1
|
Zhang YW, Gvozdenovic A, Aceto N. A Molecular Voyage: Multiomics Insights into Circulating Tumor Cells. Cancer Discov 2024; 14:920-933. [PMID: 38581442 DOI: 10.1158/2159-8290.cd-24-0218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/08/2024]
Abstract
Circulating tumor cells (CTCs) play a pivotal role in metastasis, the leading cause of cancer-associated death. Recent improvements of CTC isolation tools, coupled with a steady development of multiomics technologies at single-cell resolution, have enabled an extensive exploration of CTC biology, unlocking insights into their molecular profiles. A detailed molecular portrait requires CTC interrogation across various levels encompassing genomic, epigenetic, transcriptomic, proteomic and metabolic features. Here, we review how state-of-the-art multiomics applied to CTCs are shedding light on how cancer spreads. Further, we highlight the potential implications of CTC profiling for clinical applications aimed at enhancing cancer diagnosis and treatment. SIGNIFICANCE Exploring the complexity of cancer progression through cutting-edge multiomics studies holds the promise of uncovering novel aspects of cancer biology and identifying therapeutic vulnerabilities to suppress metastasis.
Collapse
Affiliation(s)
- Yu Wei Zhang
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
| | - Ana Gvozdenovic
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
| | - Nicola Aceto
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology Zurich (ETH Zurich), Zurich, Switzerland
| |
Collapse
|
2
|
Luo X, Li L. Effects of Solvent Evaporation Methods and Short-Term Room Temperature Storage on High-Coverage Cellular Metabolome Analysis. Metabolites 2023; 13:1052. [PMID: 37887377 PMCID: PMC10609186 DOI: 10.3390/metabo13101052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 10/28/2023] Open
Abstract
Cellular metabolomics provides insights into the metabolic processes occurring within cells and can help researchers understand how these processes are regulated and how they relate to cellular function, health, and disease. In this technical note, we investigated the effects of solvent evaporation equipment and storage condition on high-coverage cellular metabolomics. We previously introduced a robust CIL LC-MS-based cellular metabolomics workflow that encompasses various steps, including cell harvest, metabolic quenching, cell lysis, metabolite extraction, differential chemical isotope labeling, and LC-MS analysis. This workflow has consistently served as the cornerstone of our collaborative research and service projects. As a core facility catering to users with diverse research needs and financial resources, we have encountered scenarios requiring short-term sample storage. For example, the need often arises to transport samples at room temperature from user sites to our core facility. Herein, we present a study in which we compared different solvent evaporation methods (specifically, the nitrogen blowdown evaporator, SpeedVac concentrator, and lyophilizer) and diverse storage conditions (including dried samples stored in a freezer, samples stored in a freezer with methanol, dried samples stored at room temperature, and samples stored at room temperature with methanol). Our findings indicate that the choice of solvent evaporation equipment did not significantly impact the cellular metabolome. However, we observed a noteworthy change in the metabolome after 7 days of storage when cells were stored with methanol, regardless of whether they were kept at -80 °C or room temperature, in contrast to cells that were dried and frozen. Importantly, we detected no significant alterations in cells that were dried and stored at room temperature. In conclusion, to ensure the production of high-quality CIL LC-MS metabolomics results, we strongly recommend that, in situations where low-temperature storage is not feasible, cell samples should be thoroughly dried before storage or shipment at room temperature.
Collapse
Affiliation(s)
- Xian Luo
- The Metabolomics Innovation Centre, Edmonton, AB T6G 2G2, Canada;
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Liang Li
- The Metabolomics Innovation Centre, Edmonton, AB T6G 2G2, Canada;
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| |
Collapse
|
3
|
Li W, Shao C, Li C, Zhou H, Yu L, Yang J, Wan H, He Y. Metabolomics: A useful tool for ischemic stroke research. J Pharm Anal 2023; 13:968-983. [PMID: 37842657 PMCID: PMC10568109 DOI: 10.1016/j.jpha.2023.05.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/14/2023] [Accepted: 05/29/2023] [Indexed: 10/17/2023] Open
Abstract
Ischemic stroke (IS) is a multifactorial and heterogeneous disease. Despite years of studies, effective strategies for the diagnosis, management and treatment of stroke are still lacking in clinical practice. Metabolomics is a growing field in systems biology. It is starting to show promise in the identification of biomarkers and in the use of pharmacometabolomics to help patients with certain disorders choose their course of treatment. The development of metabolomics has enabled further and more biological applications. Particularly, metabolomics is increasingly being used to diagnose diseases, discover new drug targets, elucidate mechanisms, and monitor therapeutic outcomes and its potential effect on precision medicine. In this review, we reviewed some recent advances in the study of metabolomics as well as how metabolomics might be used to identify novel biomarkers and understand the mechanisms of IS. Then, the use of metabolomics approaches to investigate the molecular processes and active ingredients of Chinese herbal formulations with anti-IS capabilities is summarized. We finally summarized recent developments in single cell metabolomics for exploring the metabolic profiles of single cells. Although the field is relatively young, the development of single cell metabolomics promises to provide a powerful tool for unraveling the pathogenesis of IS.
Collapse
Affiliation(s)
- Wentao Li
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chongyu Shao
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chang Li
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Huifen Zhou
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Li Yu
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jiehong Yang
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Haitong Wan
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yu He
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| |
Collapse
|
4
|
Oliva C, Arias A, Ruiz M, Pujol A, Garrabou G, Canto-Santos J, Urreizti R, Castilla-Vallmanya L, Rodriguez-Gonzalez H, Jou C, Casado M, Ormazabal A, Artuch R. Fibroblast phenylalanine concentration as a surrogate biomarker of cellular number. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1226:123787. [PMID: 37327517 DOI: 10.1016/j.jchromb.2023.123787] [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: 03/22/2023] [Revised: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 06/18/2023]
Abstract
Metabolomics studies in human dermal fibroblasts can elucidate the biological mechanisms associated with some diseases, but several methodological issues that increase variability have been identified. We aimed to quantify the amino acid levels in cultured fibroblasts and to apply different sample-based normalization approaches. Forty-four skin biopsies from control subjects were collected. Amino acids were measured in fibroblasts supernatants by UPLC-MS/MS. Statistical supervised and unsupervised studies were used. Spearman's test showed that phenylalanine displayed the second highest correlation with the remaining amino acids (mean r = 0.8), whereas the total protein concentration from the cell pellet showed a mean of r = 0.67. The lowest percentage of variation was obtained when amino acids were normalized by phenylalanine values, with a mean of 42% vs 57% when normalized by total protein values. When amino acid levels were normalized by phenylalanine, Principal Component Analysis and clustering analyses identified different fibroblasts groups. In conclusion, phenylalanine may be a suitable biomarker to estimate cellular content in cultured fibroblasts.
Collapse
Affiliation(s)
- Clara Oliva
- Clinical Biochemistry Department, Sant Joan de Déu Research Institute, Passeig Sant Joan de Déu, 2, 08950, Esplugues de Llobregat, Barcelona, Spain
| | - Angela Arias
- Clinical Biochemistry Department, Sant Joan de Déu Research Institute, Passeig Sant Joan de Déu, 2, 08950, Esplugues de Llobregat, Barcelona, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de la Gran via de l'Hospitalet, 199, 08908 L'Hospitalet de Llobregat, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Universitat Autònoma de Barcelona, Av. de Serragalliners, s/n, 08193 Bellaterra, Barcelona, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), Avinguda de la Gran via de l'Hospitalet, 199, 08908 L'Hospitalet de Llobregat, Barcelona, Spain; Catalan Institution of Research and Advanced Studies (ICREA), Universitat Autònoma de Barcelona, Av. de Serragalliners, s/n, 08193 Bellaterra, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Avda. de Monforte de Lemos, 5, 28029 Madrid, Spain
| | - Gloria Garrabou
- Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Avda. de Monforte de Lemos, 5, 28029 Madrid, Spain; Muscle Research and Mitochondrial Function Laboratory, CELLEX-August Pi i Sunyer Biomedical Research Institute, C/ del Roselló, 149, 08036, Barcelona, Spain; Faculty of Medicine and Health Sciences-University of Barcelona, C/ de Casanova, 143, 08036 Barcelona, Spain; Internal Medicine Department-Hospital Clinic of Barcelona, C/ del Roselló, 149, 08036 Barcelona, Spain
| | - Judith Canto-Santos
- Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Avda. de Monforte de Lemos, 5, 28029 Madrid, Spain; Muscle Research and Mitochondrial Function Laboratory, CELLEX-August Pi i Sunyer Biomedical Research Institute, C/ del Roselló, 149, 08036, Barcelona, Spain
| | - Roser Urreizti
- Clinical Biochemistry Department, Sant Joan de Déu Research Institute, Passeig Sant Joan de Déu, 2, 08950, Esplugues de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Avda. de Monforte de Lemos, 5, 28029 Madrid, Spain
| | - Laura Castilla-Vallmanya
- Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Avda. de Monforte de Lemos, 5, 28029 Madrid, Spain; Department of Genetics, Microbiology and Statistics, Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona, Avinguda Diagonal, 643, 08028 Barcelona, Spain
| | - Helena Rodriguez-Gonzalez
- Clinical Biochemistry Department, Sant Joan de Déu Research Institute, Passeig Sant Joan de Déu, 2, 08950, Esplugues de Llobregat, Barcelona, Spain
| | - Cristina Jou
- Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Avda. de Monforte de Lemos, 5, 28029 Madrid, Spain; Biobank and Pathology department, Hospital Sant Joan de Deu, Passeig Sant Joan de Déu, 2, 08950, Esplugues de Llobregat, Barcelona, Spain
| | - Mercedes Casado
- Clinical Biochemistry Department, Sant Joan de Déu Research Institute, Passeig Sant Joan de Déu, 2, 08950, Esplugues de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Avda. de Monforte de Lemos, 5, 28029 Madrid, Spain
| | - Aida Ormazabal
- Clinical Biochemistry Department, Sant Joan de Déu Research Institute, Passeig Sant Joan de Déu, 2, 08950, Esplugues de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Avda. de Monforte de Lemos, 5, 28029 Madrid, Spain
| | - Rafael Artuch
- Clinical Biochemistry Department, Sant Joan de Déu Research Institute, Passeig Sant Joan de Déu, 2, 08950, Esplugues de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Avda. de Monforte de Lemos, 5, 28029 Madrid, Spain.
