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Karmaus PWF. Application of Single Cell Methods in Immunometabolism and Immunotoxicology. CURRENT OPINION IN TOXICOLOGY 2024; 39:100488. [PMID: 39091379 PMCID: PMC11290472 DOI: 10.1016/j.cotox.2024.100488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Recent developments of novel single-cell analysis techniques have rapidly advanced the fields of immunotoxicology and immunometabolism. Single-cell analyses enable the characterization of immune cells, unraveling heterogeneity, and population dynamics in response to cellular perturbations, including toxicant insults and changes in cellular metabolism. This review provides an overview of current technologies and recent discoveries, illustrating an emerging role of single-cell analyses in the field of immunotoxicology and immunometabolism. Various single-cell techniques, including flow cytometry, mass cytometry, multiplexed imaging, and sequencing, together with their applications to studying immunotoxicology and immunometabolism are discussed. This review emphasizes the potential for single-cell analyses to revolutionize our understanding of immune cell heterogeneity, uncover novel cellular therapeutic targets, and pave the way for novel mechanistic insights.
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Affiliation(s)
- Peer W F Karmaus
- National Institute of Environmental Health Sciences, US
- Institute for Integrative Toxicology, Michigan State University, US
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2
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Ren A, Chen F, Ren C, Yang M, Wang C, Feng X, Zhang F. Rapid Screening of Biomarkers in KYSE-150 Cells Exposed to Polycyclic Aromatic Hydrocarbons via Inkjet Printing Single-Cell Mass Spectrometry. Anal Chem 2024; 96:12817-12826. [PMID: 39052489 DOI: 10.1021/acs.analchem.4c02332] [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: 07/27/2024]
Abstract
Single-cell analysis by mass spectrometry (MS) is emerging as a powerful tool that not only contributes to cellular heterogeneity but also offers an unprecedented opportunity to predict pathology onset and facilitates novel biomarker discovery. However, the development of single-cell MS analysis techniques with a focus on sample extraction, separation, and ionization methods for volume-limited samples and complexity of cellular samples are still a big challenge. In this study, we present a high-throughput approach to inkjet drop on demand printing single-cell MS for rapid screening of biomarkers of polycyclic aromatic hydrocarbon (PAH) exposure at the KYSE-150 cell, aiming to elucidate the pathogenesis of PAH-induced esophageal cancer. With an analytical bulk KYSE-150 cell throughput of up to 51 cells per minute, the method provides a new opportunity for simultaneous single-cell analysis of multiple biomarkers. We screened 930 characteristic ions from 3,683 detected peak signals and identified 91 distinctive molecules that exhibited significant differences under various concentrations of PAH exposure. These molecules have potential as clinical diagnostic biomarkers. Additionally, the current study identifies specific biomarkers that behave completely opposite in single-cell and multicell lipidomics as the concentration of PAH changes. These biomarkers potentially subdivide KYSE-150 cells into PAH-sensitive and PAH-insensitive types, providing a basis for revealing PAH toxicity and disease pathogenesis from the heterogeneity of cellular metabolism.
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Affiliation(s)
- Ai Ren
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- Key Laboratory of Food Quality and Safety for State Market Regulation, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Fengming Chen
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- Key Laboratory of Food Quality and Safety for State Market Regulation, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Chenjie Ren
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- Key Laboratory of Food Quality and Safety for State Market Regulation, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Minli Yang
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- Key Laboratory of Food Quality and Safety for State Market Regulation, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Chang Wang
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
- Key Laboratory of Food Quality and Safety for State Market Regulation, School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Xuesong Feng
- School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Feng Zhang
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
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3
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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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Liu J, Yang M, Chen F, Xu X, Chen Y, Zhang F. A Novel Multiarmed Bifunctional PEG Derivative for the Preparation of Mass Spectrometry Ion Sources with Antifouling Property and High Selectivity. Anal Chem 2024; 96:8484-8491. [PMID: 38753368 DOI: 10.1021/acs.analchem.4c00346] [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: 05/29/2024]
Abstract
It is challenging to prepare a highly selective mass spectrometry (MS) ion source for the rapid and highly sensitive detection of analytes, especially mycotoxins. In this study, an amino and tetrazine bifunctionalized multiarm PEG derivative (NH2HCl-4armPEG10K-(MTz)3), which can be easily immobilized on the substrate by the addition reaction between amino and polydopamine, was used for the preparation of MS ionization substrate. NH2HCl-4armPEG10K-(MTz)3 can also be used as a linker to immobilize sufficient streptavidin (SA) on the surface of the substrate by a click reaction. The process further promotes the immobilization of broad-spectrum antibodies (3D4), which were used as the recognition element for ZEN and its metabolites. The prepared SSS-Au-PDA-4armPEG10K-SA-3D4 not only can rapidly enrich ZEN and its metabolites with high selectivity but also shows good antifouling properties in the matrix. After simple sample preparation, the prepared SSS-Au-PDA-4armPEG10K-SA-3D4 can be directly coupled with MS to achieve high sensitivity (LODs: 0.18-0.66 ng/mL, LOQs: 0.5-1.0 ng/mL) and selective detection of ZEN and its metabolites in the matrix. At the same time, satisfactory recoveries (83.60-97.80%) and precision (RSD: 2.80-9.10%) can also be obtained. The prepared SSS-Au-PDA-4armPEG10K-SA-3D4 is expected to provide a powerful tool for the rapid and highly sensitive determination of multiple targets by MS.
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Affiliation(s)
- Jiawei Liu
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China
- Key Laboratory of Food Quality and Safety for State Market Regulation, Beijing 100176, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Minli Yang
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China
- Key Laboratory of Food Quality and Safety for State Market Regulation, Beijing 100176, China
| | - Fengming Chen
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China
- Key Laboratory of Food Quality and Safety for State Market Regulation, Beijing 100176, China
| | - Xiuli Xu
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China
- Key Laboratory of Food Quality and Safety for State Market Regulation, Beijing 100176, China
| | - Yiping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Feng Zhang
- Institute of Food Safety, Chinese Academy of Inspection & Quarantine, Beijing 100176, China
- Key Laboratory of Food Quality and Safety for State Market Regulation, Beijing 100176, China
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5
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Fan Y, Zhang Z, Zhang X, Xu A, Zhu JJ, Min Q. DNA Walker-Driven Mass Nanotag Assembly System for Simultaneously Profiling Dual Markers of Oxidative Stress at Different Cellular Locations. Anal Chem 2024; 96:8754-8762. [PMID: 38740024 DOI: 10.1021/acs.analchem.4c01115] [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: 05/16/2024]
Abstract
Simultaneous profiling of redox-regulated markers at different cellular sublocations is of great significance for unraveling the upstream and downstream molecular mechanisms of oxidative stress in living cells. Herein, by synchronizing dual target-triggered DNA machineries in one nanoentity, we engineered a DNA walker-driven mass nanotag (MNT) assembly system (w-MNT-AS) that can be sequentially activated by oxidative stress-associated mucin 1 (MUC1) and apurinic/apyrimidinic endonuclease 1 (APE1) from plasma membrane to cytoplasm and induce recycled assembly of MNTs for multiplex detection of the two markers by matrix-assisted laser desorption ionization mass spectrometry (MALDI MS). In the working cascade, the sensing process governs the separate activation of w-MNT-AS by MUC1 and APE1 in diverse locations, while the assembly process contributes to the parallel amplification of the ion signal of the characteristic mass tags. In this manner, the differences between MCF-7, HeLa, HepG2, and L02 cells in membrane MUC1 expression and cytoplasmic APE1 activation were fully characterized. Furthermore, the oxidative stress level and dynamics caused by exogenous H2O2, doxorubicin, and simvastatin were comprehensively demonstrated by tracking the fate of the two markers across different cellular locations. The proposed w-MNT-AS coupled MS method provides an effective route to probe multiple functional molecules that lie at different locations while participating in the same cellular event, facilitating the mechanistic studies on cellular response to oxidative stress and other disease-related cellular processes.
