1
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Hu H, Liu G, Li Y. The isolation strategy and chemical analysis of oil cells from Asari Radix et Rhizoma. PLANT METHODS 2024; 20:72. [PMID: 38760854 PMCID: PMC11100110 DOI: 10.1186/s13007-024-01184-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 04/15/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Single-cell analysis, a rapidly evolving field, encounters significant challenges in detecting individual cells within complex plant tissues, particularly oil cells (OCs). The intricate process of single-cell isolation, coupled with the inherent chemical volatility of oil cells, necessitates a comprehensive methodology. RESULTS This study presents a method for obtaining intact OC from Asari Radix et Rhizoma (ARR), a traditional herbal medicine. The developed approach facilitates both qualitative and quantitative analysis of diverse OCs. To determine the most reliable approach, four practical methods-laser capture microdissection, micromanipulation capturing, micromanipulation piping, and cell picking-were systematically compared and evaluated, unequivocally establishing cell picking as the most effective method for OC isolation and chemical analysis. Microscopic observations showed that OCs predominantly distribute in the cortex of adventitious and fibrous roots, as well as the pith and cortex of the rhizome, with distinct morphologies-oblong in roots and circular in rhizomes. Sixty-three volatile constituents were identified in OCs, with eighteen compounds exhibiting significant differences. Safrole, methyleugenol, and asaricin emerged as the most abundant constituents in OCs. Notably, cis-4-thujanol and tetramethylpyrazine were exclusive to rhizome OCs, while isoeugenol methyl ether was specific to fibrous root OCs based on the detections. ARR roots and rhizomes displayed marked disparities in OC distribution, morphology, and constituents. CONCLUSION The study highlights the efficacy of cell picking coupled with HS-SPME-GC-MS as a flexible, reliable, and sensitive method for OC isolation and chemical analysis, providing a robust methodology for future endeavors in single-cell analyses.
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Affiliation(s)
- Haibo Hu
- National Engineering Research Center for Modernization of Traditional Chinese Medicine-Hakka Medical Resources Branch, School of Pharmacy, Gannan Medical University, Ganzhou, 341000, China
- School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Guangxue Liu
- School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yaoli Li
- School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.
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2
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Agostini M, Traldi P, Hamdan M. Mass Spectrometry-Based Proteomics: Analyses Related to Drug-Resistance and Disease Biomarkers. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1722. [PMID: 37893440 PMCID: PMC10608342 DOI: 10.3390/medicina59101722] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023]
Abstract
Mass spectrometry-based proteomics is a key player in research efforts to characterize aberrant epigenetic alterations, including histone post-translational modifications and DNA methylation. Data generated by this approach complements and enrich datasets generated by genomic, epigenetic and transcriptomics approaches. These combined datasets can provide much-needed information on various mechanisms responsible for drug resistance, the discovery and validation of potential biomarkers for different diseases, the identification of signaling pathways, and genes and enzymes to be targeted by future therapies. The increasing use of high-resolution, high-accuracy mass spectrometers combined with more refined protein labeling and enrichment procedures enhanced the role of this approach in the investigation of these epigenetic modifications. In this review, we discuss recent MS-based studies, which are contributing to current research efforts to understand certain mechanisms behind drug resistance to therapy. We also discuss how these MS-based analyses are contributing to biomarkers discovery and validation.
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Affiliation(s)
| | - Pietro Traldi
- Istituto di Ricerca Pediatrica Città della Speranza, Corso Stati Uniti 4, 35100 Padova, Italy; (M.A.); (M.H.)
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3
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Hu R, Li Y, Yang Y, Liu M. Mass spectrometry-based strategies for single-cell metabolomics. MASS SPECTROMETRY REVIEWS 2023; 42:67-94. [PMID: 34028064 DOI: 10.1002/mas.21704] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
Single cell analysis has drawn increasing interest from the research community due to its capability to interrogate cellular heterogeneity, allowing refined tissue classification and facilitating novel biomarker discovery. With the advancement of relevant instruments and techniques, it is now possible to perform multiple omics including genomics, transcriptomics, metabolomics or even proteomics at single cell level. In comparison with other omics studies, single-cell metabolomics (SCM) represents a significant challenge since it involves many types of dynamically changing compounds with a wide range of concentrations. In addition, metabolites cannot be amplified. Although difficult, considerable progress has been made over the past decade in mass spectrometry (MS)-based SCM in terms of processing technologies and biochemical applications. In this review, we will summarize recent progress in the development of promising MS platforms, sample preparation methods and SCM analysis of various cell types (including plant cell, cancer cell, neuron, embryo cell, and yeast cell). Current limitations and future research directions in the field of SCM will also be discussed.
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Affiliation(s)
- Rui Hu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yunhuang Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
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4
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Zhao C, Cai Z. Three-dimensional quantitative mass spectrometry imaging in complex system: From subcellular to whole organism. MASS SPECTROMETRY REVIEWS 2022; 41:469-487. [PMID: 33300181 DOI: 10.1002/mas.21674] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/13/2020] [Accepted: 10/22/2020] [Indexed: 06/12/2023]
Abstract
Mass spectrometry imaging (MSI) has been applied for label-free three-dimensional (3D) imaging from position array across the whole organism, which provides high-dimensional quantitative data of inorganic or organic compounds that may play an important role in the regulation of cellular signaling, including metals, metabolites, lipids, drugs, peptides, and proteins. While MSI is suitable for investigation of the spatial distribution of molecules, it has a limitation with visualization and quantification of multiple molecules. 3D-MSI, however, can be applied toward exploring metabolic pathway as well as the interactions of lipid-protein, protein-protein, and metal-protein in complex systems from subcellular to the whole organism through an untargeted methodology. In this review, we highlight the methods and applications of MS-based 3D imaging to address the complexity of molecular interaction from nano- to micrometer lateral resolution, with particular focus on: (a) common and hybrid 3D-MSI techniques; (b) quantitative MSI methodology, including the methods using a stable isotope labeling internal standard (SILIS) and SILIS-free approaches with tissue extinction coefficient or virtual calibration; (c) reconstruction of the 3D organ; (d) application of 3D-MSI for biomarker screening and environmental toxicological research. 3D-MSI quantitative analysis provides accurate spatial information and quantitative variation of biomolecules, which may be valuable for the exploration of the molecular mechanism of the disease progresses and toxicological assessment of environmental pollutants in the whole organism. Additionally, we also discuss the challenges and perspectives on the future of 3D quantitative MSI.
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Affiliation(s)
- Chao Zhao
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong SAR, China
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5
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Recent advances for cancer detection and treatment by microfluidic technology, review and update. Biol Proced Online 2022; 24:5. [PMID: 35484481 PMCID: PMC9052508 DOI: 10.1186/s12575-022-00166-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 04/18/2022] [Indexed: 12/16/2022] Open
Abstract
Numerous cancer-associated deaths are owing to a lack of effective diagnostic and therapeutic approaches. Microfluidic systems for analyzing a low volume of samples offer a precise, quick, and user-friendly technique for cancer diagnosis and treatment. Microfluidic devices can detect many cancer-diagnostic factors from biological fluids and also generate appropriate nanoparticles for drug delivery. Thus, microfluidics may be valuable in the cancer field due to its high sensitivity, high throughput, and low cost. In the present article, we aim to review recent achievements in the application of microfluidic systems for the diagnosis and treatment of various cancers. Although microfluidic platforms are not yet used in the clinic, they are expected to become the main technology for cancer diagnosis and treatment. Microfluidic systems are proving to be more sensitive and accurate for the detection of cancer biomarkers and therapeutic strategies than common assays. Microfluidic lab-on-a-chip platforms have shown remarkable potential in the designing of novel procedures for cancer detection, therapy, and disease follow-up as well as the development of new drug delivery systems for cancer treatment.