| |
Collapse
|
5
|
Neef SK, Hofmann U, Mürdter TE, Schwab M, Haag M. Performance comparison of narrow-bore and capillary liquid-chromatography for non-targeted metabolomics profiling by HILIC-QTOF-MS. Talanta 2023; 260:124578. [PMID: 37119797 DOI: 10.1016/j.talanta.2023.124578] [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: 11/25/2022] [Revised: 03/13/2023] [Accepted: 04/19/2023] [Indexed: 05/01/2023]
Abstract
Clinical metabolomics studies often have to cope with limited sample amounts, thus miniaturized liquid chromatography (LC) systems are a promising alternative. Their applicability has already been demonstrated in various fields, including a few metabolomics studies that mainly used reversed-phase chromatography. However, hydrophilic interaction chromatography (HILIC), which is widely used in metabolomics due to its particular suitability for the analysis of polar molecules, has rarely been tested for miniaturized LC-MS analysis of small molecules. In the present work, the suitability of a capillary HILIC (CapHILIC)-QTOF-MS system for non-targeted metabolomics was evaluated based on extracts of porcine formalin-fixed, paraffin-embedded (FFPE) tissue samples. The performance was assessed with respect to the number and retention time span of metabolic features as well as the analytical repeatability, the signal-to-noise ratio and the signal intensity of 16 annotated metabolites from different compound classes. The results were compared with a well established narrow-bore HILIC-QTOF-MS system. Both platforms have detected a similar number of features and performed excellent with respect to retention time stability (median RT span <0.05 min) and analytical repeatability (>75% of features with CV < 20%). The signal areas of all metabolites assessed were increased up to 18-fold by the use of CapHILIC, although the signal-to-noise ratio was only improved for 50% of the metabolites. An even better reproducibility (median CV = 5.2%) and up to 80-fold increase in signal intensity were observed after optimization of CapHILIC conditions for analysis of bile acid standard solutions. Even though the observed improvement for specific bile acids (e.g. taurocholic acid) in biological matrix needs to be evaluated, the platform comparison indicates, that the tested CapHILIC system is particularly suitable for analyses of a less broad metabolite spectrum, and specifically optimized chromatography.
Collapse
Affiliation(s)
- Sylvia K Neef
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, Tuebingen, Germany
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, Tuebingen, Germany
| | - Thomas E Mürdter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, Tuebingen, Germany
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, Tuebingen, Germany; Departments of Clinical Pharmacology, and of Pharmacy and Biochemistry, University of Tuebingen, Tuebingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany and University of Tuebingen, Tuebingen, Germany.
| |
Collapse
|
6
|
Schönberger K, Mitterer M, Glaser K, Stecher M, Hobitz S, Schain-Zota D, Schuldes K, Lämmermann T, Rambold AS, Cabezas-Wallscheid N, Buescher JM. LC-MS-Based Targeted Metabolomics for FACS-Purified Rare Cells. Anal Chem 2023; 95:4325-4334. [PMID: 36812587 PMCID: PMC9996616 DOI: 10.1021/acs.analchem.2c04396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Metabolism plays a fundamental role in regulating cellular functions and fate decisions. Liquid chromatography-mass spectrometry (LC-MS)-based targeted metabolomic approaches provide high-resolution insights into the metabolic state of a cell. However, the typical sample size is in the order of 105-107 cells and thus not compatible with rare cell populations, especially in the case of a prior flow cytometry-based purification step. Here, we present a comprehensively optimized protocol for targeted metabolomics on rare cell types, such as hematopoietic stem cells and mast cells. Only 5000 cells per sample are required to detect up to 80 metabolites above background. The use of regular-flow liquid chromatography allows for robust data acquisition, and the omission of drying or chemical derivatization avoids potential sources of error. Cell-type-specific differences are preserved while the addition of internal standards, generation of relevant background control samples, and targeted metabolite with quantifiers and qualifiers ensure high data quality. This protocol could help numerous studies to gain thorough insights into cellular metabolic profiles and simultaneously reduce the number of laboratory animals and the time-consuming and costly experiments associated with rare cell-type purification.
Collapse
Affiliation(s)
- Katharina Schönberger
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.,International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), 79108 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79085 Freiburg, Germany
| | - Michael Mitterer
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Katharina Glaser
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.,International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-IEM), 79108 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79085 Freiburg, Germany
| | - Manuel Stecher
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.,Faculty of Biology, University of Freiburg, 79085 Freiburg, Germany.,International Max Planck Research School for Immunobiology, Epigenetics and Metabolism (IMPRS-MCB), 79108 Freiburg, Germany
| | - Sebastian Hobitz
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Dominik Schain-Zota
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Konrad Schuldes
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Tim Lämmermann
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Angelika S Rambold
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | | | - Joerg M Buescher
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| |
Collapse
|
7
|
Gao S, Zhou X, Yue M, Zhu S, Liu Q, Zhao XE. Advances and perspectives in chemical isotope labeling-based mass spectrometry methods for metabolome and exposome analysis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
|
8
|
Zhang Y, Liang F, Zhang D, Qi S, Liu Y. Metabolites as extracellular vesicle cargo in health, cancer, pleural effusion, and cardiovascular diseases: An emerging field of study to diagnostic and therapeutic purposes. Biomed Pharmacother 2023; 157:114046. [PMID: 36469967 DOI: 10.1016/j.biopha.2022.114046] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/19/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Extracellular vesicles (EVs) are highly diverse nanoscale membrane-bound structures released from different cell types into the extracellular environment. They play essential functions in cell signaling by transporting their cargo, such as proteins, RNA, DNA, lipids, metabolites, and small molecules, to recipient cells. It has recently been shown that EVs might modulate carcinogenesis by delivering cargo to recipient cells. Furthermore, recent discoveries revealed that changes in plasma-derived EV levels and cargo in subjects with metabolic diseases were documented by many researchers, suggesting that EVs might be a promising source of disease biomarkers. One of the cargos of EVs that has recently attracted the most attention is metabolites. The metabolome of these vesicles introduces a plethora of disease indicators; hence, examining the metabolomics of EVs detected in human biofluids would be an effective approach. On the other hand, metabolites have various roles in biological systems, including the production of energies, synthesizing macromolecules, and serving as signaling molecules and hormones. Metabolome rewiring in cancer and stromal cells is a characteristic of malignancy, but the current understanding of how this affects the metabolite composition and activity of tumor-derived EVs remains in its infancy. Since new findings and studies in the field of exosome biology and metabolism are constantly being published, it is likely that diagnostic and treatment techniques, including the use of exosome metabolites, will be launched in the coming years. Recent years have seen increased interest in the EV metabolome as a possible source for biomarker development. However, our understanding of the role of these molecules in health and disease is still immature. In this work, we have provided the latest findings regarding the role of metabolites as EV cargoes in the pathophysiology of diseases, including cancer, pleural effusion (PE), and cardiovascular disease (CVD). We also discussed the significance of metabolites as EV cargoes of microbiota and their role in host-microbe interaction. In addition, the latest findings on metabolites in the form of EV cargoes as biomarkers for disease diagnosis and treatment are presented in this study.
Collapse
Affiliation(s)
- Yan Zhang
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China
| | - Feng Liang
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China
| | - DuoDuo Zhang
- Department of Thoracic Surgery, The First Hospital of Jilin University, Changchun, Jilin Province 130021, People's Republic of China
| | - Shuang Qi
- Department of Anesthesiology, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China.
| | - Yan Liu
- Department of Hand Surgery, China-Japan Union Hospital of Jilin University, Changchun, 130033, People's Republic of China.
| |
Collapse
|
9
|
Hu R, Li Y, Yang Y, Liu M. Mass spectrometry-based strategies for single-cell metabolomics. MASS SPECTROMETRY REVIEWS 2023; 42:67-94. [PMID: 34028064 DOI: 10.1002/mas.21704] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
Single cell analysis has drawn increasing interest from the research community due to its capability to interrogate cellular heterogeneity, allowing refined tissue classification and facilitating novel biomarker discovery. With the advancement of relevant instruments and techniques, it is now possible to perform multiple omics including genomics, transcriptomics, metabolomics or even proteomics at single cell level. In comparison with other omics studies, single-cell metabolomics (SCM) represents a significant challenge since it involves many types of dynamically changing compounds with a wide range of concentrations. In addition, metabolites cannot be amplified. Although difficult, considerable progress has been made over the past decade in mass spectrometry (MS)-based SCM in terms of processing technologies and biochemical applications. In this review, we will summarize recent progress in the development of promising MS platforms, sample preparation methods and SCM analysis of various cell types (including plant cell, cancer cell, neuron, embryo cell, and yeast cell). Current limitations and future research directions in the field of SCM will also be discussed.
Collapse
Affiliation(s)
- Rui Hu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yunhuang Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
10
|
Li M, Wu S, Zhuang C, Shi C, Gu L, Wang P, Guo F, Wang Y, Liu Z. Metabolomic analysis of circulating tumor cells derived liver metastasis of colorectal cancer. Heliyon 2022; 9:e12515. [PMID: 36691542 PMCID: PMC9860459 DOI: 10.1016/j.heliyon.2022.e12515] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/17/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Metabolic reprogramming is one of the essential features of tumor that may dramatically contribute to metastasis and collapse. The metabolic profiling is investigated on the patient derived tissue and cancer cell line derived mouse metastasis xenograft. As well-recognized "seeds" for remote metastasis of tumor, role of circulating tumor cells (CTCs) in the study of metabolic reprogramming feature of tumor is yet to be elucidated. More specifically, whether there is difference of metabolic features of liver metastasis in colorectal cancer (CRC) derived from either CTCs or cancer cell line is still unknown. In this study, comprehensive untargeted metabolomics was performed using high performance liquid chromatography-mass spectrometry (HPLC-MS) in liver metastasis tissues from CT26 cells and CTCs derived mouse models. We identified 288 differential metabolites associated with the pathways such as one carbon pool by folate, folate biosynthesis and histidine metabolism through bioinformation analysis. Multiple gene expression was upregulated in the CTCs derived liver metastasis, specifically some specific enzymes. These results indicated that the metabolite phenotype and corresponding gene expression in the CTCs derived liver metastasis tissues was different from the parental CT26 cells, displaying a specific up-regulation of mRNAs involved in the above metabolism-related pathways. The metabolic profile of CTCs was characterized on the liver metastatic process in colorectal cancer. The invasion ability and chemo drug tolerance of the CTCs derived tumor and metastasis was found to be overwhelming higher than cell line derived counterpart. Identification of the differential metabolites will lead to a better understanding of the hallmarks of the cancer progression and metastasis, which may suggest potential attractive target for treating metastatic CRC.
