1
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Singh R, Fatima E, Thakur L, Singh S, Ratan C, Kumar N. Advancements in CHO metabolomics: techniques, current state and evolving methodologies. Front Bioeng Biotechnol 2024; 12:1347138. [PMID: 38600943 PMCID: PMC11004234 DOI: 10.3389/fbioe.2024.1347138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/28/2024] [Indexed: 04/12/2024] Open
Abstract
Background: Investigating the metabolic behaviour of different cellular phenotypes, i.e., good/bad grower and/or producer, in production culture is important to identify the key metabolite(s)/pathway(s) that regulate cell growth and/or recombinant protein production to improve the overall yield. Currently, LC-MS, GC-MS and NMR are the most used and advanced technologies for investigating the metabolome. Although contributed significantly in the domain, each technique has its own biasness towards specific metabolites or class of metabolites due to various reasons including variability in the concept of working, sample preparation, metabolite-extraction methods, metabolite identification tools, and databases. As a result, the application of appropriate analytical technique(s) is very critical. Purpose and scope: This review provides a state-of-the-art technological insights and overview of metabolic mechanisms involved in regulation of cell growth and/or recombinant protein production for improving yield from CHO cultures. Summary and conclusion: In this review, the advancements in CHO metabolomics over the last 10 years are traced based on a bibliometric analysis of previous publications and discussed. With the technical advancement in the domain of LC-MS, GC-MS and NMR, metabolites of glycolytic and nucleotide biosynthesis pathway (glucose, fructose, pyruvate and phenylalanine, threonine, tryptophan, arginine, valine, asparagine, and serine, etc.) were observed to be upregulated in exponential-phase thereby potentially associated with cell growth regulation, whereas metabolites/intermediates of TCA, oxidative phosphorylation (aspartate, glutamate, succinate, malate, fumarate and citrate), intracellular NAD+/NADH ratio, and glutathione metabolic pathways were observed to be upregulated in stationary-phase and hence potentially associated with increased cell-specific productivity in CHO bioprocess. Moreover, each of technique has its own bias towards metabolite identification, indicating their complementarity, along with a number of critical gaps in the CHO metabolomics pipeline and hence first time discussed here to identify their potential remedies. This knowledge may help in future study designs to improve the metabolomic coverage facilitating identification of the metabolites/pathways which might get missed otherwise and explore the full potential of metabolomics for improving the CHO bioprocess performances.
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Affiliation(s)
- Rita Singh
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Eram Fatima
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Lovnish Thakur
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Sevaram Singh
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Chandra Ratan
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Niraj Kumar
- Translational Health Science and Technology Institute, Faridabad, India
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2
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Almalki AH. Recent Analytical Advances for Decoding Metabolic Reprogramming in Lung Cancer. Metabolites 2023; 13:1037. [PMID: 37887362 PMCID: PMC10609104 DOI: 10.3390/metabo13101037] [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: 08/24/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 10/28/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related death worldwide. Metabolic reprogramming is a fundamental trait associated with lung cancer development that fuels tumor proliferation and survival. Monitoring such metabolic pathways and their intermediate metabolites can provide new avenues concerning treatment strategies, and the identification of prognostic biomarkers that could be utilized to monitor drug responses in clinical practice. In this review, recent trends in the analytical techniques used for metabolome mapping of lung cancer are capitalized. These techniques include nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and imaging mass spectrometry (MSI). The advantages and limitations of the application of each technique for monitoring the metabolite class or type are also highlighted. Moreover, their potential applications in the analysis of many biological samples will be evaluated.