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6
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Cortés-Llanos B, Wang Y, Sims CE, Allbritton NL. A technology of a different sort: microraft arrays. LAB ON A CHIP 2021; 21:3204-3218. [PMID: 34346456 PMCID: PMC8387436 DOI: 10.1039/d1lc00506e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A common procedure performed throughout biomedical research is the selection and isolation of biological entities such as organelles, cells and organoids from a mixed population. In this review, we describe the development and application of microraft arrays, an analysis and isolation platform which enables a vast range of criteria and strategies to be used when separating biological entities. The microraft arrays are comprised of elastomeric microwells with detachable polymer bases (microrafts) that act as capture and culture sites as well as supporting carriers during cell isolation. The technology is elegant in its simplicity and can be implemented for samples possessing tens to millions of objects yielding a flexible platform for applications such as single-cell RNA sequencing, subcellular organelle capture and assay, high-throughput screening and development of CRISPR gene-edited cell lines, and organoid manipulation and selection. The transparent arrays are compatible with a multitude of imaging modalities enabling selection based on 2D or 3D spatial phenotypes or temporal properties. Each microraft can be individually isolated on demand with retention of high viability due to the near zero hydrodynamic stress imposed upon the cells during microraft release, capture and deposition. The platform has been utilized as a simple manual add-on to a standard microscope or incorporated into fully automated instruments that implement state-of-the-art imaging algorithms and machine learning. The vast array of selection criteria enables separations not possible with conventional sorting methods, thus garnering widespread interest in the biological and pharmaceutical sciences.
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7
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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.
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8
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Wang J, Han X. Analytical challenges of shotgun lipidomics at different resolution of measurements. Trends Analyt Chem 2019; 121:115697. [PMID: 32713986 PMCID: PMC7382544 DOI: 10.1016/j.trac.2019.115697] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The essence of shotgun lipidomics is to maintain consistency of the chemical environment of lipid samples during mass spectrometry acquisition. This strategy is suitable for large-scale quantitative analysis. This strategy also allows sufficient time to collect data to improve the signal-to-noise ratio. The initial approach of shotgun lipidomics was the electrospray ionization (ESI)-based direct infusion mass spectrometry strategy. With development of mass spectrometry for small molecules, shotgun lipidomics methods have been extended to matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) and ambient mass spectrometry, including MS imaging methods. Furthermore, the object of analysis has extended from organ and body fluid levels to tissue and cell levels with technological developments. In this article, we summarize the status and technical challenges of shotgun lipidomics at different resolution of measurements from the mass spectrometry perspective.
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Affiliation(s)
- Jianing Wang
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
- Department of Medicine – Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
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9
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Rodogiannis K, Duong JT, Kovarik ML. Microfluidic single-cell analysis of oxidative stress in Dictyostelium discoideum. Analyst 2019; 143:3643-3650. [PMID: 29969508 DOI: 10.1039/c8an00752g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Microfluidic chemical cytometry is a powerful technique for examining chemical contents of individual cells, but applications have focused on cells from multicellular organisms, especially mammals. We demonstrate the first use of microfluidic chemical cytometry to examine a unicellular organism, the social amoeba Dictyostelium discoideum. We used the reactive oxygen species indicator dichlorodihydrofluorescein diacetate to report on oxidative stress and controlled for variations in indicator loading and retention using carboxyfluorescein diacetate as an internal standard. After optimizing indicator concentration, we investigated the effect of peroxide treatment through single-cell measurements of 353 individual cells. The peak area ratio of dichlorofluorescein to carboxyfluorescein increased from 1.69 ± 0.89 for untreated cells to 5.19 ± 2.72 for cells treated with 40 mM hydrogen peroxide. Interestingly, the variance of the data also increased with oxidative stress. While preliminary, these results are consistent with the hypothesis that heterogeneous stress responses in unicellular organisms may be adaptive.
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Affiliation(s)
- Kathy Rodogiannis
- Department of Chemistry, Trinity College, 300 Summit St., Hartford, CT 06106, USA.
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10
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Nadappuram BP, Cadinu P, Barik A, Ainscough AJ, Devine MJ, Kang M, Gonzalez-Garcia J, Kittler JT, Willison KR, Vilar R, Actis P, Wojciak-Stothard B, Oh SH, Ivanov AP, Edel JB. Nanoscale tweezers for single-cell biopsies. NATURE NANOTECHNOLOGY 2019; 14:80-88. [PMID: 30510280 DOI: 10.1038/s41565-018-0315-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 10/19/2018] [Indexed: 05/19/2023]
Abstract
Much of the functionality of multicellular systems arises from the spatial organization and dynamic behaviours within and between cells. Current single-cell genomic methods only provide a transcriptional 'snapshot' of individual cells. The real-time analysis and perturbation of living cells would generate a step change in single-cell analysis. Here we describe minimally invasive nanotweezers that can be spatially controlled to extract samples from living cells with single-molecule precision. They consist of two closely spaced electrodes with gaps as small as 10-20 nm, which can be used for the dielectrophoretic trapping of DNA and proteins. Aside from trapping single molecules, we also extract nucleic acids for gene expression analysis from living cells without affecting their viability. Finally, we report on the trapping and extraction of a single mitochondrion. This work bridges the gap between single-molecule/organelle manipulation and cell biology and can ultimately enable a better understanding of living cells.
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Affiliation(s)
| | - Paolo Cadinu
- Department of Chemistry, Imperial College London, London, UK
| | - Avijit Barik
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Alexander J Ainscough
- Department of Chemistry, Imperial College London, London, UK
- Department of Experimental Medicine and Toxicology, Imperial College London, London, UK
| | - Michael J Devine
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Minkyung Kang
- Department of Chemistry, Imperial College London, London, UK
| | | | - Josef T Kittler
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | | | - Ramon Vilar
- Department of Chemistry, Imperial College London, London, UK
| | - Paolo Actis
- School of Electronic and Electrical Engineering, Pollard Institute, University of Leeds, Leeds, UK
| | | | - Sang-Hyun Oh
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, USA
| | | | - Joshua B Edel
- Department of Chemistry, Imperial College London, London, UK.
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11
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De Silva IW, Kretsch AR, Lewis HM, Bailey M, Verbeck GF. True one cell chemical analysis: a review. Analyst 2019; 144:4733-4749. [DOI: 10.1039/c9an00558g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The constantly growing field of True One Cell (TOC) analysis has provided important information on the direct chemical composition of various cells and cellular components.
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12
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Berry SB, Zhang T, Day JH, Su X, Wilson IZ, Berthier E, Theberge AB. Upgrading well plates using open microfluidic patterning. LAB ON A CHIP 2017; 17:4253-4264. [PMID: 29164190 DOI: 10.1039/c7lc00878c] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cellular communication between multiple cell types is a ubiquitous process that is responsible for vital physiological responses observed in vivo (e.g., immune response, organ function). Many in vitro coculture strategies have been developed, both in traditional culture and microscale systems, and have shown the potential to recreate some of the physiological behaviors of organs or groups of cells. A fundamental limitation of current systems is the difficulty of reconciling the additional engineering requirements for creating soluble factor signaling systems (e.g., segregated cell culture) with the use of well-characterized materials and platforms that have demonstrated successful results and biocompatibility in assays. We present a new open-microfluidic platform, the Monorail Device, that is placed in any existing well plate or Petri dish and enables patterning of segregated coculture regions, thereby allowing the direct upgrade of monoculture experiments into multiculture assays. Our platform patterns biocompatible hydrogel walls via microfluidic spontaneous capillary flow (SCF) along a rail insert set inside commercially available cultureware, creating customized pipette-accessible cell culture chambers that require fewer cells than standard macroscale culture. Importantly, the device allows the use of native surfaces without additional modification or treatments, while creating permeable dividers for the diffusion of soluble factors. Additionally, the ease of patterning afforded by our platform makes reconfiguration of the culture region as simple as changing the rail insert. We demonstrate the ability of the device to pattern flows on a variety of cell culture surfaces and create hydrogel walls in complex and precise shapes. We characterize the physical parameters that enable a reproducible SCF-driven flow and highlight specialized design features that increase the ease of use of the device and control of the open microfluidic flow. Further, we present the performance of our platform according to useful coculture criteria, including permeability and integrity of our hydrogel walls and surface-sensitive cell culture. Lastly, we show the potential of this type of platform to create modular multikingdom culture systems that can be used to study soluble factor signaling between mammalian cells, bacteria, and fungi, as well as the potential for adaptation of this technology by researchers across multiple fields.
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Affiliation(s)
- Samuel B Berry
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA.
