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Colón Rosado J, Sun L. Solid-Phase Microextraction-Aided Capillary Zone Electrophoresis-Mass Spectrometry: Toward Bottom-Up Proteomics of Single Human Cells. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1120-1127. [PMID: 38514245 PMCID: PMC11157658 DOI: 10.1021/jasms.3c00429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/02/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
Capillary zone electrophoresis-mass spectrometry (CZE-MS) has been recognized as a valuable technique for the proteomics of mass-limited biological samples (i.e., single cells). However, its broad adoption for single cell proteomics (SCP) of human cells has been impeded by the low sample loading capacity of CZE, only allowing us to use less than 5% of the available peptide material for each measurement. Here we present a reversed-phase-based solid-phase microextraction (RP-SPME)-CZE-MS platform to solve the issue, paving the way for SCP of human cells using CZE-MS. The RP-SPME-CZE system was constructed in one fused silica capillary with zero dead volume for connection via in situ synthesis of a frit, followed by packing C8 beads into the capillary to form a roughly 2 mm long SPME section. Peptides captured by SPME were eluted with a buffer containing 30% (v/v) acetonitrile and 50 mM ammonium acetate (pH 6.5), followed by dynamic pH junction-based CZE-MS. The SPME-CZE-MS enabled the injection of nearly 40% of the available peptide sample for each measurement. The system identified 257 ± 24 proteins and 523 ± 69 peptides (N = 2) using a Q-Exactive HF mass spectrometer when only 0.25 ng of a commercial HeLa cell digest was available in the sample vial and 0.1 ng of the sample was injected. The amount of available peptide is equivalent to the protein mass of one HeLa cell. The data indicate that SPME-CZE-MS is ready for SCP of human cells.
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Affiliation(s)
- Jorge
A. Colón Rosado
- Department of Chemistry, Michigan
State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
| | - Liangliang Sun
- Department of Chemistry, Michigan
State University, 578 S Shaw Lane, East Lansing, Michigan 48824, United States
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2
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Weigert Muñoz A, Zhao W, Sieber SA. Monitoring host-pathogen interactions using chemical proteomics. RSC Chem Biol 2024; 5:73-89. [PMID: 38333198 PMCID: PMC10849124 DOI: 10.1039/d3cb00135k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/09/2023] [Indexed: 02/10/2024] Open
Abstract
With the rapid emergence and the dissemination of microbial resistance to conventional chemotherapy, the shortage of novel antimicrobial drugs has raised a global health threat. As molecular interactions between microbial pathogens and their mammalian hosts are crucial to establish virulence, pathogenicity, and infectivity, a detailed understanding of these interactions has the potential to reveal novel therapeutic targets and treatment strategies. Bidirectional molecular communication between microbes and eukaryotes is essential for both pathogenic and commensal organisms to colonise their host. In particular, several devastating pathogens exploit host signalling to adjust the expression of energetically costly virulent behaviours. Chemical proteomics has emerged as a powerful tool to interrogate the protein interaction partners of small molecules and has been successfully applied to advance host-pathogen communication studies. Here, we present recent significant progress made by this approach and provide a perspective for future studies.
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Affiliation(s)
- Angela Weigert Muñoz
- Center for Functional Protein Assemblies, Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich Ernst-Otto-Fischer-Straße 8 D-85748 Garching Germany
| | - Weining Zhao
- College of Pharmacy, Shenzhen Technology University Shenzhen 518118 China
| | - Stephan A Sieber
- Center for Functional Protein Assemblies, Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich Ernst-Otto-Fischer-Straße 8 D-85748 Garching Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) Germany
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3
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Zhang H, Jiang H, Liu X, Wang X. A review of innovative electrochemical strategies for bioactive molecule detection and cell imaging: Current advances and challenges. Anal Chim Acta 2024; 1285:341920. [PMID: 38057043 DOI: 10.1016/j.aca.2023.341920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/13/2023] [Accepted: 10/14/2023] [Indexed: 12/08/2023]
Abstract
Cellular heterogeneity poses a major challenge for tumor theranostics, requiring high-resolution intercellular bioanalysis strategies. Over the past decades, the advantages of electrochemical analysis, such as high sensitivity, good spatio-temporal resolution, and ease of use, have made it the preferred method to uncover cellular differences. To inspire more creative research, herein, we highlight seminal works in electrochemical techniques for biomolecule analysis and bioimaging. Specifically, micro/nano-electrode-based electrochemical techniques enable real-time quantitative analysis of electroactive substances relevant to life processes in the micro-nanostructure of cells and tissues. Nanopore-based technique plays a vital role in biosensing by utilizing nanoscale pores to achieve high-precision detection and analysis of biomolecules with exceptional sensitivity and single-molecule resolution. Electrochemiluminescence (ECL) technology is utilized for real-time monitoring of the behavior and features of individual cancer cells, enabling observation of their dynamic processes due to its capability of providing high-resolution and highly sensitive bioimaging of cells. Particularly, scanning electrochemical microscopy (SECM) and scanning ion conductance microscopy (SICM) which are widely used in real-time observation of cell surface biological processes and three-dimensional imaging of micro-nano structures, such as metabolic activity, ion channel activity, and cell morphology are introduced in this review. Furthermore, the expansion of the scope of cellular electrochemistry research by innovative functionalized electrodes and electrochemical imaging models and strategies to address future challenges and potential applications is also discussed in this review.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Hui Jiang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Xiaohui Liu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China.
| | - Xuemei Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China.
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4
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Zhang Z, Lee KCM, Siu DMD, Lo MCK, Lai QTK, Lam EY, Tsia KK. Morphological profiling by high-throughput single-cell biophysical fractometry. Commun Biol 2023; 6:449. [PMID: 37095203 PMCID: PMC10126163 DOI: 10.1038/s42003-023-04839-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
Complex and irregular cell architecture is known to statistically exhibit fractal geometry, i.e., a pattern resembles a smaller part of itself. Although fractal variations in cells are proven to be closely associated with the disease-related phenotypes that are otherwise obscured in the standard cell-based assays, fractal analysis with single-cell precision remains largely unexplored. To close this gap, here we develop an image-based approach that quantifies a multitude of single-cell biophysical fractal-related properties at subcellular resolution. Taking together with its high-throughput single-cell imaging performance (~10,000 cells/sec), this technique, termed single-cell biophysical fractometry, offers sufficient statistical power for delineating the cellular heterogeneity, in the context of lung-cancer cell subtype classification, drug response assays and cell-cycle progression tracking. Further correlative fractal analysis shows that single-cell biophysical fractometry can enrich the standard morphological profiling depth and spearhead systematic fractal analysis of how cell morphology encodes cellular health and pathological conditions.
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Affiliation(s)
- Ziqi Zhang
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kelvin C M Lee
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Dickson M D Siu
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Michelle C K Lo
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Queenie T K Lai
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Edmund Y Lam
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kevin K Tsia
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong.
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5
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A rapid and sensitive single-cell proteomic method based on fast liquid-chromatography separation, retention time prediction and MS1-only acquisition. Anal Chim Acta 2023; 1251:341038. [PMID: 36925302 DOI: 10.1016/j.aca.2023.341038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Single-cell analysis has received much attention in recent years for elucidating the widely existing cellular heterogeneity in biological systems. However, the ability to measure the proteome in single cells is still far behind that of transcriptomics due to the lack of sensitive and high-throughput mass spectrometry methods. Herein, we report an integrated strategy termed "SCP-MS1" that combines fast liquid chromatography (LC) separation, deep learning-based retention time (RT) prediction and MS1-only acquisition for rapid and sensitive single-cell proteome analysis. In SCP-MS1, the peptides were identified via four-dimensional MS1 feature (m/z, RT, charge and FAIMS CV) matching, therefore relieving MS acquisition from the time consuming and information losing MS2 step and making this method particularly compatible with fast LC separation. By completely omitting the MS2 step, all the MS analysis time was utilized for MS1 acquisition in SCP-MS1 and therefore led to 65%-138% increased MS1 feature collection. Unlike "match between run" methods that still needed MS2 information for RT alignment, SCP-MS1 used deep learning-based RT prediction to transfer the measured RTs in long gradient bulk analyses to short gradient single cell analyses, which was the key step to enhance both identification scale and matching accuracy. Using this strategy, more than 2000 proteins were obtained from 0.2 ng of peptides with a 14-min active gradient at a false discovery rate (FDR) of 0.8%. Comparing with the DDA method, improved quantitative performance was also observed for SCP-MS1 with approximately 50% decreased median coefficient of variation of quantified proteins. For single-cell analysis, 1715 ± 204 and 1604 ± 224 proteins were quantified in single 293T and HeLa cells, respectively. Finally, SCP-MS1 was applied to single-cell proteome analysis of sorafenib resistant and non-resistant HepG2 cells and revealed clear cellular heterogeneity in the resistant population that may be masked in bulk studies.