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Affiliation(s)
- Atiah H. Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
- Addiction and Neuroscience Research Unit, Health Science Campus, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
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3
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Lysak DH, Wolff WW, Soong R, Bermel W, Kupče ER, Jenne A, Biswas RG, Lane D, Gasmi-Seabrook G, Simpson A. Application of 15N-Edited 1H- 13C Correlation NMR Spectroscopy─Toward Fragment-Based Metabolite Identification and Screening via HCN Constructs. Anal Chem 2023; 95:11926-11933. [PMID: 37535003 DOI: 10.1021/acs.analchem.3c01362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Many key building blocks of life contain nitrogen moieties. Despite the prevalence of nitrogen-containing metabolites in nature, 15N nuclei are seldom used in NMR-based metabolite assignment due to their low natural abundance and lack of comprehensive chemical shift databases. However, with advancements in isotope labeling strategies, 13C and 15N enriched metabolites are becoming more common in metabolomic studies. Simple multidimensional nuclear magnetic resonance (NMR) experiments that correlate 1H and 15N via single bond 1JNH or multiple bond 2-3JNH couplings using heteronuclear single quantum coherence (HSQC) or heteronuclear multiple bond coherence are well established and routinely applied for structure elucidation. However, a 1H-15N correlation spectrum of a metabolite mixture can be difficult to deconvolute, due to the lack of a 15N specific database. In order to bridge this gap, we present here a broadband 15N-edited 1H-13C HSQC NMR experiment that targets metabolites containing 15N moieties. Through this approach, nitrogen-containing metabolites, such as amino acids, nucleotide bases, and nucleosides, are identified based on their 13C, 1H, and 15N chemical shift information. This approach was tested and validated using a [15N, 13C] enriched Daphnia magna (water flea) metabolite extract, where the number of clearly resolved 15N-containing peaks increased from only 11 in a standard HSQC to 51 in the 15N-edited HSQC, and the number of obscured peaks decreased from 59 to just 7. The approach complements the current repertoire of NMR techniques for mixture deconvolution and holds considerable potential for targeted metabolite NMR in 15N, 13C enriched systems.
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Affiliation(s)
- Daniel H Lysak
- University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C1A4, Canada
| | - William W Wolff
- University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C1A4, Canada
| | - Ronald Soong
- University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C1A4, Canada
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Rudolf-Plank-Str. 23, Ettlingen 76275, Germany
| | | | - Amy Jenne
- University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C1A4, Canada
| | - Rajshree Ghosh Biswas
- University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C1A4, Canada
| | - Daniel Lane
- University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C1A4, Canada
| | | | - Andre Simpson
- University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario M1C1A4, Canada
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4
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Ribay V, Praud C, Letertre MPM, Dumez JN, Giraudeau P. Hyperpolarized NMR metabolomics. Curr Opin Chem Biol 2023; 74:102307. [PMID: 37094508 DOI: 10.1016/j.cbpa.2023.102307] [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: 12/07/2022] [Revised: 02/20/2023] [Accepted: 03/21/2023] [Indexed: 04/26/2023]
Abstract
Hyperpolarized NMR is a promising approach to address the sensitivity limits of conventional NMR metabolomics approaches, which currently fails to detect minute metabolite concentrations in biological samples. This review describes how tremendous signal enhancement offered by dissolution-dynamic nuclear polarization and parahydrogen-based techniques can be fully exploited for molecular omics sciences. Recent developments, including the combination of hyperpolarization techniques with fast multi-dimensional NMR implementation and quantitative workflows are described, and a comprehensive comparison of existing hyperpolarization techniques is proposed. High-throughput, sensitivity, resolution and other relevant challenges that should be tackled for a general application of hyperpolarized NMR in metabolomics are discussed.
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Affiliation(s)
- Victor Ribay
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
| | - Clément Praud
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
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5
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Zhang N, Kandalai S, Zhou X, Hossain F, Zheng Q. Applying multi-omics toward tumor microbiome research. IMETA 2023; 2:e73. [PMID: 38868335 PMCID: PMC10989946 DOI: 10.1002/imt2.73] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/30/2022] [Accepted: 11/28/2022] [Indexed: 06/14/2024]
Abstract
Rather than a "short-term tenant," the tumor microbiome has been shown to play a vital role as a "permanent resident," affecting carcinogenesis, cancer development, metastasis, and cancer therapies. As the tumor microbiome has great potential to become a target for the early diagnosis and treatment of cancer, recent research on the relevance of the tumor microbiota has attracted a wide range of attention from various scientific fields, resulting in remarkable progress that benefits from the development of interdisciplinary technologies. However, there are still a great variety of challenges in this emerging area, such as the low biomass of intratumoral bacteria and unculturable character of some microbial species. Due to the complexity of tumor microbiome research (e.g., the heterogeneity of tumor microenvironment), new methods with high spatial and temporal resolution are urgently needed. Among these developing methods, multi-omics technologies (combinations of genomics, transcriptomics, proteomics, and metabolomics) are powerful approaches that can facilitate the understanding of the tumor microbiome on different levels of the central dogma. Therefore, multi-omics (especially single-cell omics) will make enormous impacts on the future studies of the interplay between microbes and tumor microenvironment. In this review, we have systematically summarized the advances in multi-omics and their existing and potential applications in tumor microbiome research, thus providing an omics toolbox for investigators to reference in the future.