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13
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Gupta SD, Sachs Z. Novel single-cell technologies in acute myeloid leukemia research. Transl Res 2017; 189:123-135. [PMID: 28802867 PMCID: PMC6584944 DOI: 10.1016/j.trsl.2017.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 12/29/2022]
Abstract
Acute myeloid leukemia (AML) is a lethal malignancy because patients who initially respond to chemotherapy eventually relapse with treatment refractory disease. Relapse is caused by leukemia stem cells (LSCs) that reestablish the disease through self-renewal. Self-renewal is the ability of a stem cell to produce copies of itself and give rise to progeny cells. Therefore, therapeutic strategies eradicating LSCs are essential to prevent relapse and achieve long-term remission in AML. AML is a heterogeneous disease both at phenotypic and genotypic levels, and this heterogeneity extends to LSCs. Classical studies in AML have aimed at characterization of the bulk tumor population, thereby masking cellular heterogeneity. Single-cell approaches provide a novel opportunity to elucidate molecular mechanisms in heterogeneous diseases such as AML. In recent years, major advancements in single-cell measurement systems have revolutionized our understanding of the pathophysiology of AML and enabled the characterization of LSCs. Identifying the molecular mechanisms critical to AML LSCs will aid in the development of targeted therapeutic strategies to combat this deadly disease.
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Affiliation(s)
- Soumyasri Das Gupta
- Division of Hematology, Oncology, and Transplantation, Department Medicine, University of Minnesota, Minneapolis, Minn
| | - Zohar Sachs
- Division of Hematology, Oncology, and Transplantation, Department Medicine, University of Minnesota, Minneapolis, Minn; Masonic Cancer Center, University of Minnesota, Minneapolis, Minn.
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Proctor A, Sims CE, Allbritton NL. Chemical fixation to arrest phospholipid signaling for chemical cytometry. J Chromatogr A 2017; 1523:97-106. [PMID: 28528682 DOI: 10.1016/j.chroma.2017.05.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/28/2017] [Accepted: 05/07/2017] [Indexed: 12/18/2022]
Abstract
Chemical cytometry is a powerful tool for measuring biological processes such as enzymatic signaling at the single cell level. Among these technologies, single-cell capillary zone electrophoresis (CZE) has emerged as a powerful tool to assay a wide range of cellular metabolites. However, analysis of dynamic processes within cells remains challenging as signaling pathways are rapidly altered in response to changes in the cellular environment, including cell manipulation and storage. To address these limitations, we describe a method for chemical fixation of cells to stop the cellular reactions to preserve the integrity of key signaling molecules or reporters within the cell and to enable the cell to act as a storage reservoir for the reporter and its metabolites prior to assay by single-cell CZE. Fluorescent phosphatidylinositol 4,5-bisphosphate reporters were loaded into cells and the cells were chemically fixed and stored prior to analysis. The reporter and its metabolites were electrophoretically separated by single-cell CZE. Chemical fixation parameters such as fixative, fixation time, storage solution, storage duration, and extraction solution were optimized. When cells were loaded with a fluorescent C6- or C16-PIP2 followed by glutaraldehyde fixation and immediate analysis, 24±2% and 139±12% of the lipid was recoverable, respectively, when compared to an unfixed control. Storage of the cells for 24h yielded recoverable lipid of 61±3% (C6-PIP2) and 55±5% (C16-PIP2) when compared to cells analyzed immediately after fixation. The metabolites observed with and without fixation were identical. Measurement of phospholipase C activity in single leukemic cells in response to an agonist demonstrated the capability of chemical fixation coupled to single-cell CZE to yield an accurate snapshot of cellular reactions with the probe. This methodology enables cell assay with the reporter to be separated in space and time from reporter metabolite quantification while preserving assay integrity.
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Affiliation(s)
- Angela Proctor
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, United States.
| | - Christopher E Sims
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, United States.
| | - Nancy L Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599, United States; Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599, United States and North Carolina State University, Raleigh, NC 27695, United States.
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15
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Affiliation(s)
- Lucas Armbrecht
- Department of Biosystems Science and Engineering, ETH Zurich, CH-8093 Zurich, Switzerland
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16
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Onjiko RM, Morris SE, Moody SA, Nemes P. Single-cell mass spectrometry with multi-solvent extraction identifies metabolic differences between left and right blastomeres in the 8-cell frog (Xenopus) embryo. Analyst 2016; 141:3648-56. [PMID: 27004603 PMCID: PMC4899105 DOI: 10.1039/c6an00200e] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Single-cell metabolic mass spectrometry enables the discovery (untargeted) analysis of small molecules in individual cells. Using single-cell capillary electrophoresis high-resolution mass spectrometry (CE-HRMS), we recently uncovered small-molecule differences between embryonic cells located along the animal-vegetal and dorsal-ventral axes of the 16-cell frog (Xenopus laevis) embryo, raising the question whether metabolic cell heterogeneity also exists along the left-right body axis. To address this question, we here advance single-cell CE-HRMS for identifying and quantifying metabolites in higher analytical sensitivity, and then use the methodology to compare metabolite production between left and right cells. Our strategy utilizes multiple solvents with complementary physicochemical properties to extract small molecules from single cells and improve electrophoretic separation, increasing metabolite ion signals for quantification and tandem HRMS. As a result, we were able to identify 55 different small molecules in D1 cells that were isolated from 8-cell embryos. To quantify metabolite production between left and right cells, we analyzed n = 24 different D1 cells in technical duplicate-triplicate measurements. Statistical and multivariate analysis based on 80 of the most repeatedly quantified compounds revealed 10 distinct metabolites that were significantly differentially accumulated in the left or right cells (p < 0.05 and fold change ≥1.5). These metabolites were enriched in the arginine-proline metabolic pathway in the right, but not the left D1 cells. Besides providing analytical benefits for single-cell HRMS, this work provides new metabolic data on the establishment of normal body asymmetry in the early developing embryo.
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Affiliation(s)
- Rosemary M Onjiko
- Department of Chemistry, The George Washington University, Washington, DC 20052, USA.
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17
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Li X, Zhao S, Hu H, Liu YM. A microchip electrophoresis-mass spectrometric platform with double cell lysis nano-electrodes for automated single cell analysis. J Chromatogr A 2016; 1451:156-163. [PMID: 27207575 DOI: 10.1016/j.chroma.2016.05.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/01/2016] [Accepted: 05/04/2016] [Indexed: 01/11/2023]
Abstract
Capillary electrophoresis-based single cell analysis has become an essential approach in researches at the cellular level. However, automation of single cell analysis has been a challenge due to the difficulty to control the number of cells injected and the irreproducibility associated with cell aggregation. Herein we report the development of a new microfluidic platform deploying the double nano-electrode cell lysis technique for automated analysis of single cells with mass spectrometric detection. The proposed microfluidic chip features integration of a cell-sized high voltage zone for quick single cell lysis, a microfluidic channel for electrophoretic separation, and a nanoelectrospray emitter for ionization in MS detection. Built upon this platform, a microchip electrophoresis-mass spectrometric method (MCE-MS) has been developed for automated single cell analysis. In the method, cell introduction, cell lysis, and MCE-MS separation are computer controlled and integrated as a cycle into consecutive assays. Analysis of large numbers of individual PC-12 neuronal cells (both intact and exposed to 25mM KCl) was carried out to determine intracellular levels of dopamine (DA) and glutamic acid (Glu). It was found that DA content in PC-12 cells was higher than Glu content, and both varied from cell to cell. The ratio of intracellular DA to Glu was 4.20±0.8 (n=150). Interestingly, the ratio drastically decreased to 0.38±0.20 (n=150) after the cells are exposed to 25mM KCl for 8min, suggesting the cells released DA promptly and heavily while they released Glu at a much slower pace in response to KCl-induced depolarization. These results indicate that the proposed MCE-MS analytical platform may have a great potential in researches at the cellular level.