Collapse
Affiliation(s)
- Meng Li
- Department of General Surgery, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200092, PR China
| | - Shengming Wu
- The Institute for Translational Nanomedicine, Shanghai East Hospital, The Institute for Biomedical Engineering & Nano Science, School of Medicine, Tongji University, Shanghai 200092, PR China
| | - Chengle Zhuang
- Department of General Surgery, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200092, PR China
| | - Chenzhang Shi
- Department of General Surgery, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200092, PR China
| | - Lei Gu
- Department of General Surgery, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200092, PR China
| | - Peng Wang
- The Institute for Translational Nanomedicine, Shanghai East Hospital, The Institute for Biomedical Engineering & Nano Science, School of Medicine, Tongji University, Shanghai 200092, PR China
| | - Fangfang Guo
- The Institute for Translational Nanomedicine, Shanghai East Hospital, The Institute for Biomedical Engineering & Nano Science, School of Medicine, Tongji University, Shanghai 200092, PR China
| | - Yilong Wang
- The Institute for Translational Nanomedicine, Shanghai East Hospital, The Institute for Biomedical Engineering & Nano Science, School of Medicine, Tongji University, Shanghai 200092, PR China,Corresponding author.
| | - Zhongchen Liu
- Department of General Surgery, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200092, PR China,Corresponding author.
| |
Collapse
|
11
|
Nascentes Melo LM, Lesner NP, Sabatier M, Ubellacker JM, Tasdogan A. Emerging metabolomic tools to study cancer metastasis. Trends Cancer 2022; 8:988-1001. [PMID: 35909026 DOI: 10.1016/j.trecan.2022.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/24/2022] [Accepted: 07/06/2022] [Indexed: 12/24/2022]
Abstract
Metastasis is responsible for 90% of deaths in patients with cancer. Understanding the role of metabolism during metastasis has been limited by the development of robust and sensitive technologies that capture metabolic processes in metastasizing cancer cells. We discuss the current technologies available to study (i) metabolism in primary and metastatic cancer cells and (ii) metabolic interactions between cancer cells and the tumor microenvironment (TME) at different stages of the metastatic cascade. We identify advantages and disadvantages of each method and discuss how these tools and technologies will further improve our understanding of metastasis. Studies investigating the complex metabolic rewiring of different cells using state-of-the-art metabolomic technologies have the potential to reveal novel biological processes and therapeutic interventions for human cancers.
Collapse
Affiliation(s)
| | - Nicholas P Lesner
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marie Sabatier
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jessalyn M Ubellacker
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Alpaslan Tasdogan
- Department of Dermatology, University Hospital Essen and German Cancer Consortium, Partner Site, Essen, Germany.
| |
Collapse
|
12
|
Ogrizek M, Kroflič A, Šala M. Determination of trace concentrations of simple phenols in ambient PM samples. CHEMOSPHERE 2022; 303:135313. [PMID: 35697106 DOI: 10.1016/j.chemosphere.2022.135313] [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: 05/04/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Phenols are hazardous, but yet ubiquitous in the environment, including in atmospheric aerosols due to combustion emissions. There, phenols are subjected to secondary transformations, producing even more toxic nitrophenolic air pollutants. However, primary simple phenols, i.e. those containing only hydroxyl, methyl and methoxy substituents are not easy to detect. Trace concentrations, semi-volatile character and poorly ionizable functional groups prevent us from their determination by the most common analytical techniques, such as gas and liquid chromatography with mass spectrometric detection (GC/LC-MS). Here, we present a new derivatization method for MS/MS detection with positive ion electrospray ionization (+ESI-MS/MS) of simple phenols in atmospheric particulate matter (PM) extracts. The method is sensitive, selective, and robust, and requires no sample concentration step, which is critical due to the volatile character of the target analytes. After derivatization with dansyl chloride, phenol, catechol, cresols and guaiacol were detected in urban PM samples from Ljubljana, Slovenia. This method finally enables to study the abundance of primary phenols in atmospheric PM from different sources, which will improve understanding of secondary aerosol (trans)formation pathways and allow for more targeted mitigation strategies in respect to airborne phenolic pollutants.
Collapse
Affiliation(s)
- Monika Ogrizek
- Department of Analytical Chemistry, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova Cesta 39, 1000, Ljubljana, Slovenia
| | - Ana Kroflič
- Department of Analytical Chemistry, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.
| | - Martin Šala
- Department of Analytical Chemistry, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.
| |
Collapse
|
13
|
Fitz V, El Abiead Y, Berger D, Koellensperger G. Systematic Investigation of LC Miniaturization to Increase Sensitivity in Wide-Target LC-MS-Based Trace Bioanalysis of Small Molecules. Front Mol Biosci 2022; 9:857505. [PMID: 35923463 PMCID: PMC9340153 DOI: 10.3389/fmolb.2022.857505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/06/2022] [Indexed: 01/23/2023] Open
Abstract
Covering a wide spectrum of molecules is essential for global metabolome assessment. While metabolomics assays are most frequently carried out in microbore LC-MS analysis, reducing the size of the analytical platform has proven its ability to boost sensitivity for specific -omics applications. In this study, we elaborate the impact of LC miniaturization on exploratory small-molecule LC-MS analysis, focusing on chromatographic properties with critical impact on peak picking and statistical analysis. We have assessed a panel of small molecules comprising endogenous metabolites and environmental contaminants covering three flow regimes—analytical, micro-, and nano-flow. Miniaturization to the micro-flow regime yields moderately increased sensitivity as compared to the nano setup, where median sensitivity gains around 80-fold are observed in protein-precipitated blood plasma extract. This gain resulting in higher coverage at low µg/L concentrations is compound dependent. At the same time, the nano-LC-high-resolution mass spectrometry (HRMS) approach reduces the investigated chemical space as a consequence of the trap-and-elute nano-LC platform. Finally, while all three setups show excellent retention time stabilities, rapid gradients jeopardize the peak area repeatability of the nano-LC setup. Micro-LC offers the best compromise between improving signal intensity and metabolome coverage, despite the fact that only incremental gains can be achieved. Hence, we recommend using micro-LC for wide-target small-molecule trace bioanalysis and global metabolomics of abundant samples.
Collapse
Affiliation(s)
- Veronika Fitz
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna, Austria
| | - Yasin El Abiead
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Daniel Berger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
- Chemistry Meets Biology, University of Vienna, Vienna, Austria
- *Correspondence: Gunda Koellensperger,
| |
Collapse
|
14
|
A rapid and robust method for amino acid quantification using a simple N-hydroxysuccinimide ester derivatization and liquid chromatography-ion mobility-mass spectrometry. Anal Bioanal Chem 2022; 414:5549-5559. [PMID: 35338375 DOI: 10.1007/s00216-022-03993-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/14/2022] [Accepted: 02/25/2022] [Indexed: 11/01/2022]
Abstract
The vast majority of mass spectrometry (MS)-based metabolomics studies employ reversed-phase liquid chromatography (RPLC) to separate analytes prior to MS detection. Highly polar metabolites, such as amino acids (AAs), are poorly retained by RPLC, making quantitation of these key species challenging across the broad concentration ranges typically observed in biological specimens, such as cell extracts. To improve the detection and quantitation of AAs in microglial cell extracts, the implementation of a 4-dimethylaminobenzoylamido acetic acid N-hydroxysuccinimide ester (DBAA-NHS) derivatization agent was explored for its ability to improve both analyte retention and detection limits in RPLC-MS. In addition to the introduction of the DBAA-NHS labeling reagent, a uniformly (U) 13C-labeled yeast extract was also introduced during the sample preparation workflow as an internal standard (IS) to eliminate artifacts and to enable targeted quantitation of AAs, as well as untargeted amine submetabolome profiling. To improve method sensitivity and selectivity, multiplexed drift-tube ion mobility (IM) was integrated into the LC-MS workflow, facilitating the separation of isomeric metabolites, and improving the structural identification of unknown metabolites. Implementation of the U-13C-labeled yeast extract during the multiplexed LC-IM-MS analysis enabled the quantitation of 19 of the 20 common AAs, supporting a linear dynamic range spanning up to three orders of magnitude in concentration for microglial cell extracts, in addition to reducing the required cell count for reliable quantitation from 10 to 5 million cells per sample.
Collapse
|
15
|
Patel SB, Nemkov T, D'Alessandro A, Welner RS. Deciphering Metabolic Adaptability of Leukemic Stem Cells. Front Oncol 2022; 12:846149. [PMID: 35756656 PMCID: PMC9213881 DOI: 10.3389/fonc.2022.846149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Therapeutic targeting of leukemic stem cells is widely studied to control leukemia. An emerging approach gaining popularity is altering metabolism as a potential therapeutic opportunity. Studies have been carried out on hematopoietic and leukemic stem cells to identify vulnerable pathways without impacting the non-transformed, healthy counterparts. While many metabolic studies have been conducted using stem cells, most have been carried out in vitro or on a larger population of progenitor cells due to challenges imposed by the low frequency of stem cells found in vivo. This creates artifacts in the studies carried out, making it difficult to interpret and correlate the findings to stem cells directly. This review discusses the metabolic difference seen between hematopoietic stem cells and leukemic stem cells across different leukemic models. Moreover, we also shed light on the advancements of metabolic techniques and current limitations and areas for additional research of the field to study stem cell metabolism.
