1
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Wang X, Li Y, Hou X, Li J, Ma X. Lipid metabolism reprogramming in endometrial cancer: biological functions and therapeutic implications. Cell Commun Signal 2024; 22:436. [PMID: 39256811 PMCID: PMC11385155 DOI: 10.1186/s12964-024-01792-7] [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: 05/30/2024] [Accepted: 08/15/2024] [Indexed: 09/12/2024] Open
Abstract
BACKGROUND Endometrial cancer is one of the major gynecological cancers, with increasing incidence and mortality in the past decades. Emerging preclinical and clinical data have indicated its close association with obesity and dyslipidemia. Metabolism reprogramming has been considered as the hallmark of cancer, to satisfy the extensive need of nutrients and energy for survival and growth. Particularly, lipid metabolism reprogramming has aroused the researchers' interest in the field of cancer, including tumorigenesis, invasiveness, metastasis, therapeutic resistance and immunity modulation, etc. But the roles of lipid metabolism reprogramming in endometrial cancer have not been fully understood. This review has summarized how lipid metabolism reprogramming induces oncogenesis and progression of endometrial cancer, including the biological functions of aberrant lipid metabolism pathway and altered transcription regulation of lipid metabolism pathway. Besides, we proposed novel therapeutic strategies of targeting lipid metabolism pathway and concentrated on its potential of sensitizing immunotherapy and hormonal therapy, to further optimize the existing treatment modalities of patients with advanced/metastatic endometrial cancer. Moreover, we expect that targeting lipid metabolism plus hormone therapy may block the endometrial malignant transformation and enrich the preventative approaches of endometrial cancer. CONCLUSION Lipid metabolism reprogramming plays an important role in tumor initiation and cancer progression of endometrial cancer. Targeting the core enzymes and transcriptional factors of lipid metabolism pathway alone or in combination with immunotherapy/hormone treatment is expected to decrease the tumor burden and provide promising treatment opportunity for patients with advanced/metastatic endometrial cancer.
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Affiliation(s)
- Xiangyu Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095, Jiefang Avenue, Wuhan, Hubei Province, 430030, China
| | - Yinuo Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095, Jiefang Avenue, Wuhan, Hubei Province, 430030, China
| | - Xin Hou
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095, Jiefang Avenue, Wuhan, Hubei Province, 430030, China
| | - Jingfang Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095, Jiefang Avenue, Wuhan, Hubei Province, 430030, China
| | - Xiangyi Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095, Jiefang Avenue, Wuhan, Hubei Province, 430030, China.
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2
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Buglakova E, Ekelöf M, Schwaiger-Haber M, Schlicker L, Molenaar MR, Shahraz M, Stuart L, Eisenbarth A, Hilsenstein V, Patti GJ, Schulze A, Snaebjornsson MT, Alexandrov T. Spatial single-cell isotope tracing reveals heterogeneity of de novo fatty acid synthesis in cancer. Nat Metab 2024; 6:1695-1711. [PMID: 39251875 PMCID: PMC11422168 DOI: 10.1038/s42255-024-01118-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 07/26/2024] [Indexed: 09/11/2024]
Abstract
While heterogeneity is a key feature of cancer, understanding metabolic heterogeneity at the single-cell level remains a challenge. Here we present 13C-SpaceM, a method for spatial single-cell isotope tracing that extends the previously published SpaceM method with detection of 13C6-glucose-derived carbons in esterified fatty acids. We validated 13C-SpaceM on spatially heterogeneous models using liver cancer cells subjected to either normoxia-hypoxia or ATP citrate lyase depletion. This revealed substantial single-cell heterogeneity in labelling of the lipogenic acetyl-CoA pool and in relative fatty acid uptake versus synthesis hidden in bulk analyses. Analysing tumour-bearing brain tissue from mice fed a 13C6-glucose-containing diet, we found higher glucose-dependent synthesis of saturated fatty acids and increased elongation of essential fatty acids in tumours compared with healthy brains. Furthermore, our analysis uncovered spatial heterogeneity in lipogenic acetyl-CoA pool labelling in tumours. Our method enhances spatial probing of metabolic activities in single cells and tissues, providing insights into fatty acid metabolism in homoeostasis and disease.
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Affiliation(s)
- Elena Buglakova
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL, Heidelberg, Germany
| | - Måns Ekelöf
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Michaela Schwaiger-Haber
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Lisa Schlicker
- Division of Tumor Metabolism and Microenvironment, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Martijn R Molenaar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mohammed Shahraz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Lachlan Stuart
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas Eisenbarth
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Volker Hilsenstein
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Gary J Patti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Almut Schulze
- Division of Tumor Metabolism and Microenvironment, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Marteinn T Snaebjornsson
- Division of Tumor Metabolism and Microenvironment, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Metabolomics Core Facility, EMBL, Heidelberg, Germany.
- Molecular Medicine Partnership Unit, EMBL and Heidelberg University, Heidelberg, Germany.
- BioStudio, BioInnovation Institute, Copenhagen, Denmark.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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3
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Fu Y, Tao J, Liu T, Liu Y, Qiu J, Su D, Wang R, Luo W, Cao Z, Weng G, Zhang T, Zhao Y. Unbiasedly decoding the tumor microenvironment with single-cell multiomics analysis in pancreatic cancer. Mol Cancer 2024; 23:140. [PMID: 38982491 PMCID: PMC11232163 DOI: 10.1186/s12943-024-02050-7] [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: 05/07/2024] [Accepted: 06/21/2024] [Indexed: 07/11/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with a poor prognosis and limited therapeutic options. Research on the tumor microenvironment (TME) of PDAC has propelled the development of immunotherapeutic and targeted therapeutic strategies with a promising future. The emergence of single-cell sequencing and mass spectrometry technologies, coupled with spatial omics, has collectively revealed the heterogeneity of the TME from a multiomics perspective, outlined the development trajectories of cell lineages, and revealed important functions of previously underrated myeloid cells and tumor stroma cells. Concurrently, these findings necessitated more refined annotations of biological functions at the cell cluster or single-cell level. Precise identification of all cell clusters is urgently needed to determine whether they have been investigated adequately and to identify target cell clusters with antitumor potential, design compatible treatment strategies, and determine treatment resistance. Here, we summarize recent research on the PDAC TME at the single-cell multiomics level, with an unbiased focus on the functions and potential classification bases of every cellular component within the TME, and look forward to the prospects of integrating single-cell multiomics data and retrospectively reusing bulk sequencing data, hoping to provide new insights into the PDAC TME.