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Affiliation(s)
- Nan Zhang
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Shruthi Kandalai
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Xiaozhuang Zhou
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Farzana Hossain
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Qingfei Zheng
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
- Department of Biological Chemistry and Pharmacology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
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6
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Abdelzaher H, Tawfik SM, Nour A, Abdelkader S, Elbalkiny ST, Abdelkader M, Abbas WA, Abdelnaser A. Climate change, human health, and the exposome: Utilizing OMIC technologies to navigate an era of uncertainty. Front Public Health 2022; 10:973000. [PMID: 36211706 PMCID: PMC9533016 DOI: 10.3389/fpubh.2022.973000] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/17/2022] [Indexed: 01/25/2023] Open
Abstract
Climate change is an anthropogenic phenomenon that is alarming scientists and non-scientists alike. The emission of greenhouse gases is causing the temperature of the earth to rise and this increase is accompanied by a multitude of climate change-induced environmental exposures with potential health impacts. Tracking human exposure has been a major research interest of scientists worldwide. This has led to the development of exposome studies that examine internal and external individual exposures over their lifetime and correlate them to health. The monitoring of health has also benefited from significant technological advances in the field of "omics" technologies that analyze physiological changes on the nucleic acid, protein, and metabolism levels, among others. In this review, we discuss various climate change-induced environmental exposures and their potential health implications. We also highlight the potential integration of the technological advancements in the fields of exposome tracking, climate monitoring, and omics technologies shedding light on important questions that need to be answered.
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Affiliation(s)
| | | | | | | | | | | | | | - Anwar Abdelnaser
- Institute of Global Health and Human Ecology, The American University in Cairo, New Cairo, Egypt
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7
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Opekar S, Kvíčala J, Moos M, Pejchal V, Šimek P. Mechanism of Alkyl Chloroformate-Mediated Esterification of Carboxylic Acids in Aqueous Media. J Org Chem 2021; 86:16293-16299. [PMID: 34546734 DOI: 10.1021/acs.joc.1c01546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The protection of carboxyl groups by esterification has been the most common method in macroscale and microscale chemistries. The esterification is usually conducted under anhydrous conditions; however, in biological chemistry and related fields, the reaction is of major concern in aqueous environments. Immediate esterification of the carboxyl in aqueous alcoholic media driven by an alkyl chloroformate and pyridine has been such a method which has found widespread use in many research and industrial laboratories. Nevertheless, the reaction mechanism has not yet been investigated, to our knowledge, and is not well understood. Herein, we describe the reaction intermediates and demonstrate that the reaction proceeds via a continual formation of the N-acylpyridinium intermediate decomposed by several reaction channels to the final ester. The understanding of the mechanism could encourage novel laboratory applications of this important esterification method.