Collapse
Affiliation(s)
- Sweta B Patel
- Department of Medicine, Division of Hematology/Oncology, O'Neal Comprehensive Cancer Center, University of Alabama at, Birmingham, AL, United States.,Divison of Hematology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Robert S Welner
- Department of Medicine, Division of Hematology/Oncology, O'Neal Comprehensive Cancer Center, University of Alabama at, Birmingham, AL, United States
| |
Collapse
|
16
|
Malinowska JM, Palosaari T, Sund J, Carpi D, Bouhifd M, Weber RJM, Whelan M, Viant MR. Integrating in vitro metabolomics with a 96-well high-throughput screening platform. Metabolomics 2022; 18:11. [PMID: 35000038 PMCID: PMC8743266 DOI: 10.1007/s11306-021-01867-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 12/16/2021] [Indexed: 02/07/2023]
Abstract
INTRODUCTION High-throughput screening (HTS) is emerging as an approach to support decision-making in chemical safety assessments. In parallel, in vitro metabolomics is a promising approach that can help accelerate the transition from animal models to high-throughput cell-based models in toxicity testing. OBJECTIVE In this study we establish and evaluate a high-throughput metabolomics workflow that is compatible with a 96-well HTS platform employing 50,000 hepatocytes of HepaRG per well. METHODS Low biomass cell samples were extracted for metabolomics analyses using a newly established semi-automated protocol, and the intracellular metabolites were analysed using a high-resolution spectral-stitching nanoelectrospray direct infusion mass spectrometry (nESI-DIMS) method that was modified for low sample biomass. RESULTS The method was assessed with respect to sensitivity and repeatability of the entire workflow from cell culturing and sampling to measurement of the metabolic phenotype, demonstrating sufficient sensitivity (> 3000 features in hepatocyte extracts) and intra- and inter-plate repeatability for polar nESI-DIMS assays (median relative standard deviation < 30%). The assays were employed for a proof-of-principle toxicological study with a model toxicant, cadmium chloride, revealing changes in the metabolome across five sampling times in the 48-h exposure period. To allow the option for lipidomics analyses, the solvent system was extended by establishing separate extraction methods for polar metabolites and lipids. CONCLUSIONS Experimental, analytical and informatics workflows reported here met pre-defined criteria in terms of sensitivity, repeatability and ability to detect metabolome changes induced by a toxicant and are ready for application in metabolomics-driven toxicity testing to complement HTS assays.
Collapse
Affiliation(s)
- Julia M Malinowska
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Taina Palosaari
- European Commission, Joint Research Centre (JRC), 21027, Ispra, Italy
| | - Jukka Sund
- European Commission, Joint Research Centre (JRC), 21027, Ispra, Italy
| | - Donatella Carpi
- European Commission, Joint Research Centre (JRC), 21027, Ispra, Italy
| | - Mounir Bouhifd
- European Commission, Joint Research Centre (JRC), 21027, Ispra, Italy
- European Chemicals Agency, Helsinki, Finland
| | - Ralf J M Weber
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
- Phenome Centre Birmingham, University of Birmingham, Birmingham, B15 2TT, UK
| | - Maurice Whelan
- European Commission, Joint Research Centre (JRC), 21027, Ispra, Italy
| | - Mark R Viant
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
- Phenome Centre Birmingham, University of Birmingham, Birmingham, B15 2TT, UK.
| |
Collapse
|
17
|
He B, Zhang W, Guled F, Harms A, Ramautar R, Hankemeier T. Analytical techniques for biomass-restricted metabolomics: An overview of the state-of-the-art. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
18
|
Mass spectrometry based metabolomics of volume-restricted in-vivo brain samples: Actual status and the way forward. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
19
|
Marchev AS, Vasileva LV, Amirova KM, Savova MS, Balcheva-Sivenova ZP, Georgiev MI. Metabolomics and health: from nutritional crops and plant-based pharmaceuticals to profiling of human biofluids. Cell Mol Life Sci 2021; 78:6487-6503. [PMID: 34410445 PMCID: PMC8558153 DOI: 10.1007/s00018-021-03918-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 12/19/2022]
Abstract
During the past decade metabolomics has emerged as one of the fastest developing branches of “-omics” technologies. Metabolomics involves documentation, identification, and quantification of metabolites through modern analytical platforms in various biological systems. Advanced analytical tools, such as gas chromatography–mass spectrometry (GC/MS), liquid chromatography–mass spectroscopy (LC/MS), and non-destructive nuclear magnetic resonance (NMR) spectroscopy, have facilitated metabolite profiling of complex biological matrices. Metabolomics, along with transcriptomics, has an influential role in discovering connections between genetic regulation, metabolite phenotyping and biomarkers identification. Comprehensive metabolite profiling allows integration of the summarized data towards manipulation of biosynthetic pathways, determination of nutritional quality markers, improvement in crop yield, selection of desired metabolites/genes, and their heritability in modern breeding. Along with that, metabolomics is invaluable in predicting the biological activity of medicinal plants, assisting the bioactivity-guided fractionation process and bioactive leads discovery, as well as serving as a tool for quality control and authentication of commercial plant-derived natural products. Metabolomic analysis of human biofluids is implemented in clinical practice to discriminate between physiological and pathological state in humans, to aid early disease biomarker discovery and predict individual response to drug therapy. Thus, metabolomics could be utilized to preserve human health by improving the nutritional quality of crops and accelerating plant-derived bioactive leads discovery through disease diagnostics, or through increasing the therapeutic efficacy of drugs via more personalized approach. Here, we attempt to explore the potential value of metabolite profiling comprising the above-mentioned applications of metabolomics in crop improvement, medicinal plants utilization, and, in the prognosis, diagnosis and management of complex diseases.
Collapse
Affiliation(s)
- Andrey S Marchev
- Department Plant Cell Biotechnology, Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.,Laboratory of Metabolomics, Department of Biotechnology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4000, Plovdiv, Bulgaria
| | - Liliya V Vasileva
- Department Plant Cell Biotechnology, Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.,Laboratory of Metabolomics, Department of Biotechnology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4000, Plovdiv, Bulgaria
| | - Kristiana M Amirova
- Department Plant Cell Biotechnology, Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.,Laboratory of Metabolomics, Department of Biotechnology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4000, Plovdiv, Bulgaria
| | - Martina S Savova
- Department Plant Cell Biotechnology, Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.,Laboratory of Metabolomics, Department of Biotechnology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4000, Plovdiv, Bulgaria
| | - Zhivka P Balcheva-Sivenova
- Department Plant Cell Biotechnology, Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.,Laboratory of Metabolomics, Department of Biotechnology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4000, Plovdiv, Bulgaria
| | - Milen I Georgiev
- Department Plant Cell Biotechnology, Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria. .,Laboratory of Metabolomics, Department of Biotechnology, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, 4000, Plovdiv, Bulgaria.
| |
Collapse
|
20
|
Xu T, Li H, Feng D, Dou P, Shi X, Hu C, Xu G. Lipid Profiling of 20 Mammalian Cells by Capillary Microsampling Combined with High-Resolution Spectral Stitching Nanoelectrospray Ionization Direct-Infusion Mass Spectrometry. Anal Chem 2021; 93:10031-10038. [PMID: 34270220 DOI: 10.1021/acs.analchem.1c00373] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Studies of cellular metabolism can provide profound insights into the underlying molecular mechanisms and metabolic function. To date, the majority of cellular metabolism studies based on chromatography-mass spectrometry (MS) require population cells to obtain informative metabolome. These methods are not only time-consuming but also not suitable for amount-limited cell samples such as circulating tumor cells, stem cells, and neurons. Therefore, it is extremely essential to develop analytical methods enabling to detect metabolome from tens of cells in a high-throughput and high-sensitivity way. In this work, a novel platform for rapid and sensitive detection of lipidome in 20 mammalian cells was proposed using capillary microsampling combined with high-resolution spectral stitching nanoelectrospray ionization direct-infusion MS. It can be used to collect cells rapidly and accurately via the capillary microprobe, extract lipids directly in a 96-well plate using a spray solvent, and detect more than 500 lipids covering 19 lipid subclasses within 3 min. This novel platform was successfully applied to study the lipid features of different cancer cell types and subtypes as well as target cells from tissue samples. This study provides a strategy for determining the lipid species with rich information in tens of cells and demonstrates great potential for clinical applications.
Collapse
Affiliation(s)
- Tianrun Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Disheng Feng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Dou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xianzhe Shi
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chunxiu Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
21
|
Zago G, Saavedra PHV, Keshari KR, Perry JSA. Immunometabolism of Tissue-Resident Macrophages - An Appraisal of the Current Knowledge and Cutting-Edge Methods and Technologies. Front Immunol 2021; 12:665782. [PMID: 34025667 PMCID: PMC8138590 DOI: 10.3389/fimmu.2021.665782] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/07/2021] [Indexed: 12/23/2022] Open
Abstract
Tissue-resident macrophages exist in unique environments, or niches, that inform their identity and function. There is an emerging body of literature suggesting that the qualities of this environment, such as the types of cells and debris they eat, the intercellular interactions they form, and the length of time spent in residence, collectively what we call habitare, directly inform their metabolic state. In turn, a tissue-resident macrophage’s metabolic state can inform their function, including whether they resolve inflammation and protect the host from excessive perturbations of homeostasis. In this review, we summarize recent work that seeks to understand the metabolic requirements for tissue-resident macrophage identity and maintenance, for how they respond to inflammatory challenges, and for how they perform homeostatic functions or resolve inflammatory insults. We end with a discussion of the emerging technologies that are enabling, or will enable, in situ study of tissue-resident macrophage metabolism.