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Affiliation(s)
- Yinyin Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhenzhen Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xue Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Aobo Xu
- Nanjing Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210023, China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Sciences, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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6
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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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Wu J, Xu QQ, Jiang YR, Chen JB, Ying WX, Fan QX, Wang HF, Wang Y, Shi SW, Pan JZ, Fang Q. One-Shot Single-Cell Proteome and Metabolome Analysis Strategy for the Same Single Cell. Anal Chem 2024; 96:5499-5508. [PMID: 38547315 DOI: 10.1021/acs.analchem.3c05659] [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: 04/10/2024]
Abstract
Characterizing the profiles of proteome and metabolome at the single-cell level is of great significance in single-cell multiomic studies. Herein, we proposed a novel strategy called one-shot single-cell proteome and metabolome analysis (scPMA) to acquire the proteome and metabolome information in a single-cell individual in one injection of LC-MS/MS analysis. Based on the scPMA strategy, a total workflow was developed to achieve the single-cell capture, nanoliter-scale sample pretreatment, one-shot LC injection and separation of the enzyme-digested peptides and metabolites, and dual-zone MS/MS detection for proteome and metabolome profiling. Benefiting from the scPMA strategy, we realized dual-omic analysis of single tumor cells, including A549, HeLa, and HepG2 cells with 816, 578, and 293 protein groups and 72, 91, and 148 metabolites quantified on average. A single-cell perspective experiment for investigating the doxorubicin-induced antitumor effects in both the proteome and metabolome aspects was also performed.
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Affiliation(s)
- Jie Wu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Qin-Qin Xu
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Yi-Rong Jiang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Jian-Bo Chen
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Wei-Xin Ying
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Qian-Xi Fan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
| | - Hui-Feng Wang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Yu Wang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Shao-Wen Shi
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Jian-Zhang Pan
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
| | - Qun Fang
- Institute of Microanalytical Systems, Department of Chemistry, Zhejiang University, Hangzhou 310058, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
- Key Laboratory for Biomedical Engineering of Ministry of Education, Cancer Center, Zhejiang University, Hangzhou 310007, China
- Key Laboratory of Excited-State Materials of Zhejiang Province, Zhejiang University, Hangzhou 310007, China
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
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9
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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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10
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Xie Q, Liu S, Zhang S, Liao L, Xiao Z, Wang S, Zhang P. Research progress on the multi-omics and survival status of circulating tumor cells. Clin Exp Med 2024; 24:49. [PMID: 38427120 PMCID: PMC10907490 DOI: 10.1007/s10238-024-01309-z] [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: 11/22/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024]
Abstract
In the dynamic process of metastasis, circulating tumor cells (CTCs) emanate from the primary solid tumor and subsequently acquire the capacity to disengage from the basement membrane, facilitating their infiltration into the vascular system via the interstitial tissue. Given the pivotal role of CTCs in the intricate hematogenous metastasis, they have emerged as an essential resource for a deeper comprehension of cancer metastasis while also serving as a cornerstone for the development of new indicators for early cancer screening and new therapeutic targets. In the epoch of precision medicine, as CTC enrichment and separation technologies continually advance and reach full fruition, the domain of CTC research has transcended the mere straightforward detection and quantification. The rapid advancement of CTC analysis platforms has presented a compelling opportunity for in-depth exploration of CTCs within the bloodstream. Here, we provide an overview of the current status and research significance of multi-omics studies on CTCs, including genomics, transcriptomics, proteomics, and metabolomics. These studies have contributed to uncovering the unique heterogeneity of CTCs and identifying potential metastatic targets as well as specific recognition sites. We also review the impact of various states of CTCs in the bloodstream on their metastatic potential, such as clustered CTCs, interactions with other blood components, and the phenotypic states of CTCs after undergoing epithelial-mesenchymal transition (EMT). Within this context, we also discuss the therapeutic implications and potential of CTCs.
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Affiliation(s)
- Qingming Xie
- NHC Key Laboratory of Cancer Proteomics, Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Shilei Liu
- NHC Key Laboratory of Cancer Proteomics, Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Sai Zhang
- NHC Key Laboratory of Cancer Proteomics, Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Liqiu Liao
- Department of Breast Surgery, Hunan Clinical Meditech Research Center for Breast Cancer, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Zhi Xiao
- Department of Breast Surgery, Hunan Clinical Meditech Research Center for Breast Cancer, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Shouman Wang
- Department of Breast Surgery, Hunan Clinical Meditech Research Center for Breast Cancer, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
| | - Pengfei Zhang
- NHC Key Laboratory of Cancer Proteomics, Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
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11
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Zhang X, Wei X, Wu CX, Men X, Wang J, Bai JJ, Sun XY, Wang Y, Yang T, Lim CT, Chen ML, Wang JH. Multiplex Profiling of Biomarker and Drug Uptake in Single Cells Using Microfluidic Flow Cytometry and Mass Spectrometry. ACS NANO 2024; 18:6612-6622. [PMID: 38359901 PMCID: PMC10906074 DOI: 10.1021/acsnano.3c12803] [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: 12/19/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/17/2024]
Abstract
To perform multiplex profiling of single cells and eliminate the risk of potential sample loss caused by centrifugation, we developed a microfluidic flow cytometry and mass spectrometry system (μCytoMS) to evaluate the drug uptake and induced protein expression at the single cell level. It involves a microfluidic chip for the alignment and purification of single cells followed by detection with laser-induced fluorescence (LIF) and inductively coupled plasma mass spectrometry (ICP-MS). Biofunctionalized nanoprobes (BioNPs), conjugating ∼3000 6-FAM-Sgc8 aptamers on a single gold nanoparticle (AuNP) (Kd = 0.23 nM), were engineered to selectively bind with protein tyrosine kinase 7 (PTK7) on target cells. PTK7 expression induced by oxaliplatin (OXA) uptake was assayed with LIF, while ICP-MS measurement of 195Pt revealed OXA uptake of the drug in individual cells, which provided further in-depth information about the drug in relation to PTK7 expression. At an ultralow flow of ∼0.043 dyn/cm2 (20 μL/min), the chip facilitates the extremely fast focusing of BioNPs labeled single cells without the need for centrifugal purification. It ensures multiplex profiling of single cells at a throughput speed of 500 cells/min as compared to 40 cells/min in previous studies. Using a machine learning algorithm to initially profile drug uptake and marker expression in tumor cell lines, μCytoMS was able to perform in situ profiling of the PTK7 response to the OXA at single-cell resolution for tests done on clinical samples from 10 breast cancer patients. It offers great potential for multiplex single-cell phenotypic analysis and clinical diagnosis.
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Affiliation(s)
- Xuan Zhang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
- Institute
for Health Innovation and Technology, National
University of Singapore, 117599, Singapore
- Academy
of Medical Science, Shanxi Medical University, Taiyuan 030001, China
| | - Xing Wei
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Cheng-Xin Wu
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Xue Men
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jiao Wang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jun-Jie Bai
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Xiao-Yan Sun
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Yu Wang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Ting Yang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Chwee Teck Lim
- Institute
for Health Innovation and Technology, National
University of Singapore, 117599, Singapore
- Department
of Biomedical Engineering, National University
of Singapore, 117576, Singapore
| | - Ming-Li Chen
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, China
| | - Jian-Hua Wang
- Research
Center for Analytical Sciences, Department of Chemistry, College of
Sciences, Northeastern University, Box 332, Shenyang 110819, 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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Zeng Q, Xia MC, Yin X, Cheng S, Xue Z, Tan S, Gong X, Ye Z. Recent developments in ionization techniques for single-cell mass spectrometry. Front Chem 2023; 11:1293533. [PMID: 38130875 PMCID: PMC10733462 DOI: 10.3389/fchem.2023.1293533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
The variation among individual cells plays a significant role in many biological functions. Single-cell analysis is advantageous for gaining insight into intricate biochemical mechanisms rarely accessible when studying tissues as a whole. However, measurement on a unicellular scale is still challenging due to unicellular complex composition, minute substance quantities, and considerable differences in compound concentrations. Mass spectrometry has recently gained extensive attention in unicellular analytical fields due to its exceptional sensitivity, throughput, and compound identification abilities. At present, single-cell mass spectrometry primarily concentrates on the enhancement of ionization methods. The principal ionization approaches encompass nanoelectrospray ionization (nano-ESI), laser desorption ionization (LDI), secondary ion mass spectrometry (SIMS), and inductively coupled plasma (ICP). This article summarizes the most recent advancements in ionization techniques and explores their potential directions within the field of single-cell mass spectrometry.
