51
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Gao W, Zhang Q, Su Y, Huang P, Lu X, Gong Q, Chen W, Xu R, Tian R. Multiomic analysis of a dried single-drop plasma sample using an integrated mass spectrometry approach. Analyst 2020; 145:6441-6446. [PMID: 32785396 DOI: 10.1039/d0an01149e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An easy-to-use and fast approach was developed for integrated proteomic and metabolic profiling in a dried single-drop plasma sample. Plasma collection, room temperature storage, and sample preparation for both proteins and metabolites were seamlessly integrated in one spintip device. MS-based multiomic profiling using the same nano LC-MS system identified more than 150 proteins and 160 metabolites from the 1 μL plasma sample in 6 hours. Further combination with micro-flow LC and targeted MS made it a promising approach for the fast profiling of molecular biomarkers with high sensitivity and accuracy.
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Affiliation(s)
- Weina Gao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China.
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52
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Bacigalupa ZA, Rathmell WK. Beyond glycolysis: Hypoxia signaling as a master regulator of alternative metabolic pathways and the implications in clear cell renal cell carcinoma. Cancer Lett 2020; 489:19-28. [PMID: 32512023 PMCID: PMC7429250 DOI: 10.1016/j.canlet.2020.05.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/17/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022]
Abstract
The relationship between kidney cancer, specifically clear cell renal cell carcinoma (ccRCC), and the hypoxia signaling program has been extensively characterized. Its underlying role as the primary driver of the disease has led to the development of the most effective targeted therapies to date. Cellular responses to hypoxia or mutations affecting the von Hippel-Lindau (VHL) tumor suppressor gene stabilize the hypoxia inducible factor (HIF) transcription factors which then orchestrate elaborate downstream signaling events resulting in adaptations to key biological processes, such as reprogramming metabolism. The direct link of hypoxia signaling to glucose uptake and glycolysis has long been appreciated; however, the HIF family of proteins directly regulate many downstream targets, including other transcription factors with their own extensive networks. In this review, we will summarize our current understanding of how hypoxia signaling regulates other metabolic pathways and how this contributes to the development and progression of clear cell renal cell carcinomas.
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Affiliation(s)
- Zachary A Bacigalupa
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - W Kimryn Rathmell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
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53
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A new opening for the tricky untargeted investigation of natural and modified short peptides. Talanta 2020; 219:121262. [PMID: 32887153 DOI: 10.1016/j.talanta.2020.121262] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/16/2022]
Abstract
Short peptides are of extreme interest in clinical and food research fields, nevertheless they still represent a crucial analytical issue. The main aim of this paper was the development of an analytical platform for a considerable advancement in short peptides identification. For the first time, short sequences presenting both natural and post-translationally modified amino acids were comprehensively studied thanks to the generation of specific databases. Short peptide databases had a dual purpose. First, they were employed as inclusion lists for a suspect screening mass-spectrometric analysis, overcoming the limits of data dependent acquisition mode and allowing the fragmentation of such low-abundance substances. Moreover, the databases were implemented in Compound Discoverer 3.0, a software dedicated to the analysis of short molecules, for the creation of a data processing workflow specifically dedicated to short peptide tentative identification. For this purpose, a detailed study of short peptide fragmentation pathways was carried out for the first time. The proposed method was applied to the study of short peptide sequences in enriched urine samples and led to the tentative identification more than 200 short natural and modified short peptides, the highest number ever reported.
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54
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Yin J, Sun W, Li F, Hong J, Li X, Zhou Y, Lu Y, Liu M, Zhang X, Chen N, Jin X, Xue J, Zeng S, Yu L, Zhu F. VARIDT 1.0: variability of drug transporter database. Nucleic Acids Res 2020; 48:D1042-D1050. [PMID: 31495872 PMCID: PMC6943059 DOI: 10.1093/nar/gkz779] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/20/2019] [Accepted: 08/29/2019] [Indexed: 12/11/2022] Open
Abstract
The absorption, distribution and excretion of drugs are largely determined by their transporters (DTs), the variability of which has thus attracted considerable attention. There are three aspects of variability: epigenetic regulation and genetic polymorphism, species/tissue/disease-specific DT abundances, and exogenous factors modulating DT activity. The variability data of each aspect are essential for clinical study, and a collective consideration among multiple aspects becomes crucial in precision medicine. However, no database is constructed to provide the comprehensive data of all aspects of DT variability. Herein, the Variability of Drug Transporter Database (VARIDT) was introduced to provide such data. First, 177 and 146 DTs were confirmed, for the first time, by the transporting drugs approved and in clinical/preclinical, respectively. Second, for the confirmed DTs, VARIDT comprehensively collected all aspects of their variability (23 947 DNA methylations, 7317 noncoding RNA/histone regulations, 1278 genetic polymorphisms, differential abundance profiles of 257 DTs in 21 781 patients/healthy individuals, expression of 245 DTs in 67 tissues of human/model organism, 1225 exogenous factors altering the activity of 148 DTs), which allowed mutual connection between any aspects. Due to huge amount of accumulated data, VARIDT made it possible to generalize characteristics to reveal disease etiology and optimize clinical treatment, and is freely accessible at: https://db.idrblab.org/varidt/ and http://varidt.idrblab.net/.
