1
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Wang X, Peng R, Zhao L. Multiscale metabolomics techniques: Insights into neuroscience research. Neurobiol Dis 2024; 198:106541. [PMID: 38806132 DOI: 10.1016/j.nbd.2024.106541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 05/30/2024] Open
Abstract
The field of metabolomics examines the overall composition and dynamic patterns of metabolites in living organisms. The primary methods used in metabolomics include liquid chromatography (LC), nuclear magnetic resonance (NMR), and mass spectrometry (MS) analysis. These methods enable the identification and examination of metabolite types and contents within organisms, as well as modifications to metabolic pathways and their connection to the emergence of diseases. Research in metabolomics has extensive value in basic and applied sciences. The field of metabolomics is growing quickly, with the majority of studies concentrating on biomedicine, particularly early disease diagnosis, therapeutic management of human diseases, and mechanistic knowledge of biochemical processes. Multiscale metabolomics is an approach that integrates metabolomics techniques at various scales, including the holistic, tissue, cellular, and organelle scales, to enable more thorough and in-depth studies of metabolic processes in organisms. Multiscale metabolomics can be combined with methods from systems biology and bioinformatics. In recent years, multiscale metabolomics approaches have become increasingly important in neuroscience research due to the nervous system's high metabolic demands. Multiscale metabolomics can offer novel concepts and approaches for the diagnosis, treatment, and development of medication for neurological illnesses in addition to a more thorough understanding of brain metabolism and nervous system function. In this review, we summarize the use of multiscale metabolomics techniques in neuroscience, address the promise and constraints of these techniques, and provide an overview of the metabolome and its applications in neuroscience.
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Affiliation(s)
- Xiaoya Wang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Ruiyun Peng
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
| | - Li Zhao
- Beijing Institute of Radiation Medicine, Beijing 100850, China.
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2
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Cui N, Xu X, Zhou F. Single-cell technologies in psoriasis. Clin Immunol 2024; 264:110242. [PMID: 38750947 DOI: 10.1016/j.clim.2024.110242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 03/30/2024] [Accepted: 05/01/2024] [Indexed: 05/24/2024]
Abstract
Psoriasis is a chronic and recurrent inflammatory skin disorder. The primary manifestation of psoriasis arises from disturbances in the cutaneous immune microenvironment, but the specific functions of the cellular components within this microenvironment remain unknown. Recent advancements in single-cell technologies have enabled the detection of multi-omics at the level of individual cells, including single-cell transcriptome, proteome, and metabolome, which have been successfully applied in studying autoimmune diseases, and other pathologies. These techniques allow the identification of heterogeneous cell clusters and their varying contributions to disease development. Considering the immunological traits of psoriasis, an in-depth exploration of immune cells and their interactions with cutaneous parenchymal cells can markedly advance our comprehension of the mechanisms underlying the onset and recurrence of psoriasis. In this comprehensive review, we present an overview of recent applications of single-cell technologies in psoriasis, aiming to improve our understanding of the underlying mechanisms of this disorder.
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Affiliation(s)
- Niannian Cui
- First School of Clinical Medicine, Anhui Medical University, Hefei 230032, China
| | - Xiaoqing Xu
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230031, China; Institute of Dermatology, Anhui Medical University, Hefei, Anhui 230022, China; The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui 230022, China
| | - Fusheng Zhou
- Department of Dermatology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230031, China; Institute of Dermatology, Anhui Medical University, Hefei, Anhui 230022, China; The Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui 230022, China.
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3
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Li L, Zhang Y, Zhou J, Wang J, Wang L. Single-cell metabolomics in rare disease: From technology to disease. Intractable Rare Dis Res 2024; 13:99-103. [PMID: 38836176 PMCID: PMC11145402 DOI: 10.5582/irdr.2023.01073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 05/12/2024] [Accepted: 05/22/2024] [Indexed: 06/06/2024] Open
Abstract
With the development of clinical experience and technology, rare diseases (RDs) are gradually coming into the limelight. As they often lead to poor prognosis, it is urgent to promote the accuracy and rapidity of diagnosis and promote the development of therapeutic drugs. In recent years, with the rapid improvement of single-cell sequencing technology, the advantages of multi-omics combined application in diseases have been continuously explored. Single-cell metabolomics represents a powerful tool for advancing our understanding of rare diseases, particularly metabolic RDs, and transforming clinical practice. By unraveling the intricacies of cellular metabolism at a single-cell resolution, this innovative approach holds the potential to revolutionize diagnosis, treatment, and management strategies, ultimately improving outcomes for RDs patients. Continued research and technological advancements in single-cell metabolomics are essential for realizing its full potential in the field of RDs diagnosis and therapeutics. It is expected that single-cell metabolomics can be better applied to RDs research in the future, for the benefit of patients and society.
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Affiliation(s)
- Lisha Li
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
| | - Yiqin Zhang
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- Shanghai Key Laboratory Embryo Original Diseases, Shanghai, China
| | - Jing Zhou
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
| | - Jing Wang
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
| | - Ling Wang
- Laboratory for Reproductive Immunology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- The Academy of Integrative Medicine of Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-related Diseases, Shanghai, China
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4
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Sun X, Yu Y, Qian K, Wang J, Huang L. Recent Progress in Mass Spectrometry-Based Single-Cell Metabolic Analysis. SMALL METHODS 2024; 8:e2301317. [PMID: 38032130 DOI: 10.1002/smtd.202301317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/10/2023] [Indexed: 12/01/2023]
Abstract
Single-cell analysis enables the measurement of biomolecules at the level of individual cells, facilitating in-depth investigations into cellular heterogeneity and precise interpretation of the related biological mechanisms. Among these biomolecules, cellular metabolites exhibit remarkable sensitivity to environmental and biochemical changes, unveiling a hidden world underlying cellular heterogeneity and allowing for the determination of cell physiological states. However, the metabolic analysis of single cells is challenging due to the extremely low concentrations, substantial content variations, and rapid turnover rates of cellular metabolites. Mass spectrometry (MS), characterized by its high sensitivity, wide dynamic range, and excellent selectivity, is employed in single-cell metabolic analysis. This review focuses on recent advances and applications of MS-based single-cell metabolic analysis, encompassing three key steps of single-cell isolation, detection, and application. It is anticipated that MS will bring profound implications in biomedical practices, serving as advanced tools to depict the single-cell metabolic landscape.
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Affiliation(s)
- Xuming Sun
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Engineering Technology Research Center of Neurosense and Control of Henan Province, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Xinxiang Key Laboratory of Neurobiosensor, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Yi Yu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Engineering Technology Research Center of Neurosense and Control of Henan Province, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Xinxiang Key Laboratory of Neurobiosensor, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Kun Qian
- School of Biomedical Engineering, Institute of Medical Robotics and Med X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Jiayi Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
| | - Lin Huang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
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5
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Sánchez-Ramírez E, Ung TPL, Stringari C, Aguilar-Arnal L. Emerging Functional Connections Between Metabolism and Epigenetic Remodeling in Neural Differentiation. Mol Neurobiol 2024:10.1007/s12035-024-04006-w. [PMID: 38340204 DOI: 10.1007/s12035-024-04006-w] [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: 09/13/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
Stem cells possess extraordinary capacities for self-renewal and differentiation, making them highly valuable in regenerative medicine. Among these, neural stem cells (NSCs) play a fundamental role in neural development and repair processes. NSC characteristics and fate are intricately regulated by the microenvironment and intracellular signaling. Interestingly, metabolism plays a pivotal role in orchestrating the epigenome dynamics during neural differentiation, facilitating the transition from undifferentiated NSC to specialized neuronal and glial cell types. This intricate interplay between metabolism and the epigenome is essential for precisely regulating gene expression patterns and ensuring proper neural development. This review highlights the mechanisms behind metabolic regulation of NSC fate and their connections with epigenetic regulation to shape transcriptional programs of stemness and neural differentiation. A comprehensive understanding of these molecular gears appears fundamental for translational applications in regenerative medicine and personalized therapies for neurological conditions.
