1
|
Marchante-Gayón JM, Nicolás Carcelén J, Potes Rodríguez H, Pineda-Cevallos D, Rodas Sánchez L, González-Gago A, Rodríguez-González P, García Alonso JI. Quantification of modified nucleotides and nucleosides by isotope dilution mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:998-1018. [PMID: 37597182 DOI: 10.1002/mas.21865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/26/2023] [Accepted: 08/06/2023] [Indexed: 08/21/2023]
Abstract
Epigenetic modifications are closely related to certain disorders of the organism, including the development of tumors. One of the main epigenetic modifications is the methylation of DNA cytosines, 5-methyl-2'-deoxycycytidine. Furthermore, 5-mdC can be oxidized to form three new modifications, 5-(hydroxymethyl)-2'-deoxycytidine, 5-formyl-2'-deoxycytidine, and 5-carboxy-2'-deoxycytidine. The coupling of liquid chromatography with tandem mass spectrometry has been widely used for the total determination of methylated DNA cytosines in samples of biological and clinical interest. These methods are based on the measurement of the free compounds (e.g., urine) or after complete hydrolysis of the DNA (e.g., tissues) followed by a preconcentration, derivatization, and/or clean-up step. This review highlights the main advances in the quantification of modified nucleotides and nucleosides by isotope dilution using isotopically labeled analogs combined with liquid or gas chromatography coupled to mass spectrometry reported in the last 20 years. The different possible sources of labeled compounds are indicated. Special emphasis has been placed on the different types of chromatography commonly used (reverse phase and hydrophilic interaction liquid chromatography) and the derivatization methods developed to enhance chromatographic resolution and ionization efficiency. We have also revised the application of bidimensional chromatography and indicated significant biological and clinical applications of these determinations.
Collapse
Affiliation(s)
- Juan M Marchante-Gayón
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Jesús Nicolás Carcelén
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Helí Potes Rodríguez
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Daniela Pineda-Cevallos
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Laura Rodas Sánchez
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Adriana González-Gago
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Pablo Rodríguez-González
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Jose I García Alonso
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| |
Collapse
|
2
|
Sattler C, Ceylan B, Hoffmann L, Juric A, Kraus J, Marandi S, Shahnazari A, Rühl M. Sequence confirmation of synthetic DNA exceeding 100 nucleotides using restriction enzyme mediated digestion combined with high-resolution tandem mass spectrometry. J Pharm Biomed Anal 2024; 245:116180. [PMID: 38703748 DOI: 10.1016/j.jpba.2024.116180] [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: 12/21/2023] [Revised: 04/11/2024] [Accepted: 04/23/2024] [Indexed: 05/06/2024]
Abstract
Oligonucleotides have emerged as important therapeutic options for inherited diseases. In recent years, RNA therapeutics, especially mRNA, have been pushed to the market. Analytical methods for these molecules have been published extensively in the last few years. Notably, mass spectrometry has proven as a state-of-the-art quality control method. For RNA based therapeutics, numerous methods are available, while DNA therapeutics lack of suitable MS-based methods when it comes to molecules exceeding approximately 60 nucleotides. We present a method which combines the use of common restriction enzymes and short enzyme-directing oligonucleotides to generate DNA digestion products with the advantages of high-resolution tandem mass spectrometry. The instrumentation includes ion pair reverse phase chromatography coupled to a time-of-flight mass spectrometer with a collision induced dissociation (CID) for sequence analysis. Utilizing this approach, we increased the sequence coverage from 23.3% for a direct CID-MS/MS experiment of a 100 nucleotide DNA molecule to 100% sequence coverage using the restriction enzyme mediated approach presented in this work. This approach is suitable for research and development and quality control purposes in a regulated environment, which makes it a versatile tool for drug development.
