bims-mascan 2021-03-21 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2021–03–21
twenty-two papers selected by
Giovanny Rodríguez Blanco, University of Edinburgh

A combined flow injection/reversed-phase chromatography-high-resolution mass spectrometry workflow for accurate absolute lipid quantification with 13C internal standards.
Lipid Metabolism in Cancer Cells.
Lipid Metabolism and Lipidomics Applications in Cancer Research.
Quantitative Top-Down Proteomics in Complex Samples Using Protein-Level Tandem Mass Tag Labeling.
Rewiring of purine metabolism in response to acidosis stress in glioma stem cells.
Metabolic Reprogramming in Anticancer Drug Resistance: A Focus on Amino Acids.
Direct LC-MS/MS Analysis of Extra- and Intracellular Glycerophosphoinositol in Model Cancer Cell Lines.
Gas chromatography-mass spectrometry based 18O stable isotope labeling of Krebs cycle intermediates.
Triboelectric Nanogenerator Ion Mobility-Mass Spectrometry for In-Depth Lipid Annotation.
SGK1 signaling promotes glucose metabolism and survival in extracellular matrix detached cells.
Role of Aberrant Lipid Metabolism of Cancer Stem Cells in Cancer Progression.
Applications of Lipidomics in Tumor Diagnosis and Therapy.
Lipid Metabolism in Tumor-Associated Fibroblasts.
Lipid Metabolism and Tumor Antigen Presentation.
Validation of plasma amino acid profile using UHPLC-mass spectrometer (QDa) as a screening method in a metabolic disorders reference centre: performance and accreditation concerns.
metabCombiner: Paired Untargeted LC-HRMS Metabolomics Feature Matching and Concatenation of Disparately Acquired Data Sets.
G protein-coupled receptors as potential targets for nonalcoholic fatty liver disease treatment.
Carbamate and N-Pyrimidine Mitigate Amide Hydrolysis: Structure-Based Drug Design of Tetrahydroquinoline IDO1 Inhibitors.
Mass Spectrometry-Based Steroid Profiling: Meeting Unmet Clinical Needs.
Amadori rearrangement products as potential biomarkers for inborn errors of amino-acid metabolism.
Triglyceride lowering by omega-3 fatty acids: a mechanism mediated by N-acyl taurines.
Proteomics in aging research: A roadmap to clinical, translational research.

Analyst. 2021 Mar 18.

A combined flow injection/reversed-phase chromatography-high-resolution mass spectrometry workflow for accurate absolute lipid quantification with 13C internal standards.

Harald Schoeny, Evelyn Rampler, Yasin El Abiead, Felina Hildebrand, Olivia Zach, Gerrit Hermann, Gunda Koellensperger.

We propose a fully automated novel workflow for lipidomics based on flow injection, followed by liquid chromatography-high-resolution mass spectrometry (FI/LC-HRMS). The workflow combined in-depth characterization of the lipidome achieved via reversed-phase LC-HRMS with absolute quantification by using a large number of lipid species-specific and/or retention time (RT)-matched/class-specific calibrants. The lipidome of 13C-labelled yeast (LILY) provided a large panel of cost-effective internal standards (ISTDs) covering triacylglycerols (TG), steryl esters (SE), free fatty acids (FA), diacylglycerols (DG), sterols (ST), ceramides (Cer), hexosyl ceramides (HexCer), phosphatidylglycerols (PG), phosphatidylethanolamines (PE), phosphatidic acids (PA), cardiolipins (CL), phosphatidylinositols (PI), phosphatidylserines (PS), phosphatidylcholines (PC), lysophosphatidylcholines (LPC) and lysophosphatidylethanolamines (LPE). The workflow in combination with the LILY lipid panel enables simultaneous quantification via (1) external multi-point calibration with internal standardization and (2) internal one-point calibration with LILY as a surrogate ISTD, increasing the coverage while keeping the accuracy and throughput high. Extensive measures on quality control allowed us to rank the calibration strategies and to automatically select the calibration strategy of the highest metrological order for the respective lipid species. Overall, the workflow enabled a streamlined analysis, with a limit of detection in the low femtomolar range, and provided validation tools together with absolute concentration values for >350 lipids in human plasma on a species level. Based on the selected standard panel, lipids from 7 classes (LPC, LPE, PC, PE, PI, DG, TG) passed stringent quality filters, which included QC accuracy, a precision and recovery bias of <30% and concentrations within the 99% confidence interval of the international laboratory comparison of SRM 1950, NIST, USA. The quantitative values are independent of common deuterated or non-endogenous ISTDs, thus offering cross-validation of different lipid methods and further standardizing lipidomics.

DOI: https://doi.org/10.1039/d0an02443k
Adv Exp Med Biol. 2021 ;1316 49-69

Lipid Metabolism in Cancer Cells.

