1
|
Pandian K, de Matos LDDAHEA, Hetzel LA, Zwier R, Veldhuizen PV, Schubert C, Karuppusamy J, Harms AC, Ali A, Hankemeier T. Enabling high-sensitivity live single-cell mass spectrometry using an integrated electrical lysis and nano electrospray ionization interface. Anal Chim Acta 2024; 1324:343068. [PMID: 39218570 DOI: 10.1016/j.aca.2024.343068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 08/03/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Live single-cell metabolomic studies encounter inherent difficulties attributed to the limited sample volume, minimal compound quantity, and insufficient sensitivity in the Mass Spectrometry (MS) method used to obtain single-cell data. However, understanding cellular heterogeneity, functional diversity, and metabolic processes within individual cells is essential. Exploring how individual cells respond to stimuli, including drugs, environmental changes, or signaling molecules, offers insights into biology, oncology, and drug discovery. Efficient release of cell contents (lysis) is vital for accurate metabolite detection at the single-cell level. Despite this, traditional approaches in live single cell metabolomics methods do not emphasize efficient lysis to prevent sample dilution. Instead, current live single cell metabolomics methods use direct infusion to introduce the cell into the mass spectrometry without prior chromatographic separation or a lysis step, which adversely affects sensitivity and metabolic coverage. RESULTS To address this, we developed an integrated single-cell electrical lysis and nano spray (SCEL-nS) platform coupled to an Orbitrap MS capable of efficiently lysing a single cell after being sampled with specially manufactured micropipettes. Lysis efficiency was validated by comparing live cell stain fluorescent intensities of intact and electrically lysed cells through microscopy imaging. The SCEL-nS platform successfully induced the breakdown of a single cell, significantly reducing the live cell stain's fluorescent intensity indicating cell membrane breakdown. Additionally, SCEL-nS was validated by measuring single cells spiked with the anti-cancer drug tamoxifen by MS. SCEL-nS use resulted in statistically significant increase in the peak measured by the method compared to the traditional non-lysis method. SIGNIFICANCE Overall, our results demonstrate that the newly incorporated SCEL-nS platform achieved higher sensitivities compared to traditional live single cell analysis methods.
Collapse
Affiliation(s)
- Kanchana Pandian
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | | | - Laura A Hetzel
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Raphaël Zwier
- Fine Mechanical Department, Leiden Institute of Physics (LION), Leiden University, Leiden, the Netherlands
| | - Peter van Veldhuizen
- Electronics Department, Leiden Institute of Physics (LION), Leiden University, Leiden, the Netherlands
| | - Charelle Schubert
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Jayaprakash Karuppusamy
- Department of Mechanical Engineering, Birla Institute of Technology and Science, Pilani, Hyderabad, India
| | - Amy C Harms
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands.
| | - Thomas Hankemeier
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| |
Collapse
|
2
|
Pan X, Pan S, Du M, Yang J, Yao H, Zhang X, Zhang S. SCMeTA: a pipeline for single-cell metabolic analysis data processing. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae545. [PMID: 39240328 PMCID: PMC11401741 DOI: 10.1093/bioinformatics/btae545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 09/02/2024] [Accepted: 09/04/2024] [Indexed: 09/07/2024]
Abstract
SUMMARY To address the challenges in single-cell metabolomics (SCM) research, we have developed an open-source Python-based modular library, named SCMeTA, for SCM data processing. We designed standardized pipeline and inter-container communication format and have developed modular components to adapt to the diverse needs of SCM studies. The validation was carried out on multiple SCM experiment data. The results demonstrated significant improvements in batch effects, accuracy of results, metabolic extraction rate, cell matching rate, as well as processing speed. This library is of great significance in advancing the practical application of SCM analysis and makes a foundation for wide-scale adoption in biological studies. AVAILABILITY AND IMPLEMENTATION SCMeTA is freely available on https://github.com/SCMeTA/SCMeTA and https://doi.org/10.5281/zenodo.13569643.
Collapse
Affiliation(s)
- 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
| | - Jinlei Yang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Huan Yao
- Division of Chemical Metrology and Analytical Science, National Institute of Metrology China, Beijing 100029, China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| |
Collapse
|
3
|
Wevers D, Ramautar R, Clark C, Hankemeier T, Ali A. Opportunities and challenges for sample preparation and enrichment in mass spectrometry for single-cell metabolomics. Electrophoresis 2023; 44:2000-2024. [PMID: 37667867 DOI: 10.1002/elps.202300105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/08/2023] [Accepted: 08/19/2023] [Indexed: 09/06/2023]
Abstract
Single-cell heterogeneity in metabolism, drug resistance and disease type poses the need for analytical techniques for single-cell analysis. As the metabolome provides the closest view of the status quo in the cell, studying the metabolome at single-cell resolution may unravel said heterogeneity. A challenge in single-cell metabolome analysis is that metabolites cannot be amplified, so one needs to deal with picolitre volumes and a wide range of analyte concentrations. Due to high sensitivity and resolution, MS is preferred in single-cell metabolomics. Large numbers of cells need to be analysed for proper statistics; this requires high-throughput analysis, and hence automation of the analytical workflow. Significant advances in (micro)sampling methods, CE and ion mobility spectrometry have been made, some of which have been applied in high-throughput analyses. Microfluidics has enabled an automation of cell picking and metabolite extraction; image recognition has enabled automated cell identification. Many techniques have been used for data analysis, varying from conventional techniques to novel combinations of advanced chemometric approaches. Steps have been set in making data more findable, accessible, interoperable and reusable, but significant opportunities for improvement remain. Herein, advances in single-cell analysis workflows and data analysis are discussed, and recommendations are made based on the experimental goal.
Collapse
Affiliation(s)
- Dirk Wevers
- Wageningen University and Research, Wageningen, The Netherlands
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Rawi Ramautar
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Charlie Clark
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| |
Collapse
|
4
|
Pandian K, Matsui M, Hankemeier T, Ali A, Okubo-Kurihara E. Advances in single-cell metabolomics to unravel cellular heterogeneity in plant biology. PLANT PHYSIOLOGY 2023; 193:949-965. [PMID: 37338502 PMCID: PMC10517197 DOI: 10.1093/plphys/kiad357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/03/2023] [Accepted: 05/17/2023] [Indexed: 06/21/2023]
Abstract
Single-cell metabolomics is a powerful tool that can reveal cellular heterogeneity and can elucidate the mechanisms of biological phenomena in detail. It is a promising approach in studying plants, especially when cellular heterogeneity has an impact on different biological processes. In addition, metabolomics, which can be regarded as a detailed phenotypic analysis, is expected to answer previously unrequited questions which will lead to expansion of crop production, increased understanding of resistance to diseases, and in other applications as well. In this review, we will introduce the flow of sample acquisition and single-cell techniques to facilitate the adoption of single-cell metabolomics. Furthermore, the applications of single-cell metabolomics will be summarized and reviewed.
Collapse
Affiliation(s)
- Kanchana Pandian
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einstein Road 55, 2333 CC Leiden, The Netherlands
| | - Minami Matsui
- RIKEN, Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einstein Road 55, 2333 CC Leiden, The Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Einstein Road 55, 2333 CC Leiden, The Netherlands
| | - Emiko Okubo-Kurihara
- RIKEN, Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
- College of Science, Rikkyo University, Tokyo 171-8501, Japan
| |
Collapse
|
5
|
Lee S, Vu HM, Lee JH, Lim H, Kim MS. Advances in Mass Spectrometry-Based Single Cell Analysis. BIOLOGY 2023; 12:395. [PMID: 36979087 PMCID: PMC10045136 DOI: 10.3390/biology12030395] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Technological developments and improvements in single-cell isolation and analytical platforms allow for advanced molecular profiling at the single-cell level, which reveals cell-to-cell variation within the admixture cells in complex biological or clinical systems. This helps to understand the cellular heterogeneity of normal or diseased tissues and organs. However, most studies focused on the analysis of nucleic acids (e.g., DNA and RNA) and mass spectrometry (MS)-based analysis for proteins and metabolites of a single cell lagged until recently. Undoubtedly, MS-based single-cell analysis will provide a deeper insight into cellular mechanisms related to health and disease. This review summarizes recent advances in MS-based single-cell analysis methods and their applications in biology and medicine.
Collapse
Affiliation(s)
- Siheun Lee
- School of Undergraduate Studies, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Hung M. Vu
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Jung-Hyun Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Heejin Lim
- Center for Scientific Instrumentation, Korea Basic Science Institute (KBSI), Cheongju 28119, Republic of Korea
| | - Min-Sik Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
- New Biology Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
- Center for Cell Fate Reprogramming and Control, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| |
Collapse
|
6
|
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.