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Affiliation(s)
- Yifan Fu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- 4+4 Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jinxin Tao
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Tao Liu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yueze Liu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Jiangdong Qiu
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Dan Su
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Ruobing Wang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Wenhao Luo
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Zhe Cao
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Guihu Weng
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Taiping Zhang
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
- Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Yupei Zhao
- General Surgery Department, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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4
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Zhu J, Pan S, Chai H, Zhao P, Feng Y, Cheng Z, Zhang S, Wang W. Microfluidic Impedance Cytometry Enabled One-Step Sample Preparation for Efficient Single-Cell Mass Spectrometry. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310700. [PMID: 38483007 DOI: 10.1002/smll.202310700] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/05/2024] [Indexed: 06/27/2024]
Abstract
Single-cell mass spectrometry (MS) is significant in biochemical analysis and holds great potential in biomedical applications. Efficient sample preparation like sorting (i.e., separating target cells from the mixed population) and desalting (i.e., moving the cells off non-volatile salt solution) is urgently required in single-cell MS. However, traditional sample preparation methods suffer from complicated operation with various apparatus, or insufficient performance. Herein, a one-step sample preparation strategy by leveraging label-free impedance flow cytometry (IFC) based microfluidics is proposed. Specifically, the IFC framework to characterize and sort single-cells is adopted. Simultaneously with sorting, the target cell is transferred from the local high-salinity buffer to the MS-compatible solution. In this way, one-step sorting and desalting are achieved and the collected cells can be directly fed for MS analysis. A high sorting efficiency (>99%), cancer cell purity (≈87%), and desalting efficiency (>99%), and the whole workflow of impedance-based separation and MS analysis of normal cells (MCF-10A) and cancer cells (MDA-MB-468) are verified. As a standalone sample preparation module, the microfluidic chip is compatible with a variety of MS analysis methods, and envisioned to provide a new paradigm in efficient MS sample preparation, and further in multi-modal (i.e., electrical and metabolic) characterization of single-cells.
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Affiliation(s)
- Junwen Zhu
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Siyuan Pan
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Huichao Chai
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Peng Zhao
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Yongxiang Feng
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Zhen Cheng
- Department of Automation, Tsinghua University, Beijing, 100084, China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Wenhui Wang
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
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5
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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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6
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von Gerichten J, Saunders KDG, Kontiza A, Newman CF, Mayson G, Beste DJV, Velliou E, Whetton AD, Bailey MJ. Single-Cell Untargeted Lipidomics Using Liquid Chromatography and Data-Dependent Acquisition after Live Cell Selection. Anal Chem 2024; 96:6922-6929. [PMID: 38653330 PMCID: PMC11079853 DOI: 10.1021/acs.analchem.3c05677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
We report the development and validation of an untargeted single-cell lipidomics method based on microflow chromatography coupled to a data-dependent mass spectrometry method for fragmentation-based identification of lipids. Given the absence of single-cell lipid standards, we show how the methodology should be optimized and validated using a dilute cell extract. The methodology is applied to dilute pancreatic cancer and macrophage cell extracts and standards to demonstrate the sensitivity requirements for confident assignment of lipids and classification of the cell type at the single-cell level. The method is then coupled to a system that can provide automated sampling of live, single cells into capillaries under microscope observation. This workflow retains the spatial information and morphology of cells during sampling and highlights the heterogeneity in lipid profiles observed at the single-cell level. The workflow is applied to show changes in single-cell lipid profiles as a response to oxidative stress, coinciding with expanded lipid droplets. This demonstrates that the workflow is sufficiently sensitive to observing changes in lipid profiles in response to a biological stimulus. Understanding how lipids vary in single cells will inform future research into a multitude of biological processes as lipids play important roles in structural, biophysical, energy storage, and signaling functions.
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Affiliation(s)
- Johanna von Gerichten
- School
of Chemistry and Chemical Engineering, Faculty of Engineering and
Physical Sciences, University of Surrey, GU2 7XH Guildford, U.K.
| | - Kyle D. G. Saunders
- School
of Chemistry and Chemical Engineering, Faculty of Engineering and
Physical Sciences, University of Surrey, GU2 7XH Guildford, U.K.
| | - Anastasia Kontiza
- School
of Chemistry and Chemical Engineering, Faculty of Engineering and
Physical Sciences, University of Surrey, GU2 7XH Guildford, U.K.
| | - Carla F. Newman
- Cellular
Imaging and Dynamics, GlaxoSmithKline, Stevenage SG1 2NY, U.K.
| | - George Mayson
- School
of Bioscience, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, U.K.
| | - Dany J. V. Beste
- School
of Bioscience, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, U.K.
| | - Eirini Velliou
- Centre
for 3D Models of Health and Disease, University
College London, Division of Surgery and Interventional Science, London W1W 7TY, U.K.
| | - Anthony D. Whetton
- vHive,
School of Veterinary Medicine, School of Biosciences and Medicine, University of Surrey, Guildford GU2 7XH, U.K.
| | - Melanie J. Bailey
- School
of Chemistry and Chemical Engineering, Faculty of Engineering and
Physical Sciences, University of Surrey, GU2 7XH Guildford, U.K.