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6
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Chen L, Ghiasvand A, Paull B. Applications of thread-based microfluidics: Approaches and options for detection. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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7
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Sciurti E, Biscaglia F, Prontera C, Giampetruzzi L, Blasi L, Francioso L. Nanoelectrodes for Intracellular and Intercellular electrochemical detection: working principles, fabrication techniques and applications. J Electroanal Chem (Lausanne) 2022. [DOI: 10.1016/j.jelechem.2022.117125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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8
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Cupp-Sutton KA, Fang M, Wu S. Separation methods in single-cell proteomics: RPLC or CE? INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2022; 481:116920. [PMID: 36211475 PMCID: PMC9542495 DOI: 10.1016/j.ijms.2022.116920] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Cellular heterogeneity is commonly investigated using single-cell genomics and transcriptomics to investigate biological questions such as disease mechanism, therapeutic screening, and genomic and transcriptomic diversity between cellular populations and subpopulations at the cellular level. Single-cell mass spectrometry (MS)-based proteomics enables the high-throughput examination of protein expression at the single-cell level with wide applicability, and with spatial and temporal resolution, applicable to the study of cellular development, disease, effect of treatment, etc. The study of single-cell proteomics has lagged behind genomics and transcriptomics largely because proteins from single-cell samples cannot be amplified as DNA and RNA can using well established techniques such as PCR. Therefore, analytical methods must be robust, reproducible, and sensitive enough to detect the very small amount of protein within a single cell. To this end, nearly every step of the proteomics process has been extensively altered and improved to facilitate the proteomics analysis of single cells including cell counting and sorting, lysis, protein digestion, sample cleanup, separation, MS data acquisition, and data analysis. Here, we have reviewed recent advances in single-cell protein separation using nano reversed phase liquid chromatography (nRPLC) and capillary electrophoresis (CE) to inform application driven selection of separation techniques in the laboratory setting.
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Affiliation(s)
| | - Mulin Fang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
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9
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Bien T, Koerfer K, Schwenzfeier J, Dreisewerd K, Soltwisch J. Mass spectrometry imaging to explore molecular heterogeneity in cell culture. Proc Natl Acad Sci U S A 2022; 119:e2114365119. [PMID: 35858333 PMCID: PMC9303856 DOI: 10.1073/pnas.2114365119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 05/13/2022] [Indexed: 01/13/2023] Open
Abstract
Molecular analysis on the single-cell level represents a rapidly growing field in the life sciences. While bulk analysis from a pool of cells provides a general molecular profile, it is blind to heterogeneities between individual cells. This heterogeneity, however, is an inherent property of every cell population. Its analysis is fundamental to understanding the development, function, and role of specific cells of the same genotype that display different phenotypical properties. Single-cell mass spectrometry (MS) aims to provide broad molecular information for a significantly large number of cells to help decipher cellular heterogeneity using statistical analysis. Here, we present a sensitive approach to single-cell MS based on high-resolution MALDI-2-MS imaging in combination with MALDI-compatible staining and use of optical microscopy. Our approach allowed analyzing large amounts of unperturbed cells directly from the growth chamber. Confident coregistration of both modalities enabled a reliable compilation of single-cell mass spectra and a straightforward inclusion of optical as well as mass spectrometric features in the interpretation of data. The resulting multimodal datasets permit the use of various statistical methods like machine learning-driven classification and multivariate analysis based on molecular profile and establish a direct connection of MS data with microscopy information of individual cells. Displaying data in the form of histograms for individual signal intensities helps to investigate heterogeneous expression of specific lipids within the cell culture and to identify subpopulations intuitively. Ultimately, t-MALDI-2-MSI measurements at 2-µm pixel sizes deliver a glimpse of intracellular lipid distributions and reveal molecular profiles for subcellular domains.
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Affiliation(s)
- Tanja Bien
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, 48149 Münster, Germany
| | - Krischan Koerfer
- Institute for Psychology, University of Münster, 48149 Münster, Germany
- Otto Creutzfeldt Center for Cognitive and Behavioural Neuroscience, University of Münster, 48149 Münster, Germany
| | - Jan Schwenzfeier
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
| | - Klaus Dreisewerd
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, 48149 Münster, Germany
| | - Jens Soltwisch
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
- Interdisciplinary Center for Clinical Research (IZKF), University of Münster, 48149 Münster, Germany
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10
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Wang L, Abdulla A, Wang A, Warden AR, Ahmad KZ, Xin Y, Ding X. Sickle-like Inertial Microfluidic System for Online Rare Cell Separation and Tandem Label-Free Quantitative Proteomics (Orcs-Proteomics). Anal Chem 2022; 94:6026-6035. [PMID: 35380437 DOI: 10.1021/acs.analchem.2c00679] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Label-free proteomics with trace clinical samples provides a wealth of actionable insights for personalized medicine. Clinically acquired primary cells, such as circulating tumor cells (CTCs), are usually with low abundance that is prohibitive for conventional label-free proteomics analysis. Here, we present a sickle-like inertial microfluidic system for online rare cell separation and tandem label-free proteomics (namely, Orcs-proteomics). Orcs-proteomics adopts a buffer system with 0.1% N-dodecyl β-d-maltoside (DDM), 1 mM Tris (2-carboxyethyl) phosphine (TCEP), and 2 mM 2-chloroacetamide (CAA) for cell lysis and reductive alkylation. We demonstrate the application of Orcs-proteomics with 293T cells and manage to identify 913, 1563, 2271, and 2770 protein groups with 4, 13, 68, and 119 cells, respectively. We then spike MCF7 cells with white blood cells (WBCs) to simulate the patient's blood sample. Orcs-proteomics identifies more than 2000 protein groups with an average of 61 MCF7 cells. We further recruit two advanced breast cancer patients and collect 5 and 7 CTCs from each patient through minimally invasive blood drawing. Orcs-proteomics manages to identify 973 and 1135 protein groups for each patient. Therefore, Orcs-proteomics empowers rare cells simultaneously to be separated and counted for proteomics and provides technical support for personalized treatment decision making with rare primary patient samples.
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Affiliation(s)
- Liping Wang
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Aynur Abdulla
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Aiting Wang
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Antony R Warden
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Khan Zara Ahmad
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yufang Xin
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xianting Ding
- Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
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11
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Amarakoon TN, Ke N, Aspinwall CA, Miranda KM. Quantification of intracellular HNO delivery with capillary zone electrophoresis. Nitric Oxide 2022; 118:49-58. [PMID: 34715361 PMCID: PMC8758193 DOI: 10.1016/j.niox.2021.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 01/03/2023]
Abstract
Redox signaling, wherein reactive and diffusible small molecules are channeled into specific messenger functions, is a critical component of signal transduction. A central principle of redox signaling is that the redox modulators are produced in a highly controlled fashion to specifically modify biotargets. Thiols serve as primary mediators of redox signaling as a function of the rich variety of adducts, which allows initiation of distinct cellular effects. Coupling the inherent reactivity of thiols with highly sensitive and selective chemical analysis protocols can facilitate identification of redox signaling agents, both in solution and in cultured cells. Here, we describe use of capillary zone electrophoresis to both identify and quantify sulfinamides, which are specific markers of the reaction of thiols with nitroxyl (HNO), a putative biologically relevant reactive nitrogen species.
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Affiliation(s)
- Thilini N Amarakoon
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Neng Ke
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA
| | - Craig A Aspinwall
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA; BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA; Department of Biomedical Engineering, University of Arizona, Tucson, AZ, 85721, USA
| | - Katrina M Miranda
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA; BIO5 Institute, University of Arizona, Tucson, AZ, 85721, USA.
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Zhao Y, Lou J, Zhang H, Sun H, Zhang M, Wang S, Sha X, Zhan Z, Wang Y, Ma C, Li WJ. Measurement methods of single cell drug response. Talanta 2021; 239:123035. [PMID: 34839926 DOI: 10.1016/j.talanta.2021.123035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/25/2022]
Abstract
In the last decades, a wide multitude of research activity has been focused on the development of new drugs, and devoted to overcome the challenges of high cost and low efficiency in drug evaluation. The measurement of drug response at the single cell level is a quicker, more direct and more accurate way to reflect drug efficacy, which can shorten the drug development period and reduce research costs. Therefore, the single cell drug response (SCDR) measurement technology has aroused extensive attention from researchers, and has become a hot topic in the fields of drug research and cell biology. Recent years have seen the emergence of various SCDR measurement technologies that feature different working principles and different levels of measurement performance. To better examine, compare and summarize the characteristics and functions of these technologies, we select signal-to-noise ratio, throughput, content, invasion, and device complexity as the criteria to evaluate them from the drug efficacy perspective. This review aims to highlight sixteen kinds of SCDR measurement technologies, including patch-clamp technique, live-cell interferometry, capillary electrophoresis, secondary ion mass spectrometry, and more, and report widespread representative examples of SCDR measurement the recent approaches for over the past forty years. Based on their reaction principles, these technologies are classified into four categories: electrical, optical, electrochemical, and mass spectrometry, and a detailed comparison is made between them. After in-depth understanding of these technologies, it is expected to improve or integrate these technologies to propose better SCDR measurement strategies, and explore methods in new drug development and screening, as well as disease diagnosis and treatment.