Collapse
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
| | | |
Collapse
|
7
|
Zhang Z, Bao C, Jiang L, Wang S, Wang K, Lu C, Fang H. When cancer drug resistance meets metabolomics (bulk, single-cell and/or spatial): Progress, potential, and perspective. Front Oncol 2023; 12:1054233. [PMID: 36686803 PMCID: PMC9854130 DOI: 10.3389/fonc.2022.1054233] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/20/2022] [Indexed: 01/07/2023] Open
Abstract
Resistance to drug treatment is a critical barrier in cancer therapy. There is an unmet need to explore cancer hallmarks that can be targeted to overcome this resistance for therapeutic gain. Over time, metabolic reprogramming has been recognised as one hallmark that can be used to prevent therapeutic resistance. With the advent of metabolomics, targeting metabolic alterations in cancer cells and host patients represents an emerging therapeutic strategy for overcoming cancer drug resistance. Driven by technological and methodological advances in mass spectrometry imaging, spatial metabolomics involves the profiling of all the metabolites (metabolomics) so that the spatial information is captured bona fide within the sample. Spatial metabolomics offers an opportunity to demonstrate the drug-resistant tumor profile with metabolic heterogeneity, and also poses a data-mining challenge to reveal meaningful insights from high-dimensional spatial information. In this review, we discuss the latest progress, with the focus on currently available bulk, single-cell and spatial metabolomics technologies and their successful applications in pre-clinical and translational studies on cancer drug resistance. We provide a summary of metabolic mechanisms underlying cancer drug resistance from different aspects; these include the Warburg effect, altered amino acid/lipid/drug metabolism, generation of drug-resistant cancer stem cells, and immunosuppressive metabolism. Furthermore, we propose solutions describing how to overcome cancer drug resistance; these include early detection during cancer initiation, monitoring of clinical drug response, novel anticancer drug and target metabolism, immunotherapy, and the emergence of spatial metabolomics. We conclude by describing the perspectives on how spatial omics approaches (integrating spatial metabolomics) could be further developed to improve the management of drug resistance in cancer patients.
Collapse
Affiliation(s)
- Zhiqiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chaohui Bao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kankan Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chang Lu
- MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
8
|
Václavek T, Foret F. Microfluidic device integrating single-cell extraction and electrical lysis for mass spectrometry detection of intracellular compounds. Electrophoresis 2023; 44:313-322. [PMID: 35315940 DOI: 10.1002/elps.202100379] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 02/01/2023]
Abstract
Analysis of cellular composition and metabolism at a single-cell resolution allows gaining more information about complex relationships of cells within tissues or whole living organisms by resolving the variance stemming from the cellular heterogeneity. Mass spectrometry (MS) is a perfect analytical tool satisfying the demanding requirements of detecting and identifying compounds present in such ultralow-volume samples of high chemical complexity. However, the method of sampling and sample ionization is crucial in obtaining relevant information. In this work, we present a microfluidic sampling platform that integrates single-cell extraction from MS-incompatible media with electrical cell lysis and nanoESI-MS analysis of human erythrocytes. Hemoglobin alpha and beta chains (300 amol/cell) were successfully identified in mass spectra of single-erythrocyte lysates.
Collapse
Affiliation(s)
- Tomáš Václavek
- Department of Bioanalytical Instrumentation, Institute of Analytical Chemistry of the CAS, Brno, Czech Republic.,Department of Biochemistry, Masaryk University, Brno, Czech Republic
| | - František Foret
- Department of Bioanalytical Instrumentation, Institute of Analytical Chemistry of the CAS, Brno, Czech Republic
| |
Collapse
|
9
|
Hu R, Li Y, Yang Y, Liu M. Mass spectrometry-based strategies for single-cell metabolomics. MASS SPECTROMETRY REVIEWS 2023; 42:67-94. [PMID: 34028064 DOI: 10.1002/mas.21704] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
Single cell analysis has drawn increasing interest from the research community due to its capability to interrogate cellular heterogeneity, allowing refined tissue classification and facilitating novel biomarker discovery. With the advancement of relevant instruments and techniques, it is now possible to perform multiple omics including genomics, transcriptomics, metabolomics or even proteomics at single cell level. In comparison with other omics studies, single-cell metabolomics (SCM) represents a significant challenge since it involves many types of dynamically changing compounds with a wide range of concentrations. In addition, metabolites cannot be amplified. Although difficult, considerable progress has been made over the past decade in mass spectrometry (MS)-based SCM in terms of processing technologies and biochemical applications. In this review, we will summarize recent progress in the development of promising MS platforms, sample preparation methods and SCM analysis of various cell types (including plant cell, cancer cell, neuron, embryo cell, and yeast cell). Current limitations and future research directions in the field of SCM will also be discussed.
Collapse
Affiliation(s)
- Rui Hu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yunhuang Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
10
|
Ali A, Davidson S, Fraenkel E, Gilmore I, Hankemeier T, Kirwan JA, Lane AN, Lanekoff I, Larion M, McCall LI, Murphy M, Sweedler JV, Zhu C. Single cell metabolism: current and future trends. Metabolomics 2022; 18:77. [PMID: 36181583 PMCID: PMC10063251 DOI: 10.1007/s11306-022-01934-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
Single cell metabolomics is an emerging and rapidly developing field that complements developments in single cell analysis by genomics and proteomics. Major goals include mapping and quantifying the metabolome in sufficient detail to provide useful information about cellular function in highly heterogeneous systems such as tissue, ultimately with spatial resolution at the individual cell level. The chemical diversity and dynamic range of metabolites poses particular challenges for detection, identification and quantification. In this review we discuss both significant technical issues of measurement and interpretation, and progress toward addressing them, with recent examples from diverse biological systems. We provide a framework for further directions aimed at improving workflow and robustness so that such analyses may become commonly applied, especially in combination with metabolic imaging and single cell transcriptomics and proteomics.
Collapse
Affiliation(s)
- Ahmed Ali
- Leiden Academic Centre for Drug Research, University of Leiden, Gorlaeus Building Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Shawn Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Ernest Fraenkel
- Department of Biological Engineering and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ian Gilmore
- National Physical Laboratory, Teddington, TW11 0LW, Middlesex, UK
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research, University of Leiden, Room number GW4.07, Gorlaeus Building, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jennifer A Kirwan
- Berlin Institute of Health, Metabolomics Platform, Translational Research Unit of the Charite-Universitätsmedizin Berlin, Anna-Louisa-Karsch-Str 2, 10178, Berlin, Germany
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology, and Center for Environmental and Systems Biochemistry, University of Kentucky, 789 S. Limestone St, Lexington, KY, 40536, USA.
| | - Ingela Lanekoff
- Department of Chemistry-BMC, Uppsala University, Husargatan 3 (576), 751 23, Uppsala, Sweden
| | - Mioara Larion
- Center for Cancer Research, National Cancer Institute, Building 37, Room 1136A, Bethesda, MD, 20892, USA
| | - Laura-Isobel McCall
- Department of Chemistry & Biochemistry, Department of Microbiology and Plant Biology, Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 Stephenson Parkway, room 3750, Norman, OK, 73019-5251, USA
| | - Michael Murphy
- Departments of Biological Engineering, Department of Electrical Engineering, and Computer Science and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, USA
| | - Jonathan V Sweedler
- Department of Chemistry, and the Beckman Institute, University of Illinois Urbana-Champaign, 505 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Caigang Zhu
- Department of Biomedical Engineering, University of Kentucky, Lexington, KY, 40536, USA
| |
Collapse
|
11
|
Nguyen TD, Lan Y, Kane SS, Haffner JJ, Liu R, McCall LI, Yang Z. Single-Cell Mass Spectrometry Enables Insight into Heterogeneity in Infectious Disease. Anal Chem 2022; 94:10567-10572. [PMID: 35863111 PMCID: PMC10064790 DOI: 10.1021/acs.analchem.2c02279] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cellular heterogeneity is generally overlooked in infectious diseases. In this study, we investigated host cell heterogeneity during infection with Trypanosoma cruzi (T. cruzi) parasites, causative agents of Chagas disease (CD). In chronic-stage CD, only a few host cells are infected with a large load of parasites and symptoms may appear at sites distal to parasite colonization. Furthermore, recent work has revealed T. cruzi heterogeneity with regard to replication rates and drug susceptibility. However, the role of cellular-level metabolic heterogeneity in these processes has yet to be assessed. To fill this knowledge gap, we developed a Single-probe SCMS (single-cell mass spectrometry) method compatible with biosafety protocols, to acquire metabolomics data from individual cells during T. cruzi infection. This study revealed heterogeneity in the metabolic response of the host cells to T. cruzi infection in vitro. Our results showed that parasite-infected cells possessed divergent metabolism compared to control cells. Strikingly, some uninfected cells adjacent to infected cells showed metabolic impacts as well. Specific metabolic changes include increases in glycerophospholipids with infection. These results provide novel insight into the pathogenesis of CD. Furthermore, they represent the first application of bioanalytical SCMS to the study of mammalian-infectious agents, with the potential for broad applications to study infectious diseases.