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Affiliation(s)
- Xiangtang Li
- Department of Chemistry and Biochemistry, Jackson State University, 1400 Lynch St., Jackson, MS, 39217, United States
| | - Shulin Zhao
- College of Chemistry and Chemical Engineering, Guangxi Normal University, Guilin, 51004, China
| | - Hankun Hu
- Wuhan University Zhongnan Hospital, Wuhan 430071, China; Wuhan Yaogu Bio-tech, Wuhan 430075, China
| | - Yi-Ming Liu
- Department of Chemistry and Biochemistry, Jackson State University, 1400 Lynch St., Jackson, MS, 39217, United States; Wuhan Yaogu Bio-tech, Wuhan 430075, China.
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18
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Chen F, Lin L, Zhang J, He Z, Uchiyama K, Lin JM. Single-Cell Analysis Using Drop-on-Demand Inkjet Printing and Probe Electrospray Ionization Mass Spectrometry. Anal Chem 2016; 88:4354-60. [DOI: 10.1021/acs.analchem.5b04749] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Fengming Chen
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Luyao Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Jie Zhang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Ziyi He
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Katsumi Uchiyama
- Department
of Applied Chemistry, Graduate School of Urban Environmental Sciences, Tokyo Metropolitan University, Minamiohsawa, Hachioji,
Tokyo 192-0397, Japan
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, The Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing 100084, China
- Collaborative
Innovation Center of Functionalized Probes for Chemical Imaging in
University of Shandong, Shandong Normal University, Jinan 250014, China
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19
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Development of Microfluidic Systems Enabling High-Throughput Single-Cell Protein Characterization. SENSORS 2016; 16:232. [PMID: 26891303 PMCID: PMC4801608 DOI: 10.3390/s16020232] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 01/21/2016] [Accepted: 02/02/2016] [Indexed: 01/09/2023]
Abstract
This article reviews recent developments in microfluidic systems enabling high-throughput characterization of single-cell proteins. Four key perspectives of microfluidic platforms are included in this review: (1) microfluidic fluorescent flow cytometry; (2) droplet based microfluidic flow cytometry; (3) large-array micro wells (microengraving); and (4) large-array micro chambers (barcode microchips). We examine the advantages and limitations of each technique and discuss future research opportunities by focusing on three key performance parameters (absolute quantification, sensitivity, and throughput).
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20
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Phelps MS, Sturtevant D, Chapman KD, Verbeck GF. Nanomanipulation-Coupled Matrix-Assisted Laser Desorption/ Ionization-Direct Organelle Mass Spectrometry: A Technique for the Detailed Analysis of Single Organelles. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:187-193. [PMID: 26238327 DOI: 10.1007/s13361-015-1232-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 06/04/2023]
Abstract
We describe a novel technique combining precise organelle microextraction with deposition and matrix-assisted laser desorption/ionization (MALDI) for a rapid, minimally invasive mass spectrometry (MS) analysis of single organelles from living cells. A dual-positioner nanomanipulator workstation was utilized for both extraction of organelle content and precise co-deposition of analyte and matrix solution for MALDI-direct organelle mass spectrometry (DOMS) analysis. Here, the triacylglycerol (TAG) profiles of single lipid droplets from 3T3-L1 adipocytes were acquired and results validated with nanoelectrospray ionization (NSI) MS. The results demonstrate the utility of the MALDI-DOMS technique as it enabled longer mass analysis time, higher ionization efficiency, MS imaging of the co-deposited spot, and subsequent MS/MS capabilities of localized lipid content in comparison to NSI-DOMS. This method provides selective organellar resolution, which complements current biochemical analyses and prompts for subsequent subcellular studies to be performed where limited samples and analyte volume are of concern. Graphical Abstract ᅟ.
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21
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Sarkar S, Cohen N, Sabhachandani P, Konry T. Phenotypic drug profiling in droplet microfluidics for better targeting of drug-resistant tumors. LAB ON A CHIP 2015; 15:4441-50. [PMID: 26456240 PMCID: PMC4666301 DOI: 10.1039/c5lc00923e] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Acquired drug resistance is a key factor in the failure of chemotherapy. Due to intratumoral heterogeneity, cancer cells depict variations in intracellular drug uptake and efflux at the single cell level, which may not be detectable in bulk assays. In this study we present a droplet microfluidics-based approach to assess the dynamics of drug uptake, efflux and cytotoxicity in drug-sensitive and drug-resistant breast cancer cells. An integrated droplet generation and docking microarray was utilized to encapsulate single cells as well as homotypic cell aggregates. Drug-sensitive cells showed greater death in the presence or absence of Doxorubicin (Dox) compared to the drug-resistant cells. We observed heterogeneous Dox uptake in individual drug-sensitive cells while the drug-resistant cells showed uniformly low uptake and retention. Dox-resistant cells were classified into distinct subsets based on their efflux properties. Cells that showed longer retention of extracellular reagents also demonstrated maximal death. We further observed homotypic fusion of both cell types in droplets, which resulted in increased cell survival in the presence of high doses of Dox. Our results establish the applicability of this microfluidic platform for quantitative drug screening in single cells and multicellular interactions.
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Affiliation(s)
- S Sarkar
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, 02115 MA, USA.
| | - N Cohen
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, 02115 MA, USA.
| | - P Sabhachandani
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, 02115 MA, USA.
| | - T Konry
- Department of Pharmaceutical Sciences, Northeastern University, 360 Huntington Avenue, Boston, 02115 MA, USA.
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22
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Duay J, Elliott J, Shear JB, Stevenson KJ. Transparent Carbon Ultramicroelectrode Arrays: Figures of Merit for Quantitative Spectroelectrochemistry for Biogenic Analysis of Reactive Oxygen Species. Anal Chem 2015; 87:10109-16. [DOI: 10.1021/acs.analchem.5b02804] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jonathon Duay
- Department of Chemistry,
Center for Nano and Molecular Science and Technology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Janine Elliott
- Department of Chemistry,
Center for Nano and Molecular Science and Technology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jason B. Shear
- Department of Chemistry,
Center for Nano and Molecular Science and Technology, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Keith J. Stevenson
- Department of Chemistry,
Center for Nano and Molecular Science and Technology, The University of Texas at Austin, Austin, Texas 78712, United States
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23
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Kast RE, Tucker SC, Killian K, Trexler M, Honn KV, Auner GW. Emerging technology: applications of Raman spectroscopy for prostate cancer. Cancer Metastasis Rev 2015; 33:673-93. [PMID: 24510129 DOI: 10.1007/s10555-013-9489-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There is a need in prostate cancer diagnostics and research for a label-free imaging methodology that is nondestructive, rapid, objective, and uninfluenced by water. Raman spectroscopy provides a molecular signature, which can be scaled from micron-level regions of interest in cells to macroscopic areas of tissue. It can be used for applications ranging from in vivo or in vitro diagnostics to basic science laboratory testing. This work describes the fundamentals of Raman spectroscopy and complementary techniques including surface enhanced Raman scattering, resonance Raman spectroscopy, coherent anti-Stokes Raman spectroscopy, confocal Raman spectroscopy, stimulated Raman scattering, and spatially offset Raman spectroscopy. Clinical applications of Raman spectroscopy to prostate cancer will be discussed, including screening, biopsy, margin assessment, and monitoring of treatment efficacy. Laboratory applications including cell identification, culture monitoring, therapeutics development, and live imaging of cellular processes are discussed. Potential future avenues of research are described, with emphasis on multiplexing Raman spectroscopy with other modalities.
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Affiliation(s)
- Rachel E Kast
- Smart Sensors and Integrated Microsystems Laboratories, Department of Electrical and Computer Engineering, Wayne State University, 5050 Anthony Wayne Drive, Room 3100, Detroit, MI, 48202, USA
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24
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Stenken JA, Poschenrieder AJ. Bioanalytical chemistry of cytokines--a review. Anal Chim Acta 2015; 853:95-115. [PMID: 25467452 PMCID: PMC4717841 DOI: 10.1016/j.aca.2014.10.009] [Citation(s) in RCA: 192] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/30/2014] [Accepted: 10/08/2014] [Indexed: 02/06/2023]
Abstract
Cytokines are bioactive proteins produced by many different cells of the immune system. Due to their role in different inflammatory disease states and maintaining homeostasis, there is enormous clinical interest in the quantitation of cytokines. The typical standard methods for quantitation of cytokines are immunoassay-based techniques including enzyme-linked immusorbent assays (ELISA) and bead-based immunoassays read by either standard or modified flow cytometers. A review of recent developments in analytical methods for measurements of cytokine proteins is provided. This review briefly covers cytokine biology and the analysis challenges associated with measurement of these biomarker proteins for understanding both health and disease. New techniques applied to immunoassay-based assays are presented along with the uses of aptamers, electrochemistry, mass spectrometry, optical resonator-based methods. Methods used for elucidating the release of cytokines from single cells as well as in vivo collection methods are described.