Collapse
Affiliation(s)
| | - Burak Ceylan
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Luisa Hoffmann
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Andela Juric
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Julia Kraus
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Shima Marandi
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Aref Shahnazari
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany
| | - Michael Rühl
- BioSpring GmbH, Alt-Fechenheim 34, Frankfurt am Main 60386, Germany.
| |
Collapse
|
3
|
De Graeve M, Van de Walle E, Van Hecke T, De Smet S, Vanhaecke L, Hemeryck LY. Exploration and optimization of extraction, analysis and data normalization strategies for mass spectrometry-based DNA adductome mapping and modeling. Anal Chim Acta 2023; 1274:341578. [PMID: 37455087 DOI: 10.1016/j.aca.2023.341578] [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: 03/10/2023] [Revised: 06/23/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
Although interest in characterizing DNA damage by means of DNA adductomics has substantially grown, the field of DNA adductomics is still in its infancy, with room for optimization of methods for sample analysis, data processing and DNA adduct identification. In this context, the first objective of this study was to evaluate the use of hydrophilic interaction (HILIC) vs. reversed phase liquid chromatography (RPLC) coupled to high resolution mass spectrometry (HRMS) and thermal acidic vs. enzymatic hydrolysis of DNA followed by DNA adduct purification and enrichment using solid-phase extraction (SPE) or fraction collection for DNA adductome mapping. The second objective was to assess the use of total ion count (TIC) and median intensity (MedI) normalization compared to QC (quality control), iQC (internal QC) and quality control-based robust locally estimated scatterplot smoothing (LOESS) signal correction (QC-RLSC) normalization for processing of the acquired data. The results demonstrate that HILIC compared to RPLC allowed better modeling of the tentative DNA adductome, particularly in combination with thermal acidic hydrolysis and SPE (more valid models, with an average Q2(Y) and R2(Y) of 0.930 and 0.998, respectively). Regarding the need for data normalization and the management of (limited) system instability and signal drift, QC normalization outperformed TIC, MedI, iQC and LOESS normalization. As such, QC normalization can be put forward as the default data normalization strategy. In case of momentous signal drift and/or batch effects however, comparison to other normalization strategies (like e.g. LOESS) is recommended. In future work, further optimization of DNA adductomics may be achieved by merging of HILIC and RPLC datasets and/or application of 2D-LC, as well as the inclusion of Schiff base stabilization and/or fraction collection in the thermal acidic hydrolysis-SPE sample preparation workflow.
Collapse
Affiliation(s)
- Marilyn De Graeve
- Laboratory of Integrative Metabolomics, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium.
| | - Emma Van de Walle
- Laboratory of Integrative Metabolomics, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium.
| | - Thomas Van Hecke
- Laboratory for Animal Nutrition and Animal Product Quality, Faculty of Bioscience Engineering, Ghent University, Coupure Links, 653, B-9000, Ghent, Belgium.
| | - Stefaan De Smet
- Laboratory for Animal Nutrition and Animal Product Quality, Faculty of Bioscience Engineering, Ghent University, Coupure Links, 653, B-9000, Ghent, Belgium.
| | - Lynn Vanhaecke
- Laboratory of Integrative Metabolomics, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium; Institute for Global Food Security, School of Biological Sciences, Queen's University, University Road, Belfast, United Kingdom.
| | - Lieselot Y Hemeryck
- Laboratory of Integrative Metabolomics, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820, Merelbeke, Belgium.
| |
Collapse
|
4
|
Abd El-Aleem FS, Lotfy SN, Saad R, Ahmed MYS, Fadel HHM. Production of nutty-like flavour from soybean protein isolate hydrolysate pretreated or assisted by microwave irradiation: impact of encapsulation on nutty flavour quality. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2022; 59:1958-1967. [PMID: 35531421 PMCID: PMC9046492 DOI: 10.1007/s13197-021-05211-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 06/29/2021] [Accepted: 07/11/2021] [Indexed: 05/03/2023]
Abstract
The aim of this study was to prepare a nutty-like flavour from enzymatic hydrolysates of soybean protein isolate pretreated or assisted by microwave heating. In both cases the time of microwave heating was optimized and degree of hydrolysis (DH) and content of free amino acids in each hydrolysate were determined and compared with those of hydrolysate prepared by conventional method (E-HSC). The hydrolysates showed the best results were used as main precursors of nutty flavour. The generated volatiles were subjected to GC-MS analysis and odour evaluation. The effect of encapsulation and storage on the nutty flavour was evaluated. The results revealed that the hydrolysates pretreated (E-HSMP7) or assisted (E-HSMA6) by microwave at 7 and 6 min, respectively showed a significant increase in DH. The nutty flavour generated from these hydrolysates (NFMP7 and NFMA6) were dominated with pyrazines whereas, the volatiles from E-HSC (NFC) dominated with furans. NFMA6 showed the highest intensity of nutty and overall acceptability notes, compared with NFMP7 and NFC. Encapsulation resulted in a significant decrease in pyrazines, which are responsible for the nutty note. The significant increase in nutty aroma intensity of the stored encapsulated sample was correlated to the increase in pyrazines.