Collapse
Affiliation(s)
- Tra D Nguyen
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Yunpeng Lan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Shelley S Kane
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Jacob J Haffner
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma 73019, United States.,Department of Anthropology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Renmeng Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Laura-Isobel McCall
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States.,Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma 73019, United States.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| |
Collapse
|
12
|
Chen X, Peng Z, Yang Z. Metabolomics studies of cell-cell interactions using single cell mass spectrometry combined with fluorescence microscopy. Chem Sci 2022; 13:6687-6695. [PMID: 35756524 PMCID: PMC9172575 DOI: 10.1039/d2sc02298b] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 05/15/2022] [Indexed: 11/21/2022] Open
Abstract
Cell-cell interactions are critical for transmitting signals among cells and maintaining their normal functions from the single-cell level to tissues. In cancer studies, interactions between drug-resistant and drug-sensitive cells play an important role in the development of chemotherapy resistance of tumors. As metabolites directly reflect the cell status, metabolomics studies provide insight into cell-cell communication. Mass spectrometry (MS) is a powerful tool for metabolomics studies, and single cell MS (SCMS) analysis can provide unique information for understanding interactions among heterogeneous cells. In the current study, we utilized a direct co-culture system (with cell-cell contact) to study metabolomics of single cells affected by cell-cell interactions in their living status. A fluorescence microscope was utilized to distinguish these two types of cells for SCMS metabolomics studies using the Single-probe SCMS technique under ambient conditions. Our results show that through interactions with drug-resistant cells, drug-sensitive cancer cells acquired significantly increased drug resistance and exhibited drastically altered metabolites. Further investigation found that the increased drug resistance was associated with multiple metabolism regulations in drug-sensitive cells through co-culture such as the upregulation of sphingomyelins lipids and lactic acid and the downregulation of TCA cycle intermediates. The method allows for direct MS metabolomics studies of individual cells labeled with fluorescent proteins or dyes among heterogeneous populations.
Collapse
Affiliation(s)
- Xingxiu Chen
- Chemistry and Biochemistry Department, University of Oklahoma Norman Oklahoma 73072 USA
| | - Zongkai Peng
- Chemistry and Biochemistry Department, University of Oklahoma Norman Oklahoma 73072 USA
| | - Zhibo Yang
- Chemistry and Biochemistry Department, University of Oklahoma Norman Oklahoma 73072 USA
| |
Collapse
|
13
|
Sun M, Chen X, Yang Z. Single cell mass spectrometry studies reveal metabolomic features and potential mechanisms of drug-resistant cancer cell lines. Anal Chim Acta 2022; 1206:339761. [PMID: 35473873 PMCID: PMC9046687 DOI: 10.1016/j.aca.2022.339761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 12/28/2022]
Abstract
Irinotecan (Iri) is a key drug to treat metastatic colorectal cancer, but its clinical activity is often limited by de novo and acquired drug resistance. Studying the underlying mechanisms of drug resistance is necessary for developing novel therapeutic strategies. In this study, we used both regular and irinotecan-resistant (Iri-resistant) colorectal cell lines as models, and performed single cell mass spectrometry (SCMS) metabolomics studies combined with analyses from cytotoxicity assay, western blot, flow cytometry, quantitative real-time polymerase chain reaction (qPCR), and reactive oxygen species (ROS). Our SCMS results indicate that Iri-resistant cancer cells possess higher levels of unsaturated lipids compared with the regular cancer cells. In addition, multiple protein biomarkers and their corresponding mRNAs of colon cancer stem cells are overexpressed in Iri-resistance cells. Particularly, stearoyl-CoA desaturase 1 (SCD1) is upregulated with the development of drug resistance in Iri-resistant cells, whereas inhibiting the activity of SCD1 efficiently increase their sensitivity to Iri treatment. In addition, we demonstrated that SCD1 directly regulates the expression of ALDH1A1, which contributes to the cancer stemness and ROS level in Iri-resistant cell lines.
Collapse
|
14
|
Chin S, Blancaflor EB. Plant Gravitropism: From Mechanistic Insights into Plant Function on Earth to Plants Colonizing Other Worlds. Methods Mol Biol 2022; 2368:1-41. [PMID: 34647245 DOI: 10.1007/978-1-0716-1677-2_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Gravitropism, the growth of roots and shoots toward or away from the direction of gravity, has been studied for centuries. Such studies have not only led to a better understanding of the gravitropic process itself, but also paved new paths leading to deeper mechanistic insights into a wide range of research areas. These include hormone biology, cell signal transduction, regulation of gene expression, plant evolution, and plant interactions with a variety of environmental stimuli. In addition to contributions to basic knowledge about how plants function, there is accumulating evidence that gravitropism confers adaptive advantages to crops, particularly under marginal agricultural soils. Therefore, gravitropism is emerging as a breeding target for enhancing agricultural productivity. Moreover, research on gravitropism has spawned several studies on plant growth in microgravity that have enabled researchers to uncouple the effects of gravity from other tropisms. Although rapid progress on understanding gravitropism witnessed during the past decade continues to be driven by traditional molecular, physiological, and cell biological tools, these tools have been enriched by technological innovations in next-generation omics platforms and microgravity analog facilities. In this chapter, we review the field of gravitropism by highlighting recent landmark studies that have provided unique insights into this classic research topic while also discussing potential contributions to agriculture on Earth and beyond.
Collapse
Affiliation(s)
- Sabrina Chin
- Department of Botany, University of Wisconsin, Madison, WI, USA.
| | | |
Collapse
|
15
|
Chatzimichail S, Supramaniam P, Salehi-Reyhani A. Absolute Quantification of Protein Copy Number in Single Cells With Immunofluorescence Microscopy Calibrated Using Single-Molecule Microarrays. Anal Chem 2021; 93:6656-6664. [PMID: 33876929 DOI: 10.1021/acs.analchem.0c05177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Great strides toward routine single-cell analyses have been made over the last decade, particularly in the field of transcriptomics. For proteomics, amplification is not currently possible and has necessitated the development of ultrasensitive platforms capable of performing such analyses on single cells. These platforms are improving in terms of throughput and multiplexability but still fall short in relation to more established methods such as fluorescence microscopy. However, microscopy methods rely on fluorescence intensity as a proxy for protein abundance and are not currently capable of reporting this in terms of an absolute copy number. Here, a microfluidic implementation of single-molecule microarrays for single-cell analysis is assessed in its ability to calibrate fluorescence microscopy data. We show that the equivalence of measurements of the steady-state distribution of protein abundance to single-molecule microarray data can be exploited to pave the way for absolute quantitation by fluorescence and immunofluorescence microscopy. The methods presented have been developed using GFP but are extendable to other proteins and other biomolecules of interest.
Collapse
Affiliation(s)
| | | | - Ali Salehi-Reyhani
- Department of Surgery & Cancer, Imperial College London, London W12 0HS, U.K
| |
Collapse
|
16
|
Sakamoto W, Azegami N, Konuma T, Akashi S. Single-Cell Native Mass Spectrometry of Human Erythrocytes. Anal Chem 2021; 93:6583-6588. [PMID: 33871982 DOI: 10.1021/acs.analchem.1c00588] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Native mass spectrometry (MS) enables the determination of the molecular mass of protein complexes. Generally, samples for native MS are isolated, purified, and prepared in volatile solutions. However, to understand the function of proteins in living cells, it is essential to characterize the protein complex as is, without isolation/purification of the protein, using the smallest possible amount of the sample. In the present study, we modified the "live single-cell MS" method, which has mainly been used in metabolomics, and applied it to observe hemoglobin directly sampled from human erythrocytes. By optimizing the experimental methods and conditions, we obtained native mass spectra of hemoglobin using only a single erythrocyte, which was directly sampled into a nanoelectrospray ionization emitter using a micromanipulator and microinjector system. That is, our method enables the analysis of ∼0.45 fmol of hemoglobin directly sampled from an erythrocyte. To our knowledge, this is the first report of native MS for endogenous proteins using a single intact human cell.