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Affiliation(s)
- Julie A Stenken
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Andreas J Poschenrieder
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA; Pharmaceutical Radiochemistry, Technische Universität München, Walther-Meißner-Street 3, D-85748 Garching, Germany
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25
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Vasdekis AE, Stephanopoulos G. Review of methods to probe single cell metabolism and bioenergetics. Metab Eng 2015; 27:115-135. [PMID: 25448400 PMCID: PMC4399830 DOI: 10.1016/j.ymben.2014.09.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 11/26/2022]
Abstract
Single cell investigations have enabled unexpected discoveries, such as the existence of biological noise and phenotypic switching in infection, metabolism and treatment. Herein, we review methods that enable such single cell investigations specific to metabolism and bioenergetics. Firstly, we discuss how to isolate and immobilize individuals from a cell suspension, including both permanent and reversible approaches. We also highlight specific advances in microbiology for its implications in metabolic engineering. Methods for probing single cell physiology and metabolism are subsequently reviewed. The primary focus therein is on dynamic and high-content profiling strategies based on label-free and fluorescence microspectroscopy and microscopy. Non-dynamic approaches, such as mass spectrometry and nuclear magnetic resonance, are also briefly discussed.
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Affiliation(s)
- Andreas E Vasdekis
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, PO Box 999, Richland, WA 99354, USA.
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, Cambridge, MA 02139, USA.
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26
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Abstract
Unprecedented access to the biology of single cells is now feasible, enabled by recent technological advancements that allow us to manipulate and measure sparse samples and achieve a new level of resolution in space and time. This review focuses on advances in tools to study single cells for specific areas of biology. We examine both mature and nascent techniques to study single cells at the genomics, transcriptomics, and proteomics level. In addition, we provide an overview of tools that are well suited for following biological responses to defined perturbations with single-cell resolution. Techniques to analyze and manipulate single cells through soluble and chemical ligands, the microenvironment, and cell-cell interactions are provided. For each of these topics, we highlight the biological motivation, applications, methods, recent advances, and opportunities for improvement. The toolbox presented in this review can function as a starting point for the design of single-cell experiments.
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27
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28
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Real-time quantification of protein expression and translocation at individual cell resolution using imaging-dish-based live cell array. Anal Bioanal Chem 2014; 406:7085-101. [PMID: 25258284 DOI: 10.1007/s00216-014-8157-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/19/2014] [Accepted: 09/02/2014] [Indexed: 01/19/2023]
Abstract
Cell populations represent intrinsically heterogeneous systems with a high level of spatiotemporal complexity. Monitoring and understanding cell-to-cell diversity is essential for the research and application of intra- and interpopulation variations. Optical analysis of live cells is challenging since both adherent and nonadherent cells change their spatial location. However, most currently available single-cell techniques do not facilitate treatment and monitoring of the same live cells over time throughout multistep experiments. An imaging-dish-based live cell array (ID-LCA) has been developed and produced for cell handling, culturing, and imaging of numerous live cells. The dish is composed of an array of pico scale cavities-pico wells (PWs) embossed on its glass bottom. Cells are seeded, cultured, treated, and spatiotemporally measured on the ID-LCA, while each cell or small group of cells are locally constrained in the PWs. Finally, predefined cells can be retrieved for further evaluation. Various types of ID-LCAs were used in this proof-of-principle work, to demonstrate on-ID-LCA transfection of fluorescently tagged chimeric proteins, as well as the detection and kinetic analysis of their induced translocation. High variability was evident within cell populations with regard to protein expression levels as well as the extent and dynamics of protein redistribution. The association of these parameters with cell morphology and functional parameters was examined. Both the new methodology and the device facilitate research of the translocation process at individual cell resolution within large populations and thus, can potentially be used in high-throughput fashion.
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29
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Zhang K, Han X, Li Y, Li SY, Zu Y, Wang Z, Qin L. Hand-held and integrated single-cell pipettes. J Am Chem Soc 2014; 136:10858-61. [PMID: 25036187 PMCID: PMC4133013 DOI: 10.1021/ja5053279] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
Successful single-cell isolation is a primary step for subsequent
chemical and biological analyses of single cells. Conventional single-cell
isolation methods often encounter operational complexity, limited
efficiency, deterioration of cell viability, incompetence in the isolation
of a single-cell into nanoliter liquid, and/or inability to select
single adherent cells with specific phenotypes. Here, we develop a
hand-held single-cell pipet (hSCP) that is rapid, operationally simple,
highly efficient, and inexpensive for unbiased isolation of single
viable suspended cells directly from submicroliter cell suspensions
into nanoliter droplets without the assistance of any additional equipment.
An integrated SCP (iSCP) has also been developed for selective isolation
of single suspended and adherent cells according to the fluorescence
imaging and morphological features. The isolated single cells can
be conveniently transferred into standard 96-/384-well plates, Petri
dishes, or vials for cloning, PCR, and other single-cell biochemical
assays.
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Affiliation(s)
- Kai Zhang
- Department of Nanomedicine, Houston Methodist Research Institute , Houston, Texas 77030, United States
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30
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Deng B, Tian Y, Yu X, Song J, Guo F, Xiao Y, Zhang Z. Laminar flow mediated continuous single-cell analysis on a novel poly(dimethylsiloxane) microfluidic chip. Anal Chim Acta 2014; 820:104-11. [DOI: 10.1016/j.aca.2014.02.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 02/10/2014] [Accepted: 02/22/2014] [Indexed: 01/06/2023]
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31
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Shintaku H, Nishikii H, Marshall LA, Kotera H, Santiago JG. On-Chip Separation and Analysis of RNA and DNA from Single Cells. Anal Chem 2014; 86:1953-7. [DOI: 10.1021/ac4040218] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hirofumi Shintaku
- Department
of Micro Engineering, Kyoto University, Kyoto 606-8501, Japan
| | | | | | - Hidetoshi Kotera
- Department
of Micro Engineering, Kyoto University, Kyoto 606-8501, Japan
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32
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33
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Klepárník K, Foret F. Recent advances in the development of single cell analysis--a review. Anal Chim Acta 2013; 800:12-21. [PMID: 24120162 DOI: 10.1016/j.aca.2013.09.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 08/23/2013] [Accepted: 09/05/2013] [Indexed: 01/12/2023]
Abstract
Development of techniques for the analysis of the content of individual cells represents an important direction in modern bioanalytical chemistry. While the analysis of chromosomes, organelles, or location of selected proteins has been traditionally the domain of microscopic techniques, the advances in miniaturized analytical systems bring new possibilities for separations and detections of molecules inside the individual cells including smaller molecules such as hormones or metabolites. It should be stressed that the field of single cell analysis is very broad, covering advanced optical, electrochemical and mass spectrometry instrumentation, sensor technology and separation techniques. The number of papers published on single cell analysis has reached several hundred in recent years. Thus a complete literature coverage is beyond the limits of a journal article. The following text provides a critical overview of some of the latest developments with the main focus on mass spectrometry, microseparation methods, electrophoresis in capillaries and microfluidic devices and respective detection techniques for performing single cell analyses.
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Affiliation(s)
- Karel Klepárník
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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Nave M, Rubin B, Maximov V, Creager S, Kornev KG. Transport-limited electrochemical formation of long nanosharp probes from tungsten. NANOTECHNOLOGY 2013; 24:355702. [PMID: 23924892 DOI: 10.1088/0957-4484/24/35/355702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We show that electrochemical formation of long probes with nanosharp tips can be controlled by choosing an appropriate thermodynamic pathway of metal to metal oxide and hydroxide transformation. Currently, convection-limited electropolishing (CLE) is extensively used. Nanosharp probes are produced by electrochemically etching a wire until it breaks into two pieces. This process is difficult to control because of the complexity of the associated hydrodynamic flows. We introduce transport-limited electropolishing (TLE), where the electrochemical reaction results in the formation of metal oxides and hydroxides which form a porous surface layer hindering the flow of electrolyte. The developed TLE method enables one to make long tapered needles. The taper can spread over more than 6 mm while the radius of tip curvature can be decreased down to 30 nm. These needles are strong and were successfully applied for piercing single smooth vascular muscle cells.