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Affiliation(s)
- Qingli Zeng
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Meng-Chan Xia
- National Anti-Drug Laboratory Beijing Regional Center, Beijing, China
| | - Xinchi Yin
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Simin Cheng
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Zhichao Xue
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Siyuan Tan
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Xiaoyun Gong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Zihong Ye
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
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14
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Lan Y, Zhou Y, Wu M, Jia C, Zhao J. Microfluidic based single cell or droplet manipulation: Methods and applications. Talanta 2023; 265:124776. [PMID: 37348357 DOI: 10.1016/j.talanta.2023.124776] [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: 02/07/2023] [Revised: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023]
Abstract
The isolation of single cell or droplet is first and crucial step to single-cell analysis, which is important for cancer research and diagnostic methods. This review provides an overview of technologies that are currently used or in development to realize the isolation. Microfluidic based manipulation is an emerging technology with the distinct advantages of miniaturization and low cost. Therefore, recent developments in microfluidic isolated methods have attracted extensive attention. We introduced herein five strategies based on microfluid: trap, microfluidic discrete manipulation, bioprinter, capillary and inertial force. For every technology, their basic principles and features were discussed firstly. Then some modified approaches and applications were listed as the extension. Finally, we compared the advantages and drawbacks of these methods, and analyzed the trend of the manipulation based on microfluidics.
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Affiliation(s)
- Yuwei Lan
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yang Zhou
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Man Wu
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China.
| | - Chunping Jia
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jianlong Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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15
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Wevers D, Ramautar R, Clark C, Hankemeier T, Ali A. Opportunities and challenges for sample preparation and enrichment in mass spectrometry for single-cell metabolomics. Electrophoresis 2023; 44:2000-2024. [PMID: 37667867 DOI: 10.1002/elps.202300105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/08/2023] [Accepted: 08/19/2023] [Indexed: 09/06/2023]
Abstract
Single-cell heterogeneity in metabolism, drug resistance and disease type poses the need for analytical techniques for single-cell analysis. As the metabolome provides the closest view of the status quo in the cell, studying the metabolome at single-cell resolution may unravel said heterogeneity. A challenge in single-cell metabolome analysis is that metabolites cannot be amplified, so one needs to deal with picolitre volumes and a wide range of analyte concentrations. Due to high sensitivity and resolution, MS is preferred in single-cell metabolomics. Large numbers of cells need to be analysed for proper statistics; this requires high-throughput analysis, and hence automation of the analytical workflow. Significant advances in (micro)sampling methods, CE and ion mobility spectrometry have been made, some of which have been applied in high-throughput analyses. Microfluidics has enabled an automation of cell picking and metabolite extraction; image recognition has enabled automated cell identification. Many techniques have been used for data analysis, varying from conventional techniques to novel combinations of advanced chemometric approaches. Steps have been set in making data more findable, accessible, interoperable and reusable, but significant opportunities for improvement remain. Herein, advances in single-cell analysis workflows and data analysis are discussed, and recommendations are made based on the experimental goal.
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Affiliation(s)
- Dirk Wevers
- Wageningen University and Research, Wageningen, The Netherlands
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Rawi Ramautar
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Charlie Clark
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
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16
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Lu H, Zhang H, Li L. Chemical tagging mass spectrometry: an approach for single-cell omics. Anal Bioanal Chem 2023; 415:6901-6913. [PMID: 37466681 PMCID: PMC10729908 DOI: 10.1007/s00216-023-04850-0] [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: 04/10/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
Single-cell (SC) analysis offers new insights into the study of fundamental biological phenomena and cellular heterogeneity. The superior sensitivity, high throughput, and rich chemical information provided by mass spectrometry (MS) allow MS to emerge as a leading technology for molecular profiling of SC omics, including the SC metabolome, lipidome, and proteome. However, issues such as ionization suppression, low concentration, and huge span of dynamic concentrations of SC components lead to poor MS response for certain types of molecules. It is noted that chemical tagging/derivatization has been adopted in SCMS analysis, and this strategy has been proven an effective solution to circumvent these issues in SCMS analysis. Herein, we review the basic principle and general strategies of chemical tagging/derivatization in SCMS analysis, along with recent applications of chemical derivatization to single-cell metabolomics and multiplexed proteomics, as well as SCMS imaging. Furthermore, the challenges and opportunities for the improvement of chemical derivatization strategies in SCMS analysis are discussed.
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Affiliation(s)
- Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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17
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Hou Y, Yao H, Lin JM. Recent advancements in single-cell metabolic analysis for pharmacological research. J Pharm Anal 2023; 13:1102-1116. [PMID: 38024859 PMCID: PMC10658044 DOI: 10.1016/j.jpha.2023.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 12/01/2023] Open
Abstract
Cellular heterogeneity is crucial for understanding tissue biology and disease pathophysiology. Pharmacological research is being advanced by single-cell metabolic analysis, which offers a technique to identify variations in RNA, proteins, metabolites, and drug molecules in cells. In this review, the recent advancement of single-cell metabolic analysis techniques and their applications in drug metabolism and drug response are summarized. High-precision and controlled single-cell isolation and manipulation are provided by microfluidics-based methods, such as droplet microfluidics, microchamber, open microfluidic probe, and digital microfluidics. They are used in tandem with variety of detection techniques, including optical imaging, Raman spectroscopy, electrochemical detection, RNA sequencing, and mass spectrometry, to evaluate single-cell metabolic changes in response to drug administration. The advantages and disadvantages of different techniques are discussed along with the challenges and future directions for single-cell analysis. These techniques are employed in pharmaceutical analysis for studying drug response and resistance pathway, therapeutic targets discovery, and in vitro disease model evaluation.
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Affiliation(s)
- Ying Hou
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Hongren Yao
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Jin-Ming Lin
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
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18
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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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19
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Zhang H, Liu Y, Fields L, Shi X, Huang P, Lu H, Schneider AJ, Tang X, Puglielli L, Welham NV, Li L. Single-cell lipidomics enabled by dual-polarity ionization and ion mobility-mass spectrometry imaging. Nat Commun 2023; 14:5185. [PMID: 37626051 PMCID: PMC10457347 DOI: 10.1038/s41467-023-40512-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/27/2023] [Indexed: 08/27/2023] Open
Abstract
Single-cell (SC) analysis provides unique insight into individual cell dynamics and cell-to-cell heterogeneity. Here, we utilize trapped ion mobility separation coupled with dual-polarity ionization mass spectrometry imaging (MSI) to enable high-throughput in situ profiling of the SC lipidome. Multimodal SC imaging, in which dual-polarity-mode MSI is used to perform serial data acquisition runs on individual cells, significantly enhanced SC lipidome coverage. High-spatial resolution SC-MSI identifies both inter- and intracellular lipid heterogeneity; this heterogeneity is further explicated by Uniform Manifold Approximation and Projection and machine learning-driven classifications. We characterize SC lipidome alteration in response to stearoyl-CoA desaturase 1 inhibition and, additionally, identify cell-layer specific lipid distribution patterns in mouse cerebellar cortex. This integrated multimodal SC-MSI technology enables high-resolution spatial mapping of intercellular and cell-to-cell lipidome heterogeneity, SC lipidome remodeling induced by pharmacological intervention, and region-specific lipid diversity within tissue.
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Affiliation(s)
- Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Yuan Liu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Xudong Shi
- Division of Otolaryngology, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53792, USA
| | - Penghsuan Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA
| | - Andrew J Schneider
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Xindi Tang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Luigi Puglielli
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Waisman Center, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Nathan V Welham
- Division of Otolaryngology, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, 53792, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, 53705, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
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20
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Liu M, Xue J, Liu H, Bai Y. Imidazolium-based mass tags for protein biomarker detection using laser desorption ionization mass spectrometry. Chem Commun (Camb) 2023; 59:9996-9999. [PMID: 37522155 DOI: 10.1039/d3cc02907g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Novel imidazolium-based mass tags (IMTs) were designed, synthesized and applied to simultaneous in situ analysis of multiple biomarkers on less than 10 cells. The high sensitivity, flexible extensibility and excellent distinguishability of IMTs open new avenues for designing common mass tag templates suitable for mass spectrometric immunoassay and provide an ideal option for multiplex-sensitive detection at the cellular scale.