Collapse
|
17
|
Wada KI, Hosokawa K, Ito Y, Maeda M. A Microfluidic Device for Modulation of Organellar Heterogeneity in Live Single Cells. ANAL SCI 2021; 37:499-505. [PMID: 33281140 DOI: 10.2116/analsci.20scp11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The quantitatively controlled organellar transfer between living single cells provides a unique experimental platform to analyze the contribution of organellar heterogeneity on cellular phenotypes. We previously developed a microfluidic device which can perform quantitatively controlled mitochondrial transfer between live single cells by promoting strictured cytoplasmic connections between live single cells, but its application to other organelles is unclear. In this study, we investigated the quantitative properties of peroxisome transfer in our microfluidic device. When cells were fused through a 10 or 4 μm long microtunnel by a Sendai virus envelope-based method, a strictured cytoplasmic connection was achieved with a length corresponding to that of the microtunnel, and a subsequent recovery culture disconnected the fused cells. The peroxisome number being transferred through a 10 μm length of the microtunnel was smaller than that of 4 μm. These data suggest that our microfuidic device can perform a quantitative control of peroxisome transfer.
Collapse
Affiliation(s)
- Ken-Ichi Wada
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Kazuo Hosokawa
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, RIKEN Cluster for Pioneering Research
| | - Mizuo Maeda
- Bioengineering Laboratory, RIKEN Cluster for Pioneering Research
| |
Collapse
|
18
|
Sero JE, Stevens MM. Nanoneedle-Based Materials for Intracellular Studies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1295:191-219. [PMID: 33543461 DOI: 10.1007/978-3-030-58174-9_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nanoneedles, defined as high aspect ratio structures with tip diameters of 5 to approximately 500 nm, are uniquely able to interface with the interior of living cells. Their nanoscale dimensions mean that they are able to penetrate the plasma membrane with minimal disruption of normal cellular functions, allowing researchers to probe the intracellular space and deliver or extract material from individual cells. In the last decade, a variety of strategies have been developed using nanoneedles, either singly or as arrays, to investigate the biology of cancer cells in vitro and in vivo. These include hollow nanoneedles for soluble probe delivery, nanocapillaries for single-cell biopsy, nano-AFM for direct physical measurements of cytosolic proteins, and a wide range of fluorescent and electrochemical nanosensors for analyte detection. Nanofabrication has improved to the point that nanobiosensors can detect individual vesicles inside the cytoplasm, delineate tumor margins based on intracellular enzyme activity, and measure changes in cell metabolism almost in real time. While most of these applications are currently in the proof-of-concept stage, nanoneedle technology is poised to offer cancer biologists a powerful new set of tools for probing cells with unprecedented spatial and temporal resolution.
Collapse
Affiliation(s)
- Julia E Sero
- Biology and Biochemistry Department, University of Bath, Claverton Down, Bath, UK
| | - Molly M Stevens
- Institute for Biomedical Engineering, Imperial College London, London, UK.
| |
Collapse
|
19
|
de Souza LP, Borghi M, Fernie A. Plant Single-Cell Metabolomics-Challenges and Perspectives. Int J Mol Sci 2020; 21:E8987. [PMID: 33256100 PMCID: PMC7730874 DOI: 10.3390/ijms21238987] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
Omics approaches for investigating biological systems were introduced in the mid-1990s and quickly consolidated to become a fundamental pillar of modern biology. The idea of measuring the whole complement of genes, transcripts, proteins, and metabolites has since become widespread and routinely adopted in the pursuit of an infinity of scientific questions. Incremental improvements over technical aspects such as sampling, sensitivity, cost, and throughput pushed even further the boundaries of what these techniques can achieve. In this context, single-cell genomics and transcriptomics quickly became a well-established tool to answer fundamental questions challenging to assess at a whole tissue level. Following a similar trend as the original development of these techniques, proteomics alternatives for single-cell exploration have become more accessible and reliable, whilst metabolomics lag behind the rest. This review summarizes state-of-the-art technologies for spatially resolved metabolomics analysis, as well as the challenges hindering the achievement of sensu stricto metabolome coverage at the single-cell level. Furthermore, we discuss several essential contributions to understanding plant single-cell metabolism, finishing with our opinion on near-future developments and relevant scientific questions that will hopefully be tackled by incorporating these new exciting technologies.
Collapse
Affiliation(s)
- Leonardo Perez de Souza
- Max Planck Institute of Molecular Plant Physiology, Am Müehlenberg 1, Golm, 14476 Potsdam, Germany
| | - Monica Borghi
- Department of Biology, Utah State University, 1435 Old Main Hill, Logan, UT 84322, USA;
| | - Alisdair Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Müehlenberg 1, Golm, 14476 Potsdam, Germany
| |
Collapse
|
20
|
Cao YQ, Zhang L, Zhang J, Guo YL. Single-Cell On-Probe Derivatization-Noncontact Nanocarbon Fiber Ionization: Unraveling Cellular Heterogeneity of Fatty Alcohol and Sterol Metabolites. Anal Chem 2020; 92:8378-8385. [PMID: 32420735 DOI: 10.1021/acs.analchem.0c00954] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Currently in single-cell mass spectrometry, the analysis of low-abundance cell metabolites such as fatty alcohols and sterols remains a challenge. In most research studies, single-cell samples are analyzed directly after sampling. However, this workflow may exclude many effective sample pretreatment methods such as derivatization for the improvement of detection sensitivity for specific cell metabolites in a single-cell sample. Metabolites in low abundance in a cell may not be detected. Herein on-probe derivatization coupled with noncontact nanocarbon fiber ionization is proposed for sensitive fatty alcohol and sterol metabolite analysis at the single-cell level. Fatty alcohol and sterol metabolites were rapidly quaternized by the single-cell on-probe derivatization method. The reaction products were directly ionized with no postreaction processing. Furthermore, a new ionization source for noncontact nanocarbon fiber ionization was developed to show good compatibility with dichloromethane, a low-polarity solvent used in on-probe derivatization. The quaternized fatty alcohols and sterols exhibited evidently enhanced ionization efficiency in mass spectra. In applications of the developed method, seven kinds of even-numbered-carbon fatty alcohols (C12-C22) and five kinds of sterols were detected in single L-02 and HepG2 cells. Then the L-02 and HepG2 cells were readily discriminated through principal component analysis. Additionally, a rough quantitative analysis of the detected fatty alcohols and sterols in single cells was performed. The mass intensities of fatty alcohols show a significant difference between L-02 and HepG2 cells while those of sterols remain stable.
Collapse
Affiliation(s)
- Yu-Qi Cao
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Li Zhang
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Jing Zhang
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| | - Yin-Long Guo
- State Key Laboratory of Organometallic Chemistry and National Center for Organic Mass Spectrometry in Shanghai, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China
| |
Collapse
|
21
|
Single-cell Metabolomics Analysis by Microfluidics and Mass Spectrometry: Recent New Advances. JOURNAL OF ANALYSIS AND TESTING 2020. [DOI: 10.1007/s41664-020-00138-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
22
|
Fang Z, Wang R, Zhao H, Yao H, Ouyang J, Zhang X. Mannose Promotes Metabolic Discrimination of Osteosarcoma Cells at Single-Cell Level by Mass Spectrometry. Anal Chem 2020; 92:2690-2696. [DOI: 10.1021/acs.analchem.9b04773] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Zhuyin Fang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ruihua Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hansen Zhao
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Huan Yao
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jin Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xinrong Zhang
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Department of Chemistry, Tsinghua University, Beijing 100084, China
| |
Collapse
|
23
|
Huang L, Wang Z, Cupp-Sutton KA, Smith K, Wu S. Spray-Capillary: An Electrospray-Assisted Device for Quantitative Ultralow-Volume Sample Handling. Anal Chem 2020; 92:640-646. [PMID: 31793760 PMCID: PMC7558432 DOI: 10.1021/acs.analchem.9b04131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The analysis of low-volume samples provides valuable insight into complex biological systems. However, the proteomic and metabolomic analysis of low-volume samples remains challenging due to the lack of simple, efficient, and reproducible microsampling techniques. We have developed an electrospray-assisted device for quantitative low-volume sample extraction, referred to here as "Spray-Capillary". Stable electrospray was achieved through a chemically etched tip from a long (e.g., 50 cm) capillary with a conductive sheath flow. This electrospray provided the driving force to quantitatively draw low-volume samples into the capillary. We evaluated the precision and accuracy of sample injection volumes using our spray-capillary as the electrospray voltage, capillary ID, and column length were varied. Our results demonstrate that spray-capillary allows for reproducible and quantitative microsampling with low injection flow rates (as low as 15 pL/s). Furthermore, spray-capillary can be directly coupled with capillary zone electrophoresis (CZE) for separation. Overall, spray-capillary is a simple microsampling device that holds great potential for high-throughput quantitative omics analysis of ultralow-volume samples.
