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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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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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Zhu J, Pan S, Chai H, Zhao P, Feng Y, Cheng Z, Zhang S, Wang W. Microfluidic Impedance Cytometry Enabled One-Step Sample Preparation for Efficient Single-Cell Mass Spectrometry. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310700. [PMID: 38483007 DOI: 10.1002/smll.202310700] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/05/2024] [Indexed: 06/27/2024]
Abstract
Single-cell mass spectrometry (MS) is significant in biochemical analysis and holds great potential in biomedical applications. Efficient sample preparation like sorting (i.e., separating target cells from the mixed population) and desalting (i.e., moving the cells off non-volatile salt solution) is urgently required in single-cell MS. However, traditional sample preparation methods suffer from complicated operation with various apparatus, or insufficient performance. Herein, a one-step sample preparation strategy by leveraging label-free impedance flow cytometry (IFC) based microfluidics is proposed. Specifically, the IFC framework to characterize and sort single-cells is adopted. Simultaneously with sorting, the target cell is transferred from the local high-salinity buffer to the MS-compatible solution. In this way, one-step sorting and desalting are achieved and the collected cells can be directly fed for MS analysis. A high sorting efficiency (>99%), cancer cell purity (≈87%), and desalting efficiency (>99%), and the whole workflow of impedance-based separation and MS analysis of normal cells (MCF-10A) and cancer cells (MDA-MB-468) are verified. As a standalone sample preparation module, the microfluidic chip is compatible with a variety of MS analysis methods, and envisioned to provide a new paradigm in efficient MS sample preparation, and further in multi-modal (i.e., electrical and metabolic) characterization of single-cells.
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Affiliation(s)
- Junwen Zhu
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Siyuan Pan
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Huichao Chai
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Peng Zhao
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Yongxiang Feng
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Zhen Cheng
- Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Wenhui Wang
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
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4
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Wang H, Tang H, Qiu X, Li Y. Solid-State Glass Nanopipettes: Functionalization and Applications. Chemistry 2024; 30:e202400281. [PMID: 38507278 DOI: 10.1002/chem.202400281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/28/2024] [Accepted: 03/19/2024] [Indexed: 03/22/2024]
Abstract
Solid-state glass nanopipettes provide a promising confined space that offers several advantages such as controllable size, simple preparation, low cost, good mechanical stability, and good thermal stability. These advantages make them an ideal choice for various applications such as biosensors, DNA sequencing, and drug delivery. In this review, we first delve into the functionalized nanopipettes for sensing various analytes and the methods used to develop detection means with them. Next, we provide an in-depth overview of the advanced functionalization methodologies of nanopipettes based on diversified chemical kinetics. After that, we present the latest state-of-the-art achievements and potential applications in detecting a wide range of targets, including ions, molecules, biological macromolecules, and single cells. We examine the various challenges that arise when working with these targets, as well as the innovative solutions developed to overcome them. The final section offers an in-depth overview of the current development status, newest trends, and application prospects of sensors. Overall, this review provides a comprehensive and detailed analysis of the current state-of-the-art functionalized nanopipette perception sensing and development of detection means and offers valuable insights into the prospects for this exciting field.
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Affiliation(s)
- Hao Wang
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education, School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, 235000, Anhui, P.R. China
| | - Haoran Tang
- Key Laboratory of Green and Precise Synthetic Chemistry and Applications, Ministry of Education, School of Chemistry and Materials Science, Huaibei Normal University, Huaibei, 235000, Anhui, P.R. China
| | - Xia Qiu
- Key Laboratory of Functional Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, P.R. China
| | - Yongxin Li
- Key Laboratory of Functional Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing College of Chemistry and Materials Science, Anhui Normal University, Wuhu, 241000, P.R. China
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Qin S, Zhang Y, Shi M, Miao D, Lu J, Wen L, Bai Y. In-depth organic mass cytometry reveals differential contents of 3-hydroxybutanoic acid at the single-cell level. Nat Commun 2024; 15:4387. [PMID: 38782922 PMCID: PMC11116506 DOI: 10.1038/s41467-024-48865-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
Comprehensive single-cell metabolic profiling is critical for revealing phenotypic heterogeneity and elucidating the molecular mechanisms underlying biological processes. However, single-cell metabolomics remains challenging because of the limited metabolite coverage and inability to discriminate isomers. Herein, we establish a single-cell metabolomics platform for in-depth organic mass cytometry. Extended single-cell analysis time guarantees sufficient MS/MS acquisition for metabolite identification and the isomers discrimination while online sampling ensures the high-throughput of the method. The largest number of identified metabolites (approximately 600) are achieved in single cells and fine subtyping of MCF-7 cells is first demonstrated by an investigation on the differential levels of 3-hydroxybutanoic acid among clusters. Single-cell transcriptome analysis reveals differences in the expression of 3-hydroxybutanoic acid downstream antioxidative stress genes, such as metallothionein 2 (MT2A), while a fluorescence-activated cell sorting assay confirms the positive relationship between 3-hydroxybutanoic acid and target proteins; these results suggest that the heterogeneity of 3-hydroxybutanoic acid provides cancer cells with different ability to resist surrounding oxidative stress. Our method paves the way for deep single-cell metabolome profiling and investigations on the physiological and pathological processes that occur during cancer.
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Affiliation(s)
- Shaojie Qin
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Yi Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Mingying Shi
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Daiyu Miao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Jiansen Lu
- Biomedical Pioneering Innovative Center, School of Life Sciences, Peking University, Beijing, China
| | - Lu Wen
- Biomedical Pioneering Innovative Center, School of Life Sciences, Peking University, Beijing, China
| | - Yu Bai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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Cheng S, Cao C, Qian Y, Yao H, Gong X, Dai X, Ouyang Z, Ma X. High-throughput single-cell mass spectrometry enables metabolic network analysis by resolving phospholipid C[double bond, length as m-dash]C isomers. Chem Sci 2024; 15:6314-6320. [PMID: 38699276 PMCID: PMC11062128 DOI: 10.1039/d3sc06573a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
Single-cell mass spectrometry (MS) is an essential technology for sensitive and multiplexed analysis of metabolites and lipids for cell phenotyping and pathway studies. However, the structural elucidation of lipids from single cells remains a challenge, especially in the high-throughput scenario. Technically, there is a contradiction between the inadequate sample amount (i.e. a single cell, 0.5-20 pL) for replicate or multiple analysis, on the one hand, and the high metabolite coverage and multidimensional structure analysis that needs to be performed for each single cell, on the other hand. Here, we have developed a high-throughput single-cell MS platform that can perform both lipid profiling and lipid carbon-carbon double bond (C[double bond, length as m-dash]C) location isomer resolution analysis, aided by C[double bond, length as m-dash]C activation in unsaturated lipids by the Paternò-Büchi (PB) reaction and tandem MS, termed single-cell structural lipidomics analysis. The method can achieve a single-cell analysis throughput of 51 cells per minute. A total of 145 lipids were structurally characterized at the subclass level, of which the relative abundance of 17 isomeric lipids differing in the location of C[double bond, length as m-dash]C from 5 lipid precursors was determined. While cell-to-cell variations in MS1-based lipid profiling can be large, an advantage of quantifying lipid C[double bond, length as m-dash]C location isomers is the significantly improved quantitation accuracy. For example, the relative standard deviations (RSDs) of the relative amounts of PC 34:1 C[double bond, length as m-dash]C position isomers in MDA-MB-468 cells are half smaller than those measured for PC 34:1 as a whole by MS1 abundance profiling. Taken together, the developed method can be effectively used for in-depth structural lipid metabolism network analysis by high-throughput analysis of 142 MDA-MB-468 human breast cancer cells.
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Affiliation(s)
- Simin Cheng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology Bejing 100029 China
| | - Chenxi Cao
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University Beijing 100084 China
| | - Yao Qian
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University Beijing 100084 China
| | - Huan Yao
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology Beijing 100029 China
| | - Xiaoyun Gong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology Bejing 100029 China
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology Bejing 100029 China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University Beijing 100084 China
| | - Xiaoxiao Ma
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University Beijing 100084 China
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Xu T, Li H, Dou P, Luo Y, Pu S, Mu H, Zhang Z, Feng D, Hu X, Wang T, Tan G, Chen C, Li H, Shi X, Hu C, Xu G. Concentric Hybrid Nanoelectrospray Ionization-Atmospheric Pressure Chemical Ionization Source for High-Coverage Mass Spectrometry Analysis of Single-Cell Metabolomics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306659. [PMID: 38359005 DOI: 10.1002/advs.202306659] [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: 09/14/2023] [Revised: 02/04/2024] [Indexed: 02/17/2024]
Abstract
High-coverage mass spectrometry analysis of single-cell metabolomics remains challenging due to the extremely low abundance and wide polarity of metabolites and ultra-small volume in single cells. Herein, a novel concentric hybrid ionization source, nanoelectrospray ionization-atmospheric pressure chemical ionization (nanoESI-APCI), is ingeniously designed to detect polar and nonpolar metabolites simultaneously in single cells. The source is constructed by inserting a pulled glass capillary coaxially into a glass tube that acts as a dielectric barrier layer. Benefitting from the integrated advantages of nanoESI and APCI, its limit of detection is improved by one order of magnitude to 10 pg mL-1. After the operational parameter optimization, 254 metabolites detected in nanoESI-APCI are tentatively identified from a single cell, and 82 more than those in nanoESI. The developed nanoESI-APCI is successively applied to study the metabolic heterogeneity of human hepatocellular carcinoma tissue microenvironment united with laser capture microdissection (LCM), the discrimination of cancer cell types and subtypes, the metabolic perturbations to glucose starvation in MCF7 cells and the metabolic regulation of cancer stem cells. These results demonstrated that the nanoESI-APCI not only opens a new avenue for high-coverage and high-sensitivity metabolomics analysis of single cell, but also facilitates spatially resolved metabolomics study coupled with LCM.