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Affiliation(s)
- Yuliang Zhao
- School of Control Engineering, Northeastern University at Qinhuangdao, Qinhuangdao, 066004, China
| | - Jiazhi Lou
- School of Control Engineering, Northeastern University at Qinhuangdao, Qinhuangdao, 066004, China
| | - Hongyu Zhang
- School of Control Engineering, Northeastern University at Qinhuangdao, Qinhuangdao, 066004, China
| | - Hui Sun
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China
| | - Menglin Zhang
- School of Control Engineering, Northeastern University at Qinhuangdao, Qinhuangdao, 066004, China
| | - Shuyu Wang
- School of Control Engineering, Northeastern University at Qinhuangdao, Qinhuangdao, 066004, China
| | - Xiaopeng Sha
- School of Control Engineering, Northeastern University at Qinhuangdao, Qinhuangdao, 066004, China
| | - Zhikun Zhan
- School of Electrical Engineering, Yanshan University at Qinhuangdao, Qinhuangdao, 066004, China.
| | - Ying Wang
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing, 100191, China
| | - Cuihua Ma
- Department of Clinical Laboratory, First Hospital of Qinhuangdao, Qinhuangdao, 066004, China.
| | - Wen Jung Li
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon, Hong Kong, 999077, China.
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13
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Cho SY, Koman VB, Gong X, Moon SJ, Gordiichuk P, Strano MS. Nanosensor Chemical Cytometry for Characterizing the Efflux Heterogeneity of Nitric Oxide from Macrophages. ACS NANO 2021; 15:13683-13691. [PMID: 34398614 DOI: 10.1021/acsnano.1c04958] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Macrophages are a critical part of the human immune response, and their collective heterogeneity is implicated in disease progression and prevention. A nondestructive, label-free tool does not currently exist for profiling the dynamic, antigenic responses of single macrophages in a collection to correlate with specific molecular expression and correlated biophysical properties at the cellular level, despite the potential for diagnosis and therapeutics. Herein, we develop a nanosensor chemical cytometry (NCC) that can profile the heterogeneity of inducible nitric oxide synthase (iNOS) responses from macrophage populations. By integrating a near-infrared (nIR) fluorescent nanosensor array and collagen layer with microfluidics, the cellular lensing effect of the macrophage was utilized to characterize both nitric oxide (NO) efflux and refractive index (RI) changes at a single-cell level. Using a parallel, multichannel approach, distinct iNOS heterogeneities of macrophages can be monitored at an attomolar (10-18 mol) sensitivity in a nondestructive and real-time manner with a throughput of exceeding the 200 cells/frame. We demonstrate that estimated mean NO efflux rates of macrophage populations are elevated from 342 (σ = 199) to 464 (σ = 206) attomol/cell·hr with a 3% larger increase in the heterogeneity, and estimated RI of macrophage decrease from 1.366 (σ = 0.015) to 1.359 (σ = 0.009) with trimodal subpopulations under lipopolysaccharide (LPS) activation. These measured values are also in good agreement with Griess assay results and previously reported measurements. This work provides an efficient strategy for single-cell analysis of macrophage populations for cellular manufacturing and biopharmaceutical engineering.
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Affiliation(s)
- Soo-Yeon Cho
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Volodymyr B Koman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Xun Gong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sun Jin Moon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Pavlo Gordiichuk
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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14
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Wolfbeis OS. Fluorescent chameleon labels for bioconjugation and imaging of proteins, nucleic acids, biogenic amines and surface amino groups. a review. Methods Appl Fluoresc 2021; 9. [PMID: 34340216 DOI: 10.1088/2050-6120/ac1a0a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/02/2021] [Indexed: 12/14/2022]
Abstract
Chameleon labels (ChLs) possess the unique property of changing (visible) color and fluorescence on binding to amino groups of biomolecules. MostChLs react with primary aliphatic amino groups such as those in lysine or with amino groups artificially introduced into polynucleic acids or saccharides, but someothers also react with secondary amino groups. Under controlled circumstances, the reactions are fairly specific. The review is subdivided into the following sections: (1) An introduction and classification of fluorescent labels; (2) pyrylium labels that undergo shortwave color changes upon labelling, typically from blue to red; (3) polymethine type of labels (that also undergo shortwave color changes, typically from green to blue; (4) various other (less common) chromogenic and fluorogenic systems; (5) hemicyanine labels that undergolongwavecolor changes, typically from yellow to purple; (6) the application of ChLs to labeling of proteins and oligonucleotides; (7) applications to fluorometric assays and sensing; (8) applications to fluorescence imaging of biomolecules; (9) applications in studies on affinity interactions (receptor-ligand binding); (10) applications in surface and interface chemistry; and (11) applications in chromatography, electrophoresis and isotachophoresis of biomolecules.
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Affiliation(s)
- Otto S Wolfbeis
- University of Regensburg, Institute of Analytical Chemistry, Chemo- and Biosensors, 94040 Regensburg, Germany
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15
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Wang N, Wang D, Pan R, Wang D, Jiang D, Chen HY. Self-Referenced Nanopipette for Electrochemical Analysis of Hydrogen Peroxide in the Nucleus of a Single Living Cell. Anal Chem 2021; 93:10744-10749. [PMID: 34314583 DOI: 10.1021/acs.analchem.0c05025] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In a typical intracellular electroanalytical measurement, a nanoelectrode is located inside a living cell and a reference electrode outside the cell. This setup faces a problem to drop a certain potential across the cellular plasma membrane that might interrupt the cellular activity. To solve this problem, a self-referenced nanopipette is assembled by incorporating a reference electrode inside the nanocapillary, with a Pt ring at the tip as the electrochemical surface. The potential applied between the Pt ring and the reference electrode is restricted inside the capillary and thus has a negligible effect on the surrounding cellular environment. Using this new setup, the nanopipette pierces into the nucleus of a single living cell for the measurement of hydrogen peroxide under oxidative stress. It is found that a lesser amount of hydrogen peroxide is measured in the nucleus compared with the cytoplasm, revealing uneven oxidative stress inside the cell. The result will not only greatly improve the current setup for intracellular electrochemical analysis but also provide biological information of the compartment inside the living cell.
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Affiliation(s)
- Nina Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210092, China
| | - Dongni Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210092, China
| | - Rongrong Pan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210092, China
| | - Dengchao Wang
- School of Chemical Sciences, University of Chinese Academy of Science, Beijing 100190, China
| | - Dechen Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210092, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210092, China
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16
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Yang Z, Zhang Z, Chen D, Xu T, Wang Y, Sun L. Nanoparticle-Aided Nanoreactor for Nanoproteomics. Anal Chem 2021; 93:10568-10576. [PMID: 34297524 DOI: 10.1021/acs.analchem.1c01704] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Large-scale bottom-up proteomics of few even single cells is crucial for a better understanding of the roles played by cell-to-cell heterogeneity in disease and development. Novel proteomic methodologies with extremely high sensitivity are required for few even single-cell proteomics. Sample processing with high recovery and no contaminants is one key step. Here we developed a nanoparticle-aided nanoreactor for nanoproteomics (Nano3) technique for processing low-nanograms of mammalian cell proteins for proteome profiling. The Nano3 technique employed nanoparticles packed in a capillary channel to form a nanoreactor (≤30 nL) for concentrating, cleaning, and digesting proteins originally in a lysis buffer containing sodium dodecyl sulfate (SDS), followed by nanoRPLC-MS/MS analysis. The Nano3 method identified a 40-times higher number of proteins based on MS/MS from 2-ng mouse brain protein samples compared to the SP3 (single-pot solid-phase-enhanced sample preparation) method, which performed the sample processing using the nanoparticles in a 10 μL solution in an Eppendorf tube. The data indicates a drastically higher sample recovery of the Nano3 compared to the SP3 method for processing mass-limited proteome samples. In this pilot study, the Nano3 method was further applied in processing 10-1000 HeLa cells for bottom-up proteomics, producing 441 ± 263 (n = 4) (MS/MS) and 983 ± 292 (n = 4) [match between runs (MBR)+MS/MS] protein identifications from only 10 HeLa cells using a Q-Exactive HF mass spectrometer. The preliminary results render the Nano3 method a useful approach for processing few mammalian cells for proteome profiling.
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Affiliation(s)
- Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824 United States
| | - Zhaoran Zhang
- Department of Animal Sciences, Michigan State University, 766 Service Road, East Lansing, Michigan 48824 United States
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824 United States
| | - Tian Xu
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824 United States
| | - Yuan Wang
- Department of Animal Sciences, Michigan State University, 766 Service Road, East Lansing, Michigan 48824 United States
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824 United States
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17
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Cho SY, Gong X, Koman VB, Kuehne M, Moon SJ, Son M, Lew TTS, Gordiichuk P, Jin X, Sikes HD, Strano MS. Cellular lensing and near infrared fluorescent nanosensor arrays to enable chemical efflux cytometry. Nat Commun 2021; 12:3079. [PMID: 34035262 PMCID: PMC8149711 DOI: 10.1038/s41467-021-23416-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/20/2021] [Indexed: 02/07/2023] Open
Abstract
Nanosensors have proven to be powerful tools to monitor single cells, achieving spatiotemporal precision even at molecular level. However, there has not been way of extending this approach to statistically relevant numbers of living cells. Herein, we design and fabricate nanosensor array in microfluidics that addresses this limitation, creating a Nanosensor Chemical Cytometry (NCC). nIR fluorescent carbon nanotube array is integrated along microfluidic channel through which flowing cells is guided. We can utilize the flowing cell itself as highly informative Gaussian lenses projecting nIR profiles and extract rich information. This unique biophotonic waveguide allows for quantified cross-correlation of biomolecular information with various physical properties and creates label-free chemical cytometer for cellular heterogeneity measurement. As an example, the NCC can profile the immune heterogeneities of human monocyte populations at attomolar sensitivity in completely non-destructive and real-time manner with rate of ~600 cells/hr, highest range demonstrated to date for state-of-the-art chemical cytometry.