Collapse
Affiliation(s)
- Lushuang Huang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Kellye A. Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Kenneth Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, United States
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, United States
| |
Collapse
|
24
|
Abstract
Mass spectrometry (MS) is an indispensable analytical technique for bioanalysis. Based on the measurement of mass/charge ratios (m/z) of ions, MS can be used for sensitive detection and accurate identification of species of interest. In traditional studies, MS is utilized to measure analytes in prepared solutions or gas-phase samples. Benefited from recent development of sampling and ionization approaches, MS has been extensively applied to the analysis of broad ranges of biological samples. We have developed a new device, the Single-probe, that can be used for in situ, real-time MS analysis of metabolites inside individual living cells. The Single-probe is a miniaturized multifunctional sampling and ionization device that is directly coupled to the mass spectrometer. With a sampling tip size smaller than 10 μm, we can insert the Single-probe tip into single cells to extract intracellular compounds, which are analyzed using MS in real-time. We have successfully used the Single-probe MS technique to detect a variety of endogenous and exogenous cellular metabolites in individual eukaryotic cells. Single cell mass spectrometry (SCMS) is a new scientific technology that has the potential to reshape approaches in biological and pharmaceutical bioanalytical research.
Collapse
Affiliation(s)
- Ning Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Wei Rao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA.
| |
Collapse
|
25
|
Analysis of Lipids in Single Cells and Organelles Using Nanomanipulation-Coupled Mass Spectrometry. Methods Mol Biol 2020; 2064:19-30. [PMID: 31565764 DOI: 10.1007/978-1-4939-9831-9_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The ability to discriminately analyze the chemical constituents of single cells and organelles is highly sought after and necessary to establish true biomarkers. Some major challenges of individual cell analysis include requirement and expenditure of a large sample of cells as well as extensive extraction and separation techniques. Here, we describe methods to perform individual cell and organelle extractions of both tissues and cells in vitro using nanomanipulation coupled to mass spectrometry. Lipid profiles display heterogeneity from extracted adipocytes and lipid droplets, demonstrating the necessity for single cell analysis. The application of these techniques can be applied to other cell and organelle types for selective and thorough monitoring of disease progression and biomarker discovery.
Collapse
|
26
|
Zhu Y, Liu R, Yang Z. Redesigning the T-probe for mass spectrometry analysis of online lysis of non-adherent single cells. Anal Chim Acta 2019; 1084:53-59. [PMID: 31519234 PMCID: PMC6746249 DOI: 10.1016/j.aca.2019.07.059] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/25/2019] [Accepted: 07/28/2019] [Indexed: 12/16/2022]
Abstract
Single cell mass spectrometry (SCMS) allows for molecular analysis of individual cells while avoiding the inevitable drawbacks of using cell lysate prepared from populations of cells. Based on our previous design of the T-probe, a microscale sampling and ionization device for SCMS analysis, we further developed the device to perform online, and real time lysis of non-adherent live single cells for mass spectrometry (MS) analysis at ambient conditions. This redesigned T-probe includes three parts: a sampling probe with a small tip to withdraw a whole cell, a solvent-providing capillary to deliver lysis solution (i.e., acetonitrile), and a nano-ESI emitter in which rapid cell lysis and ionization occur followed by MS analysis. These three components are embedded between two polycarbonate slides and are jointed through a T-junction to form an integrated device. Colon cancer cells (HCT-116) under control and treatment (using anticancer drug irinotecan) conditions were analyzed. We detected a variety of intracellular species, and structural identification of selected ions was conducted using tandem MS (MS2). We further conducted statistical analysis (e.g., PLS-DA and t-test) to gain biological insights of cellular metabolism. Our results indicate that the influence of anticancer drugs on cellular metabolism of live non-adherent cells can be obtained using the SCMS experiments combined with statistical data analysis.
Collapse
Affiliation(s)
- Yanlin Zhu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Renmeng Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| |
Collapse
|
27
|
Huang Q, Mao S, Khan M, Li W, Zhang Q, Lin JM. Single-cell identification by microfluidic-based in situ extracting and online mass spectrometric analysis of phospholipids expression. Chem Sci 2019; 11:253-256. [PMID: 34040719 PMCID: PMC8132990 DOI: 10.1039/c9sc05143k] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 11/11/2019] [Indexed: 12/12/2022] Open
Abstract
This work describes a microfluidic system for in situ extraction of a single-cell and its phosphatidylcholine analysis through mass spectrometry. This approach uncovered cellular heterogeneity among seemingly identical cells and provided a new platform for identification and classification of cells.
Collapse
Affiliation(s)
- Qiushi Huang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| | - Sifeng Mao
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| | - Mashooq Khan
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| | - Weiwei Li
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| | - Qiang Zhang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University Beijing 100084 China
| |
Collapse
|
28
|
Li Q, Tang F, Huo X, Huang X, Zhang Y, Wang X, Zhang X. Native State Single-Cell Printing System and Analysis for Matrix Effects. Anal Chem 2019; 91:8115-8122. [DOI: 10.1021/acs.analchem.9b00344] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Qi Li
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Fei Tang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Xinming Huo
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Xi Huang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yan Zhang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Xiaohao Wang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| |
Collapse
|
29
|
Yin L, Zhang Z, Liu Y, Gao Y, Gu J. Recent advances in single-cell analysis by mass spectrometry. Analyst 2019; 144:824-845. [PMID: 30334031 DOI: 10.1039/c8an01190g] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells are the most basic structural units that play vital roles in the functioning of living organisms. Analysis of the chemical composition and content of a single cell plays a vital role in ensuring precise investigations of cellular metabolism, and is a crucial aspect of lipidomic and proteomic studies. In addition, structural knowledge provides a better understanding of cell behavior as well as the cellular and subcellular mechanisms. However, single-cell analysis can be very challenging due to the very small size of each cell as well as the large variety and extremely low concentrations of substances found in individual cells. On account of its high sensitivity and selectivity, mass spectrometry holds great promise as an effective technique for single-cell analysis. Numerous mass spectrometric techniques have been developed to elucidate the molecular profiles at the cellular level, including electrospray ionization mass spectrometry (ESI-MS), secondary ion mass spectrometry (SIMS), laser-based mass spectrometry and inductively coupled plasma mass spectrometry (ICP-MS). In this review, the recent advances in single-cell analysis by mass spectrometry are summarized. The strategies of different ionization modes to achieve single-cell analysis are classified and discussed in detail.
Collapse
Affiliation(s)
- Lei Yin
- Research Institute of Translational Medicine, The First Hospital of Jilin University, Jilin University, Dongminzhu Street, Changchun 130061, PR China.