Collapse
Affiliation(s)
| | - Shereen Nazeh Lotfy
- Chemistry of Flavour and Aroma Department, National Research Centre, Dokki, Cairo, 12622 Egypt
| | - Rasha Saad
- Chemistry of Flavour and Aroma Department, National Research Centre, Dokki, Cairo, 12622 Egypt
| | | | | |
Collapse
|
5
|
Chilakala S, Feng Y, Li L, Mahfouz R, Quteba E, Saunthararajah Y, Xu Y. Tracking Decitabine Incorporation into Malignant Myeloid Cell DNA in vitro and in vivo by LC-MS/MS with Enzymatic Digestion. Sci Rep 2019; 9:4558. [PMID: 30872721 PMCID: PMC6418203 DOI: 10.1038/s41598-019-41070-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 02/27/2019] [Indexed: 12/31/2022] Open
Abstract
The DNA hypomethylating agents decitabine and 5-azacytidine are the only two drugs approved for treatment of all subtypes of the myeloid malignancy myelodysplastic syndromes (MDS). The key to drug activity is incorporation into target cell DNA, however, a practical method to measure this incorporation is un-available. Here, we report a sensitive and specific LC-MS/MS method to simultaneously measure decitabine incorporation and DNA hypomethylation. A stable heavy isotope of 2'-deoxycytidine was used as an internal standard and one-step multi-enzyme digestion was used to release the DNA bound drug. Enzyme-released decitabine along with other mononucleosides were separated by a reverse-phase C18 column and quantified by mass spectrometry using multiple-reaction-monitoring (MRM) mode, with a lower limit of quantitation at 1.00 nM. In vitro studies demonstrated dosage and time-dependent incorporation of decitabine into myeloid leukemia cell DNA that correlated with extent of DNA hypomethylation. When applied to clinical samples serially collected from MDS patients treated with decitabine, the method again demonstrated correlation between decitabine DNA-incorporation and DNA hypomethylation. This novel assay to measure the intended molecular pharmacodynamic effect of decitabine therapy can therefore potentially provide insights into mechanisms underlying sensitivity versus resistance to therapy.
Collapse
Affiliation(s)
- Sujatha Chilakala
- Department of Chemistry, Cleveland State University, 2121 Euclid Avenue, Cleveland, Ohio, 44115, USA
| | - Ye Feng
- Department of Chemistry, Cleveland State University, 2121 Euclid Avenue, Cleveland, Ohio, 44115, USA
| | - Lan Li
- Department of Chemistry, Cleveland State University, 2121 Euclid Avenue, Cleveland, Ohio, 44115, USA
| | - Reda Mahfouz
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, 2010 East 90th Street, Cleveland, OH, 44195, USA
| | - Ebrahem Quteba
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, 2010 East 90th Street, Cleveland, OH, 44195, USA
| | - Yogen Saunthararajah
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, 2010 East 90th Street, Cleveland, OH, 44195, USA
| | - Yan Xu
- Department of Chemistry, Cleveland State University, 2121 Euclid Avenue, Cleveland, Ohio, 44115, USA.
| |
Collapse
|
6
|
Lai W, Mo J, Yin J, Lyu C, Wang H. Profiling of epigenetic DNA modifications by advanced liquid chromatography-mass spectrometry technologies. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.10.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|