Minhua Zheng, Wei Wang, Jun Liu, Xiao Zhang, Rui Zhang.

  Metabolic reprogramming is one of the most critical hallmarks in cancer cells. In the past decades, mounting evidence has demonstrated that, besides the Warburg Effect, lipid metabolism dysregulation is also one of the essential characteristics of cancer cell metabolism. Lipids are water-insoluble molecules with diverse categories of phosphoglycerides, triacylglycerides, sphingolipids, sterols, etc. As the major utilization for energy storage, fatty acids are the primary building blocks for synthesizing triacylglycerides. And phosphoglycerides, sphingolipids, and sterols are the main components constructing biological membranes. More importantly, lipids play essential roles in signal transduction by functioning as second messengers or hormones. Much evidence has shown specific alterations of lipid metabolism in cancer cells. Consequently, the structural configuration of biological membranes, the energy homeostasis under nutrient stress, and the abundance of lipids in the intracellular signal transduction are affected by these alterations. Furthermore, lipid droplets accumulate in cancer cells and function adaptively to different types of harmful stress. This chapter reviews the regulation, functions, and therapeutic benefits of targeting lipid metabolism in cancer cells. Overall, this chapter highlights the significance of exploring more potential therapeutic strategies for malignant diseases by unscrambling lipid metabolism regulation in cancer cells.

Keywords:  Cancer; Cancer therapy; Lipid metabolism; Metabolic reprogramming

DOI:  https://doi.org/10.1007/978-981-33-6785-2_4
Adv Exp Med Biol. 2021 ;1316 1-24

Lipid Metabolism and Lipidomics Applications in Cancer Research.

Meixia Pan, Chao Qin, Xianlin Han.

  Lipids are the critical components of cellular and plasma membrane, which constitute an impermeable barrier of cellular compartments, and play important roles on numerous cellular processes including cell growth, proliferation, differentiation, and signaling. Alterations in lipid metabolism have been implicated in the development and progression of cancers. However, unlike other biomolecules, the diversity in the structures and characteristics of lipid species results in the limited understanding of their metabolic alterations in cancers. Lipidomics is an emerging discipline that studies lipids in a large scale based on analytical chemistry principles and technological tools. Multidimensional mass spectrometry-based shotgun lipidomics (MDMS-SL) uses direct infusion to avoid difficulties from alterations in concentration, chromatographic anomalies, and ion-pairing alterations to improve resolution and achieve rapid and accurate qualitative and quantitative analysis. In this chapter, lipids and lipid metabolism relevant to cancer research are introduced, followed by a brief description of MDMS-SL and other shotgun lipidomics techniques and some applications for cancer research.

Keywords:  Cancer; Immunity; Lipid metabolism; Lipidomics; Lipids; Mass spectrometry

DOI:  https://doi.org/10.1007/978-981-33-6785-2_1
J Am Soc Mass Spectrom. 2021 Mar 16.

Quantitative Top-Down Proteomics in Complex Samples Using Protein-Level Tandem Mass Tag Labeling.

Dahang Yu, Zhe Wang, Kellye A Cupp-Sutton, Yanting Guo, Qiang Kou, Kenneth Smith, Xiaowen Liu, Si Wu.

  Labeling approaches using isobaric chemical tags (e.g., isobaric tagging for relative and absolute quantification, iTRAQ and tandem mass tag, TMT) have been widely applied for the quantification of peptides and proteins in bottom-up MS. However, until recently, successful applications of these approaches to top-down proteomics have been limited because proteins tend to precipitate and "crash" out of solution during TMT labeling of complex samples making the quantification of such samples difficult. In this study, we report a top-down TMT MS platform for confidently identifying and quantifying low molecular weight intact proteoforms in complex biological samples. To reduce the sample complexity and remove large proteins from complex samples, we developed a filter-SEC technique that combines a molecular weight cutoff filtration step with high-performance size exclusion chromatography (SEC) separation. No protein precipitation was observed in filtered samples under the intact protein-level TMT labeling conditions. The proposed top-down TMT MS platform enables high-throughput analysis of intact proteoforms, allowing for the identification and quantification of hundreds of intact proteoforms from Escherichia coli cell lysates. To our knowledge, this represents the first high-throughput TMT labeling-based, quantitative, top-down MS analysis suitable for complex biological samples.

Keywords:  isobaric labeling; liquid chromatography; mass spectrometry; quantitative proteomics; tandem mass tags (TMT); top-down proteomics

DOI:  https://doi.org/10.1021/jasms.0c00464
Cell Death Dis. 2021 Mar 15. 12(3): 277

Rewiring of purine metabolism in response to acidosis stress in glioma stem cells.

Xiaoyu Xu, Liping Wang, Qingce Zang, Shanshan Li, Limei Li, Zhixing Wang, Jiuming He, Boqin Qiang, Wei Han, Ruiping Zhang, Xiaozhong Peng, Zeper Abliz.