| | | | | | | | | |
Collapse
|
30
|
Cahill JF, Riba J, Kertesz V. Rapid, Untargeted Chemical Profiling of Single Cells in Their Native Environment. Anal Chem 2019; 91:6118-6126. [DOI: 10.1021/acs.analchem.9b00680] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- John F. Cahill
- Mass Spectrometry and Laser Spectroscopy Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| | - Julian Riba
- Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103, 79110 Freiburg, Germany
- Cytena GmbH, Neuer Messplatz 3, 79108 Freiburg, Germany
| | - Vilmos Kertesz
- Mass Spectrometry and Laser Spectroscopy Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6131, United States
| |
Collapse
|
31
|
Begg M, Edwards CD, Hamblin JN, Pefani E, Wilson R, Gilbert J, Vitulli G, Mallett D, Morrell J, Hingle MI, Uddin S, Ehtesham F, Marotti M, Harrell A, Newman CF, Fernando D, Clark J, Cahn A, Hessel EM. Translation of Inhaled Drug Optimization Strategies into Clinical Pharmacokinetics and Pharmacodynamics Using GSK2292767A, a Novel Inhaled Phosphoinositide 3-Kinase δ Inhibitor. J Pharmacol Exp Ther 2019; 369:443-453. [PMID: 30940692 DOI: 10.1124/jpet.119.257311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 03/27/2019] [Indexed: 11/22/2022] Open
Abstract
This study describes the pharmacokinetic (PK) and pharmaco-dynamic (PD) profile of N-(5-(4-(5-(((2R,6S)-2,6-dimethylmorpholino)methyl)oxazol-2-yl)-1H-indazol-6-yl)-2-methoxypyridin-3-yl)methanesulfonamide (GSK2292767A), a novel low-solubility inhaled phosphoinositide 3-kinase delta (PI3Kδ) inhibitor developed as an alternative to 2-(6-(1H-indol-4-yl)-1H-indazol-4-yl)-5-((4-isopropylpiperazin-1-yl)methyl)oxazole (nemiralisib), which is a highly soluble inhaled inhibitor of PI3Kδ with a lung profile consistent with once-daily dosing. GSK2292767A has a similar in vitro cellular profile to nemiralisib and reduces eosinophilia in a murine PD model by 63% (n = 5, P < 0.05). To explore whether a low-soluble compound results in effective PI3Kδ inhibition in humans, a first time in human study was conducted with GSK2292767A in healthy volunteers who smoke. GSK2292767A was generally well tolerated, with headache being the most common reported adverse event. PD changes in induced sputum were measured in combination with drug concentrations in plasma from single (0.05-2 mg, n = 37), and 14-day repeat (2 mg, n = 12) doses of GSK2292767A. Trough bronchoalveolar lavage (BAL) for PK was taken after 14 days of repeat dosing. GSK2292767A displayed a linear increase in plasma exposure with dose, with marginal accumulation after 14 days. Induced sputum showed a 27% (90% confidence interval 15%, 37%) reduction in phosphatidylinositol-trisphosphate (the product of phosphoinositide 3-kinase activation) 3 hours after a single dose. Reduction was not maintained 24 hours after single or repeat dosing. BAL analysis confirmed the presence of GSK2292767A in lung at 24 hours, consistent with the preclinical lung retention profile. Despite good lung retention, target engagement was only present at 3 hours. This exposure-response disconnect is an important observation for future inhaled drug design strategies considering low solubility to drive lung retention.
Collapse
Affiliation(s)
- Malcolm Begg
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Chris D Edwards
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - J Nicole Hamblin
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Eleni Pefani
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Robert Wilson
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Jane Gilbert
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Giovanni Vitulli
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - David Mallett
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Josie Morrell
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Martin I Hingle
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Sorif Uddin
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Filzah Ehtesham
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Miriam Marotti
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Andrew Harrell
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Carla F Newman
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Disala Fernando
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Jonathan Clark
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Anthony Cahn
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| | - Edith M Hessel
- Refractory Respiratory Inflammation Discovery Performance Unit, GlaxoSmithKline, Stevenage, United Kingdom (M.B., C.D.E., J.N.H., E.M.H.); Clinical Pharmacology & Model Stimulation, (E.P., R.W.), Drug Metabolism & Pharmacokinetics, (G.V., D.M., J.M.), Refractory Respiratory Inflammation DPU, (S.U.), In Vitro In Vivo Translation, (C.F.N.), Discovery Medicine, (A.C) GlaxoSmithKline, Stevenage, United Kingdom; Global Clinical Science & Delivery, GlaxoSmithKline, Stockley Park, Uxbridge, United Kingdom (M.M., J.G.); In Vitro In Vivo Translation, (A.H.), Drug Product Design & Development, (M.I.H.), GlaxoSmithKline, Ware, United Kingdom (M.I.H.); Department of Biological Chemistry, Babraham Institute, Cambridge, United Kingdom (J.C.); and Clinical Unit Cambridge, Addenbrookes Hospital, Cambridge, United Kingdom (F.E., D.F.)
| |
Collapse
|
32
|
Liu R, Zhang G, Yang Z. Towards rapid prediction of drug-resistant cancer cell phenotypes: single cell mass spectrometry combined with machine learning. Chem Commun (Camb) 2019; 55:616-619. [PMID: 30525135 DOI: 10.1039/c8cc08296k] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Combined single cell mass spectrometry and machine learning methods is demonstrated for the first time to achieve rapid and reliable prediction of the phenotype of unknown single cells based on their metabolomic profiles, with experimental validation. This approach can be potentially applied towards prediction of drug-resistant phenotypes prior to chemotherapy.
Collapse
Affiliation(s)
- Renmeng Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA.
| | | | | |
Collapse
|
33
|
Abouleila Y, Onidani K, Ali A, Shoji H, Kawai T, Lim CT, Kumar V, Okaya S, Kato K, Hiyama E, Yanagida T, Masujima T, Shimizu Y, Honda K. Live single cell mass spectrometry reveals cancer-specific metabolic profiles of circulating tumor cells. Cancer Sci 2019; 110:697-706. [PMID: 30549153 PMCID: PMC6361580 DOI: 10.1111/cas.13915] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/05/2018] [Accepted: 12/09/2018] [Indexed: 02/06/2023] Open
Abstract
Recently, there has been increased attention on the analysis of circulating tumor cells (CTCs), also known as liquid biopsy, owing to its potential benefits in cancer diagnosis and treatment. Circulating tumor cells are released from primary tumor lesions into the blood stream and eventually metastasize to distant body organs. However, a major hurdle with CTC analysis is their natural scarcity. Existing methods lack sensitivity, specificity, or reproducibility required in CTC characterization and detection. Here, we report untargeted molecular profiling of single CTCs obtained from gastric cancer and colorectal cancer patients, using live single cell mass spectrometry integrated with microfluidics-based cell enrichment techniques. Using this approach, we showed the difference in the metabolomic profile between CTCs originating from different cancer groups. Moreover, potential biomarkers were putatively annotated to be specific to each cancer type.
Collapse
Affiliation(s)
- Yasmine Abouleila
- RIKEN Center for Biosystems Dynamics research (BDR)OsakaJapan
- Natural Science for Basic Research and DevelopmentHiroshima UniversityHiroshimaJapan
- Misr International University Research Center (MIU‐RC)CairoEgypt
| | - Kaoru Onidani
- Department of Biomarkers for Early Detection of CancerNational Cancer Center Research InstituteTokyoJapan
- Department of Oral and Maxillofacial SurgeryTokyo Dental CollegeTokyoJapan
| | - Ahmed Ali
- RIKEN Center for Biosystems Dynamics research (BDR)OsakaJapan
- Natural Science for Basic Research and DevelopmentHiroshima UniversityHiroshimaJapan
- Misr International University Research Center (MIU‐RC)CairoEgypt
| | - Hirokazu Shoji
- Department of Biomarkers for Early Detection of CancerNational Cancer Center Research InstituteTokyoJapan
- Gastrointestinal Medical Oncology DivisionNational Cancer Center HospitalTokyoJapan
| | - Takayuki Kawai
- RIKEN Center for Biosystems Dynamics research (BDR)OsakaJapan
- Japan Science and Technology AgencyPRESTOSaitamaJapan
- Graduate School of Frontier BiosciencesOsaka UniversityOsakaJapan
| | - Chwee Teck Lim
- Department of Biomedical EngineeringNational University of SingaporeSingapore
- Biomedical Institute for Global Health Research and TechnologyNational University of SingaporeSingapore
| | - Vipin Kumar
- RIKEN Center for Biosystems Dynamics research (BDR)OsakaJapan
| | - Shinobu Okaya
- Department of Biomarkers for Early Detection of CancerNational Cancer Center Research InstituteTokyoJapan
| | - Ken Kato
- Gastrointestinal Medical Oncology DivisionNational Cancer Center HospitalTokyoJapan
| | - Eiso Hiyama
- Natural Science for Basic Research and DevelopmentHiroshima UniversityHiroshimaJapan
| | - Toshio Yanagida
- RIKEN Center for Biosystems Dynamics research (BDR)OsakaJapan
| | | | | | - Kazufumi Honda
- Department of Biomarkers for Early Detection of CancerNational Cancer Center Research InstituteTokyoJapan
- Japan Agency for Medical Research and Development (AMED) CRESTTokyoJapan
| |
Collapse
|
34
|
Kempa EE, Hollywood KA, Smith CA, Barran PE. High throughput screening of complex biological samples with mass spectrometry – from bulk measurements to single cell analysis. Analyst 2019; 144:872-891. [DOI: 10.1039/c8an01448e] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We review the state of the art in HTS using mass spectrometry with minimal sample preparation from complex biological matrices. We focus on industrial and biotechnological applications.