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Affiliation(s)
- Mingxia Liu
- 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 100871, China.
- Beijing Key Laboratory of Mental Disorders, National Clinical Research Center for Mental Disorders & National Center for Mental Disorders, Beijing Anding Hospital, Capital Medical University, Beijing 100088, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing 100069, China
| | - Jinjuan Xue
- 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 100871, China.
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Huwei Liu
- 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 100871, 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 100871, China.
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21
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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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22
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Wu P, Song J, Zuo W, Zhu J, Meng X, Yang J, Liu X, Jiang H, Zhang D, Dai J, Ju Y. A universal boronate affinity capture-antibody-independent lateral flow immunoassay for point-of-care glycoprotein detection. Talanta 2023; 265:124927. [PMID: 37441999 DOI: 10.1016/j.talanta.2023.124927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023]
Abstract
Protein glycosylation and other post-translational modifications are involved in many biological processes including growth, development and immune responses, and glycoproteins are also known as biomarkers for cancer, diabetes and cardiovascular diseases. In traditional lateral flow immunoassay (LFIA) for glycoprotein detection, capture antibody (CA) is often required to label targets. However, the production of CA is complicated and expensive, restricting the wide application of LFIA. In this study, we developed a universal boronate affinity CA-independent LFIA method for glycoprotein detection. 4-Mercaptophenylboronic acid (4-MPBA)-modified Au nanoparticles (namely 4-MPBA-AuNPs) were used as LFIA labels, which could generate colorimetric signal and showed outstanding capability to bind glycoprotein. Compared with CA, 4-MPBA molecular as a glycoprotein recognition element had more prominent advantages, e.g., low cost, easy availability and good quality controllability. Take carcinoembryonic antigen (CEA) as model glycoprotein, the limit of detection of this CA-independent LFIA was 1.25 ng/mL by naked eyes, which was 8-fold lower than conventional CA-dependent sandwich LFIA. Significantly, the developed 4-MPBA-AuNPs-based CA-independent LFIA successfully detected 23 CEA-positive samples from 64 suspected human serum samples within 50 min in a nonlaboratory environment, with a 100% accuracy compared to clinical detection method. Therefore, this diagnostic platform could provide an effective tool for point-of-care glycoprotein detection with excellent reproducibility and high specificity.
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Affiliation(s)
- Pengcheng Wu
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang, 524045, China; College of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiaren Song
- College of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Wanchao Zuo
- College of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Jiaying Zhu
- College of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Xiangming Meng
- College of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Jun Yang
- Nanjing Institute for Food and Drug Control, Nanjing, 210038, China
| | - Xinmei Liu
- Nanjing Institute for Food and Drug Control, Nanjing, 210038, China
| | - Hui Jiang
- Nanjing Institute for Food and Drug Control, Nanjing, 210038, China
| | - Donghui Zhang
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Guangdong Medical University Zhanjiang Central Hospital, Zhanjiang, 524045, China.
| | - Jianjun Dai
- College of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Yanmin Ju
- College of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
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23
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Zhu G, Zhang W, Zhao Y, Chen T, Yuan H, Liu Y, Guo G, Liu Z, Wang X. Single-Cell Metabolomics-Based Strategy for Studying the Mechanisms of Drug Action. Anal Chem 2023; 95:4712-4720. [PMID: 36857711 DOI: 10.1021/acs.analchem.2c05351] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Studying the mechanisms of drug antitumor activity at the single-cell level can provide information about the responses of cell subpopulations to drug therapy, which is essential for the accurate treatment of cancer. Due to the small size of single cells and the low contents of metabolites, metabolomics-based approaches to studying the mechanisms of drug action at the single-cell level are lacking. Herein, we develop a label-free platform for studying the mechanisms of drug action based on single-cell metabolomics (sMDA-scM) by integrating intact living-cell electro-launching ionization mass spectrometry (ILCEI-MS) with metabolomics analysis. Using this platform, we reveal that non-small-cell lung cancer (NSCLC) cells treated by gefitinib can be clustered into two cell subpopulations with different metabolic responses. The glutathione metabolic pathway of the subpopulation containing 14.4% of the cells is not significantly affected by gefitinib, exhibiting certain resistance characteristics. The presence of these cells masked the judgment of whether cysteine and methionine metabolic pathway was remarkably influenced in the analysis of overall average results, revealing the heterogeneity of the response of single NSCLC cells to gefitinib treatment. The findings provide a basis for evaluating the early therapeutic effects of clinical medicines and insights for overcoming drug resistance in NSCLC subpopulations.
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Affiliation(s)
- Guizhen Zhu
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
| | - Wenmei Zhang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
| | - Yaoyao Zhao
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
| | - Tian Chen
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
| | - Hanyu Yuan
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
| | - Yuanxing Liu
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
| | - Guangsheng Guo
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China.,Minzu University of China, Beijing 100081, China
| | - Zhihong Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xiayan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry, Beijing University of Technology, Beijing 100124, China
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24
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Zhang Z, Xu H, Fan Y, Zhang X, Wang W, Zhu JJ, Min Q. Mass Nanotags Mediate Parallel Amplifications on Nanointerfaces for Multiplexed Profiling of RNAs. NANO LETTERS 2023; 23:1820-1829. [PMID: 36790360 DOI: 10.1021/acs.nanolett.2c04690] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Multiplexed profiling of RNAs aids in a comprehensive understanding of multiparameter-defined cellular processes and pathological states. We herein present a mass nanotags-enabled interfacial assembly system (MNTs-AS) with parallel amplification motors for simultaneous assaying of multiple RNAs in biosystems by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS). Four kinds of MNTs encoding corresponding RNA can be cyclically assembled on magnetic beads by target-triggered catalytic hairpin assembly (CHA) machineries on nanointerfaces, generating multiplexed and amplified characteristic ion signals assigned to target RNAs upon MALDI MS interrogation. By virtue of high sensitivity and multiplexing capability, the MNTs-AS-based MS assay allows precision subtyping of diverse breast cancer cells and their exosomes by multiplexed profiling of miRNA-21, miRNA-373, miRNA-155, and manganese superoxide dismutase mRNA via a single MS inquiry. This method provides a promising tool for unraveling multiple RNA-involved biological events in fundamental research and distinguishing different cancer subtypes in clinical practice.
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Affiliation(s)
- Zhenzhen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Hongmei Xu
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, P. R. China
| | - Yinyin Fan
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Xue Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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25
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Saffari H, Hajiaghalou S, Hajari MA, Gourabi H, Fathi D, Fathi R. Design and fabrication of aspiration microfluidic channel for oocyte characterization. Talanta 2023; 254:124098. [PMID: 36462279 DOI: 10.1016/j.talanta.2022.124098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/05/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022]
Abstract
The development potential for oocytes can be predicted by their mechanical properties. One important parameter that is measured to calculate oocyte hardness is Cortical Tension (CT). In this work, for the first time, we present the design, simulation, and fabrication of a new aspiration microfluidic chip to measure the CT of oocytes and then predict their maturation capability in the Germinal Vesicle (GV) stage. This high-performance technique facilitates oocyte characterization and is a promising alternative to traditional methods such as MicroPipette Aspiration (MPA). The proposed technique involves considerably simpler operation, less specialized equipment, and less technical skill than MPA. The proposed microfluidic channel also promises faster measurements. It is shown that in order to completely continue the growth process of oocytes in GV stage, the CT should be in a certain range: very low or very high CTs lead to unsuccessful growth. The obtained results show that 79% of oocytes with the CT between 1.5 and 3 nN/μm reach the Metaphase II (MII) stage, whereas the growth for 78% of oocytes with the CT less than 1.5 nN/μm or higher than 3 nN/μm stops at the GV or Germinal Vesicle Break Down (GVBD) stages. Another property, kvis, that points to the viscous behavior of oocytes is also measured. It is seen that 80% of GV oocytes with the kvis values between 15 and 30 k Pa s/m reach the MII stage.