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Affiliation(s)
- Jiayi Yin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Wen Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jiajun Hong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaoxu Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ying Zhou
- The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang 310000, China
| | - Yinjing Lu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Mengzhi Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xue Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Na Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiuping Jin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jia Xue
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Su Zeng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lushan Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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55
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Kim JT, Terrell SM, Li VL, Wei W, Fischer CR, Long JZ. Cooperative enzymatic control of N-acyl amino acids by PM20D1 and FAAH. eLife 2020; 9:55211. [PMID: 32271712 PMCID: PMC7145423 DOI: 10.7554/elife.55211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/21/2020] [Indexed: 12/28/2022] Open
Abstract
The N-acyl amino acids are a family of bioactive lipids with pleiotropic physiologic functions, including in energy homeostasis. Their endogenous levels are regulated by an extracellular mammalian N-acyl amino acid synthase/hydrolase called PM20D1 (peptidase M20 domain containing 1). Using an activity-guided biochemical approach, we report the molecular identification of fatty acid amide hydrolase (FAAH) as a second intracellular N-acyl amino acid synthase/hydrolase. In vitro, FAAH exhibits a more restricted substrate scope compared to PM20D1. In mice, genetic ablation or selective pharmacological inhibition of FAAH bidirectionally dysregulates intracellular, but not circulating, N-acyl amino acids. Dual blockade of both PM20D1 and FAAH reveals a dramatic and non-additive biochemical engagement of these two enzymatic pathways. These data establish FAAH as a second intracellular pathway for N-acyl amino acid metabolism and underscore enzymatic division of labor as an enabling strategy for the regulation of a structurally diverse bioactive lipid family.
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Affiliation(s)
- Joon T Kim
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
| | - Stephanie M Terrell
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
| | - Veronica L Li
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
| | - Wei Wei
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States.,Department of Biology, Stanford University, Stanford, United States
| | - Curt R Fischer
- Stanford ChEM-H, Stanford University, Stanford, United States
| | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, United States.,Stanford ChEM-H, Stanford University, Stanford, United States
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56
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Walach J, Filzmoser P, Kouřil Š, Friedecký D, Adam T. Cellwise outlier detection and biomarker identification in metabolomics based on pairwise log ratios. JOURNAL OF CHEMOMETRICS 2020; 34:e3182. [PMID: 32189829 PMCID: PMC7063692 DOI: 10.1002/cem.3182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 07/19/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
Data outliers can carry very valuable information and might be most informative for the interpretation. Nevertheless, they are often neglected. An algorithm called cellwise outlier diagnostics using robust pairwise log ratios (cell-rPLR) for the identification of outliers in single cell of a data matrix is proposed. The algorithm is designed for metabolomic data, where due to the size effect, the measured values are not directly comparable. Pairwise log ratios between the variable values form the elemental information for the algorithm, and the aggregation of appropriate outlyingness values results in outlyingness information. A further feature of cell-rPLR is that it is useful for biomarker identification, particularly in the presence of cellwise outliers. Real data examples and simulation studies underline the good performance of this algorithm in comparison with alternative methods.
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Affiliation(s)
- Jan Walach
- Institute of Statistics and Mathematical Methods in EconomicsTU WienViennaAustria
| | - Peter Filzmoser
- Institute of Statistics and Mathematical Methods in EconomicsTU WienViennaAustria
| | - Štěpán Kouřil
- Laboratory of Metabolomics, Institute of Molecular and Translational Medicine, Faculty of Medicine and DentistryPalacký University OlomoucOlomoucCzech Republic
- Department of Clinical BiochemistryUniversity Hospital OlomoucOlomoucCzech Republic
| | - David Friedecký
- Laboratory of Metabolomics, Institute of Molecular and Translational Medicine, Faculty of Medicine and DentistryPalacký University OlomoucOlomoucCzech Republic
- Department of Clinical BiochemistryUniversity Hospital OlomoucOlomoucCzech Republic
| | - Tomáš Adam
- Laboratory of Metabolomics, Institute of Molecular and Translational Medicine, Faculty of Medicine and DentistryPalacký University OlomoucOlomoucCzech Republic
- Department of Clinical BiochemistryUniversity Hospital OlomoucOlomoucCzech Republic
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57
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Kim JT, Li VL, Terrell SM, Fischer CR, Long JZ. Family-wide Annotation of Enzymatic Pathways by Parallel In Vivo Metabolomics. Cell Chem Biol 2019; 26:1623-1629.e3. [PMID: 31587987 PMCID: PMC6874721 DOI: 10.1016/j.chembiol.2019.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/19/2019] [Accepted: 09/16/2019] [Indexed: 12/21/2022]
Abstract
Enzymes catalyze fundamental biochemical reactions that control cellular and organismal homeostasis. Here we present an approach for de novo biochemical pathway discovery across entire mammalian enzyme families using parallel viral transduction in mice and untargeted liquid chromatography-mass spectrometry. Applying this method to the M20 peptidases uncovers both known pathways of amino acid metabolism as well as a previously unknown CNDP2-regulated pathway for threonyl dipeptide catabolism. Ablation of CNDP2 in mice elevates threonyl dipeptides across multiple tissues, establishing the physiologic relevance of our biochemical assignments. Taken together, these data underscore the utility of parallel in vivo metabolomics for the family-wide discovery of enzymatic pathways.