Collapse
Affiliation(s)
- Emily E. Kempa
- Michael Barber Centre for Collaborative Mass Spectrometry
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester
- UK
| | - Katherine A. Hollywood
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM)
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester M1 7DN
- UK
| | - Clive A. Smith
- Sphere Fluidics Limited
- The Jonas-Webb Building
- Babraham Research Campus
- Cambridge
- UK
| | - Perdita E. Barran
- Michael Barber Centre for Collaborative Mass Spectrometry
- Manchester Institute of Biotechnology
- The University of Manchester
- Manchester
- UK
| |
Collapse
|
35
|
|
36
|
Zhang L, Khattar N, Kemenes I, Kemenes G, Zrinyi Z, Pirger Z, Vertes A. Subcellular Peptide Localization in Single Identified Neurons by Capillary Microsampling Mass Spectrometry. Sci Rep 2018; 8:12227. [PMID: 30111831 PMCID: PMC6093924 DOI: 10.1038/s41598-018-29704-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/17/2018] [Indexed: 12/22/2022] Open
Abstract
Single cell mass spectrometry (MS) is uniquely positioned for the sequencing and identification of peptides in rare cells. Small peptides can take on different roles in subcellular compartments. Whereas some peptides serve as neurotransmitters in the cytoplasm, they can also function as transcription factors in the nucleus. Thus, there is a need to analyze the subcellular peptide compositions in identified single cells. Here, we apply capillary microsampling MS with ion mobility separation for the sequencing of peptides in single neurons of the mollusk Lymnaea stagnalis, and the analysis of peptide distributions between the cytoplasm and nucleus of identified single neurons that are known to express cardioactive Phe-Met-Arg-Phe amide-like (FMRFamide-like) neuropeptides. Nuclei and cytoplasm of Type 1 and Type 2 F group (Fgp) neurons were analyzed for neuropeptides cleaved from the protein precursors encoded by alternative splicing products of the FMRFamide gene. Relative abundances of nine neuropeptides were determined in the cytoplasm. The nuclei contained six of these peptides at different abundances. Enabled by its relative enrichment in Fgp neurons, a new 28-residue neuropeptide was sequenced by tandem MS.
Collapse
Affiliation(s)
- Linwen Zhang
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Nikkita Khattar
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA
| | - Ildiko Kemenes
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Gyorgy Kemenes
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK
| | - Zita Zrinyi
- Department of Experimental Zoology, Balaton Limnological Institute, MTA Center for Ecological Research, 8237, Tihany, Hungary
| | - Zsolt Pirger
- Department of Experimental Zoology, Balaton Limnological Institute, MTA Center for Ecological Research, 8237, Tihany, Hungary
| | - Akos Vertes
- Department of Chemistry, The George Washington University, Washington, DC, 20052, USA.
| |
Collapse
|
37
|
Bioinspired, nanoscale approaches in contemporary bioanalytics (Review). Biointerphases 2018; 13:040801. [DOI: 10.1116/1.5037582] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
|
38
|
Saha-Shah A, Karty JA, Baker LA. Local collection, reaction and analysis with theta pipette emitters. Analyst 2018; 142:1512-1518. [PMID: 28361146 DOI: 10.1039/c7an00109f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A mobile nanofluidic device based on theta pipettes was developed for "collect-react-analyze" measurements of small volumes of a sample collected locally from biological samples. Specifically, we demonstrate execution of local reactions inside single cells and on Pseudomonas aeruginosa biofilms for targeted analysis of metabolites. Nanoliter volumes of the sample, post-reaction, were delivered to a mass spectrometer via electrospray ionization (ESI) for chemical analysis. A new strategy was developed where the additional barrel of a theta pipette was utilized both to enable chemical manipulations after sample collection and to electrospray the nanoliter sample volumes collected directly from the pipette tip. This strategy proved a robust method for ESI from nanometer sized tips without clogging or degradation of the emitter and obviated the need to coat glass pipettes with a conductive metal coating. Chemical reactions investigated include acid catalyzed degradation of oligosaccharides inside the pipette tip to increase the detection sensitivity of minor metabolites found in Allium cepa cells. Additionally, phenylboronic acid complexation of carbohydrates from single cells and liposaccharides from biofilms was also performed inside the pipette tip for selective detection of carbohydrates and liposaccharides with cis-diols.
Collapse
Affiliation(s)
- Anumita Saha-Shah
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, USA.
| | | | | |
Collapse
|
39
|
Zhang XC, Zang Q, Zhao H, Ma X, Pan X, Feng J, Zhang S, Zhang R, Abliz Z, Zhang X. Combination of Droplet Extraction and Pico-ESI-MS Allows the Identification of Metabolites from Single Cancer Cells. Anal Chem 2018; 90:9897-9903. [DOI: 10.1021/acs.analchem.8b02098] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Qingce Zang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | | | | | | | | | | | - Ruiping Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zeper Abliz
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Centre for Bioimaging and Systems Biology, Minzu University of China, Beijing 100081, China
| | | |
Collapse
|
40
|
Yang B, Patterson NH, Tsui T, Caprioli RM, Norris JL. Single-Cell Mass Spectrometry Reveals Changes in Lipid and Metabolite Expression in RAW 264.7 Cells upon Lipopolysaccharide Stimulation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29. [PMID: 29536413 PMCID: PMC5943162 DOI: 10.1007/s13361-018-1899-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
It has been widely recognized that individual cells that exist within a large population of cells, even if they are genetically identical, can have divergent molecular makeups resulting from a variety of factors, including local environmental factors and stochastic processes within each cell. Presently, numerous approaches have been described that permit the resolution of these single-cell expression differences for RNA and protein; however, relatively few techniques exist for the study of lipids and metabolites in this manner. This study presents a methodology for the analysis of metabolite and lipid expression at the level of a single cell through the use of imaging mass spectrometry on a high-performance Fourier transform ion cyclotron resonance mass spectrometer. This report provides a detailed description of the overall experimental approach, including sample preparation as well as the data acquisition and analysis strategy for single cells. Applying this approach to the study of cultured RAW264.7 cells, we demonstrate that this method can be used to study the variation in molecular expression with cell populations and is sensitive to alterations in that expression that occurs upon lipopolysaccharide stimulation. Graphical Abstract.
Collapse
Affiliation(s)
- Bo Yang
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37240, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37240, USA
| | - Nathan Heath Patterson
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37240, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37240, USA
| | - Tina Tsui
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37240, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37240, USA
| | - Richard M Caprioli
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37240, USA
- Department of Biochemistry, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37240, USA
- Department of Chemistry, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37240, USA
| | - Jeremy L Norris
- Mass Spectrometry Research Center, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37240, USA.
- Department of Biochemistry, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN, 37240, USA.
- Department of Chemistry, Vanderbilt University, 465 21st Avenue South, Nashville, TN, 37240, USA.
| |
Collapse
|
41
|
Zhang L, Vertes A. Einzelzell‐Massenspektrometrie zur Untersuchung zellulärer Heterogenität. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201709719] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Linwen Zhang
- Department of Chemistry The George Washington University Washington DC 20052 USA
| | - Akos Vertes
- Department of Chemistry The George Washington University Washington DC 20052 USA
| |
Collapse
|
42
|
Zhang L, Vertes A. Single‐Cell Mass Spectrometry Approaches to Explore Cellular Heterogeneity. Angew Chem Int Ed Engl 2018; 57:4466-4477. [DOI: 10.1002/anie.201709719] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/27/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Linwen Zhang
- Department of Chemistry The George Washington University Washington DC 20052 USA
| | - Akos Vertes
- Department of Chemistry The George Washington University Washington DC 20052 USA
| |
Collapse
|
43
|
Lee MCG, Sun B. Quantitation of nonspecific protein adsorption at solid–liquid interfaces for single-cell proteomics. CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Protein nonspecific adsorption that occurred at the solid–liquid interface has been subjected to intense physical and chemical characterizations due to its crucial role in a wide range of applications, including food and pharmaceutical industries, medical implants, biosensing, and so on. Protein-adsorption caused sample loss has largely hindered the studies of single-cell proteomics; the prevention of such loss requires the understanding of protein–surface adsorption at the proteome level, in which the competitive adsorption of thousands and millions of proteins with vast dynamic range occurs. To this end, we feel the necessity to review current methodologies on their potentials to characterize — more specifically to quantify — the proteome-wide adsorption. We hope this effort can help advancing single-cell proteomics and trace proteomics.
