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Liu YM, Wang S, Dickenson A, Mao J, Bai X, Liao X. An on-line SPE-LC-MS/MS method for quantification of nucleobases and nucleosides present in biological fluids. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:2505-2512. [PMID: 38584507 DOI: 10.1039/d4ay00100a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Solid phase extraction (SPE) and liquid chromatographic (LC) separation of nucleobases and nucleosides are challenging due to the high hydrophilicity of these compounds. Herein we report a novel on-line SPE-LC-MS/MS method for their quantification after pre-column derivatization with chloroacetaldehyde (CAA). The method proposed is selective and sensitive with limits of detection at the nano-molar level. Analysis of urine and saliva samples by using this method is demonstrated. Adenine, guanine, cytosine, adenosine, guanosine, and cytidine were found in the range from 0.19 (guanosine) to 1.83 μM (cytidine) in urine and from 0.015 (guanosine) to 0.79 μM (adenine) in saliva. Interestingly, methylation of cytidine was found to be significantly different in urine from that in saliva. While 5-hydroxymethylcytidine was detected at a very low level (<0.05 μM) in saliva, it was found to be the most prominent methylated cytidine in urine at a high level of 3.33 μM. Since on-line SPE is deployed, the proposed LC-MS/MS quantitative assay is convenient to carry out and offers good assay accuracy and repeatability.
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Affiliation(s)
- Yi-Ming Liu
- Department of Chemistry, Physics, and Atmospheric Science, Jackson State University, Jackson, MS 39217, USA.
| | - Shuguan Wang
- Department of Chemistry, Physics, and Atmospheric Science, Jackson State University, Jackson, MS 39217, USA.
| | - Amani Dickenson
- Department of Chemistry, Physics, and Atmospheric Science, Jackson State University, Jackson, MS 39217, USA.
| | - Jinghe Mao
- Department of Biology, Tougaloo College, Tougaloo, MS 39174, USA
| | - Xiaolin Bai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
| | - Xun Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China.
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2
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Zhao J, Adiele N, Gomes D, Malovichko M, Conklin DJ, Ekuban A, Luo J, Gripshover T, Watson WH, Banerjee M, Smith ML, Rouchka EC, Xu R, Zhang X, Gondim DD, Cave MC, O’Toole TE. Obesogenic polystyrene microplastic exposures disrupt the gut-liver-adipose axis. Toxicol Sci 2024; 198:210-220. [PMID: 38291899 PMCID: PMC10964747 DOI: 10.1093/toxsci/kfae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Abstract
Microplastics (MP) derived from the weathering of polymers, or synthesized in this size range, have become widespread environmental contaminants and have found their way into water supplies and the food chain. Despite this awareness, little is known about the health consequences of MP ingestion. We have previously shown that the consumption of polystyrene (PS) beads was associated with intestinal dysbiosis and diabetes and obesity in mice. To further evaluate the systemic metabolic effects of PS on the gut-liver-adipose tissue axis, we supplied C57BL/6J mice with normal water or that containing 2 sizes of PS beads (0.5 and 5 µm) at a concentration of 1 µg/ml. After 13 weeks, we evaluated indices of metabolism and liver function. As observed previously, mice drinking the PS-containing water had a potentiated weight gain and adipose expansion. Here we found that this was associated with an increased abundance of adipose F4/80+ macrophages. These exposures did not cause nonalcoholic fatty liver disease but were associated with decreased liver:body weight ratios and an enrichment in hepatic farnesoid X receptor and liver X receptor signaling. PS also increased hepatic cholesterol and altered both hepatic and cecal bile acids. Mice consuming PS beads and treated with the berry anthocyanin, delphinidin, demonstrated an attenuated weight gain compared with those mice receiving a control intervention and also exhibited a downregulation of cyclic adenosine monophosphate (cAMP) and peroxisome proliferator-activated receptor (PPAR) signaling pathways. This study highlights the obesogenic role of PS in perturbing the gut-liver-adipose axis and altering nuclear receptor signaling and intermediary metabolism. Dietary interventions may limit the adverse metabolic effects of PS consumption.
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Affiliation(s)
- Jingjing Zhao
- Division of Environmental Medicine, Department of Medicine, School of Medicine, Christina Lee Brown Envirome Institute, University of Louisville, Louisville, Kentucky 40202, USA
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, Kentucky 40202, USA
| | - Ngozi Adiele
- Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
| | - Daniel Gomes
- Division of Environmental Medicine, Department of Medicine, School of Medicine, Christina Lee Brown Envirome Institute, University of Louisville, Louisville, Kentucky 40202, USA
- Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
| | - Marina Malovichko
- Division of Environmental Medicine, Department of Medicine, School of Medicine, Christina Lee Brown Envirome Institute, University of Louisville, Louisville, Kentucky 40202, USA
- The Superfund Research Center, University of Louisville, Louisville, Kentucky 40202, USA
| | - Daniel J Conklin
- Division of Environmental Medicine, Department of Medicine, School of Medicine, Christina Lee Brown Envirome Institute, University of Louisville, Louisville, Kentucky 40202, USA
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, Kentucky 40202, USA
- The Superfund Research Center, University of Louisville, Louisville, Kentucky 40202, USA
| | - Abigail Ekuban
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
- The Hepatobiology and Toxicology Center, University of Louisville, Louisville, Kentucky 40202, USA
| | - Jianzhu Luo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
| | - Tyler Gripshover
- Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
- The Superfund Research Center, University of Louisville, Louisville, Kentucky 40202, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
| | - Walter H Watson
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, Kentucky 40202, USA
- Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
- The Hepatobiology and Toxicology Center, University of Louisville, Louisville, Kentucky 40202, USA
| | - Mayukh Banerjee
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, Kentucky 40202, USA
- Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
| | - Melissa L Smith
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, Kentucky 40202, USA
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
| | - Eric C Rouchka
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
- KY INBRE Bioinformatics Core, University of Louisville, Louisville, Kentucky 40202, USA
| | - Raobo Xu
- Department of Chemistry, School of Arts and Sciences, University of Louisville, Louisville, Kentucky 40292, USA
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, Kentucky 40292, USA
| | - Xiang Zhang
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, Kentucky 40202, USA
- The Hepatobiology and Toxicology Center, University of Louisville, Louisville, Kentucky 40202, USA
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, Kentucky 40292, USA
- Division of Analytic Chemistry, Department of Chemistry, School of Arts and Sciences, University of Louisville, Louisville, Kentucky 40292, USA
- The Alcohol Research Center, University of Louisville, Louisville, Kentucky 40202, USA
| | - Dibson D Gondim
- Department of Pathology and Laboratory, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
| | - Matthew C Cave
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, Kentucky 40202, USA
- Department of Pharmacology and Toxicology, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
- The Superfund Research Center, University of Louisville, Louisville, Kentucky 40202, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
- The Hepatobiology and Toxicology Center, University of Louisville, Louisville, Kentucky 40202, USA
- Department of Biochemistry & Molecular Genetics, School of Medicine, University of Louisville, Louisville, Kentucky 40202, USA
- The Robley Rex Veterans Affairs Medical Center, Louisville, KY 40206, USA
| | - Timothy E O’Toole
- Division of Environmental Medicine, Department of Medicine, School of Medicine, Christina Lee Brown Envirome Institute, University of Louisville, Louisville, Kentucky 40202, USA
- The Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, Kentucky 40202, USA
- The Superfund Research Center, University of Louisville, Louisville, Kentucky 40202, USA
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3
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Ishima T, Kimura N, Kobayashi M, Nagai R, Osaka H, Aizawa K. A Simple, Fast, Sensitive LC-MS/MS Method to Quantify NAD(H) in Biological Samples: Plasma NAD(H) Measurement to Monitor Brain Pathophysiology. Int J Mol Sci 2024; 25:2325. [PMID: 38397001 PMCID: PMC10888655 DOI: 10.3390/ijms25042325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/08/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Nicotinamide adenine dinucleotide (NAD) is a cofactor in redox reactions and an essential mediator of energy metabolism. The redox balance between NAD+ and NADH affects various diseases, cell differentiation, and aging, and in recent years there has been a growing need for measurement techniques with improved accuracy. However, NAD(H) measurements, representing both NAD+ and NADH, have been limited by the compound's properties. We achieved highly sensitive simultaneous measurement of NAD+ and NADH under non-ion pairing, mobile phase conditions of water, or methanol containing 5 mM ammonium acetate. These were achieved using a simple pre-treatment and 7-min analysis time. Use of the stable isotope 13C5-NAD+ as an internal standard enabled validation close to BMV criteria and demonstrated the robustness of NAD(H) determination. Measurements using this method showed that brain NAD(H) levels correlate strongly with plasma NAD(H) levels in the same mouse, indicating that NAD(H) concentrations in brain tissue are reflected in plasma. As NAD(H) is involved in various neurodegenerative diseases and cerebral ischemia, as well as brain diseases such as mitochondrial myopathies, monitoring changes in NADH levels in plasma after drug administration will be useful for development of future diagnostics and therapeutics.
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Affiliation(s)
- Tamaki Ishima
- Division of Clinical Pharmacology, Department of Pharmacology, Jichi Medical University, Shimotsuke 329-0498, Japan; (T.I.); (N.K.)
| | - Natsuka Kimura
- Division of Clinical Pharmacology, Department of Pharmacology, Jichi Medical University, Shimotsuke 329-0498, Japan; (T.I.); (N.K.)
| | - Mizuki Kobayashi
- Department of Pediatrics, Jichi Medical University, Shimotsuke 329-0498, Japan; (M.K.); (H.O.)
| | - Ryozo Nagai
- Jichi Medical University, Shimotsuke 329-0498, Japan;
| | - Hitoshi Osaka
- Department of Pediatrics, Jichi Medical University, Shimotsuke 329-0498, Japan; (M.K.); (H.O.)
| | - Kenichi Aizawa
- Division of Clinical Pharmacology, Department of Pharmacology, Jichi Medical University, Shimotsuke 329-0498, Japan; (T.I.); (N.K.)