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Affiliation(s)
- Edgar Sánchez-Ramírez
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Thi Phuong Lien Ung
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau, France
| | - Chiara Stringari
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, Palaiseau, France
| | - Lorena Aguilar-Arnal
- Departamento de Biología Celular y Fisiología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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6
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Wevers D, Ramautar R, Clark C, Hankemeier T, Ali A. Opportunities and challenges for sample preparation and enrichment in mass spectrometry for single-cell metabolomics. Electrophoresis 2023; 44:2000-2024. [PMID: 37667867 DOI: 10.1002/elps.202300105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/08/2023] [Accepted: 08/19/2023] [Indexed: 09/06/2023]
Abstract
Single-cell heterogeneity in metabolism, drug resistance and disease type poses the need for analytical techniques for single-cell analysis. As the metabolome provides the closest view of the status quo in the cell, studying the metabolome at single-cell resolution may unravel said heterogeneity. A challenge in single-cell metabolome analysis is that metabolites cannot be amplified, so one needs to deal with picolitre volumes and a wide range of analyte concentrations. Due to high sensitivity and resolution, MS is preferred in single-cell metabolomics. Large numbers of cells need to be analysed for proper statistics; this requires high-throughput analysis, and hence automation of the analytical workflow. Significant advances in (micro)sampling methods, CE and ion mobility spectrometry have been made, some of which have been applied in high-throughput analyses. Microfluidics has enabled an automation of cell picking and metabolite extraction; image recognition has enabled automated cell identification. Many techniques have been used for data analysis, varying from conventional techniques to novel combinations of advanced chemometric approaches. Steps have been set in making data more findable, accessible, interoperable and reusable, but significant opportunities for improvement remain. Herein, advances in single-cell analysis workflows and data analysis are discussed, and recommendations are made based on the experimental goal.
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Affiliation(s)
- Dirk Wevers
- Wageningen University and Research, Wageningen, The Netherlands
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Rawi Ramautar
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Charlie Clark
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
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7
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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.
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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
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8
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Gao P. Exploring Single-Cell Exposomics by Mass Spectrometry. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:12201-12209. [PMID: 37561608 PMCID: PMC10448745 DOI: 10.1021/acs.est.3c04524] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Indexed: 08/12/2023]
Abstract
Single-cell exposomics, a revolutionary approach that investigates cell-environment interactions at cellular and subcellular levels, stands distinct from conventional bulk exposomics. Leveraging advancements in mass spectrometry, it provides a detailed perspective on cellular dynamics, interactions, and responses to environmental stimuli and their impacts on human health. This work delves into this innovative realm, highlighting the nuanced interplay between environmental stressors and biological responses at cellular and subcellular levels. The application of spatial mass spectrometry in single-cell exposomics is discussed, revealing the intricate spatial organization and molecular composition within individual cells. Cell-type-specific exposomics, shedding light on distinct susceptibilities and adaptive strategies of various cell types to environmental exposures, is also examined. The Perspective further emphasizes the integration with molecular and cellular biology approaches to validate hypotheses derived from single-cell exposomics in a comprehensive biological context. Looking toward the future, we anticipate continued technological advancements and convergence with other -omics approaches and discuss implications for environmental health research, disease progression studies, and precision medicine. The final emphasis is on the need for robust computational tools and interdisciplinary collaboration to fully leverage the potential of single-cell exposomics, acknowledging the complexities inherent to this paradigm.
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Affiliation(s)
- Peng Gao
- Department
of Environmental and Occupational Health and Department of Civil and
Environmental Engineering, University of
Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- UPMC
Hillman Cancer Center, Pittsburgh, Pennsylvania 15232, United States
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9
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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.
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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
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10
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Recent advances and typical applications in mass spectrometry-based technologies for single-cell metabolite analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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11
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Advances in measuring cancer cell metabolism with subcellular resolution. Nat Methods 2022; 19:1048-1063. [PMID: 36008629 DOI: 10.1038/s41592-022-01572-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 07/05/2022] [Indexed: 11/08/2022]
Abstract
Characterizing metabolism in cancer is crucial for understanding tumor biology and for developing potential therapies. Although most metabolic investigations analyze averaged metabolite levels from all cell compartments, subcellular metabolomics can provide more detailed insight into the biochemical processes associated with the disease. Methodological limitations have historically prevented the wider application of subcellular metabolomics in cancer research. Recently, however, ways to distinguish and identify metabolic pathways within organelles have been developed, including state-of-the-art methods to monitor metabolism in situ (such as mass spectrometry-based imaging, Raman spectroscopy and fluorescence microscopy), to isolate key organelles via new approaches and to use tailored isotope-tracing strategies. Herein, we examine the advantages and limitations of these developments and look to the future of this field of research.
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Portero EP, Pade L, Li J, Choi SB, Nemes P. Single-Cell Mass Spectrometry of Metabolites and Proteins for Systems and Functional Biology. NEUROMETHODS 2022; 184:87-114. [PMID: 36699808 PMCID: PMC9872963 DOI: 10.1007/978-1-0716-2525-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Molecular composition is intricately intertwined with cellular function, and elucidation of this relationship is essential for understanding life processes and developing next-generational therapeutics. Technological innovations in capillary electrophoresis (CE) and liquid chromatography (LC) mass spectrometry (MS) provide previously unavailable insights into cellular biochemistry by allowing for the unbiased detection and quantification of molecules with high specificity. This chapter presents our validated protocols integrating ultrasensitive MS with classical tools of cell, developmental, and neurobiology to assess the biological function of important biomolecules. We use CE and LC MS to measure hundreds of metabolites and thousands of proteins in single cells or limited populations of tissues in chordate embryos and mammalian neurons, revealing molecular heterogeneity between identified cells. By pairing microinjection and optical microscopy, we demonstrate cell lineage tracing and testing the roles the dysregulated molecules play in the formation and maintenance of cell heterogeneity and tissue specification in frog embryos (Xenopus laevis). Electrophysiology extends our workflows to characterizing neuronal activity in sections of mammalian brain tissues. The information obtained from these studies mutually strengthen chemistry and biology and highlight the importance of interdisciplinary research to advance basic knowledge and translational applications forward.
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Affiliation(s)
| | | | - Jie Li
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Sam B. Choi
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, 8051 Regents Drive, College Park, MD 20742
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13
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Lee JW, Profant M, Wang C. Metabolic Sex Dimorphism of the Brain at the Gene, Cell, and Tissue Level. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:212-220. [PMID: 35017210 DOI: 10.4049/jimmunol.2100853] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/09/2021] [Indexed: 12/21/2022]
Abstract
The palpable observation in the sex bias of disease prevalence in the CNS has fascinated scientists for several generations. Brain sex dimorphism has been visualized by imaging and analytical tools at the tissue, cellular, and molecular levels. Recent work highlighted the specificity of such sex bias in the brain and its subregions, offering a unique lens through which disease pathogenesis can be investigated. The brain is the largest consumer of energy in the body and provides a unique metabolic environment for diverse lineages of cells. Immune cells are increasingly recognized as an integral part of brain physiology, and their function depends on metabolic homeostasis. This review focuses on metabolic sex dimorphism in brain tissue, resident, and infiltrating immune cells. In this context, we highlight the relevance of recent advances in metabolomics and RNA sequencing technologies at the single cell resolution and the development of novel computational approaches.