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Affiliation(s)
- Joon T Kim
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Veronica L Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Stephanie M Terrell
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Curt R Fischer
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Jonathan Z Long
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA.
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58
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Barupal DK, Fiehn O. Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. ENVIRONMENTAL HEALTH PERSPECTIVES 2019; 127:97008. [PMID: 31557052 PMCID: PMC6794490 DOI: 10.1289/ehp4713] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Blood chemicals are routinely measured in clinical or preclinical research studies to diagnose diseases, assess risks in epidemiological research, or use metabolomic phenotyping in response to treatments. A vast volume of blood-related literature is available via the PubMed database for data mining. OBJECTIVES We aimed to generate a comprehensive blood exposome database of endogenous and exogenous chemicals associated with the mammalian circulating system through text mining and database fusion. METHODS Using NCBI resources, we retrieved PubMed abstracts, PubChem chemical synonyms, and PMC supplementary tables. We then employed text mining and PubChem crowdsourcing to associate phrases relating to blood with PubChem chemicals. False positives were removed by a phrase pattern and a compound exclusion list. RESULTS A query to identify blood-related publications in the PubMed database yielded 1.1 million papers. Matching a total of 15 million synonyms from 6.5 million relevant PubChem chemicals against all blood-related publications yielded 37,514 chemicals and 851,999 publications records. Mapping PubChem compound identifiers to the PubMed database yielded 49,940 unique chemicals linked to 676,643 papers. Analysis of open-access metabolomics papers related to blood phrases in the PMC database yielded 4,039 unique compounds and 204 papers. Consolidating these three approaches summed up to a total of 41,474 achiral structures that were linked to 65,957 PubChem CIDs and to over 878,966 PubMed articles. We mapped these compounds to 50 databases such as those covering metabolites and pathways, governmental and toxicological databases, pharmacology resources, and bioassay repositories. In comparison, HMDB, the Human Metabolome Database, links 1,075 compounds to blood-related primary publications. CONCLUSION This new Blood Exposome Database can be used for prioritizing chemicals for systematic reviews, developing target assays in exposome research, identifying compounds in untargeted mass spectrometry, and biological interpretation in metabolomics data. The database is available at http://bloodexposome.org. https://doi.org/10.1289/EHP4713.
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Affiliation(s)
- Dinesh Kumar Barupal
- National Institutes of Health (NIH) West Coast Metabolomics Center, Genome Center, University of California, Davis, Davis, California, USA
| | - Oliver Fiehn
- National Institutes of Health (NIH) West Coast Metabolomics Center, Genome Center, University of California, Davis, Davis, California, USA
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59
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Cyranka M, Veprik A, McKay EJ, van Loon N, Thijsse A, Cotter L, Hare N, Saibudeen A, Lingam S, Pires E, Larraufie P, Reimann F, Gribble F, Stewart M, Bentley E, Lear P, McCullagh J, Cantley J, Cox RD, de Wet H. Abcc5 Knockout Mice Have Lower Fat Mass and Increased Levels of Circulating GLP-1. Obesity (Silver Spring) 2019; 27:1292-1304. [PMID: 31338999 PMCID: PMC6658130 DOI: 10.1002/oby.22521] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/09/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVE A previous genome-wide association study linked overexpression of an ATP-binding cassette transporter, ABCC5, in humans with a susceptibility to developing type 2 diabetes with age. Specifically, ABCC5 gene overexpression was shown to be strongly associated with increased visceral fat mass and reduced peripheral insulin sensitivity. Currently, the role of ABCC5 in diabetes and obesity is unknown. This study reports the metabolic phenotyping of a global Abcc5 knockout mouse. METHODS A global Abcc5-/- mouse was generated by CRISPR/Cas9. Fat mass was determined by weekly EchoMRI and fat pads were dissected and weighed at week 18. Glucose homeostasis was ascertained by an oral glucose tolerance test, intraperitoneal glucose tolerance test, and intraperitoneal insulin tolerance test. Energy expenditure and locomotor activity were measured using PhenoMaster cages. Glucagon-like peptide 1 (GLP-1) levels in plasma, primary gut cell cultures, and GLUTag cells were determined by enzyme-linked immunosorbent assay. RESULTS Abcc5-/- mice had decreased fat mass and increased plasma levels of GLP-1, and they were more insulin sensitive and more active. Recombinant overexpression of ABCC5 protein in GLUTag cells decreased GLP-1 release. CONCLUSIONS ABCC5 protein expression levels are inversely related to fat mass and appear to play a role in the regulation of GLP-1 secretion from enteroendocrine cells.
