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Li M, Zuo J, Yang K, Wang P, Zhou S. Proteomics mining of cancer hallmarks on a single-cell resolution. MASS SPECTROMETRY REVIEWS 2024; 43:1019-1040. [PMID: 37051664 DOI: 10.1002/mas.21842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 11/25/2022] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Dysregulated proteome is an essential contributor in carcinogenesis. Protein fluctuations fuel the progression of malignant transformation, such as uncontrolled proliferation, metastasis, and chemo/radiotherapy resistance, which severely impair therapeutic effectiveness and cause disease recurrence and eventually mortality among cancer patients. Cellular heterogeneity is widely observed in cancer and numerous cell subtypes have been characterized that greatly influence cancer progression. Population-averaged research may not fully reveal the heterogeneity, leading to inaccurate conclusions. Thus, deep mining of the multiplex proteome at the single-cell resolution will provide new insights into cancer biology, to develop prognostic biomarkers and treatments. Considering the recent advances in single-cell proteomics, herein we review several novel technologies with particular focus on single-cell mass spectrometry analysis, and summarize their advantages and practical applications in the diagnosis and treatment for cancer. Technological development in single-cell proteomics will bring a paradigm shift in cancer detection, intervention, and therapy.
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Affiliation(s)
- Maomao Li
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Jing Zuo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan, China
| | - Kailin Yang
- Department of Radiation Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, Ohio, USA
| | - Ping Wang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, Sichuan, China
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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: 23] [Impact Index Per Article: 23.0] [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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Wink K, van der Loh M, Hartner N, Polack M, Dusny C, Schmid A, Belder D. Quantification of Biocatalytic Transformations by Single Microbial Cells Enabled by Tailored Integration of Droplet Microfluidics and Mass Spectrometry. Angew Chem Int Ed Engl 2022; 61:e202204098. [PMID: 35511505 PMCID: PMC9401594 DOI: 10.1002/anie.202204098] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Indexed: 12/23/2022]
Abstract
Improving the performance of chemical transformations catalysed by microbial biocatalysts requires a deep understanding of cellular processes. While the cellular heterogeneity of cellular characteristics, such as the concentration of high abundant cellular content, is well studied, little is known about the reactivity of individual cells and its impact on the chemical identity, quantity, and purity of excreted products. Biocatalytic transformations were monitored chemically specific and quantifiable at the single-cell level by integrating droplet microfluidics, cell imaging, and mass spectrometry. Product formation rates for individual Saccharomyces cerevisiae cells were obtained by i) incubating nanolitre-sized droplets for product accumulation in microfluidic devices, ii) an imaging setup to determine the number of cells in the droplets, and iii) electrospray ionisation mass spectrometry for reading the chemical contents of individual droplets. These findings now enable the study of whole-cell biocatalysis at single-cell resolution.
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Affiliation(s)
- Konstantin Wink
- University of LeipzigInstitute of Analytical Chemistry04107LeipzigGermany
| | - Marie van der Loh
- University of LeipzigInstitute of Analytical Chemistry04107LeipzigGermany
| | - Nora Hartner
- University of LeipzigInstitute of Analytical Chemistry04107LeipzigGermany
| | - Matthias Polack
- University of LeipzigInstitute of Analytical Chemistry04107LeipzigGermany
| | - Christian Dusny
- Department Solar MaterialsHelmholtz Centre for Environmental Research (UFZ)04318LeipzigGermany
| | - Andreas Schmid
- Department Solar MaterialsHelmholtz Centre for Environmental Research (UFZ)04318LeipzigGermany
| | - Detlev Belder
- University of LeipzigInstitute of Analytical Chemistry04107LeipzigGermany
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Wink K, Loh M, Hartner N, Polack M, Dusny C, Schmid A, Belder D. Quantifizierung biokatalytischer Umwandlungen durch einzelne mikrobielle Zellen mittels maßgeschneiderter Integration von Tröpfchenmikrofluidik und Massenspektrometrie. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Konstantin Wink
- Universität Leipzig Institut für Analytische Chemie 04107 Leipzig Deutschland
| | - Marie Loh
- Universität Leipzig Institut für Analytische Chemie 04107 Leipzig Deutschland
| | - Nora Hartner
- Universität Leipzig Institut für Analytische Chemie 04107 Leipzig Deutschland
| | - Matthias Polack
- Universität Leipzig Institut für Analytische Chemie 04107 Leipzig Deutschland
| | - Christian Dusny
- Department Solare Materialien Helmholtz-Zentrum für Umweltforschung (UFZ) 04318 Leipzig Deutschland
| | - Andreas Schmid
- Department Solare Materialien Helmholtz-Zentrum für Umweltforschung (UFZ) 04318 Leipzig Deutschland
| | - Detlev Belder
- Universität Leipzig Institut für Analytische Chemie 04107 Leipzig Deutschland