- Clinical Pharmacology Center, Jichi Medical University Hospital, Shimotsuke 329-0498, Japan
- Division of Translational Research, Clinical Research Center, Jichi Medical University Hospital, Shimotsuke 329-0498, Japan
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4
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Warner JB, Hardesty JE, Song YL, Floyd AT, Deng Z, Jebet A, He L, Zhang X, McClain CJ, Hammock BD, Warner DR, Kirpich IA. Hepatic Transcriptome and Its Regulation Following Soluble Epoxide Hydrolase Inhibition in Alcohol-Associated Liver Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:71-84. [PMID: 37925018 PMCID: PMC10768534 DOI: 10.1016/j.ajpath.2023.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 09/02/2023] [Accepted: 09/27/2023] [Indexed: 11/06/2023]
Abstract
Alcohol-associated liver disease (ALD) is a serious public health problem with limited pharmacologic options. The goal of the current study was to investigate the efficacy of pharmacologic inhibition of soluble epoxide hydrolase (sEH), an enzyme involved in lipid metabolism, in experimental ALD, and to examine the underlying mechanisms. C57BL/6J male mice were subjected to acute-on-chronic ethanol (EtOH) feeding with or without the sEH inhibitor 4-[[trans-4-[[[[4-trifluoromethoxy phenyl]amino]carbonyl]-amino]cyclohexyl]oxy]-benzoic acid (TUCB). Liver injury was assessed by multiple end points. Liver epoxy fatty acids and dihydroxy fatty acids were measured by targeted metabolomics. Whole-liver RNA sequencing was performed, and free modified RNA bases were measured by mass spectrometry. EtOH-induced liver injury was ameliorated by TUCB treatment as evidenced by reduced plasma alanine aminotransferase levels and was associated with attenuated alcohol-induced endoplasmic reticulum stress, reduced neutrophil infiltration, and increased numbers of hepatic M2 macrophages. TUCB altered liver epoxy and dihydroxy fatty acids and led to a unique hepatic transcriptional profile characterized by decreased expression of genes involved in apoptosis, inflammation, fibrosis, and carcinogenesis. Several modified RNA bases were robustly changed by TUCB, including N6-methyladenosine and 2-methylthio-N6-threonylcarbamoyladenosine. These findings show the beneficial effects of sEH inhibition by TUCB in experimental EtOH-induced liver injury, warranting further mechanistic studies to explore the underlying mechanisms, and highlighting the translational potential of sEH as a drug target for this disease.
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Affiliation(s)
- Jeffrey B Warner
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky; Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky
| | - Josiah E Hardesty
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky; Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky
| | - Ying L Song
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - Alison T Floyd
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - Zhongbin Deng
- Division of Immunotherapy, Department of Surgery, University of Louisville, Louisville, Kentucky; Brown Cancer Center, University of Louisville, Louisville, Kentucky
| | - Audriy Jebet
- Department of Chemistry, University of Louisville, Louisville, Kentucky
| | - Liqing He
- Department of Chemistry, University of Louisville, Louisville, Kentucky
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, Kentucky
| | - Craig J McClain
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky; Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky; University of Louisville Alcohol Center, University of Louisville School of Medicine, Louisville, Kentucky; University of Louisville Hepatobiology & Toxicology Center, University of Louisville School of Medicine, Louisville, Kentucky; Robley Rex Veterans Medical Center, Louisville, Kentucky
| | - Bruce D Hammock
- Department of Entomology and Nematology, Comprehensive Cancer Center, University of California, Davis, California
| | - Dennis R Warner
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky
| | - Irina A Kirpich
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky; Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky; University of Louisville Alcohol Center, University of Louisville School of Medicine, Louisville, Kentucky; University of Louisville Hepatobiology & Toxicology Center, University of Louisville School of Medicine, Louisville, Kentucky; Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, Kentucky.
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5
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Ross RL, Yu N, Zhao R, Wood A, Limbach PA. Automated Identification of Modified Nucleosides during HRAM-LC-MS/MS using a Metabolomics ID Workflow with Neutral Loss Detection. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2785-2792. [PMID: 37948765 DOI: 10.1021/jasms.3c00298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The role of post-transcriptional modification in biological processes has been an ongoing field of study for several decades. Improvements in liquid chromatography platforms and mass spectrometry instrumentation have resulted in the enhanced identification, characterization, and quantification of modified nucleosides in biological systems. One consequence of the rapid technological improvements in the analytical acquisition of modified nucleosides has been a dearth of robust data processing workflows for analyzing more than a handful of samples at a time. To improve the utility of LC-MS/MS for batch analyses of modified nucleosides, a workflow for automated nucleoside identification has been developed. We adapted the Thermo Fisher Scientific metabolomics identification software package, Compound Discoverer, to accurately identify modified nucleosides from batch LC-MS/MS acquisitions. Three points of identification are used: accurate mass from a monoisotopic mass list, spectral matching from a spectral library, and neutral loss identification. This workflow was applied to a batch (n = 24) of urinary nucleosides, resulting in the accurate identification and relative quantification of 16 known nucleosides in less than 1 h.
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Affiliation(s)
- Robert L Ross
- Thermo Fisher Scientific, Lexington, Massachusetts 04241, United States
| | - Ningxi Yu
- Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Ruoxia Zhao
- Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Andrew Wood
- Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
| | - Patrick A Limbach
- Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, Ohio 45221-0172, United States
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6
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Kopra K, Mahran R, Yli-Hollo T, Tabata S, Vuorinen E, Fujii Y, Vuorinen I, Ogawa-Iio A, Hirayama A, Soga T, Sasaki AT, Härmä H. Homogeneous luminescent quantitation of cellular guanosine and adenosine triphosphates (GTP and ATP) using QT-Luc GTP&ATP assay. Anal Bioanal Chem 2023; 415:6689-6700. [PMID: 37714971 PMCID: PMC10598090 DOI: 10.1007/s00216-023-04944-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/17/2023]
Abstract
Guanosine triphosphate (GTP) and adenosine triphosphate (ATP) are essential nucleic acid building blocks and serve as energy molecules for a wide range of cellular reactions. Cellular GTP concentration fluctuates independently of ATP and is significantly elevated in numerous cancers, contributing to malignancy. Quantitative measurement of ATP and GTP has become increasingly important to elucidate how concentration changes regulate cell function. Liquid chromatography-coupled mass spectrometry (LC-MS) and capillary electrophoresis-coupled MS (CE-MS) are powerful methods widely used for the identification and quantification of biological metabolites. However, these methods have limitations related to specialized instrumentation and expertise, low throughput, and high costs. Here, we introduce a novel quantitative method for GTP concentration monitoring (GTP-quenching resonance energy transfer (QRET)) in homogenous cellular extracts. CE-MS analysis along with pharmacological control of cellular GTP levels shows that GTP-QRET possesses high dynamic range and accuracy. Furthermore, we combined GTP-QRET with luciferase-based ATP detection, leading to a new technology, termed QT-LucGTP&ATP, enabling high-throughput compatible dual monitoring of cellular GTP and ATP in a homogenous fashion. Collectively, GTP-QRET and QT-LucGTP&ATP offer a unique, high-throughput opportunity to explore cellular energy metabolism, serving as a powerful platform for the development of novel therapeutics and extending its usability across a range of disciplines.
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Affiliation(s)
- Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland.
| | - Randa Mahran
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Titta Yli-Hollo
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Sho Tabata
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
| | - Emmiliisa Vuorinen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Yuki Fujii
- Department of Internal Medicine, University of Cincinnati College of Medicine, 3125 Eden Ave, Cincinnati, OH, 45267-0508, USA
| | - Iida Vuorinen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Aki Ogawa-Iio
- Department of Internal Medicine, University of Cincinnati College of Medicine, 3125 Eden Ave, Cincinnati, OH, 45267-0508, USA
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
| | - Atsuo T Sasaki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
- Department of Internal Medicine, University of Cincinnati College of Medicine, 3125 Eden Ave, Cincinnati, OH, 45267-0508, USA
- Department of Clinical and Molecular Genetics, Hiroshima University Hospital, Hiroshima, 734-8551, Japan
| | - Harri Härmä
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
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7
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Sun Z, Sun Y, Shen J, Wang C, Wei Y. Simultaneous enrichment and sequential elution of cis-diol containing molecules and deoxyribonucleotides with bifunctional boronate and titanium (Ⅳ) ion modified-magnetic nanoparticles prior to quantitation by high performance liquid chromatography. J Chromatogr A 2023; 1709:464386. [PMID: 37722178 DOI: 10.1016/j.chroma.2023.464386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 09/20/2023]
Abstract
Some diseases can cause abnormal concentrations of catecholamines (CAs), nucleosides (NSs) and nucleotides (NTs) in patients. Previous studies normally focused on the detection of the three types of substances separately. In this work, a bifunctional boronate and titanium (Ⅳ) ion affinity magnetic adsorbent with high-capacity was prepared. The adsorbent can simultaneously enrich CAs, NSs and NTs in a single extraction process, and the adsorbed analytes can be sequentially eluted by 1.0% trifluoroacetic acid and 20.0 mmol L-1 Na3PO4. An analytical method of the analytes has been established by coupling the adsorbent with RP-HPLC. The method has low detection limits (0.039-0.708 ng mL-1) and good reproducibility (inter- and intra-day of assay RSDs less than 15.0%). Serum sample from healthy volunteer was successfully quantified for two CAs, four NSs and five NTs. Compared with the reported methods, the proposed method is simpler to operate, consume less samples, and has enough accurate and sensitivity to obtain comprehensive information on the concentrations of analytes in a single extraction process.
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Affiliation(s)
- Zhian Sun
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, China
| | - Yao Sun
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, China
| | - Jiwei Shen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, China
| | - Chaozhan Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, China
| | - Yinmao Wei
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, China.
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8
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Hiefner J, Rische J, Bunders MJ, Worthmann A. A liquid chromatography-tandem mass spectrometry based method for the quantification of adenosine nucleotides and NAD precursors and products in various biological samples. Front Immunol 2023; 14:1250762. [PMID: 37799723 PMCID: PMC10548204 DOI: 10.3389/fimmu.2023.1250762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/18/2023] [Indexed: 10/07/2023] Open
Abstract
Adenine nucleotides (AN) are ubiquitous metabolites that regulate cellular energy metabolism and modulate cell communication and inflammation. To understand how disturbances in AN balance arise and affect cellular function, robust quantification techniques for these metabolites are crucial. However, due to their hydrophilicity, simultaneous quantification of AN across various biological samples has been challenging. Here we present a hydrophilic interaction high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) based method for the quantification of 26 adenosine nucleotides and precursors as well as metabolic products of nicotinamide adenine dinucleotide (NAD) in plasma, liver, and adipose tissue samples as well as cell culture supernatants and cells. Method validation was performed with regard to linearity, accuracy, precision, matrix effects, and carryover. Finally, analysis of cell culture supernatants derived from intestinal organoids and RAW 264.7 cells illustrates that the here described method is a reliable and easy-to-use tool to quantify AN and opens up new avenues to understand the role of AN generation and breakdown for cellular functions.