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Affiliation(s)
- Soo-Yeon Cho
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xun Gong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Volodymyr B Koman
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Matthias Kuehne
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sun Jin Moon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manki Son
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tedrick Thomas Salim Lew
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Pavlo Gordiichuk
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xiaojia Jin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hadley D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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18
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Hong S, Pawel GT, Pei R, Lu Y. Recent progress in developing fluorescent probes for imaging cell metabolites. Biomed Mater 2021; 16. [PMID: 33915523 DOI: 10.1088/1748-605x/abfd11] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 04/29/2021] [Indexed: 01/12/2023]
Abstract
Cellular metabolites play a crucial role in promoting and regulating cellular activities, but it has been difficult to monitor these cellular metabolites in living cells and in real time. Over the past decades, iterative development and improvements of fluorescent probes have been made, resulting in the effective monitoring of metabolites. In this review, we highlight recent progress in the use of fluorescent probes for tracking some key metabolites, such as adenosine triphosphate, cyclic adenosine monophosphate, cyclic guanosine 5'-monophosphate, Nicotinamide adenine dinucleotide (NADH), reactive oxygen species, sugar, carbon monoxide, and nitric oxide for both whole cell and subcellular imaging.
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Affiliation(s)
- Shanni Hong
- Department of Medical Imaging Technology, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, People's Republic of China.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America.,CAS Key Laboratory of Nano-Bio Interfaces, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, People's Republic of China
| | - Gregory T Pawel
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interfaces, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, People's Republic of China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
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19
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Abstract
The ultimate goal of single-cell analyses is to obtain the biomolecular content for each cell in unicellular and multicellular organisms at different points of their life cycle under variable environmental conditions. These require an assessment of: a) the total number of cells, b) the total number of cell types, and c) the complete and quantitative single molecular detection and identification for all classes of biopolymers, and organic and inorganic compounds, in each individual cell. For proteins, glycans, lipids, and metabolites, whose sequences cannot be amplified by copying as in the case of nucleic acids, the detection limit by mass spectrometry is about 105 molecules. Therefore, proteomic, glycomic, lipidomic, and metabolomic analyses do not yet permit the assembly of the complete single-cell omes. The construction of novel nanoelectrophoretic arrays and nano in microarrays on a single 1-cm-diameter chip has shown proof of concept for a high throughput platform for parallel processing of thousands of individual cells. Combined with dynamic secondary ion mass spectrometry, with 3D scanning capability and lateral resolution of 50 nm, the sensitivity of single molecular quantification and identification for all classes of biomolecules could be reached. Further development and routine application of such technological and instrumentation solution would allow assembly of complete omes with a quantitative assessment of structural and functional cellular diversity at the molecular level.
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20
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Petersen BV, Gallion L, Allbritton NL. Silicon Photomultipliers as a Low-Cost Fluorescence Detector for Capillary Electrophoresis. Anal Chem 2020; 92:13683-13687. [PMID: 32967426 PMCID: PMC7728455 DOI: 10.1021/acs.analchem.0c03105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Capillary electrophoresis (CE) is a highly efficient separation method capable of handling small sample volumes (∼pL) and low (∼yoctomole) detection limits and, as such, is ideal for applications that require high sensitivity, such as single-cell analysis (Chen et al. Anal. Chem. 1996, 68 (4), 690-696; Cohen et al. Annu. Rev. Anal. Chem. 2008, 1 (1), 165-190; Vickerman et al. ACS Chem. Biol. 2018, 13 (7), 1741-1751). Low-cost CE instrumentation is quickly expanding, but low-cost, open-source fluorescence detectors with ultrasensitive detection limits are lacking (Vickerman et al. ACS Chem. Biol. 2018, 13 (7), 1741-1751; Fang et al. Electrophoresis 2016, 37 (17-18), 2376-2383; Casto et al. Anal. Chem. 2019, 40 (1), 65-78). Silicon photomultipliers (SiPM) are inexpensive, low-footprint detectors with the potential to fill the role as a detector when cost, size, and customization are important. In this work, we demonstrate the use of a SiPM in CE with zeptomolar detection limits and a dynamic range spanning 5 orders of magnitude, comparable to photomultiplier detectors. The performance of these detectors was measured using a continuous wave excitation laser in an epifluorescence detection configuration. We characterize the performance of the SiPM as a highly sensitive detector by measuring enzyme activity in single cells. This simple, small footprint, and low-cost (<$130) light detection circuit will be beneficial for open-source, portable, and budget-friendly instrumentation requiring high sensitivity.
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Affiliation(s)
- Brae V. Petersen
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Luke Gallion
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nancy L. Allbritton
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, United States
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21
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Hong S, Dechaumphai E, Green CR, Lal R, Murphy AN, Metallo CM, Chen R. Sub-nanowatt microfluidic single-cell calorimetry. Nat Commun 2020; 11:2982. [PMID: 32532969 PMCID: PMC7292832 DOI: 10.1038/s41467-020-16697-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 05/18/2020] [Indexed: 12/02/2022] Open
Abstract
Non-invasive and label-free calorimetry could become a disruptive technique to study single cell metabolic heat production without altering the cell behavior, but it is currently limited by insufficient sensitivity. Here, we demonstrate microfluidic single-cell calorimetry with 0.2-nW sensitivity, representing more than ten-fold enhancement over previous record, which is enabled by (i) a low-noise thermometry platform with ultralow long-term (10-h) temperature noise (80 μK) and (ii) a microfluidic channel-in-vacuum design allowing cell flow and nutrient delivery while maintaining a low thermal conductance of 2.5 μW K−1. Using Tetrahymena thermophila as an example, we demonstrate on-chip single-cell calorimetry measurement with metabolic heat rates ranging from 1 to 4 nW, which are found to correlate well with the cell size. Finally, we perform real-time monitoring of metabolic rate stimulation by introducing a mitochondrial uncoupling agent to the microchannel, enabling determination of the spare respiratory capacity of the cells. Calorimetrically measuring the heat of single cells is currently not possible due to the sensitivity of existing calorimeters. Here the authors present on-chip single cell calorimetry, with a sensitivity over ten-fold greater than the current gold-standard.
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Affiliation(s)
- Sahngki Hong
- Materials Science and Engineering Program, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Edward Dechaumphai
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Courtney R Green
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Ratneshwar Lal
- Materials Science and Engineering Program, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, 92093, USA.,Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Anne N Murphy
- Department of Pharmacology, University of California San Diego, La Jolla, CA, 92093, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Renkun Chen
- Materials Science and Engineering Program, University of California San Diego, La Jolla, CA, 92093, USA. .,Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, 92093, USA.
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22
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Zhu C, Luo X, Espulgar WV, Koyama S, Kumanogoh A, Saito M, Takamatsu H, Tamiya E. Real-Time Monitoring and Detection of Single-Cell Level Cytokine Secretion Using LSPR Technology. MICROMACHINES 2020; 11:E107. [PMID: 31963848 PMCID: PMC7019717 DOI: 10.3390/mi11010107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/08/2020] [Accepted: 01/15/2020] [Indexed: 01/14/2023]
Abstract
Cytokine secretion researches have been a main focus of studies among the scientists in the recent decades for its outstanding contribution to clinical diagnostics. Localized surface plasmon resonance (LSPR) technology is one of the conventional methods utilized to analyze these issues, as it could provide fast, label-free and real-time monitoring of biomolecule binding events. However, numerous LSPR-based biosensors in the past are usually utilized to monitor the average performance of cell groups rather than single cells. Meanwhile, the complicated sensor structures will lead to the fabrication and economic budget problems. Thus, in this paper, we report a simple synergistic integration of the cell trapping of microwell chip and gold-capped nanopillar-structured cyclo-olefin-polymer (COP) film for single cell level Interleukin 6 (IL-6) detection. Here, in-situ cytokine secreted from the trapped cell can be directly observed and analyzed through the peak red-shift in the transmittance spectrum. The fabricated device also shows the potential to conduct the real-time monitoring which would greatly help us identify the viability and biological variation of the tested single cell.
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Affiliation(s)
- Chen Zhu
- Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (C.Z.); (W.V.E.); (M.S.)
| | - Xi Luo
- Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (C.Z.); (W.V.E.); (M.S.)
- AIST-Osaka University Advanced Photonics and Biosensing Open Innovation Laboratory, AIST, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Wilfred Villariza Espulgar
- Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (C.Z.); (W.V.E.); (M.S.)
| | - Shohei Koyama
- Immunology Frontier Research Center, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; (S.K.); (A.K.); (H.T.)
| | - Atsushi Kumanogoh
- Immunology Frontier Research Center, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; (S.K.); (A.K.); (H.T.)
| | - Masato Saito
- Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (C.Z.); (W.V.E.); (M.S.)