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Affiliation(s)
- Malgorzata Cyranka
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Anna Veprik
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Eleanor J. McKay
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Nienke van Loon
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Amber Thijsse
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Luke Cotter
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Nisha Hare
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Affan Saibudeen
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Swathi Lingam
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | | | - Pierre Larraufie
- Wellcome Trust‐MRC Institute of Metabolic ScienceAddenbrooke's HospitalCambridgeUK
| | - Frank Reimann
- Wellcome Trust‐MRC Institute of Metabolic ScienceAddenbrooke's HospitalCambridgeUK
| | - Fiona Gribble
- Wellcome Trust‐MRC Institute of Metabolic ScienceAddenbrooke's HospitalCambridgeUK
| | - Michelle Stewart
- MRC Harwell Institute, Genetics of Type 2 DiabetesMammalian Genetics Unit, Harwell CampusOxfordshireUK
| | - Elizabeth Bentley
- MRC Harwell Institute, Genetics of Type 2 DiabetesMammalian Genetics Unit, Harwell CampusOxfordshireUK
| | - Pamela Lear
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | | | - James Cantley
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
| | - Roger D. Cox
- MRC Harwell Institute, Genetics of Type 2 DiabetesMammalian Genetics Unit, Harwell CampusOxfordshireUK
| | - Heidi de Wet
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
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60
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Andreyeva EN, Ogienko AA, Dubatolova TD, Oshchepkova AL, Kozhevnikova EN, Ivankin AV, Pavlova GA, Kopyl SA, Pindyurin AV. A toolset to study functions of Cytosolic non-specific dipeptidase 2 (CNDP2) using Drosophila as a model organism. BMC Genet 2019; 20:31. [PMID: 30885138 PMCID: PMC6421639 DOI: 10.1186/s12863-019-0726-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Expression of the CNDP2 gene is frequently up- or down-regulated in different types of human cancers. However, how the product of this gene is involved in cell growth and proliferation is poorly understood. Moreover, our knowledge of the functions of the CNDP2 orthologs in well-established model organisms is scarce. In particular, the function of the D. melanogaster ortholog of CNDP2, encoded by the CG17337 gene (hereafter referred to as dCNDP2), is still unknown. Results This study was aimed at developing a set of genetic and molecular tools to study the roles of dCNDP2. We generated a dCNDP2 null mutation (hereafter ∆dCNDP2) using CRISPR/Cas9-mediated homologous recombination (HR) and found that the ∆dCNDP2 mutants are homozygous viable, morphologically normal and fertile. We also generated transgenic fly lines expressing eGFP-tagged and non-tagged dCNDP2 protein, all under the control of the UAS promoter, as well as polyclonal antibodies specific to dCNDP2. Using these tools, we demonstrate that only one of the two predicted dCNDP2 isoforms is expressed throughout the different tissues tested. dCNDP2 was detected in both the cytoplasm and the nucleus, and was found to be associated with multiple sites in the salivary gland polytene chromosomes. Conclusions The dCNDP2 gene is not essential for fly viability under standard laboratory conditions. The subcellular localization pattern of dCNDP2 suggests that this protein might have roles in both the cytoplasm and the nucleus. The genetic and molecular tools developed in this study will allow further functional characterization of the conserved CNDP2 protein using D. melanogaster as a model system. Electronic supplementary material The online version of this article (10.1186/s12863-019-0726-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Evgeniya N Andreyeva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Anna A Ogienko
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Tatiana D Dubatolova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Anastasiya L Oshchepkova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Elena N Kozhevnikova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Anton V Ivankin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Gera A Pavlova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Sergei A Kopyl
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
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Buñay J, Larriba E, Patiño-Garcia D, Urriola-Muñoz P, Moreno RD, del Mazo J. Combined proteomic and miRNome analyses of mouse testis exposed to an endocrine disruptors chemicals mixture reveals altered toxicological pathways involved in male infertility. ACTA ACUST UNITED AC 2019; 25:156-169. [DOI: 10.1093/molehr/gaz003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 12/23/2018] [Accepted: 01/24/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Julio Buñay
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Catolica de Chile (PUC), Santiago, Chile
| | - Eduardo Larriba
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biologicas (CIB-CSIC), Madrid, Spain
| | - Daniel Patiño-Garcia
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Catolica de Chile (PUC), Santiago, Chile
| | - Paulina Urriola-Muñoz
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Catolica de Chile (PUC), Santiago, Chile
- Chemistry Institute, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Ricardo D Moreno
- Department of Physiology, Faculty of Biological Sciences, Pontificia Universidad Catolica de Chile (PUC), Santiago, Chile
| | - Jesús del Mazo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biologicas (CIB-CSIC), Madrid, Spain
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62
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Occurrence of non-proteolytic amino acyl derivatives in dry-cured ham. Food Res Int 2018; 114:38-46. [DOI: 10.1016/j.foodres.2018.07.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/04/2018] [Accepted: 07/30/2018] [Indexed: 11/19/2022]
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63
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Knott ME, Manzi M, Zabalegui N, Salazar MO, Puricelli LI, Monge ME. Metabolic Footprinting of a Clear Cell Renal Cell Carcinoma in Vitro Model for Human Kidney Cancer Detection. J Proteome Res 2018; 17:3877-3888. [PMID: 30260228 DOI: 10.1021/acs.jproteome.8b00538] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A protocol for harvesting and extracting extracellular metabolites from an in vitro model of human renal cell lines was developed to profile the exometabolome by means of a discovery-based metabolomics approach using ultraperformance liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry. Metabolic footprints provided by conditioned media (CM) samples ( n = 66) of two clear cell Renal Cell Carcinoma (ccRCC) cell lines with different genetic backgrounds and a nontumor renal cell line, were compared with the human serum metabolic profile of a pilot cohort ( n = 10) comprised of stage IV ccRCC patients and healthy individuals. Using a cross-validated orthogonal projection to latent structures-discriminant analysis model, a panel of 21 discriminant features selected by iterative multivariate classification, allowed differentiating control from tumor cell lines with 100% specificity, sensitivity, and accuracy. Isoleucine/leucine, phenylalanine, N-lactoyl-leucine, and N-acetyl-phenylalanine, and cysteinegluthatione disulfide (CYSSG) were identified by chemical standards, and hydroxyprolyl-valine was identified with MS and MS/MS experiments. A subset of 9 discriminant features, including the identified metabolites except for CYSSG, produced a fingerprint of classification value that enabled discerning ccRCC patients from healthy individuals. To our knowledge, this is the first time that N-lactoyl-leucine is associated with ccRCC. Results from this study provide a proof of concept that CM can be used as a serum proxy to obtain disease-related metabolic signatures.