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Affiliation(s)
- Johanna Hiefner
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Johann Rische
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Madeleine J. Bunders
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
- Hamburg Center of Translational Immunology, Hamburg, Germany
| | - Anna Worthmann
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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9
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Xu R, Vatsalya V, He L, Ma X, Feng W, McClain CJ, Zhang X. Altered urinary tryptophan metabolites in alcohol-associated liver disease. ALCOHOL, CLINICAL & EXPERIMENTAL RESEARCH 2023; 47:1665-1676. [PMID: 37431708 PMCID: PMC10782820 DOI: 10.1111/acer.15148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/12/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023]
Abstract
BACKGROUND Alcohol-associated liver disease (ALD) leads to millions of deaths worldwide annually. A few potential biomarkers of ALD have been discovered through metabolomic or proteomic analysis. Tryptophan (Trp), one of nine essential amino acids, has been extensively studied and shown to play significant roles in many mammalian physiological processes. However, Trp metabolism changes in ALD are not yet fully understood. Whereas urine is an abundant and non-invasive source for disease biomarker discovery the current study investigated whether the abundance of Trp metabolites in the urine of ALD patients differs from that of healthy subjects. We also examined whether, if present in ALD, changes in urinary Trp metabolites can serve as markers for differentiating between mild/moderate and severe ALD. METHODS We quantified the concentration of Trp and its metabolites in urine samples of healthy controls (n = 18), patients with mild or moderate alcohol-related liver injury (non-severe ALD; n = 21), and patients with severe alcohol-associated hepatitis (severe AH; n = 25) using both untargeted and targeted metabolomics. RESULTS Eighteen Trp metabolites were identified and quantified from the untargeted metabolomics data. We developed a targeted metabolomics method to quantify the Trp and its metabolites and quantified 17 metabolites from the human urine samples. The data acquired in the untargeted and targeted platforms agreed and showed that the Trp concentration is not affected by the severity of ALD. However, the abundance of 10 Trp metabolites was correlated with the model for end-stage liver disease (MELD) score, with the abundance of nine metabolites significantly different between the healthy control and ALD patient groups. CONCLUSION We found that Trp metabolism differs between ALD patients and healthy controls even though the concentration of Trp was not affected. Two Trp metabolites, quinolinic acid and indoxyl sulfate, correlate highly with the severity of ALD.
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Affiliation(s)
- Raobo Xu
- Department of Chemistry, University of Louisville, Louisville, KY 40208, U.S.A
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40208, U.S.A
- University of Louisville Hepatobiology & Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, KY 40208, U.S.A
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40208, U.S.A
| | - Vatsalya Vatsalya
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40208, U.S.A
- Department of Medicine, University of Louisville, Louisville, KY 40208, U.S.A
| | - Liqing He
- Department of Chemistry, University of Louisville, Louisville, KY 40208, U.S.A
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40208, U.S.A
- University of Louisville Hepatobiology & Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, KY 40208, U.S.A
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40208, U.S.A
| | - Xipeng Ma
- Department of Chemistry, University of Louisville, Louisville, KY 40208, U.S.A
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40208, U.S.A
- University of Louisville Hepatobiology & Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, KY 40208, U.S.A
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40208, U.S.A
| | - Wenke Feng
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40208, U.S.A
- University of Louisville Hepatobiology & Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, KY 40208, U.S.A
- Department of Medicine, University of Louisville, Louisville, KY 40208, U.S.A
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40208, U.S.A
| | - Craig J. McClain
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40208, U.S.A
- University of Louisville Hepatobiology & Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, KY 40208, U.S.A
- Department of Medicine, University of Louisville, Louisville, KY 40208, U.S.A
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40208, U.S.A
- Robley Rex Louisville VAMC, Louisville, KY 40292, U.S.A
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, KY 40208, U.S.A
- University of Louisville Alcohol Research Center, University of Louisville, Louisville, KY 40208, U.S.A
- University of Louisville Hepatobiology & Toxicology Center of Biomedical Research Excellence, University of Louisville, Louisville, KY 40208, U.S.A
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40208, U.S.A
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40208, U.S.A
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10
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Ghosh S, Kundu R, Chandana M, Das R, Anand A, Beura S, Bobde RC, Jain V, Prabhu SR, Behera PK, Mohanty AK, Chakrapani M, Satyamoorthy K, Suryawanshi AR, Dixit A, Padmanaban G, Nagaraj VA. Distinct evolution of type I glutamine synthetase in Plasmodium and its species-specific requirement. Nat Commun 2023; 14:4216. [PMID: 37452051 PMCID: PMC10349072 DOI: 10.1038/s41467-023-39670-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
Malaria parasite lacks canonical pathways for amino acid biosynthesis and depends primarily on hemoglobin degradation and extracellular resources for amino acids. Interestingly, a putative gene for glutamine synthetase (GS) is retained despite glutamine being an abundant amino acid in human and mosquito hosts. Here we show Plasmodium GS has evolved as a unique type I enzyme with distinct structural and regulatory properties to adapt to the asexual niche. Methionine sulfoximine (MSO) and phosphinothricin (PPT) inhibit parasite GS activity. GS is localized to the parasite cytosol and abundantly expressed in all the life cycle stages. Parasite GS displays species-specific requirement in Plasmodium falciparum (Pf) having asparagine-rich proteome. Targeting PfGS affects asparagine levels and inhibits protein synthesis through eIF2α phosphorylation leading to parasite death. Exposure of artemisinin-resistant Pf parasites to MSO and PPT inhibits the emergence of viable parasites upon artemisinin treatment.
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Affiliation(s)
- Sourav Ghosh
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Rajib Kundu
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Manjunatha Chandana
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, 751024, Odisha, India
| | - Rahul Das
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Aditya Anand
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Subhashree Beura
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Ruchir Chandrakant Bobde
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Vishal Jain
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Sowmya Ramakant Prabhu
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | | | - Akshaya Kumar Mohanty
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Ispat General Hospital, Sector 19, Rourkela, 769005, Odisha, India
| | - Mahabala Chakrapani
- Department of Medicine, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | | | - Anshuman Dixit
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Govindarajan Padmanaban
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
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11
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Liu S, He L, Bannister OB, Li J, Schnegelberger RD, Vanderpuye CM, Althouse AD, Schopfer FJ, Wahlang B, Cave MC, Monga SP, Zhang X, Arteel GE, Beier JI. Western diet unmasks transient low-level vinyl chloride-induced tumorigenesis; potential role of the (epi-)transcriptome. Toxicol Appl Pharmacol 2023; 468:116514. [PMID: 37061008 PMCID: PMC10164119 DOI: 10.1016/j.taap.2023.116514] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/17/2023]
Abstract
BACKGROUND & AIMS Vinyl chloride (VC) monomer is a volatile organic compound commonly used in industry. At high exposure levels, VC causes liver cancer and toxicant-associated steatohepatitis. However, lower exposure levels (i.e., sub-regulatory exposure limits) that do not directly damage the liver, enhance injury caused by Western diet (WD). It is still unknown if the long-term impact of transient low-concentration VC enhances the risk of liver cancer development. This is especially a concern given that fatty liver disease is in and of itself a risk factor for the development of liver cancer. METHODS C57Bl/6 J mice were fed WD or control diet (CD) for 1 year. During the first 12 weeks of feeding only, mice were also exposed to VC via inhalation at sub-regulatory limit concentrations (<1 ppm) or air for 6 h/day, 5 days/week. RESULTS Feeding WD for 1 year caused significant hepatic injury, which was exacerbated by VC. Additionally, VC increased the number of tumors which ranged from moderately to poorly differentiated hepatocellular carcinoma (HCC). Transcriptomic analysis demonstrated VC-induced changes in metabolic but also ribosomal processes. Epitranscriptomic analysis showed a VC-induced shift of the modification pattern that has been associated with metabolic disease, mitochondrial dysfunction, and cancer. CONCLUSIONS These data indicate that VC sensitizes the liver to other stressors (e.g., WD), resulting in enhanced tumorigenesis. These data raise concerns about potential interactions between VC exposure and WD. It also emphasizes that current safety restrictions may be insufficient to account for other factors that can influence hepatotoxicity.
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Affiliation(s)
- Silvia Liu
- Department of Pathology, University of Pittsburgh, United States of America; Pittsburgh Liver Research Center, Pittsburgh, PA 15213, United States of America.
| | - Liqing He
- Department of Chemistry, University of Louisville, Louisville, KY 40208, United States of America.
| | - Olivia B Bannister
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition University of Pittsburgh, United States of America.
| | - Jiang Li
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition University of Pittsburgh, United States of America.
| | - Regina D Schnegelberger
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, United States of America.
| | - Charis-Marie Vanderpuye
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition University of Pittsburgh, United States of America.
| | - Andrew D Althouse
- Division of General Internal Medicine, University of Pittsburgh, Pittsburgh, PA 15213, United States of America.
| | - Francisco J Schopfer
- Pittsburgh Liver Research Center, Pittsburgh, PA 15213, United States of America; Department of Pharmacology and Chemical Biology, University of Pittsburgh, United States of America.
| | - Banrida Wahlang
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, United States of America; Superfund Research Center, University of Louisville, Louisville, KY 40202, United States of America; Hepatobiology and Toxicology Center, University of Louisville, Louisville, KY 40202, United States of America; Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, KY 40202, United States of America; University of Louisville Alcohol Research Center, Louisville, KY 40202, United States of America.
| | - Matthew C Cave
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, United States of America; Superfund Research Center, University of Louisville, Louisville, KY 40202, United States of America; Hepatobiology and Toxicology Center, University of Louisville, Louisville, KY 40202, United States of America; Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, KY 40202, United States of America; University of Louisville Alcohol Research Center, Louisville, KY 40202, United States of America; Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40202, United States of America; Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, United States of America; Liver Transplant Program at UofL Health-Jewish Hospital Trager Transplant Center, Louisville, KY 40202, United States of America; The Robley Rex Veterans Affairs Medical Center, Louisville, KY 40206, United States of America.
| | - Satdarshan P Monga
- Department of Pathology, University of Pittsburgh, United States of America; Pittsburgh Liver Research Center, Pittsburgh, PA 15213, United States of America; Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition University of Pittsburgh, United States of America.
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, KY 40208, United States of America; Hepatobiology and Toxicology Center, University of Louisville, Louisville, KY 40202, United States of America; Center for Integrative Environmental Health Sciences, University of Louisville, Louisville, KY 40202, United States of America; University of Louisville Alcohol Research Center, Louisville, KY 40202, United States of America.
| | - Gavin E Arteel
- Pittsburgh Liver Research Center, Pittsburgh, PA 15213, United States of America; Department of Environmental and Occupational Health University of Pittsburgh, Pittsburgh, PA 15213, United States of America.
| | - Juliane I Beier
- Pittsburgh Liver Research Center, Pittsburgh, PA 15213, United States of America; Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition University of Pittsburgh, United States of America; Department of Environmental and Occupational Health University of Pittsburgh, Pittsburgh, PA 15213, United States of America.