Collapse
Affiliation(s)
| | - Bingyun Sun
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| |
Collapse
|
44
|
Masuda K, Abouleila Y, Ali A, Yanagida T, Masujima T. Live Single-Cell Mass Spectrometry (LSC-MS) for Plant Metabolomics. Methods Mol Biol 2018; 1778:269-282. [PMID: 29761445 DOI: 10.1007/978-1-4939-7819-9_19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Live single-cell mass spectrometry (LSC-MS) allows for the detection of hundreds to thousands of metabolite peaks acquired from a single plant cell within a few minutes. Plant cells are first observed under a stereomicroscope, a cell of interest is chosen, and then sampled using a metal-coated glass microcapillary for subsequent analysis. A few microliters of ionization solvent is then added to the rear end of the capillary followed by the introduction of the capillary's content directly into the mass spectrometer. High voltage is applied between the capillary and the mass spectrometer inlet to induce nanospray ionization. Metabolite structural confirmation is performed using tandem mass spectrometry analysis (MS/MS) and fragments are matched with MS/MS databases to predict metabolic pathways. This method enables swift and direct molecular detection and identification of specific metabolites from a single plant cell along with their localization within the cell, which will allow for comprehensive understanding of plant metabolomics on a single cell level.
Collapse
Affiliation(s)
- Keiko Masuda
- Laboratory for Single-Cell Mass Spectrometry, Quantitative Biology Center, RIKEN, Osaka, Japan.
| | - Yasmine Abouleila
- Laboratory for Single-Cell Mass Spectrometry, Quantitative Biology Center, RIKEN, Osaka, Japan
| | - Ahmed Ali
- Laboratory for Single-Cell Mass Spectrometry, Quantitative Biology Center, RIKEN, Osaka, Japan
| | - Toshio Yanagida
- Laboratory for Single-Cell Mass Spectrometry, Quantitative Biology Center, RIKEN, Osaka, Japan
| | - Tsutomu Masujima
- Laboratory for Single-Cell Mass Spectrometry, Quantitative Biology Center, RIKEN, Osaka, Japan
| |
Collapse
|
45
|
Yang Y, Huang Y, Wu J, Liu N, Deng J, Luan T. Single-cell analysis by ambient mass spectrometry. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.02.009] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
46
|
Guillaume-Gentil O, Rey T, Kiefer P, Ibáñez AJ, Steinhoff R, Brönnimann R, Dorwling-Carter L, Zambelli T, Zenobi R, Vorholt JA. Single-Cell Mass Spectrometry of Metabolites Extracted from Live Cells by Fluidic Force Microscopy. Anal Chem 2017; 89:5017-5023. [PMID: 28363018 DOI: 10.1021/acs.analchem.7b00367] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Single-cell metabolite analysis provides valuable information on cellular function and response to external stimuli. While recent advances in mass spectrometry reached the sensitivity required to investigate metabolites in single cells, current methods commonly isolate and sacrifice cells, inflicting a perturbed state and preventing complementary analyses. Here, we propose a two-step approach that combines nondestructive and quantitative withdrawal of intracellular fluid with subpicoliter resolution using fluidic force microscopy, followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The developed method enabled the detection and identification of 20 metabolites recovered from the cytoplasm of individual HeLa cells. The approach was further validated in 13C-glucose feeding experiments, which showed incorporation of labeled carbon atoms into different metabolites. Metabolite sampling, followed by mass spectrometry measurements, enabled the preservation of the physiological context and the viability of the analyzed cell, providing opportunities for complementary analyses of the cell before, during, and after metabolite analysis.
Collapse
Affiliation(s)
- Orane Guillaume-Gentil
- Department of Biology, Institute of Microbiology, ETH Zurich , Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Timo Rey
- Department of Biology, Institute of Microbiology, ETH Zurich , Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Patrick Kiefer
- Department of Biology, Institute of Microbiology, ETH Zurich , Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| | - Alfredo J Ibáñez
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich , 8093 Zurich, Switzerland
| | - Robert Steinhoff
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich , 8093 Zurich, Switzerland
| | - Rolf Brönnimann
- Swiss Federal Laboratories for Material Science and Technology EMPA , 8600 Dübendorf, Switzerland
| | - Livie Dorwling-Carter
- Department of Information Technology and Electrical Engineering, Institute for Biomedical Engineering, ETH Zurich , 8093 Zurich, Switzerland
| | - Tomaso Zambelli
- Department of Information Technology and Electrical Engineering, Institute for Biomedical Engineering, ETH Zurich , 8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zurich , 8093 Zurich, Switzerland
| | - Julia A Vorholt
- Department of Biology, Institute of Microbiology, ETH Zurich , Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland
| |
Collapse
|
47
|
Single-neuron identification of chemical constituents, physiological changes, and metabolism using mass spectrometry. Proc Natl Acad Sci U S A 2017; 114:2586-2591. [PMID: 28223513 DOI: 10.1073/pnas.1615557114] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The use of single-cell assays has emerged as a cutting-edge technique during the past decade. Although single-cell mass spectrometry (MS) has recently achieved remarkable results, deep biological insights have not yet been obtained, probably because of various technical issues, including the unavoidable use of matrices, the inability to maintain cell viability, low throughput because of sample pretreatment, and the lack of recordings of cell physiological activities from the same cell. In this study, we describe a patch clamp/MS-based platform that enables the sensitive, rapid, and in situ chemical profiling of single living neurons. This approach integrates modified patch clamp technique and modified MS measurements to directly collect and detect nanoliter-scale samples from the cytoplasm of single neurons in mice brain slices. Abundant possible cytoplasmic constituents were detected in a single neuron at a relatively fast rate, and over 50 metabolites were identified in this study. The advantages of direct, rapid, and in situ sampling and analysis enabled us to measure the biological activities of the cytoplasmic constituents in a single neuron, including comparing neuron types by cytoplasmic chemical constituents; observing changes in constituent concentrations as the physiological conditions, such as age, vary; and identifying the metabolic pathways of small molecules.
Collapse
|
48
|
|
49
|
Vanbellingen QP, Castellanos A, Rodriguez-Silva M, Paudel I, Chambers JW, Fernandez-Lima FA. Analysis of Chemotherapeutic Drug Delivery at the Single Cell Level Using 3D-MSI-TOF-SIMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:2033-2040. [PMID: 27582118 PMCID: PMC5088064 DOI: 10.1007/s13361-016-1485-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/08/2016] [Accepted: 08/13/2016] [Indexed: 05/18/2023]
Abstract
In this work, we show the advantages of label-free, tridimensional mass spectrometry imaging using dual beam analysis (25 keV Bi3+) and depth profiling (20 keV with a distribution centered at Ar1500+) coupled to time of flight secondary ion mass spectrometry (3D-MSI-TOF-SIMS) for the study of A-172 human glioblastoma cell line treated with B-cell lymphoma 2 (Bcl-2) inhibitor ABT-737. The high spatial (~250 nm) and high mass resolution (m/Δm ~10,000) of TOF-SIMS permitted the localization and identification of the intact, unlabeled drug molecular ion (m/z 811.26 C42H44ClN6O5S2- [M - H]-) as well as characteristic fragment ions. We propose a novel approach based on the inspection of the drug secondary ion yield, which showed a good correlation with the drug concentration during cell treatment at therapeutic dosages (0-200 μM with 4 h incubation). Chemical maps using endogenous molecular markers showed that the ABT-737 is mainly localized in subsurface regions and absent in the nucleus. A semiquantitative workflow is proposed to account for the biological cell diversity based on the spatial distribution of endogenous molecular markers (e.g., nuclei and cytoplasm) and secondary ion confirmation based on the ratio of drug-specific fragments to molecular ion as a function of the therapeutic dosage. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Quentin P Vanbellingen
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Anthony Castellanos
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Monica Rodriguez-Silva
- Department of Cellular Biology and Pharmacology, Department of Neuroscience, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Iru Paudel
- Department of Cellular Biology and Pharmacology, Department of Neuroscience, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Jeremy W Chambers
- Department of Cellular Biology and Pharmacology, Department of Neuroscience, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Biomolecular Science Institute, Florida International University, Miami, FL, USA
| | - Francisco A Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA.
- Biomolecular Science Institute, Florida International University, Miami, FL, USA.
| |
Collapse
|
50
|
Esaki T, Masujima T. Fluorescence Probing Live Single-cell Mass Spectrometry for Direct Analysis of Organelle Metabolism. ANAL SCI 2016; 31:1211-3. [PMID: 26656807 DOI: 10.2116/analsci.31.1211] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Mitochondria in a live HepG2 cell were visualized with a fluorescent probe to specify their location and state in a living cell. Then, mitochondria were selectively captured with a nanospray tip under fluorescence microscope, and thousands of small molecular peaks were revealed and unique steroids specific to mitochondria were also found. This fluorescence imaging combined with live single-cell mass spectrometry opens the door to the analysis of site- and state-specific molecular detection to elucidate precise molecular mechanisms at the single-cell and organelle level.
Collapse
|