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Affiliation(s)
- María Elena Knott
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Godoy Cruz 2390 , C1425FQD , Ciudad de Buenos Aires , Argentina
| | - Malena Manzi
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Godoy Cruz 2390 , C1425FQD , Ciudad de Buenos Aires , Argentina
| | - Nicolás Zabalegui
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Godoy Cruz 2390 , C1425FQD , Ciudad de Buenos Aires , Argentina
| | - Mario O Salazar
- Farmacognosia, Departamento de Química Orgánica, Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario , Suipacha 531 , Rosario S-2002LRK , Santa Fe, Argentina
| | - Lydia I Puricelli
- Instituto de Oncología Ángel H. Roffo, Facultad de Medicina , Universidad de Buenos Aires , Av. San Martín 5481 , C1417DTB , Ciudad de Buenos Aires , Argentina
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Godoy Cruz 2390 , C1425FQD , Ciudad de Buenos Aires , Argentina
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64
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Václavík J, Coene KLM, Vrobel I, Najdekr L, Friedecký D, Karlíková R, Mádrová L, Petsalo A, Engelke UFH, van Wegberg A, Kluijtmans LAJ, Adam T, Wevers RA. Structural elucidation of novel biomarkers of known metabolic disorders based on multistage fragmentation mass spectra. J Inherit Metab Dis 2018; 41:407-414. [PMID: 29139026 DOI: 10.1007/s10545-017-0109-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/02/2017] [Accepted: 10/22/2017] [Indexed: 10/18/2022]
Abstract
Specific diagnostic markers are the key to effective diagnosis and treatment of inborn errors of metabolism (IEM). Untargeted metabolomics allows for the identification of potential novel diagnostic biomarkers. Current separation techniques coupled to high-resolution mass spectrometry provide a powerful tool for structural elucidation of unknown compounds in complex biological matrices. This is a proof-of-concept study testing this methodology to determine the molecular structure of as yet uncharacterized m/z signals that were significantly increased in plasma samples from patients with phenylketonuria and 3-hydroxy-3-methylglutaryl-CoA lyase deficiency. A hybrid linear ion trap-orbitrap high resolution mass spectrometer, capable of multistage fragmentation, was used to acquire accurate masses and product ion spectra of the uncharacterized m/z signals. In order to determine the molecular structures, spectral databases were searched and fragmentation prediction software was used. This approach enabled structural elucidation of novel compounds potentially useful as biomarkers in diagnostics and follow-up of IEM patients. Two new conjugates, glutamyl-glutamyl-phenylalanine and phenylalanine-hexose, were identified in plasma of phenylketonuria patients. These novel markers showed high inter-patient variation and did not correlate to phenylalanine levels, illustrating their potential added value for follow-up. As novel biomarkers for 3-hydroxy-3-methylglutaryl-CoA lyase deficiency, three positional isomers of 3-methylglutaconyl carnitine could be detected in patient plasma. Our results highlight the applicability of current accurate mass multistage fragmentation techniques for structural elucidation of unknown metabolites in human biofluids, offering an unprecedented opportunity to gain further biochemical insights in known inborn errors of metabolism by enabling high confidence identification of novel biomarkers.