  Glioma stem cells (GSCs) contribute to therapy resistance and poor outcomes for glioma patients. A significant feature of GSCs is their ability to grow in an acidic microenvironment. However, the mechanism underlying the rewiring of their metabolism in low pH remains elusive. Here, using metabolomics and metabolic flux approaches, we cultured GSCs at pH 6.8 and pH 7.4 and found that cells cultured in low pH exhibited increased de novo purine nucleotide biosynthesis activity. The overexpression of glucose-6-phosphate dehydrogenase, encoded by G6PD or H6PD, supports the metabolic dependency of GSCs on nucleotides when cultured under acidic conditions, by enhancing the pentose phosphate pathway (PPP). The high level of reduced glutathione (GSH) under acidic conditions also causes demand for the PPP to provide NADPH. Taken together, upregulation of G6PD/H6PD in the PPP plays an important role in acidic-driven purine metabolic reprogramming and confers a predilection toward glioma progression. Our findings indicate that targeting G6PD/H6PD, which are closely related to glioma patient survival, may serve as a promising therapeutic target for improved glioblastoma therapeutics. An integrated metabolomics and metabolic flux analysis, as well as considering microenvironment and cancer stem cells, provide a precise insight into understanding cancer metabolic reprogramming.

Keywords:  Acidic microenvironment; Glioma stem cells; Glucose-6-phosphate dehydrogenase; Metabolomics; Purine metabolism

DOI:  https://doi.org/10.1038/s41419-021-03543-9
Trends Cancer. 2021 Mar 15. pii: S2405-8033(21)00046-7. [Epub ahead of print]

Metabolic Reprogramming in Anticancer Drug Resistance: A Focus on Amino Acids.

Erica Pranzini, Elisa Pardella, Paolo Paoli, Sarah-Maria Fendt, Maria Letizia Taddei.

  Overcoming anticancer drug resistance is a major challenge in cancer therapy, requiring innovative strategies that consider the extensive tumor heterogeneity and adaptability. We provide recent evidence highlighting the key role of amino acid (AA) metabolic reprogramming in cancer cells and the supportive microenvironment in driving resistance to anticancer therapies. AAs sustain the acquisition of anticancer resistance by providing essential building blocks for biosynthetic pathways and for maintaining a balanced redox status, and modulating the epigenetic profile of both malignant and non-malignant cells. In addition, AAs support the reduced intrinsic susceptibility of cancer stem cells to antineoplastic therapies. These findings shed new light on the possibility of targeting nonresponding tumors by modulating AA availability through pharmacological or dietary interventions.

Keywords:  amino acids; anticancer drug resistance; cancer metabolism

DOI:  https://doi.org/10.1016/j.trecan.2021.02.004
Front Immunol. 2021 ;12 646681

Direct LC-MS/MS Analysis of Extra- and Intracellular Glycerophosphoinositol in Model Cancer Cell Lines.

Ana Margarida Campos, Genoveffa Nuzzo, Alessia Varone, Paola Italiani, Diana Boraschi, Daniela Corda, Angelo Fontana.

  Glycerophosphoinositols (GPIs) are water-soluble bioactive phospholipid derivatives of increasing interest as intracellular and paracrine mediators of eukaryotic cell functions. The most representative compound of the family is glycerophosphoinositol (GroPIns), an ubiquitous component of mammalian cells that participates in cell proliferation, cell survival and cell response to stimuli. Levels and activity of this compound vary among cell types and deciphering these functions requires accurate measurements in in vitro and in vivo models. The conventional approaches for the analysis of GroPIns pose several issues in terms of sensitivity and product resolution, especially when the product is in the extracellular milieu. Here we present an UPLC-MS study for the quantitative analysis of this lipid derivative in cells and, for the first time, culture supernatants. The method is based on a solid-phase extraction that allows for fast desalting and analyte concentration. The robustness of the procedure was tested on the simultaneous measurements of intra- and extracellular levels of GroPIns in a number of human cell lines where it has been shown that the non-transformed cells are characterized by high extracellular level of GroPIns, whereas the tumor cells tended to have higher intracellular levels.

Keywords:  autocrine and paracrine mechanism; cancer; inflammation; lipid metabolism; mass spectrometry; second messenger; solid phase extraction

DOI:  https://doi.org/10.3389/fimmu.2021.646681
Anal Chim Acta. 2021 Apr 15. pii: S0003-2670(21)00151-3. [Epub ahead of print]1154 338325

Gas chromatography-mass spectrometry based 18O stable isotope labeling of Krebs cycle intermediates.

Cemil Can Eylem, İpek Baysal, Acelya Erikci, Samiye Yabanoglu-Ciftci, Song Zhang, Sedef Kır, Andre Terzic, Petras Dzeja, Emirhan Nemutlu.

