealed the essential role of NPRA in metabolic profiles and may elucidate new underlying pathophysiological mechanisms of NPRA in cardiovascular diseases.

Keywords:  Metabolism; Myocardium; NPRA; Natriuretic peptides; Proteome

DOI:  https://doi.org/10.1016/j.mcpro.2021.100072
JCI Insight. 2021 Apr 06. pii: 137761. [Epub ahead of print]

Coordination of asparagine uptake and asparagine synthetase expression modulates CD8+ T cell activation.

Helen Carrasco Hope, Rebecca J Brownlie, Christopher M Fife, Lynette Steele, Mihaela Lorger, Robert J Salmond.

  T cell receptor (TCR) triggering by antigen results in metabolic reprogramming that, in turn, facilitates T cells' exit from quiescence. The increased nutrient requirements of activated lymphocytes are met in part by upregulation of cell surface transporters and enhanced uptake of amino acids, fatty acids and glucose from the environment. However, the role of intracellular pathways of amino acid biosynthesis in T cell activation is relatively unexplored. Asparagine (Asn) is a non-essential amino acid that can be synthesized intracellularly through the glutamine-hydrolyzing enzyme asparagine synthetase (ASNS). We set out to define the requirements for uptake of extracellular Asn and ASNS activity in CD8+ T cell activation. At early timepoints of activation in vitro, CD8+ T cells expressed little or no ASNS and, as a consequence, viability and TCR-stimulated growth, activation and metabolic reprogramming were substantially impaired under conditions of Asn deprivation. At later timepoints (>24h of activation), TCR-induced mTOR-dependent signals resulted in upregulation of ASNS, that endowed CD8+ T cells with the capacity to function independently of extracellular Asn. Thus, our data suggest that the coordinated upregulation of ASNS expression and uptake of extracellular Asn is involved in optimal T cell effector responses.

Keywords:  Amino acid metabolism; Immunology; T cells

DOI:  https://doi.org/10.1172/jci.insight.137761
PLoS Comput Biol. 2021 Apr;17(4): e1008860

Genome Scale-Differential Flux Analysis reveals deregulation of lung cell metabolism on SARS-CoV-2 infection.

Piyush Nanda, Amit Ghosh.

The COVID-19 pandemic is posing an unprecedented threat to the whole world. In this regard, it is absolutely imperative to understand the mechanism of metabolic reprogramming of host human cells by SARS-CoV-2. A better understanding of the metabolic alterations would aid in design of better therapeutics to deal with COVID-19 pandemic. We developed an integrated genome-scale metabolic model of normal human bronchial epithelial cells (NHBE) infected with SARS-CoV-2 using gene-expression and macromolecular make-up of the virus. The reconstructed model predicts growth rates of the virus in high agreement with the experimental measured values. Furthermore, we report a method for conducting genome-scale differential flux analysis (GS-DFA) in context-specific metabolic models. We apply the method to the context-specific model and identify severely affected metabolic modules predominantly comprising of lipid metabolism. We conduct an integrated analysis of the flux-altered reactions, host-virus protein-protein interaction network and phospho-proteomics data to understand the mechanism of flux alteration in host cells. We show that several enzymes driving the altered reactions inferred by our method to be directly interacting with viral proteins and also undergoing differential phosphorylation under diseased state. In case of SARS-CoV-2 infection, lipid metabolism particularly fatty acid oxidation, cholesterol biosynthesis and beta-oxidation cycle along with arachidonic acid metabolism are predicted to be most affected which confirms with clinical metabolomics studies. GS-DFA can be applied to existing repertoire of high-throughput proteomic or transcriptomic data in diseased condition to understand metabolic deregulation at the level of flux.

DOI: https://doi.org/10.1371/journal.pcbi.1008860
Biochim Biophys Acta Proteins Proteom. 2021 Mar 31. pii: S1570-9639(21)00061-3. [Epub ahead of print]1869(7): 140655

Towards low false discovery rate estimation for protein-protein interactions detected by chemical cross-linking.