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Affiliation(s)
- Tianrun Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Hang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Peng Dou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Yuanyuan Luo
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Siming Pu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Hua Mu
- The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116023, P. R. China
| | - Zhihao Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Science, Dalian Key Laboratory for Online Analytical Instrumentation, Dalian, Liaoning, 116023, P. R. China
| | - Disheng Feng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Xuesen Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Ting Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Guang Tan
- The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116023, P. R. China
| | - Chuang Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Science, Dalian Key Laboratory for Online Analytical Instrumentation, Dalian, Liaoning, 116023, P. R. China
| | - Haiyang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Science, Dalian Key Laboratory for Online Analytical Instrumentation, Dalian, Liaoning, 116023, P. R. China
| | - Xianzhe Shi
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Chunxiu Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
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8
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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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9
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Qi H, Duan S, Xu Y, Zhang H. Frontiers and future perspectives of neuroimmunology. FUNDAMENTAL RESEARCH 2024; 4:206-217. [PMID: 38933499 PMCID: PMC11197808 DOI: 10.1016/j.fmre.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 08/16/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Neuroimmunology is an interdisciplinary branch of biomedical science that emerges from the intersection of studies on the nervous system and the immune system. The complex interplay between the two systems has long been recognized. Research efforts directed at the underlying functional interface and associated pathophysiology, however, have garnered attention only in recent decades. In this narrative review, we highlight significant advances in research on neuroimmune interplay and modulation. A particular focus is on early- and middle-career neuroimmunologists in China and their achievements in frontier areas of "neuroimmune interface", "neuro-endocrine-immune network and modulation", "neuroimmune interactions in diseases", "meningeal lymphatic and glymphatic systems in health and disease", and "tools and methodologies in neuroimmunology research". Key scientific questions and future directions for potential breakthroughs in neuroimmunology research are proposed.
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Affiliation(s)
- Hai Qi
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shumin Duan
- Faculty of Medicine and Pharmaceutical Sciences, Zhejiang University, Hangzhou 310014, China
| | - Yanying Xu
- Department of Life Sciences, National Natural Science Foundation of China, Beijing 100085, China
| | - Hongliang Zhang
- Department of Life Sciences, National Natural Science Foundation of China, Beijing 100085, China
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10
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Deng J, Xie J, Wang C, Wu Y, Luan T, Yang Y. Inner-Wall Coated Nanopipette Microextraction for Quantitative Analysis of Per- and Polyfluoroalkyl Substances in Single Cells Using Mass Spectrometry. Anal Chem 2024; 96:1391-1396. [PMID: 38227719 DOI: 10.1021/acs.analchem.3c05141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Per- and polyfluoroalkyl substances (PFASs) are a series of organic pollutants with potential cytotoxicity and biotoxicity. Accurate and sensitive detection of trace PFASs in single cells can provide insights into investigating their cytotoxicity, carcinogenicity, and mutagenicity. Here we report the development of an inner-wall coated nanopipette microextraction coupled with induced nanoelectrospray ionization mass spectrometry (InESI-MS) method and its application for rapid, sensitive, and accurate analysis of trace PFASs in single cells. A specially designed inner-wall coated nanopipette was prepared for sampling of the cytoplasm from a single cell, and the trace PFASs in the cytoplasm were selectively enriched into the coating via reversed-phase adsorption, ion bonding adsorption, and π-π interaction mechanisms. After the extraction, the cytoplasm was removed, and the enriched PFASs were then desorbed into some organic solvent, applying an alternating current (AC) voltage to the inner-wall coated nanopipette for InESI-MS analysis. The inner-wall coated nanopipette showed an exhaustive extraction to the trace PFASs in one single cell, and thus, the mass of each target analyte in the cytoplasm can be calculated via an internal standard calibration curve method, avoiding the measurement of ultrasmall volume cytoplasm for one single cell. By using the inner-wall coated nanopipette microextraction coupled with InESI-MS method, trace PFASs accumulated in the LO2 cells with pollutant exposure were successfully detected, and the accumulative behaviors and heterogeneities of PFASs in single cells were explored.
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Affiliation(s)
- Jiewei Deng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
- Smart Medical Innovation Technology Center, Guangdong University of Technology, Guangzhou 510006, China
| | - Jialiang Xie
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Chao Wang
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - YueHua Wu
- Guangdong Women and Children Hospital, Guangzhou 511400, China
| | - Tiangang Luan
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
- School of Environmental and Chemical Engineering, Wuyi University, Jiangmen 529020, China
| | - Yunyun Yang
- Guangdong Provincial Engineering Research Center for Ambient Mass Spectrometry, Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou 510070, China
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11
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Cao J, Yao QJ, Wu J, Chen X, Huang L, Liu W, Qian K, Wan JJ, Zhou BO. Deciphering the metabolic heterogeneity of hematopoietic stem cells with single-cell resolution. Cell Metab 2024; 36:209-221.e6. [PMID: 38171334 DOI: 10.1016/j.cmet.2023.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/14/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
Metabolic status is crucial for stem cell functions; however, the metabolic heterogeneity of endogenous stem cells has never been directly assessed. Here, we develop a platform for high-throughput single-cell metabolomics (hi-scMet) of hematopoietic stem cells (HSCs). By combining flow cytometric isolation and nanoparticle-enhanced laser desorption/ionization mass spectrometry, we routinely detected >100 features from single cells. We mapped the single-cell metabolomes of all hematopoietic cell populations and HSC subpopulations with different division times, detecting 33 features whose levels exhibited trending changes during HSC proliferation. We found progressive activation of the oxidative pentose phosphate pathway (OxiPPP) from dormant to active HSCs. Genetic or pharmacological interference with OxiPPP increased reactive oxygen species level in HSCs, reducing HSC self-renewal upon oxidative stress. Together, our work uncovers the metabolic dynamics during HSC proliferation, reveals a role of OxiPPP for HSC activation, and illustrates the utility of hi-scMet in dissecting metabolic heterogeneity of immunophenotypically defined cell populations.
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Affiliation(s)
- Jing Cao
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai 200030, PRC; Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC; Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC
| | - Qi Jason Yao
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiao Wu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai 200030, PRC; Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC; Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC
| | - Xiaonan Chen
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Lin Huang
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai 200030, PRC; Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC; Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC
| | - Wanshan Liu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai 200030, PRC; Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC; Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC
| | - Kun Qian
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Institute of Medical Robotics and Shanghai Academy of Experimental Medicine, Shanghai Jiao Tong University, Shanghai 200030, PRC; Shanghai Key Laboratory of Gynecologic Oncology, Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC; Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, PRC.
| | - Jing-Jing Wan
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China.
| | - Bo O Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China; State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences, Tianjin 300020, China.
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12
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Zhang D, Qiao L. Microfluidics Coupled Mass Spectrometry for Single Cell Multi-Omics. SMALL METHODS 2024; 8:e2301179. [PMID: 37840412 DOI: 10.1002/smtd.202301179] [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: 09/01/2023] [Revised: 10/02/2023] [Indexed: 10/17/2023]
Abstract
Population-level analysis masks significant heterogeneity between individual cells, making it difficult to accurately reflect the true intricacies of life activities. Microfluidics is a technique that can manipulate individual cells effectively and is commonly coupled with a variety of analytical methods for single-cell analysis. Single-cell omics provides abundant molecular information at the single-cell level, fundamentally revealing differences in cell types and biological states among cell individuals, leading to a deeper understanding of cellular phenotypes and life activities. Herein, this work summarizes the microfluidic chips designed for single-cell isolation, manipulation, trapping, screening, and sorting, including droplet microfluidic chips, microwell arrays, hydrodynamic microfluidic chips, and microchips with microvalves. This work further reviews the studies on single-cell proteomics, metabolomics, lipidomics, and multi-omics based on microfluidics and mass spectrometry. Finally, the challenges and future application of single-cell multi-omics are discussed.