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7
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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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8
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Xu T, Li H, Dou P, Luo Y, Pu S, Mu H, Zhang Z, Feng D, Hu X, Wang T, Tan G, Chen C, Li H, Shi X, Hu C, Xu G. Concentric Hybrid Nanoelectrospray Ionization-Atmospheric Pressure Chemical Ionization Source for High-Coverage Mass Spectrometry Analysis of Single-Cell Metabolomics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306659. [PMID: 38359005 DOI: 10.1002/advs.202306659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/04/2024] [Indexed: 02/17/2024]
Abstract
High-coverage mass spectrometry analysis of single-cell metabolomics remains challenging due to the extremely low abundance and wide polarity of metabolites and ultra-small volume in single cells. Herein, a novel concentric hybrid ionization source, nanoelectrospray ionization-atmospheric pressure chemical ionization (nanoESI-APCI), is ingeniously designed to detect polar and nonpolar metabolites simultaneously in single cells. The source is constructed by inserting a pulled glass capillary coaxially into a glass tube that acts as a dielectric barrier layer. Benefitting from the integrated advantages of nanoESI and APCI, its limit of detection is improved by one order of magnitude to 10 pg mL-1. After the operational parameter optimization, 254 metabolites detected in nanoESI-APCI are tentatively identified from a single cell, and 82 more than those in nanoESI. The developed nanoESI-APCI is successively applied to study the metabolic heterogeneity of human hepatocellular carcinoma tissue microenvironment united with laser capture microdissection (LCM), the discrimination of cancer cell types and subtypes, the metabolic perturbations to glucose starvation in MCF7 cells and the metabolic regulation of cancer stem cells. These results demonstrated that the nanoESI-APCI not only opens a new avenue for high-coverage and high-sensitivity metabolomics analysis of single cell, but also facilitates spatially resolved metabolomics study coupled with LCM.
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Affiliation(s)
- Tianrun Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Hang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Peng Dou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Yuanyuan Luo
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Siming Pu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Hua Mu
- The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116023, P. R. China
| | - Zhihao Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Science, Dalian Key Laboratory for Online Analytical Instrumentation, Dalian, Liaoning, 116023, P. R. China
| | - Disheng Feng
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Xuesen Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Ting Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Guang Tan
- The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116023, P. R. China
| | - Chuang Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Science, Dalian Key Laboratory for Online Analytical Instrumentation, Dalian, Liaoning, 116023, P. R. China
| | - Haiyang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Science, Dalian Key Laboratory for Online Analytical Instrumentation, Dalian, Liaoning, 116023, P. R. China
| | - Xianzhe Shi
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Chunxiu Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), University of Chinese Academy of Sciences, Liaoning Province Key Laboratory of Metabolomics, Dalian, Liaoning, 116023, P. R. China
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9
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Liu Q, Lan J, Martínez-Jarquín S, Ge W, Zenobi R. Screening Metabolic Biomarkers in KRAS Mutated Mouse Acinar and Human Pancreatic Cancer Cells via Single-Cell Mass Spectrometry. Anal Chem 2024; 96:4918-4924. [PMID: 38471062 DOI: 10.1021/acs.analchem.3c05741] [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: 03/14/2024]
Abstract
Pancreatic cancer is a highly aggressive and rapidly progressing disease, often diagnosed in advanced stages due to the absence of early noticeable symptoms. The KRAS mutation is a hallmark of pancreatic cancer, yet the underlying mechanisms driving pancreatic carcinogenesis remain elusive. Cancer cells display significant metabolic heterogeneity, which is relevant to the pathogenesis of cancer. Population measurements may obscure information about the metabolic heterogeneity among cancer cells. Therefore, it is crucial to analyze metabolites at the single-cell level to gain a more comprehensive understanding of metabolic heterogeneity. In this study, we employed a 3D-printed ionization source for metabolite analysis in both mice and human pancreatic cancer cells at the single-cell level. Using advanced machine learning algorithms and mass spectral feature selection, we successfully identified 23 distinct metabolites that are statistically significantly different in KRAS mutant human pancreatic cancer cells and mouse acinar cells bearing the oncogenic KRAS mutation. These metabolites encompass a variety of chemical classes, including organic nitrogen compounds, organic acids and derivatives, organoheterocyclic compounds, benzenoids, and lipids. These findings shed light on the metabolic remodeling associated with KRAS-driven pancreatic cancer initiation and indicate that the identified metabolites hold promise as potential diagnostic markers for early detection in pancreatic cancer patients.