- AIST-Osaka University Advanced Photonics and Biosensing Open Innovation Laboratory, AIST, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hyota Takamatsu
- Immunology Frontier Research Center, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan; (S.K.); (A.K.); (H.T.)
| | - Eiichi Tamiya
- Department of Applied Physics, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (C.Z.); (W.V.E.); (M.S.)
- AIST-Osaka University Advanced Photonics and Biosensing Open Innovation Laboratory, AIST, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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23
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24
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Yang Z, Shen X, Chen D, Sun L. Improved Nanoflow RPLC-CZE-MS/MS System with High Peak Capacity and Sensitivity for Nanogram Bottom-up Proteomics. J Proteome Res 2019; 18:4046-4054. [PMID: 31610113 DOI: 10.1021/acs.jproteome.9b00545] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Novel mass spectrometry (MS)-based proteomic tools with extremely high sensitivity and high peak capacity are required for comprehensive characterization of protein molecules in mass-limited samples. We reported a nanoRPLC-CZE-MS/MS system for deep bottom-up proteomics of low micrograms of human cell samples in previous work. In this work, we improved the sensitivity of the nanoRPLC-CZE-MS/MS system drastically via employing bovine serum albumin (BSA)-treated sample vials, improving the nanoRPLC fraction collection procedure, and using a short capillary for fast CZE separation. The improved nanoRPLC-CZE produced a peak capacity of 8500 for peptide separation. The improved system identified 6500 proteins from a MCF7 proteome digest starting with only 500 ng of peptides using a Q-Exactive HF mass spectrometer. The system produced a comparable number of protein identifications (IDs) to our previous system and the two-dimensional (2D) nanoRPLC-MS/MS system developed by Mann's group with 10-fold and 4-fold less sample consumption, respectively. We coupled the single-spot solid phase sample preparation (SP3) method to the improved nanoRPLC-CZE-MS/MS for bottom-up proteomics of 5000 HEK293T cells, resulting in 3689 protein IDs with the consumption of a peptide amount that corresponded to only roughly 1000 cells.
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Affiliation(s)
- Zhichang Yang
- Department of Chemistry , Michigan State University , 578 S Shaw Lane , East Lansing , Michigan 48824 , United States
| | - Xiaojing Shen
- Department of Chemistry , Michigan State University , 578 S Shaw Lane , East Lansing , Michigan 48824 , United States
| | - Daoyang Chen
- Department of Chemistry , Michigan State University , 578 S Shaw Lane , East Lansing , Michigan 48824 , United States
| | - Liangliang Sun
- Department of Chemistry , Michigan State University , 578 S Shaw Lane , East Lansing , Michigan 48824 , United States
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25
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Abraham DH, Anttila MM, Gallion LA, Petersen BV, Proctor A, Allbritton NL. Design of an automated capillary electrophoresis platform for single-cell analysis. Methods Enzymol 2019; 628:191-221. [PMID: 31668230 DOI: 10.1016/bs.mie.2019.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Single-cell analysis of cellular contents by highly sensitive analytical instruments is known as chemical cytometry. A chemical cytometer typically samples one cell at a time, quantifies the cellular contents of interest, and then processes and reports that data. Automation adds the potential to perform this entire sequence of events with minimal intervention, increasing throughput and repeatability. In this chapter, we discuss the design considerations for an automated capillary electrophoresis-based instrument for assay of enzymatic activity within single cells. We describe the key requirements of the microscope base and capillary electrophoresis platforms. We also provide detailed protocols and schematic designs of our cell isolation, lysis, sampling, and detection strategies. Additionally, we describe our signal processing and instrument automation workflows. The described automated system has demonstrated single-cell throughput at rates above 100cells/h and analyte limits of detection as low as 10-20mol.
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Affiliation(s)
- David H Abraham
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States
| | - Matthew M Anttila
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States
| | - Luke A Gallion
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States
| | - Brae V Petersen
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States
| | - Angela Proctor
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States
| | - Nancy L Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, United States; Joint Department of Biomedical Engineering, University of North Carolina, Chapel and North Carolina State University, Raleigh, NC, USA.
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26
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Abstract
A microfluidic device as a pivotal research tool in chemistry and life science is now widely recognized. Indeed, microfluidic techniques have made significant advancements in fundamental research, such as the inherent heterogeneity of single-cells studies in cell populations, which would be helpful in understanding cellular molecular mechanisms and clinical diagnosis of major diseases. Single-cell analyses on microdevices have shown great potential for precise fluid control, cell manipulation, and signal output with rapid and high throughput. Moreover, miniaturized devices also have open functions such as integrating with traditional detection methods, for example, optical, electrochemical or mass spectrometry for single-cell analysis. In this review, we summarized recent advances of single-cell analysis based on various microfluidic approaches from different dimensions, such as in vitro, ex vivo, and in vivo analysis of single cells.
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Affiliation(s)
- Xiaowen Ou
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology
| | - Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology
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27
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Lombard-Banek C, Moody SA, Manzini MC, Nemes P. Microsampling Capillary Electrophoresis Mass Spectrometry Enables Single-Cell Proteomics in Complex Tissues: Developing Cell Clones in Live Xenopus laevis and Zebrafish Embryos. Anal Chem 2019; 91:4797-4805. [PMID: 30827088 PMCID: PMC6688183 DOI: 10.1021/acs.analchem.9b00345] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Label-free single-cell proteomics by mass spectrometry (MS) is currently incompatible with complex tissues without requiring cell culturing, single-cell dissection, or tissue dissociation. We here report the first example of label-free single-cell MS-based proteomics directly in single cells in live vertebrate embryos. Our approach integrates optically guided in situ subcellular capillary microsampling, one-pot extraction-digestion of the collected proteins, peptide separation by capillary electrophoresis, ionization by an ultrasensitive electrokinetically pumped nanoelectrospray, and detection by high-resolution MS (Orbitrap). With a 700 zmol (420 000 copies) lower limit of detection, this trace-sensitive technology confidently identified and quantified ∼750-800 protein groups (<1% false-discovery rate) by analyzing just ∼5 ng of protein digest, viz. <0.05% of the total protein content from individual cells in a 16-cell Xenopus laevis (frog) embryo. After validating the approach by recovering animal-vegetal-pole proteomic asymmetry in the frog zygote, the technology was applied to uncover proteomic reorganization as the animal-dorsal (D11) cell of the 16-cell embryo gave rise to its neural-tissue-fated clone in the embryo developing to the 32-, 64-, and 128-cell stages. In addition to enabling proteomics on smaller cells in X. laevis, we also demonstrated this technology to be scalable to single cells in live zebrafish embryos. Microsampling single-cell MS-based proteomics raises exciting opportunities to study cell and developmental processes directly in complex tissues and whole organisms at the level of the building block of life: the cell.
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Affiliation(s)
- Camille Lombard-Banek
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742
| | - Sally A. Moody
- Department of Anatomy & Regenerative Biology, The George Washington University, Washington, DC 20052
| | - M. Chiara Manzini
- Department of Pharmacology & Physiology, The George Washington University, Washington, DC 20052
| | - Peter Nemes
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD 20742
- Department of Anatomy & Regenerative Biology, The George Washington University, Washington, DC 20052
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28
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Wang Z, Zhang X. Single Cell Proteomics for Molecular Targets in Lung Cancer: High-Dimensional Data Acquisition and Analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1068:73-87. [PMID: 29943297 DOI: 10.1007/978-981-13-0502-3_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the proteomic and genomic era, lung cancer researchers are increasingly under challenge with traditional protein analyzing tools. High output, multiplexed analytical procedures are in demand for disclosing the post-translational modification, molecular interactions and signaling pathways of proteins precisely, specifically, dynamically and systematically, as well as for identifying novel proteins and their functions. This could be better realized by single-cell proteomic methods than conventional proteomic methods. Using single-cell proteomic tools including flow cytometry, mass cytometry, microfluidics and chip technologies, chemical cytometry, single-cell western blotting, the quantity and functions of proteins are analyzed simultaneously. Aside from deciphering disease mechanisms, single-cell proteomic techniques facilitate the identification and screening of biomarkers, molecular targets and promising compounds as well. This review summarized single-cell proteomic tools and their use in lung cancer.
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Affiliation(s)
- Zheng Wang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Zhengzhou, China
| | - Xiaoju Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Zhengzhou, China. .,Biomedical Research Center, Zhengzhou University People's Hospital, Zhengzhou, China.