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Affiliation(s)
- H Saffari
- Department of Electrical and Computer Engineering, Tarbiat Modares University (TMU), Tehran, Iran
| | - S Hajiaghalou
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - M A Hajari
- Department of Cell Engineering, Cell Science Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - H Gourabi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
| | - D Fathi
- Department of Electrical and Computer Engineering, Tarbiat Modares University (TMU), Tehran, Iran.
| | - R Fathi
- Department of Embryology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
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26
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Yin H, Chu Y, Wang W, Zhang Z, Meng Z, Min Q. Mass tag-encoded nanointerfaces for multiplexed mass spectrometric analysis and imaging of biomolecules. NANOSCALE 2023; 15:2529-2540. [PMID: 36688447 DOI: 10.1039/d2nr06020e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Revealing multiple biomolecules in the physiopathological environment simultaneously is crucial in biological and biomedical research. Mass spectrometry (MS) features unique technical advantages in multiplexed and label-free analyses. However, owing to comparably low abundance and poor ionization efficiency of target biomolecules, direct MS profiling of these biological species in vitro or in situ remains a challenge. An emerging route to solve this issue is to devise mass tag (MT)-encoded nanointerfaces which specifically convert the abundance or activity of biomolecules into amplified ion signals of mass tags, offering an ideal strategy for synchronous MS assaying and mapping of multiple targets in biofluids, cells and tissues. This review provides a thorough and organized overview of recent advances in MT-encoded nanointerfaces elaborately tailored for several practical applications in multiplexed MS bioanalysis and biomedical research. First, we start with elucidation of the structural characteristics and working principle of MT-encoded nanointerfaces in specific labeling and sensing of multiple biological targets. In addition, we further discuss the application scenarios of MT-encoded nanointerfaces particularly in multiplexed biomarker assays, cell analysis, and tissue imaging. Finally, the current challenges are pointed out and future prospects of these nanointerfaces in MS analysis are forecast.
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Affiliation(s)
- Hao Yin
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Yanxin Chu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Zhenzhen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Zhen Meng
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
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27
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Xu ST, Yang C, Yan XP. Organic Mass Cytometry Discriminating Cycle Stages of Single Cells with Small Molecular Indicators. Anal Chem 2023; 95:2312-2320. [PMID: 36651064 DOI: 10.1021/acs.analchem.2c04165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cell cycle is a significant factor toward cellular heterogeneity, so cell cycle discrimination is a precise measurement on the top of single-cell analysis. Single-cell analysis based on organic mass spectrometry has received great attention for its unique ability to profile single-cell metabolome, but the influence of cell cycle on cellular metabolome heterogeneity has been overlooked until now due to the lack of a compatible cell cycle discrimination method. Here, we report a robust protocol based on the combination of three small molecular indicators, consisting of two small molecular labels (Hoechst and docetaxel) and one cellular endogenous compound [phosphocholine (34:1)], to discriminate single cells at different cycle stages in real time by organic mass cytometry. More than 6000 HeLa cells were acquired by an improved organic mass cytometry system to build a cell cycle differentiation model. The model successfully discriminated single HeLa cells, SCC7, and Hep G2 cells, at G0/G1, S, and G2/M stages with larger than 85% sensitivity and larger than 89% specificity. Along with cell cycle discrimination, obvious heterogeneity of amino acids, nucleotides, energy metabolic intermediates, and phospholipids was observed among single cells at different cycle stages by this protocol, further demonstrating the necessity of cell cycle discrimination for cellular metabolome heterogeneity research and the potential of more endogenous small molecular compounds for cell cycle discrimination.
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Affiliation(s)
- Shu-Ting Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Cheng Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiu-Ping Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Jiangnan University, Wuxi 214122, China
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28
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Liu Q, Martínez-Jarquín S, Ge W, Zenobi R. Development of a 3D-Printed Ionization Source for Single-Cell Analysis. Anal Chem 2023; 95:1823-1828. [PMID: 36622658 DOI: 10.1021/acs.analchem.2c04279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Understanding the physiologies and pathologies of diseases requires a thorough understanding of metabolic heterogeneity in cells. This technical note presents a 3D printing technology for manufacturing an ionization source that is specially adapted for mass spectrometry-based single-cell analysis. This all-in-one 3D-printed electrospray ionization source integrates the sample introduction, metabolite extraction, and ionization into one device, simplifying the process of single-cell analysis and improving the reproducibility of the measurement. We successfully used it for high-throughput analysis of three types of cancer cells (around 17 cells/min) and used the t-distributed stochastic neighbor embedding algorithm to distinguish different cell types based on detected metabolites. By simply adjusting the printing parameters of the 3D-printed ionization source, it can be applied to cells with different sizes. The proposed 3D-printed ionization source promises to open new possibilities for single-cell analysis.
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Affiliation(s)
- Qinlei Liu
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich CH-8093, Switzerland
| | | | - Wenjie Ge
- Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich CH-8093, Switzerland
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29
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Ren J, Li HW, Chen L, Zhang M, Liu YX, Zhang BW, Xu R, Miao YY, Xu XM, Hua X, Sun XG, Yu RJ, Long YT, Hu SS. Mass Spectrometry Imaging-Based Single-Cell Lipidomics Profiles Metabolic Signatures of Heart Failure. RESEARCH 2023; 6:0019. [PMID: 37040505 PMCID: PMC10076023 DOI: 10.34133/research.0019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/14/2022] [Indexed: 01/13/2023]
Abstract
Heart failure (HF), leading as one of the main causes of mortality, has become a serious public health issue with high prevalence around the world. Single cardiomyocyte (CM) metabolomics promises to revolutionize the understanding of HF pathogenesis since the metabolic remodeling in the human hearts plays a vital role in the disease progression. Unfortunately, current metabolic analysis is often limited by the dynamic features of metabolites and the critical needs for high-quality isolated CMs. Here, high-quality CMs were directly isolated from transgenic HF mice biopsies and further employed in the cellular metabolic analysis. The lipids landscape in individual CMs was profiled with a delayed extraction mode in time-of-flight secondary ion mass spectrometry. Specific metabolic signatures were identified to distinguish HF CMs from the control subjects, presenting as possible single-cell biomarkers. The spatial distributions of these signatures were imaged in single cells, and those were further found to be strongly associated with lipoprotein metabolism, transmembrane transport, and signal transduction. Taken together, we systematically studied the lipid metabolism of single CMs with a mass spectrometry imaging method, which directly benefited the identification of HF-associated signatures and a deeper understanding of HF-related metabolic pathways.
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Affiliation(s)
- Jie Ren
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
| | - Hao-Wen Li
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Liang Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
| | - Min Zhang
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yan-Xiang Liu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
| | - Bo-Wen Zhang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
| | - Rui Xu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Yan-Yan Miao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Xue-Mei Xu
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
| | - Xin Hua
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, P. R. China
| | - Xiao-Gang Sun
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
| | - Ru-Jia Yu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Yi-Tao Long
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, P. R. China
| | - Sheng-Shou Hu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Disease, Chinese Academy of Medicine Science (CAMS) and Perking Union Medical College (PUMC), Beijing, 100037, P. R. China
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30
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Feng M, Gao B, Garcia LR, Sun Q. Microbiota-derived metabolites in regulating the development and physiology of Caenorhabditis elegans. Front Microbiol 2023; 14:1035582. [PMID: 36925470 PMCID: PMC10011103 DOI: 10.3389/fmicb.2023.1035582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 02/09/2023] [Indexed: 03/08/2023] Open
Abstract
Microbiota consist of microorganisms that provide essential health benefits and contribute to the animal's physiological homeostasis. Microbiota-derived metabolites are crucial mediators in regulating host development, system homeostasis, and overall fitness. In this review, by focusing on the animal model Caenorhabditis elegans, we summarize key microbial metabolites and their molecular mechanisms that affect animal development. We also provide, from a bacterial perspective, an overview of host-microbiota interaction networks used for maintaining host physiological homeostasis. Moreover, we discuss applicable methodologies for profiling new bacterial metabolites that modulate host developmental signaling pathways. Microbiota-derived metabolites have the potential to be diagnostic biomarkers for diseases, as well as promising targets for engineering therapeutic interventions against animal developmental or health-related defects.