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Affiliation(s)
- Jun Won Lee
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada; and
| | - Martin Profant
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada; and.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Chao Wang
- Biological Sciences Platform, Sunnybrook Research Institute, Toronto, Ontario, Canada; and .,Department of Immunology, University of Toronto, Toronto, Ontario, Canada
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14
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Yamagishi A, Takimoto K, Tamura K, Sato F, Sato H. Chiral Discrimination of Dansylated Alanine Methyl Ester on a Modified Clay Surface: Vibrational Circular Dichroism Approach. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Akihiko Yamagishi
- Department of Medicine, Faculty of Medicine, Toho University, Ota-ku, Tokyo 143-8540, Japan
- Research Center for Functional Materials, National Institute of Materials Science, Tsukuba, Ibaraki 305-0044, Japan
| | - Kazuyoshi Takimoto
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Kenji Tamura
- Research Center for Functional Materials, National Institute of Materials Science, Tsukuba, Ibaraki 305-0044, Japan
| | - Fumi Sato
- Department of Medicine, Faculty of Medicine, Toho University, Ota-ku, Tokyo 143-8540, Japan
| | - Hisako Sato
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790-8577, Japan
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15
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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]
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16
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17
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The limitless applications of single-cell metabolomics. Curr Opin Biotechnol 2021; 71:115-122. [PMID: 34339935 DOI: 10.1016/j.copbio.2021.07.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/08/2021] [Accepted: 07/11/2021] [Indexed: 12/28/2022]
Abstract
Single-cell metabolomics (SCM) is currently one of the most powerful tools for performing high-throughput metabolic analysis at the cellular level. The power of single-cell metabolomics to determine the metabolic profiles of individual cells makes it very suitable for decoding cell heterogeneity. SCM bears great potential in cell type identification and differentiation within cell colonies. With the development of various equipment and techniques, SCM analysis has become possible for a wide range of biological samples. Many fields have incorporated this cutting-edge analytic tool to generate fruitful findings. This review article pays close attention to the prevalent techniques utilized in SCM and the exciting new findings and applications developed by studies in phytology, neurology, and oncology using SCM.
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18
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Abstract
A growing appreciation of the importance of cellular metabolism and revelations concerning the extent of cell-cell heterogeneity demand metabolic characterization of individual cells. We present SpaceM, an open-source method for in situ single-cell metabolomics that detects >100 metabolites from >1,000 individual cells per hour, together with a fluorescence-based readout and retention of morpho-spatial features. We validated SpaceM by predicting the cell types of cocultured human epithelial cells and mouse fibroblasts. We used SpaceM to show that stimulating human hepatocytes with fatty acids leads to the emergence of two coexisting subpopulations outlined by distinct cellular metabolic states. Inducing inflammation with the cytokine interleukin-17A perturbs the balance of these states in a process dependent on NF-κB signaling. The metabolic state markers were reproduced in a murine model of nonalcoholic steatohepatitis. We anticipate SpaceM to be broadly applicable for investigations of diverse cellular models and to democratize single-cell metabolomics.
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19
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Vaziri A, Dus M. Brain on food: The neuroepigenetics of nutrition. Neurochem Int 2021; 149:105099. [PMID: 34133954 DOI: 10.1016/j.neuint.2021.105099] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/29/2021] [Accepted: 06/10/2021] [Indexed: 12/17/2022]
Abstract
Humans have known for millennia that nutrition has a profound influence on health and disease, but it is only recently that we have begun mapping the mechanisms via which the dietary environment impacts brain physiology and behavior. Here we review recent evidence on the effects of energy-dense and methionine diets on neural epigenetic marks, gene expression, and behavior in invertebrate and vertebrate model organisms. We also discuss limitations, open questions, and future directions in the emerging field of the neuroepigenetics of nutrition.
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Affiliation(s)
- Anoumid Vaziri
- Molecular, Cellular and Developmental Biology Graduate Program, The University of Michigan, Ann Arbor, USA; Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, USA
| | - Monica Dus
- Molecular, Cellular and Developmental Biology Graduate Program, The University of Michigan, Ann Arbor, USA; Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, USA.
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20
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Taylor M, Lukowski JK, Anderton CR. Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:872-894. [PMID: 33656885 PMCID: PMC8033567 DOI: 10.1021/jasms.0c00439] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 05/02/2023]
Abstract
Biological systems are composed of heterogeneous populations of cells that intercommunicate to form a functional living tissue. Biological function varies greatly across populations of cells, as each single cell has a unique transcriptome, proteome, and metabolome that translates to functional differences within single species and across kingdoms. Over the past decade, substantial advancements in our ability to characterize omic profiles on a single cell level have occurred, including in multiple spectroscopic and mass spectrometry (MS)-based techniques. Of these technologies, spatially resolved mass spectrometry approaches, including mass spectrometry imaging (MSI), have shown the most progress for single cell proteomics and metabolomics. For example, reporter-based methods using heavy metal tags have allowed for targeted MS investigation of the proteome at the subcellular level, and development of technologies such as laser ablation electrospray ionization mass spectrometry (LAESI-MS) now mean that dynamic metabolomics can be performed in situ. In this Perspective, we showcase advancements in single cell spatial metabolomics and proteomics over the past decade and highlight important aspects related to high-throughput screening, data analysis, and more which are vital to the success of achieving proteomic and metabolomic profiling at the single cell scale. Finally, using this broad literature summary, we provide a perspective on how the next decade may unfold in the area of single cell MS-based proteomics and metabolomics.
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Affiliation(s)
- Michael
J. Taylor
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jessica K. Lukowski
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Christopher R. Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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21
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Lita A, Pliss A, Kuzmin A, Yamasaki T, Zhang L, Dowdy T, Burks C, de Val N, Celiku O, Ruiz-Rodado V, Nicoli ER, Kruhlak M, Andresson T, Das S, Yang C, Schmitt R, Herold-Mende C, Gilbert MR, Prasad PN, Larion M. IDH1 mutations induce organelle defects via dysregulated phospholipids. Nat Commun 2021; 12:614. [PMID: 33504762 PMCID: PMC7840755 DOI: 10.1038/s41467-020-20752-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 12/11/2020] [Indexed: 01/25/2023] Open
Abstract
Infiltrating gliomas are devastating and incurable tumors. Amongst all gliomas, those harboring a mutation in isocitrate dehydrogenase 1 mutation (IDH1mut) acquire a different tumor biology and clinical manifestation from those that are IDH1WT. Understanding the unique metabolic profile reprogrammed by IDH1 mutation has the potential to identify new molecular targets for glioma therapy. Herein, we uncover increased monounsaturated fatty acids (MUFA) and their phospholipids in endoplasmic reticulum (ER), generated by IDH1 mutation, that are responsible for Golgi and ER dilation. We demonstrate a direct link between the IDH1 mutation and this organelle morphology via D-2HG-induced stearyl-CoA desaturase (SCD) overexpression, the rate-limiting enzyme in MUFA biosynthesis. Inhibition of IDH1 mutation or SCD silencing restores ER and Golgi morphology, while D-2HG and oleic acid induces morphological defects in these organelles. Moreover, addition of oleic acid, which tilts the balance towards elevated levels of MUFA, produces IDH1mut-specific cellular apoptosis. Collectively, these results suggest that IDH1mut-induced SCD overexpression can rearrange the distribution of lipids in the organelles of glioma cells, providing new insight into the link between lipid metabolism and organelle morphology in these cells, with potential and unique therapeutic implications. The understanding of altered lipid metabolism by isocitrate dehydrogenase 1 (IDH1) mutations in gliomas at a compartment-specific level is limited. Here, the authors use Raman spectroscopy to monitor organelle-specific metabolic changes and report that IDH1 mutations induce phospholipid imbalances which lead to ER and Golgi dilation.
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Affiliation(s)
- Adrian Lita
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Artem Pliss
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Andrey Kuzmin
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA.,Advanced Cytometry Instrumentation Systems, LLC, Buffalo, NY, 14260, USA
| | - Tomohiro Yamasaki
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Lumin Zhang
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Tyrone Dowdy
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Christina Burks
- Electron Microscopy Laboratory, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Natalia de Val
- Electron Microscopy Laboratory, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.,Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Orieta Celiku
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Victor Ruiz-Rodado
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Elena-Raluca Nicoli
- Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Michael Kruhlak
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory of the Cancer Research Technology Program (CRTP), National Cancer Institute, Frederick, MD, 21702, USA
| | - Sudipto Das
- Protein Characterization Laboratory of the Cancer Research Technology Program (CRTP), National Cancer Institute, Frederick, MD, 21702, USA
| | - Chunzhang Yang
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Rebecca Schmitt
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Christel Herold-Mende
- Division of Neurosurgical Research, Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Paras N Prasad
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA.,Advanced Cytometry Instrumentation Systems, LLC, Buffalo, NY, 14260, USA
| | - Mioara Larion
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA.