Collapse
Affiliation(s)
- Giulia Zago
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Pedro H V Saavedra
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Kayvan R Keshari
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Justin S A Perry
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY, United States
| |
Collapse
|
22
|
Guan F, Xiang X, Xie Y, Li H, Zhang W, Shu Y, Wang J, Qin W. Simultaneous metabolomics and proteomics analysis of plasma-derived extracellular vesicles. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:1930-1938. [PMID: 33913941 DOI: 10.1039/d1ay00060h] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Extracellular vesicles (EVs) are nanoscale vesicles with a phospholipid bilayer. In the past few decades, EVs have gained more and more attention, which is attributed to their important roles in cell-to-cell communication. They are regarded as promising sources for disease biomarkers and have been explored for applications in early-stage diagnostics, monitoring of disease status, therapeutics and drug delivery. Nevertheless, EVs are a heterogeneous group of vesicles, and include two predominant classes: exosomes and microvesicles. The origins of these vesicles are diverse, which determines their differences in features and functions. To study the diversity of these EV subpopulations, it is essential to elucidate their compositions including proteins, metabolites, etc. Here, we presented a tandem extraction method to obtain metabolites and proteins from the same batch of EVs simultaneously, enabling a multi-omics differential analysis of exosomes and microvesicles in human plasma. As a result, we found 112 different proteins and 50 different metabolites between exosomes and microvesicles, demonstrating the diversity of these EV subpopulations. Furthermore, compared with human plasma, these two major classes of EVs showed distinct metabolome features, which indicated the necessity of analysing the metabolites derived from EVs to obtain a more comprehensive profile of the plasma metabolome, and the potential of EVs as important sources for biomarker screening.
Collapse
Affiliation(s)
- Fulin Guan
- Research Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, P. R. China
| | | | | | | | | | | | | | | |
Collapse
|
23
|
Roberg-Larsen H, Wilson SR, Lundanes E. Recent advances in on-line upfront devices for sensitive bioanalytical nano LC methods. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116190] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
24
|
Luo X, Wu Y, Li L. Normalization of Samples of Limited Amounts in Quantitative Metabolomics Using Liquid Chromatography Fluorescence Detection with Dansyl Labeling of Metabolites. Anal Chem 2021; 93:3418-3425. [PMID: 33554593 DOI: 10.1021/acs.analchem.0c04508] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Quantitative metabolomics requires the analysis of the same or a very similar amount of samples in order to accurately determine the concentration differences of individual metabolites in comparative samples. Ideally, the total amount or concentration of metabolites in each sample is measured to normalize all the analyzed samples. In this work, we describe a very sensitive method to measure a subclass of metabolites as a surrogate quantifier for normalization of samples with limited amounts. This method starts with low-volume dansyl labeling of all metabolites containing a primary/secondary amine or phenol group in a sample to produce a final solution of 21 μL. The dansyl-labeled metabolites generate fluorescence signals at 520 nm with photoexcitation at 250 nm. To remove the interference of dansyl hydroxyl products (Dns-OH) formed from the labeling reagents used, a fast-gradient liquid chromatography separation is used to elute Dns-OH using aqueous solution, followed by organic solvent elution to produce a chromatographic peak of labeled metabolites, giving a measurement throughput of 6 min per sample. The integrated fluorescence signals of the peak are found to be related to the injection amount of the dansyl-labeled metabolites. A calibration curve using mixtures of dansyl-labeled amino acids is used to determine the total concentration of labeled metabolites in a sample. This concentration is used for normalization of samples in the range from 2 to 120 μM in 21 μL with only 1 μL consumed for fluorescence quantification (i.e., 2-120 pmol). We demonstrate the application of this sensitive sample normalization method in comparative metabolome analysis of human cancer cells, MCF-7 cells, treated with and without resveratrol, using a starting material of as low as 500 cells.
Collapse
Affiliation(s)
- Xian Luo
- Department of Chemistry, University of Alberta, Edmonton Alberta T6G 2G2, Canada
| | - Yiman Wu
- Department of Chemistry, University of Alberta, Edmonton Alberta T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton Alberta T6G 2G2, Canada
| |
Collapse
|
25
|
Zaikin VG, Borisov RS. Options of the Main Derivatization Approaches for Analytical ESI and MALDI Mass Spectrometry. Crit Rev Anal Chem 2021; 52:1287-1342. [PMID: 33557614 DOI: 10.1080/10408347.2021.1873100] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The inclusion of preliminary chemical labeling (derivatization) in the analysis process by such powerful and widespread methods as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a popular and widely used methodological approach. This is due to the need to remove some fundamental limitations inherent in these powerful analytic methods. Although a number of special reviews has been published discussing the utilization of derivatization approaches, the purpose of the present critical review is to comprehensively summarize, characterize and evaluate most of the previously developed and practically applied, as well as recently proposed representative derivatization reagents for ESI-MS and MALDI-MS platforms in their mostly sensitive positive ion mode and frequently hyphenated with separation techniques. The review is focused on the use of preliminary chemical labeling to facilitate the detection, identification, structure elucidation, quantification, profiling or MS imaging of compounds within complex matrices. Two main derivatization approaches, namely the introduction of permanent charge-fixed or highly proton affinitive residues into analytes are critically evaluated. In situ charge-generation, charge-switch and charge-transfer derivatizations are considered separately. The potential of using reactive matrices in MALDI-MS and chemical labeling in MS-based omics sciences is given.
Collapse
Affiliation(s)
- Vladimir G Zaikin
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
| | - Roman S Borisov
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
| |
Collapse
|
26
|
Majuta SN, DeBastiani A, Li P, Valentine SJ. Combining Field-Enabled Capillary Vibrating Sharp-Edge Spray Ionization with Microflow Liquid Chromatography and Mass Spectrometry to Enhance 'Omics Analyses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:473-485. [PMID: 33417454 PMCID: PMC8132193 DOI: 10.1021/jasms.0c00376] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Field-enabled capillary vibrating sharp-edge spray ionization (cVSSI) has been combined with high-flow liquid chromatography (LC) and mass spectrometry (MS) to establish current ionization capabilities for metabolomics and proteomics investigations. Comparisons are made between experiments employing cVSSI and a heated electrospray ionization probe representing the state-of-the-art in microflow LC-MS methods for 'omics studies. For metabolomics standards, cVSSI is shown to provide an ionization enhancement by factors of 4 ± 2 for both negative and positive ion mode analyses. For chymotryptic peptides, cVSSI is shown to provide an ionization enhancement by factors of 5 ± 2 and 2 ± 1 for negative and positive ion mode analyses, respectively. Slightly broader high-performance liquid chromatography peaks are observed in the cVSSI datasets, and several studies suggest that this results from a slightly decreased post-split flow rate. This may result from partial obstruction of the pulled-tip emitter over time. Such a challenge can be remedied with the use of LC pumps that operate in the 10 to 100 μL·min-1 flow regime. At this early stage, the proof-of-principle studies already show ion signal advantages over state-of-the-art electrospray ionization (ESI) for a wide variety of analytes in both positive and negative ion mode. Overall, this represents a ∼20-50-fold improvement over the first demonstration of LC-MS analyses by voltage-free cVSSI. Separate comparisons of the ion abundances of compounds eluting under identical solvent conditions reveal ionization efficiency differences between cVSSI and ESI and may suggest varied contributions to ionization from different physicochemical properties of the compounds. Future investigations of parameters that could further increase ionization gains in negative and positive ion mode analyses with the use of cVSSI are briefly presented.
Collapse
Affiliation(s)
- Sandra N. Majuta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| | - Stephen J. Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown WV 26501
| |
Collapse
|
27
|
Liu R, Yang Z. Single cell metabolomics using mass spectrometry: Techniques and data analysis. Anal Chim Acta 2021; 1143:124-134. [PMID: 33384110 PMCID: PMC7775990 DOI: 10.1016/j.aca.2020.11.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/10/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023]
Abstract
Mass spectrometry (MS) based techniques are gaining popularity for metabolomics research due to their high sensitivity, wide detection range, and capability of molecular identification. Utilizing such powerful technique to explore the cellular metabolism at the single cell level not only appreciates the subtle cell-to-cell difference (i.e., cell heterogeneity), but also gains biological merits corresponding to individual cells or small cell subpopulations. In this review article, we first briefly summarize recent advances in single cell MS experimental techniques, and then emphasize on the single cell metabolomics data analysis approaches. Through implementation of statistical analysis and more advanced data analysis methods, single cell metabolomics is expected to find more potential applications in the translational and clinical fields in the future.
Collapse
Affiliation(s)
- Renmeng Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA; Alliance Pharma. Inc., Malvern, PA, 19355, USA
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.
| |
Collapse
|
28
|
DeVilbiss AW, Zhao Z, Martin-Sandoval MS, Ubellacker JM, Tasdogan A, Agathocleous M, Mathews TP, Morrison SJ. Metabolomic profiling of rare cell populations isolated by flow cytometry from tissues. eLife 2021; 10:61980. [PMID: 33470192 PMCID: PMC7847306 DOI: 10.7554/elife.61980] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/19/2021] [Indexed: 12/16/2022] Open
Abstract
Little is known about the metabolic regulation of rare cell populations because most metabolites are hard to detect in small numbers of cells. We previously described a method for metabolomic profiling of flow cytometrically isolated hematopoietic stem cells (HSCs) that detects 60 metabolites in 10,000 cells (Agathocleous et al., 2017). Here we describe a new method involving hydrophilic liquid interaction chromatography and high-sensitivity orbitrap mass spectrometry that detected 160 metabolites in 10,000 HSCs, including many more glycolytic and lipid intermediates. We improved chromatographic separation, increased mass resolution, minimized ion suppression, and eliminated sample drying. Most metabolite levels did not significantly change during cell isolation. Mouse HSCs exhibited increased glycerophospholipids relative to bone marrow cells and methotrexate treatment altered purine biosynthesis. Circulating human melanoma cells were depleted for purine intermediates relative to subcutaneous tumors, suggesting decreased purine synthesis during metastasis. These methods facilitate the routine metabolomic analysis of rare cells from tissues.