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Affiliation(s)
- Min Feng
- Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Baizhen Gao
- Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - L Rene Garcia
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - Qing Sun
- Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
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31
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Stiborek M, Jindřichová L, Meliorisová S, Bednařík A, Prysiazhnyi V, Kroupa J, Houška P, Adamová B, Navrátilová J, Kanický V, Preisler J. Infrared Laser Desorption of Intact Nanoparticles for Digital Tissue Imaging. Anal Chem 2022; 94:18114-18120. [PMID: 36514811 DOI: 10.1021/acs.analchem.2c05216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We report a new technique for the digital mapping of biomarkers in tissues based on desorption and counting intact gold nanoparticle (Au NP) tags using infrared laser ablation single-particle inductively coupled plasma mass spectrometry (IR LA SP ICP MS). In contrast to conventional UV laser ablation, Au NPs are not disintegrated during the desorption process due to their low absorption at 2940 nm. A mass spectrometer detects up to 83% of Au NPs. The technique is demonstrated on mapping a proliferation marker, nuclear protein Ki-67, in three-dimensional (3D) aggregates of colorectal carcinoma cells, and the results are compared with confocal fluorescence microscopy and UV LA ICP MS. Precise counting of 20 nm Au NPs with a single-particle detection limit in each pixel by the new approach generates sharp distribution maps of a specific biomarker in the tissue. Advantageously, the desorption of Au NPs from regions outside the tissue is strongly suppressed. The developed methodology promises multiplex mapping of low-abundant biomarkers in numerous biological and medical applications using multielemental mass spectrometers.
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Affiliation(s)
- Marek Stiborek
- Department of Chemistry, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Lenka Jindřichová
- Department of Chemistry, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Stanislava Meliorisová
- Department of Chemistry, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Antonín Bednařík
- Department of Chemistry, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Vadym Prysiazhnyi
- Department of Chemistry, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Jiří Kroupa
- Research Center of Automatic Manipulation, Faculty of Mechanical Engineering, Brno University of Technology, 616 69 Brno, Czech Republic
| | - Pavel Houška
- Research Center of Automatic Manipulation, Faculty of Mechanical Engineering, Brno University of Technology, 616 69 Brno, Czech Republic
| | - Barbora Adamová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Jarmila Navrátilová
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, 602 00 Brno, Czech Republic
| | - Viktor Kanický
- Department of Chemistry, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Jan Preisler
- Department of Chemistry, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
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32
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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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33
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Wu Y, Zhang W, Zhao Y, Wang X, Guo G. Technology development trend of electrospray ionization mass spectrometry for single-cell proteomics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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34
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Zhang D, Qin Q, Qiao L. Mass spectrometry profiling of single bacterial cells reveals metabolic regulation during antibiotics induced bacterial filamentation. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.107938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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35
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Tan S, Yin X, Feng L, Wang J, Li C, Jiang Y, Gong X, Fang X, Dai X. Investigation on the binary ionization choices for large conjugated amines during electrospray ionization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2022; 36:e9330. [PMID: 35637635 DOI: 10.1002/rcm.9330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/29/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
RATIONALE Generally, amines form protonated cations ([M + H]+ ) in positive polarity during electrospray ionization (ESI). However, it was found that large conjugated amines (LCAs) had binary ionization choices of generating either radical cations (M•+ ) or [M + H]+ during ESI. Investigation on the mechanism would further our understanding of ESI. METHODS In this work, the binary ionization behavior of LCAs was reported and studied. Internal factors (functional groups and sizes of conjugated systems) and external factors (solvent type, flow rate, and electrode position) were systematically investigated and discussed. RESULTS For the internal factors, electron-donating groups and large conjugated structures of LCAs were conducive to the generation of M•+ . For the external factors, aprotic solvent, higher flow rate, and shorter distance from the electrode to the spray cone facilitated the formation of M•+ but hampered the generation of [M + H]+ . CONCLUSION The present study illustrated that the formations of M•+ and [M + H]+ for LCAs were two independent processes. The M•+ cations of LCAs were formed on the surface of the electrode through electrochemical oxidation, whereas the [M + H]+ cations were generated following the typical ESI evolution process. By regulating the external factors, the ionization results of LCAs could be well modulated.
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Affiliation(s)
- Siyuan Tan
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People's Republic of China
| | - Xinchi Yin
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People's Republic of China
| | - Lulu Feng
- Department of Chemistry, Zhejiang University, Zhejiang, Hangzhou, People's Republic of China
| | - Juduo Wang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People's Republic of China
| | - Chang Li
- College of Instrumentation & Electrical Engineering, Jilin University, Changchun, People's Republic of China
| | - You Jiang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People's Republic of China
| | - Xiaoyun Gong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People's Republic of China
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People's Republic of China
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People's Republic of China
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36
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Liu M, Miao D, Qin S, Liu H, Bai Y. Mass tags-based mass spectrometric immunoassay and its bioanalysis applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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37
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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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38
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Xie T, Zhang Q, Zhang W, Feng S, Lin JM. Inkjet-Patterned Microdroplets as Individual Microenvironments for Adherent Single Cell Culture. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107992. [PMID: 35362237 DOI: 10.1002/smll.202107992] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/26/2022] [Indexed: 06/14/2023]
Abstract
Adhesion of single cells is the foundation of manifold cellular behaviors and life processes. However, investigating the function of a specific cell is still challenging due to deficiency of adhesion or interference from surrounding cells. Herein, an open microfluidic system is reported for culturing adherent single cells, implemented by a micrometer-scale droplet matrix on an inkjet-printed polylysine template. The target cells are isolated from any cell from other droplets, and their adhesion strength is determined to be comparable to conventional petri dishes via an in-situ investigation with a microfluidic extractor. On this proposed platform, isolated single cells are observed to display an entirely distinct spreading behavior featuring total absence of elongation, indicating drastic cell behavior change from their "singleness." This system has high versatility and compatibility for various assaying methods, assuring a promising potential in detailed single cell behavior and cell heterogeneity studies.
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Affiliation(s)
- Tianze Xie
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, P. R. China
| | - Qiang Zhang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, P. R. China
| | - Weifei Zhang
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology, N 3rd Ring Road E 18, Beijing, 100029, P. R. China
| | - Shuo Feng
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, P. R. China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, P. R. China
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39
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Xu H, Zhang Z, Wang Y, Zhang X, Zhu JJ, Min Q. Sense and Validate: Fluorophore/Mass Dual-Encoded Nanoprobes for Fluorescence Imaging and MS Quantification of Intracellular Multiple MicroRNAs. Anal Chem 2022; 94:6329-6337. [PMID: 35412806 DOI: 10.1021/acs.analchem.2c00513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Simultaneously monitoring and quantifying intracellular multiple microRNAs (miRNAs) is highly essential to clinical diagnosis and pathological research. However, revealing the intracellular distribution of multiple miRNAs while determining their content in a multiplex and quantitative format remains challenging. Considering the respective technical merit of fluorescence imaging and mass spectrometry (MS) in in situ detection and multiplex assaying, we herein propose fluorophore/mass dual-encoded nanoprobes (FMNPs) that can execute target-triggered hairpin self-assembly to enable in situ amplified imaging and follow-up MS quantification of intracellular multiple miRNAs. The FMNPs responsive to the target miRNA were constructed by codecorating gold nanoparticles (AuNPs) with locked hairpin DNA probes (LH1) and corresponding mass tags (MTs) for fluorescent and mass spectrometric dual-modal readout. Cellular miRNAs can separately trigger recycled hairpin self-assembly, leading to the continuous liberation of fluorophore-labeled bolt DNA (bDNA) for fluorescence imaging in cells. Moreover, the postreaction FMNPs afford an extra chance to validate the fluorescence output of miRNA-21 and miRNA-141 by accurate MS quantification relying on the ion signal of the barcoded MTs. Fluorescence imaging and MS quantification of miRNA-21 and miRNA-141 have also been successfully accomplished in different cell lines, highlighting its potential in cell subtyping. This "sense-and-validate" strategy creates a new modality for assaying multiple intracellular miRNAs and holds great promise in unveiling multicomponent-involved events in cellular processes and determining multiple biomarkers in accurate clinical diagnosis.