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Yang Z, Shen X, Chen D, Sun L. Microscale Reversed-Phase Liquid Chromatography/Capillary Zone Electrophoresis-Tandem Mass Spectrometry for Deep and Highly Sensitive Bottom-Up Proteomics: Identification of 7500 Proteins with Five Micrograms of an MCF7 Proteome Digest. Anal Chem 2018; 90:10479-10486. [PMID: 30102516 PMCID: PMC6156779 DOI: 10.1021/acs.analchem.8b02466] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) has been well recognized for bottom-up proteomics. It has approached 4000-8000 protein identifications (IDs) from a human cell line, mouse brains, or Xenopus embryos via coupling with liquid chromatography (LC) prefractionation. However, at least 500 μg of complex proteome digests were required for the LC/CZE-MS/MS studies. This requirement of a large amount of initial peptide material impedes the application of CZE-MS/MS for deep bottom-up proteomics of mass-limited samples. In this work, we coupled microscale reversed-phase LC (μRPLC)-based peptide prefractionation to dynamic pH-junction-based CZE-MS/MS for deep bottom-up proteomics of the MCF7 breast cancer cell proteome starting with only 5 μg of peptides. The dynamic pH-junction-based CZE enabled a 500 nL sample injection from as low as a 1.5 μL peptide sample, using up to 33% of the available peptide material for an analysis. Two kinds of μRPLC prefractionation were investigated, C18 ZipTip and nanoflow RPLC. C18 ZipTip/CZE-MS/MS identified 4453 proteins from 5 μg of the MCF7 proteome digest and showed good qualitative and quantitative reproducibility. Nanoflow RPLC/CZE-MS/MS produced over 7500 protein IDs and nearly 60 000 peptide IDs from the 5 μg of MCF7 proteome digest. The nanoflow RPLC/CZE-MS/MS platform reduced the required amount of complex proteome digests for LC/CZE-MS/MS-based deep bottom-up proteomics by 2 orders of magnitude. Our work provides the proteomics community with a powerful tool for deep and highly sensitive proteomics.
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Affiliation(s)
- Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Xiaojing Shen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Ln, East Lansing, MI 48824 USA
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30
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Vickerman BM, Anttila MM, Petersen BV, Allbritton NL, Lawrence DS. Design and Application of Sensors for Chemical Cytometry. ACS Chem Biol 2018; 13:1741-1751. [PMID: 29376326 DOI: 10.1021/acschembio.7b01009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The bulk cell population response to a stimulus, be it a growth factor or a cytotoxic agent, neglects the cell-to-cell variability that can serve as a friend or as a foe in human biology. Biochemical variations among closely related cells furnish the basis for the adaptability of the immune system but also act as the root cause of resistance to chemotherapy by tumors. Consequently, the ability to probe for the presence of key biochemical variables at the single-cell level is now recognized to be of significant biological and biomedical impact. Chemical cytometry has emerged as an ultrasensitive single-cell platform with the flexibility to measure an array of cellular components, ranging from metabolite concentrations to enzyme activities. We briefly review the various chemical cytometry strategies, including recent advances in reporter design, probe and metabolite separation, and detection instrumentation. We also describe strategies for improving intracellular delivery, biochemical specificity, metabolic stability, and detection sensitivity of probes. Recent applications of these strategies to small molecules, lipids, proteins, and other analytes are discussed. Finally, we assess the current scope and limitations of chemical cytometry and discuss areas for future development to meet the needs of single-cell research.
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Affiliation(s)
- Brianna M. Vickerman
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Matthew M. Anttila
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Brae V. Petersen
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nancy L. Allbritton
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Joint Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, and North Carolina State University,
Raleigh, North Carolina 27695, United States
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - David S. Lawrence
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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31
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Kepinska M, Kizek R, Milnerowicz H. Fullerene as a doxorubicin nanotransporter for targeted breast cancer therapy: Capillary electrophoresis analysis. Electrophoresis 2018; 39:2370-2379. [PMID: 29931716 DOI: 10.1002/elps.201800148] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/14/2018] [Accepted: 06/17/2018] [Indexed: 12/31/2022]
Abstract
The clinical use of doxorubicin (DOX) is limited by dose-related cardiomyopathy, which becomes more prevalent with increasing cumulative doses of the drug. Complexes of fullerene with DOX were designed and studied using biophysical methods. The ability of DOX to release from fullerene at different pHs was analyzed. It has been shown that the size of the fullerene-DOX complexes was ∼280 nm. The zeta potential for fullerene was -30 mV, for DOX -8 mV, and for fullerene-DOX conjugates -24 mV. Drug release was studied by CE with LIF detection. When fullerene-DOX conjugates were separated in a pH 7.5 buffer, 43% of all DOX signals were derived from free DOX, with the signal increasing as pH decreased. At pH 5.25, all DOX had been released and 100% of the signal was derived from free DOX. The release of DOX from complexes with fullerene at lower pH can be used in targeted antineoplastic therapy, resulting in lower toxicity for less acidic non-target tissue.
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Affiliation(s)
- Marta Kepinska
- Department of Biomedical and Environmental Analyses, Faculty of Pharmacy with Division of Laboratory Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Rene Kizek
- Department of Biomedical and Environmental Analyses, Faculty of Pharmacy with Division of Laboratory Medicine, Wroclaw Medical University, Wroclaw, Poland.,Central Laboratory, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Halina Milnerowicz
- Department of Biomedical and Environmental Analyses, Faculty of Pharmacy with Division of Laboratory Medicine, Wroclaw Medical University, Wroclaw, Poland
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32
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Li ZY, Huang M, Wang XK, Zhu Y, Li JS, Wong CCL, Fang Q. Nanoliter-Scale Oil-Air-Droplet Chip-Based Single Cell Proteomic Analysis. Anal Chem 2018; 90:5430-5438. [PMID: 29551058 DOI: 10.1021/acs.analchem.8b00661] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single cell proteomic analysis provides crucial information on cellular heterogeneity in biological systems. Herein, we describe a nanoliter-scale oil-air-droplet (OAD) chip for achieving multistep complex sample pretreatment and injection for single cell proteomic analysis in the shotgun mode. By using miniaturized stationary droplet microreaction and manipulation techniques, our system allows all sample pretreatment and injection procedures to be performed in a nanoliter-scale droplet with minimum sample loss and a high sample injection efficiency (>99%), thus substantially increasing the analytical sensitivity for single cell samples. We applied the present system in the proteomic analysis of 100 ± 10, 50 ± 5, 10, and 1 HeLa cell(s), and protein IDs of 1360, 612, 192, and 51 were identified, respectively. The OAD chip-based system was further applied in single mouse oocyte analysis, with 355 protein IDs identified at the single oocyte level, which demonstrated its special advantages of high enrichment of sequence coverage, hydrophobic proteins, and enzymatic digestion efficiency over the traditional in-tube system.
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Affiliation(s)
- Zi-Yi Li
- Institute of Microanalytical Systems, Chemistry Department and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
| | - Min Huang
- National Center for Protein Science (Shanghai), Institute of Biochemistry and Cell Biology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , 200031 , China
| | - Xiu-Kun Wang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science , Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai , 200031 , China
| | - Ying Zhu
- Institute of Microanalytical Systems, Chemistry Department and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
| | - Jin-Song Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science , Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai , 200031 , China
| | - Catherine C L Wong
- Center for Precision Medicine Multi-Omics Research , Peking University Health Science Center , Beijing , 100191 , China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences , Peking University , Beijing , 100191 , China.,National Center for Protein Science (Shanghai), Institute of Biochemistry and Cell Biology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , 200031 , China
| | - Qun Fang
- Institute of Microanalytical Systems, Chemistry Department and Innovation Center for Cell Signaling Network , Zhejiang University , Hangzhou , 310058 , China
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Biswas S, Pal K, Kumar P, Koner AL. A fluorogenic probe for in vitro and in vivo detection of biothiols and vitamin-C with an in-depth mechanistic understanding. SENSORS AND ACTUATORS B: CHEMICAL 2018; 256:186-194. [DOI: 10.1016/j.snb.2017.10.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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Zhang J, Zhou J, Pan R, Jiang D, Burgess JD, Chen HY. New Frontiers and Challenges for Single-Cell Electrochemical Analysis. ACS Sens 2018; 3:242-250. [PMID: 29276834 DOI: 10.1021/acssensors.7b00711] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Previous measurements of cell populations might obscure many important cellular differences, and new strategies for single-cell analyses are urgently needed to re-examine these fundamental biological principles for better diagnosis and treatment of diseases. Electrochemistry is a robust technique for the analysis of single living cells that has the advantages of minor interruption of cellular activity and provides the capability of high spatiotemporal resolution. The achievements of the past 30 years have revealed significant information about the exocytotic events of single cells to elucidate the mechanisms of cellular activity. Currently, the rapid developments of micro/nanofabrication and optoelectronic technologies drive the development of multifunctional electrodes and novel electrochemical approaches with higher resolution for single cells. In this Perspective, three new frontiers in this field, namely, electrochemical microscopy, intracellular analysis, and single-cell analysis in a biological system (i.e., neocortex and retina), are reviewed. The unique features and remaining challenges of these techniques are discussed.
