1
|
Osik N, Lukzen NN, Yanshole VV, Tsentalovich YP. Loss of Volatile Metabolites during Concentration of Metabolomic Extracts. ACS OMEGA 2024; 9:24015-24024. [PMID: 38854568 PMCID: PMC11154959 DOI: 10.1021/acsomega.4c02439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/02/2024] [Accepted: 05/16/2024] [Indexed: 06/11/2024]
Abstract
Volatile metabolites can be lost during the preanalytical stage of metabolomic analysis. This work is aimed at the experimental and theoretical study of mechanisms of volatile substance evaporation and retention in the residues during the drying of extract solutions. We demonstrate that solvent evaporation leads to the unavoidable loss of nondissociating volatile metabolites with low boiling points and high vapor pressures (such as acetone and ethanol). The retention of dissociating volatile compounds (primarily organic acids RH) during the evaporation depends on the presence of buffer salts in solution, which are responsible for maintaining the neutral pH. An acid remains in the solution as long as it is present predominantly in the dissociated R- state. At the very last stage of solvent evaporation, buffer salts precipitate, forming a solid matrix for metabolite trapping in the residue. At the same time, buffer precipitation leads to a decrease of the solution pH, increase of the portion of RH in associated state, and acceleration of RH volatilization. The RH recovery is thus determined by the competition between the solute volatilization in the associated RH form and metabolite trapping in the solid matrix. The retention of volatile acids in the residue after extract drying can be improved either by adding buffer salts to maintain high pH or by incomplete sample drying.
Collapse
Affiliation(s)
- Nataliya
A. Osik
- International
Tomography Center Siberian Branch of Russian Academy of Sciences, Institutskaya str. 3a, Novosibirsk 630090, Russia
| | - Nikita N. Lukzen
- International
Tomography Center Siberian Branch of Russian Academy of Sciences, Institutskaya str. 3a, Novosibirsk 630090, Russia
- Novosibirsk
State University, Pirogova
str. 1, Novosibirsk 630090, Russia
| | - Vadim V. Yanshole
- International
Tomography Center Siberian Branch of Russian Academy of Sciences, Institutskaya str. 3a, Novosibirsk 630090, Russia
- Novosibirsk
State University, Pirogova
str. 1, Novosibirsk 630090, Russia
| | - Yuri P. Tsentalovich
- International
Tomography Center Siberian Branch of Russian Academy of Sciences, Institutskaya str. 3a, Novosibirsk 630090, Russia
| |
Collapse
|
2
|
Ellisor DL, Bayless AL, Schock TB, Davis WC, Knott BT, Seghers J, Leys H, Emteborg H. Multi-omics characterization of NIST seafood reference materials and alternative matrix preparations. Anal Bioanal Chem 2024; 416:773-785. [PMID: 37723254 DOI: 10.1007/s00216-023-04928-9] [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: 06/01/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/20/2023]
Abstract
The National Institute of Standards and Technology (NIST) has prepared four seafood reference materials (RMs) for use in food safety and nutrition studies: wild-caught and aquacultured salmon (RM 8256 and RM 8257) and wild-caught and aquacultured shrimp (RM 8258 and RM 8259). These materials were characterized using genetic, metabolomic (1H-NMR, nuclear magnetic resonance and LC-HRMS/MS, liquid chromatography high-resolution tandem mass spectrometry), lipidomic, and proteomic methods to explore their use as matrix-matched, multi-omic differential materials for method development towards identifying product source and/or as quality control in untargeted omics studies. The results from experimental replicates were reproducible for each reference material and analytical method, with the most abundant features reported. Additionally, differences between the materials could be detected, where wild-caught and aquacultured seafood could be distinguished using untargeted metabolite, lipid, and protein analyses. Further processing of the fresh-frozen RMs by freeze-drying revealed the freeze-dried seafoods could still be reliably discerned. These results demonstrate the usefulness of these reference materials as tools for omics instrument validation and measurement harmonization in seafood-related studies. Furthermore, their use as differential quality control (QC) materials, regardless of preparation method, may also provide a tool for laboratories to demonstrate proficiency at discriminating between products based on source/species.
Collapse
Affiliation(s)
- Debra L Ellisor
- National Institute of Standards and Technology Materials Measurement Laboratory, Charleston, SC, USA.