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Affiliation(s)
- M Nave
- Department of Materials Science and Engineering, Clemson University, Clemson, SC 29634, USA
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35
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Xu W, Allbritton N, Lawrence DS. SRC kinase regulation in progressively invasive cancer. PLoS One 2012; 7:e48867. [PMID: 23145001 PMCID: PMC3492248 DOI: 10.1371/journal.pone.0048867] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 10/01/2012] [Indexed: 11/18/2022] Open
Abstract
Metastatic progression is a multistep process that involves tumor growth and survival, motility and invasion, and subsequent proliferation in an inappropriate environment. The Src protein tyrosine kinase has been implicated in many of the biochemical pathways that drive these behaviors. Although Src itself is only rarely mutated in human tumors, its aberrant activity has been noted in various cancers and suggested to serve as a barometer of metastatic potential. With these features in mind, we examined Src kinase regulation at the structural, enzymatic, and expression levels as a function of progressively invasive prostate cancer cell lines. Surprisingly, both total Src content and kinase activity decrease with increasing cell line aggressiveness, an observation that appears to be inconsistent with the well-documented role of Src in the signaling pathways that drive growth and invasion. However, we do observe a direct correlation between Src kinase specific activity (total Src kinase activity/total Src content) and metastatic aggressiveness, possibly suggesting that in highly aggressive cell lines, key signaling enzymes are globally recruited to drive the cancerous phenotype. In addition, although the expected enhanced phosphorylation of Src at Tyr-416 (activation site) is present in the most aggressive prostate cancer cell lines, unexpectedly high phosphorylation levels at the Tyr-527 inhibitory site are observed as well. The latter, rather than representative of inhibited enzyme, is more indicative of primed Src responsive to local phosphorylated binding partners.
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Affiliation(s)
- Weichen Xu
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Nancy Allbritton
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Pharmacology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David S. Lawrence
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Pharmacology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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36
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Nemes P, Knolhoff AM, Rubakhin SS, Sweedler JV. Single-cell metabolomics: changes in the metabolome of freshly isolated and cultured neurons. ACS Chem Neurosci 2012; 3:782-92. [PMID: 23077722 PMCID: PMC3474288 DOI: 10.1021/cn300100u] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 08/24/2012] [Indexed: 02/07/2023] Open
Abstract
![]()
Metabolites are involved in a diverse range of intracellular
processes,
including a cell’s response to a changing extracellular environment.
Using single-cell capillary electrophoresis coupled to electrospray
ionization mass spectrometry, we investigated how placing individual
identified neurons in culture affects their metabolic profile. First,
glycerol-based cell stabilization was evaluated using metacerebral
neurons from Aplysia californica; the
measurement error was reduced from ∼24% relative standard deviation
to ∼6% for glycerol-stabilized cells compared to those isolated
without glycerol stabilization. In order to determine the changes
induced by culturing, 14 freshly isolated and 11 overnight-cultured
neurons of two metabolically distinct cell types from A. californica, the B1 and B2 buccal neurons, were
characterized. Of the more than 300 distinctive cell-related signals
detected, 35 compounds were selected for their known biological roles
and compared among each measured cell. Unsupervised multivariate and
statistical analysis revealed robust metabolic differences between
these two identified neuron types. We then compared the changes induced
by overnight culturing; metabolite concentrations were distinct for
26 compounds in the cultured B1 cells. In contrast, culturing had
less influence on the metabolic profile of the B2 neurons, with only
five compounds changing significantly. As a result of these culturing-induced
changes, the metabolic composition of the B1 neurons became indistinguishable
from the cultured B2 cells. This observation suggests that the two
cell types differentially regulate their in vivo or in vitro metabolomes in response to a changing environment.
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Affiliation(s)
- Peter Nemes
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews
Avenue, Urbana, Illinois 61801, United States
| | - Ann M. Knolhoff
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews
Avenue, Urbana, Illinois 61801, United States
| | - Stanislav S. Rubakhin
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews
Avenue, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews
Avenue, Urbana, Illinois 61801, United States
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37
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Naves T, Battu S, Jauberteau MO, Cardot PJ, Ratinaud MH, Verdier M. Autophagic Subpopulation Sorting by Sedimentation Field-Flow Fractionation. Anal Chem 2012; 84:8748-55. [DOI: 10.1021/ac302032v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Thomas Naves
- Université de Limoges, Institut 145 GEIST, EA 3842 “Homéostasie
cellulaire et pathologies”, Faculté de Médecine,
2 rue du Dr Marcland, 87025 Limoges Cedex, France
| | - Serge Battu
- Université de Limoges, Institut 145 GEIST, EA 3842 “Homéostasie
cellulaire et pathologies”, Faculté de Médecine,
2 rue du Dr Marcland, 87025 Limoges Cedex, France
- Faculté de Pharmacie, Laboratoire de Chimie Analytique et Bromatologie, 87025
Limoges Cedex, France
| | - Marie-Odile Jauberteau
- Université de Limoges, Institut 145 GEIST, EA 3842 “Homéostasie
cellulaire et pathologies”, Faculté de Médecine,
2 rue du Dr Marcland, 87025 Limoges Cedex, France
| | - Philippe J.P. Cardot
- Université de Limoges, Institut 145 GEIST, EA 3842 “Homéostasie
cellulaire et pathologies”, Faculté de Médecine,
2 rue du Dr Marcland, 87025 Limoges Cedex, France
- Faculté de Pharmacie, Laboratoire de Chimie Analytique et Bromatologie, 87025
Limoges Cedex, France
| | - Marie-Hélène Ratinaud
- Université de Limoges, Institut 145 GEIST, EA 3842 “Homéostasie
cellulaire et pathologies”, Faculté de Médecine,
2 rue du Dr Marcland, 87025 Limoges Cedex, France
| | - Mireille Verdier
- Université de Limoges, Institut 145 GEIST, EA 3842 “Homéostasie
cellulaire et pathologies”, Faculté de Médecine,
2 rue du Dr Marcland, 87025 Limoges Cedex, France
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38
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Iourov IY, Vorsanova SG, Yurov YB. Single cell genomics of the brain: focus on neuronal diversity and neuropsychiatric diseases. Curr Genomics 2012; 13:477-88. [PMID: 23449087 PMCID: PMC3426782 DOI: 10.2174/138920212802510439] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Revised: 01/30/2012] [Accepted: 06/12/2012] [Indexed: 12/21/2022] Open
Abstract
Single cell genomics has made increasingly significant contributions to our understanding of the role that somatic genome variations play in human neuronal diversity and brain diseases. Studying intercellular genome and epigenome variations has provided new clues to the delineation of molecular mechanisms that regulate development, function and plasticity of the human central nervous system (CNS). It has been shown that changes of genomic content and epigenetic profiling at single cell level are involved in the pathogenesis of neuropsychiatric diseases (schizophrenia, mental retardation (intellectual/leaning disability), autism, Alzheimer's disease etc.). Additionally, several brain diseases were found to be associated with genome and chromosome instability (copy number variations, aneuploidy) variably affecting cell populations of the human CNS. The present review focuses on the latest advances of single cell genomics, which have led to a better understanding of molecular mechanisms of neuronal diversity and neuropsychiatric diseases, in the light of dynamically developing fields of systems biology and "omics".