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Affiliation(s)
- Qinlei Liu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610065, China
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Jiayi Lan
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Sandra Martínez-Jarquín
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
- Advanced Materials and Healthcare Technologies Division, School of Pharmacym, University of Nottingha, University Park, NG7 2RD Nottingham, United Kingdom
| | - Wenjie Ge
- Cancer Institute, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu 221004, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 West Huaihai Road, Xuzhou, Jiangsu 221002, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu 221004, China
- Department of Biology, ETH Zurich, Otto-Stern-Weg 7, CH-8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
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10
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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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11
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Buglakova E, Ekelöf M, Schwaiger-Haber M, Schlicker L, Molenaar MR, Mohammed S, Stuart L, Eisenbarth A, Hilsenstein V, Patti GJ, Schulze A, Snaebjornsson MT, Alexandrov T. 13C-SpaceM: Spatial single-cell isotope tracing reveals heterogeneity of de novo fatty acid synthesis in cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.18.553810. [PMID: 38464218 PMCID: PMC10925155 DOI: 10.1101/2023.08.18.553810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Metabolism has emerged as a key factor in homeostasis and disease including cancer. Yet, little is known about the heterogeneity of metabolic activity of cancer cells due to the lack of tools to directly probe it. Here, we present a novel method, 13C-SpaceM for spatial single-cell isotope tracing of glucose-dependent de novo lipogenesis. The method combines imaging mass spectrometry for spatially-resolved detection of 13C6-glucose-derived 13C label incorporated into esterified fatty acids with microscopy and computational methods for data integration and analysis. We validated 13C-SpaceM on a spatially-heterogeneous normoxia-hypoxia model of liver cancer cells. Investigating cultured cells, we revealed single-cell heterogeneity of lipogenic acetyl-CoA pool labelling degree upon ACLY knockdown that is hidden in the bulk analysis and its effect on synthesis of individual fatty acids. Next, we adapted 13C-SpaceM to analyze tissue sections of mice harboring isocitrate dehydrogenase (IDH)-mutant gliomas. We found a strong induction of de novo fatty acid synthesis in the tumor tissue compared to the surrounding brain. Comparison of fatty acid isotopologue patterns revealed elevated uptake of mono-unsaturated and essential fatty acids in the tumor. Furthermore, our analysis uncovered substantial spatial heterogeneity in the labelling of the lipogenic acetyl-CoA pool indicative of metabolic reprogramming during microenvironmental adaptation. Overall, 13C-SpaceM enables novel ways for spatial probing of metabolic activity at the single cell level. Additionally, this methodology provides unprecedented insight into fatty acid uptake, synthesis and modification in normal and cancerous tissues.
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Affiliation(s)
- Elena Buglakova
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Måns Ekelöf
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Michaela Schwaiger-Haber
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Lisa Schlicker
- Division of Tumor Metabolism and Microenvironment, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Martijn R. Molenaar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Shahraz Mohammed
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Lachlan Stuart
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas Eisenbarth
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Volker Hilsenstein
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Gary J. Patti
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Almut Schulze
- Division of Tumor Metabolism and Microenvironment, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marteinn T. Snaebjornsson
- Division of Tumor Metabolism and Microenvironment, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Metabolomics Core Facility, EMBL, Heidelberg, Germany
- Molecular Medicine Partnership Unit, EMBL and Heidelberg University, Heidelberg, Germany
- BioStudio, BioInnovation Institute, Copenhagen, Denmark
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12
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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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13
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Yang J, Cheng R, Pan X, Pan S, Du M, Yao H, Hu Z, Zhang S, Zhang X. Single-Cell Unsaturated Lipid Profiling for Studying Chemoresistance Heterogeneity of Triple-Negative Breast Cancer Cells. Anal Chem 2024. [PMID: 38334074 DOI: 10.1021/acs.analchem.3c04887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Chemoresistance to triple-negative breast cancer (TNBC) is a critical issue in clinical practice. Lipid metabolism takes a unique role in breast cancer cells; especially, unsaturated lipids involving cell membrane fluidity and peroxidation are highly remarked. At present, for the lack of a high-resolution molecular recognition platform at the single-cell level, it is still hard to systematically study chemoresistance heterogeneity based on lipid unsaturation proportion. By designing a single-cell mass spectrometry workflow based on CyESI-MS, we profiled the unsaturated lipids of TNBC cells to evaluate lipidomic remodeling under platinum stress. Profiling revealed the heterogeneity of the polyunsaturated lipid proportion of TNBC cells under cisplatin treatment. A cluster of cells identified by polyunsaturated lipid accumulation was found to be involved in platinum sensitivity. Furthermore, we found that the chemoresistance of TNBC cells could be regulated by fatty acid supplementation, which determinates the composition of unsaturated lipids. These discoveries provide insights for monitoring and controlling cellular unsaturated lipid proportions to overcome chemoresistance in breast cancer.
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Affiliation(s)
- Jinlei Yang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Runsong Cheng
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xingyu Pan
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Siyuan Pan
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Murong Du
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Huan Yao
- National Institute of Metrology, Beijing 100029, China
- Key Laboratory of Chemical Metrology and Applications on Nutrition and Health for State Market Regulation, Beijing 100029, China
| | - Zhian Hu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology, Beijing 100083, China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
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14
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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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15
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Yan Z, Liu K, Xu P, Chen Z, Zhang P, Pei S, Cheng Q, Huang S, Li B, Lv J, Xu Z, Xu H, Yang L, Zhang D. ACLY promotes gastric tumorigenesis and accelerates peritoneal metastasis of gastric cancer regulated by HIF-1A. Cell Cycle 2023; 22:2288-2301. [PMID: 38009671 PMCID: PMC10730177 DOI: 10.1080/15384101.2023.2286805] [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: 07/16/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023] Open
Abstract
Mounting evidence indicates the potential involvement of ATP-citrate lyase (ACLY) in the modulation of various cancer types. Nevertheless, the precise biological significance of ACLY in gastric cancer (GC) remains elusive. This study sought to elucidate the biological function of ACLY and uncover its influence on peritoneal metastasis in GC. The expression of ACLY was assessed using both real-time quantitative PCR and western blot techniques. To investigate the impact of ACLY on the proliferation of gastric cancer (GC) cells, colony formation and 5-ethynyl-2'-deoxyuridine (EdU) assays were performed. The migratory and invasive abilities of GC were evaluated using wound healing and transwell assays. Additionally, a bioinformatics analysis was employed to predict the correlation between ACLY and HIF-1A. This interaction was subsequently confirmed through a chromatin immunoprecipitation (ChIP) assay. ACLY exhibited upregulation in gastric cancer (GC) as well as in peritoneal metastasis. Its overexpression was found to facilitate the proliferation and metastasis of GC cells in both in vitro and in vivo experiments. Moreover, ACLY was observed to play a role in promoting angiogenesis and epithelial-mesenchymal transition (EMT). Notably, under hypoxic conditions, HIF-1A levels were elevated, thereby acting as a transcription factor to upregulate ACLY expression. Under the regulatory influence of HIF-1A, ACLY exerts a significant impact on the progression of gastric cancer, thereby facilitating peritoneal metastasis.