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Affiliation(s)
- Stanislav Opekar
- Czech Academy of Sciences, Biology Centre, Institute of Entomology, Branišovská 31/1160, České Budějovice 37005, Czech Republic
| | - Jaroslav Kvíčala
- Department of Organic Chemistry, University of Chemistry and Technology Prague, Technická 5, 16628 Prague 6, Czech Republic
| | - Martin Moos
- Czech Academy of Sciences, Biology Centre, Institute of Entomology, Branišovská 31/1160, České Budějovice 37005, Czech Republic
| | - Vladimír Pejchal
- Faculty of Chemical Technology, University of Pardubice, Studentská 95, 53210 Pardubice, Czech Republic
| | - Petr Šimek
- Czech Academy of Sciences, Biology Centre, Institute of Entomology, Branišovská 31/1160, České Budějovice 37005, Czech Republic
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8
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Letertre MPM, Giraudeau P, de Tullio P. Nuclear Magnetic Resonance Spectroscopy in Clinical Metabolomics and Personalized Medicine: Current Challenges and Perspectives. Front Mol Biosci 2021; 8:698337. [PMID: 34616770 PMCID: PMC8488110 DOI: 10.3389/fmolb.2021.698337] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022] Open
Abstract
Personalized medicine is probably the most promising area being developed in modern medicine. This approach attempts to optimize the therapies and the patient care based on the individual patient characteristics. Its success highly depends on the way the characterization of the disease and its evolution, the patient’s classification, its follow-up and the treatment could be optimized. Thus, personalized medicine must combine innovative tools to measure, integrate and model data. Towards this goal, clinical metabolomics appears as ideally suited to obtain relevant information. Indeed, the metabolomics signature brings crucial insight to stratify patients according to their responses to a pathology and/or a treatment, to provide prognostic and diagnostic biomarkers, and to improve therapeutic outcomes. However, the translation of metabolomics from laboratory studies to clinical practice remains a subsequent challenge. Nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) are the two key platforms for the measurement of the metabolome. NMR has several advantages and features that are essential in clinical metabolomics. Indeed, NMR spectroscopy is inherently very robust, reproducible, unbiased, quantitative, informative at the structural molecular level, requires little sample preparation and reduced data processing. NMR is also well adapted to the measurement of large cohorts, to multi-sites and to longitudinal studies. This review focus on the potential of NMR in the context of clinical metabolomics and personalized medicine. Starting with the current status of NMR-based metabolomics at the clinical level and highlighting its strengths, weaknesses and challenges, this article also explores how, far from the initial “opposition” or “competition”, NMR and MS have been integrated and have demonstrated a great complementarity, in terms of sample classification and biomarker identification. Finally, a perspective discussion provides insight into the current methodological developments that could significantly raise NMR as a more resolutive, sensitive and accessible tool for clinical applications and point-of-care diagnosis. Thanks to these advances, NMR has a strong potential to join the other analytical tools currently used in clinical settings.
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Affiliation(s)
| | | | - Pascal de Tullio
- Metabolomics Group, Center for Interdisciplinary Research of Medicine (CIRM), Department of Pharmacy, Université de Liège, Liège, Belgique
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9
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Wei Y, Jasbi P, Shi X, Turner C, Hrovat J, Liu L, Rabena Y, Porter P, Gu H. Early Breast Cancer Detection Using Untargeted and Targeted Metabolomics. J Proteome Res 2021; 20:3124-3133. [PMID: 34033488 DOI: 10.1021/acs.jproteome.1c00019] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Breast cancer (BC) is a common cause of morbidity and mortality, particularly in women. Moreover, the discovery of diagnostic biomarkers for early BC remains a challenging task. Previously, we [Jasbi et al. J. Chromatogr. B. 2019, 1105, 26-37] demonstrated a targeted metabolic profiling approach capable of identifying metabolite marker candidates that could enable highly sensitive and specific detection of BC. However, the coverage of this targeted method was limited and exhibited suboptimal classification of early BC (EBC). To expand the metabolome coverage and articulate a better panel of metabolites or mass spectral features for classification of EBC, we evaluated untargeted liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) data, both individually as well as in conjunction with previously published targeted LC-triple quadruple (QQQ)-MS data. Variable importance in projection scores were used to refine the biomarker panel, whereas orthogonal partial least squares-discriminant analysis was used to operationalize the enhanced biomarker panel for early diagnosis. In this approach, 33 altered metabolites/features were detected by LC-QTOF-MS from 124 BC patients and 86 healthy controls. For EBC diagnosis, significance testing and analysis of the area under receiver operating characteristic (AUROC) curve identified six metabolites/features [ethyl (R)-3-hydroxyhexanoate; caprylic acid; hypoxanthine; and m/z 358.0018, 354.0053, and 356.0037] with p < 0.05 and AUROC > 0.7. These metabolites informed the construction of EBC diagnostic models; evaluation of model performance for the prediction of EBC showed an AUROC = 0.938 (95% CI: 0.895-0.975), with sensitivity = 0.90 when specificity = 0.90. Using the combined untargeted and targeted data set, eight metabolic pathways of potential biological relevance were indicated to be significantly altered as a result of EBC. Metabolic pathway analysis showed fatty acid and aminoacyl-tRNA biosynthesis as well as inositol phosphate metabolism to be most impacted in response to the disease. The combination of untargeted and targeted metabolomics platforms has provided a highly predictive and accurate method for BC and EBC diagnosis from plasma samples. Furthermore, such a complementary approach yielded critical information regarding potential pathogenic mechanisms underlying EBC that, although critical to improved prognosis and enhanced survival, are understudied in the current literature. All mass spectrometry data and deidentified subject metadata analyzed in this study have been deposited to Mendeley Data and are publicly available (DOI: 10.17632/kcjg8ybk45.1).