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Affiliation(s)
- Hongmei Xu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.,Institute of Environmental Science, Shanxi University, Taiyuan 030006, P. R. China
| | - Zhenzhen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yihan Wang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Xuemeng Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Qianhao Min
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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40
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Xie H, Ding X. The Intriguing Landscape of Single-Cell Protein Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105932. [PMID: 35199955 PMCID: PMC9036017 DOI: 10.1002/advs.202105932] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Indexed: 05/15/2023]
Abstract
Profiling protein expression at single-cell resolution is essential for fundamental biological research (such as cell differentiation and tumor microenvironmental examination) and clinical precision medicine where only a limited number of primary cells are permitted. With the recent advances in engineering, chemistry, and biology, single-cell protein analysis methods are developed rapidly, which enable high-throughput and multiplexed protein measurements in thousands of individual cells. In combination with single cell RNA sequencing and mass spectrometry, single-cell multi-omics analysis can simultaneously measure multiple modalities including mRNAs, proteins, and metabolites in single cells, and obtain a more comprehensive exploration of cellular signaling processes, such as DNA modifications, chromatin accessibility, protein abundance, and gene perturbation. Here, the recent progress and applications of single-cell protein analysis technologies in the last decade are summarized. Current limitations, challenges, and possible future directions in this field are also discussed.
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Affiliation(s)
- Haiyang Xie
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
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41
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Wu Y, Chang Y, Shao Y, Guo G, Liu Z, Wang X. Controllable Fabrication of Small-Size Holding Pipets for the Nondestructive Manipulation of Suspended Living Single Cells. Anal Chem 2022; 94:4924-4929. [PMID: 35298884 DOI: 10.1021/acs.analchem.2c00418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The capture and manipulation of single cells are an important premise and basis for intracellular delivery, which provides abundant molecular and omics information for biomedical development. However, for intracellular delivery of cargos into/from small-size suspended living single cells, the capture methods are limited by the lack of small-size holding pipets, poor cell activity, and the low spatial accuracy of intracellular delivery. To solve these problems, a method for the controllable fabrication of small-size holding pipets was proposed. A simple, homemade microforge instrument including an imaging device was built to cut and melt the glass capillary tip by controlling the heat production of a nichrome wire. The controllable fabrication of small-size holding pipets was realized by observing the fabrication process in real time. Combined with an electroosmotic drive system and a micromanipulation system with high spatial resolution, the holding pipet achieved the active capture, movement, and sampling of suspended living single cells. Moreover, solid-phase microextraction was performed on captured single pheochromocytoma cells, and the extracted dopamine was successfully detected using an electrochemical method. The homemade microforge instrument overcame the limitations of traditional microforges, resulting in holding pipets that were sufficiently small for small-size suspended single living cells (5-30 μm). This proactive capture method overcame the shortcomings of existing methods to achieve the multiangle, high-precision manipulation of single cells, thereby allowing the intracellular delivery of small-size single cells in suspension with high spatiotemporal resolution.
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Affiliation(s)
- Yuanyuan Wu
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing 100124, China
| | - Yaran Chang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing 100124, China
| | - Yunlong Shao
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing 100124, China
| | - Guangsheng Guo
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing 100124, China.,Minzu University of China, Beijing 100081, China
| | - Zhihong Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xiayan Wang
- Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Department of Chemistry and Biology, Beijing University of Technology, Beijing 100124, China
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42
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Xu S, Liu H, Bai Y. Highly sensitive and multiplexed mass spectrometric immunoassay techniques and clinical applications. Anal Bioanal Chem 2022; 414:5121-5138. [PMID: 35165779 DOI: 10.1007/s00216-022-03945-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/17/2022] [Accepted: 01/31/2022] [Indexed: 11/29/2022]
Abstract
Immunoassay is one of the most important clinical techniques for disease/pathological diagnosis. Mass spectrometry (MS) has been a popular and powerful readout technique for immunoassays, generating the mass spectrometric immunoassays (MSIAs) with unbeatable channels for multiplexed detection. The sensitivity of MSIAs has been greatly improved with the development of mass labels from element labels to small-molecular labels. MSIAs are also expended from the representative element MS-based methods to the laser-based organic MS and latest ambient MS, improving in both technology and methodology. Various MSIAs present high potential for clinical applications, including the biomarker screening, the immunohistochemistry, and the advanced single-cell analysis. Here, we give an overall review of the development of MSIAs in recent years, highlighting the latest improvement of mass labels and MS techniques for clinical immunoassays.
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Affiliation(s)
- Shuting Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,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, 100871, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Huwei Liu
- 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, 100871, 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, 100871, China.
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43
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Wang Y, Li B, Tian T, Liu Y, Zhang J, Qian K. Advanced on-site and in vitro signal amplification biosensors for biomolecule analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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44
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Shao Y, Zhou Y, Liu Y, Zhang W, Zhu G, Zhao Y, Zhang Q, Yao H, Zhao H, Guo G, Zhang S, Zhang X, Wang X. Intact living-cell electrolaunching ionization mass spectrometry for single-cell metabolomics. Chem Sci 2022; 13:8065-8073. [PMID: 35919431 PMCID: PMC9278508 DOI: 10.1039/d2sc02569h] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
A novel living-cell mass spectrometry method allows a whole cell to enter entirely into the MS inlet and ionize with almost no sample dilution and matrix interference, which greatly improves the sensitivity of single-cell metabolite detection.
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Affiliation(s)
- Yunlong Shao
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
| | - Yingyan Zhou
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
| | - Yuanxing Liu
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
| | - Wenmei Zhang
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
| | - Guizhen Zhu
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
| | - Yaoyao Zhao
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
| | - Qi Zhang
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
| | - Huan Yao
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Hansen Zhao
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Guangsheng Guo
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
- Minzu University of China, Beijing 100081, 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
| | - Xiayan Wang
- Department of Chemistry and Biology, Center of Excellence for Environmental Safety and Biological Effects, Beijing Key Laboratory for Green Catalysis and Separation, Beijing University of Technology, Beijing 100124, P. R. China
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45
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Shen Z, Zhao H, Yao H, Pan X, Yang J, Zhang S, Han G, Zhang X. Dynamic metabolic change of cancer cells induced by natural killer cells at single-cell level studied by label-free mass cytometry. Chem Sci 2022; 13:1641-1647. [PMID: 35282636 PMCID: PMC8827047 DOI: 10.1039/d1sc06366a] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/31/2021] [Indexed: 01/10/2023] Open
Abstract
Natural killer cells (NK cells) are important immune cells which have attracted increasing attention in cancer immunotherapy. Due to the heterogeneity of cells, individual cancer cells show different resistance to NK cytotoxicity, which has been revealed by flow cytometry. Here we used label-free mass cytometry (CyESI-MS) as a new tool to analyze the metabolites in Human Hepatocellular Carcinoma (HepG2) cells at the single-cell level after the interaction with different numbers of NK92 MI cells. A large amount of chemical information from individual HepG2 cells was obtained showing the process of cell apoptosis induced by NK cells. Nineteen metabolites which consecutively change during cell apoptosis were revealed by calculating their average relative intensity. Four metabolic pathways were impacted during cell apoptosis which hit 4 metabolites including glutathione (GSH), creatine, glutamic acid and taurine. We found that the HepG2 cells could be divided into two phenotypes after co-culturing with NK cells according to the bimodal distribution of concentration of these 4 metabolites. The correlation between metabolites and different apoptotic pathways in the early apoptosis cell group was established by the 4 metabolites at the single-cell level. This is a new idea of using single-cell specific metabolites to reveal the metabolic heterogeneity in cell apoptosis which would be a powerful means for evaluating the cytotoxicity of NK cells. Label-free mass cytometry is utilized to study the dynamic metabolic change during apoptosis in HepG2 cells induced by NK92 MI cells at the single-cell level. The metabolic heterogeneity of individual HepG2 cells during apoptosis was revealed.![]()
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Affiliation(s)
- Zizheng Shen
- Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Hansen Zhao
- Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Huan Yao
- Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Xingyu Pan
- Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Jinlei Yang
- Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University Beijing 100084 China
| | - Guojun Han
- Institute of Medical Technology, Peking University Health Science Center Beijing 100191 China
- Peking University School and Hospital of Stomatology Beijing 100081 P. R. China
- Department of Biomedical Engineering, Peking University Health Science Center Beijing 100191 P. R. China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University Beijing 100084 China
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46
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Xu ST, Yang C, Yan XP. Nanothorn Filter-Facilitated Online Cell Lysis for Rapid and Deep Intracellular Profiling by Single-Cell Mass Spectrometry. Anal Chem 2021; 93:15677-15686. [PMID: 34784185 DOI: 10.1021/acs.analchem.1c03529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry combined with flow cytometry is emerging for high-throughput single-cell metabolite analysis but still has problems with limited intracellular information coverage. Here, we show a simple and efficient all-in-one system integrating cell injection, cell extraction, online cell lysis, analyte ionization, and mass spectrometric detection for rapid single-HeLa-cell screening with in-depth profiling of cellular metabolites and drugs. Zinc oxide nanothorn-decorated filters with three bore sizes (5.22, 8.36, and 16.75 μm) were fabricated for efficient online lysis of the cell membrane (even nuclear membrane) to facilitate intracellular analyte release and demonstrated to have a size effect for potential subcellular discrimination. The two smaller-bore filters gave 2-11-fold improvements in signal response for representative intracellular metabolites, such as adenosine, glutamine, and leucine/isoleucine. Especially, the smallest-bore filter enabled successful detection of the metabolites in the nucleus, including tetrahydrobiopterin and cyclic guanosine monophosphate. The developed all-in-one system was explored to monitor the uptake of four anticancer drugs, including 5-fluorouracil, doxorubicin, gambogic acid, and paclitaxel in single cells, and further to investigate the drug uptake trends at the subcellular level. The all-in-one system integrates the merits of high-throughput single-cell screening and in-depth intracellular information profiling and is promising for high-coverage single-cell metabolome analysis to serve cell biology research and cancer research.