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Affiliation(s)
- Dongxue Zhang
- Department of Chemistry, Institutes of Biomedical Sciences, and Minhang Hospital, Fudan University, Shanghai, 20000, China
| | - Liang Qiao
- Department of Chemistry, Institutes of Biomedical Sciences, and Minhang Hospital, Fudan University, Shanghai, 20000, China
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13
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Li C, Cheng K, Zhao Q, Jin L, Wang X, Liufu T, Zhao X, Li X, Wang X, Lyu J, Huang D, Li P, Chen XW, Wang Z, Hu X, Quan L, Chen Z. Diazo-carboxyl Click Derivatization Enables Sensitive Analysis of Carboxylic Acid Metabolites in Biosamples. Anal Chem 2023; 95:16976-16986. [PMID: 37943785 DOI: 10.1021/acs.analchem.3c03277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Carboxylic acids are central metabolites in bioenergetics, signal transduction, and post-translation protein regulation. However, the quantitative analysis of carboxylic acids as an indispensable part of metabolomics is prohibitively challenging, particularly in trace amounts of biosamples. Here we report a diazo-carboxyl/hydroxylamine-ketone double click derivatization method for the sensitive analysis of hydrophilic, low-molecular-weight carboxylic acids. In general, our method renders a 5- to 2000-fold higher response in mass spectrometry along with improved chromatographic separation. With this method, we presented the near-single-cell analysis of carboxylic acid metabolites in 10 mouse egg cells before and after fertilization. Malate, fumarate, and β-hydroxybutyrate were found to decrease after fertilization. We also monitored the isotope labeling kinetics of carboxylic acids inside adherent cells cultured in 96-well plates during drug treatment. Finally, we applied this method to plasma or serum samples (5 μL) collected from mice and humans under pathological and physiological conditions. The double click derivatization method paves a way toward single-cell metabolomics and bedside diagnostics.
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Affiliation(s)
- Cong Li
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Kunlun Cheng
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Qijin Zhao
- 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
| | - Li Jin
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Xuelian Wang
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Tongling Liufu
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Xutong Zhao
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Xiaochuan Li
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Xiao Wang
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Jia Lyu
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Dong Huang
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Pingping Li
- 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
| | - Xiao-Wei Chen
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
- Beijing Key Laboratory of Neurovascular Disease Discovery, Beijing 100034, China
| | - Xinli Hu
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Li Quan
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
| | - Zhixing Chen
- College of Future Technology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- National Biomedical Imaging Center, Beijing 100871, China
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14
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Wang Z, Zhu H, Xiong W. Advances in mass spectrometry-based multi-scale metabolomic methodologies and their applications in biological and clinical investigations. Sci Bull (Beijing) 2023; 68:2268-2284. [PMID: 37666722 DOI: 10.1016/j.scib.2023.08.047] [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: 06/15/2023] [Revised: 07/25/2023] [Accepted: 08/22/2023] [Indexed: 09/06/2023]
Abstract
Metabolomics is a nascent field of inquiry that emerged in the late 20th century. It encompasses the comprehensive profiling of metabolites across a spectrum of organisms, ranging from bacteria and cells to tissues. The rapid evolution of analytical methods and data analysis has greatly accelerated progress in this dynamic discipline over recent decades. Sophisticated techniques such as liquid chromatograph mass spectrometry (MS), gas chromatograph MS, capillary electrophoresis MS, and nuclear magnetic resonance serve as the cornerstone of metabolomic analysis. Building upon these methods, a plethora of modifications and combinations have emerged to propel the advancement of metabolomics. Despite this progress, scrutinizing metabolism at the single-cell or single-organelle level remains an arduous task over the decades. Some of the most thrilling advancements, such as single-cell and single-organelle metabolic profiling techniques, offer profound insights into the intricate mechanisms within cells and organelles. This allows for a comprehensive study of metabolic heterogeneity and its pivotal role in multiple biological processes. The progress made in MS imaging has enabled high-resolution in situ metabolic profiling of tissue sections and even individual cells. Spatial reconstruction techniques enable the direct representation of metabolic distribution and alteration in three-dimensional space. The application of novel metabolomic techniques has led to significant breakthroughs in biological and clinical studies, including the discovery of novel metabolic pathways, determination of cell fate in differentiation, anti-aging intervention through modulating metabolism, metabolomics-based clinicopathologic analysis, and surgical decision-making based on on-site intraoperative metabolic analysis. This review presents a comprehensive overview of both conventional and innovative metabolomic techniques, highlighting their applications in groundbreaking biological and clinical studies.
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Affiliation(s)
- Ziyi Wang
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Hongying Zhu
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China; Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; CAS Key Laboratory of Brain Function and Disease, Hefei 230026, China; Anhui Province Key Laboratory of Biomedical Aging Research, Hefei 230026, China.
| | - Wei Xiong
- Department of Neurology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China; Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; CAS Key Laboratory of Brain Function and Disease, Hefei 230026, China; Anhui Province Key Laboratory of Biomedical Aging Research, Hefei 230026, China.
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15
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Pandian K, Matsui M, Hankemeier T, Ali A, Okubo-Kurihara E. Advances in single-cell metabolomics to unravel cellular heterogeneity in plant biology. PLANT PHYSIOLOGY 2023; 193:949-965. [PMID: 37338502 PMCID: PMC10517197 DOI: 10.1093/plphys/kiad357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/03/2023] [Accepted: 05/17/2023] [Indexed: 06/21/2023]
Abstract
Single-cell metabolomics is a powerful tool that can reveal cellular heterogeneity and can elucidate the mechanisms of biological phenomena in detail. It is a promising approach in studying plants, especially when cellular heterogeneity has an impact on different biological processes. In addition, metabolomics, which can be regarded as a detailed phenotypic analysis, is expected to answer previously unrequited questions which will lead to expansion of crop production, increased understanding of resistance to diseases, and in other applications as well. In this review, we will introduce the flow of sample acquisition and single-cell techniques to facilitate the adoption of single-cell metabolomics. Furthermore, the applications of single-cell metabolomics will be summarized and reviewed.
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Affiliation(s)
- Kanchana Pandian
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einstein Road 55, 2333 CC Leiden, The Netherlands
| | - Minami Matsui
- RIKEN, Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einstein Road 55, 2333 CC Leiden, The Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einstein Road 55, 2333 CC Leiden, The Netherlands
| | - Emiko Okubo-Kurihara
- RIKEN, Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
- College of Science, Rikkyo University, Tokyo 171-8501, Japan
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16
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Deng J, Zeng X, He C, Zhong D, Wu Y, Liu N, Luan T, Yang Y. Exploring the Accumulation Behavior and Heterogeneity of Perfluorooctanesulfonic Acid in Zebrafish Primary Organ Cells by Single-Cell Mass Cytometry. Anal Chem 2023; 95:13750-13755. [PMID: 37669419 DOI: 10.1021/acs.analchem.3c02398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Perfluorooctanesulfonic acid (PFOS) is a commonly found environmental pollutant with potential toxicity and health risks to biosystems and ecosystems. Study of the accumulation behavior and heterogeneity of PFOS in biological primary organ cells provides us significant insights to explore its cytotoxicity, carcinogenicity, and mutagenicity. Here a single-cell mass cytometry system was established for the high-throughput analysis of trace PFOS and the exploration of its accumulation behavior and heterogeneity in zebrafish primary organ cells. The single-cell mass cytometry system applied a ∼25 μm constant-inner-diameter capillary as the single-cell generation and transportation channel with an etched tip-end of 40 μm as the nanoelectrospray emitter for mass spectrometric analysis. The single-cell mass cytometry system showed satisfactory semiquantitative performance and sensitivity for analysis of PFOS in single cells, with a high detection throughput of ∼35 cells/min. Subsequently, the liver, intestine, heart, and brain from PFOS-exposed zebrafish (100 pg/μL, 28 days) were dissociated and prepared as cell suspensions, and the cell suspensions were introduced into the single-cell mass cytometry system for high-throughput analysis of PFOS in individual primary organ cells. Significant cellular accumulation heterogeneities were observed, with the highest content in liver cells, followed by intestine cells, then heart cells, and the lowest in brain cells. In addition, the dynamics of PFOS in the zebrafish liver, intestine, heart, and brain cells showed typical violin plot distributions and were well-described using a gamma (γ) function.