  New technologies permit determining metabolomic profiles of human diseases by fingerprinting metabolites levels. However, to fully understand metabolomic phenotypes, metabolite levels and turnover rates are necessary to know. Krebs cycle is the major hub of energy metabolism and cell signaling. Traditionally, 13C stable isotope labeled substrates were used to track the carbon turnover rates in Krebs cycle metabolites. In this study, for the first time we introduce H2[18O] based stable isotope marker that permit tracking oxygen exchange rates in separate segments of Krebs cycle. The chromatographic and non-chromatographic parameters were systematically tested on the effect of labeling ratio of Krebs cycle mediators to increase selectivity and sensitivity of the method. We have developed a rapid, precise, and robust GC-MS method for determining the percentage of 18O incorporation to Krebs cycle metabolites. The developed method was applied to track the cancer-induced shift in the Krebs cycle dynamics of Caco-2 cells as compared to the control FHC cells revealing Warburg effects in Caco-2 cells. We demonstrate that unique information could be obtained using this newly developed 18O-labeling analytical technology by following the oxygen exchange rates of Krebs cycle metabolites. Thus, 18O-labeling of Krebs cycle metabolites expands the arsenal of techniques for monitoring the dynamics of cellular metabolism. Moreover, the developed method will allow to apply the 18O-labeling technique to numerous other metabolic pathways where oxygen exchange with water takes place.

Keywords:  (18)O stable isotope labeling; Citric acid cycle; Colon adenocarcinoma; Gas chromatography-mass spectrometry; Krebs cycle; Warburg effect

DOI:  https://doi.org/10.1016/j.aca.2021.338325
Anal Chem. 2021 Mar 15.

Triboelectric Nanogenerator Ion Mobility-Mass Spectrometry for In-Depth Lipid Annotation.

Marcos Bouza, Yafeng Li, Aurelia C Wang, Zhong Lin Wang, Facundo M Fernández.

Lipids play a critical role in cell membrane integrity, signaling, and energy storage. However, in-depth structural characterization of lipids is still challenging and not routinely possible in lipidomics experiments. Techniques such as collision-induced dissociation (CID) tandem mass spectrometry (MS/MS), ion mobility (IM) spectrometry, and ultrahigh-performance liquid chromatography are not yet capable of fully characterizing double-bond and sn-chain position of lipids in a high-throughput manner. Herein, we report on the ability to structurally characterize lipids using large-area triboelectric nanogenerators (TENG) coupled with time-aligned parallel (TAP) fragmentation IM-MS analysis. Gas-phase lipid epoxidation during TENG ionization, coupled to mobility-resolved MS3 via TAP IM-MS, enabled the acquisition of detailed information on the presence and position of lipid C═C double bonds, the fatty acyl sn-chain position and composition, and the cis/trans geometrical C═C isomerism. The proposed methodology proved useful for the shotgun lipidomics analysis of lipid extracts from biological samples, enabling the detailed annotation of numerous lipid isobars.

DOI: https://doi.org/10.1021/acs.analchem.0c05145
Cell Rep. 2021 Mar 16. pii: S2211-1247(21)00135-2. [Epub ahead of print]34(11): 108821

SGK1 signaling promotes glucose metabolism and survival in extracellular matrix detached cells.

Joshua A Mason, Jordan A Cockfield, Daniel J Pape, Hannah Meissner, Michael T Sokolowski, Taylor C White, José C Valentín López, Juan Liu, Xiaojing Liu, Inmaculada Martínez-Reyes, Navdeep S Chandel, Jason W Locasale, Zachary T Schafer.

  Loss of integrin-mediated attachment to extracellular matrix (ECM) proteins can trigger a variety of cellular changes that affect cell viability. Foremost among these is the activation of anoikis, caspase-mediated cell death induced by ECM detachment. In addition, loss of ECM attachment causes profound alterations in cellular metabolism, which can lead to anoikis-independent cell death. Here, we describe a surprising role for serum and glucocorticoid kinase-1 (SGK1) in the promotion of energy production when cells are detached. Our data demonstrate that SGK1 activation is necessary and sufficient for ATP generation during ECM detachment and anchorage-independent growth. More specifically, SGK1 promotes a substantial elevation in glucose uptake because of elevated GLUT1 transcription. In addition, carbon flux into the pentose phosphate pathway (PPP) is necessary to accommodate elevated glucose uptake and PPP-mediated glyceraldehyde-3-phosphate (G3P) is necessary for ATP production. Thus, our data show SGK1 as master regulator of glucose metabolism and cell survival during ECM-detached conditions.

Keywords:  SGK1; anoikis; glucose metabolism; pentose phosphate pathway; signal transduction

DOI:  https://doi.org/10.1016/j.celrep.2021.108821
Curr Cancer Drug Targets. 2021 Mar 16.