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Affiliation(s)
- Ivan Y Iourov
- National Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow, Russia
- Institute of Pediatrics and Children Surgery, Minzdravsotsrazvitia, Moscow, Russia
| | - Svetlana G Vorsanova
- National Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow, Russia
- Institute of Pediatrics and Children Surgery, Minzdravsotsrazvitia, Moscow, Russia
- Center for Neurobiological Diagnosis of Genetic Psychiatric Disorders, Moscow City University of Psychology and Education, Russia
| | - Yuri B Yurov
- National Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow, Russia
- Institute of Pediatrics and Children Surgery, Minzdravsotsrazvitia, Moscow, Russia
- Center for Neurobiological Diagnosis of Genetic Psychiatric Disorders, Moscow City University of Psychology and Education, Russia
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39
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Janssen KGH, Li J, Hoang HT, Vulto P, van den Berg RJBHN, Overkleeft HS, Eijkel JCT, Tas NR, van der Linden HJ, Hankemeier T. Limits of miniaturization: assessing ITP performance in sub-micron and nanochannels. LAB ON A CHIP 2012; 12:2888-2893. [PMID: 22691967 DOI: 10.1039/c2lc21011h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The feasibility of isotachophoresis in channels of sub micrometer and nanometer dimension is investigated. A sample injection volume of 0.4 pL is focused and separated in a 330 nm deep channel. The sample consists of a biomatrix containing the fluorescently-labeled amino acids glutamate and phenylalanine, 20 attomoles of each. Isotachophoretic focusing is successfully demonstrated in a 50 nm deep channel. Separation of the two amino acids in the 50 nm deep channel however, could not be performed as the maximum applicable voltage was insufficient. This limit is imposed by bubble formation that we contribute to cavitation as a result of the mismatch in electro-osmotic flow, so called electrocavitation. This represents an unexpected limit on the miniaturization of ITP. Nonetheless, we report the smallest isotachophoretic separation and focusing experiment to date, both in terms of controlled sample injection volume and channel height.
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Affiliation(s)
- Kjeld G H Janssen
- Department of Analytical Biosciences, Leiden/Amsterdam Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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40
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Isolated microbial single cells and resulting micropopulations grow faster in controlled environments. Appl Environ Microbiol 2012; 78:7132-6. [PMID: 22820335 DOI: 10.1128/aem.01624-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Singularized cells of Pichia pastoris, Hansenula polymorpha, and Corynebacterium glutamicum displayed specific growth rates under chemically and physically constant conditions that were consistently higher than those obtained in populations. This highlights the importance of single-cell analyses by uncoupling physiology and the extracellular environment, which is now possible using the Envirostat 2.0 concept.
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41
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Eyer K, Kuhn P, Hanke C, Dittrich PS. A microchamber array for single cell isolation and analysis of intracellular biomolecules. LAB ON A CHIP 2012; 12:765-72. [PMID: 22183159 DOI: 10.1039/c2lc20876h] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We present a microfluidic device that enables the determination of intracellular biomolecules in multiple single cells. The cells are individually trapped and isolated in a microchamber array. Since the microchambers can be opened and closed reversibly, the cells can be exposed to different solutions sequentially, e.g. for incubation, washing steps, labelling and finally, for lysis. The tightly sealed microchambers enable the retention and analysis of cell lysate derived from single cells. The performance of the device is demonstrated by monitoring the levels of the cofactors NADPH and NADH both in healthy mammalian cells and in cells exposed to oxidative stress. The platform was also used to determine the toxic impact of the alkaloid camptothecin on the intracellular enzyme glucose-6-phosphate dehydrogenase levels. In general, the device is applicable for the analysis of cell auto-stimulation and the detection of intracellular metabolite concentration or expression levels of proteins.
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Affiliation(s)
- Klaus Eyer
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
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42
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Grohman JK, Kottegoda S, Gorelick RJ, Allbritton NL, Weeks KM. Femtomole SHAPE reveals regulatory structures in the authentic XMRV RNA genome. J Am Chem Soc 2011; 133:20326-34. [PMID: 22126209 PMCID: PMC3241870 DOI: 10.1021/ja2070945] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Higher-order structure influences critical functions in nearly all noncoding and coding RNAs. Most single-nucleotide resolution RNA structure determination technologies cannot be used to analyze RNA from scarce biological samples, like viral genomes. To make quantitative RNA structure analysis applicable to a much wider array of RNA structure-function problems, we developed and applied high-sensitivity selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) to structural analysis of authentic genomic RNA of the xenotropic murine leukemia virus-related virus (XMRV). For analysis of fluorescently labeled cDNAs generated in high-sensitivity SHAPE experiments, we developed a two-color capillary electrophoresis approach with zeptomole molecular detection limits and subfemtomole sensitivity for complete SHAPE experiments involving hundreds of individual RNA structure measurements. High-sensitivity SHAPE data correlated closely (R = 0.89) with data obtained by conventional capillary electrophoresis. Using high-sensitivity SHAPE, we determined the dimeric structure of the XMRV packaging domain, examined dynamic interactions between the packaging domain RNA and viral nucleocapsid protein inside virion particles, and identified the packaging signal for this virus. Despite extensive sequence differences between XMRV and the intensively studied Moloney murine leukemia virus, architectures of the regulatory domains are similar and reveal common principles of gammaretrovirus RNA genome packaging.
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Affiliation(s)
- Jacob K. Grohman
- Department of Chemistry, University of North Carolina, Chapel Hill 27599-3290
| | - Sumith Kottegoda
- Department of Chemistry, University of North Carolina, Chapel Hill 27599-3290
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Science Applications International Corporation-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21702-1201
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill 27599-3290
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC 27599 and North Carolina State University, Raleigh, NC 27695
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill 27599-3290
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43
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Hargis AD, Alarie JP, Ramsey J. Characterization of cell lysis events on a microfluidic device for high-throughput single cell analysis. Electrophoresis 2011; 32:3172-9. [PMID: 22025127 PMCID: PMC3517164 DOI: 10.1002/elps.201100229] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 08/03/2011] [Accepted: 08/05/2011] [Indexed: 11/09/2022]
Abstract
A microfluidic device capable of rapidly analyzing cells in a high-throughput manner using electrical cell lysis is further characterized. In the experiments performed, cell lysis events were studied using an electron multiplying charge coupled device camera with high frame rate (>100 fps) data collection. It was found that, with this microfluidic design, the path that a cell follows through the electric field affects the amount of lysate injected into the analysis channel. Elimination of variable flow paths through the electric field was achieved by coating the analysis channel with a polyamine compound to reverse the electroosmotic flow (EOF). EOF reversal forced the cells to take the same path through the electric field. The improved control of the cell trajectory will reduce device-imposed bias on the analysis and maximizes the amount of lysate injected into the analysis channel for each cell, resulting in improved analyte detection capabilities.
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Affiliation(s)
- Amy D Hargis
- Department of Chemistry, Chapman Hall Room 251, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3216
| | - JP Alarie
- Department of Chemistry, Chapman Hall Room 251, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3216
| | - J.M. Ramsey
- Department of Chemistry, Chapman Hall Room 251, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3216
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44
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Analysis of doxorubicin uptake in single human leukemia K562 cells using capillary electrophoresis coupled with laser-induced fluorescence detection. Anal Bioanal Chem 2011; 401:2143-52. [DOI: 10.1007/s00216-011-5315-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 07/30/2011] [Accepted: 08/03/2011] [Indexed: 10/17/2022]
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45
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Huang W, Jiang D, Wang X, Wang K, Sims CE, Allbritton NL, Zhang Q. Kinetic analysis of PI3K reactions with fluorescent PIP2 derivatives. Anal Bioanal Chem 2011; 401:1881-8. [PMID: 21789487 DOI: 10.1007/s00216-011-5257-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 07/05/2011] [Accepted: 07/13/2011] [Indexed: 01/25/2023]
Abstract
Phosphatidylinositol 3-kinase (PI3K) signaling plays important roles in cell differentiation, proliferation, and migration. Increased mutations and expression levels of PI3K are hallmarks for the development of certain cancers. Pharmacological targeting of PI3K activity has also been actively pursued as a novel cancer therapeutic. Consequently, measurement of PI3K activity in different cell types or patient samples holds the promise as being a novel diagnostic tool. However, the direct measurement of cellular PI3K activity has been a challenging task. We report here the characterization of two fluorescent PIP(2) derivatives as reporters for PI3K enzymatic activity. The reporters are efficiently separated from their corresponding PI3K enzymatic products through either thin layer chromatography (TLC) or capillary electrophoresis (CE), and can be detected with high sensitivity by fluorescence. The biophysical and kinetic properties of the two probes are measured, and their suitability to characterize PI3K inhibitors is explored. Both probes show similar capacity as PI3K substrates for inhibitor characterization, yet also possess distinct properties that may suggest their different applications. These characterizations have laid the groundwork to systematically measure cellular PI3K activity, and have the potential to generate molecular fingerprints for diagnostic and therapeutic applications.