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12
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Kurt Z, Çimen D, Denizli A, Bereli N. Development of Optical-Based Molecularly Imprinted Nanosensors for Adenosine Detection. ACS OMEGA 2023; 8:18839-18850. [PMID: 37273602 PMCID: PMC10233842 DOI: 10.1021/acsomega.3c01028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/28/2023] [Indexed: 06/06/2023]
Abstract
Adenosine nucleoside is an important molecule in human physiology. The levels of adenosine nucleoside in urine and plasma are directly or indirectly related to diseases such as neurodegenerative diseases and cancer. In the present study, adenosine-imprinted and non-imprinted poly(2-hydroxyethyl methacrylate-methacrylic acid) (poly(HEMA-MAA)) surface plasmon resonance (SPR) nanosensors were prepared for the determination of adenosine nucleoside. First, MAA/adenosine pre-polymerization complexes were prepared at different molar ratios using adenosine as a template molecule and methacrylic acid (MAA) as a monomer, and SPR nanosensor surfaces were optimized by determining the highest imprinting factor of the chip surfaces. The surfaces of adenosine-imprinted and non-imprinted SPR nanosensors were characterized by using atomic force microscopy, ellipsometry, and contact angle measurements. Kinetic analyses were made with different concentrations in the range of 0.5-400.0 nM for the detection range with a pH 7.4 phosphate buffer solution. The limit of detection in adenosine aqueous solutions, artificial plasma, and artificial urine was determined to be 0.018, 0.015, and 0.013 nM, respectively. In the selectivity analysis of the developed nanosensors, the selectivity of adenosine SPR nanosensors in solutions at different concentrations was determined by using guanosine and cytidine nucleosides. The relative selectivity coefficients of adenosine-imprinted SPR nanosensors for adenosine/cytidine and adenosine/guanosine are 3.836 and 3.427, respectively. Since adenosine-imprinted SPR nanosensors are intended to be used in medical analysis and research, adenosine analysis has also been studied in artificial urine and artificial plasma samples.
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Affiliation(s)
- Zehra
Tuğçe Kurt
- Bioengineering
Division, Hacettepe University, Ankara 06230, Turkey
| | - Duygu Çimen
- Department
of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Adil Denizli
- Department
of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Nilay Bereli
- Department
of Chemistry, Hacettepe University, Ankara 06800, Turkey
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13
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Huang G, Zhang F, Xie D, Ma Y, Wang P, Cao G, Chen L, Lin S, Zhao Z, Cai Z. High-throughput profiling of RNA modifications by ultra-performance liquid chromatography coupled to complementary mass spectrometry: Methods, quality control, and applications. Talanta 2023; 263:124697. [PMID: 37262985 DOI: 10.1016/j.talanta.2023.124697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/17/2023] [Accepted: 05/20/2023] [Indexed: 06/03/2023]
Abstract
Although next-generation sequencing technology has been used to delineate RNA modifications in recent years, the paucity of appropriate converting reactions or specific antibodies impedes the accurate characterization and quantification of numerous RNA modifications, especially when these modifications demonstrate wide variations across developmental stages and cell types. In this study, we developed a high-throughput analytical platform coupling ultra-performance liquid chromatograph (UPLC) with complementary mass spectrometry (MS) to identify and quantify RNA modifications in both synthetic and biological samples. Sixty-four types of RNA modifications, including positional isomers and hypermodified ribonucleosides, were successfully monitored within a 16-min single run of UPLC-MS. Two independent methods to cross-validate the purity of RNA extracted from Caenorhabditis elegans (C. elegans) were developed using the coexisting C. elegans and Escherichia coli (E. coli) as a surveillance system. To test the validity of the method, we investigated the RNA modification landscape of three model organisms, C. elegans, E. coli, and Arabidopsis thaliana (A. thaliana). Both the identity and molarity of modified ribonucleosides markedly varied among the species. Moreover, our platform is not only useful for exploring the dynamics of RNA modifications in response to environmental cues (e.g., cold shock) but can also help with the identification of RNA-modifying enzymes in genetic studies. Cumulatively, our method presents a novel platform for the comprehensive analysis of RNA modifications, which will be of benefit to both analytical chemists involved in biomarker discovery and biologists conducting functional studies of RNA modifications.
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Affiliation(s)
- Gefei Huang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Feng Zhang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Yiming Ma
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Pengxi Wang
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Guodong Cao
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Leijian Chen
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Siyi Lin
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, 999077, China.
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, 999077, China.
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14
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Liu S, Lai Z, Zhang M, Tian H, Zhou J, Li Z. Facile synthesis of amino-functionalized magnetic materials for efficient enrichment of anionic metabolites from biological samples. Anal Chim Acta 2023; 1250:340977. [PMID: 36898822 DOI: 10.1016/j.aca.2023.340977] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023]
Abstract
The analysis of biological samples is often affected by the background matrix. Proper sample preparation is a critical step in the analytical procedure for complex samples. In this study, a simple and efficient enrichment strategy based on Amino-functionalized Polymer-Magnetic MicroParticles (NH2-PMMPs) with coral-like porous structures was developed to enable the detection of 320 anionic metabolites, providing detailed coverage of phosphorylation metabolism. Among them, 102 polar phosphate metabolites including nucleotides, cyclic nucleotides, sugar nucleotides, phosphate sugars, and phosphates, were enriched and identified from serum, tissues, and cells. Furthermore, the detection of 34 previously unknown polar phosphate metabolites in serum samples demonstrates the advantages of this efficient enrichment method for mass spectrometric analysis. The limit of detections (LODs) were between 0.02 and 4 nmol/L for most anionic metabolites and its high sensitivity enabled the detection of 36 polar anion metabolites from 10 cell equivalent samples. This study has provided a promising tool for the efficient enrichment and analysis of anionic metabolites in biological samples with high sensitivity and broad coverage, facilitating the knowledge of the phosphorylation processes of life.
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Affiliation(s)
- Shuai Liu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Zhizhen Lai
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Mo Zhang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Hongtao Tian
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Jiang Zhou
- Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Beijing, 100871, China.
| | - Zhili Li
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
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15
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Xu R, He L, Vatsalya V, Ma X, Kim S, Mueller EG, Feng W, McClain CJ, Zhang X. Metabolomics analysis of urine from patients with alcohol-associated liver disease reveals dysregulated caffeine metabolism. Am J Physiol Gastrointest Liver Physiol 2023; 324:G142-G154. [PMID: 36513601 PMCID: PMC9870580 DOI: 10.1152/ajpgi.00228.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/28/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022]
Abstract
Excess alcohol intake causes millions of deaths annually worldwide. Asymptomatic early-stage, alcohol-associated liver disease (ALD) is easily overlooked, and ALD is usually only diagnosed in more advanced stages. We explored the possibility of using polar urine metabolites as biomarkers of ALD for early-stage diagnosis and functional assessment of disease severity by quantifying the abundance of polar metabolites in the urine samples of healthy controls (n = 18), patients with mild or moderate liver injury (n = 21), and patients with severe alcohol-associated hepatitis (n = 25). The polar metabolites in human urine were first analyzed by untargeted metabolomics, showing that 209 urine metabolites are significantly changed in patients, and 17 of these are highly correlated with patients' model for end-stage liver disease (MELD) score. Pathway enrichment analysis reveals that the caffeine metabolic pathway is the most affected in ALD. We then developed a targeted metabolomics method and measured the concentration of caffeine and its metabolites in urine using internal and external standard calibration, respectively. The described method can quantify caffeine and its 14 metabolites in 35 min. The results of targeted metabolomics analysis agree with the results of untargeted metabolomics, showing that 13 caffeine metabolites are significantly decreased in patients. In particular, the concentrations of 1-methylxanthine, paraxanthine, and 5-acetylamino-6-amino-3-methyluracil are markedly decreased with increased disease severity. We suggest that these three metabolites could serve as functional biomarkers for differentiating early-stage ALD from more advanced liver injury.NEW & NOTEWORTHY Our study using both untargeted and targeted metabolomics reveals the caffeine metabolic pathway is dysregulated in ALD. Three caffeine metabolites, 1-methylxanthine, paraxanthine, and 5-acetylamino-6-amino-3-methyluracil, can differentiate the severity of early-stage ALD.
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Affiliation(s)
- Raobo Xu
- Department of Chemistry, University of Louisville, Louisville, Kentucky
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, Kentucky
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville School of Medicine Louisville, Louisville, Kentucky
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, Kentucky
| | - Liqing He
- Department of Chemistry, University of Louisville, Louisville, Kentucky
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, Kentucky
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville School of Medicine Louisville, Louisville, Kentucky
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, Kentucky
| | - Vatsalya Vatsalya
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, Kentucky
- Department of Medicine, University of Louisville, Louisville, Kentucky
| | - Xipeng Ma
- Department of Chemistry, University of Louisville, Louisville, Kentucky
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, Kentucky
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville School of Medicine Louisville, Louisville, Kentucky
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, Kentucky
| | - Seongho Kim
- Department of Oncology, Wayne State University, Detroit, Michigan
- Biostatistics and Bioinformatics Core, Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Eugene G Mueller
- Department of Chemistry, University of Louisville, Louisville, Kentucky
| | - Wenke Feng
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, Kentucky
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville School of Medicine Louisville, Louisville, Kentucky
- Department of Medicine, University of Louisville, Louisville, Kentucky
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky
| | - Craig J McClain
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, Kentucky
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville School of Medicine Louisville, Louisville, Kentucky
- Department of Medicine, University of Louisville, Louisville, Kentucky
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky
- Robley Rex Louisville Veterans Affairs Medical Center, Louisville, Kentucky
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, Kentucky
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, Kentucky
- Hepatobiology and Toxicology Center of Biomedical Research Excellence, University of Louisville School of Medicine Louisville, Louisville, Kentucky
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, Kentucky
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, Kentucky
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16
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Sit I, Quirk E, Hettiarachchi E, Grassian VH. Differential Surface Interactions and Surface Templating of Nucleotides (dGMP, dCMP, dAMP, and dTMP) on Oxide Particle Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15038-15049. [PMID: 36445255 PMCID: PMC9753757 DOI: 10.1021/acs.langmuir.2c01604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 11/07/2022] [Indexed: 06/16/2023]
Abstract
The fate of biomolecules in the environment depends in part on understanding the surface chemistry occurring at the biological-geochemical (bio-geo) interface. Little is known about how environmental DNA (eDNA) or smaller components, like nucleotides and oligonucleotides, persist in aquatic environments and the role of surface interactions. This study aims to probe surface interactions and adsorption behavior of nucleotides on oxide surfaces. We have investigated the interactions of individual nucleotides (dGMP, dCMP, dAMP, and dTMP) on TiO2 particle surfaces as a function of pH and in the presence of complementary and noncomplementary base pairs. Using attenuated total reflectance-Fourier transform infrared spectroscopy, there is an increased number of adsorbed nucleotides at lower pH with a preferential interaction of the phosphate group with the oxide surface. Additionally, differential adsorption behavior is seen where purine nucleotides are preferentially adsorbed, with higher surface saturation coverage, over their pyrimidine derivatives. These differences may be a result of intermolecular interactions between coadsorbed nucleotides. When the TiO2 surface was exposed to two-component solutions of nucleotides, there was preferential adsorption of dGMP compared to dCMP and dTMP, and dAMP compared to dTMP and dCMP. Complementary nucleotide base pairs showed hydrogen-bond interactions between a strongly adsorbed purine nucleotide layer and a weaker interacting hydrogen-bonded pyrimidine second layer. Noncomplementary base pairs did not form a second layer. These results highlight several important findings: (i) there is differential adsorption of nucleotides; (ii) complementary coadsorbed nucleotides show base pairing with a second layer, and the stability depends on the strength of the hydrogen bonding interactions and; (iii) the first layer coverage strongly depends on pH. Overall, the importance of surface interactions in the adsorption of nucleotides and the templating of specific interactions between nucleotides are discussed.