Role of Aberrant Lipid Metabolism of Cancer Stem Cells in Cancer Progression.

Juan Zhou, Jing Zhao, Chunxia Su.

  Cancer stem cells (CSCs) represent a small population of cancer cells that are able to self-renew and initiate tumors, which undergo epigenetic, epithelial-mesenchymal, immunological, and metabolic reprogramming to adapt to the tumor microenvironment as well as survive host defense or therapeutic insults. The metabolic reprogramming that accompanies cancer onset is known to be critical for the disease pathogenesis. A coordinated dysregulation of lipid metabolism is observed in nearly all cancer types. In addition to fulfilling basic requirements of structural lipids for membrane synthesis, lipids function importantly as signaling molecules and contribute to energy homeostasis. In this review, we summarize the current progress in the attractive research field of aberrant lipid metabolism regarding CSCs in cancer progression, which provides insights into therapeutic agents targeting CSCs based upon their modulation of lipid metabolism.

Keywords:  Cancer stem cells (CSCs); cancer progression; dysregulation of lipid metabolism; energy homeostasis.; lipid metabolism; tumor microenvironment

DOI:  https://doi.org/10.2174/1568009619666210316112333
Adv Exp Med Biol. 2021 ;1316 25-39

Applications of Lipidomics in Tumor Diagnosis and Therapy.

Yuping Wang.

  Lipids have many critical biological functions in cancer. There are characteristic changes of lipid metabolism and metabolites in different physiological and pathological processes. Lipidomics is an emerging discipline of metabolomics for systematic analysis of lipids in organisms, tissues, or cells and the molecules that interact with them. With the development of new analytical techniques, especially the application and development of mass spectrometry techniques, the determination of lipids can be carried out quickly and accurately and has a high throughput. A large number of studies have shown that abnormal lipid metabolism is closely related to the occurrence and development of tumors. The application of lipidomics technology can reveal changes in lipids and relative abnormal metabolic pathways associated with tumors. Moreover, it shows a wide range of application prospects in the identification of tumor lipid biomarkers, early tumor diagnosis, and the discovery of antitumor drug targets. This chapter mainly introduces the application and development direction of lipidomics in the diagnosis and therapy of different tumors.

Keywords:  Diagnosis; Lipid; Lipidomics; Therapy; Tumor

DOI:  https://doi.org/10.1007/978-981-33-6785-2_2
Adv Exp Med Biol. 2021 ;1316 117-131

Lipid Metabolism in Tumor-Associated Fibroblasts.

Hongzhong Li, Jingyuan Wan.

  Tumor- or cancer-associated fibroblasts (TAFs), one of the most abundant stromal cell types in various carcinomas, consist of a heterogeneous cell population. Typically, TAFs are assigned with pro-tumor activities to promote tumor growth and progression. One of the key features of solid tumors is the metabolic reprogramming that induces alterations of bioenergetics and biosynthesis in both tumor cells and TAFs. Therefore, this review emphasizes TAFs lipid metabolism related to both TAFs differentiation process and TAFs crosstalk with cancer cells. We hope that this review will help understand lipid metabolism in tumor microenvironment, and support the rational design of metabolism-based approaches to improve the efficacy of cancer therapy.

Keywords:  Cancer cells; Lipid metabolism; Metabolism; Tumor microenvironment; Tumor-associated fibroblasts

DOI:  https://doi.org/10.1007/978-981-33-6785-2_8
Adv Exp Med Biol. 2021 ;1316 169-189

Lipid Metabolism and Tumor Antigen Presentation.

Hong Qin, Yaxi Chen.

  Tumors always evade immune surveillance and block T cell activation in a poorly immunogenic and immunosuppressive environment. Cancer cells and immune cells exhibit metabolic reprogramming in the tumor microenvironment (TME), which intimately links immune cell function and edits tumor immunology. In addition to glucose metabolism, amino acid and lipid metabolism also provide the materials for biological processes crucial in cancer biology and pathology. Furthermore, lipid metabolism is synergistically or negatively involved in the interactions between tumors and the microenvironment and contributes to the regulation of immune cells. Antigen processing and presentation as the initiation of adaptive immune response play a critical role in antitumor immunity. Therefore, a relationship exists between antigen-presenting cells and lipid metabolism in TME. This chapter introduces the updated understandings of lipid metabolism of tumor antigen-presenting cells and describes new directions in the manipulation of immune responses for cancer treatment.

Keywords:  Antigen presentation; Immune response; Lipid metabolism; Tumor microenvironment

DOI:  https://doi.org/10.1007/978-981-33-6785-2_11
Clin Biochem. 2021 Mar 15. pii: S0009-9120(21)00073-4. [Epub ahead of print]

Validation of plasma amino acid profile using UHPLC-mass spectrometer (QDa) as a screening method in a metabolic disorders reference centre: performance and accreditation concerns.