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Affiliation(s)
- Zhengyuan Yan
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
- Department of Surgery, Nanjing Lishui People’s Hospital, Nanjing, China
| | - Kanghui Liu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Peng Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Zhengwei Chen
- Department of Surgery, Nanjing Lishui People’s Hospital, Nanjing, China
| | - Pengpeng Zhang
- Department of Thoracic Surgery, The Second Hospital of Nanjing, Nanjing, China
| | - Shengbin Pei
- Department of Breast Surgical Oncology, National Cancer Center Cancer Hospital, Beijing, China
| | - Quan Cheng
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Shansong Huang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Bowen Li
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Jialun Lv
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Zekuan Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Hao Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Li Yang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Diancai Zhang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
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16
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Deng J, Zeng X, He C, Zhong D, Wu Y, Liu N, Luan T, Yang Y. Exploring the Accumulation Behavior and Heterogeneity of Perfluorooctanesulfonic Acid in Zebrafish Primary Organ Cells by Single-Cell Mass Cytometry. Anal Chem 2023; 95:13750-13755. [PMID: 37669419 DOI: 10.1021/acs.analchem.3c02398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Perfluorooctanesulfonic acid (PFOS) is a commonly found environmental pollutant with potential toxicity and health risks to biosystems and ecosystems. Study of the accumulation behavior and heterogeneity of PFOS in biological primary organ cells provides us significant insights to explore its cytotoxicity, carcinogenicity, and mutagenicity. Here a single-cell mass cytometry system was established for the high-throughput analysis of trace PFOS and the exploration of its accumulation behavior and heterogeneity in zebrafish primary organ cells. The single-cell mass cytometry system applied a ∼25 μm constant-inner-diameter capillary as the single-cell generation and transportation channel with an etched tip-end of 40 μm as the nanoelectrospray emitter for mass spectrometric analysis. The single-cell mass cytometry system showed satisfactory semiquantitative performance and sensitivity for analysis of PFOS in single cells, with a high detection throughput of ∼35 cells/min. Subsequently, the liver, intestine, heart, and brain from PFOS-exposed zebrafish (100 pg/μL, 28 days) were dissociated and prepared as cell suspensions, and the cell suspensions were introduced into the single-cell mass cytometry system for high-throughput analysis of PFOS in individual primary organ cells. Significant cellular accumulation heterogeneities were observed, with the highest content in liver cells, followed by intestine cells, then heart cells, and the lowest in brain cells. In addition, the dynamics of PFOS in the zebrafish liver, intestine, heart, and brain cells showed typical violin plot distributions and were well-described using a gamma (γ) function.
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Affiliation(s)
- Jiewei Deng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
- Smart Medical Innovation Technology Center, Guangdong University of Technology, Guangzhou 510006, China
- Guangdong Laboratory of Chemistry and Fine Chemical Engineering Jieyang Center, Jieyang 515200, China
| | - Xiliu Zeng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Cai He
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
- Guangdong Provincial Engineering Research Center for Ambient Mass Spectrometry, Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences, (China National Analytical Center, Guangzhou), 100 Xianlie Middle Road, Guangzhou 510070, China
| | - Dahao Zhong
- Guangdong Provincial Key Laboratory of Water Quality Improvement and Ecological Restoration for Watersheds, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou 510006, China
| | - Yuehua Wu
- Guangdong Women and Children Hospital, Guangzhou 511400, China
| | - Ning Liu
- Guangdong Provincial Engineering Research Center for Ambient Mass Spectrometry, Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences, (China National Analytical Center, Guangzhou), 100 Xianlie Middle Road, Guangzhou 510070, China
| | - Tiangang Luan
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
- Guangdong Laboratory of Chemistry and Fine Chemical Engineering Jieyang Center, Jieyang 515200, China
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yunyun Yang
- Guangdong Provincial Engineering Research Center for Ambient Mass Spectrometry, Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences, (China National Analytical Center, Guangzhou), 100 Xianlie Middle Road, Guangzhou 510070, China
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17
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Li Y, Jia K, Pan Y, Han J, Chen J, Wang Y, Ma X, Chen H, Wang S, Xie D, Xiong C, Nie Z. Pocket-Size Wireless Nanoelectrospray Ionization Mass Spectrometry for Metabolic Analysis of Salty Biofluids and Single Cells. Anal Chem 2023; 95:4612-4618. [PMID: 36862115 DOI: 10.1021/acs.analchem.2c04268] [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
Analysis of volume-limited biological samples such as single cells and biofluids not only benefits clinical purposes but also promotes fundamental research in life sciences. Detection of these samples, however, imposes strict requirements on measurement performance because of the minimal volume and concentrated salts of the samples. Herein, we developed a self-cleaning nanoelectrospray ionization device powered by a pocket-size "MasSpec Pointer" (MSP-nanoESI) for metabolic analysis of salty biological samples with limited volume. The self-cleaning effect induced by Maxwell-Wagner electric stress helps with keeping the borosilicate glass capillary tip free from clogging and thus increasing salt tolerance. This device possesses a high sample economy (about 0.1 μL per test) due to its pulsed high voltage supply, sampling method (dipping the nanoESI tip into analyte solution), and contact-free electrospray ionization (ESI) (the electrode does not touch the analyte solution during ESI). High repeatable results could be acquired by the device with a relative standard deviation (RSD) of 1.02% for voltage output and 12.94% for MS signals of caffeine standard. Single MCF-7 cells were metabolically analyzed directly from phosphate buffered saline, and two types of untreated cerebrospinal fluid from hydrocephalus patients were distinguished with 84% accuracy. MSP-nanoESI gets rid of the bulky apparatus and could be held in hand or put into one's pocket for transportation, and it could operate for more than 4 h without recharge. We believe this device will boost scientific research and clinical usage of volume-limited biological samples with high-concentration salts in a low-cost, convenient, and rapid manner.