Collapse
Affiliation(s)
- Andrew W DeVilbiss
- Children's Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Zhiyu Zhao
- Children's Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Misty S Martin-Sandoval
- Children's Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jessalyn M Ubellacker
- Children's Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Alpaslan Tasdogan
- Children's Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Michalis Agathocleous
- Children's Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Thomas P Mathews
- Children's Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Sean J Morrison
- Children's Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| |
Collapse
|
29
|
Zhao S, Li L. Chemical Isotope Labeling LC-MS for Metabolomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1280:1-18. [PMID: 33791971 DOI: 10.1007/978-3-030-51652-9_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Due to the great diversity of chemical and physical properties of metabolites as well as a wide range of concentrations of metabolites present in metabolomic samples, performing comprehensive and quantitative metabolome analysis is a major analytical challenge. Conventional approach of combining various techniques and methods with each detecting a fraction of the metabolome can lead to the increase in overall metabolomic coverage. However, this approach requires extensive investment in equipment and analytical expertise with still relatively low coverage and low sample throughput. Chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS) offers an alternative means of increasing metabolomic coverage while maintaining high quantification precision and accuracy. This chapter describes the CIL LC-MS method and its key features for metabolomic analysis.
Collapse
Affiliation(s)
- Shuang Zhao
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada.
| |
Collapse
|
30
|
Willacey CC, Karu N, Harms AC, Hankemeier T. Metabolic profiling of material-limited cell samples by dimethylaminophenacyl bromide derivatization with UPLC-MS/MS analysis. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
31
|
Li Y, Bouza M, Wu C, Guo H, Huang D, Doron G, Temenoff JS, Stecenko AA, Wang ZL, Fernández FM. Sub-nanoliter metabolomics via mass spectrometry to characterize volume-limited samples. Nat Commun 2020; 11:5625. [PMID: 33159052 PMCID: PMC7648103 DOI: 10.1038/s41467-020-19444-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/28/2020] [Indexed: 01/18/2023] Open
Abstract
The human metabolome provides a window into the mechanisms and biomarkers of various diseases. However, because of limited availability, many sample types are still difficult to study by metabolomic analyses. Here, we present a mass spectrometry (MS)-based metabolomics strategy that only consumes sub-nanoliter sample volumes. The approach consists of combining a customized metabolomics workflow with a pulsed MS ion generation method, known as triboelectric nanogenerator inductive nanoelectrospray ionization (TENGi nanoESI) MS. Samples tested with this approach include exhaled breath condensate collected from cystic fibrosis patients as well as in vitro-cultured human mesenchymal stromal cells. Both test samples are only available in minimum amounts. Experiments show that picoliter-volume spray pulses suffice to generate high-quality spectral fingerprints, which increase the information density produced per unit sample volume. This TENGi nanoESI strategy has the potential to fill in the gap in metabolomics where liquid chromatography-MS-based analyses cannot be applied. Our method opens up avenues for future investigations into understanding metabolic changes caused by diseases or external stimuli.
Collapse
Affiliation(s)
- Yafeng Li
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Marcos Bouza
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Changsheng Wu
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Hengyu Guo
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Danning Huang
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Gilad Doron
- W.H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Johnna S Temenoff
- W.H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA.,Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Arlene A Stecenko
- Emory + Children's Center for Cystic Fibrosis and Airways Disease Research and Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Zhong Lin Wang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 100083, China
| | - Facundo M Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA. .,Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| |
Collapse
|
32
|
Domenick TM, Gill EL, Vedam-Mai V, Yost RA. Mass Spectrometry-Based Cellular Metabolomics: Current Approaches, Applications, and Future Directions. Anal Chem 2020; 93:546-566. [PMID: 33146525 DOI: 10.1021/acs.analchem.0c04363] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Taylor M Domenick
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Emily L Gill
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104-4283, United States.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-4283, United States
| | - Vinata Vedam-Mai
- Department of Neurology, University of Florida, Gainesville, Florida 32610, United States
| | - Richard A Yost
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| |
Collapse
|
33
|
Abshiru NA, Sikora JW, Camarillo JM, Morris JA, Compton PD, Lee T, Neelamraju Y, Haddox S, Sheridan C, Carroll M, Cripe LD, Tallman MS, Paietta EM, Melnick AM, Thomas PM, Garrett-Bakelman FE, Kelleher NL. Targeted detection and quantitation of histone modifications from 1,000 cells. PLoS One 2020; 15:e0240829. [PMID: 33104722 PMCID: PMC7588077 DOI: 10.1371/journal.pone.0240829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/02/2020] [Indexed: 01/30/2023] Open
Abstract
Histone post-translational modifications (PTMs) create a powerful regulatory mechanism for maintaining chromosomal integrity in cells. Histone acetylation and methylation, the most widely studied histone PTMs, act in concert with chromatin-associated proteins to control access to genetic information during transcription. Alterations in cellular histone PTMs have been linked to disease states and have crucial biomarker and therapeutic potential. Traditional bottom-up mass spectrometry of histones requires large numbers of cells, typically one million or more. However, for some cell subtype-specific studies, it is difficult or impossible to obtain such large numbers of cells and quantification of rare histone PTMs is often unachievable. An established targeted LC-MS/MS method was used to quantify the abundance of histone PTMs from cell lines and primary human specimens. Sample preparation was modified by omitting nuclear isolation and reducing the rounds of histone derivatization to improve detection of histone peptides down to 1,000 cells. In the current study, we developed and validated a quantitative LC-MS/MS approach tailored for a targeted histone assay of 75 histone peptides with as few as 10,000 cells. Furthermore, we were able to detect and quantify 61 histone peptides from just 1,000 primary human stem cells. Detection of 37 histone peptides was possible from 1,000 acute myeloid leukemia patient cells. We anticipate that this revised method can be used in many applications where achieving large cell numbers is challenging, including rare human cell populations.
Collapse
Affiliation(s)
- Nebiyu A. Abshiru
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Jacek W. Sikora
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Jeannie M. Camarillo
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Juliette A. Morris
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Philip D. Compton
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Tak Lee
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States of America
| | - Samuel Haddox
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States of America
| | - Caroline Sheridan
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
| | - Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States of America
| | - Larry D. Cripe
- Indiana University/Melvin and Bren Simon Cancer Center, Indianapolis, IN, United States of America
| | - Martin S. Tallman
- Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | | | - Ari M. Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
| | - Paul M. Thomas
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Francine E. Garrett-Bakelman
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States of America
- Division of Hematology/Medical Oncology, Department of Medicine, University of Virginia, Charlottesville, VA, United States of America
- * E-mail: (FEGB); (NLK)
| | - Neil L. Kelleher
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
- * E-mail: (FEGB); (NLK)
| |
Collapse
|
34
|
|
35
|
Neef SK, Winter S, Hofmann U, Mürdter TE, Schaeffeler E, Horn H, Buck A, Walch A, Hennenlotter J, Ott G, Fend F, Bedke J, Schwab M, Haag M. Optimized protocol for metabolomic and lipidomic profiling in formalin-fixed paraffin-embedded kidney tissue by LC-MS. Anal Chim Acta 2020; 1134:125-135. [DOI: 10.1016/j.aca.2020.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/31/2020] [Accepted: 08/02/2020] [Indexed: 12/16/2022]
|
36
|
Sanders KL, Edwards JL. Nano-liquid chromatography-mass spectrometry and recent applications in omics investigations. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4404-4417. [PMID: 32901622 PMCID: PMC7530103 DOI: 10.1039/d0ay01194k] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Liquid chromatography coupled to mass spectrometry (LC-MS) is one of the most powerful tools in identifying and quantitating molecular species. Decreasing column diameter from the millimeter to micrometer scale is now a well-developed method which allows for sample limited analysis. Specific fabrication of capillary columns is required for proper implementation and optimization when working in the nanoflow regime. Coupling the capillary column to the mass spectrometer for electrospray ionization (ESI) requires reduction of the subsequent emitter tip. Reduction of column diameter to capillary scale can produce improved chromatographic efficiency and the reduction of emitter tip size increased sensitivity of the electrospray process. This improved sensitivity and ionization efficiency is valuable in analysis of precious biological samples where analytes vary in size, ion affinity, and concentration. In this review we will discuss common approaches and challenges in implementing nLC-MS methods and how the advantages can be leveraged to investigate a wide range of biomolecules.
Collapse
|
37
|
Balcerczyk A, Damblon C, Elena-Herrmann B, Panthu B, Rautureau GJP. Metabolomic Approaches to Study Chemical Exposure-Related Metabolism Alterations in Mammalian Cell Cultures. Int J Mol Sci 2020; 21:E6843. [PMID: 32961865 PMCID: PMC7554780 DOI: 10.3390/ijms21186843] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 12/12/2022] Open
Abstract
Biological organisms are constantly exposed to an immense repertoire of molecules that cover environmental or food-derived molecules and drugs, triggering a continuous flow of stimuli-dependent adaptations. The diversity of these chemicals as well as their concentrations contribute to the multiplicity of induced effects, including activation, stimulation, or inhibition of physiological processes and toxicity. Metabolism, as the foremost phenotype and manifestation of life, has proven to be immensely sensitive and highly adaptive to chemical stimuli. Therefore, studying the effect of endo- or xenobiotics over cellular metabolism delivers valuable knowledge to apprehend potential cellular activity of individual molecules and evaluate their acute or chronic benefits and toxicity. The development of modern metabolomics technologies such as mass spectrometry or nuclear magnetic resonance spectroscopy now offers unprecedented solutions for the rapid and efficient determination of metabolic profiles of cells and more complex biological systems. Combined with the availability of well-established cell culture techniques, these analytical methods appear perfectly suited to determine the biological activity and estimate the positive and negative effects of chemicals in a variety of cell types and models, even at hardly detectable concentrations. Metabolic phenotypes can be estimated from studying intracellular metabolites at homeostasis in vivo, while in vitro cell cultures provide additional access to metabolites exchanged with growth media. This article discusses analytical solutions available for metabolic phenotyping of cell culture metabolism as well as the general metabolomics workflow suitable for testing the biological activity of molecular compounds. We emphasize how metabolic profiling of cell supernatants and intracellular extracts can deliver valuable and complementary insights for evaluating the effects of xenobiotics on cellular metabolism. We note that the concepts and methods discussed primarily for xenobiotics exposure are widely applicable to drug testing in general, including endobiotics that cover active metabolites, nutrients, peptides and proteins, cytokines, hormones, vitamins, etc.