C Bruno, C Veyrat-Durebex, C H LumbuLukuntonda, C R Andres, C Moreau, C Bendavid, C Homedan, F Labarthe, M Tardieu, A Bigot, F Maillot, I Benz-de Bretagne, H Blasco.

   INTRODUCTION: Amino acid (AA) analysis in plasma is essential for diagnosis and monitoring of inborn errors of metabolism (IEM). The efficacy of patient management is governed by the rapidity of AA profile availability, along with the robustness of the method. French quality guidelines and progress made in analytical techniques have led biologists to develop AA profile exploration via mass spectrometry (MS).
OBJECTIVES: The aim of this study was to validate an analytical method with a single quadrupole mass spectrometer (MS) and to suggest reference values in regard to French quality and IEM society recommendations.
DESIGN AND METHODS: Plasma samples from patients were deproteinised and derivatised with AccqTag™ reagent. Analysis was performed by reverse-phase chromatography coupled to QDA detector. We evaluated accuracy, intra-days and inter-days precision and limit of quantification by the β-expectation tolerance interval method for 27 AA. Method comparison was performed with the standard method (ion exchange chromatography, IEC) on Jeol Aminotac® and to tandem MS. Reference values were established on AA concentrations of the cohort of patients who had no IEM.
RESULTS: Our method allowed the separations of almost all amino acids with a total run time of 12minutes. Separation of isoleucine and alloisoleucine was incomplete (R = 0.55) but without impact on biological interpretation. Precision, accuracy and quantification were satisfactory (intra-days coefficient of variation (CV) was <5%, inter-days precision CV <10% and accuracy <15%). The limits of quantification were validated between 1 and 900 µmol/L. Results were comparable between the new method and IEC.
CONCLUSION: Ultimately, we validated a rapid method on plasma for quantifying 27 amino acids that can be used in routine practice, according to French quality laboratories and SFEIM (French Society of Inborn Error of Metabolism) recommendations. Furthermore, estimated reference values were similar to those found in published studies focusing on other methods. Despite a lower specificity compared to tandem MS, the simplicity and rapidity of our method are the main advantage of this technique and place it as a major tool in IEM diagnosis and management.

Keywords:  Aminoacids; Derivatization; Liquid chromatography; Mass Spectrometry

DOI:  https://doi.org/10.1016/j.clinbiochem.2021.03.004
Anal Chem. 2021 Mar 16.

metabCombiner: Paired Untargeted LC-HRMS Metabolomics Feature Matching and Concatenation of Disparately Acquired Data Sets.

Hani Habra, Maureen Kachman, Kevin Bullock, Clary Clish, Charles R Evans, Alla Karnovsky.

LC-HRMS experiments detect thousands of compounds, with only a small fraction of them identified in most studies. Traditional data processing pipelines contain an alignment step to assemble the measurements of overlapping features across samples into a unified table. However, data sets acquired under nonidentical conditions are not amenable to this process, mostly due to significant alterations in chromatographic retention times. Alignment of features between disparately acquired LC-MS metabolomics data could aid collaborative compound identification efforts and enable meta-analyses of expanded data sets. Here, we describe metabCombiner, a new computational pipeline for matching known and unknown features in a pair of untargeted LC-MS data sets and concatenating their abundances into a combined table of intersecting feature measurements. metabCombiner groups features by mass-to-charge (m/z) values to generate a search space of possible feature pair alignments, fits a spline through a set of selected retention time ordered pairs, and ranks alignments by m/z, mapped retention time, and relative abundance similarity. We evaluated this workflow on a pair of plasma metabolomics data sets acquired with different gradient elution methods, achieving a mean absolute retention time prediction error of roughly 0.06 min and a weighted per-compound matching accuracy of approximately 90%. We further demonstrate the utility of this method by comprehensively mapping features in urine and muscle metabolomics data sets acquired from different laboratories. metabCombiner has the potential to bridge the gap between otherwise incompatible metabolomics data sets and is available as an R package at https://github.com/hhabra/metabCombiner and Bioconductor.

DOI: https://doi.org/10.1021/acs.analchem.0c03693
World J Gastroenterol. 2021 Feb 28. 27(8): 677-691

G protein-coupled receptors as potential targets for nonalcoholic fatty liver disease treatment.

Ming Yang, Chun-Ye Zhang.