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Affiliation(s)
- Shu-Ting Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cheng Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiu-Ping Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,International Joint Laboratory on Food Safety, Wuxi 214122, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Key Laboratory of Synthetic and Biological Colloids, Ministry of Education, Jiangnan University, Wuxi 214122, China
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47
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Liu Q, Ge W, Wang T, Lan J, Martínez‐Jarquín S, Wolfrum C, Stoffel M, Zenobi R. High‐Throughput Single‐Cell Mass Spectrometry Reveals Abnormal Lipid Metabolism in Pancreatic Ductal Adenocarcinoma. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Qinlei Liu
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Wenjie Ge
- Department of Biology ETH Zurich Otto-Stern-Weg 7 8093 Zurich Switzerland
| | - Tongtong Wang
- Department of Health Sciences and Technology ETH Zurich Schorenstrasse 16 8603 Schwerzenbach Switzerland
| | - Jiayi Lan
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Sandra Martínez‐Jarquín
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Christian Wolfrum
- Department of Health Sciences and Technology ETH Zurich Schorenstrasse 16 8603 Schwerzenbach Switzerland
| | - Markus Stoffel
- Department of Biology ETH Zurich Otto-Stern-Weg 7 8093 Zurich Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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48
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Liu Q, Ge W, Wang T, Lan J, Martínez‐Jarquín S, Wolfrum C, Stoffel M, Zenobi R. High-Throughput Single-Cell Mass Spectrometry Reveals Abnormal Lipid Metabolism in Pancreatic Ductal Adenocarcinoma. Angew Chem Int Ed Engl 2021; 60:24534-24542. [PMID: 34505339 PMCID: PMC8597026 DOI: 10.1002/anie.202107223] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/17/2021] [Indexed: 01/02/2023]
Abstract
Even populations of clonal cells are heterogeneous, which requires high-throughput analysis methods with single-cell sensitivity. Here, we propose a rapid, label-free single-cell analytical method based on active capillary dielectric barrier discharge ionization mass spectrometry, which can analyze multiple metabolites in single cells at a rate of 38 cells/minute. Multiple cell types (HEK-293T, PANC-1, CFPAC-1, H6c7, HeLa and iBAs) were discriminated successfully. We found evidence for abnormal lipid metabolism in pancreatic cancer cells. We also analyzed gene expression in a cancer genome atlas dataset and found that the mRNA level of a critical enzyme of lipid synthesis (ATP citrate lyase, ACLY) was upregulated in human pancreatic ductal adenocarcinoma (PDAC). Moreover, both an ACLY chemical inhibitor and a siRNA approach targeting ACLY could suppress the viability of PDAC cells. A significant reduction in lipid content in treated cells indicates that ACLY could be a potential target for treating pancreatic cancer.
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Affiliation(s)
- Qinlei Liu
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Wenjie Ge
- Department of BiologyETH ZurichOtto-Stern-Weg 78093ZurichSwitzerland
| | - Tongtong Wang
- Department of Health Sciences and TechnologyETH ZurichSchorenstrasse 168603SchwerzenbachSwitzerland
| | - Jiayi Lan
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Sandra Martínez‐Jarquín
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
| | - Christian Wolfrum
- Department of Health Sciences and TechnologyETH ZurichSchorenstrasse 168603SchwerzenbachSwitzerland
| | - Markus Stoffel
- Department of BiologyETH ZurichOtto-Stern-Weg 78093ZurichSwitzerland
| | - Renato Zenobi
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 38093ZurichSwitzerland
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49
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Hu J, Liu F, Chen Y, Shangguan G, Ju H. Mass Spectrometric Biosensing: A Powerful Approach for Multiplexed Analysis of Clinical Biomolecules. ACS Sens 2021; 6:3517-3535. [PMID: 34529414 DOI: 10.1021/acssensors.1c01394] [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] [Indexed: 12/13/2022]
Abstract
Rapid and sensitive detection of clinical biomolecules in a multiplexed fashion is of great importance for accurate diagnosis of diseases. Mass spectrometric (MS) approaches are exceptionally suitable for clinical analysis due to its high throughput, high sensitivity, and reliable qualitative and quantitative capabilities. To break through the bottleneck of MS technique for detecting high-molecular-weight substances with low ionization efficiency, the concept of mass spectrometric biosensing has been put forward by adopting mass spectrometric chips to recognize the targets and mass spectrometry to detect the signals switched by the recognition. In this review, the principle of mass spectrometric sensing, the construction of different mass tags used for biosensing, and the typical combination mode of mass spectrometric imaging (MSI) technique are summarized. Future perspectives including the design of portable matching platforms, exploitation of novel mass tags, development of effective signal amplification strategies, and standardization of MSI methodologies are proposed to promote the advancements and practical applications of mass spectrometric biosensing.
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Affiliation(s)
- Junjie Hu
- College of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining 272067, China
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Fei Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yunlong Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Guoqiang Shangguan
- College of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining 272067, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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50
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Xu S, Yang C, Yan X, Liu H. Towards high throughput and high information coverage: advanced single-cell mass spectrometric techniques. Anal Bioanal Chem 2021; 414:219-233. [PMID: 34435209 DOI: 10.1007/s00216-021-03624-w] [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: 06/29/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/23/2022]
Abstract
Mass spectrometry (MS) is attractive for single-cell analysis because of its high sensitivity, rich information, and large dynamic ranges, especially for the single-cell metabolome and proteome analysis. Efforts have been made to deal with the throughput and information coverage problems in typical manual single-cell MS techniques. In this review, advanced techniques to improve the automation and throughput for single-cell sampling and single-cell metabolome and proteome MS detection have been discussed. Furthermore, representative MS-based strategies that can increase the in-depth cellular information coverage and achieve the more comprehensive single-cell multiomics information during high throughput detection have been highlighted, providing an ongoing perspective of the MS performance for the single-cell research.
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Affiliation(s)
- Shuting Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Cheng Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xiuping Yan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China. .,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Huwei Liu
- Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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