| | - Amanda L Bayless
- National Institute of Standards and Technology Materials Measurement Laboratory, Charleston, SC, USA
| | - Tracey B Schock
- National Institute of Standards and Technology Materials Measurement Laboratory, Charleston, SC, USA
| | - W Clay Davis
- National Institute of Standards and Technology Materials Measurement Laboratory, Charleston, SC, USA
| | - B Trey Knott
- National Oceanic and Atmospheric Administration Northwest Fisheries Science Center Forensic Laboratory, Charleston, SC, USA
| | - John Seghers
- European Commission - Joint Research Centre, Directorate Health and Food, Geel, Belgium
| | - Hanne Leys
- European Commission - Joint Research Centre, Directorate Health and Food, Geel, Belgium
| | - Håkan Emteborg
- European Commission - Joint Research Centre, Directorate Health and Food, Geel, Belgium
| |
Collapse
|
3
|
Ross IL, Beardslee JA, Steil MM, Chihanga T, Kennedy MA. Statistical considerations and database limitations in NMR-based metabolic profiling studies. Metabolomics 2023; 19:64. [PMID: 37378680 DOI: 10.1007/s11306-023-02027-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
INTRODUCTION Interpretation and analysis of NMR-based metabolic profiling studies is limited by substantially incomplete commercial and academic databases. Statistical significance tests, including p-values, VIP scores, AUC values and FC values, can be largely inconsistent. Data normalization prior to statistical analysis can cause erroneous outcomes. OBJECTIVES The objectives were (1) to quantitatively assess consistency among p-values, VIP scores, AUC values and FC values in representative NMR-based metabolic profiling datasets, (2) to assess how data normalization can impact statistical significance outcomes, (3) to determine resonance peak assignment completion potential using commonly used databases and (4) to analyze intersection and uniqueness of metabolite space in these databases. METHODS P-values, VIP scores, AUC values and FC values, and their dependence on data normalization, were determined in orthotopic mouse model of pancreatic cancer and two human pancreatic cancer cell lines. Completeness of resonance assignments were evaluated using Chenomx, the human metabolite database (HMDB) and the COLMAR database. The intersection and uniqueness of the databases was quantified. RESULTS P-values and AUC values were strongly correlated compared to VIP or FC values. Distributions of statistically significant bins depended strongly on whether or not datasets were normalized. 40-45% of peaks had either no or ambiguous database matches. 9-22% of metabolites were unique to each database. CONCLUSIONS Lack of consistency in statistical analyses of metabolomics data can lead to misleading or inconsistent interpretation. Data normalization can have large effects on statistical analysis and should be justified. About 40% of peak assignments remain ambiguous or impossible with current databases. 1D and 2D databases should be made consistent to maximize metabolite assignment confidence and validation.
Collapse
Affiliation(s)
- Imani L Ross
- Department of Chemistry and Biochemistry, University of California, San Diego, CA, 92093, USA
| | - Julie A Beardslee
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA
| | - Maria M Steil
- Division of Plastic Surgery, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Tafadzwa Chihanga
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA.
| |
Collapse
|
4
|
Holderman NR, Ferrer-González FX, Glushka J, Moran MA, Edison AS. Dissolved organic metabolite extraction from high-salt media. NMR IN BIOMEDICINE 2023; 36:e4797. [PMID: 35799308 DOI: 10.1002/nbm.4797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 06/13/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
We describe considerations and strategies for developing a nuclear magnetic resonance (NMR) sample preparation method to extract low molecular weight metabolites from high-salt spent media in a model coculture system of phytoplankton and marine bacteria. Phytoplankton perform half the carbon fixation and oxygen generation on Earth. A substantial fraction of fixed carbon becomes part of a metabolite pool of small molecules known as dissolved organic matter (DOM), which are taken up by marine bacteria proximate to phytoplankton. There is an urgent need to elucidate these metabolic exchanges due to widespread anthropogenic transformations on the chemical, phenotypic, and species composition of seawater. These changes are increasing water temperature and the amount of CO2 absorbed by the ocean at energetic costs to marine microorganisms. Little is known about the metabolite-mediated, structured interactions occurring between phytoplankton and associated marine bacteria, in part because of challenges in studying high-salt solutions on various analytical platforms. NMR analysis is problematic due to the high-salt content of both natural seawater and culture media for marine microbes. High-salt concentration degrades the performance of the radio frequency coil, reduces the efficiency of some pulse sequences, limits signal-to-noise, and prolongs experimental time. The method described herein can reproducibly extract low molecular weight DOM from small-volume, high-salt cultures. It is a promising tool for elucidating metabolic flux between marine microorganisms and facilitates genetic screens of mutant microorganisms.
Collapse
Affiliation(s)
- Nicole R Holderman
- Department of Biochemistry and Molecular Biology and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | | | - John Glushka
- Department of Biochemistry and Molecular Biology and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
| | - Arthur S Edison
- Department of Biochemistry and Molecular Biology and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| |
Collapse
|
5
|
Lutz NW, Bernard M. Methodological Developments for Metabolic NMR Spectroscopy from Cultured Cells to Tissue Extracts: Achievements, Progress and Pitfalls. Molecules 2022; 27:molecules27134214. [PMID: 35807461 PMCID: PMC9268249 DOI: 10.3390/molecules27134214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/08/2022] [Accepted: 06/20/2022] [Indexed: 12/04/2022] Open
Abstract
This is a broad overview and critical review of a particular group of closely related ex vivo and in vitro metabolic NMR spectroscopic methods. The scope of interest comprises studies of cultured cells and excised tissue, either intact or after physicochemical extraction of metabolites. Our detailed discussion includes pitfalls that have led to erroneous statements in the published literature, some of which may cause serious problems in metabolic and biological interpretation of results. To cover a wide range of work from relevant research areas, we consider not only the most recent achievements in the field, but also techniques that proved to be valid and successful in the past, although they may not have generated a very significant number of papers more recently. Thus, this comparative review also aims at providing background information useful for judiciously choosing between the metabolic ex vivo/in vitro NMR methods presented. Finally, the methods of interest are discussed in the context of, and in relation to, other metabolic analysis protocols such as HR-MAS and cell perfusion NMR, as well as the mass spectrometry approach.