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Affiliation(s)
- Izaac Sit
- Department
of Nanoengineering and Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Eleanor Quirk
- Department
of Nanoengineering and Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Eshani Hettiarachchi
- Department
of Nanoengineering and Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Vicki H. Grassian
- Department
of Nanoengineering and Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
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17
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He L, Vatsalya V, Ma X, Klinge CM, Cave MC, Feng W, McClain CJ, Zhang X. Metabolic Analysis of Nucleosides/Bases in the Urine and Serum of Patients with Alcohol-Associated Liver Disease. Metabolites 2022; 12:metabo12121187. [PMID: 36557225 PMCID: PMC9783452 DOI: 10.3390/metabo12121187] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/15/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Accumulating evidence supports the important role of RNA modifications in liver disease pathogenesis. However, RNA modifications in alcohol-associated liver disease (ALD) have not yet been reported. Modified ribonucleosides/bases are products of RNA degradation; therefore, we investigated whether modified ribonucleosides/bases in human urine and serum are changed and whether these changes are associated with the severity of ALD. Human urine and serum samples from patients with ALD and appropriate controls were collected. Free nucleosides/bases were extracted from these samples and quantified using untargeted and targeted metabolomic approaches. Thirty-nine and forty free nucleosides/bases were respectively detected in human urine and serum samples. Twelve and eleven modified nucleosides are significantly changed in patients’ urine and serum (q < 0.05 and fold-change > 20%). The abundance of modified nucleobase and ribonucleoside, 7,9-dimethylguanine in urine and 2-methylthio-N6-threonylcarbamoyladenosine (ms2t6A) in serum are strongly associated with the severity of ALD. Spearman’s rank correlation coefficient of these two metabolites with the Model for End-stage Liver Disease (MELD) score are 0.66 and 0.74, respectively. Notably, the abundance changes in these two metabolites are sufficiently large to distinguish severe alcohol-associate hepatitis (AH) from non-severe ALD and non-severe ALD from healthy controls.
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Affiliation(s)
- Liqing He
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Hepatobiology & Toxicology Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40292, USA
| | - Vatsalya Vatsalya
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Xipeng Ma
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Hepatobiology & Toxicology Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40292, USA
| | - Carolyn M. Klinge
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Matthew C. Cave
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Hepatobiology & Toxicology Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Wenke Feng
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Hepatobiology & Toxicology Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Craig J. McClain
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Hepatobiology & Toxicology Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Robley Rex Department of Veterans Affairs Medical Center, Louisville, KY 40206, USA
- Correspondence: (C.J.M.); (X.Z.)
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA
- Alcohol Research Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Hepatobiology & Toxicology Center, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Center for Regulatory and Environmental Analytical Metabolomics, University of Louisville, Louisville, KY 40292, USA
- Department of Pharmacology & Toxicology, University of Louisville School of Medicine, Louisville, KY 40202, USA
- Correspondence: (C.J.M.); (X.Z.)
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18
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Development of an Ultra-high Performance Liquid Chromatography Method for the Separation and Determination of Nucleotides and Nucleosides in Extracts From Infant Milk Formulas and Human Milk Samples. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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19
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Hayter EA, Azibere S, Skrajewski LA, Soule LD, Spence DM, Martin RS. A 3D-printed, multi-modal microfluidic device for measuring nitric oxide and ATP release from flowing red blood cells. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:3171-3179. [PMID: 35959771 PMCID: PMC10227723 DOI: 10.1039/d2ay00931e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this paper, a 3D-printed multi-modal device was designed and fabricated to simultaneously detect nitric oxide (NO) and adenosine triphosphate (ATP) in red blood cell suspensions prepared from whole blood. Once a sample was injected into the device, NO was first detected (via amperometry) using a three-electrode, dual-opposed, electrode configuration with a platinum-black/Nafion coated gold working electrode. After in-line amperometric detection of NO, ATP was detected via a chemiluminescence reaction, with a luciferin/luciferase solution continuously pumped into an integrated mixing T and the resulting light being measured with a PMT underneath the channel. The device was optimized for mixing/reaction conditions, limits of detection (40 nM for NO and 30 nM for ATP), and sensitivity. This device was used to determine the basal (normoxic) levels of NO and ATP in red blood cells, as well as an increase in concentration of both analytes under hypoxic conditions. Finally, the effect of storing red blood cells in a commonly used storage solution was also investigated by monitoring the production of NO and ATP over a three-week storage time.
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Affiliation(s)
- Elizabeth A Hayter
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave St. Louis, MO, USA, 63103.
| | - Samuel Azibere
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave St. Louis, MO, USA, 63103.
| | - Lauren A Skrajewski
- Department of Biomedical Engineering, Institute for Quantitative Health Science & Engineering, Michigan State University, USA
| | - Logan D Soule
- Department of Biomedical Engineering, Institute for Quantitative Health Science & Engineering, Michigan State University, USA
| | - Dana M Spence
- Department of Biomedical Engineering, Institute for Quantitative Health Science & Engineering, Michigan State University, USA
| | - R Scott Martin
- Department of Chemistry, Saint Louis University, 3501 Laclede Ave St. Louis, MO, USA, 63103.
- Center for Additive Manufacturing, Saint Louis University, USA
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20
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Nanoconfined liquid phase nanoextraction combined with in-fiber derivatization for simultaneous quantification of seventy amino-containing metabolites in plasma by LC-MS/MS: Exploration of lung cancer screening model. Talanta 2022; 245:123452. [DOI: 10.1016/j.talanta.2022.123452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/30/2022] [Accepted: 04/03/2022] [Indexed: 11/23/2022]
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21
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Liu S, Zhang M, Lai Z, Tian H, Qiu Y, Li Z. Coral-like Magnetic Particles for Chemoselective Extraction of Anionic Metabolites. ACS APPLIED MATERIALS & INTERFACES 2022; 14:32890-32900. [PMID: 35819264 DOI: 10.1021/acsami.2c06922] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
To date, advanced chemical biology tools for chemoselective extraction of metabolites are limited. In this study, unique coral-like polymer particles were synthesized via high concentrations of 1-ethyl-3-(3-(dimethylamino)propyl) carbodiimide hydrochloride (EDC)/N-hydroxysuccinimide (NHS), which are usually used as condensation agents. The polymers can wrap or adhere Fe3O4 nanoparticles (Fe3O4-NPs) to form polymer magnetic microparticles (PMMPs). With abundant NHS-activated moieties on their surface, the coral-like PMMPs could be modified by cystamine for the chemoselective extraction of phosphate/carboxylate anion metabolites from complex biological samples. Finally, 97 metabolites including nucleotides, phosphates, phosphate sugars, carboxylate sugars, and organic acids were extracted and identified from serum, tissues, and cells. These metabolites are involved in four major metabolic pathways including glycolysis, the tricarboxylic acid cycle, the pentose phosphate pathway, and nucleotide metabolism. This study has provided a cost-effective and easy-to-implement preparation of PMMPs with a robust chemoselective extraction ability and versatile applications.
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Affiliation(s)
- Shuai Liu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005, China
| | - Mo Zhang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005, China
| | - Zhizhen Lai
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005, China
| | - Hongtao Tian
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005, China
| | - Yuming Qiu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005, China
| | - Zhili Li
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 5 Dongdan San Tiao, Beijing 100005, China
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22
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Stochastic dynamic quantitative and 3D structural matrix assisted laser desorption/ionization mass spectrometric analyses of mixture of nucleosides. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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In-situ growth of boronic acid-decorated metal-organic framework on Fe3O4 nanospheres for specific enrichment of cis-diol containing nucleosides. Anal Chim Acta 2022; 1206:339772. [DOI: 10.1016/j.aca.2022.339772] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 03/09/2022] [Accepted: 03/24/2022] [Indexed: 12/26/2022]
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24
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Krämer J, Kang R, Grimm LM, De Cola L, Picchetti P, Biedermann F. Molecular Probes, Chemosensors, and Nanosensors for Optical Detection of Biorelevant Molecules and Ions in Aqueous Media and Biofluids. Chem Rev 2022; 122:3459-3636. [PMID: 34995461 PMCID: PMC8832467 DOI: 10.1021/acs.chemrev.1c00746] [Citation(s) in RCA: 100] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Synthetic molecular probes, chemosensors, and nanosensors used in combination with innovative assay protocols hold great potential for the development of robust, low-cost, and fast-responding sensors that are applicable in biofluids (urine, blood, and saliva). Particularly, the development of sensors for metabolites, neurotransmitters, drugs, and inorganic ions is highly desirable due to a lack of suitable biosensors. In addition, the monitoring and analysis of metabolic and signaling networks in cells and organisms by optical probes and chemosensors is becoming increasingly important in molecular biology and medicine. Thus, new perspectives for personalized diagnostics, theranostics, and biochemical/medical research will be unlocked when standing limitations of artificial binders and receptors are overcome. In this review, we survey synthetic sensing systems that have promising (future) application potential for the detection of small molecules, cations, and anions in aqueous media and biofluids. Special attention was given to sensing systems that provide a readily measurable optical signal through dynamic covalent chemistry, supramolecular host-guest interactions, or nanoparticles featuring plasmonic effects. This review shall also enable the reader to evaluate the current performance of molecular probes, chemosensors, and nanosensors in terms of sensitivity and selectivity with respect to practical requirement, and thereby inspiring new ideas for the development of further advanced systems.
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Affiliation(s)
- Joana Krämer
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Rui Kang
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Laura M. Grimm
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Luisa De Cola
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Dipartimento
DISFARM, University of Milano, via Camillo Golgi 19, 20133 Milano, Italy
- Department
of Molecular Biochemistry and Pharmacology, Instituto di Ricerche Farmacologiche Mario Negri, IRCCS, 20156 Milano, Italy
| | - Pierre Picchetti
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- P.P.: email,
| | - Frank Biedermann
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- F.B.: email,
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25
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Geiger M, Hayter E, Martin R, Spence D. Red blood cells in type 1 diabetes and multiple sclerosis and technologies to measure their emerging roles. J Transl Autoimmun 2022; 5:100161. [PMID: 36039310 PMCID: PMC9418496 DOI: 10.1016/j.jtauto.2022.100161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 11/15/2022] Open
Affiliation(s)
- M. Geiger
- Institute of Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - E. Hayter
- Department of Chemistry, Saint Louis University, St. Louis, MO 63103, USA
| | - R.S. Martin
- Department of Chemistry, Saint Louis University, St. Louis, MO 63103, USA
| | - D. Spence
- Institute of Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI 48824, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI 48824, USA
- Corresponding author. 775 Woodlot Drive, East Lansing, MI 48824, USA.