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Affiliation(s)
- Yiping Wei
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
| | - Paniz Jasbi
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
| | - Xiaojian Shi
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States.,Systems Biology Institute, Cellular and Molecular Physiology, Yale School of Medicine, West Haven, Connecticut 06516, United States
| | - Cassidy Turner
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
| | - Jonathon Hrovat
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
| | - Li Liu
- College of Health Solutions, Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States.,Department of Neurology, Mayo Clinic, Scottsdale, Arizona 85259, United States
| | - Yuri Rabena
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Peggy Porter
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Haiwei Gu
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, Scottsdale, Arizona 85259, United States
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10
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Liang L, Sun F, Wang H, Hu Z. Metabolomics, metabolic flux analysis and cancer pharmacology. Pharmacol Ther 2021; 224:107827. [PMID: 33662451 DOI: 10.1016/j.pharmthera.2021.107827] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Metabolic reprogramming is a hallmark of cancer and increasing evidence suggests that reprogrammed cell metabolism supports tumor initiation, progression, metastasis and drug resistance. Understanding metabolic dysregulation may provide therapeutic targets and facilitate drug research and development for cancer therapy. Metabolomics enables the high-throughput characterization of a large scale of small molecule metabolites in cells, tissues and biofluids, while metabolic flux analysis (MFA) tracks dynamic metabolic activities using stable isotope tracer methods. Recent advances in metabolomics and MFA technologies make them powerful tools for metabolic profiling and characterizing metabolic activities in health and disease, especially in cancer research. In this review, we introduce recent advances in metabolomics and MFA analytical technologies, and provide the first comprehensive summary of the most commonly used isotope tracing methods. In addition, we highlight how metabolomics and MFA are applied in cancer pharmacology studies particularly for discovering targetable metabolic vulnerabilities, understanding the mechanisms of drug action and drug resistance, exploring potential strategies with dietary intervention, identifying cancer biomarkers, as well as enabling precision treatment with pharmacometabolomics.
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Affiliation(s)
- Lingfan Liang
- School of Pharmaceutical Sciences; Tsinghua-Peking Joint Center for Life Sciences; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Fei Sun
- School of Pharmaceutical Sciences; Tsinghua-Peking Joint Center for Life Sciences; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Hongbo Wang
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China.
| | - Zeping Hu
- School of Pharmaceutical Sciences; Tsinghua-Peking Joint Center for Life Sciences; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China.
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11
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Xu N, Lin H, Lin S, Zhang W, Han S, Nakajima H, Mao S, Lin JM. A Fluidic Isolation-Assisted Homogeneous-Flow-Pressure Chip-Solid Phase Extraction-Mass Spectrometry System for Online Dynamic Monitoring of 25-Hydroxyvitamin D 3 Biotransformation in Cells. Anal Chem 2021; 93:2273-2280. [PMID: 33443406 DOI: 10.1021/acs.analchem.0c04147] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
It is well known that cell can response to various chemical and mechanical stimuli. Therefore, flow pressure variation induced by sample loading and elution should be small enough to ignore the physical impact on cells when we use a Chip-SPE-MS system for cells. However, most existent Chip-SPE-MS systems ignored the pressure alternation because it is extremely difficult to develop a homogeneous-flow-pressure hyphenated module. Herein, we developed an interesting fluidic isolation-assisted homogeneous-flow-pressure Chip-SPE-MS system and demonstrated that it is adequate for online high-throughput determination and quantification of the 25-hydroxyvitamin D3 (25(OH)D3) biotransformation in different cells. Briefly, the homogeneous ambient flow pressure is achieved by fluidic isolation between the cell culture channel and the SPE column, and an automatic sampling probe could accomplish the sample loading and dispensing to fulfill online pretreatment of the sample. Through this new system, the expression levels of 24,25-dihydroxyvitamin D3 (24,25(OH)2D3) can be determined in real time with a detection limit of 2.54 nM. In addition, the results revealed that 25(OH)D3 metabolic activity differed significantly between normal L-02 cells and cancerous HepG2 cells. Treatment of L-02 cells with a high dose of 25(OH)D3 was found to increase significant formation of 24,25(OH)2D3, but this change was not apparent in HepG2 cells. The presented system promises to be a versatile tool for online accurate molecule biotransformation investigation and drug screening processes.