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22
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Palermo A. Charting Metabolism Heterogeneity by Nanostructure Imaging Mass Spectrometry: From Biological Systems to Subcellular Functions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2392-2400. [PMID: 33595331 DOI: 10.1021/jasms.0c00204] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The study of metabolism heterogeneity is essential to understand the role of metabolites in supporting and regulating biological functions. To this end, several mass spectrometry imaging (MSI) approaches have been proposed for the detection of small molecule metabolites. However, high noise from the ionization matrix and low metabolome coverage hinder their applicability for untargeted metabolomics studies across space. In this context, nanostructure imaging (/initiator) mass spectrometry (NIMS) and NIMS with fluorinated gold nanoparticles (f-AuNPs) are attractive strategies for comprehensive MSI of metabolites in biological systems, which can provide heterogeneous metabolome coverage, ultrahigh sensitivity, and high lateral resolution. In particular, NIMS with f-AuNPs permits the simultaneous detection of polar metabolites and lipids in a single and cohesive analytical session, thus allowing the systems-level interpretation of metabolic changes. In this Perspective article, we discuss the use of NIMS and f-AuNPs in the exploration of metabolism heterogeneity and provide a critical outlook on future applications of this technology for revealing the metabolic architecture that supports biological functions in health and disease, from whole organisms to tissues, single cells, and subcellular compartments.
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Affiliation(s)
- Amelia Palermo
- Department of Medicine, School of Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, California 92093-0412, United States
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23
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Systems Biology in Neuroscience: the Paramount Importance of Data Sharing and Citation. NEUROSCI 2020. [DOI: 10.3390/neurosci1020009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The emergence and maturation, in the last decade, of high powerful technologies in the fields of neurogenomics, neurometabolomics, and neuroproteomics has opened exciting novel possibilities of research [...]
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24
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Solid-state vibrational circular dichroism studies on the conformation of an amino acid molecule in crystalline state. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140439. [DOI: 10.1016/j.bbapap.2020.140439] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/18/2020] [Accepted: 04/29/2020] [Indexed: 11/20/2022]
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25
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Kumar R, Ghosh M, Kumar S, Prasad M. Single Cell Metabolomics: A Future Tool to Unmask Cellular Heterogeneity and Virus-Host Interaction in Context of Emerging Viral Diseases. Front Microbiol 2020; 11:1152. [PMID: 32582094 PMCID: PMC7286130 DOI: 10.3389/fmicb.2020.01152] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022] Open
Abstract
Viral emergence is an unpredictable but obvious event, particularly in the era of climate change and globalization. Efficient management of viral outbreaks depends on pre-existing knowledge and alertness. The potential hotspots of viral emergence often remain neglected and the information related to them is insufficient, particularly for emerging viruses. Viral replication and transmission rely upon usurping the host metabolic machineries. So altered host metabolic pathways can be exploited for containment of these viruses. Metabolomics provides the insight for tracing out such checkpoints. Consequently introspection of metabolic alteration at virus-host interface has evolved as prime area in current virology research. Chromatographic separation followed by mass spectrometry has been used as the predominant analytical platform in bulk of the analyses followed by nuclear magnetic resonance (NMR) and fluorescence based techniques. Although valuable information regarding viral replication and modulation of host metabolic pathways have been extracted but ambiguity often superseded the real events due to population effect over the infected cells. Exploration of cellular heterogeneity and differentiation of infected cells from the nearby healthy ones has become essential. Single cell metabolomics (SCM) emerges as necessity to explore such minute details. Mass spectrometry imaging (MSI) coupled with several soft ionization techniques such as electrospray ionization (ESI), laser ablation electrospray ionization (LAESI), matrix assisted laser desorption/ionization (MALDI), matrix-free laser desorption ionization (LDI) have evolved as the best suited platforms for SCM analyses. The potential of SCM has already been exploited to resolve several biological conundrums. Thus SCM is knocking at the door of virus-host interface.
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Affiliation(s)
- Rajesh Kumar
- Department of Veterinary Physiology and Biochemistry, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Mayukh Ghosh
- Department of Veterinary Physiology and Biochemistry, RGSC, Banaras Hindu University, Mirzapur, India
| | - Sandeep Kumar
- Department of Veterinary Surgery and Radiology, College of Veterinary Sciences, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
| | - Minakshi Prasad
- Department of Animal Biotechnology, Lala Lajpat Rai University of Veterinary and Animal Sciences, Hisar, India
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26
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Lanznaster D, Veyrat-Durebex C, Vourc’h P, Andres CR, Blasco H, Corcia P. Metabolomics: A Tool to Understand the Impact of Genetic Mutations in Amyotrophic Lateral Sclerosis. Genes (Basel) 2020; 11:genes11050537. [PMID: 32403313 PMCID: PMC7288444 DOI: 10.3390/genes11050537] [Citation(s) in RCA: 8] [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: 03/31/2020] [Revised: 04/27/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022] Open
Abstract
Metabolomics studies performed in patients with amyotrophic lateral sclerosis (ALS) reveal a set of distinct metabolites that can shed light on the pathological alterations taking place in each individual. Metabolites levels are influenced by disease status, and genetics play an important role both in familial and sporadic ALS cases. Metabolomics analysis helps to unravel the differential impact of the most common ALS-linked genetic mutations (as C9ORF72, SOD1, TARDBP, and FUS) in specific signaling pathways. Further, studies performed in genetic models of ALS reinforce the role of TDP-43 pathology in the vast majority of ALS cases. Studies performed in differentiated cells from ALS-iPSC (induced Pluripotent Stem Cells) reveal alterations in the cell metabolism that are also found in ALS models and ultimately in ALS patients. The development of metabolomics approaches in iPSC derived from ALS patients allow addressing and ultimately understanding the pathological mechanisms taking place in any patient. Lately, the creation of a "patient in a dish" will help to identify patients that may benefit from specific treatments and allow the implementation of personalized medicine.
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Affiliation(s)
- Débora Lanznaster
- UMR 1253, iBrain, University of Tours, Inserm, 37000 Tours, France; (C.V.-D.); (P.V.); (C.R.A.); (H.B.); (P.C.)
- Correspondence:
| | - Charlotte Veyrat-Durebex
- UMR 1253, iBrain, University of Tours, Inserm, 37000 Tours, France; (C.V.-D.); (P.V.); (C.R.A.); (H.B.); (P.C.)
- CHU de Tours, Service de Biochimie et Biologie Moléculaire, 37000 Tours, France
| | - Patrick Vourc’h
- UMR 1253, iBrain, University of Tours, Inserm, 37000 Tours, France; (C.V.-D.); (P.V.); (C.R.A.); (H.B.); (P.C.)
- CHU de Tours, Service de Biochimie et Biologie Moléculaire, 37000 Tours, France
| | - Christian R. Andres
- UMR 1253, iBrain, University of Tours, Inserm, 37000 Tours, France; (C.V.-D.); (P.V.); (C.R.A.); (H.B.); (P.C.)
- CHU de Tours, Service de Biochimie et Biologie Moléculaire, 37000 Tours, France
| | - Hélène Blasco
- UMR 1253, iBrain, University of Tours, Inserm, 37000 Tours, France; (C.V.-D.); (P.V.); (C.R.A.); (H.B.); (P.C.)
- CHU de Tours, Service de Biochimie et Biologie Moléculaire, 37000 Tours, France
| | - Philippe Corcia
- UMR 1253, iBrain, University of Tours, Inserm, 37000 Tours, France; (C.V.-D.); (P.V.); (C.R.A.); (H.B.); (P.C.)