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Affiliation(s)
- Jiewei Deng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
- Smart Medical Innovation Technology Center, Guangdong University of Technology, Guangzhou 510006, China
- Guangdong Laboratory of Chemistry and Fine Chemical Engineering Jieyang Center, Jieyang 515200, China
| | - Xiliu Zeng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Cai He
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
- Guangdong Provincial Engineering Research Center for Ambient Mass Spectrometry, Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences, (China National Analytical Center, Guangzhou), 100 Xianlie Middle Road, Guangzhou 510070, China
| | - Dahao Zhong
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Yuehua Wu
- Guangdong Women and Children Hospital, Guangzhou 511400, China
| | - Ning Liu
- Guangdong Provincial Engineering Research Center for Ambient Mass Spectrometry, Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences, (China National Analytical Center, Guangzhou), 100 Xianlie Middle Road, Guangzhou 510070, China
| | - Tiangang Luan
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
- Guangdong Laboratory of Chemistry and Fine Chemical Engineering Jieyang Center, Jieyang 515200, China
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yunyun Yang
- Guangdong Provincial Engineering Research Center for Ambient Mass Spectrometry, Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences, (China National Analytical Center, Guangzhou), 100 Xianlie Middle Road, Guangzhou 510070, China
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17
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Meng Y, Hang W, Zare RN. Microlensed fiber allows subcellular imaging by laser-based mass spectrometry. Nat Protoc 2023; 18:2558-2578. [PMID: 37479826 DOI: 10.1038/s41596-023-00848-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 05/02/2023] [Indexed: 07/23/2023]
Abstract
Mass spectrometry imaging (MSI) enables the chemical mapping of molecules and elements in a label-free, high-throughput manner. Because this approach can be accomplished rapidly, it also enables chemical changes to be monitored. Here, we describe a protocol for MSI with subcellular spatial resolution. This is achieved by using a microlensed fiber, which is made by grinding an optical fiber. It is a universal and economic technique that can be adapted to most laser-based mass spectrometry methods. In this protocol, the output of laser radiation from the microlensed fiber causes laser ablation of the sample, and the resulting plume is mass spectrometrically analyzed. The microlensed fiber can be used with matrix-assisted laser desorption ionization, laser desorption ionization, laser ablation electrospray desorption ionization and laser ablation inductively coupled plasma, in each case to achieve submicroscale imaging of single cells and biological tissues. This report provides a detailed introduction of the microlensed fiber design and working principles, sample preparation, microlensed fiber ion source setup and multiple MSI platforms with different kinds of mass spectrometers. A researcher with a little background (such as a trained graduate student) is able to complete all the steps for the experimental setup in ~2 h, including fiber test, laser coupling and ion source modification. The imaging time spent mainly depends on the size of the imaging area. It is suggested that most existing laser-based MSI platforms, especially atmospheric pressure applications, can achieve breakthroughs in spatial resolution by introducing a microlensed fiber module.
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Affiliation(s)
- Yifan Meng
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Wei Hang
- Ministry of Education (MOE) Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
| | - Richard N Zare
- Department of Chemistry, Stanford University, Stanford, CA, USA.
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18
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Xia D, Jin R, Pan R, Chen HY, Jiang D. In Situ Spatial Analysis of Metabolic Heterogeneity in Single Living Tumor Spheroids Using Nanocapillary-Based Electrospray Ionization Mass Spectroscopy. Anal Chem 2023. [PMID: 37358923 DOI: 10.1021/acs.analchem.3c00479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
Spatial metabolomic analysis of individual tumor spheroids can help investigate metabolic rearrangements in different cellular regions of a spheroid. In this work, a nanocapillary-based electrospray ionization mass spectroscopy (ESI-MS) method is established that could realize the spatial sampling of cellular components in different regions of a single living tumor spheroid and the subsequent MS analysis for a metabolic study. During the penetration of the nanocapillary into the spheroid for sampling, this "wound surface" at the outer layer of the spheroid takes only 0.1% of the whole area that maximally maintains the cellular activity inside the spheroid for the metabolic analysis. Using the ESI-MS analysis, different metabolic activities in the inner and outer (upper and lower) layers of a single spheroid are revealed, giving a full investigation of the metabolic heterogeneity inside one living tumor spheroid for the first time. In addition, the metabolic activities between the outer layer of the spheroid and two-dimensional (2D)-cultured cells show obvious differences, which suggests more frequent cell-cell and cell-extracellular environment interactions during the culture of the spheroid. This observation not only establishes a powerful tool for the in situ spatial analysis of the metabolic heterogeneity in single living tumor spheroids but also provides molecular information to elucidate the metabolic heterogeneity in this three-dimensional (3D)-cultured cell model.
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Affiliation(s)
- Dandan Xia
- The State Key Lab of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210093, P. R. China
| | - Rong Jin
- The State Key Lab of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210093, P. R. China
| | - Rongrong Pan
- The State Key Lab of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210093, P. R. China
| | - Hong-Yuan Chen
- The State Key Lab of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210093, P. R. China
| | - Dechen Jiang
- The State Key Lab of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210093, P. R. China
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19
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Liu R, Li J, Lan Y, Nguyen TD, Chen YA, Yang Z. Quantifying Cell Heterogeneity and Subpopulations Using Single Cell Metabolomics. Anal Chem 2023; 95:7127-7133. [PMID: 37115510 DOI: 10.1021/acs.analchem.2c05245] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Mass spectrometry (MS) has become an indispensable tool for metabolomics studies. However, due to the lack of applicable experimental platforms, suitable algorithm, software, and quantitative analyses of cell heterogeneity and subpopulations, investigating global metabolomics profiling at the single cell level remains challenging. We combined the Single-probe single cell MS (SCMS) experimental technique with a bioinformatics software package, SinCHet-MS (Single Cell Heterogeneity for Mass Spectrometry), to characterize changes of tumor heterogeneity, quantify cell subpopulations, and prioritize the metabolite biomarkers of each subpopulation. As proof of principle studies, two melanoma cancer cell lines, the primary (WM115; with a lower drug resistance) and the metastatic (WM266-4; with a higher drug resistance), were used as models. Our results indicate that after the treatment of the anticancer drug vemurafenib, a new subpopulation emerged in WM115 cells, while the proportion of the existing subpopulations was changed in the WM266-4 cells. In addition, metabolites for each subpopulation can be prioritized. Combining the SCMS experimental technique with a bioinformatics tool, our label-free approach can be applied to quantitatively study cell heterogeneity, prioritize markers for further investigation, and improve the understanding of cell metabolism in human diseases and response to therapy.
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Affiliation(s)
- Renmeng Liu
- Chemistry and Biochemistry Department, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Jiannong Li
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida 33647, United States
| | - Yunpeng Lan
- Chemistry and Biochemistry Department, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Tra D Nguyen
- Chemistry and Biochemistry Department, University of Oklahoma, Norman, Oklahoma 73072, United States
| | - Y Ann Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida 33647, United States
| | - Zhibo Yang
- Chemistry and Biochemistry Department, University of Oklahoma, Norman, Oklahoma 73072, United States
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20
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Zheng X, Hou Z, Qian Y, Zhang Y, Cui Q, Wang X, Shen Y, Liu Z, Zhou Y, Fu B, Sun R, Tian Z, Huang G, Wei H. Tumors evade immune cytotoxicity by altering the surface topology of NK cells. Nat Immunol 2023; 24:802-813. [PMID: 36959292 DOI: 10.1038/s41590-023-01462-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 02/14/2023] [Indexed: 03/25/2023]
Abstract
The highly variable response rates to immunotherapies underscore our limited knowledge about how tumors can manipulate immune cells. Here the membrane topology of natural killer (NK) cells from patients with liver cancer showed that intratumoral NK cells have fewer membrane protrusions compared with liver NK cells outside tumors and with peripheral NK cells. Dysregulation of these protrusions prevented intratumoral NK cells from recognizing tumor cells, from forming lytic immunological synapses and from killing tumor cells. The membranes of intratumoral NK cells have altered sphingomyelin (SM) content and dysregulated serine metabolism in tumors contributed to the decrease in SM levels of intratumoral NK cells. Inhibition of SM biosynthesis in peripheral NK cells phenocopied the disrupted membrane topology and cytotoxicity of the intratumoral NK cells. Targeting sphingomyelinase confers powerful antitumor efficacy, both as a monotherapy and as a combination therapy with checkpoint blockade.
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Affiliation(s)
- Xiaohu Zheng
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Institute of Immunology, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China.
- The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China.
| | - Zhuanghao Hou
- The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China
- School of Chemistry and Materials Science and National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China
| | - Yeben Qian
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yongwei Zhang
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Quanwei Cui
- Department of General Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xuben Wang
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Immunology, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Yiqing Shen
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Immunology, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Zhenbang Liu
- Core Facility Center for Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yonggang Zhou
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Immunology, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Binqing Fu
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Immunology, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Rui Sun
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Immunology, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China
| | - Zhigang Tian
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Institute of Immunology, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China.
- Research Unit Of NK Cells, Chinese Academy Of Medical Sciences, Hefei, China.
| | - Guangming Huang
- The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China.
- School of Chemistry and Materials Science and National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, China.
| | - Haiming Wei
- Hefei National Research Center for Physical Sciences at the Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Institute of Immunology, Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, China.
- The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China.