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Affiliation(s)
- Yuze Li
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering, College of Chemistry and Chemical Engineering, Ningxia University, Yinchuan 750021, China.,Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ke Jia
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yixin Pan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Han
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Junyu Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiran Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaobing Ma
- Aerospace Information Research Institute, Chinese Academy of Sciences Beijing 100094, China
| | - Hongwei Chen
- Department of Neurosurgery for Cerebrospinal Fluid Diseases, Aviation General Hospital, Beijing 100012, China
| | - Shengjie Wang
- Department of Neurosurgery for Cerebrospinal Fluid Diseases, Aviation General Hospital, Beijing 100012, China
| | - Dongcheng Xie
- Department of Neurosurgery for Cerebrospinal Fluid Diseases, Aviation General Hospital, Beijing 100012, China
| | - Caiqiao Xiong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Zongxiu Nie
- State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering, College of Chemistry and Chemical Engineering, Ningxia University, Yinchuan 750021, China.,Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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18
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Lewis HM, Gupta P, Saunders KDG, Briones S, von Gerichten J, Townsend PA, Velliou E, Beste DJV, Cexus O, Webb R, Bailey MJ. Nanocapillary sampling coupled to liquid chromatography mass spectrometry delivers single cell drug measurement and lipid fingerprints. Analyst 2023; 148:1041-1049. [PMID: 36723178 PMCID: PMC9969958 DOI: 10.1039/d2an01732f] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/27/2023] [Indexed: 01/28/2023]
Abstract
This work describes the development of a new approach to measure drug levels and lipid fingerprints in single living mammalian cells. Nanocapillary sampling is an approach that enables the selection and isolation of single living cells under microscope observation. Here, live single cell nanocapillary sampling is coupled to liquid chromatography for the first time. This allows molecular species to be separated prior to ionisation and improves measurement precision of drug analytes. The efficiency of transferring analytes from the sampling capillary into a vial was optimised in this work. The analysis was carried out using standard flow liquid chromatography coupled to widely available mass spectrometry instrumentation, highlighting opportunities for widespread adoption. The method was applied to 30 living cells, revealing cell-to-cell heterogeneity in the uptake of different drug molecules. Using this system, we detected 14-158 lipid features per single cell, revealing the association between bedaquiline uptake and lipid fingerprints.
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Affiliation(s)
- Holly-May Lewis
- Department of Chemistry, University of Surrey, Guildford, UK.
| | - Priyanka Gupta
- Department of Chemical and Process Engineering, University of Surrey, Guildford, UK
- Centre for 3D Models of Health and Disease, University College London - Division of Surgery and Interventional Science, London, UK
| | | | - Shazneil Briones
- School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | | | - Paul A Townsend
- School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Eirini Velliou
- Department of Chemical and Process Engineering, University of Surrey, Guildford, UK
- Centre for 3D Models of Health and Disease, University College London - Division of Surgery and Interventional Science, London, UK
| | - Dany J V Beste
- School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Olivier Cexus
- School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Roger Webb
- Ion Beam Centre, University of Surrey, Guildford, UK
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19
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Zhao X, Liang J, Chen Z, Jian R, Qian Y, Wang Y, Guo Z, Zhang W, Zhang Y, Yin H, Xia Y. sn-1 Specificity of Lysophosphatidylcholine Acyltransferase-1 Revealed by a Mass Spectrometry-Based Assay. Angew Chem Int Ed Engl 2023; 62:e202215556. [PMID: 36478519 DOI: 10.1002/anie.202215556] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022]
Abstract
Lysophosphatidylcholine acyltransferase-1 (LPCAT1) plays a critical role in the remodeling of phosphatidylcholines (PCs) in cellular lipidome. However, evidence is scarce regarding its sn-selectivity, viz. the preference of assembling acyl-Coenzyme A (CoA) at the C1 or C2-hydroxyl on a glycerol backbone because of difficulty to quantify the thus-formed PC sn-isomers. We have established a multiplexed assay to measure both sn- and acyl-chain selectivity of LPCAT1 toward a mixture of acyl-CoAs by integrating isomer-resolving tandem mass spectrometry. Our findings reveal that LPCAT1 shows exclusive sn-1 specificity regardless of the identity of acyl-CoAs. We further confirm that elevated PC 18 : 1/16:0 relative to its sn-isomer results from an increased expression of LPCAT1 in human hepatocellular carcinoma (HCC) tissue as compared to normal liver tissue. MS imaging via desorption electrospray ionization of PC 18 : 1/16:0 thus enables visualization of HCC margins in human liver tissue at a molecular level.