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Affiliation(s)
- Jan Václavík
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Hněvotínská 5, 775 15, Olomouc, Czech Republic
- Laboratory of Inherited Metabolic Disorders, Department of Clinical Chemistry, University Hospital in Olomouc, I.P. Pavlova 6, 775 20, Olomouc, Czech Republic
| | - Karlien L M Coene
- Translational Metabolic Laboratory - 830 TML, Department of Laboratory Medicine, Radboud University Medical Centre, Geert Grooteplein 10, 6525, GA, Nijmegen, the Netherlands
| | - Ivo Vrobel
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Hněvotínská 5, 775 15, Olomouc, Czech Republic
- Laboratory of Inherited Metabolic Disorders, Department of Clinical Chemistry, University Hospital in Olomouc, I.P. Pavlova 6, 775 20, Olomouc, Czech Republic
| | - Lukáš Najdekr
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Hněvotínská 5, 775 15, Olomouc, Czech Republic
- Laboratory of Inherited Metabolic Disorders, Department of Clinical Chemistry, University Hospital in Olomouc, I.P. Pavlova 6, 775 20, Olomouc, Czech Republic
| | - David Friedecký
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Hněvotínská 5, 775 15, Olomouc, Czech Republic
- Laboratory of Inherited Metabolic Disorders, Department of Clinical Chemistry, University Hospital in Olomouc, I.P. Pavlova 6, 775 20, Olomouc, Czech Republic
| | - Radana Karlíková
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Hněvotínská 5, 775 15, Olomouc, Czech Republic
- Laboratory of Inherited Metabolic Disorders, Department of Clinical Chemistry, University Hospital in Olomouc, I.P. Pavlova 6, 775 20, Olomouc, Czech Republic
| | - Lucie Mádrová
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Hněvotínská 5, 775 15, Olomouc, Czech Republic
- Laboratory of Inherited Metabolic Disorders, Department of Clinical Chemistry, University Hospital in Olomouc, I.P. Pavlova 6, 775 20, Olomouc, Czech Republic
| | - Aleksanteri Petsalo
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Hněvotínská 5, 775 15, Olomouc, Czech Republic
| | - Udo F H Engelke
- Translational Metabolic Laboratory - 830 TML, Department of Laboratory Medicine, Radboud University Medical Centre, Geert Grooteplein 10, 6525, GA, Nijmegen, the Netherlands
| | - Annemiek van Wegberg
- Department of Gastroenterology, Radboud University Medical Centre, Geert Grooteplein 10, 6525, GA, Nijmegen, the Netherlands
| | - Leo A J Kluijtmans
- Translational Metabolic Laboratory - 830 TML, Department of Laboratory Medicine, Radboud University Medical Centre, Geert Grooteplein 10, 6525, GA, Nijmegen, the Netherlands
| | - Tomáš Adam
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Hněvotínská 5, 775 15, Olomouc, Czech Republic.
- Laboratory of Inherited Metabolic Disorders, Department of Clinical Chemistry, University Hospital in Olomouc, I.P. Pavlova 6, 775 20, Olomouc, Czech Republic.
| | - Ron A Wevers
- Translational Metabolic Laboratory - 830 TML, Department of Laboratory Medicine, Radboud University Medical Centre, Geert Grooteplein 10, 6525, GA, Nijmegen, the Netherlands
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Peters V, Zschocke J, Schmitt CP. Carnosinase, diabetes mellitus and the potential relevance of carnosinase deficiency. J Inherit Metab Dis 2018; 41:39-47. [PMID: 29027595 DOI: 10.1007/s10545-017-0099-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/20/2017] [Accepted: 09/26/2017] [Indexed: 12/15/2022]
Abstract
Carnosinase (CN1) is a dipeptidase, encoded by the CNDP1 gene, that degrades histidine-containing dipeptides, such as carnosine, anserine and homocarnosine. Loss of CN1 function (also called carnosinase deficiency or aminoacyl-histidine dipeptidase deficiency) has been reported in a small number of patients with highly elevated blood carnosine concentrations, denoted carnosinaemia; it is unclear whether the variety of clinical symptoms in these individuals is causally related to carnosinase deficiency. Reduced CN1 function should increase serum carnosine concentrations but the genetic basis of carnosinaemia has not been formally confirmed to be due to CNDP1 mutations. A CNDP1 polymorphism associated with low CN1 activity correlates with significantly reduced risk for diabetic nephropathy, especially in women with type 2 diabetes, and may slow progression of chronic kidney disease in children with glomerulonephritis. Studies in rodents demonstrate antiproteinuric and vasculoprotective effects of carnosine, the precise molecular mechanisms, however, are still incompletely understood. Thus, carnosinemia due to CN1 deficiency may be a non-disease; in contrast, carnosine may potentially protect against long-term sequelae of reactive metabolites accumulating, e.g. in diabetes and chronic renal failure.
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MESH Headings
- Amino Acid Metabolism, Inborn Errors/diagnosis
- Amino Acid Metabolism, Inborn Errors/enzymology
- Amino Acid Metabolism, Inborn Errors/epidemiology
- Amino Acid Metabolism, Inborn Errors/genetics
- Animals
- Brain Diseases, Metabolic, Inborn/diagnosis
- Brain Diseases, Metabolic, Inborn/enzymology
- Brain Diseases, Metabolic, Inborn/epidemiology
- Brain Diseases, Metabolic, Inborn/genetics
- Diabetes Mellitus, Type 2/diagnosis
- Diabetes Mellitus, Type 2/enzymology
- Diabetes Mellitus, Type 2/epidemiology
- Diabetes Mellitus, Type 2/genetics
- Diabetic Nephropathies/diagnosis
- Diabetic Nephropathies/enzymology
- Diabetic Nephropathies/epidemiology
- Diabetic Nephropathies/genetics
- Dipeptidases/deficiency
- Dipeptidases/genetics
- Humans
- Mutation
- Polymorphism, Genetic
- Prognosis
- Protective Factors
- Risk Factors
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Affiliation(s)
- Verena Peters
- Centre for Paediatric and Adolescent Medicine, University of Heidelberg, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany.