Collapse
Affiliation(s)
- Aneta Balcerczyk
- Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland;
| | - Christian Damblon
- Unité de Recherche MolSys, Faculté des sciences, Université de Liège, 4000 Liège, Belgium;
| | | | - Baptiste Panthu
- CarMeN Laboratory, INSERM, INRA, INSA Lyon, Univ Lyon, Université Claude Bernard Lyon 1, 69921 Oullins CEDEX, France;
- Hospices Civils de Lyon, Faculté de Médecine, Hôpital Lyon Sud, 69921 Oullins CEDEX, France
| | - Gilles J. P. Rautureau
- Centre de Résonance Magnétique Nucléaire à Très Hauts Champs (CRMN FRE 2034 CNRS, UCBL, ENS Lyon), Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
| |
Collapse
|
38
|
Vargas Medina DA, Maciel EVS, de Toffoli AL, Lanças FM. Miniaturization of liquid chromatography coupled to mass spectrometry. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115910] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
39
|
Miniaturized liquid chromatography focusing on analytical columns and mass spectrometry: A review. Anal Chim Acta 2020; 1103:11-31. [DOI: 10.1016/j.aca.2019.12.064] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/19/2019] [Accepted: 12/20/2019] [Indexed: 12/17/2022]
|
40
|
Lkhagva A, Shen CC, Leung YS, Tai HC. Comparative study of five different amine-derivatization methods for metabolite analyses by liquid chromatography-tandem mass spectrometry. J Chromatogr A 2020; 1610:460536. [PMID: 31563299 DOI: 10.1016/j.chroma.2019.460536] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/17/2019] [Accepted: 09/09/2019] [Indexed: 01/21/2023]
Abstract
Current metabolomics research utilizes liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses to handle biological samples that contain thousands of quantifiable metabolites. However, no LC-MS/MS condition is suitable for directly analyzing all metabolites. An alternative approach is to derivatize metabolites to impart desirable properties such as better chromatographic separation, enhanced ionization efficiency, or fluorescence detection. An important category of metabolites is amine-containing compounds, which includes amino acids, neurotransmitters, alkaloids, biogenic amines, etc. Various derivatization methods have been developed for amine groups, but few studies have compared their relative strengths and weaknesses. We chose Dansyl-Cl, o-phthalaldehyde (OPA), Fmoc-Cl, Dabsyl-Cl, and Marfey's reagent to systematically compare their reactivity, absorbance, fluorescence, chromatographic separation, and ionization efficiencies under three pH conditions-2.6, 5.0, and 8.0. Their MS/MS fragmentation patterns were also examined under different collision energies. Overall, Dansyl-Cl is a very versatile derivatization method, generating products with fluorescence and high ionization efficiency. Fmoc-Cl is similarly useful under highly acidic chromatography conditions. Dabsyl-Cl may be a good alternative at weakly acidic and weakly basic conditions. OPA is a versatile fluorogenic reagent and its chemistry may be fine-tuned by incorporating different thiol molecules. Marfey's reagent is suboptimal in general, but its chiral property is useful for the separation of enantiomers. All five were applied to the analyses of Coptis chinensis, a Chinese medical herb, identifying hundreds of amine-containing metabolites through MS/MS analyses. None of the five methods is clearly superior, and their compound coverage profiles are rather distinct. A combination of multiple derivatization reagents is required for comprehensive coverage. Our comparative data provide useful guidelines for designing more efficient metabolomics experiments for different analytical goals.
Collapse
Affiliation(s)
- Ankhbayar Lkhagva
- Department of Chemistry, National Taiwan University, Taipei, Taiwan; Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Ching-Chieh Shen
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yun-Shiuan Leung
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hwan-Ching Tai
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
41
|
Fukui S, Takayama T, Toyo’oka T, Mizuno H, Todoroki K. An accurate differential analysis of carboxylic acids in beer using ultra high-performance liquid chromatography–quadrupole time-of-flight mass spectrometry based on chiral derivatization combining three isotopic reagents. Talanta 2019; 205:120146. [DOI: 10.1016/j.talanta.2019.120146] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/08/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022]
|
42
|
González-Riano C, Dudzik D, Garcia A, Gil-de-la-Fuente A, Gradillas A, Godzien J, López-Gonzálvez Á, Rey-Stolle F, Rojo D, Ruperez FJ, Saiz J, Barbas C. Recent Developments along the Analytical Process for Metabolomics Workflows. Anal Chem 2019; 92:203-226. [PMID: 31625723 DOI: 10.1021/acs.analchem.9b04553] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Carolina González-Riano
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Danuta Dudzik
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain.,Department of Biopharmaceutics and Pharmacodynamics, Faculty of Pharmacy , Medical University of Gdańsk , 80-210 Gdańsk , Poland
| | - Antonia Garcia
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Alberto Gil-de-la-Fuente
- Department of Information Technology, Escuela Politécnica Superior , Universidad San Pablo-CEU , 28003 Madrid , Spain
| | - Ana Gradillas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Joanna Godzien
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain.,Clinical Research Centre , Medical University of Bialystok , 15-089 Bialystok , Poland
| | - Ángeles López-Gonzálvez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Fernanda Rey-Stolle
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - David Rojo
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Francisco J Ruperez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Jorge Saiz
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty , Universidad San Pablo-CEU , Boadilla del Monte , 28668 Madrid , Spain
| |
Collapse
|
43
|
Wu ZE, Kruger MC, Cooper GJS, Poppitt SD, Fraser K. Tissue-Specific Sample Dilution: An Important Parameter to Optimise Prior to Untargeted LC-MS Metabolomics. Metabolites 2019; 9:metabo9070124. [PMID: 31252691 PMCID: PMC6680868 DOI: 10.3390/metabo9070124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 12/27/2022] Open
Abstract
When developing a sample preparation protocol for LC–MS untargeted metabolomics of a new sample matrix unfamiliar to the laboratory, selection of a suitable injection concentration is rarely described. Here we developed a simple workflow to address this issue prior to untargeted LC–MS metabolomics using pig adipose tissue and liver tissue. Bi-phasic extraction was performed to enable simultaneous optimisation of parameters for analysis of both lipids and polar extracts. A series of diluted pooled samples were analysed by LC–MS and used to evaluate signal linearity. Suitable injected concentrations were determined based on both the number of reproducible features and linear features. With our laboratory settings, the optimum concentrations of tissue mass to reconstitution solvent of liver and adipose tissue lipid fractions were found to be 125 mg/mL and 7.81 mg/mL respectively, producing 2811 (ESI+) and 4326 (ESI−) linear features from liver, 698 (ESI+) and 498 (ESI−) linear features from adipose tissue. For analysis of the polar fraction of both tissues, 250 mg/mL was suitable, producing 403 (ESI+) and 235 (ESI−) linear features from liver, 114 (ESI+) and 108 (ESI−) linear features from adipose tissue. Incorrect reconstitution volumes resulted in either severe overloading or poor linearity in our lipid data, while too dilute polar fractions resulted in a low number of reproducible features (<50) compared to hundreds of reproducible features from the optimum concentration used. Our study highlights on multiple matrices and multiple extract and chromatography types, the critical importance of determining a suitable injected concentration prior to untargeted LC–MS metabolomics, with the described workflow applicable to any matrix and LC–MS system.
Collapse
Affiliation(s)
- Zhanxuan E Wu
- Food Nutrition & Health, Food and Bio-based Products, AgResearch Limited, Palmerston North 4442, New Zealand
- School of Food and Advanced Technology, Massey University, Palmerston North 4442, New Zealand
- High-Value Nutrition National Science Challenge, Auckland 1142, New Zealand
| | - Marlena C Kruger
- School of Health Sciences, Massey University, Palmerston North 4442, New Zealand
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand
| | - Garth J S Cooper
- Centre for Advanced Discovery and Experimental Therapeutics, Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9NT, UK
- Human Nutrition Unit, School of Biological Sciences and Department of Medicine, University of Auckland, Auckland 1010, New Zealand
| | - Sally D Poppitt
- High-Value Nutrition National Science Challenge, Auckland 1142, New Zealand
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand
- Human Nutrition Unit, School of Biological Sciences and Department of Medicine, University of Auckland, Auckland 1010, New Zealand
| | - Karl Fraser
- Food Nutrition & Health, Food and Bio-based Products, AgResearch Limited, Palmerston North 4442, New Zealand.
- High-Value Nutrition National Science Challenge, Auckland 1142, New Zealand.
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand.
| |
Collapse
|
44
|
Kumar A, Misra BB. Challenges and Opportunities in Cancer Metabolomics. Proteomics 2019; 19:e1900042. [PMID: 30950571 DOI: 10.1002/pmic.201900042] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/22/2019] [Indexed: 12/23/2022]
Abstract
Challenges in metabolomics for a given spectrum of disease are more or less comparable, ranging from the accurate measurement of metabolite abundance, compound annotation, identification of unknown constituents, and interpretation of untargeted and analysis of high throughput targeted metabolomics data leading to the identification of biomarkers. However, metabolomics approaches in cancer studies specifically suffer from several additional challenges and require robust ways to sample the cells and tissues in order to tackle the constantly evolving cancer landscape. These constraints include, but are not limited to, discriminating the signals from given cell types and those that are cancer specific, discerning signals that are systemic and confounded, cell culture-based challenges associated with cell line identities and media standardizations, the need to look beyond Warburg effects, citrate cycle, lactate metabolism, and identifying and developing technologies to precisely and effectively sample and profile the heterogeneous tumor environment. This review article discusses some of the current and pertinent hurdles in cancer metabolomics studies. In addition, it addresses some of the most recent and exciting developments in metabolomics that may address some of these issues. The aim of this article is to update the oncometabolomics research community about the challenges and potential solutions to these issues.