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26
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Zheng J, Zhao M, Yang L, Chen Y, Gu X, Huang Q. Application of a HPLC-Q/TOF method with post-column compensation for separation and identification of polar impurities in Cytidine disodium triphosphate for injection. CURR PHARM ANAL 2021. [DOI: 10.2174/1573412918666211214095347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Cytidine Disodium Triphosphate (CTP-2Na) for injection is mainly used
for treating nervous system diseases. Currently, there are few studies focused on the separation and
identification of polar impurities in CTP-2Na for injection, which is important for ensuring drug
safety and efficacy.
Objective:
The study aimed to establish an HPLC-Q/TOF method for the separation and identification of polar impurities in CTP-2Na for injection.
Methods:
Chromatographic separation was achieved on a Waters Atlantis T3 column using 5 mM
aqueous ammonium acetate solution as the mobile phase in an isocratic elution mode. A postcolumn compensation technology was used to improve the ionization efficiency of impurities in the
spray chamber.
Results:
Three polar impurities (disodium cytidine tetraphosphate, disodium cytidine diphosphate,
disodium cytidine monophosphate) were detected in CTP-2Na for injection. The former one is
probably the overreaction product during the production of CTP-2Na, the latter two were reported
as degradation products. The fragmentation patterns of cytidine phosphate compounds in negative
ion mode are summarized.
Conclusion:
This study provides a good reference for the separation and identification of polar impurities in nucleotide drugs.
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Affiliation(s)
- Jinqi Zheng
- Zhejiang Institute for Food and Drug Control (Key Laboratory of Core Technology for Generic Drug Evaluation, China Drug Administration), Hangzhou, Zhejiang, China
| | - Mingjuan Zhao
- Zhejiang Institute for Food and Drug Control (Key Laboratory of Core Technology for Generic Drug Evaluation, China Drug Administration), Hangzhou, Zhejiang, China
| | - Lishi Yang
- Zhejiang Institute for Food and Drug Control (Key Laboratory of Core Technology for Generic Drug Evaluation, China Drug Administration), Hangzhou, Zhejiang, China
| | - Yue Chen
- Zhejiang Institute for Food and Drug Control (Key Laboratory of Core Technology for Generic Drug Evaluation, China Drug Administration), Hangzhou, Zhejiang, China
| | - Xiao Gu
- Zhejiang Institute for Food and Drug Control (Key Laboratory of Core Technology for Generic Drug Evaluation, China Drug Administration), Hangzhou, Zhejiang, China
| | - Qiaoqiao Huang
- Zhejiang Institute for Food and Drug Control (Key Laboratory of Core Technology for Generic Drug Evaluation, China Drug Administration), Hangzhou, Zhejiang, China
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27
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Huang G, Ding Q, Xie D, Cai Z, Zhao Z. Technical challenges in defining RNA modifications. Semin Cell Dev Biol 2021; 127:155-165. [PMID: 34838434 DOI: 10.1016/j.semcdb.2021.11.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/28/2021] [Accepted: 11/10/2021] [Indexed: 01/27/2023]
Abstract
It is well established that DNA base modifications play a key role in gene regulation during development and in response to environmental stress. This type of epigenetic control of development and environmental responses has been intensively studied over the past few decades. Similar to DNA, various RNA species also undergo modifications that play important roles in, for example, RNA splicing, protein translation, and the avoidance of immune surveillance by host. More than 160 different types of RNA modifications have been identified. In addition to base modifications, RNA modification also involves splicing of pre-mRNAs, leading to as many as tens of transcript isoforms from a single pre-RNA, especially in higher organisms. However, the function, prevalence and distribution of RNA modifications are poorly understood. The lack of a suitable method for the reliable identification of RNA modifications constitutes a significant challenge to studying their functions. This review focuses on the technologies that enable de novo identification of RNA base modifications and the alternatively spliced mRNA transcripts.
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Affiliation(s)
- Gefei Huang
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
| | - Qiutao Ding
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zongwei Cai
- Department of Chemistry, Hong Kong Baptist University, Hong Kong, China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China.
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China.
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28
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Klinge CM, Piell KM, Petri BJ, He L, Zhang X, Pan J, Rai SN, Andreeva K, Rouchka EC, Wahlang B, Beier JI, Cave MC. Combined exposure to polychlorinated biphenyls and high-fat diet modifies the global epitranscriptomic landscape in mouse liver. ENVIRONMENTAL EPIGENETICS 2021; 7:dvab008. [PMID: 34548932 PMCID: PMC8448424 DOI: 10.1093/eep/dvab008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/13/2021] [Accepted: 08/10/2021] [Indexed: 05/30/2023]
Abstract
Exposure to a single dose of polychlorinated biphenyls (PCBs) and a 12-week high-fat diet (HFD) results in nonalcoholic steatohepatitis (NASH) in mice by altering intracellular signaling and inhibiting epidermal growth factor receptor signaling. Post-transcriptional chemical modification (PTM) of RNA regulates biological processes, but the contribution of epitranscriptomics to PCB-induced steatosis remains unknown. This study tested the hypothesis that PCB and HFD exposure alters the global RNA epitranscriptome in male mouse liver. C57BL/6J male mice were fed a HFD for 12 weeks and exposed to a single dose of Aroclor 1260 (20 mg/kg), PCB 126 (20 µg/kg), both Aroclor 1260 and PCB 126 or vehicle control after 2 weeks on HFD. Chemical RNA modifications were identified at the nucleoside level by liquid chromatography-mass spectrometry. From 22 PTM global RNA modifications, we identified 10 significant changes in RNA modifications in liver with HFD and PCB 126 exposure. Only two modifications were significantly different from HFD control liver in all three PCB exposure groups: 2'-O-methyladenosine (Am) and N(6)-methyladenosine (m6A). Exposure to HFD + PCB 126 + Aroclor 1260 increased the abundance of N(6), O(2)-dimethyladenosine (m6Am), which is associated with the largest number of transcript changes. Increased m6Am and pseudouridine were associated with increased protein expression of the writers of these modifications: Phosphorylated CTD Interacting Factor 1 (PCIF1) and Pseudouridine Synthase 10 (PUS10), respectively, in HFD + PCB 126- + Aroclor 1260-exposed mouse liver. Increased N1-methyladenosine (m1A) and m6A were associated with increased transcript levels of the readers of these modifications: YTH N6-Methyladenosine RNA Binding Protein 2 (YTHDF2), YTH Domain Containing 2 (YTHDC2), and reader FMRP Translational Regulator 1 (FMR1) transcript and protein abundance. The results demonstrate that PCB exposure alters the global epitranscriptome in a mouse model of NASH; however, the mechanism for these changes requires further investigation.
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Affiliation(s)
- Carolyn M Klinge
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
| | - Kellianne M Piell
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Belinda J Petri
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Liqing He
- Department of Chemistry, University of Louisville College of Arts and Sciences, Louisville, KY 40292, USA
| | - Xiang Zhang
- Department of Chemistry, University of Louisville College of Arts and Sciences, Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
| | - Jianmin Pan
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Shesh N Rai
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
- Department of Bioinformatics and Biostatistics, University of Louisville School of Public Health and Information Sciences, Louisville, KY 40292, USA
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville School of Medicine, Louisville, KY 40292, USA
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
| | - Kalina Andreeva
- Bioinformatics and Biomedical Computing Laboratory, Department of Computer Engineering and Computer Science, JB Speed School of Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Eric C Rouchka
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Banrida Wahlang
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
- Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Juliane I Beier
- Department of Medicine, Division of Gastroenterology, Hepatology & Nutrition, University of Pittsburgh, Louisville, KY 40292, USA
- Pittsburgh Liver Research Center (PLRC), Louisville, KY 40292, USA
- Department of Environmental and Occupational Health Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Matthew C Cave
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), Louisville, KY 40292, USA
- University of Louisville Hepatobiology and Toxicology Center, Louisville, KY 40292, USA
- University of Louisville Alcohol Research Center, Louisville, KY 40292, USA
- The University of Louisville Superfund Research Center, Louisville, KY 40292, USA
- Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, KY 40292, USA
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, KY 40292, USA
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29
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Ding T, Song G, Liu X, Xu M, Li Y. Nucleotides as optimal candidates for essential nutrients in living organisms: A review. J Funct Foods 2021. [DOI: 10.1016/j.jff.2021.104498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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30
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Lei C, Teng Y, He L, Sayed M, Mu J, Xu F, Zhang X, Kumar A, Sundaram K, Sriwastva MK, Zhang L, Chen SY, Feng W, Zhang S, Yan J, Park JW, Merchant ML, Zhang X, Zhang HG. Lemon exosome-like nanoparticles enhance stress survival of gut bacteria by RNase P-mediated specific tRNA decay. iScience 2021; 24:102511. [PMID: 34142028 PMCID: PMC8188359 DOI: 10.1016/j.isci.2021.102511] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/29/2021] [Accepted: 04/30/2021] [Indexed: 11/30/2022] Open
Abstract
Diet and bile play critical roles in shaping gut microbiota, but the molecular mechanism underlying interplay with intestinal microbiota is unclear. Here, we showed that lemon-derived exosome-like nanoparticles (LELNs) enhance lactobacilli toleration to bile. To decipher the mechanism, we used Lactobacillus rhamnosus GG (LGG) as proof of concept to show that LELNs enhance LGG bile resistance via limiting production of Msp1 and Msp3, resulting in decrease of bile accessibility to cell membrane. Furthermore, we found that decline of Msps protein levels was regulated through specific tRNAser UCC and tRNAser UCG decay. We identified RNase P, an essential housekeeping endonuclease, being responsible for LELNs-induced tRNAser UCC and tRNAser UCG decay. We further identified galacturonic acid-enriched pectin-type polysaccharide as the active factor in LELNs to increase bile resistance and downregulate tRNAser UCC and tRNAser UCG level in the LGG. Our study demonstrates a tRNA-based gene expression regulation mechanism among lactobacilli to increase bile resistance.