- CHU de Tours, Service de Neurologie, 37000 Tours, France
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27
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Adhikari SS, Zhao L, Dickmeis T, Korvink JG, Badilita V. Inductively coupled magic angle spinning microresonators benchmarked for high-resolution single embryo metabolomic profiling. Analyst 2019; 144:7192-7199. [PMID: 31696868 DOI: 10.1039/c9an01634a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The magic angle coil spinning (MACS) technique has been introduced as a very promising extension for solid state NMR detection, demonstrating sensitivity enhancements by a factor of 14 from the very first time it has been reported. The main beneficiary of this technique is the scientific community dealing with mass- and volume-limited, rare, or expensive samples. However, more than a decade after the first report on MACS, there is a very limited number of groups who have continued to develop the technique, let alone it being widely adopted by practitioners. This might be due to several drawbacks associated with the MACS technology until now, including spectral linewidth, heating due to eddy currents, and imprecise manufacturing. Here, we report a device overcoming all these remaining issues, therefore achieving: (1) spectral resolution of approx 0.01 ppm and normalized limit of detection of approx. 13 nmol s0.5 calculated using the anomeric proton of sucrose at 3 kHz MAS frequency; (2) limited temperature increase inside the MACS insert of only 5 °C at 5 kHz MAS frequency in an 11.74 T magnetic field, rendering MACS suitable to study live biological samples. The wafer-scale fabrication process yields MACS inserts with reproducible properties, readily available to be used on a large scale in bio-chemistry labs. To illustrate the potential of these devices for metabolomic studies, we further report on: (3) ultra-fine 1H-1H and 13C-13C J-couplings resolved within 10 min for a 340 mM uniformly 13C-labeled glucose sample; and (4) single zebrafish embryo measurements through 1H-1H COSY within 4.5 h, opening the gate for the single embryo NMR studies.
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Affiliation(s)
- Shyam S Adhikari
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Li Zhao
- Voxalytic GmbH, Rosengarten 3, 76228, Karlsruhe, Germany
| | - Thomas Dickmeis
- Institute of Toxicology and Genetics (ITG), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Jan G Korvink
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| | - Vlad Badilita
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
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28
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Kawai T, Ota N, Okada K, Imasato A, Owa Y, Morita M, Tada M, Tanaka Y. Ultrasensitive Single Cell Metabolomics by Capillary Electrophoresis-Mass Spectrometry with a Thin-Walled Tapered Emitter and Large-Volume Dual Sample Preconcentration. Anal Chem 2019; 91:10564-10572. [PMID: 31357863 DOI: 10.1021/acs.analchem.9b01578] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Single cell metabolome analysis is essential for studying microscale life phenomena such as neuronal networks and tumor microenvironments. Capillary electrophoresis-mass spectrometry (CE-MS) is one of the most sensitive technologies; however, its sensitivity is still not enough for single cell analysis on general human cells such as HeLa. To address these issues, we first developed an efficient ionization emitter, named as a "nanoCESI" emitter, that had a thin-walled (∼10 μm) and tapered (5-10 μm) end. The thin conductive wall enabled sheathless ionization and minimized the flow rate of ionizing sample, and the tapered end efficiently ionized analytes via an electrospray ionization mechanism, providing up to 3.5-fold increase in sensitivity compared with a conventional sheathless emitter. Fifty repetitive analyses on 20 amino acids were successfully achieved with a nanoCESI emitter. Relative standard deviations of 50 analyses were 1.5%, 4.4%, and 6.8% for migration time, peak height, and peak area, respectively, where a limit of detection (LOD) of 170 pM (850 zmol) was achieved. Second, a sample enrichment method, large-volume dual preconcentration by isotachophoresis and stacking (LDIS), was applied to a newly designed protocol of nanoCESI-MS. This approach achieved up to 380-fold enhanced sensitivity and LOD of 450 fM. Compared with normal sheathless CE-MS, coupling of nanoCESI and LDIS provided up to 800-fold increase of sensitivity in total. Finally, metabolome analyses of single HeLa cells were performed, where 20 amino acids were successfully quantified with triple-quadrupole MS and 40 metabolites were identified with quadrupole-time-of-flight MS, as a promising analytical platform for microscale bioanalysis for the next generation.
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Affiliation(s)
- Takayuki Kawai
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan.,Japan Science and Technology Agency , PRESTO, Kawaguchi , Saitama 332-0012 , Japan.,Graduate School of Frontier Biosciences , Osaka University , Suita , Osaka 565-0871 , Japan
| | - Nobutoshi Ota
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan
| | - Kaori Okada
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan
| | - Akiko Imasato
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan
| | - Yuri Owa
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan
| | - Makiko Morita
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan
| | - Misa Tada
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan
| | - Yo Tanaka
- RIKEN Center for Biosystems Dynamics Research , Suita , Osaka 565-0874 , Japan.,Graduate School of Frontier Biosciences , Osaka University , Suita , Osaka 565-0871 , Japan
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29
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Neumann EK, Do TD, Comi TJ, Sweedler JV. Exploring the Fundamental Structures of Life: Non-Targeted, Chemical Analysis of Single Cells and Subcellular Structures. Angew Chem Int Ed Engl 2019; 58:9348-9364. [PMID: 30500998 PMCID: PMC6542728 DOI: 10.1002/anie.201811951] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Indexed: 01/14/2023]
Abstract
Cells are a basic functional and structural unit of living organisms. Both unicellular communities and multicellular species produce an astonishing chemical diversity, enabling a wide range of divergent functions, yet each cell shares numerous aspects that are common to all living organisms. While there are many approaches for studying this chemical diversity, only a few are non-targeted and capable of analyzing hundreds of different chemicals at cellular resolution. Here, we review the non-targeted approaches used to perform comprehensive chemical analyses, provide chemical imaging information, or obtain high-throughput single-cell profiling data. Single-cell measurement capabilities are rapidly increasing in terms of throughput, limits of detection, and completeness of the chemical analyses; these improvements enable their application to understand ever more complex physiological phenomena, such as learning, memory, and behavior.
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Affiliation(s)
- Elizabeth K. Neumann
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Thanh D. Do
- Department of Chemistry, 1420 Circle Drive, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Troy J. Comi
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, 405 N. Mathews Avenue, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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30
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Vasiljevic T, Singh V, Pawliszyn J. Miniaturized SPME tips directly coupled to mass spectrometry for targeted determination and untargeted profiling of small samples. Talanta 2019; 199:689-697. [DOI: 10.1016/j.talanta.2019.03.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/02/2019] [Accepted: 03/02/2019] [Indexed: 10/27/2022]
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31
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Neumann EK, Do TD, Comi TJ, Sweedler JV. Erforschung der fundamentalen Strukturen des Lebens: Nicht zielgerichtete chemische Analyse von Einzelzellen und subzellulären Strukturen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811951] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Elizabeth K. Neumann
- Department of Chemistry and the Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-Champaign 405 N. Mathews Avenue Urbana IL 61801 USA
| | - Thanh D. Do
- Department of ChemistryUniversity of Tennessee 1420 Circle Drive Knoxville TN 37996 USA
| | - Troy J. Comi
- Department of Chemistry and the Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-Champaign 405 N. Mathews Avenue Urbana IL 61801 USA
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and TechnologyUniversity of Illinois at Urbana-Champaign 405 N. Mathews Avenue Urbana IL 61801 USA
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Schmitt ND, Rawlins CM, Randall EC, Wang X, Koller A, Auclair JR, Kowalski JM, Kowalski PJ, Luther E, Ivanov AR, Agar NYR, Agar JN. Genetically Encoded Fluorescent Proteins Enable High-Throughput Assignment of Cell Cohorts Directly from MALDI-MS Images. Anal Chem 2019; 91:3810-3817. [PMID: 30839199 DOI: 10.1021/acs.analchem.8b03454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) provides a unique in situ chemical profile that can include drugs, nucleic acids, metabolites, lipids, and proteins. MSI of individual cells (of a known cell type) affords a unique insight into normal and disease-related processes and is a prerequisite for combining the results of MSI and other single-cell modalities (e.g. mass cytometry and next-generation sequencing). Technological barriers have prevented the high-throughput assignment of MSI spectra from solid tissue preparations to their cell type. These barriers include obtaining a suitable cell-identifying image (e.g. immunohistochemistry) and obtaining sufficiently accurate registration of the cell-identifying and MALDI-MS images. This study introduces a technique that overcame these barriers by assigning cell type directly from mass spectra. We hypothesized that, in MSI from mice with a defined fluorescent protein expression pattern, the fluorescent protein's molecular ion could be used to identify cell cohorts. A method was developed for the purification of enhanced yellow fluorescent protein (EYFP) from mice. To determine EYFP's molecular mass for MSI studies, we performed intact mass analysis and characterized the protein's primary structure and post-translational modifications through various techniques. MALDI-MSI methods were developed to enhance the detection of EYFP in situ, and by extraction of EYFP's molecular ion from MALDI-MS images, automated, whole-image assignment of cell cohorts was achieved. This method was validated using a well-characterized mouse line that expresses EYFP in motor and sensory neurons and should be applicable to hundreds of commercially available mice (and other animal) strains comprising a multitude of cell-specific fluorescent labels.