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Affiliation(s)
- Xue Zhao
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biological, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Jiaqi Liang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biological, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | | | - Ruijun Jian
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biological, Department of Chemistry, 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
| | - Yunfang Wang
- Hepato-pancreato-biliary Center, Beijing Tsinghua Changgung Hospital, Institute for Precision Medicine, Tsinghua University, Beijing, 102218, China
| | - Zhiying Guo
- Hepato-pancreato-biliary Center, Beijing Tsinghua Changgung Hospital, Institute for Precision Medicine, Tsinghua University, Beijing, 102218, China
| | - Wenpeng Zhang
- State key laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Ying Zhang
- School of Pharmaceutical Sciences, Tsinghua University-Peking University Joint Center for Life Sciences, and Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Hang Yin
- School of Pharmaceutical Sciences, Tsinghua University-Peking University Joint Center for Life Sciences, and Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biological, Department of Chemistry, Tsinghua University, Beijing, 100084, China
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20
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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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21
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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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22
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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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23
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Zuzčák M, Trnka J. Cellular metabolism in pancreatic cancer as a tool for prognosis and treatment (Review). Int J Oncol 2022; 61:93. [PMID: 35730611 PMCID: PMC9256076 DOI: 10.3892/ijo.2022.5383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/10/2022] [Indexed: 11/28/2022] Open
Abstract
Pancreatic cancer (PC) has one of the highest fatality rates and the currently available therapeutic options are not sufficient to improve its overall poor prognosis. In addition to insufficient effectiveness of anticancer treatments, the lack of clear early symptoms and early metastatic spread maintain the PC survival rates at a low level. Metabolic reprogramming is among the hallmarks of cancer and could be exploited for the diagnosis and treatment of PC. PC is characterized by its heterogeneity and, apart from molecular subtypes, the identification of metabolic subtypes in PC could aid in the development of more individualized therapeutic approaches and may lead to improved clinical outcomes. In addition to the deregulated utilization of glucose in aerobic glycolysis, PC cells can use a wide range of substrates, including branched‑chain amino acids, glutamine and lipids to fulfil their energy requirements, as well as biosynthetic needs. The tumor microenvironment in PC supports tumor growth, metastatic spread, treatment resistance and the suppression of the host immune response. Moreover, reciprocal interactions between cancer and stromal cells enhance their metabolic reprogramming. PC stem cells (PCSCs) with an increased resistance and distinct metabolic properties are associated with disease relapses and cancer spread, and represent another significant candidate for therapeutic targeting. The present review discusses the metabolic signatures observed in PC, a disease with a multifaceted and often transient metabolic landscape. In addition, the metabolic pathways utilized by PC cells, as well as stromal cells are discussed, providing examples of how they could present novel targets for therapeutic interventions and elaborating on how interactions between the various cell types affect their metabolism. Furthermore, the importance of PCSCs is discussed, focusing specifically on their metabolic adaptations.
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Affiliation(s)
- Michal Zuzčák
- Department of Biochemistry, Cell and Molecular Biology, Third Faculty of Medicine, Charles University, 10000 Prague, Czech Republic
- Center for Research on Nutrition, Metabolism and Diabetes, Third Faculty of Medicine, Charles University, 10000 Prague, Czech Republic
| | - Jan Trnka
- Department of Biochemistry, Cell and Molecular Biology, Third Faculty of Medicine, Charles University, 10000 Prague, Czech Republic
- Center for Research on Nutrition, Metabolism and Diabetes, Third Faculty of Medicine, Charles University, 10000 Prague, Czech Republic
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24
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Han Y, Yoo HJ, Jee SH, Lee JH. High serum levels of L-carnitine and citric acid negatively correlated with alkaline phosphatase are detectable in Koreans before gastric cancer onset. Metabolomics 2022; 18:62. [PMID: 35900644 DOI: 10.1007/s11306-022-01922-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/14/2022] [Indexed: 10/16/2022]
Abstract
INTRODUCTION Monitoring metabolic biomarkers could be utilized as an effective tool for the early detection of gastric cancer (GC) risk. OBJECTIVE We aimed to discover predictive serum biomarkers for GC and investigate biomarker-related metabolism. METHODS Subjects were randomly selected from the Korean Cancer Prevention Study-II cohort and matched by age and sex. We analyzed baseline serum samples of 160 subjects (discovery set; control and GC occurrence group, 80 each) via nontargeted screening. Identified putative biomarkers were validated in baseline serum samples of 140 subjects (validation set; control and GC occurrence group, 70 each) using targeted metabolites analysis. RESULTS The final analysis was conducted on the discovery set (control, n = 52 vs. GC occurrence, n = 50) and the validation set (control, n = 43 vs. GC occurrence, n = 44) applying exclusion conditions. Eighteen putative metabolite sets differed between two groups found on nontargeted metabolic screening. We focused on fatty acid-related energy metabolism. In targeted analysis, levels of decanoyl-L-carnitine (p = 0.019), L-carnitine (p = 0.033), and citric acid (p = 0.025) were significantly lower in the GC occurrence group, even after adjusting for age, sex, and smoking status. Additionally, L-carnitine and citric acid were confirmed to have an independently significant relationship to GC development. Notably, alkaline phosphatase showed a significant correlation with these two biomarkers. CONCLUSION Changes in serum L-carnitine and citric acid levels that may result from alterations of fatty-acid-related energy metabolism are expected to be valuable biomarkers for the early diagnosis of GC risk.
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Affiliation(s)
- Youngmin Han
- National Leading Research Laboratory of Clinical Nutrigenetics/Nutrigenomics, Department of Food and Nutrition, College of Human Ecology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hye Jin Yoo
- Research Center for Silver Science, Institute of Symbiotic Life-TECH, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Sun Ha Jee
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Jong Ho Lee
- National Leading Research Laboratory of Clinical Nutrigenetics/Nutrigenomics, Department of Food and Nutrition, College of Human Ecology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
- Research Center for Silver Science, Institute of Symbiotic Life-TECH, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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25
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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] [Grants] [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
While single-cell mass spectrometry can reveal cellular heterogeneity and the molecular mechanisms of intracellular biochemical reactions, its application is limited by the insufficient detection sensitivity resulting from matrix interference and sample dilution. Herein, we propose an intact living-cell electrolaunching ionization mass spectrometry (ILCEI-MS) method. A capillary emitter with a narrow-bore, constant-inner-diameter ensures that the entire living cell enters the MS ion-transfer tube. Inlet ionization improves sample utilization, and no solvent is required, preventing sample dilution and matrix interference. Based on these features, the detection sensitivity is greatly improved, and the average signal-to-noise (S/N) ratio is about 20 : 1 of single-cell peaks in the TIC of ILCEI-MS. A high detection throughput of 51 cells per min was achieved by ILCEI-MS for the single-cell metabolic profiling of multiple cell lines, and 368 cellular metabolites were identified. Further, more than 4000 primary single cells digested from the fresh multi-organ tissues of mice were detected by ILCEI-MS, demonstrating its applicability and reliability.