| | - Johannes Zschocke
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Claus P Schmitt
- Centre for Paediatric and Adolescent Medicine, University of Heidelberg, Im Neuenheimer Feld 669, 69120, Heidelberg, Germany
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66
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Ma H, Delafield DG, Wang Z, You J, Wu S. Finding Biomass Degrading Enzymes Through an Activity-Correlated Quantitative Proteomics Platform (ACPP). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:655-663. [PMID: 28083757 PMCID: PMC5373979 DOI: 10.1007/s13361-016-1569-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/29/2016] [Accepted: 11/21/2016] [Indexed: 06/06/2023]
Abstract
The microbial secretome, known as a pool of biomass (i.e., plant-based materials) degrading enzymes, can be utilized to discover industrial enzyme candidates for biofuel production. Proteomics approaches have been applied to discover novel enzyme candidates through comparing protein expression profiles with enzyme activity of the whole secretome under different growth conditions. However, the activity measurement of each enzyme candidate is needed for confident "active" enzyme assignments, which remains to be elucidated. To address this challenge, we have developed an Activity-Correlated Quantitative Proteomics Platform (ACPP) that systematically correlates protein-level enzymatic activity patterns and protein elution profiles using a label-free quantitative proteomics approach. The ACPP optimized a high performance anion exchange separation for efficiently fractionating complex protein samples while preserving enzymatic activities. The detected enzymatic activity patterns in sequential fractions using microplate-based assays were cross-correlated with protein elution profiles using a customized pattern-matching algorithm with a correlation R-score. The ACPP has been successfully applied to the identification of two types of "active" biomass-degrading enzymes (i.e., starch hydrolysis enzymes and cellulose hydrolysis enzymes) from Aspergillus niger secretome in a multiplexed fashion. By determining protein elution profiles of 156 proteins in A. niger secretome, we confidently identified the 1,4-α-glucosidase as the major "active" starch hydrolysis enzyme (R = 0.96) and the endoglucanase as the major "active" cellulose hydrolysis enzyme (R = 0.97). The results demonstrated that the ACPP facilitated the discovery of bioactive enzymes from complex protein samples in a high-throughput, multiplexing, and untargeted fashion. Graphical Abstract ᅟ.
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Affiliation(s)
- Hongyan Ma
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Daniel G Delafield
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Jianlan You
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.
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67
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Aguilar-Mogas A, Sales-Pardo M, Navarro M, Guimerà R, Yanes O. iMet: A Network-Based Computational Tool To Assist in the Annotation of Metabolites from Tandem Mass Spectra. Anal Chem 2017; 89:3474-3482. [DOI: 10.1021/acs.analchem.6b04512] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Antoni Aguilar-Mogas
- Departament
d’Enginyeria Química, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007 Tarragona, Catalonia, Spain
| | - Marta Sales-Pardo
- Departament
d’Enginyeria Química, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007 Tarragona, Catalonia, Spain
| | - Miriam Navarro
- Metabolomics
Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Av. Països Catalans 26, 43007 Tarragona, Catalonia, Spain
- Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Monforte de Lemos 35, 28029 Madrid, Spain
| | - Roger Guimerà
- Departament
d’Enginyeria Química, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007 Tarragona, Catalonia, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Lluís Companys 23, 08010 Barcelona, Catalonia, Spain
| | - Oscar Yanes
- Metabolomics
Platform, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Av. Països Catalans 26, 43007 Tarragona, Catalonia, Spain
- Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Monforte de Lemos 35, 28029 Madrid, Spain
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68
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Timachi MH, Hutter CA, Hohl M, Assafa T, Böhm S, Mittal A, Seeger MA, Bordignon E. Exploring conformational equilibria of a heterodimeric ABC transporter. eLife 2017; 6. [PMID: 28051765 PMCID: PMC5216877 DOI: 10.7554/elife.20236] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/01/2016] [Indexed: 01/04/2023] Open
Abstract
ABC exporters pump substrates across the membrane by coupling ATP-driven movements of nucleotide binding domains (NBDs) to the transmembrane domains (TMDs), which switch between inward- and outward-facing (IF, OF) orientations. DEER measurements on the heterodimeric ABC exporter TM287/288 from Thermotoga maritima, which contains a non-canonical ATP binding site, revealed that in the presence of nucleotides the transporter exists in an IF/OF equilibrium. While ATP binding was sufficient to partially populate the OF state, nucleotide trapping in the pre- or post-hydrolytic state was required for a pronounced conformational shift. At physiologically high temperatures and in the absence of nucleotides, the NBDs disengage asymmetrically while the conformation of the TMDs remains unchanged. Nucleotide binding at the degenerate ATP site prevents complete NBD separation, a molecular feature differentiating heterodimeric from homodimeric ABC exporters. Our data suggest hydrolysis-independent closure of the NBD dimer, which is further stabilized as the consensus site nucleotide is committed to hydrolysis. DOI:http://dx.doi.org/10.7554/eLife.20236.001
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Affiliation(s)
- M Hadi Timachi
- Faculty of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany.,Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Cedric Aj Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Michael Hohl
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Tufa Assafa
- Faculty of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany.,Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Simon Böhm
- Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Anshumali Mittal
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr-Universität Bochum, Bochum, Germany.,Department of Physics, Freie Universität Berlin, Berlin, Germany
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69
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Fletcher JI, Williams RT, Henderson MJ, Norris MD, Haber M. ABC transporters as mediators of drug resistance and contributors to cancer cell biology. Drug Resist Updat 2016; 26:1-9. [PMID: 27180306 DOI: 10.1016/j.drup.2016.03.001] [Citation(s) in RCA: 286] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 03/04/2016] [Accepted: 03/12/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Jamie I Fletcher
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, Randwick, NSW, Australia
| | - Rebekka T Williams
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, Randwick, NSW, Australia
| | - Michelle J Henderson
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, Randwick, NSW, Australia
| | - Murray D Norris
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, Randwick, NSW, Australia
| | - Michelle Haber
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, Randwick, NSW, Australia.