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Affiliation(s)
- Nicholas D Schmitt
- Department of Chemistry and Chemical Biology and Barnett Institute of Chemical and Biological Analysis , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Catherine M Rawlins
- Department of Chemistry and Chemical Biology and Barnett Institute of Chemical and Biological Analysis , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Elizabeth C Randall
- Department of Radiology , Brigham and Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Xianzhe Wang
- Department of Chemistry and Chemical Biology and Barnett Institute of Chemical and Biological Analysis , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Antonius Koller
- Department of Chemistry and Chemical Biology and Barnett Institute of Chemical and Biological Analysis , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Jared R Auclair
- Department of Chemistry and Chemical Biology and Barnett Institute of Chemical and Biological Analysis , Northeastern University , Boston , Massachusetts 02115 , United States.,Biopharmaceutical Analysis Training Laboratory (BATL) , Northeastern University Innovation Campus , Burlington , Massachusetts 01803 , United States
| | - Jane-Marie Kowalski
- Bruker Daltonics , 40 Manning Road , Billerica , Massachusetts 01821 , United States
| | - Paul J Kowalski
- Bruker Daltonics , 40 Manning Road , Billerica , Massachusetts 01821 , United States
| | - Ed Luther
- Department of Pharmaceutical Sciences , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Alexander R Ivanov
- Department of Chemistry and Chemical Biology and Barnett Institute of Chemical and Biological Analysis , Northeastern University , Boston , Massachusetts 02115 , United States
| | - Nathalie Y R Agar
- Department of Radiology , Brigham and Women's Hospital, Harvard Medical School , Boston , Massachusetts 02115 , United States.,Department of Neurosurgery, Brigham and Women's Hospital, Department of Cancer Biology , Dana-Farber Cancer Institute, Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Jeffrey N Agar
- Department of Chemistry and Chemical Biology and Barnett Institute of Chemical and Biological Analysis , Northeastern University , Boston , Massachusetts 02115 , United States.,Department of Pharmaceutical Sciences , Northeastern University , Boston , Massachusetts 02115 , United States
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Dickmeis T, Feng Y, Mione MC, Ninov N, Santoro M, Spaink HP, Gut P. Nano-Sampling and Reporter Tools to Study Metabolic Regulation in Zebrafish. Front Cell Dev Biol 2019; 7:15. [PMID: 30873407 PMCID: PMC6401643 DOI: 10.3389/fcell.2019.00015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 01/31/2019] [Indexed: 01/09/2023] Open
Abstract
In the past years, evidence has emerged that hallmarks of human metabolic disorders can be recapitulated in zebrafish using genetic, pharmacological or dietary interventions. An advantage of modeling metabolic diseases in zebrafish compared to other "lower organisms" is the presence of a vertebrate body plan providing the possibility to study the tissue-intrinsic processes preceding the loss of metabolic homeostasis. While the small size of zebrafish is advantageous in many aspects, it also has shortcomings such as the difficulty to obtain sufficient amounts for biochemical analyses in response to metabolic challenges. A workshop at the European Zebrafish Principal Investigator meeting in Trento, Italy, was dedicated to discuss the advantages and disadvantages of zebrafish to study metabolic disorders. This perspective article by the participants highlights strategies to achieve improved tissue-resolution for read-outs using "nano-sampling" approaches for metabolomics as well as live imaging of zebrafish expressing fluorescent reporter tools that inform on cellular or subcellular metabolic processes. We provide several examples, including the use of reporter tools to study the heterogeneity of pancreatic beta-cells within their tissue environment. While limitations exist, we believe that with the advent of new technologies and more labs developing methods that can be applied to minimal amounts of tissue or single cells, zebrafish will further increase their utility to study energy metabolism.
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Affiliation(s)
- Thomas Dickmeis
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Yi Feng
- Centre for Inflammation Research, Queen’s Medical Research Institute, The University of Edinburgh, Edinburgh, Scotland
| | | | - Nikolay Ninov
- DFG-Center for Regenerative Therapies Dresden, Cluster of Excellence, Technische Universität Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden, Helmholtz Zentrum München, Faculty of Medicine, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | | | - Herman P. Spaink
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Philipp Gut
- Nestlé Research, EPFL Innovation Park, Lausanne, Switzerland
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Thaler DS, Head MG, Horsley A. Precision public health to inhibit the contagion of disease and move toward a future in which microbes spread health. BMC Infect Dis 2019; 19:120. [PMID: 30727964 PMCID: PMC6364421 DOI: 10.1186/s12879-019-3715-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 01/10/2019] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance continues to outpace the development of new chemotherapeutics. Novel pathogens continue to evolve and emerge. Public health innovation has the potential to open a new front in the war of "our wits against their genes" (Joshua Lederberg). Dense sampling coupled to next generation sequencing can increase the spatial and temporal resolution of microbial characterization while sensor technologies precisely map physical parameters relevant to microbial survival and spread. Microbial, physical, and epidemiological big data could be combined to improve prospective risk identification. However, applied in the wrong way, these approaches may not realize their maximum potential benefits and could even do harm. Minimizing microbial-human interactions would be a mistake. There is evidence that microbes previously thought of at best "benign" may actually enhance human health. Benign and health-promoting microbiomes may, or may not, spread via mechanisms similar to pathogens. Infectious vaccines are approaching readiness to make enhanced contributions to herd immunity. The rigorously defined nature of infectious vaccines contrasts with indigenous "benign or health-promoting microbiomes" but they may converge. A "microbial Neolithic revolution" is a possible future in which human microbial-associations are understood and managed analogously to the macro-agriculture of plants and animals. Tradeoffs need to be framed in order to understand health-promoting potentials of benign, and/or health-promoting microbiomes and infectious vaccines while also discouraging pathogens. Super-spreaders are currently defined as individuals who play an outsized role in the contagion of infectious disease. A key unanswered question is whether the super-spreader concept may apply similarly to health-promoting microbes. The complex interactions of individual rights, community health, pathogen contagion, the spread of benign, and of health-promoting microbiomes including infectious vaccines require study. Advancing the detailed understanding of heterogeneity in microbial spread is very likely to yield important insights relevant to public health.
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Affiliation(s)
- David S. Thaler
- Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Michael G. Head
- Clinical Informatics Research Unit, Faculty of Medicine, University of Southampton, University Hospital Southampton, Coxford Road, Southampton, SO16 6YD UK
| | - Andrew Horsley
- Research School of Physics and Engineering, The Australian National University, Mills Rd., Canberra, ACT 2601 Australia
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Duncan KD, Fyrestam J, Lanekoff I. Advances in mass spectrometry based single-cell metabolomics. Analyst 2019; 144:782-793. [DOI: 10.1039/c8an01581c] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Single cell metabolomics using mass spectrometry can contribute to understanding biological activities in health and disease.