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Affiliation(s)
- Jingjing Zhang
- The
State Key Laboratory of Analytical Chemistry for Life Science, School
of Chemistry and Chemical Engineering, Nanjing University, Jiangsu 210093, China
| | - Junyu Zhou
- The
State Key Laboratory of Analytical Chemistry for Life Science, School
of Chemistry and Chemical Engineering, Nanjing University, Jiangsu 210093, China
| | - Rongrong Pan
- The
State Key Laboratory of Analytical Chemistry for Life Science, School
of Chemistry and Chemical Engineering, Nanjing University, Jiangsu 210093, China
| | - Dechen Jiang
- The
State Key Laboratory of Analytical Chemistry for Life Science, School
of Chemistry and Chemical Engineering, Nanjing University, Jiangsu 210093, China
| | - James D. Burgess
- Department
of Medical Laboratory, Imaging, and Radiologic Sciences, College of
Allied Health Sciences, Augusta University, Augusta, Georgia 30912, United States
| | - Hong-Yuan Chen
- The
State Key Laboratory of Analytical Chemistry for Life Science, School
of Chemistry and Chemical Engineering, Nanjing University, Jiangsu 210093, China
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35
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36
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Sun M, Yang Z, Wawrik B. Metabolomic Fingerprints of Individual Algal Cells Using the Single-Probe Mass Spectrometry Technique. FRONTIERS IN PLANT SCIENCE 2018; 9:571. [PMID: 29760716 PMCID: PMC5936784 DOI: 10.3389/fpls.2018.00571] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/11/2018] [Indexed: 05/21/2023]
Abstract
Traditional approaches for the assessment of physiological responses of microbes in the environment rely on bulk filtration techniques that obscure differences among populations as well as among individual cells. Here, were report on the development on a novel micro-scale sampling device, referred to as the "Single-probe," which allows direct extraction of metabolites from living, individual phytoplankton cells for mass spectrometry (MS) analysis. The Single-probe is composed of dual-bore quartz tubing which is pulled using a laser pipette puller and fused to a silica capillary and a nano-ESI. For this study, we applied Single-probe MS technology to the marine dinoflagellate Scrippsiella trochoidea, assaying cells grown under different illumination levels and under nitrogen (N) limiting conditions as a proof of concept for the technology. In both experiments, significant differences in the cellular metabolome of individual cells could readily be identified, though the vast majority of detected metabolites could not be assigned to KEGG pathways. Using the same approach, significant changes in cellular lipid complements were observed, with individual lipids being both up- and down-regulated under light vs. dark conditions. Conversely, lipid content increased across the board under N limitation, consistent with an adjustment of Redfield stoichiometry to reflect higher C:N and C:P ratios. Overall, these data suggest that the Single-probe MS technique has the potential to allow for near in situ metabolomic analysis of individual phytoplankton cells, opening the door to targeted analyses that minimize cell manipulation and sampling artifacts, while preserving metabolic variability at the cellular level.
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Affiliation(s)
- Mei Sun
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Boris Wawrik
- Department of Botany and Microbiology, University of Oklahoma, Norman, OK, United States
- *Correspondence: Boris Wawrik,
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37
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Labas V, Teixeira-Gomes AP, Bouguereau L, Gargaros A, Spina L, Marestaing A, Uzbekova S. Intact cell MALDI-TOF mass spectrometry on single bovine oocyte and follicular cells combined with top-down proteomics: A novel approach to characterise markers of oocyte maturation. J Proteomics 2017; 175:56-74. [PMID: 28385661 DOI: 10.1016/j.jprot.2017.03.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 02/23/2017] [Accepted: 03/31/2017] [Indexed: 12/18/2022]
Abstract
Intact cell MALDI-TOF mass spectrometry (ICM-MS) was adapted to bovine follicular cells from individual ovarian follicles to obtain the protein/peptide signatures (<17kDa) of single oocytes, cumulus cells (CC) and granulosa cells (GC), which shared a total of 439 peaks. By comparing the ICM-MS profiles of single oocytes and CC before and after in vitro maturation (IVM), 71 different peaks were characterised, and their relative abundance was found to vary depending on the stage of oocyte meiotic maturation. To identify these endogenous biomolecules, top-down workflow using high resolution MS/MS (TD HR-MS) was performed on the protein extracts from oocytes, CC and GC. The TD HR-MS proteomic approach allowed for: (1) identification of 386 peptide/proteoforms encoded by 194 genes; and (2) characterisation of proteolysis products likely resulting from the action of kallikreins and caspases. In total, 136 peaks observed by ICM-MS were annotated by TD HR-MS (ProteomeXchange PXD004892). Among these, 16 markers of maturation were identified, including IGF2 binding protein 3 and hemoglobin B in the oocyte, thymosins beta-4 and beta-10, histone H2B and ubiquitin in CC. The combination of ICM-MS and TD HR-MS proved to be a suitable strategy to identify non-invasive markers of oocyte quality using limited biological samples. BIOLOGICAL SIGNIFICANCE Intact cell MALDI-TOF mass spectrometry on single oocytes and their surrounding cumulus cells, coupled to an optimised top-down HR-MS proteomic approach on ovarian follicular cells, was used to identify specific markers of oocyte meiotic maturation represented by whole low molecular weight proteins or products of degradation by specific proteases.
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Affiliation(s)
- Valérie Labas
- UMR PRC, INRA 85, CNRS, Université de Tours, IFCE, 37380 Nouzilly, France; INRA, Plateforme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, 37380 Nouzilly, France
| | - Ana-Paula Teixeira-Gomes
- UMR ISP, INRA, Université de Tours, 37380 Nouzilly, France; INRA, Plateforme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, 37380 Nouzilly, France
| | - Laura Bouguereau
- UMR ISP, INRA, Université de Tours, 37380 Nouzilly, France; INRA, Plateforme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, 37380 Nouzilly, France
| | - Audrey Gargaros
- UMR PRC, INRA 85, CNRS, Université de Tours, IFCE, 37380 Nouzilly, France; INRA, Plateforme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, 37380 Nouzilly, France
| | - Lucie Spina
- INRA, Plateforme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, 37380 Nouzilly, France; INSA/CNRS 5504 - UMR INSA/INRA 792, Toulouse, France
| | - Aurélie Marestaing
- UMR PRC, INRA 85, CNRS, Université de Tours, IFCE, 37380 Nouzilly, France; INRA, Plateforme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, 37380 Nouzilly, France
| | - Svetlana Uzbekova
- UMR PRC, INRA 85, CNRS, Université de Tours, IFCE, 37380 Nouzilly, France; INRA, Plateforme d'Analyse Intégrative des Biomolécules, Laboratoire de Spectrométrie de Masse, 37380 Nouzilly, France.
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Abstract
The development of more intricate devices for the analysis of small molecules and protein activity in single cells would advance our knowledge of cellular heterogeneity and signaling cascades. Therefore, in this study, a nanokit was produced by filling a nanometer-sized capillary with a ring electrode at the tip with components from traditional kits, which could be egressed outside the capillary by electrochemical pumping. At the tip, femtoliter amounts of the kit components were reacted with the analyte to generate hydrogen peroxide for the electrochemical measurement by the ring electrode. Taking advantage of the nanotip and small volume injection, the nanokit was easily inserted into a single cell to determine the intracellular glucose levels and sphingomyelinase (SMase) activity, which had rarely been achieved. High cellular heterogeneities of these two molecules were observed, showing the significance of the nanokit. Compared with the current methods that use a complicated structural design or surface functionalization for the recognition of the analytes, the nanokit has adapted features of the well-established kits and integrated the kit components and detector in one nanometer-sized capillary, which provides a specific device to characterize the reactivity and concentrations of cellular compounds in single cells.
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39
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Sun L, Dubiak KM, Peuchen EH, Zhang Z, Zhu G, Huber PW, Dovichi NJ. Single Cell Proteomics Using Frog (Xenopus laevis) Blastomeres Isolated from Early Stage Embryos, Which Form a Geometric Progression in Protein Content. Anal Chem 2016; 88:6653-7. [PMID: 27314579 DOI: 10.1021/acs.analchem.6b01921] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Single cell analysis is required to understand cellular heterogeneity in biological systems. We propose that single cells (blastomeres) isolated from early stage invertebrate, amphibian, or fish embryos are ideal model systems for the development of technologies for single cell analysis. For these embryos, although cell cleavage is not exactly symmetric, the content per blastomere decreases roughly by half with each cell division, creating a geometric progression in cellular content. This progression forms a ladder of single-cell targets for the development of successively higher sensitivity instruments. In this manuscript, we performed bottom-up proteomics on single blastomeres isolated by microdissection from 2-, 4-, 8-, 16-, 32-, and 50-cell Xenopus laevis (African clawed frog) embryos. Over 1 400 protein groups were identified in single-run reversed-phase liquid chromatography-electrospray ionization-tandem mass spectrometry from single balstomeres isolated from a 16-cell embryo. When the mass of yolk-free proteins in single blastomeres decreased from ∼0.8 μg (16-cell embryo) to ∼0.2 μg (50-cell embryo), the number of protein group identifications declined from 1 466 to 644. Around 800 protein groups were quantified across four blastomeres isolated from a 16-cell embryo. By comparing the protein expression among different blastomeres, we observed that the blastomere-to-blastomere heterogeneity in 8-, 16-, 32-, and 50-cell embryos increases with development stage, presumably due to cellular differentiation. These results suggest that comprehensive quantitative proteomics on single blastomeres isolated from these early stage embryos can provide valuable insights into cellular differentiation and organ development.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Kyle M Dubiak
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Elizabeth H Peuchen
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Zhenbin Zhang
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Paul W Huber
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame , Notre Dame, Indiana 46556, United States
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40
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Gavasso S, Gullaksen SE, Skavland J, Gjertsen BT. Single-cell proteomics: potential implications for cancer diagnostics. Expert Rev Mol Diagn 2016; 16:579-89. [DOI: 10.1586/14737159.2016.1156531] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Sonia Gavasso
- Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | | | - Jørn Skavland
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Bjørn T. Gjertsen
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Translational Hemato-Oncology Group, University of Bergen, Bergen, Norway
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Konry T, Sarkar S, Sabhachandani P, Cohen N. Innovative Tools and Technology for Analysis of Single Cells and Cell-Cell Interaction. Annu Rev Biomed Eng 2016; 18:259-84. [PMID: 26928209 DOI: 10.1146/annurev-bioeng-090215-112735] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Heterogeneity in single-cell responses and intercellular interactions results from complex regulation of cell-intrinsic and environmental factors. Single-cell analysis allows not only detection of individual cellular characteristics but also correlation of genetic content with phenotypic traits in the same cell. Technological advances in micro- and nanofabrication have benefited single-cell analysis by allowing precise control of the localized microenvironment, cell manipulation, and sensitive detection capabilities. Additionally, microscale techniques permit rapid, high-throughput, multiparametric screening that has become essential for -omics research. This review highlights innovative applications of microscale platforms in genetic, proteomic, and metabolic detection in single cells; cell sorting strategies; and heterotypic cell-cell interaction. We discuss key design aspects of single-cell localization and isolation in microfluidic systems, dynamic and endpoint analyses, and approaches that integrate highly multiplexed detection of various intracellular species.