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Affiliation(s)
- Ning Xu
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry &Chemical Biology, Tsinghua University, Beijing 100084, China.,Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Haifeng Lin
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Sheng Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry &Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Wanling Zhang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry &Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Shuang Han
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry &Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Hizuru Nakajima
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Sifeng Mao
- Department of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry &Chemical Biology, Tsinghua University, Beijing 100084, China
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12
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Letertre MPM, Dervilly G, Giraudeau P. Combined Nuclear Magnetic Resonance Spectroscopy and Mass Spectrometry Approaches for Metabolomics. Anal Chem 2020; 93:500-518. [PMID: 33155816 DOI: 10.1021/acs.analchem.0c04371] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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13
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Crook AA, Powers R. Quantitative NMR-Based Biomedical Metabolomics: Current Status and Applications. Molecules 2020; 25:E5128. [PMID: 33158172 PMCID: PMC7662776 DOI: 10.3390/molecules25215128] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 12/19/2022] Open
Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is a quantitative analytical tool commonly utilized for metabolomics analysis. Quantitative NMR (qNMR) is a field of NMR spectroscopy dedicated to the measurement of analytes through signal intensity and its linear relationship with analyte concentration. Metabolomics-based NMR exploits this quantitative relationship to identify and measure biomarkers within complex biological samples such as serum, plasma, and urine. In this review of quantitative NMR-based metabolomics, the advancements and limitations of current techniques for metabolite quantification will be evaluated as well as the applications of qNMR in biomedical metabolomics. While qNMR is limited by sensitivity and dynamic range, the simple method development, minimal sample derivatization, and the simultaneous qualitative and quantitative information provide a unique landscape for biomedical metabolomics, which is not available to other techniques. Furthermore, the non-destructive nature of NMR-based metabolomics allows for multidimensional analysis of biomarkers that facilitates unambiguous assignment and quantification of metabolites in complex biofluids.
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Affiliation(s)
- Alexandra A. Crook
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA;
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA;
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
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Giraudeau P. NMR-based metabolomics and fluxomics: developments and future prospects. Analyst 2020; 145:2457-2472. [DOI: 10.1039/d0an00142b] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recent NMR developments are acting as game changers for metabolomics and fluxomics – a critical and perspective review.
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Wishart DS. NMR metabolomics: A look ahead. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:155-161. [PMID: 31377153 DOI: 10.1016/j.jmr.2019.07.013] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/13/2019] [Accepted: 07/08/2019] [Indexed: 05/24/2023]
Abstract
NMR has been used to perform metabolic studies, metabolic profiling and metabolomics in biofluids and tissues for more than 40 years. This close connection between metabolic measurements and NMR has flourished because of NMR's many unique strengths for characterizing the chemical composition of complex mixtures. However, a number of other technologies, including mass spectrometry, have appeared in the past few years that are encroaching on NMR's dominance in metabolomics and metabolic studies. In this brief review, some of the current strengths and existing limitations of NMR-based metabolomics are highlighted. Additionally, a number of recent advances in NMR hardware, methodology and software are also described and these advancements are used to speculate about where NMR-based metabolomics is going, what needs to be done to make it more popular and how it will evolve in the next 5-10 years.
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Affiliation(s)
- David S Wishart
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E8, Canada; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada.
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