Collapse
Affiliation(s)
- Ashish Kumar
- Department of Genetics, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX, 78227, USA
| | - Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157, USA
| |
Collapse
|
45
|
Peñalver Bernabé B, Thiele I, Galdones E, Siletz A, Chandrasekaran S, Woodruff TK, Broadbelt LJ, Shea LD. Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development. BMC Bioinformatics 2019; 20:307. [PMID: 31182013 PMCID: PMC6558917 DOI: 10.1186/s12859-019-2825-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/16/2019] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND The maturation of the female germ cell, the oocyte, requires the synthesis and storing of all the necessary metabolites to support multiple divisions after fertilization. Oocyte maturation is only possible in the presence of surrounding, diverse, and changing layers of somatic cells. Our understanding of metabolic interactions between the oocyte and somatic cells has been limited due to dynamic nature of ovarian follicle development, thus warranting a systems approach. RESULTS Here, we developed a genome-scale metabolic model of the mouse ovarian follicle. This model was constructed using an updated mouse general metabolic model (Mouse Recon 2) and contains several key ovarian follicle development metabolic pathways. We used this model to characterize the changes in the metabolism of each follicular cell type (i.e., oocyte, granulosa cells, including cumulus and mural cells), during ovarian follicle development in vivo. Using this model, we predicted major metabolic pathways that are differentially active across multiple follicle stages. We identified a set of possible secreted and consumed metabolites that could potentially serve as biomarkers for monitoring follicle development, as well as metabolites for addition to in vitro culture media that support the growth and maturation of primordial follicles. CONCLUSIONS Our systems approach to model follicle metabolism can guide future experimental studies to validate the model results and improve oocyte maturation approaches and support growth of primordial follicles in vitro.
Collapse
Affiliation(s)
| | - Ines Thiele
- Luxembourg Center for Systems Biology, University of Luxembourg, Esch-sur-Alzette, Luxembourg, L-4365, Luxembourg
| | - Eugene Galdones
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Anaar Siletz
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Teresa K Woodruff
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.,Women's Health Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Linda J Broadbelt
- Department of Chemical and Biological Engineering, Northwestern University Feinberg School of Medicine, Evanston, IL, 60208, USA
| | - Lonnie D Shea
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
46
|
Wilkins J, Sakrikar D, Petterson XM, Lanza IR, Trushina E. A comprehensive protocol for multiplatform metabolomics analysis in patient-derived skin fibroblasts. Metabolomics 2019; 15:83. [PMID: 31123906 PMCID: PMC7928486 DOI: 10.1007/s11306-019-1544-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 05/18/2019] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Patient-derived skin fibroblasts offer a unique translational model to study molecular mechanisms of multiple human diseases. Metabolomics profiling allows to track changes in a broad range of metabolites and interconnected metabolic pathways that could inform on molecular mechanisms involved in disease development and progression, and on the efficacy of therapeutic interventions. Therefore, it is important to establish standardized protocols for metabolomics analysis in human skin fibroblasts for rigorous and reliable metabolic assessment. OBJECTIVES We aimed to develop an optimized protocol for concurrent measure of the concentration of amino acids, acylcarnitines, and components of the tricarboxylic acid (TCA) cycle in human skin fibroblasts using gas (GC) and liquid chromatography (LC) coupled with mass spectrometry (MS). METHODS The suitability of four different methods of cell harvesting on the recovery of amino acids, acylcarnitines, and TCA cycle metabolites was established using GC/MS and LC/MS analytical platforms. For each method, metabolite stability was determined after 48 h, 2 weeks and 1 month of storage at - 80 °C. RESULTS Harvesting cells in 80% methanol solution allowed the best recovery and preservation of metabolites. Storage of samples in 80% methanol up to 1 month at - 80 °C did not significantly impact metabolite concentrations. CONCLUSION We developed a robust workflow for metabolomics analysis in human skin fibroblasts suitable for a high-throughput multiplatform analysis. This method allows a direct side-by-side comparison of metabolic changes in samples collected at different time that could be used for studies in large patient cohorts.
Collapse
Affiliation(s)
- Jordan Wilkins
- Department of Neurology, Mayo Clinic, Rochester, MN, 55905, USA
| | | | | | - Ian R Lanza
- Metabolomics Core Laboratory, Mayo Clinic, Rochester, MN, 55905, USA
- Division of Endocrinology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Eugenia Trushina
- Department of Neurology, Mayo Clinic, Rochester, MN, 55905, USA.
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Guggenheim Bld., Room 1542B, Rochester, MN, 55905, USA.
| |
Collapse
|
47
|
Feng J, Zhang X, Huang L, Yao H, Yang C, Ma X, Zhang S, Zhang X. Quantitation of Glucose-phosphate in Single Cells by Microwell-Based Nanoliter Droplet Microextraction and Mass Spectrometry. Anal Chem 2019; 91:5613-5620. [DOI: 10.1021/acs.analchem.8b05226] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jiaxin Feng
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiaochao Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Liang Huang
- Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Huan Yao
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Chengdui Yang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiaoxiao Ma
- Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| |
Collapse
|
48
|
Nambiar S, Bong How S, Gummer J, Trengove R, Moodley Y. Metabolomics in chronic lung diseases. Respirology 2019; 25:139-148. [PMID: 30907495 DOI: 10.1111/resp.13530] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 01/31/2019] [Accepted: 02/25/2019] [Indexed: 12/11/2022]
Abstract
Chronic lung diseases represent a significant global burden. Their increasing incidence and complexity render a comprehensive, multidisciplinary and personalized approach to each patient, critically important. Most recently, unique biochemical pathways and disease markers have been identified through large-scale metabolomic studies. Metabolomics is the study of metabolic pathways and the measurement of unique biomolecules in a living system. Analysing samples from different compartments such as bronchoalveolar lavage fluid (BALF) and plasma has proven useful for the characterization of a number of pathological conditions and offers promise as a clinical tool. For example, several studies using mass spectrometry (MS) have shown alterations in the sphingolipid metabolism of chronic obstructive pulmonary disease (COPD) sufferers. In this article, we present a practical review of the application of metabolomics to the study of chronic lung diseases (CLD): COPD, idiopathic pulmonary fibrosis (IPF) and asthma. The insights, which the analytical strategies employed in metabolomics, have provided to the dissection of the biochemistry of CLD and future clinical biomarkers are explored.
Collapse
Affiliation(s)
- Shabarinath Nambiar
- Separation Science and Metabolomics Laboratory, Murdoch University, Perth, WA, Australia
| | - Sze Bong How
- Separation Science and Metabolomics Laboratory, Murdoch University, Perth, WA, Australia.,Metabolomics Australia, Murdoch University, Perth, WA, Australia
| | - Joel Gummer
- Separation Science and Metabolomics Laboratory, Murdoch University, Perth, WA, Australia.,Metabolomics Australia, Murdoch University, Perth, WA, Australia
| | - Robert Trengove
- Separation Science and Metabolomics Laboratory, Murdoch University, Perth, WA, Australia.,Metabolomics Australia, Murdoch University, Perth, WA, Australia
| | - Yuben Moodley
- School of Medicine, University of Western Australia, Perth, WA, Australia.,Department of Respiratory Medicine, Fiona Stanley Hospital, Perth, WA, Australia.,Institute of Respiratory Health, Sir Charles Gairdner Hospital, Perth, WA, Australia
| |
Collapse
|
49
|
Bernardo-Bermejo S, Sánchez-López E, Castro-Puyana M, Benito S, Lucio-Cazaña FJ, Marina ML. An untargeted metabolomic strategy based on liquid chromatography-mass spectrometry to study high glucose-induced changes in HK-2 cells. J Chromatogr A 2019; 1596:124-133. [PMID: 30878178 DOI: 10.1016/j.chroma.2019.03.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/06/2019] [Accepted: 03/05/2019] [Indexed: 12/20/2022]
Abstract
Diabetes mellitus is a major health concern nowadays. It is estimated that 40% of diabetics are affected by diabetic nephropathy, one of the complications derived from high glucose blood levels which can lead to chronic loss of kidney function. It is now clear that the renal proximal tubule plays a critical role in the progression of diabetic nephropathy but research focused on studying the molecular mechanisms involved is still needed. The aim of this work was to develop a liquid chromatography-mass spectrometry platform to carry out, for the first time, the untargeted metabolomic analysis of high glucose-induced changes in cultured human proximal tubular HK-2 cells. In order to find the metabolites which were affected by high glucose and to expand the metabolite coverage, intra- and extracellular fluid from HK-2 cells exposed to high glucose (25 mM), normal glucose (5.5 mM) or osmotic control (5.5 mM glucose +19.5 mM mannitol) were analyzed by two complementary chromatographic modes: hydrophilic interaction and reversed-phase liquid chromatography. Non-supervised principal components analysis showed a good separation among the three groups of samples. Statistically significant variables were chosen for further metabolite identification. Different metabolic pathways were affected mainly those derived from amino acidic, polyol, and nitrogenous bases metabolism.
Collapse
Affiliation(s)
- Samuel Bernardo-Bermejo
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain
| | - Elena Sánchez-López
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain; Instituto de Investigación Química Andrés M. del Río (IQAR), Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain
| | - María Castro-Puyana
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain; Instituto de Investigación Química Andrés M. del Río (IQAR), Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain
| | - Selma Benito
- Departamento de Biología de Sistemas, Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain
| | - Francisco Javier Lucio-Cazaña
- Departamento de Biología de Sistemas, Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain
| | - María Luisa Marina
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain; Instituto de Investigación Química Andrés M. del Río (IQAR), Universidad de Alcalá, Ctra. Madrid-Barcelona Km. 33.600, 28871 Alcalá de Henares (Madrid), Spain.
| |
Collapse
|
50
|
Takayama T, Mizuno H, Toyo’oka T, Akatsu H, Inoue K, Todoroki K. Isotope Corrected Chiral and Achiral Nontargeted Metabolomics: An Approach for High Accuracy and Precision Metabolomics Based on Derivatization and Its Application to Cerebrospinal Fluid of Patients with Alzheimer’s Disease. Anal Chem 2019; 91:4396-4404. [DOI: 10.1021/acs.analchem.8b04852] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Takahiro Takayama
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hajime Mizuno
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Toshimasa Toyo’oka
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiroyasu Akatsu
- Department of Medicine for Aging Place, Community Health Care/Community-Based Medical Education, Nagoya City University Graduate School of Medical Sciences, Nagoya 467-0001, Japan
- Department of Neuropathology, Choju Medical Institute, Fukushimura Hospital, Toyohashi 441-8124, Japan
| | - Koichi Inoue
- Laboratory of Clinical & Analytical Chemistry, College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Kenichiro Todoroki
- Laboratory of Analytical and Bio-Analytical Chemistry, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| |
Collapse
|