  Nonalcoholic fatty liver disease (NAFLD) is a broad-spectrum disease, ranging from simple hepatic steatosis to nonalcoholic steatohepatitis, which can progress to cirrhosis and liver cancer. Abnormal hepatic lipid accumulation is the major manifestation of this disease, and lipotoxicity promotes NAFLD progression. In addition, intermediate metabolites such as succinate can stimulate the activation of hepatic stellate cells to produce extracellular matrix proteins, resulting in progression of NAFLD to fibrosis and even cirrhosis. G protein-coupled receptors (GPCRs) have been shown to play essential roles in metabolic disorders, such as NAFLD and obesity, through their function as receptors for bile acids and free fatty acids. In addition, GPCRs link gut microbiota-mediated connections in a variety of diseases, such as intestinal diseases, hepatic steatosis, diabetes, and cardiovascular diseases. The latest findings show that gut microbiota-derived acetate contributes to liver lipogenesis by converting dietary fructose into hepatic acetyl-CoA and fatty acids. GPCR agonists, including peptides and natural products like docosahexaenoic acid, have been applied to investigate their role in liver diseases. Therapies such as probiotics and GPCR agonists may be applied to modulate GPCR function to ameliorate liver metabolism syndrome. This review summarizes the current findings regarding the role of GPCRs in the development and progression of NAFLD and describes some preclinical and clinical studies of GPCR-mediated treatment. Overall, understanding GPCR-mediated signaling in liver disease may provide new therapeutic options for NAFLD.

Keywords:  Bile acids; G protein-coupled receptors; Gut microbiota; Metabolism; Nonalcoholic fatty liver disease; Short-chain fatty acids

DOI:  https://doi.org/10.3748/wjg.v27.i8.677
ACS Med Chem Lett. 2021 Mar 11. 12(3): 389-396

Carbamate and N-Pyrimidine Mitigate Amide Hydrolysis: Structure-Based Drug Design of Tetrahydroquinoline IDO1 Inhibitors.

Derun Li, Yongqi Deng, Abdelghani Achab, Indu Bharathan, Brett Andrew Hopkins, Wensheng Yu, Hongjun Zhang, Sulagna Sanyal, Qinglin Pu, Hua Zhou, Kun Liu, Jongwon Lim, Xavier Fradera, Charles A Lesburg, Alfred Lammens, Theodore A Martinot, Ryan D Cohen, Amy C Doty, Heidi Ferguson, Elliott B Nickbarg, Mangeng Cheng, Peter Spacciapoli, Prasanthi Geda, Xuelei Song, Nadya Smotrov, Pravien Abeywickrema, Christine Andrews, Chad Chamberlin, Omar Mabrouk, Patrick Curran, Matthew Richards, Peter Saradjian, J Richard Miller, Ian Knemeyer, Karin M Otte, Stella Vincent, Nunzio Sciammetta, Alexander Pasternak, David Jonathan Bennett, Yongxin Han.

Indoleamine-2,3-dioxygenase-1 (IDO1) has emerged as an attractive target for cancer immunotherapy. An automated ligand identification system screen afforded the tetrahydroquinoline class of novel IDO1 inhibitors. Potency and pharmacokinetic (PK) were key issues with this class of compounds. Structure-based drug design and strategic incorporation of polarity enabled the rapid improvement on potency, solubility, and oxidative metabolic stability. Metabolite identification studies revealed that amide hydrolysis in the D-pocket was the key clearance mechanism for this class. Strategic survey of amide isosteres revealed that carbamates and N-pyrimidines, which maintained exquisite potencies, mitigated the amide hydrolysis issue and led to an improved rat PK profile. The lead compound 28 is a potent IDO1 inhibitor, with clean off-target profiles and the potential for quaque die dosing in humans.

DOI: https://doi.org/10.1021/acsmedchemlett.0c00525
Tohoku J Exp Med. 2021 ;253(3): 171-180

Mass Spectrometry-Based Steroid Profiling: Meeting Unmet Clinical Needs.

Man Ho Choi.

  Despite ongoing concerns regarding its clinical application, mass spectrometry (MS)-based steroid assay represents a promising tool in endocrine research. Recent studies indicate that monitoring the blood levels of individual sterols provides improved diagnostic insight into hyperlipidemia compared with immunoassays routinely used in clinical practice. Hypercortisolism and hyperaldosteronism can also be easily evaluated along with successful subtyping of adrenal diseases using MS-based methods, while metabolic signatures of sex steroids provide experimental evidence of abnormal puberty and male infertility. Many MS-based biological and clinical studies are based on liquid chromatography-mass spectrometry (LC-MS) coupled to electrospray ionization and tandem MS scan modes. However, gas chromatography-mass spectrometry (GC-MS) provides better chromatographic separation. Improved chromatographic resolution enables large-scale steroid profiling to allow a bird-eye view and increase the chances of identifying potent biomarkers in endocrine research. In addition to the technical advantages of MS-based assays over immunoassays, minimizing the sample amounts with acceptable analytical sensitivity and standardization of surrogate materials provides cutting-edge tools for precision and personalized medicine.

Keywords:  adrenal gland; cholesterol; clinical application; mass spectrometry; steroids

DOI:  https://doi.org/10.1620/tjem.253.171
Commun Biol. 2021 Mar 19. 4(1): 367

Amadori rearrangement products as potential biomarkers for inborn errors of amino-acid metabolism.