Collapse
|
6
|
Wang QY, You LH, Xiang LL, Zhu YT, Zeng Y. Current progress in metabolomics of gestational diabetes mellitus. World J Diabetes 2021; 12:1164-1186. [PMID: 34512885 PMCID: PMC8394228 DOI: 10.4239/wjd.v12.i8.1164] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/20/2021] [Accepted: 07/07/2021] [Indexed: 02/06/2023] Open
Abstract
Gestational diabetes mellitus (GDM) is one of the most common metabolic disorders of pregnancy and can cause short- and long-term adverse effects in both pregnant women and their offspring. However, the etiology and pathogenesis of GDM are still unclear. As a metabolic disease, GDM is well suited to metabolomics study, which can monitor the changes in small molecular metabolites induced by maternal stimuli or perturbations in real time. The application of metabolomics in GDM can be used to discover diagnostic biomarkers, evaluate the prognosis of the disease, guide the application of diet or drugs, evaluate the curative effect, and explore the mechanism. This review provides comprehensive documentation of metabolomics research methods and techniques as well as the current progress in GDM research. We anticipate that the review will contribute to identifying gaps in the current knowledge or metabolomics technology, provide evidence-based information, and inform future research directions in GDM.
Collapse
Affiliation(s)
- Qian-Yi Wang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 21000, Jiangsu Province, China
| | - Liang-Hui You
- Nanjing Maternity and Child Health Care Institute, Women’s Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing 21000, Jiangsu Province, China
| | - Lan-Lan Xiang
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing 21000, Jiangsu Province, China
| | - Yi-Tian Zhu
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing 21000, Jiangsu Province, China
| | - Yu Zeng
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing 21000, Jiangsu Province, China
| |
Collapse
|
7
|
Standage SW, Xu S, Brown L, Ma Q, Koterba A, Lahni P, Devarajan P, Kennedy MA. NMR-based serum and urine metabolomic profile reveals suppression of mitochondrial pathways in experimental sepsis-associated acute kidney injury. Am J Physiol Renal Physiol 2021; 320:F984-F1000. [PMID: 33843271 DOI: 10.1152/ajprenal.00582.2020] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Sepsis-associated acute kidney injury (SA-AKI) is a significant problem in the critically ill that causes increased death. Emerging understanding of this disease implicates metabolic dysfunction in its pathophysiology. This study sought to identify specific metabolic pathways amenable to potential therapeutic intervention. Using a murine model of sepsis, blood and tissue samples were collected for assessment of systemic inflammation, kidney function, and renal injury. Nuclear magnetic resonance (NMR)-based metabolomics quantified dozens of metabolites in serum and urine that were subsequently submitted to pathway analysis. Kidney tissue gene expression analysis confirmed the implicated pathways. Septic mice had elevated circulating levels of inflammatory cytokines and increased levels of blood urea nitrogen and creatinine, indicating both systemic inflammation and poor kidney function. Renal tissue showed only mild histological evidence of injury in sepsis. NMR metabolomic analysis identified the involvement of mitochondrial pathways associated with branched-chain amino acid metabolism, fatty acid oxidation, and de novo NAD+ biosynthesis in SA-AKI. Renal cortical gene expression of enzymes associated with those pathways was predominantly suppressed. Renal cortical fatty acid oxidation rates were lower in septic mice with high inflammation, and this correlated with higher serum creatinine levels. Similar to humans, septic mice demonstrated renal dysfunction without significant tissue disruption, pointing to metabolic derangement as an important contributor to SA-AKI pathophysiology. Metabolism of branched-chain amino acid and fatty acids and NAD+ synthesis, which all center on mitochondrial function, appeared to be suppressed. Developing interventions to activate these pathways may provide new therapeutic opportunities for SA-AKI.NEW & NOTEWORTHY NMR-based metabolomics revealed disruptions in branched-chain amino acid metabolism, fatty acid oxidation, and NAD+ synthesis in sepsis-associated acute kidney injury. These pathways represent essential processes for energy provision in renal tubular epithelial cells and may represent targetable mechanisms for therapeutic intervention.
Collapse
Affiliation(s)
- Stephen W Standage
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio
| | - Shenyuan Xu
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio
| | - Lauren Brown
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Qing Ma
- Division of Nephrology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Adeleine Koterba
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Patrick Lahni
- Division of Critical Care Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Prasad Devarajan
- Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio.,Division of Nephrology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio
| |
Collapse
|