Luitzen de Jong, Winfried Roseboom, Gertjan Kramer.

Chemical cross-linking (CX) of proteins in vivo or in cell free extracts followed by mass spectrometric (MS) identification of linked peptide pairs (CXMS) can reveal protein-protein interactions (PPIs) both at a proteome wide scale and the level of cross-linked amino acid residues. However, error estimation at the level of PPI remains challenging in large scale datasets. Here we discuss recent advances in the recognition of spurious inter-protein peptide pairs and in diminishing the FDR for these PPI-signaling cross-links, such as the use of chromatographic retention time prediction, in order to come to a more reliable reporting of PPIs.

DOI: https://doi.org/10.1016/j.bbapap.2021.140655
J Chromatogr B Analyt Technol Biomed Life Sci. 2021 Mar 04. pii: S1570-0232(21)00094-5. [Epub ahead of print]1173 122614

UHPLC-MS/HRMS method for the quantitation of pyrithione metabolites in human urine.

Ann Zoller, Kenneth Wehmeyer, Kady Krivos, Michael Karb, Peter Stoffolano, J F Nash, Guhan Balan, Lynda Behymer, Molly Seeck, Jose Brum, Yuanshu Zou, Jason Price.

  Pyrithione glucuronide (PTG) and 2-thiopyridine glucuronide (ThPG) have been reported to be the major urinary metabolites in multiple animal species following administration of zinc pyrithione (ZnPT). However, the formation of these metabolites has never been confirmed in humans. A simple and rugged ultra-high-performance liquid chromatography high resolution mass spectrometry (UHPLC-MS/HRMS) method was developed and validated for the quantification of PTG and ThPG to investigate human metabolism of pyrithione following topical application of ZnPT as a shampoo. A UHPLC-MS/HRMS method was required due to the matrix interferences that were observed with the typical industry standard HPLC/tandem mass spectrometry (LC-MS/MS) methodology based on nominal mass triple quadrupole (QQQ) platform approach. Using UPLC-MS/HRMS, both PTG and ThPG were identified in human urine following topical application of ZnPT. The presence of these human urinary metabolites of pyrithione are consistent with findings from earlier studies in multiple animal species and suggest the metabolism of pyrithione is similar amongst those mammalian species studied.

Keywords:  High resolution mass spectrometry; Pyrithione; Pyrithione glucuronide; Thiopyridine glucuronide; Urinary metabolites

DOI:  https://doi.org/10.1016/j.jchromb.2021.122614
Bioinformatics. 2021 Apr 07. pii: btab231. [Epub ahead of print]

mzRAPP - A tool for reliability assessment of data pre-processing in non-targeted metabolomics.

Yasin El Abiead, Maximilian Milford, Reza M Salek, Gunda Koellensperger.

MOTIVATION: Reliability assessment of automated pre-processing of liquid chromatography-high resolution mass spectrometry data presents a significant challenge. Here we present a tool named mzRAPP, which generates and validates a benchmark from user-supplied information and later utilises it for reliability assessment of data pre-processing. As a result, mzRAPP produces several performance metrics for different steps of the pre-processing workflow, supporting 5 of the most commonly used pre-processing tools.
AVAILABILITY: mzRAPP is implemented in R and can be downloaded from GitHub under GNU GPL v.3.0 licence. Extensive documentation, background, and examples are available at (https://github.com/YasinEl/mzRAPP).

DOI: https://doi.org/10.1093/bioinformatics/btab231
Respir Res. 2021 Apr 09. 22(1): 105

There is detectable variation in the lipidomic profile between stable and progressive patients with idiopathic pulmonary fibrosis (IPF).

Shabarinath Nambiar, Britt Clynick, Bong S How, Adam King, E Haydn Walters, Nicole S Goh, Tamera J Corte, Robert Trengove, Dino Tan, Yuben Moodley.

   BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is a chronic interstitial lung disease characterized by fibrosis and progressive loss of lung function. The pathophysiological pathways involved in IPF are not well understood. Abnormal lipid metabolism has been described in various other chronic lung diseases including asthma and chronic obstructive pulmonary disease (COPD). However, its potential role in IPF pathogenesis remains unclear.
METHODS: In this study, we used ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) to characterize lipid changes in plasma derived from IPF patients with stable and progressive disease. We further applied a data-independent acquisition (DIA) technique called SONAR, to improve the specificity of lipid identification.
RESULTS: Statistical modelling showed variable discrimination between the stable and progressive subjects, revealing differences in the detection of triglycerides (TG) and phosphatidylcholines (PC) between progressors and stable IPF groups, which was further confirmed by mass spectrometry imaging (MSI) in IPF tissue.
CONCLUSION: This is the first study to characterise lipid metabolism between stable and progressive IPF, with results suggesting disparities in the circulating lipidome with disease progression.

Keywords:  DIA; IPF; Lipids; MS; Plasma; SONAR

DOI:  https://doi.org/10.1186/s12931-021-01682-3
Adv Exp Med Biol. 2021 ;1310 533-550

The Application of Mass Spectrometry in Drug Metabolism and Pharmacokinetics.

Ji-Yoon Lee, Sang Kyum Kim, Kiho Lee, Soo Jin Oh.

  Drug metabolism and pharmacokinetics (DMPK) are fundamental in drug discovery. New chemical entities (NCEs) are typically evaluated with various in vitro and in vivo assays, which are time-consuming and labor intensive. These experiments are essential in identifying potential new drugs. Recently, mass spectrometry (MS) has played a key role in examining the drug-like properties of NCEs. Quantitative and qualitative mass spectrometry approaches are routinely utilized to obtain high-quality data in an efficient, timely, and cost-effective manner. Especially, liquid chromatography (LC) coupled with MS technology has been refined for metabolite identification (Met ID), which is critical for lead optimization. These qualitative and quantitative MS approaches and their specific utility in DMPK characterization will be described in this chapter.

Keywords:  Drug discovery; Drug metabolism; Mass spectrometry; Pharmacokinetics

DOI:  https://doi.org/10.1007/978-981-33-6064-8_20
ChemMedChem. 2021 Apr 08.

Anticancer potential of small molecule inhibitors of fatty acid amide hydrolase and monoacylglycerol lipase - A mini-review.

Shivani Jaiswal, Senthil Raja Ayyannan.

  Recently fatty acid amide hydrolase (FAAH) and monoacylglycerol lipase (MAGL) inhibitors have come in a limelight due to their anti-proliferative potential. Both FAAH and MAGL are the endocannabinoid degrading enzymes that hydrolyze several endogenous ligands, mainly anandamide (AEA) and 2-arachidonic glycerol (2-AG), which regulated the various pathophysiological condition of the body like emotion, cognition, energy balance, pain sensation, neuro-inflammation, and cancer cell proliferation. FAAH and MAGL inhibitors block the metabolism of AEA and 2-AG, and increases endogenous levels of fatty acid amides, and exert various therapeutic effects including chronic pain, metabolic disorders, psychoses, nausea and vomiting, depression, and anxiety disorders, etc. FAAH and MAGL are primarily neurotherapeutic targets but their contribution to various types of carcinomas are significant. Inhibitors of these enzymes either alone or multi-target or with supra-additive effect show the potential effect in ovarian, breast, prostate, and colorectal cancers. This review besides highlighting the role of FAAH and MAGL enzymes in cancer progression provides an update on the anti-proliferative capabilities of known and newly discovered FAAH and MAGL inhibitors and provides further directions to develop FAAH and MAGL inhibitors as new candidates for cancer therapy.

Keywords:  Fatty acid amide hydrolase; anticancer; endocannabinoids; enzyme inhibitors; monoacylglycerol lipase

DOI:  https://doi.org/10.1002/cmdc.202100120