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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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26
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Granchi C. ATP-citrate lyase (ACLY) inhibitors as therapeutic agents: a patenting perspective. Expert Opin Ther Pat 2022; 32:731-742. [PMID: 35436171 DOI: 10.1080/13543776.2022.2067478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION ATP citrate lyase (ACLY) is a key enzyme in cellular metabolism, being the main source of acetyl-Coenzyme A, an important precursor for fatty acid, cholesterol and isoprenoid biosynthesis, and it is also involved in protein acetylation. Its expression changes are related to hyperlipidemia and cardiovascular diseases. Other studies have shown that ACLY is closely related to the occurrence of cancer: the increase in lipid synthesis provides the necessary building blocks for cell growth and division. Therefore, finding effective ACLY inhibitors has very important application prospects for lipid-related pathologies and cancer. AREAS COVERED : This review covers patents concerning ACLY inhibitors and alternative strategies to modulate ACLY activity, with their potential therapeutic applications. EXPERT OPINION In recent years ACLY as a drug target has become a hot spot in the research of innovative drugs for disorders of glucose and lipid metabolism. Many types of small-molecule ACLY inhibitors have been discovered, but few ACLY inhibitors proved to be highly effective in vitro and in vivo, since their main limitations were low cell penetration and low affinity to ACLY. The search for new effective ACLY inhibitors is of great significance and has broad application prospects for the treatment of hyperlipidemia and cancer.
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27
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Rankin‐Turner S, Reynolds JC, Turner MA, Heaney LM. Applications of ambient ionization mass spectrometry in 2021: An annual review. ANALYTICAL SCIENCE ADVANCES 2022; 3:67-89. [PMID: 38715637 PMCID: PMC10989594 DOI: 10.1002/ansa.202100067] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/17/2022] [Accepted: 02/27/2022] [Indexed: 06/26/2024]
Abstract
Ambient ionization mass spectrometry (AIMS) has revolutionized the field of analytical chemistry, enabling the rapid, direct analysis of samples in their native state. Since the inception of AIMS almost 20 years ago, the analytical community has driven the further development of this suite of techniques, motivated by the plentiful advantages offered in addition to traditional mass spectrometry. Workflows can be simplified through the elimination of sample preparation, analysis times can be significantly reduced and analysis remote from the traditional laboratory space has become a real possibility. As such, the interest in AIMS has rapidly spread through analytical communities worldwide, and AIMS techniques are increasingly being integrated with standard laboratory operations. This annual review covers applications of AIMS techniques throughout 2021, with a specific focus on AIMS applications in a number of key fields of research including disease diagnostics, forensics and security, food safety testing and environmental sciences. While some new techniques are introduced, the focus in AIMS research is increasingly shifting from the development of novel techniques toward efforts to improve existing AIMS techniques, particularly in terms of reproducibility, quantification and ease-of-use.
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Affiliation(s)
- Stephanie Rankin‐Turner
- W. Harry Feinstone Department of Molecular Microbiology and ImmunologyJohns Hopkins Bloomberg School of Public HealthJohns Hopkins UniversityBaltimoreMarylandUSA
| | - James C. Reynolds
- Department of ChemistryLoughborough UniversityLoughboroughLeicestershireUK
| | - Matthew A. Turner
- Department of ChemistryLoughborough UniversityLoughboroughLeicestershireUK
| | - Liam M. Heaney
- School of SportExercise and Health SciencesLoughborough UniversityLoughboroughLeicestershireUK
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28
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Liu Q, Lan J, Wu R, Begley A, Ge W, Zenobi R. Hybrid Ionization Source Combining Nanoelectrospray and Dielectric Barrier Discharge Ionization for the Simultaneous Detection of Polar and Nonpolar Compounds in Single Cells. Anal Chem 2022; 94:2873-2881. [PMID: 35113514 DOI: 10.1021/acs.analchem.1c04759] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Single-cell metabolomics is expected to deliver fast and dynamic information on cell function; therefore, it requires rapid analysis of a wide variety of very small quantities of metabolites in living cells. In this work, a hybrid ionization source that combines nanoelectrospray ionization (nanoESI) and dielectric barrier discharge ionization (DBDI) is proposed for single-cell analysis. A capillary with a 1 μm i.d. tip was inserted into cells for sampling and then directly used as the nanoESI source for ionization of polar metabolites. In addition, a DBDI source was employed as a post-ionization source to improve the ionization of apolar metabolites in cells that are not easily ionized by ESI. By increasing the voltage of the DBDI source from 0 to 3.2 kV, the classes of detected metabolites can be shifted from mostly polar to both polar and apolar to mainly apolar. Plant cells (onion) and human cells (PANC-1) were investigated in this study. After optimization, 50 compounds in onion cells and 40 compounds in PANC-1 cells were observed in ESI mode (3.5 kV) and an additional 49 compounds in onion cells and 73 compounds in PANC-1 cells were detected in ESI (3.5 kV)-DBDI (2.6 kV) hybrid mode. This hybrid ionization source improves the coverage, ionization efficiency, and limit of detection of metabolites with different polarities and could potentially contribute to the fast-growing field of single-cell metabolomics.
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Affiliation(s)
- Qinlei Liu
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Jiayi Lan
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Ri Wu
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Alina Begley
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Wenjie Ge
- Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
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