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36
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Choi WT, Tosun M, Jeong HH, Karakas C, Semerci F, Liu Z, Maletić-Savatić M. Metabolomics of mammalian brain reveals regional differences. BMC SYSTEMS BIOLOGY 2018; 12:127. [PMID: 30577853 PMCID: PMC6302375 DOI: 10.1186/s12918-018-0644-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background The mammalian brain is organized into regions with specific biological functions and properties. These regions have distinct transcriptomes, but little is known whether they may also differ in their metabolome. The metabolome, a collection of small molecules or metabolites, is at the intersection of the genetic background of a given cell or tissue and the environmental influences that affect it. Thus, the metabolome directly reflects information about the physiologic state of a biological system under a particular condition. The objective of this study was to investigate whether various brain regions have diverse metabolome profiles, similarly to their genetic diversity. The answer to this question would suggest that not only the genome but also the metabolome may contribute to the functional diversity of brain regions. Methods We investigated the metabolome of four regions of the mouse brain that have very distinct functions: frontal cortex, hippocampus, cerebellum, and olfactory bulb. We utilized gas- and liquid- chromatography mass spectrometry platforms and identified 215 metabolites. Results Principal component analysis, an unsupervised multivariate analysis, clustered each brain region based on its metabolome content, thus providing the unique metabolic profile of each region. A pathway-centric analysis indicated that olfactory bulb and cerebellum had most distinct metabolic profiles, while the cortical parenchyma and hippocampus were more similar in their metabolome content. Among the notable differences were distinct oxidative-anti-oxidative status and region-specific lipid profiles. Finally, a global metabolic connectivity analysis using the weighted correlation network analysis identified five hub metabolites that organized a unique metabolic network architecture within each examined brain region. These data indicate the diversity of global metabolome corresponding to specialized regional brain function and provide a new perspective on the underlying properties of brain regions. Conclusion In summary, we observed many differences in the metabolome among the various brain regions investigated. All four brain regions in our study had a unique metabolic signature, but the metabolites came from all categories and were not pathway-centric. Electronic supplementary material The online version of this article (10.1186/s12918-018-0644-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- William T Choi
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA.,The National Library of Medicine Training Program in Biomedical Informatics, Houston, TX, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Mehmet Tosun
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Hyun-Hwan Jeong
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Cemal Karakas
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.,Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Fatih Semerci
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA. .,Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA. .,Quantitative Computational Biology Program, Baylor College of Medicine, Houston, TX, USA.
| | - Mirjana Maletić-Savatić
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA. .,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA. .,Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA. .,Quantitative Computational Biology Program, Baylor College of Medicine, Houston, TX, USA. .,Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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37
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Lane AN, Higashi RM, Fan TWM. NMR and MS-based Stable Isotope-Resolved Metabolomics and Applications in Cancer Metabolism. Trends Analyt Chem 2018; 120. [PMID: 32523238 DOI: 10.1016/j.trac.2018.11.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
There is considerable interest in defining metabolic reprogramming in human diseases, which is recognized as a hallmark of human cancer. Although radiotracers have a long history in specific metabolic studies, stable isotope-enriched precursors coupled with modern high resolution mass spectrometry and NMR spectroscopy have enabled systematic mapping of metabolic networks and fluxes in cells, tissues and living organisms including humans. These analytical platforms are high in information content, are complementary and cross-validating in terms of compound identification, quantification, and isotope labeling pattern analysis of a large number of metabolites simultaneously. Furthermore, new developments in chemoselective derivatization and in vivo spectroscopy enable tracking of labile/low abundance metabolites and metabolic kinetics in real-time. Here we review developments in Stable Isotope Resolved Metabolomics (SIRM) and recent applications in cancer metabolism using a wide variety of stable isotope tracers that probe both broad and specific aspects of cancer metabolism required for proliferation and survival.
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Affiliation(s)
- Andrew N Lane
- Center for Environmental and Systems Biochemistry, Dept. Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536 USA
| | - Richard M Higashi
- Center for Environmental and Systems Biochemistry, Dept. Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536 USA
| | - Teresa W-M Fan
- Center for Environmental and Systems Biochemistry, Dept. Toxicology and Cancer Biology, Markey Cancer Center, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536 USA
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38
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Fabrication of hydrophilic multilayer magnetic probe for salivary glycopeptidome analysis. J Chromatogr A 2018; 1587:24-33. [PMID: 30502035 DOI: 10.1016/j.chroma.2018.11.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/14/2018] [Accepted: 11/20/2018] [Indexed: 12/23/2022]
Abstract
Variations in salivary components are closely associated with the predisposition and state of disease, the abnormal changes of salivary glycopeptidome are usually discovered as perilous singals of serious disease. Therefore, the monitoring and analyzing of salivary glycopeptidome are of even more overriding importance. In this work, a low-cost layer-by-layer assembly strategy was adopted to fabricate a hydrophilic multilayer magnetic probe (dubbed Mag-m-G6P) for salivary glycopeptidome analysis. The successful construction of multilayer structure not only guaranteed the good dispersal of probe by protecting magnetic core from itself aggregation tendency, but also endowed the probe with multiple advantages including the good hydrophilicity, uniform mesopore size and strong magnetic responsiveness, etc. As expected, with the optimized experimental conditions, the multifunctional probe showed high enrichemnt sensitivity, unbiased enrichment ability, excellent size-exclusion ability and reusability and so on in the process of standard sample analysis. At last, the Mag-m-G6P was successfully applied to salivary glycopeptidome analysis on further combination with LC-MS/MS analysis, a total of 53 endogenous glycopeptides were identified from human saliva.
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Affiliation(s)
- Pieter E. Oomen
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg 41296, Sweden
| | - Mohaddeseh A. Aref
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg 41296, Sweden
| | - Ibrahim Kaya
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg 41296, Sweden
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the University of Gothenburg, Mölndal Hospital, House V3, 43180 Mölndal, Sweden
- The Gothenburg Imaging Mass Spectrometry (Go:IMS) Laboratory, University of Gothenburg and Chalmers University of Technology, Gothenburg 41296, Sweden
| | - Nhu T. N. Phan
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg 41296, Sweden
- The Gothenburg Imaging Mass Spectrometry (Go:IMS) Laboratory, University of Gothenburg and Chalmers University of Technology, Gothenburg 41296, Sweden
- University of Göttingen Medical Center, Institute of Neuro- and Sensory Physiology, Göttingen 37073, Germany
| | - Andrew G. Ewing
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg 41296, Sweden
- The Gothenburg Imaging Mass Spectrometry (Go:IMS) Laboratory, University of Gothenburg and Chalmers University of Technology, Gothenburg 41296, Sweden
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Buijink MR, van Weeghel M, Gülersönmez MC, Harms AC, Rohling JHT, Meijer JH, Hankemeier T, Michel S. The influence of neuronal electrical activity on the mammalian central clock metabolome. Metabolomics 2018; 14:122. [PMID: 30830420 PMCID: PMC6153692 DOI: 10.1007/s11306-018-1423-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/31/2018] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Most organisms display circadian rhythms in physiology and behaviour. In mammals, these rhythms are orchestrated by the suprachiasmatic nucleus (SCN). Recently, several metabolites have emerged as important regulators of circadian timekeeping. Metabolomics approaches have aided in identifying some key metabolites in circadian processes in peripheral tissue, but methods to routinely measure metabolites in small brain areas are currently lacking. OBJECTIVE The aim of the study was to establish a reliable method for metabolite quantifications in the central circadian clock and relate them to different states of neuronal excitability. METHODS We developed a method to collect and process small brain tissue samples (0.2 mm3), suitable for liquid chromatography-mass spectrometry. Metabolites were analysed in the SCN and one of its main hypothalamic targets, the paraventricular nucleus (PVN). Tissue samples were taken at peak (midday) and trough (midnight) of the endogenous rhythm in SCN electrical activity. Additionally, neuronal activity was altered pharmacologically. RESULTS We found a minor effect of day/night fluctuations in electrical activity or silencing activity during the day. In contrast, increasing electrical activity during the night significantly upregulated many metabolites in SCN and PVN. CONCLUSION Our method has shown to produce reliable and physiologically relevant metabolite data from small brain samples. Inducing electrical activity at night mimics the effect of a light pulses in the SCN, producing phase shifts of the circadian rhythm. The upregulation of metabolites could have a functional role in this process, since they are not solely products of physiological states, they are significant parts of cellular signalling pathways.
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Affiliation(s)
- M Renate Buijink
- Department of Cellular and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Michel van Weeghel
- Department of Cellular and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
- Analytical BioSciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - M Can Gülersönmez
- Analytical BioSciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Amy C Harms
- Analytical BioSciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jos H T Rohling
- Department of Cellular and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Johanna H Meijer
- Department of Cellular and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands
| | - Thomas Hankemeier
- Analytical BioSciences and Metabolomics, Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Stephan Michel
- Department of Cellular and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.