- Research Unit Of NK Cells, Chinese Academy Of Medical Sciences, Hefei, China.
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21
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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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22
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Pan X, Yao H, Zhang S, Zhang X. Recent progress in mass spectrometry for single-cell metabolomics. Curr Opin Chem Biol 2022; 71:102226. [PMID: 36347197 DOI: 10.1016/j.cbpa.2022.102226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/05/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022]
Abstract
Metabolites are the end products of cellular vital activities and can reflect the state of cellular to a certain extent. Rapid change of metabolites and the low abundance of signature metabolites cause difficulties in single-cell detection, which is a great challenge in single-cell metabolomics analysis. Mass spectrometry (MS) is a powerful tool that uniquely suited to detect intracellular small-molecule metabolites and has shown good application in single-cell metabolite analysis. In this mini-review, we describe three types of emerging technologies for MS-based single-cell metabolic analysis in recent years, including nano-ESI-MS based single-cell metabolomics analysis, high-throughput analysis via flow cytometry, and cellular metabolic imaging analysis. These techniques provide a large amount of single-cell metabolic data, allowing the potential of MS in single-cell metabolic analysis is gradually being explored and is of great importance in disease and life science research.
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Affiliation(s)
- Xingyu Pan
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Huan Yao
- Division of Chemistry and Analytical Science; National Institute of Metrology, Beijing, China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing, China.
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23
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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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24
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Recent advances in microfluidic single-cell analysis and its applications in drug development. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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25
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Cui H, Wu Q, Zhao Z, Wang Y, Lu H. Selective Capture-Based Single-Cell Mass Spectrometry for Enhancing Sphingolipid Profiling of Neurons with Differentiation of Cell Body from Synapse. Anal Chem 2022; 94:15729-15737. [DOI: 10.1021/acs.analchem.2c03336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hao Cui
- College of Chemistry and Chemical Engineering, Central South University, Hunan, Changsha 410083, P.R. China
| | - Qian Wu
- College of Chemistry and Chemical Engineering, Central South University, Hunan, Changsha 410083, P.R. China
| | - Zhihao Zhao
- College of Chemistry and Chemical Engineering, Central South University, Hunan, Changsha 410083, P.R. China
| | - Yang Wang
- Laboratory of Ethnopharmacology, Institute of Integrated Traditional Chinese and Western Medicine, Xiangya Hospital, Central South University, Hunan, Changsha 410008, P.R. China
| | - Hongmei Lu
- College of Chemistry and Chemical Engineering, Central South University, Hunan, Changsha 410083, P.R. China
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26
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Zhong Q, Huang X, Zhang R, Zhang K, Liu B. Optical Sensing Strategies for Probing Single-Cell Secretion. ACS Sens 2022; 7:1779-1790. [PMID: 35709496 DOI: 10.1021/acssensors.2c00474] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Measuring cell secretion events is crucial to understand the fundamental cell biology that underlies cell-cell communication, migration, proliferation, and differentiation. Although strategies targeting cell populations have provided significant information about live cell secretion, they yield ensemble profiles that obscure intrinsic cell-to-cell variations. Innovation in single-cell analysis has made breakthroughs allowing accurate sensing of a wide variety of secretions and their release dynamics with high spatiotemporal resolution. This perspective focuses on the power of single-cell protocols to revolutionize cell-secretion analysis by allowing real-time and real-space measurements on single live cell resolution. We begin by discussing recent progress on single-cell bioanalytical techniques, specifically optical sensing strategies such as fluorescence-, surface plasmon resonance-, and surface-enhanced Raman scattering-based strategies, capable of in situ real-time monitoring of single-cell released ions, metabolites, proteins, and vesicles. Single-cell sensing platforms which allow for high-throughput high-resolution analysis with enough accuracy are highlighted. Furthermore, we discuss remaining challenges that should be addressed to get a more comprehensive understanding of secretion biology. Finally, future opportunities and potential breakthroughs in secretome analysis that will arise as a result of further development of single-cell sensing approaches are discussed.
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Affiliation(s)
- Qingmei Zhong
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Xuedong Huang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Rongrong Zhang
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
| | - Kun Zhang
- Shanghai Institute for Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Baohong Liu
- Department of Chemistry, Shanghai Stomatological Hospital, State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, China
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27
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Feng D, Li H, Xu T, Zheng F, Hu C, Shi X, Xu G. High-throughput single cell metabolomics and cellular heterogeneity exploration by inertial microfluidics coupled with pulsed electric field-induced electrospray ionization-high resolution mass spectrometry. Anal Chim Acta 2022; 1221:340116. [DOI: 10.1016/j.aca.2022.340116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/15/2022]
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28
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Abouleila Y, Ali A, Masuda K, Mashaghi A, Shimizu Y. Capillary microsampling-based single-cell metabolomics by mass spectrometry and its applications in medicine and drug discovery. Cancer Biomark 2022; 33:437-447. [DOI: 10.3233/cbm-210184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Characterization of cellular metabolic states is a technical challenge in biomedicine. Cellular heterogeneity caused by inherent diversity in expression of metabolic enzymes or due to sensitivity of metabolic reactions to perturbations, necessitates single cell analysis of metabolism. Heterogeneity is typically seen in cancer and thus, single-cell metabolomics is expectedly useful in studying cancer progression, metastasis, and variations in cancer drug response. However, low sample volumes and analyte concentrations limit detection of critically important metabolites. Capillary microsampling-based mass spectrometry approaches are emerging as a promising solution for achieving single-cell omics. Herein, we focus on the recent advances in capillary microsampling-based mass spectrometry techniques for single-cell metabolomics. We discuss recent technical developments and applications to cancer medicine and drug discovery.
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Affiliation(s)
- Yasmine Abouleila
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
- Research Center, Misr International University, Cairo, Egypt
| | - Ahmed Ali
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
- Research Center, Misr International University, Cairo, Egypt
| | - Keiko Masuda
- RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Alireza Mashaghi
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
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29
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Chen X, Sun M, Yang Z. Single cell mass spectrometry analysis of drug-resistant cancer cells: Metabolomics studies of synergetic effect of combinational treatment. Anal Chim Acta 2022; 1201:339621. [PMID: 35300794 PMCID: PMC8933618 DOI: 10.1016/j.aca.2022.339621] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/30/2022] [Accepted: 02/14/2022] [Indexed: 12/24/2022]
Abstract
Irinotecan (IRI), a topoisomerase I inhibitor blocking DNA synthesis, is a widely used chemotherapy drug for metastatic colorectal cancer. Despite being an effective chemotherapy drug, its clinical effectiveness is limited by both intrinsic and acquired drug resistance. Previous studies indicate IRI induces cancer stemness in irinotecan-resistant (IRI-resistant) cells. Metformin, an oral antidiabetic drug, was recently reported for anticancer effects, likely due to its selective killing of cancer stem cells (CSCs). Given IRI-resistant cells exhibiting high cancer stemness, we hypothesize metformin can sensitize IRI-resistant cells and rescue the therapeutic effect. In this work, we utilized the Single-probe mass spectrometry technique to analyze live IRI-resistant cells under different treatment conditions. We discovered that metformin treatment was associated with the downregulation of lipids and fatty acids, potentially through the inhibition of fatty acid synthase (FASN). Importantly, certain species can be only detected from cells in their living status. The level of synergistic effect of metformin and IRI in their co-treatment of IRI-resistant cells was evaluated using Chou-Talalay combinational index. Using enzymatic activity assay, we determined that the co-treatment exhibit the highest FASN inhibition compared with the mono-treatment of IRI or metformin. To our knowledge, this is the first single-cell MS metabolomics study demonstrating metformin-IRI synergistic effect overcoming drug resistance in IRI-resistant cells.
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30
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Alarcon-Barrera JC, Kostidis S, Ondo-Mendez A, Giera M. Recent advances in metabolomics analysis for early drug development. Drug Discov Today 2022; 27:1763-1773. [PMID: 35218927 DOI: 10.1016/j.drudis.2022.02.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/25/2022] [Accepted: 02/21/2022] [Indexed: 12/25/2022]
Abstract
The pharmaceutical industry adapted proteomics and other 'omics technologies for drug research early following their initial introduction. Although metabolomics lacked behind in this development, it has now become an accepted and widely applied approach in early drug development. Over the past few decades, metabolomics has evolved from a pure exploratory tool to a more mature and quantitative biochemical technology. Several metabolomics-based platforms are now applied during the early phases of drug discovery. Metabolomics analysis assists in the definition of the physiological response and target engagement (TE) markers as well as elucidation of the mode of action (MoA) of drug candidates under investigation. In this review, we highlight recent examples and novel developments of metabolomics analyses applied during early drug development.
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Affiliation(s)
- Juan Carlos Alarcon-Barrera
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, the Netherlands; Clinical Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia
| | - Sarantos Kostidis
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Alejandro Ondo-Mendez
- Clinical Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, the Netherlands.