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Affiliation(s)
- Chao Lei
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, CTRB 309 505 Hancock Street, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Yun Teng
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, CTRB 309 505 Hancock Street, Louisville, KY 40202, USA
| | - Liqing He
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville, Louisville, KY, USA
| | - Mohammed Sayed
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40202, USA
| | - Jingyao Mu
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, CTRB 309 505 Hancock Street, Louisville, KY 40202, USA
| | - Fangyi Xu
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, CTRB 309 505 Hancock Street, Louisville, KY 40202, USA
| | - Xiangcheng Zhang
- Department of ICU, the Affiliated Huaian NO.1 People's Hospital of Nanjing Medical University, Huaian, Jiangsu 223300, China
| | - Anil Kumar
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, CTRB 309 505 Hancock Street, Louisville, KY 40202, USA
| | - Kumaran Sundaram
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, CTRB 309 505 Hancock Street, Louisville, KY 40202, USA
| | - Mukesh K. Sriwastva
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, CTRB 309 505 Hancock Street, Louisville, KY 40202, USA
| | - Lifeng Zhang
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, CTRB 309 505 Hancock Street, Louisville, KY 40202, USA
| | - Shao-yu Chen
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA
| | - Wenke Feng
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Shuangqin Zhang
- Peeples Cancer Institute, 215 Memorial Drive, Dalton, GA 30720, USA
| | - Jun Yan
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, CTRB 309 505 Hancock Street, Louisville, KY 40202, USA
| | - Juw Won Park
- Department of Computer Engineering and Computer Science, University of Louisville, Louisville, KY 40202, USA
- KBRIN Bioinformatics Core, University of Louisville, Louisville, KY 40202, USA
| | - Michael L. Merchant
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville, Louisville, KY, USA
| | - Xiang Zhang
- Kidney Disease Program and Clinical Proteomics Center, University of Louisville, Louisville, KY, USA
| | - Huang-Ge Zhang
- Robley Rex Veterans Affairs Medical Center, Louisville, KY 40206, USA
- James Graham Brown Cancer Center, Department of Microbiology & Immunology, University of Louisville, CTRB 309 505 Hancock Street, Louisville, KY 40202, USA
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31
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He L, Vatsalya V, Ma X, Zhang J, Yin X, Kim S, Feng W, McClain CJ, Zhang X. Metabolic Profiling of Bile Acids in the Urine of Patients with Alcohol-Associated Liver Disease. Hepatol Commun 2021; 5:798-811. [PMID: 34027270 PMCID: PMC8122376 DOI: 10.1002/hep4.1671] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/02/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022] Open
Abstract
Bile acids (BAs) play important functions in the development of alcohol-associated liver disease (ALD). In the current study, urine BA concentrations in 38 patients with well-described alcohol-associated hepatitis (AH) as characterized by Model for End-Stage Liver Disease (MELD), 8 patients with alcohol-use disorder (AUD), and 19 healthy controls (HCs) were analyzed using liquid chromatography-mass spectrometry. Forty-three BAs were identified, and 22 BAs had significant changes in their abundance levels in patients with AH. The potential associations of clinical data were compared to candidate BAs in this pilot proof-of-concept study. MELD score showed positive correlations with several conjugated BAs and negative correlations with certain unconjugated BAs; taurine-conjugated chenodeoxycholic acid (CDCA) and MELD score showed the highest association. Cholic acid, CDCA, and apocholic acid had nonsignificant abundance changes in patients with nonsevere ALD compared to HCs but were significantly increased in those with severe AH. Receiver operating characteristic analysis showed that the differences in these three compounds were sufficiently large to distinguish severe AH from nonsevere ALD. Notably, the abundance levels of primary BAs were significantly increased while most of the secondary BAs were markedly decreased in AH compared to AUD. Most importantly, the amount of total BAs and the ratio of primary to secondary BAs increased while the ratio of unconjugated to conjugated BAs decreased as disease severity increased. Conclusion: Abundance changes of specific BAs are closely correlated with the severity of AH in this pilot study. Urine BAs (individually or as a group) could be potential noninvasive laboratory biomarkers for detecting early stage ALD and may have prognostic value in AH morbidity.
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Affiliation(s)
- Liqing He
- Department of ChemistryUniversity of LouisvilleLouisvilleKYUSA.,Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA.,Hepatobiology and Toxicology ProgramUniversity of LouisvilleLouisvilleKYUSA.,Center for Regulatory and Environmental Analytical MetabolomicsUniversity of LouisvilleLouisvilleKYUSA
| | - Vatsalya Vatsalya
- Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA.,Department of MedicineUniversity of LouisvilleLouisvilleKYUSA.,Robley Rex Louisville Veterans Affairs Medical CenterLouisvilleKYUSA
| | - Xipeng Ma
- Department of ChemistryUniversity of LouisvilleLouisvilleKYUSA.,Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA.,Hepatobiology and Toxicology ProgramUniversity of LouisvilleLouisvilleKYUSA.,Center for Regulatory and Environmental Analytical MetabolomicsUniversity of LouisvilleLouisvilleKYUSA
| | - Jiayang Zhang
- School of DentistryUniversity of LouisvilleLouisvilleKYUSA
| | - Xinmin Yin
- Department of ChemistryUniversity of LouisvilleLouisvilleKYUSA.,Center for Regulatory and Environmental Analytical MetabolomicsUniversity of LouisvilleLouisvilleKYUSA
| | - Seongho Kim
- Department of OncologyUniversity of LouisvilleLouisvilleKYUSA.,Biostatistics Core, Karmanos Cancer InstituteWayne State UniversityDetroitMIUSA
| | - Wenke Feng
- Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA.,Hepatobiology and Toxicology ProgramUniversity of LouisvilleLouisvilleKYUSA.,Department of MedicineUniversity of LouisvilleLouisvilleKYUSA.,Department of Pharmacology and ToxicologyUniversity of LouisvilleLouisvilleKYUSA
| | - Craig J McClain
- Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA.,Hepatobiology and Toxicology ProgramUniversity of LouisvilleLouisvilleKYUSA.,Department of MedicineUniversity of LouisvilleLouisvilleKYUSA.,Robley Rex Louisville Veterans Affairs Medical CenterLouisvilleKYUSA.,Biostatistics Core, Karmanos Cancer InstituteWayne State UniversityDetroitMIUSA
| | - Xiang Zhang
- Department of ChemistryUniversity of LouisvilleLouisvilleKYUSA.,Alcohol Research CenterUniversity of LouisvilleLouisvilleKYUSA.,Hepatobiology and Toxicology ProgramUniversity of LouisvilleLouisvilleKYUSA.,Center for Regulatory and Environmental Analytical MetabolomicsUniversity of LouisvilleLouisvilleKYUSA.,Department of Pharmacology and ToxicologyUniversity of LouisvilleLouisvilleKYUSA
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32
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Wang H, Simpson JH, Kotra ME, Zhu Y, Wickramasinghe S, Mills DA, Chiu NHL. Epitranscriptomic profile of Lactobacillus agilis and its adaptation to growth on inulin. BMC Res Notes 2021; 14:154. [PMID: 33883017 PMCID: PMC8058956 DOI: 10.1186/s13104-021-05563-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/09/2021] [Indexed: 12/17/2022] Open
Abstract
Objective Ribonucleic acids (RNA) are involved in many cellular functions. In general, RNA is made up by only four different ribonucleotides. The modifications of RNA (epitranscriptome) can greatly enhance the structural diversity of RNA, which in turn support some of the RNA functions. To determine whether the epitranscriptome of a specific probiotic is associated with its adaptation to the source of energy, Lactobacillus agilis (YZ050) was selected as a model and its epitranscriptome was profiled and compared by using mass spectrometry. Results The L. agilis epitranscriptome (minus rRNA modifications) consists of 17 different RNA modifications. By capturing the L. agilis cells during exponential growth, reproducible profiling was achieved. In a comparative study, the standard source of energy (glucose) in the medium was substituted by a prebiotic inulin, and a downward trend in the L. agilis epitranscriptome was detected. This marks the first report on a system-wide variation of a bacterial epitranscriptome that resulted from adapting to an alternative energy source. No correlation was found between the down-regulated RNA modifications and the expression level of corresponding writer genes. Whereas, the expression level of a specific exonuclease gene, RNase J1, was detected to be higher in cells grown on inulin.
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Affiliation(s)
- Hongzhou Wang
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Jennifer H Simpson
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Madison E Kotra
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, USA
| | - Yuanting Zhu
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | | | - David A Mills
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Norman H L Chiu
- Department of Chemistry and Biochemistry, University of North Carolina Greensboro, Greensboro, NC, USA. .,Joint School of Nanoscience and Nanoengineering, University of North Carolina Greensboro, Greensboro, NC, USA.
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Geller S, Lieberman H, Kloss A, Ivanov AR. A systematic approach to development of analytical scale and microflow-based liquid chromatography coupled to mass spectrometry metabolomics methods to support drug discovery and development. J Chromatogr A 2021; 1642:462047. [PMID: 33744605 DOI: 10.1016/j.chroma.2021.462047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 12/21/2022]
Abstract
As the reliance on metabolic biomarkers within drug discovery and development increases, there is also an increased demand for global metabolomics methods to provide broad metabolome coverage and sensitivity towards differences in metabolite expression and reproducibility. A systematic approach is necessary for the development, and evaluation, of metabolomics methods using either conventional techniques or when establishing new methods that allow for additional gains in sensitivity and a reduction in requirements for amounts of a biological sample, such as those seen with methods based on microseparations. We developed a novel standard mixture and used a systematic approach for the development and optimization of optimal, ion-pair free, liquid chromatography-mass spectrometry (LC-MS) global profiling methods. These methods were scaled-down to microflow-based LC separations and compared with analytical flow ion-pairing reagent containing methods. Average peak volume improvements of 7- and 22-fold were observed in the positive and negative ionization mode microflow methods as compared to the ion-pairing reagent analytical flow methods, respectively. The linear range of the newly developed microflow methods showed up to a 10-fold increase in the lower limit of detection in the negative ionization mode. The developed microflow LC-MS methods were further evaluated using wild-type mouse plasma where up to a 9-fold increase in peak volume was observed.
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Affiliation(s)
| | | | - Alla Kloss
- Sanofi, Waltham, MA 02451, United States
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, United States.
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34
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Hyötyläinen T. Analytical challenges in human exposome analysis with focus on environmental analysis combined with metabolomics. J Sep Sci 2021; 44:1769-1787. [PMID: 33650238 DOI: 10.1002/jssc.202001263] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/23/2021] [Accepted: 02/23/2021] [Indexed: 12/19/2022]
Abstract
Environmental factors, such as chemical exposures, are likely to play a crucial role in the development of several human chronic diseases. However, how the specific exposures contribute to the onset and progress of various diseases is still poorly understood. In part, this is because comprehensive characterization of the chemical exposome is a highly challenging task, both due to its complex dynamic nature as well as due to the analytical challenges. Herein, the analytical challenges in the field of exposome research are reviewed, with specific emphasis on the sampling, sample preparation, and analysis, as well as challenges in the compound identification. The primary focus is on the human chemical exposome, that is, exposures to mixtures of environmental chemicals and its impact on human metabolome. In order to highlight the recent progress in the exposome research in relation to human health and disease, selected examples of human exposome studies are presented.