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Affiliation(s)
- Weigang Huang
- Division of Medicinal Chemistry and Natural Products, University of North Carolina, Chapel Hill, NC 27599, USA
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46
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Konorov SO, Schulze HG, Atkins CG, Piret JM, Aparicio SA, Turner RFB, Blades MW. Absolute Quantification of Intracellular Glycogen Content in Human Embryonic Stem Cells with Raman Microspectroscopy. Anal Chem 2011; 83:6254-8. [DOI: 10.1021/ac201581e] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Stanislav O. Konorov
- Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada, V6T 1Z4
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada, V6T 1Z1
| | - H. Georg Schulze
- Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Chad G. Atkins
- Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada, V6T 1Z4
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada, V6T 1Z1
| | - James M. Piret
- Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada, V6T 1Z4
- Department of Chemical and Biological Engineering, The University of British Columbia, 2360 East Mall, Vancouver, British Columbia, Canada, V6T 1Z3
| | - Samuel A. Aparicio
- Department of Pathology and Laboratory Medicine, The University of British Columbia, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, British Columbia, Canada, V5Z 1L3
| | - Robin F. B. Turner
- Michael Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada, V6T 1Z4
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada, V6T 1Z1
- Department of Electrical and Computer Engineering, The University of British Columbia, 2332 Main Mall, Vancouver, British Columbia, Canada, V6T 1Z4
| | - Michael W. Blades
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada, V6T 1Z1
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47
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Wu RG, Yang CS, Cheing CC, Tseng FG. Nanocapillary electrophoretic electrochemical chip: towards analysis of biochemicals released by single cells. Interface Focus 2011; 1:744-53. [PMID: 23050079 DOI: 10.1098/rsfs.2011.0049] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 06/17/2011] [Indexed: 01/09/2023] Open
Abstract
A novel nanocapillary electrophoretic electrochemical (Nano-CEEC) chip has been developed to demonstrate the possibility of zeptomole-level detection of neurotransmitters released from single living cells. The chip integrates three subunits to collect and concentrate scarce neurotransmitters released from single PC-12 cells, including a pair of targeting electrodes for single cells captured by controlling the surface charge density; a dual-asymmetry electrokinetic flow device for sample collection, pre-concentration and separation in a nanochannel; and an online electrochemical detector for zeptomole-level sample detection. This Nano-CEEC chip integrates a polydimethylsiloxane microchannel for cell sampling and biomolecule separation and a silicon dioxide nanochannel for sample pre-concentration and amperometric detection. The cell-capture voltage ranges from 0.1 to 1.5 V with a frequency of 1-10 kHz for PC-12 cells, and the single cell-capture efficiency is optimized by varying the duration of the applied field. All of the processes, from cell sampling to neurotransmitter detection, can be completed within 15 min. Catecholamines, including dopamine and norepinephrine (noradrenaline) released from coupled single cells, have been successfully detected using the Nano-CEEC chip. A detection limit of 30-75 zeptomoles was achieved, which is close to the levels released by a single neuron in vitro.
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Affiliation(s)
- Ren-Guei Wu
- Department of Engineering and Systems Science , National Tsing Hua University , 101 Section 2 Kuang Fu Road, Hsinchu 300, Taiwan , Republic of China ; National Health Research Institutes , 35 Keyan Road, Zhunan, Miaoli 350, Taiwan , Republic of China
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48
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Shi X, Lin LI, Chen SY, Chao SH, Zhang W, Meldrum DR. Real-time PCR of single bacterial cells on an array of adhering droplets. LAB ON A CHIP 2011; 11:2276-2281. [PMID: 21607246 DOI: 10.1039/c1lc20207c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Real-time PCR at the single bacterial cell level is an indispensable tool to quantitatively reveal the heterogeneity of isogenetic cells. Conventional PCR platforms that utilize microtiter plates or PCR tubes have been widely used, but their large reaction volumes are not suited for sensitive single-cell analysis. Microfluidic devices provide high density, low volume PCR chambers, but they are usually expensive and require dedicated equipment to manipulate liquid and perform detection. To address these limitations, we developed an inexpensive chip-level device that is compatible with a commercial real-time PCR thermal cycler to perform quantitative PCR for single bacterial cells. The chip contains twelve surface-adhering droplets, defined by hydrophilic patterning, that serve as real-time PCR reaction chambers when they are immersed in oil. A one-step process that premixed reagents with cell medium before loading was applied, so no on-chip liquid manipulation and DNA purification were needed. To validate its application for genetic analysis, Synechocystis PCC 6803 cells were loaded on the chip from 1000 cells to one cell per droplet, and their 16S rRNA gene (two copies per cell) was analyzed on a commercially available ABI StepOne real-time PCR thermal cycler. The result showed that the device is capable of genetic analysis at single bacterial cell level with C(q) standard deviation less than 1.05 cycles. The successful rate of this chip-based operation is more than 85% at the single bacterial cell level.
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Affiliation(s)
- Xu Shi
- Center for Biosignatures Discovery Automation, Arizona State University, PO Box 876501. Tempe, AZ, USA
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49
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Yanagisawa N, Dutta D. Kinetic ELISA in microfluidic channels. BIOSENSORS-BASEL 2011; 1:58-69. [PMID: 25586828 PMCID: PMC4264342 DOI: 10.3390/bios1020058] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Revised: 05/26/2011] [Accepted: 06/15/2011] [Indexed: 11/16/2022]
Abstract
In this article, we describe the kinetic ELISA of Blue Tongue and Epizootic Hemorrhagic Disease viral antibodies in microfluidic channels by monitoring the rate of generation of the enzyme reaction product under static conditions. It has been shown that this format of the immunoassay allows very reliable quantitation of the target species using inexpensive glass microchips and a standard epifluorescence microscope system coupled to a CCD camera. For the viral antibodies assayed here, the limit of detection (LOD) for the analyte concentration in our microchips was established to be 3–5 times lower than that obtained on commercial microwell plates using a fiftieth of the sample volume and less than a third of the incubation time. Our analyses further show that when compared to the end-point ELISA format, the kinetic mode of this assay yields an improvement in the LOD by over an order of magnitude in microfluidic devices. This benefit is primarily realized as the observed variation in the background fluorescence (signal at the start of the enzyme reaction period) was significantly larger than that in the rate of signal generation upon repeating these assays in different microchannels/microchips. Because the kinetic ELISA results depend only on the latter quantity, the noise level in them was substantially lower compared to that in its end-point counterpart in which the absolute fluorescence measurements are of greater significance. While a similar benefit was also recorded through implementation of kinetic ELISAs on the microwell platform, the improvement in LOD registered in that system was not as significant as was observed in the case of microfluidic assays.
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Affiliation(s)
- Naoki Yanagisawa
- Department of Chemistry, University of Wyoming, Laramie, WY 82071, USA.
| | - Debashis Dutta
- Department of Chemistry, University of Wyoming, Laramie, WY 82071, USA.
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50
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Ryan D, Ren K, Wu H. Single-cell assays. BIOMICROFLUIDICS 2011; 5:21501. [PMID: 21559238 PMCID: PMC3089644 DOI: 10.1063/1.3574448] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2010] [Accepted: 03/11/2011] [Indexed: 05/03/2023]
Abstract
This review presents an overview of literature that describes the applications of microfluidics to assay individual cells. We quantify the content of an individual mammalian cell, so that we can understand what criteria a single-cell assay must satisfy to be successful. We put in context the justification for single-cell assays and identify the characteristics that are relevant to single-cell assays. We review the literature from the past 24 months that describe the methods that use microfabrication-conventional or otherwise-and microfluidics in particular to study individual cells, and we present our views on how an increasing emphasis on three-dimensional cell culture and the demonstration of the first chemically defined cell might impact single-cell assays.
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Affiliation(s)
- Declan Ryan
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, People's Republic of China
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