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31
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Choi SB, Polter AM, Nemes P. Patch-Clamp Proteomics of Single Neurons in Tissue Using Electrophysiology and Subcellular Capillary Electrophoresis Mass Spectrometry. Anal Chem 2021; 94:1637-1644. [PMID: 34964611 DOI: 10.1021/acs.analchem.1c03826] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding of the relationship between cellular function and molecular composition holds a key to next-generation therapeutics but requires measurement of all types of molecules in cells. Developments in sequencing enabled semiroutine measurement of single-cell genomes and transcriptomes, but analytical tools are scarce for detecting diverse proteins in tissue-embedded cells. To bridge this gap for neuroscience research, we report the integration of patch-clamp electrophysiology with subcellular shot-gun proteomics by high-resolution mass spectrometry (HRMS). Recording of electrical activity permitted identification of dopaminergic neurons in the substantia nigra pars compacta. Ca. 20-50% of the neuronal soma content, containing an estimated 100 pg of total protein, was aspirated into the patch pipette filled with ammonium bicarbonate. About 1 pg of somal protein, or ∼0.25% of the total cellular proteome, was analyzed on a custom-built capillary electrophoresis (CE) electrospray ionization platform using orbitrap HRMS for detection. A series of experiments were conducted to systematically enhance detection sensitivity through refinements in sample processing and detection, allowing us to quantify ∼275 different proteins from somal aspirate-equivalent protein digests from cultured neurons. From single neurons, patch-clamp proteomics of the soma quantified 91, 80, and 95 different proteins from three different dopaminergic neurons or 157 proteins in total. Quantification revealed detectable proteomic differences between the somal protein samples. Analysis of canonical knowledge predicted rich interaction networks between the observed proteins. The integration of patch-clamp electrophysiology with subcellular CE-HRMS proteomics expands the analytical toolbox of neuroscience.
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Affiliation(s)
- Sam B Choi
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Abigail M Polter
- Department of Pharmacology & Physiology, The George Washington University School of Medicine and Health Sciences, Washington, D.C. 20037, United States
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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32
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Zhu G, Shao Y, Liu Y, Pei T, Li L, Zhang D, Guo G, Wang X. Single-cell metabolite analysis by electrospray ionization mass spectrometry. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116351] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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33
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Gao Y, Li Y, Zhan B, He Q, Zhu H, Chen W, Yin Q, Feng H, Pan Y. Ambient electric arc ionization for versatile sample analysis using mass spectrometry. Analyst 2021; 146:5682-5690. [PMID: 34397059 DOI: 10.1039/d1an00872b] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel, convenient ambient electric arc ionization (AEAI) device was developed as a mass spectrometry ion source for versatile sample analysis. AEAI could be considered as a soft ionization technique in which the protonated ion ([M + H]+) is the main ion species with little or no in-source fragmentation for most analytes. Coupled with a high-resolution Orbitrap mass spectrometer, AEAI could be applied to the analysis of a variety of organic compounds having a wide range of polarities, ranging from non-polar species such as polybenzenoid aromatic hydrocarbons (PAHs) to highly polar species such as amino acids. With its versatile capabilities in the mass spectrometric analysis of small molecules, AEAI has the potential to be an alternative to traditional ionization methods such as electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI), and electron impact (EI) ionization. The limitations of AEAI are also discussed.
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Affiliation(s)
- Yuanji Gao
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China. .,College of Chemistry and Materials Science, Sichuan Normal University, Chengdu 610068, Sichuan, P.R. China
| | - Yuan Li
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China.
| | - Binpeng Zhan
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China.
| | - Quan He
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China.
| | - Heping Zhu
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China.
| | - Weiwei Chen
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China.
| | - Qi Yin
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China.
| | - Hongru Feng
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China.
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou 310027, Zhejiang, P. R. China.
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34
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Pang H, Jiang Y, Li J, Wang Y, Nie M, Xiao N, Wang S, Song Z, Ji F, Chang Y, Zheng Y, Yao K, Yao L, Li S, Li P, Song L, Lan X, Xu Z, Hu Z. Aberrant NAD + metabolism underlies Zika virus-induced microcephaly. Nat Metab 2021; 3:1109-1124. [PMID: 34385701 DOI: 10.1038/s42255-021-00437-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 07/07/2021] [Indexed: 12/18/2022]
Abstract
Zika virus (ZIKV) infection during pregnancy can cause microcephaly in newborns, yet the underlying mechanisms remain largely unexplored. Here, we reveal extensive and large-scale metabolic reprogramming events in ZIKV-infected mouse brains by performing a multi-omics study comprising transcriptomics, proteomics, phosphoproteomics and metabolomics approaches. Our proteomics and metabolomics analyses uncover dramatic alteration of nicotinamide adenine dinucleotide (NAD+)-related metabolic pathways, including oxidative phosphorylation, TCA cycle and tryptophan metabolism. Phosphoproteomics analysis indicates that MAPK and cyclic GMP-protein kinase G signaling may be associated with ZIKV-induced microcephaly. Notably, we demonstrate the utility of our rich multi-omics datasets with follow-up in vivo experiments, which confirm that boosting NAD+ by NAD+ or nicotinamide riboside supplementation alleviates cell death and increases cortex thickness in ZIKV-infected mouse brains. Nicotinamide riboside supplementation increases the brain and body weight as well as improves the survival in ZIKV-infected mice. Our study provides a comprehensive resource of biological data to support future investigations of ZIKV-induced microcephaly and demonstrates that metabolic alterations can be potentially exploited for developing therapeutic strategies.
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Affiliation(s)
- Huanhuan Pang
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Yisheng Jiang
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Li
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Yushen Wang
- School of Life Sciences, Tsinghua University, Beijing, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (the PHOENIX Center), Beijing, China
| | - Meng Nie
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Nan Xiao
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Shuo Wang
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhihong Song
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Fansen Ji
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Yafei Chang
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zheng
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Ke Yao
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - LiAng Yao
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Shao Li
- Institute of TCM-X, MOE Key Laboratory of Bioinformatics / Bioinformatics Division, BNRIST, Department of Automation, Tsinghua University, Beijing, China
| | - Peng Li
- School of Life Sciences, Tsinghua University, Beijing, China
- Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
- Shanghai Qi Zhi Institute, Shanghai, China
| | - Lei Song
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (the PHOENIX Center), Beijing, China.
| | - Xun Lan
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.
| | - Zhiheng Xu
- State Key Laboratory of Molecular Developmental Biology, CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Parkinson's Disease Center, Beijing Institute for Brain Disorders, Beijing, China.
| | - Zeping Hu
- School of Pharmaceutical Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.
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Yao H, Zhao H, Pan X, Zhao X, Feng J, Yang C, Zhang S, Zhang X. Discriminating Leukemia Cellular Heterogeneity and Screening Metabolite Biomarker Candidates using Label-Free Mass Cytometry. Anal Chem 2021; 93:10282-10291. [PMID: 34259005 DOI: 10.1021/acs.analchem.1c01746] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Discriminating various leukocyte subsets with specific functions is critical due to their important roles in the development of many diseases. Here, we proposed a general strategy to unravel leukocytes heterogeneity and screen differentiated metabolites as biomarker candidates for leukocyte subtypes using the label-free mass cytometry (CyESI-MS) combined with a homemade data processing workflow. Taking leukemia cells as an example, metabolic fingerprints of single leukemia cells were obtained from 472 HL-60, 416 THP-1, 313 U937, 356 Jurkat, and 366 Ramos cells, with throughput up to 40 cells/min. Five leukemia subtypes were clearly distinguished by unsupervised learning t-SNE analysis of the single-cell metabolic fingerprints. Cell discrimination in the mixed leukemia cell samples was also realized by supervised learning of the single-cell metabolic fingerprints with high recovery and good repetition (98.31 ± 0.24%, -102.35 ± 4.82%). Statistical analysis and metabolite assignment were carried out to screen characteristic metabolites for discrimination and 36 metabolites with significant differences were annotated. Then, differentiated metabolites for pairwise discrimination of five leukemia subtypes were further selected as biomarker candidates. Furthermore, discriminating cultured leukemia cells from human normal leukocytes, separated from fresh human peripheral blood, was performed based on single-cell metabolic fingerprints as well as the proposed biomarker candidates, unveiling the potential of this strategy in clinical research. This work makes efforts to realize high-throughput single-leukocyte metabolic analysis and metabolite-based discrimination of leukocytes. It is expected to be a powerful means for the clinical molecular diagnosis of hematological diseases.