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Affiliation(s)
- Tania Konry
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
| | - Saheli Sarkar
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
| | - Pooja Sabhachandani
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
| | - Noa Cohen
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
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Guo XF, Arceo J, Huge BJ, Ludwig KR, Dovichi NJ. Chemical cytometry of thiols using capillary zone electrophoresis-laser induced fluorescence and TMPAB-o-M, an improved fluorogenic reagent. Analyst 2016; 141:1325-30. [PMID: 26814594 PMCID: PMC4747679 DOI: 10.1039/c5an02116b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Low molecular weight thiol compounds play crucial roles in many physiological processes. Most methods for determination of thiol compounds are population-averaged; few methods for quantification of thiol compounds in single cells have been reported. We report an ultrasensitive method for determination of thiol compounds in single cells by use of 1,3,5,7-tetramethyl-8-phenyl-(2-maleimide)-difluoroboradiaza-s-indacene (TMPAB-o-M), a fluorogenic probe with useful spectral properties, coupled with capillary zone electrophoresis and laser induced fluorescence detection using a post-column sheath flow cuvette. TMPAB-o-M provides low background, high sensitivity, and excellent reactivity. After optimization of the separation method, we achieved baseline separation of labeled glutathione (GSH), cysteine (Cys), homocysteine, and γ-glutamylcysteine within 11 min, and produced concentration limits of detection from 10 to 20 pM and mass LODs of 65 to 100 zmol. The method was applied for analysis of thiol containing compounds in both cell homogenates and in single HCT-29 and MCF-10A cells. GSH was the main thiol, and Cys was also detected in both cell types. Cells were treated with N-ethylmaleimide, which significantly attenuated thiol levels.
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Affiliation(s)
- Xiao-Feng Guo
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA. and Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Jennifer Arceo
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Bonnie Jaskowski Huge
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Katelyn R Ludwig
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Norman J Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
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Chen D, Fan F, Zhao X, Xu F, Chen P, Wang J, Ban L, Liu Z, Feng X, Zhang Y, Liu BF. Single Cell Chemical Proteomics with Membrane-Permeable Activity-Based Probe for Identification of Functional Proteins in Lysosome of Tumors. Anal Chem 2016; 88:2466-71. [DOI: 10.1021/acs.analchem.5b04645] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Dongjuan Chen
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Fengkai Fan
- Hubei
Key Laboratory of Purification and Application of Plant Anti-Cancer
Ingredients, College of Chemistry and Life Science, Hubei University of Education, Wuhan, 430205, China
| | - Xingfu Zhao
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Fei Xu
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Peng Chen
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jie Wang
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Lin Ban
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhihua Liu
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xiaojun Feng
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yuhui Zhang
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Bi-Feng Liu
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
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Cahill JF, Darlington TK, Fitzgerald C, Schoepp NG, Beld J, Burkart MD, Prather KA. Online Analysis of Single Cyanobacteria and Algae Cells under Nitrogen-Limited Conditions Using Aerosol Time-of-Flight Mass Spectrometry. Anal Chem 2015; 87:8039-46. [DOI: 10.1021/acs.analchem.5b02326] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- John F. Cahill
- Department
of Chemistry and Biochemistry, University of California, La Jolla, California 92093, United States
| | | | | | - Nathan G. Schoepp
- Department
of Chemistry and Biochemistry, University of California, La Jolla, California 92093, United States
| | - Joris Beld
- Department
of Chemistry and Biochemistry, University of California, La Jolla, California 92093, United States
| | - Michael D. Burkart
- Department
of Chemistry and Biochemistry, University of California, La Jolla, California 92093, United States
| | - Kimberly A. Prather
- Department
of Chemistry and Biochemistry, University of California, La Jolla, California 92093, United States
- Scripps
Institution of Oceanography, University of California, La Jolla, California 92093, United States
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Xu F, Zhao H, Feng X, Chen L, Chen D, Zhang Y, Nan F, Liu J, Liu BF. Single-cell chemical proteomics with an activity-based probe: identification of low-copy membrane proteins on primary neurons. Angew Chem Int Ed Engl 2014; 53:6730-3. [PMID: 24850238 DOI: 10.1002/anie.201402363] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/24/2014] [Indexed: 11/08/2022]
Abstract
We propose a novel single-cell chemical proteomics (SCCP) strategy to profile low-abundance membrane proteins in single cells. In this approach, the membrane protein GB1 and its splicing variants were targeted on cultured cell lines and primary neurons using a specifically designed activity-based probe. The functionally labeled single cells were encapsulated in individual buffer droplets on a PDMS microwell array, and were further picked up one at a time and loaded into a capillary electrophoresis system for cell lysis, separation, and laser-induced fluorescence detection of the targeted proteins. The results revealed the expression of GB1 splicing variants in HEK and MEF cells, which was previously only suggested at the transcriptional level. We further applied this method to investigate single primary cells and observed significant heterogeneity among individual mouse cerebellar granule neurons. Interference experiments with GB1 antagonist and agonist validated this observation.
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Affiliation(s)
- Fei Xu
- Wuhan National Laboratory for Optoelectronics-, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074 (China)
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Xu F, Zhao H, Feng X, Chen L, Chen D, Zhang Y, Nan F, Liu J, Liu BF. Single-Cell Chemical Proteomics with an Activity-Based Probe: Identification of Low-Copy Membrane Proteins on Primary Neurons. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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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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Sun L, Zhu G, Yan X, Champion MM, Dovichi NJ. Capillary zone electrophoresis for analysis of complex proteomes using an electrokinetically pumped sheath flow nanospray interface. Proteomics 2014; 14:622-8. [PMID: 24277677 PMCID: PMC3947435 DOI: 10.1002/pmic.201300295] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 08/18/2013] [Accepted: 09/02/2013] [Indexed: 12/14/2022]
Abstract
The vast majority of proteomic studies employ RP-HPLC coupled with MS/MS for analysis of the tryptic digest of a cellular lysate. This technology is quite mature, and typically provides identification of hundreds to thousands of peptides, which is used to infer the identity of hundreds to thousands of proteins. These studies usually require milligrams to micrograms of starting material. CZE provides an interesting alternative separation method based on a different separation mechanism than HPLC. CE received some attention for protein analysis beginning 25 years ago. Those efforts stalled because of the limited performance of the electrospray interfaces and the limited speed and sensitivity of mass spectrometers of that era. This review considers a new electrospray interface design coupled with Orbitrap Velos and linear Q-trap mass spectrometers. CZE coupled with this interface and these detectors provides single shot detection of >1250 peptides from an Escherichia coli digest in less than 1 h, identification of nearly 5000 peptides from analysis of seven fractions produced by SPE of the E. coli digest in a 6 h total analysis time, low attomole detection limits for peptides generated from standard proteins, and high zeptomole detection limits for selected ion monitoring of peptides. Incorporation of an integrated on-line immobilized trypsin microreactor allows digestion and analysis of picogram amounts of a complex eukaryotic proteome.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
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49
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Sun L, Li Y, Champion MM, Zhu G, Wojcik R, Dovichi NJ. Capillary zone electrophoresis-multiple reaction monitoring from 100 pg of RAW 264.7 cell lysate digest. Analyst 2013; 138:3181-8. [PMID: 23591184 DOI: 10.1039/c3an00287j] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Capillary zone electrophoresis-multiple/single reaction monitoring (CZE-MRM/SRM), which employed an electrokinetically driven sheath-flow electrospray interface, was used for the rapid and highly sensitive detection of protein analytes in complex tryptic digests. MRM channels were developed against a commercial exponential mixture of bovine proteins. Five proteins spanning four orders of magnitude concentration range were confidently detected from only 2.5 ng of the digest mixture; the mass detection limits (S/N = 3) of two detected proteins, alpha-casein and glutamate dehydrogenase were about 600 zmol and 30 amol, respectively. This technique was then applied to a RAW 264.7 cell lysate digest. Three proteins were confidently and reproducibly detected from 100 pg of this digest. The sample amount corresponds to the approximate protein content from a single cell, which suggests that CZE-MRM may be a useful analytical tool in chemical cytometry. In addition to providing highly sensitive detection of proteins in complex mixtures, this system is highly rapid; migration time of the protein digests was less than 10 min.
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Affiliation(s)
- Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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