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Affiliation(s)
- Tuulia Hyötyläinen
- MTM Research Centre, School of Science and Technology, Örebro University, Örebro, Sweden
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35
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Öngün E, Akgönüllü S, Yavuz H, Denizli A. Synthesis of molecularly imprinted magnetic nanoparticles for selective cytidine adsorption. SEPARATION SCIENCE PLUS 2021. [DOI: 10.1002/sscp.202000089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Emine Öngün
- Division of Nanotechnology and Nanomedicine Hacettepe University Ankara Turkey
| | - Semra Akgönüllü
- Division of Biochemistry Department of Chemistry Hacettepe University Ankara Turkey
| | - Handan Yavuz
- Division of Biochemistry Department of Chemistry Hacettepe University Ankara Turkey
| | - Adil Denizli
- Division of Biochemistry Department of Chemistry Hacettepe University Ankara Turkey
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36
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Kogaki T, Ohshio I, Ura H, Iyama S, Kitae K, Morie T, Fujii S, Sato S, Nagata T, Takeda AH, Aoki M, Ueda K, Minami K, Yamamoto M, Kawahara K, Furukawa T, Sato M, Ueda Y, Jingushi K, Tozuka Z, Saigusa D, Hase H, Tsujikawa K. Development of a highly sensitive method for the quantitative analysis of modified nucleosides using UHPLC-UniSpray-MS/MS. J Pharm Biomed Anal 2021; 197:113943. [PMID: 33601155 DOI: 10.1016/j.jpba.2021.113943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 01/27/2023]
Abstract
There are more than 150 types of naturally occurring modified nucleosides, which are believed to be involved in various biological processes. Recently, an ultrahigh performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UHPLC-ESI-MS/MS) technique has been developed to measure low levels of modified nucleosides. A comprehensive analysis of modified nucleosides will lead to a better understanding of intracellular ribonucleic acid modification, but this analysis requires high-sensitivity measurements. In this perspective, we established a highly sensitive and quantitative method using the newly developed ion source, UniSpray. A mass spectrometer was used with a UniSpray source in positive ion mode. Our UHPLC-UniSpray-MS/MS methodology separated and detected the four major nucleosides, 42 modified nucleosides, and dG15N5 (internal standard) in 15 min. The UniSpray method provided good correlation coefficients (>0.99) for all analyzed nucleosides, and a wide range of linearity for 35 of the 46 nucleosides. Additionally, the accuracy and precision values satisfied the criteria of <15% for higher concentrations and <20% for the lowest concentrations of all nucleosides. We also investigated whether this method could measure nucleosides in biological samples using mouse tissues and non-small cell lung cancer clinical specimens. We were able to detect 43 and 31 different modified nucleosides from mouse and clinical tissues, respectively. We also found significant differences in the levels of N6-methyl-N6-threonylcarbamoyladenosine (m6t6A), 1-methylinosine (m1I), 2'-O-methylcytidine (Cm), 5-carbamoylmethyluridine (ncm5U), 5-methoxycarbonylmethyl-2-thiouridine (mcm5S2U), and 5-methoxycarbonylmethyl-2'-O-methyluridine (mcm5Um) between cancerous and noncancerous tissues. In conclusion, we developed a highly sensitive methodology using UHPLC-UniSpray-MS/MS to simultaneously detect and quantify modified nucleosides, which can be used for analysis of biological samples.
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Affiliation(s)
- Takahiro Kogaki
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ikumi Ohshio
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hasumi Ura
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Souta Iyama
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kaori Kitae
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshiya Morie
- Center for Supporting Drug Discovery and Life Science Research Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shintarou Fujii
- Center for Supporting Drug Discovery and Life Science Research Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shohei Sato
- Center for Supporting Drug Discovery and Life Science Research Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshiyuki Nagata
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8520, Japan
| | - Aya Harada Takeda
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8520, Japan
| | - Masaya Aoki
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8520, Japan
| | - Kazuhiro Ueda
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8520, Japan
| | - Kentaro Minami
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8544, Japan
| | - Masatatsu Yamamoto
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8544, Japan
| | - Kohichi Kawahara
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8544, Japan
| | - Tatsuhiko Furukawa
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8544, Japan
| | - Masami Sato
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8520, Japan
| | - Yuko Ueda
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kentaro Jingushi
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Zenzaburo Tozuka
- Center for Supporting Drug Discovery and Life Science Research Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 1-2 Seiryocho, Aobaku, Sendai, Miyagi 980-8573, Japan
| | - Hiroaki Hase
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Kazutake Tsujikawa
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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Jayasundara K, Li C, DeBastiani A, Sharif D, Li P, Valentine SJ. Physicochemical Property Correlations with Ionization Efficiency in Capillary Vibrating Sharp-Edge Spray Ionization (cVSSI). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:84-94. [PMID: 32856909 PMCID: PMC8130659 DOI: 10.1021/jasms.0c00100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The relative contributions to ionization efficiency by three molecular chemical properties have been examined for field-free and field-enabled capillary vibrating sharp-edge spray ionization (cVSSI) using mass spectrometry (MS) analysis. Ion intensities have been recorded for model compounds under each operational ionization mode as well as for aqueous and nonaqueous (methanol) solvent systems. Multiple regression analysis suggests that for field-free cVSSI, ion intensity is mostly associated with the log of the base dissociation constant (pKb) and proton affinity (PA) for both aqueous and methanol solutions. Comparatively, for field-enabled cVSSI using aqueous solutions, the dominant factor correlated with ion intensity is the log of the partition coefficient (log P). To a lesser degree, this is observed for methanol solutions as well. For ESI, pKb is the dominant factor associated with ion signal levels from methanol and aqueous solutions. These results are supported by studies conducted on two different mass spectrometers employing different cVSSI emitter tips. The relationship of ion intensity and pKb in ESI is supported by multiple studies; however, the shift to other chemical properties with the addition of cVSSI suggests the possibility that a different (or combinations of) ionization mechanism(s) may be operative for these ionization modes. These results are briefly considered in light of the different ESI mechanisms.
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Affiliation(s)
| | | | | | | | - Peng Li
- To whom correspondence should be addressed: , and .
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38
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Sit I, Sagisaka S, Grassian VH. Nucleotide Adsorption on Iron(III) Oxide Nanoparticle Surfaces: Insights into Nano-Geo-Bio Interactions Through Vibrational Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:15501-15513. [PMID: 33331787 DOI: 10.1021/acs.langmuir.0c02633] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Molecular processes at geochemical interfaces impact many environmental processes that are critical to the fate and transport of contaminants in water systems. Often these interfaces are coated with natural organic matter, oxyanions, or biological components, yet little is understood about these coatings. Herein, we are interested in better understanding the interaction of biological components with nanoscale iron oxide minerals. In particular, we use attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy to investigate the adsorption behavior of deoxyadenosine monophosphate (dAMP) on hematite nanoparticle surfaces as a function of pH and in the presence and absence of adsorbed phosphate. These results show that fewer nucleotides adsorb at higher pH. Additionally, when phosphate anions are preadsorbed, nucleotide adsorption is significantly limited due to site-blocking by adsorbed inorganic phosphate. The pH dependence provides insights into the adsorption process and the importance of electrostatic interactions. Preadsorbed phosphate affects the binding mode of dAMP, suggesting synergistic interactions between the coadsorbates. Two-dimensional correlation spectroscopy was used to further analyze the infrared spectra. Based on this analysis, a dAMP adsorption pathway onto a preadsorbed phosphate-hematite surface was proposed, suggesting the displacement of adsorbed phosphate by dAMP. Overall, this study provides some insights into geochemical-biological interactions on nanoscale iron oxide surfaces using vibrational spectroscopy.
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Feliu C, Peyret H, Vautier D, Djerada Z. Simultaneous quantification of 8 nucleotides and adenosine in cells and their medium using UHPLC-HRMS. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1148:122156. [PMID: 32446186 DOI: 10.1016/j.jchromb.2020.122156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022]
Abstract
Purinergic signalling is involved in physiological processes, particularly during ischemia-reperfusion injuries for which it has a protective effect. The purpose of this work was to develop a method for simultaneous quantification of eight nucleotides and adenosine in biological matrices by liquid chromatography coupled with high-resolution mass spectrometry. A method was developed that was sufficiently robust to quantify the targeted analytes in 20 min with good sensitivity. Analysis of extracellular media from cultured endothelial cells detected the release of nucleotides and adenosine during 2 h of hypoxia. The quantification of cylic adenosine monophosphate (cAMP) allowed to establish a dose-response curve after receptor stimulation. Therefore, our method allows us to study the involvement of nucleotides in various processes in both the intracellular and extracellular compartment.
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Affiliation(s)
- Catherine Feliu
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims Cedex, France
| | - Hélène Peyret
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims Cedex, France
| | - Damien Vautier
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims Cedex, France
| | - Zoubir Djerada
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims Cedex, France.
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Ma YF, Yuan F, Yu Y, Zhou YL, Zhang XX. Synthesis of a pH-Responsive Functional Covalent Organic Framework via Facile and Rapid One-Step Postsynthetic Modification and Its Application in Highly Efficient N1-Methyladenosine Extraction. Anal Chem 2019; 92:1424-1430. [DOI: 10.1021/acs.analchem.9b04600] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yu-Fang Ma
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Fang Yuan
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yue Yu
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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41
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He L, Li F, Yin X, Bohman P, Kim S, McClain CJ, Feng W, Zhang X. Profiling of Polar Metabolites in Mouse Feces Using Four Analytical Platforms to Study the Effects Of Cathelicidin-Related Antimicrobial Peptide in Alcoholic Liver Disease. J Proteome Res 2019; 18:2875-2884. [PMID: 31188604 DOI: 10.1021/acs.jproteome.9b00181] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Alterations in gut bacterial homeostasis result in changes in intestinal metabolites. To investigate the effects of alcohol on fecal metabolites and the role of cathelicidin-related antimicrobial peptide (CRAMP) in alcoholic liver disease (ALD), CRAMP knockout (KO) and their control wild type (WT) mice were fed a Lieber-DeCarli liquid diet with or without alcohol. Polar metabolites in mouse feces were analyzed by GC × GC-MS and 2DLC-MS, and the concentrations of short chain fatty acids (SCFAs) were measured by GC-MS. A total of 95 and 190 metabolites were detected by GC × GC-MS and 2DLC-MS, respectively. Among the significantly changed metabolites, taurine and nicotinic acid were decreased in WT mice fed alcohol, which were also down-regulated in KO mice fed without alcohol. Interestingly, these two metabolites were increased in KO mice fed alcohol compared to them in WT controls. Additionally, SCFAs were significantly decreased in WT mice fed alcohol and in KO mice fed without alcohol, whereas two branched-chain SCFAs were increased by alcohol treatment in KO mice. In summary, the analytical platforms employed in this study successfully dissected the alterations of polar metabolites and SCFAs in fecal samples, which helped understand the effects of alcohol consumption and CRAMP in intestinal metabolism and alcohol-induced liver injury.
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Affiliation(s)
| | | | | | - Patrick Bohman
- Thermo Fisher Scientific International Inc. , 3000 Lakeside Dr. , Bannockburn , Illinois 60015 , United States
| | - Seongho Kim
- Biostatistics Core, Karmanos Cancer Institute , Wayne State University , Detroit , Michigan 48201 , United States
| | - Craig J McClain
- Robley Rex Louisville VAMC , Louisville , Kentucky 40292 , United States
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