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Affiliation(s)
- Huan Yao
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Hansen Zhao
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xingyu Pan
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xu Zhao
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Jiaxin Feng
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Chengdui Yang
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
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36
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Metabolomic profiling of single enlarged lysosomes. Nat Methods 2021; 18:788-798. [PMID: 34127857 DOI: 10.1038/s41592-021-01182-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/10/2021] [Indexed: 02/05/2023]
Abstract
Lysosomes are critical for cellular metabolism and are heterogeneously involved in various cellular processes. The ability to measure lysosomal metabolic heterogeneity is essential for understanding their physiological roles. We therefore built a single-lysosome mass spectrometry (SLMS) platform integrating lysosomal patch-clamp recording and induced nano-electrospray ionization (nanoESI)/mass spectrometry (MS) that enables concurrent metabolic and electrophysiological profiling of individual enlarged lysosomes. The accuracy and reliability of this technique were validated by supporting previous findings, such as the transportability of lysosomal cationic amino acids transporters such as PQLC2 and the lysosomal trapping of lysosomotropic, hydrophobic weak base drugs such as lidocaine. We derived metabolites from single lysosomes in various cell types and classified lysosomes into five major subpopulations based on their chemical and biological divergence. Senescence and carcinoma altered metabolic profiles of lysosomes in a type-specific manner. Thus, SLMS can open more avenues for investigating heterogeneous lysosomal metabolic changes during physiological and pathological processes.
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Recent advances in single-cell analysis: Encapsulation materials, analysis methods and integrative platform for microfluidic technology. Talanta 2021; 234:122671. [PMID: 34364472 DOI: 10.1016/j.talanta.2021.122671] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/24/2021] [Accepted: 06/26/2021] [Indexed: 12/27/2022]
Abstract
Traditional cell biology researches on cell populations by their origin, tissue, morphology, and secretions. Because of the heterogeneity of cells, research at the single-cell level can obtain more accurate and comprehensive information that reflects the physiological state and process of the cell, increasing the significance of single-cell analysis. The application of single-cell analysis is faced with the problem of contaminated or damaged cells caused by cell sample transportation. Reversible encapsulation of a single cell can protect cells from the external environment and open the encapsulation shell to release cells, thus preserving cell integrity and improving extraction efficiency of analytes. Meanwhile, microfluidic single cell analysis (MSCA) exhibits integration, miniaturization, and high throughput, which can considerably improve the efficiency of single-cell analysis. The researches on single-cell reversible encapsulation materials, single-cell analysis methods, and the MSCA integration platform are analyzed and summarized in this review. The problems of single-cell viability, network of single-cell signal, and simultaneous detection of multiple biotoxins in food based on single-cell are proposed for future research.
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38
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Li Z, Cheng S, Lin Q, Cao W, Yang J, Zhang M, Shen A, Zhang W, Xia Y, Ma X, Ouyang Z. Single-cell lipidomics with high structural specificity by mass spectrometry. Nat Commun 2021; 12:2869. [PMID: 34001877 PMCID: PMC8129106 DOI: 10.1038/s41467-021-23161-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/15/2021] [Indexed: 12/12/2022] Open
Abstract
Single-cell analysis is critical to revealing cell-to-cell heterogeneity that would otherwise be lost in ensemble analysis. Detailed lipidome characterization for single cells is still far from mature, especially when considering the highly complex structural diversity of lipids and the limited sample amounts available from a single cell. We report the development of a general strategy enabling single-cell lipidomic analysis with high structural specificity. Cell fixation is applied to retain lipids in the cell during batch treatments prior to single-cell analysis. In addition to tandem mass spectrometry analysis revealing the class and fatty acyl-chain for lipids, batch photochemical derivatization and single-cell droplet treatment are performed to identify the C=C locations and sn-positions of lipids, respectively. Electro-migration combined with droplet-assisted electrospray ionization enables single-cell mass spectrometry analysis with easy operation but high efficiency in sample usage. Four subtypes of human breast cancer cells are correctly classified through quantitative analysis of lipid C=C location or sn-position isomers in ~160 cells. Most importantly, the single-cell deep lipidomics strategy successfully discriminates gefitinib-resistant cells from a population of wild-type human lung cancer cells (HCC827), highlighting its unique capability to promote precision medicine.
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Affiliation(s)
- Zishuai Li
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
| | - Simin Cheng
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
| | - Qiaohong Lin
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Wenbo Cao
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
| | - Jing Yang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
| | - Minmin Zhang
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Aijun Shen
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Wenpeng Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Xiaoxiao Ma
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China.
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China.
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
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39
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Liang L, Sun F, Wang H, Hu Z. Metabolomics, metabolic flux analysis and cancer pharmacology. Pharmacol Ther 2021; 224:107827. [PMID: 33662451 DOI: 10.1016/j.pharmthera.2021.107827] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023]
Abstract
Metabolic reprogramming is a hallmark of cancer and increasing evidence suggests that reprogrammed cell metabolism supports tumor initiation, progression, metastasis and drug resistance. Understanding metabolic dysregulation may provide therapeutic targets and facilitate drug research and development for cancer therapy. Metabolomics enables the high-throughput characterization of a large scale of small molecule metabolites in cells, tissues and biofluids, while metabolic flux analysis (MFA) tracks dynamic metabolic activities using stable isotope tracer methods. Recent advances in metabolomics and MFA technologies make them powerful tools for metabolic profiling and characterizing metabolic activities in health and disease, especially in cancer research. In this review, we introduce recent advances in metabolomics and MFA analytical technologies, and provide the first comprehensive summary of the most commonly used isotope tracing methods. In addition, we highlight how metabolomics and MFA are applied in cancer pharmacology studies particularly for discovering targetable metabolic vulnerabilities, understanding the mechanisms of drug action and drug resistance, exploring potential strategies with dietary intervention, identifying cancer biomarkers, as well as enabling precision treatment with pharmacometabolomics.
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Affiliation(s)
- Lingfan Liang
- School of Pharmaceutical Sciences; Tsinghua-Peking Joint Center for Life Sciences; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Fei Sun
- School of Pharmaceutical Sciences; Tsinghua-Peking Joint Center for Life Sciences; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| | - Hongbo Wang
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China.
| | - Zeping Hu
- School of Pharmaceutical Sciences; Tsinghua-Peking Joint Center for Life Sciences; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China.
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40
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Jin S, Cao Q, Yang F, Zhu H, Xu S, Chen Q, Wang Z, Lin Y, Cinar R, Pawlosky RJ, Zhang Y, Xiong W, Gao B, Koob GF, Lovinger DM, Zhang L. Brain ethanol metabolism by astrocytic ALDH2 drives the behavioural effects of ethanol intoxication. Nat Metab 2021; 3:337-351. [PMID: 33758417 PMCID: PMC8294184 DOI: 10.1038/s42255-021-00357-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 02/04/2021] [Indexed: 02/08/2023]
Abstract
Alcohol is among the most widely used psychoactive substances worldwide. Ethanol metabolites such as acetate, thought to be primarily the result of ethanol breakdown by hepatic aldehyde dehydrogenase 2 (ALDH2), contribute to alcohol's behavioural effects and alcoholism. Here, we show that ALDH2 is expressed in astrocytes in the mouse cerebellum and that ethanol metabolism by astrocytic ALDH2 mediates behavioural effects associated with ethanol intoxication. We show that ALDH2 is expressed in astrocytes in specific brain regions and that astrocytic, but not hepatocytic, ALDH2 is required to produce ethanol-derived acetate in the mouse cerebellum. Cerebellar astrocytic ALDH2 mediates low-dose ethanol-induced elevation of GABA levels, enhancement of tonic inhibition and impairment of balance and coordination skills. Thus, astrocytic ALDH2 controls the production, cellular and behavioural effects of alcohol metabolites in a brain-region-specific manner. Our data indicate that astrocytic ALDH2 is an important, but previously under-recognized, target in the brain to alter alcohol pharmacokinetics and potentially treat alcohol use disorder.
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Affiliation(s)
- Shiyun Jin
- Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
- Department of Anesthesiology, Second Affiliated Hospital, Anhui Medical University, Hefei, PR China
| | - Qi Cao
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Fanghan Yang
- Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Hongying Zhu
- Department of Neuroscience, University of Science and Technology of China, Hefei, PR China
| | - Su Xu
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland, School of Medicine, Baltimore, MD, USA
| | - Qi Chen
- Department of Neuroscience, University of Science and Technology of China, Hefei, PR China
| | - Ziyi Wang
- Department of Neuroscience, University of Science and Technology of China, Hefei, PR China
| | - Yuhong Lin
- Laboratory for Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Resat Cinar
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Robert J Pawlosky
- Laboratory for Metabolic Control, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Ye Zhang
- Department of Anesthesiology, Second Affiliated Hospital, Anhui Medical University, Hefei, PR China
| | - Wei Xiong
- Department of Neuroscience, University of Science and Technology of China, Hefei, PR China
| | - Bin Gao
- Laboratory for Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - George F Koob
- National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, USA
| | - David M Lovinger
- Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Li Zhang
- Laboratory for Integrative Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA.