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Li Q, Tang F, Huo X, Huang X, Zhang Y, Wang X, Zhang X. Native State Single-Cell Printing System and Analysis for Matrix Effects. Anal Chem 2019; 91:8115-8122. [DOI: 10.1021/acs.analchem.9b00344] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Qi Li
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Fei Tang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Xinming Huo
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Xi Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yan Zhang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Xiaohao Wang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
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Yin L, Zhang Z, Liu Y, Gao Y, Gu J. Recent advances in single-cell analysis by mass spectrometry. Analyst 2019; 144:824-845. [PMID: 30334031 DOI: 10.1039/c8an01190g] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells are the most basic structural units that play vital roles in the functioning of living organisms. Analysis of the chemical composition and content of a single cell plays a vital role in ensuring precise investigations of cellular metabolism, and is a crucial aspect of lipidomic and proteomic studies. In addition, structural knowledge provides a better understanding of cell behavior as well as the cellular and subcellular mechanisms. However, single-cell analysis can be very challenging due to the very small size of each cell as well as the large variety and extremely low concentrations of substances found in individual cells. On account of its high sensitivity and selectivity, mass spectrometry holds great promise as an effective technique for single-cell analysis. Numerous mass spectrometric techniques have been developed to elucidate the molecular profiles at the cellular level, including electrospray ionization mass spectrometry (ESI-MS), secondary ion mass spectrometry (SIMS), laser-based mass spectrometry and inductively coupled plasma mass spectrometry (ICP-MS). In this review, the recent advances in single-cell analysis by mass spectrometry are summarized. The strategies of different ionization modes to achieve single-cell analysis are classified and discussed in detail.
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Affiliation(s)
- Lei Yin
- Research Institute of Translational Medicine, The First Hospital of Jilin University, Jilin University, Dongminzhu Street, Changchun 130061, PR China.
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Yang Y, Huang Y, Wu J, Liu N, Deng J, Luan T. Single-cell analysis by ambient mass spectrometry. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.02.009] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Fujii T, Matsuda S, Tejedor ML, Esaki T, Sakane I, Mizuno H, Tsuyama N, Masujima T. Direct metabolomics for plant cells by live single-cell mass spectrometry. Nat Protoc 2015; 10:1445-56. [DOI: 10.1038/nprot.2015.084] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Ketola RA, Mauriala T. Mass spectrometric tools for cell and tissue studies. Eur J Pharm Sci 2012; 46:293-314. [DOI: 10.1016/j.ejps.2012.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/14/2012] [Accepted: 03/23/2012] [Indexed: 10/28/2022]
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Abstract
Traditional ‘macroscopic’ pharmacokinetics (PK) investigates the fate of drugs or toxicants administered externally to living organisms, described by the extent and rate of absorption, distribution, metabolism and excretion. However, how a single cell affects a specific pharmaceutical after administration still remains a largely untouched area, primarily due to the technical restrictions imposed by minute amounts of chemicals involved. With the fast development of high-temporal and spatial-resolution detection techniques and single-cell handling techniques, it becomes possible to pursue single-cell PK. This review summarizes useful methodological and experimental techniques to investigate PK at the level of the single cell, including the microfluidics-based single-cell manipulation and the MS and electrochemical methods for single-cell analysis.
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Mizuno H, Tsuyama N, Harada T, Masujima T. Live single-cell video-mass spectrometry for cellular and subcellular molecular detection and cell classification. JOURNAL OF MASS SPECTROMETRY : JMS 2008; 43:1692-700. [PMID: 18615771 DOI: 10.1002/jms.1460] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The molecular content from the cytoplasm of a live, single mammalian cell and its organelle were trapped with a nano-electrospray ionization (ESI) tip acting as a micropipette under a video microscope, and hundreds of small molecular peaks were detected by direct nano-ESI mass spectrometry (MS). Granule- or cytoplasm-specific peaks in a mast cell (RBL 2H3) model were extracted by paired t-test to demonstrate their specific localization. Some of the typical and specific molecules were successfully identified by MS/MS analysis. This method was also applied to the cell classification of seven types of cell lines at the single-cellular level by principal component analysis (PCA), revealing seven clusters in the multivariate score plot.
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Affiliation(s)
- Hajime Mizuno
- Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima City 734-8551, Japan
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