Rianne E van Outersterp, Sam J Moons, Udo F H Engelke, Herman Bentlage, Tessa M A Peters, Arno van Rooij, Marleen C D G Huigen, Siebolt de Boer, Ed van der Heeft, Leo A J Kluijtmans, Clara D M van Karnebeek, Ron A Wevers, Giel Berden, Jos Oomens, Thomas J Boltje, Karlien L M Coene, Jonathan Martens.

The identification of disease biomarkers plays a crucial role in developing diagnostic strategies for inborn errors of metabolism and understanding their pathophysiology. A primary metabolite that accumulates in the inborn error phenylketonuria is phenylalanine, however its levels do not always directly correlate with clinical outcomes. Here we combine infrared ion spectroscopy and NMR spectroscopy to identify the Phe-glucose Amadori rearrangement product as a biomarker for phenylketonuria. Additionally, we find analogous amino acid-glucose metabolites formed in the body fluids of patients accumulating methionine, lysine, proline and citrulline. Amadori rearrangement products are well-known intermediates in the formation of advanced glycation end-products and have been associated with the pathophysiology of diabetes mellitus and ageing, but are now shown to also form under conditions of aminoacidemia. They represent a general class of metabolites for inborn errors of amino acid metabolism that show potential as biomarkers and may provide further insight in disease pathophysiology.

DOI: https://doi.org/10.1038/s42003-021-01909-5
J Clin Invest. 2021 Mar 15. pii: 147558. [Epub ahead of print]131(6):

Triglyceride lowering by omega-3 fatty acids: a mechanism mediated by N-acyl taurines.

Karin E Bornfeldt.

Interest in omega-3 fatty acids (colloquially known as fish oils) to lower residual cardiovascular risk in statin-treated patients has increased markedly in the wake of recent cardiovascular outcome trials. The triglyceride-lowering effects of omega-3 fatty acids are generally thought to occur by reduced hepatic VLDL production. In this issue of the JCI, Grevengoed et al. used mouse models and human plasma samples to reveal an additional mechanism whereby these polyunsaturated fatty acids can lower plasma triglycerides. Their findings indicate that omega-3 fatty acid-derived N-acyl taurines (NATs) greatly accumulate in bile and also in plasma following omega-3 supplementation. The authors further show that one of these NATs (C22:6 NAT) inhibited intestinal triglyceride hydrolysis and lipid absorption, which resulted in lower plasma triglycerides and protection against hepatic triacylglycerol accumulation in mice fed a high-fat diet. The findings open a potential avenue for triglyceride lowering by omega-3 fatty acids conjugated to taurine.

DOI: https://doi.org/10.1172/JCI147558
Aging Cell. 2021 Mar 17. e13325

Proteomics in aging research: A roadmap to clinical, translational research.

Ruin Moaddel, Ceereena Ubaida-Mohien, Toshiko Tanaka, Alexey Lyashkov, Nathan Basisty, Birgit Schilling, Richard D Semba, Claudio Franceschi, Myriam Gorospe, Luigi Ferrucci.

  The identification of plasma proteins that systematically change with age and, independent of chronological age, predict accelerated decline of health is an expanding area of research. Circulating proteins are ideal translational "omics" since they are final effectors of physiological pathways and because physicians are accustomed to use information of plasma proteins as biomarkers for diagnosis, prognosis, and tracking the effectiveness of treatments. Recent technological advancements, including mass spectrometry (MS)-based proteomics, multiplexed proteomic assay using modified aptamers (SOMAscan), and Proximity Extension Assay (PEA, O-Link), have allowed for the assessment of thousands of proteins in plasma or other biological matrices, which are potentially translatable into new clinical biomarkers and provide new clues about the mechanisms by which aging is associated with health deterioration and functional decline. We carried out a detailed literature search for proteomic studies performed in different matrices (plasma, serum, urine, saliva, tissues) and species using multiple platforms. Herein, we identified 232 proteins that were age-associated across studies. Enrichment analysis of the 232 age-associated proteins revealed metabolic pathways previously connected with biological aging both in animal models and in humans, most remarkably insulin-like growth factor (IGF) signaling, mitogen-activated protein kinases (MAPK), hypoxia-inducible factor 1 (HIF1), cytokine signaling, Forkhead Box O (FOXO) metabolic pathways, folate metabolism, advance glycation end products (AGE), and receptor AGE (RAGE) metabolic pathway. Information on these age-relevant proteins, likely expanded and validated in longitudinal studies and examined in mechanistic studies, will be essential for patient stratification and the development of new treatments aimed at improving health expectancy.

Keywords:  aging; geroscience; human; proteomics

DOI:  https://doi.org/10.1111/acel.13325