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Moroz LL. NeuroSystematics and Periodic System of Neurons: Model vs Reference Species at Single-Cell Resolution. ACS Chem Neurosci 2018; 9:1884-1903. [PMID: 29989789 DOI: 10.1021/acschemneuro.8b00100] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
There is more than one way to develop neuronal complexity, and animals frequently use different molecular toolkits to achieve similar functional outcomes (=convergent evolution). Neurons are different not only because they have different functions, but also because neurons and circuits have different genealogies, and perhaps independent origins at the broadest scale from ctenophores and cnidarians to cephalopods and primates. By combining modern phylogenomics, single-neuron sequencing (scRNA-seq), machine learning, single-cell proteomics, and metabolomic across Metazoa, it is possible to reconstruct the evolutionary histories of neurons tracing them to ancestral secretory cells. Comparative data suggest that neurons, and perhaps synapses, evolved at least 2-3 times (in ctenophore, cnidarian and bilateral lineages) during ∼600 million years of animal evolution. There were also several independent events of the nervous system centralization either from a common bilateral/cnidarian ancestor without the bona fide neurons or from the urbilaterian with diffuse, nerve-net type nervous system. From the evolutionary standpoint, (i) a neuron should be viewed as a functional rather than a genetic character, and (ii) any given neural system might be chimeric and composed of different cell lineages with distinct origins and evolutionary histories. The identification of distant neural homologies or examples of convergent evolution among 34 phyla will not only allow the reconstruction of neural systems' evolution but together with single-cell "omic" approaches the proposed synthesis would lead to the "Periodic System of Neurons" with predictive power for neuronal phenotypes and plasticity. Such a phylogenetic classification framework of Neuronal Systematics (NeuroSystematics) might be a conceptual analog of the Periodic System of Chemical Elements. scRNA-seq profiling of all neurons in an entire brain or Brain-seq is now fully achievable in many nontraditional reference species across the entire animal kingdom. Arguably, marine animals are the most suitable for the proposed tasks because the world oceans represent the greatest taxonomic and body-plan diversity.
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Affiliation(s)
- Leonid L. Moroz
- Department of Neuroscience and McKnight Brain Institute, University of Florida, 1149 Newell Drive, Gainesville, Florida 32611, United States
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd., St. Augustine, Florida 32080, United States
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Zhang L, Khattar N, Kemenes I, Kemenes G, Zrinyi Z, Pirger Z, Vertes A. Subcellular Peptide Localization in Single Identified Neurons by Capillary Microsampling Mass Spectrometry. Sci Rep 2018; 8:12227. [PMID: 30111831 PMCID: PMC6093924 DOI: 10.1038/s41598-018-29704-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/17/2018] [Indexed: 12/22/2022] Open
Abstract
Single cell mass spectrometry (MS) is uniquely positioned for the sequencing and identification of peptides in rare cells. Small peptides can take on different roles in subcellular compartments. Whereas some peptides serve as neurotransmitters in the cytoplasm, they can also function as transcription factors in the nucleus. Thus, there is a need to analyze the subcellular peptide compositions in identified single cells. Here, we apply capillary microsampling MS with ion mobility separation for the sequencing of peptides in single neurons of the mollusk Lymnaea stagnalis, and the analysis of peptide distributions between the cytoplasm and nucleus of identified single neurons that are known to express cardioactive Phe-Met-Arg-Phe amide-like (FMRFamide-like) neuropeptides. Nuclei and cytoplasm of Type 1 and Type 2 F group (Fgp) neurons were analyzed for neuropeptides cleaved from the protein precursors encoded by alternative splicing products of the FMRFamide gene. Relative abundances of nine neuropeptides were determined in the cytoplasm. The nuclei contained six of these peptides at different abundances. Enabled by its relative enrichment in Fgp neurons, a new 28-residue neuropeptide was sequenced by tandem MS.
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Affiliation(s)
- Linwen Zhang
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Nikkita Khattar
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Ildiko Kemenes
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Gyorgy Kemenes
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Zita Zrinyi
- Department of Experimental Zoology, Balaton Limnological Institute, MTA Center for Ecological Research, 8237, Tihany, Hungary
| | - Zsolt Pirger
- Department of Experimental Zoology, Balaton Limnological Institute, MTA Center for Ecological Research, 8237, Tihany, Hungary
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA.
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Zhang XC, Zang Q, Zhao H, Ma X, Pan X, Feng J, Zhang S, Zhang R, Abliz Z, Zhang X. Combination of Droplet Extraction and Pico-ESI-MS Allows the Identification of Metabolites from Single Cancer Cells. Anal Chem 2018; 90:9897-9903. [DOI: 10.1021/acs.analchem.8b02098] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Qingce Zang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | | | | | | | | | | | - Ruiping Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zeper Abliz
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Centre for Bioimaging and Systems Biology, Minzu University of China, Beijing 100081, China
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44
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Tillmaand EG, Sweedler JV. Integrating Mass Spectrometry with Microphysiological Systems for Improved Neurochemical Studies. ACTA ACUST UNITED AC 2018; 2. [PMID: 30148282 DOI: 10.21037/mps.2018.05.01] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Microphysiological systems, often referred to as "organs-on-chips", are in vitro platforms designed to model the spatial, chemical, structural, and physiological elements of in vivo cellular environments. They enhance the evaluation of complex engineered biological systems and are a step between traditional cell culture and in vivo experimentation. As neurochemists and measurement scientists studying the molecules involved in intercellular communication in the nervous system, we focus here on recent advances in neuroscience using microneurological systems and their potential to interface with mass spectrometry. We discuss a number of examples - microfluidic devices, spheroid cultures, hydrogels, scaffolds, and fibers - highlighting those that would benefit from mass spectrometric technologies to obtain improved chemical information.
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Affiliation(s)
- Emily G Tillmaand
- Department of Chemistry, the Neuroscience Program and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V Sweedler
- Department of Chemistry, the Neuroscience Program and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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Diesner M, Neupert S. Quantification of Biogenic Amines from Individual GFP-Labeled Drosophila Cells by MALDI-TOF Mass Spectrometry. Anal Chem 2018; 90:8035-8043. [DOI: 10.1021/acs.analchem.8b00961] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Max Diesner
- University of Cologne, Department of Biology, Institute for Zoology, Zülpicher Strasse 47b, 50674 Cologne, Germany
| | - Susanne Neupert
- University of Cologne, Department of Biology, Institute for Zoology, Zülpicher Strasse 47b, 50674 Cologne, Germany
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Do TD, Ellis JF, Neumann EK, Comi TJ, Tillmaand EG, Lenhart AE, Rubakhin SS, Sweedler JV. Optically Guided Single Cell Mass Spectrometry of Rat Dorsal Root Ganglia to Profile Lipids, Peptides and Proteins. Chemphyschem 2018; 19:1180-1191. [PMID: 29544029 PMCID: PMC5980748 DOI: 10.1002/cphc.201701364] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Indexed: 12/16/2022]
Abstract
The mammalian dorsal root ganglia (DRG) are located on the dorsal roots of the spinal nerves and contain cell bodies of primary sensory neurons. DRG cells have been classified into subpopulations based on their size, morphology, intracellular markers, response to stimuli, and neuropeptides. To understand the connections between DRG chemical heterogeneity and cellular function, we performed optically guided, high-throughput single cell profiling using sequential matrix-assisted laser desorption/ionization mass spectrometry (MS) to detect lipids, peptides, and several proteins in individual DRG cells. Statistical analysis of the resulting mass spectra allows stratification of the DRG population according to cellular morphology and, presumably, major cell types. A subpopulation of small cells contained myelin proteins, which are abundant in Schwann cells, and mass spectra of several larger cells contained peaks matching neurofilament, vimentin, myelin basic protein S, and thymosin beta proteins. Of the over 1000 cells analyzed, approximately 78 % produced putative peptide-rich spectra, allowing the population to be classified into three distinct cell types. Two signals with m/z 4404 and 5487 were exclusively observed in a cell type, but could not be matched to results of our previous liquid chromatography-MS analyses.
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Affiliation(s)
- Thanh D. Do
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Joseph F. Ellis
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Elizabeth K. Neumann
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Troy J. Comi
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Emily G. Tillmaand
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Ashley E. Lenhart
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Stanislav S. Rubakhin
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, Illinois 61801, United States
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