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Chen Y, Yuan S, Liu Y, Huang G. Rapid desalting during electrospray ionization mass spectrometry for investigating protein-ligand interactions in the presence of concentrated salts. Anal Chim Acta 2021; 1141:120-126. [PMID: 33248644 DOI: 10.1016/j.aca.2020.10.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/10/2020] [Accepted: 10/19/2020] [Indexed: 11/18/2022]
Abstract
Investigation of protein-ligand interactions in physiological conditions is crucial for better understanding of biochemistry because the binding stoichiometry and conformations of complexes in biological processes, such as various types of regulation and transportation, could reveal key pathways in organisms. Nanoelectrospray ionization mass spectrometry is widely used in studies of biological processes and systems biology. However, non-volatile salts in biological fluid may adversely interfere with nanoelectrospray ionization mass spectrometry. In this study, the previously developed method of induced nanoelectrospray ionization was used to facilitate in situ desalting of protein in solutions with high concentrations of non-volatile salts, and direct investigation of protein-ligand interactions for the first time. In situ desalting occurred at the tip of emitters within a short period lasting for a few to tens of milliseconds, enabling the maintenance of nativelike conditions compatible with mass spectrometry measurements. Induced nanoelectrospray ionization was driven by pulsed potential and exhibited microelectrophoresis effect in each spray cycle, which is not observed in conventional nanoelectrospray ionization because the continuous spray procedure is driven by direct current. Microelectrophoresis caused desalting through micron-sized spray emitters (1-20 μm), as confirmed experimentally with proteins in 100 mM NaCl solution. The method developed in this study has been further illustrated as a potential option for fast and direct identification of protein-ligand (small molecules or metal ions) interactions in complex samples. The results of this study demonstrate that the newly developed method may represent a reliable approach for investigations of proteins and protein complexes in biological samples.
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Affiliation(s)
- Yuting Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China
| | - Siming Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China
| | - Yangzhong Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China
| | - Guangming Huang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, 230026, Hefei, China; National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, 230029, PR China.
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42
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Yao L, Liu C, Wang N, Du F, Fan S, Guo Y, Zhang L, Pan Y, Xiong W. Cholesterol regulates cannabinoid analgesia through glycine receptors. Neuropharmacology 2020; 177:108242. [DOI: 10.1016/j.neuropharm.2020.108242] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 06/20/2020] [Accepted: 07/13/2020] [Indexed: 12/11/2022]
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43
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Longuespée R, Theile D, Fresnais M, Burhenne J, Weiss J, Haefeli WE. Approaching sites of action of drugs in clinical pharmacology: New analytical options and their challenges. Br J Clin Pharmacol 2020; 87:858-874. [PMID: 32881012 DOI: 10.1111/bcp.14543] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 12/13/2022] Open
Abstract
Clinical pharmacology is an important discipline for drug development aiming to define pharmacokinetics (PK), pharmacodynamics (PD) and optimum exposure to drugs, i.e. the concentration-response relationship and its modulators. For this purpose, information on drug concentrations at the anatomical, cellular and molecular sites of action is particularly valuable. In pharmacological assays, the limited accessibility of target cells in readily available samples (i.e. blood) often hampers mass spectrometry-based monitoring of the absolute quantity of a compound and the determination of its molecular action at the cellular level. Recently, new sample collection methods have been developed for the specific capture of rare circulating cells, especially for the diagnosis of circulating tumour cells. In parallel, new advances and developments in mass spectrometric instrumentation now allow analyses to be scaled down to the cellular level. Together, these developments may permit the monitoring of minute drug quantities and show their effect at the cellular level. In turn, such PK/PD associations on a cellular level would not only enrich our pharmacological knowledge of a given compound but also expand the basis for PK/PD simulations. In this review, we describe novel concepts supporting clinical pharmacology at the anatomical, cellular and molecular sites of action, and highlight the new challenges in mass spectrometry-based monitoring. Moreover, we present methods to tackle these challenges and define future needs.
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Affiliation(s)
- Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, University Hospital of Heidelberg, Heidelberg, Germany
| | - Dirk Theile
- Department of Clinical Pharmacology and Pharmacoepidemiology, University Hospital of Heidelberg, Heidelberg, Germany
| | - Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, University Hospital of Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK)-German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jürgen Burhenne
- Department of Clinical Pharmacology and Pharmacoepidemiology, University Hospital of Heidelberg, Heidelberg, Germany
| | - Johanna Weiss
- Department of Clinical Pharmacology and Pharmacoepidemiology, University Hospital of Heidelberg, Heidelberg, Germany
| | - Walter E Haefeli
- Department of Clinical Pharmacology and Pharmacoepidemiology, University Hospital of Heidelberg, Heidelberg, Germany
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44
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Zhu Y, Wang W, Yang Z. Combining Mass Spectrometry with Paternò-Büchi Reaction to Determine Double-Bond Positions in Lipids at the Single-Cell Level. Anal Chem 2020; 92:11380-11387. [PMID: 32678580 PMCID: PMC7482314 DOI: 10.1021/acs.analchem.0c02245] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Single cell MS (SCMS) techniques are under rapid development for molecular analysis of individual cells among heterogeneous populations. Lipids are basic cellular constituents playing essential functions in energy storage and the cellular signaling processes of cells. Unsaturated lipids are characterized with one or multiple carbon-carbon double (C═C) bonds, and they are critical for cell functions and human diseases. Characterizing unsaturated lipids in single cells allows for better understanding of metabolomic biomarkers and therapeutic targets of rare cells (e.g., cancer stem cells); however, these studies remain challenging. We developed a new technique using a micropipette needle, in which Paternò-Büchi (PB) reactions at C═C bond can be induced, to determine locations of C═C bonds in unsaturated lipids at the single-cell level. The micropipette needle is produced by combining a pulled glass capillary needle with a fused silica capillary. Cell lysis solvent and PB reagent (acetone or benzophenone) are delivered into the micropipette needle (tip size ≈ 15 um) through a fused silica capillary. The capillary needle plays multiple functions (i.e., single cell sampling probe, cell lysis container, microreactor, and nano-ESI emitter) in the experiments. Both regular (no reaction) and reactive (with PB reaction) SCMS analyses of the same cell can be achieved. C═C bond locations were determined from MS scan and MS/MS of PB products assisted by Python programs. This technique can potentially be used for other reactive SCMS studies to enhance molecular analysis for broad ranges of single cells.
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Affiliation(s)
- Yanlin Zhu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Wenhua Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
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45
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Recent Advances in Single Cell Analysis Methods Based on Mass Spectrometry. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60038-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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46
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Zhuang M, Hou Z, Chen P, Liang G, Huang G. Introducing charge tag via click reaction in living cells for single cell mass spectrometry. Chem Sci 2020; 11:7308-7312. [PMID: 34123015 PMCID: PMC8159379 DOI: 10.1039/d0sc00259c] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/23/2020] [Indexed: 12/13/2022] Open
Abstract
For single living cell mass spectrometry measurement, sensitivity is of great significance due to the extremely complicated chemical components of the cytoplasm. Higher sensitivity is always highly desired, especially for chemicals with low concentrations or poor mass spectrometry responses. Here, a quaternary ammonium salt group-based charge tag was designed to enhance the analytical performance for cysteine within single cells using induced nanoelectrospray mass spectrometry. While the charge tag was coupled to the analyte via biocompatible click reaction, viability of the living cells was maintained during in situ derivatization and following analysis. Enhanced sensitivity under physiological conditions for cysteine, at pH 7.4 and with highly concentrated salts, was achieved due to higher ionization efficiency of the charge tag. Therefore, the cysteine levels in single living HeLa cells and HepG2 cells were found to be in the range of 62.0 ± 3.4 μM and 49.6 ± 7.2 μM, respectively. Furthermore, the low cysteine levels in living single HeLa cells could be monitored, in the presence of cystine transporter inhibitor. Thus, this method provides a general strategy for in situ chemical derivatization for signal amplification in the field of single cell mass spectrometry.
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Affiliation(s)
- Meihui Zhuang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Zhuanghao Hou
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Peiyao Chen
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Gaolin Liang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Guangming Huang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China Hefei Anhui 230026 P. R. China
- National Synchrotron Radiation Laboratory, University of Science and Technology of China Hefei Anhui 230029 P. R. China
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Li Z, Wang Z, Pan J, Ma X, Zhang W, Ouyang Z. Single-Cell Mass Spectrometry Analysis of Metabolites Facilitated by Cell Electro-Migration and Electroporation. Anal Chem 2020; 92:10138-10144. [DOI: 10.1021/acs.analchem.0c02147] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Zishuai Li
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Zhengmao Wang
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Junmin Pan
- MOE Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaoxiao Ma
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Wenpeng Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
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48
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Single-cell Metabolomics Analysis by Microfluidics and Mass Spectrometry: Recent New Advances. JOURNAL OF ANALYSIS AND TESTING 2020. [DOI: 10.1007/s41664-020-00138-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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49
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50
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