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70
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Borst P. Maxi-circles, glycosomes, gene transposition, expression sites, transsplicing, transferrin receptors and base J. Mol Biochem Parasitol 2016; 205:39-52. [DOI: 10.1016/j.molbiopara.2016.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 03/22/2016] [Accepted: 03/22/2016] [Indexed: 01/05/2023]
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71
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Jansen RS, Mahakena S, de Haas M, Borst P, van de Wetering K. ATP-binding Cassette Subfamily C Member 5 (ABCC5) Functions as an Efflux Transporter of Glutamate Conjugates and Analogs. J Biol Chem 2015; 290:30429-40. [PMID: 26515061 DOI: 10.1074/jbc.m115.692103] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Indexed: 01/12/2023] Open
Abstract
The ubiquitous efflux transporter ABCC5 (ATP-binding cassette subfamily C member 5) is present at high levels in the blood-brain barrier, neurons, and glia, but its in vivo substrates and function are not known. Using untargeted metabolomic screens, we show that Abcc5(-/-) mice accumulate endogenous glutamate conjugates in several tissues, but brain in particular. The abundant neurotransmitter N-acetylaspartylglutamate was 2.4-fold higher in Abcc5(-/-) brain. The metabolites that accumulated in Abcc5(-/-) tissues were depleted in cultured cells that overexpressed human ABCC5. In a vesicular membrane transport assay, ABCC5 also transported exogenous glutamate analogs, like the classic excitotoxic neurotoxins kainic acid, domoic acid, and NMDA; the therapeutic glutamate analog ZJ43; and, as previously shown, the anti-cancer drug methotrexate. Glutamate conjugates and analogs are of physiological relevance because they can affect the function of glutamate, the principal excitatory neurotransmitter in the brain. After CO2 asphyxiation, several immediate early genes were expressed at lower levels in Abcc5(-/-) brains than in wild type brains, suggesting altered glutamate signaling. Our results show that ABCC5 is a general glutamate conjugate and analog transporter that affects the disposition of endogenous metabolites, toxins, and drugs.
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Affiliation(s)
- Robert S Jansen
- From the Division of Molecular Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Sunny Mahakena
- From the Division of Molecular Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Marcel de Haas
- From the Division of Molecular Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Piet Borst
- From the Division of Molecular Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Koen van de Wetering
- From the Division of Molecular Oncology, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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72
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Shipp LE, Hill RZ, Moy GW, Gökırmak T, Hamdoun A. ABCC5 is required for cAMP-mediated hindgut invagination in sea urchin embryos. Development 2015; 142:3537-48. [PMID: 26395488 DOI: 10.1242/dev.126144] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 08/14/2015] [Indexed: 12/31/2022]
Abstract
ATP-binding cassette (ABC) transporters are evolutionarily conserved proteins that pump diverse substrates across membranes. Many are known to efflux signaling molecules and are extensively expressed during development. However, the role of transporters in moving extracellular signals that regulate embryogenesis is largely unexplored. Here, we show that a mesodermal ABCC (MRP) transporter is necessary for endodermal gut morphogenesis in sea urchin embryos. This transporter, Sp-ABCC5a (C5a), is expressed in pigment cells and their precursors, which are a subset of the non-skeletogenic mesoderm (NSM) cells. C5a expression depends on Delta/Notch signaling from skeletogenic mesoderm and is downstream of Gcm in the aboral NSM gene regulatory network. Long-term imaging of development reveals that C5a knockdown embryos gastrulate, but ∼90% develop a prolapse of the hindgut by the late prism stage (∼8 h after C5a protein expression normally peaks). Since C5a orthologs efflux cyclic nucleotides, and cAMP-dependent protein kinase (Sp-CAPK/PKA) is expressed in pigment cells, we examined whether C5a could be involved in gastrulation through cAMP transport. Consistent with this hypothesis, membrane-permeable pCPT-cAMP rescues the prolapse phenotype in C5a knockdown embryos, and causes archenteron hyper-invagination in control embryos. In addition, the cAMP-producing enzyme soluble adenylyl cyclase (sAC) is expressed in pigment cells, and its inhibition impairs gastrulation. Together, our data support a model in which C5a transports sAC-derived cAMP from pigment cells to control late invagination of the hindgut. Little is known about the ancestral functions of ABCC5/MRP5 transporters, and this study reveals a novel role for these proteins in mesoderm-endoderm signaling during embryogenesis.
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Affiliation(s)
- Lauren E Shipp
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202, USA
| | - Rose Z Hill
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202, USA
| | - Gary W Moy
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202, USA
| | - Tufan Gökırmak
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202, USA
| | - Amro Hamdoun
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0202, USA
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