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Ledvina V, Janečková E, Matalová E, Klepárník K. Parallel single-cell analysis of active caspase-3/7 in apoptotic and non-apoptotic cells. Anal Bioanal Chem 2016; 409:269-274. [PMID: 27757513 DOI: 10.1007/s00216-016-9998-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 09/08/2016] [Accepted: 09/30/2016] [Indexed: 01/17/2023]
Abstract
Analysing the chemical content of individual cells has already been proven to reveal unique information on various biological processes. Single-cell analysis provides more accurate and reliable results for biology and medicine than analyses of extracts from cell populations, where a natural heterogeneity is averaged. To meet the requirements in the research of important biologically active molecules, such as caspases, we have developed a miniaturized device for simultaneous analyses of individual cells. A stainless steel body with a carousel holder enables high-sensitivity parallel detections in eight microvials. The holder is mounted in front of a photomultiplier tube with cooled photocathode working in photon counting mode. The detection of active caspase-3/7, central effector caspases in apoptosis, in single cells is based on the bioluminescence chemistry commercially available as Caspase-Glo® 3/7 reagent developed by Promega. Individual cells were captured from a culture medium under microscope and transferred by micromanipulator into detection microvial filled with the reagent. As a result of testing, the limits of detection and quantification were determined to be 0.27/0.86 of active caspase-3/7 content in an average apoptotic cell and 0.46/2.92 for non-apoptotic cells. Application potential of this technology in laboratory diagnostics and related medical research is discussed. Graphical abstract Miniaturized device for simultaneous analyses of individual cells.
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Affiliation(s)
- Vojtěch Ledvina
- Institute of Analytical Chemistry, v.v.i., Czech Academy of Sciences, Veveří 97, 60200, Brno, Czech Republic.,Faculty of Science, Masaryk University, Kotlářská 267/2, 61137, Brno, Czech Republic
| | - Eva Janečková
- Faculty of Science, Masaryk University, Kotlářská 267/2, 61137, Brno, Czech Republic.,Institute of Animal Physiology and Genetics, v.v.i., Czech Academy of Sciences, Veveří 97, 60200, Brno, Czech Republic
| | - Eva Matalová
- Institute of Animal Physiology and Genetics, v.v.i., Czech Academy of Sciences, Veveří 97, 60200, Brno, Czech Republic.,Department of Physiology, University of Veterinary and Pharmaceutical Sciences, Palackého 1/3, 61242, Brno, Czech Republic
| | - Karel Klepárník
- Institute of Analytical Chemistry, v.v.i., Czech Academy of Sciences, Veveří 97, 60200, Brno, Czech Republic.
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52
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Ahrberg CD, Manz A, Chung BG. Polymerase chain reaction in microfluidic devices. LAB ON A CHIP 2016; 16:3866-3884. [PMID: 27713993 DOI: 10.1039/c6lc00984k] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The invention of the polymerase chain reaction (PCR) has caused a revolution in molecular biology, giving access to a method of amplifying deoxyribonucleic acid (DNA) molecules across several orders of magnitude. Since the first application of PCR in a microfluidic device was developed in 1998, an increasing number of researchers have continued the development of microfluidic PCR systems. In this review, we introduce recent developments in microfluidic-based space and time domain devices as well as discuss various designs integrated with multiple functions for sample preparation and detection. The development of isothermal nucleic acid amplification and digital PCR microfluidic devices within the last five years is also highlighted. Furthermore, we introduce various commercial microfluidic PCR devices.
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Affiliation(s)
| | - Andreas Manz
- Microfluidics group, KIST-Europe, Saarbrücken, Germany and Mechanotronics Department, Universität des Saarlandes, Saarbrücken, Germany
| | - Bong Geun Chung
- Department of Mechanical Engineering, Sogang University, Seoul, Korea.
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53
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Chen HIH, Jin Y, Huang Y, Chen Y. Detection of high variability in gene expression from single-cell RNA-seq profiling. BMC Genomics 2016; 17 Suppl 7:508. [PMID: 27556924 PMCID: PMC5001205 DOI: 10.1186/s12864-016-2897-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background The advancement of the next-generation sequencing technology enables mapping gene expression at the single-cell level, capable of tracking cell heterogeneity and determination of cell subpopulations using single-cell RNA sequencing (scRNA-seq). Unlike the objectives of conventional RNA-seq where differential expression analysis is the integral component, the most important goal of scRNA-seq is to identify highly variable genes across a population of cells, to account for the discrete nature of single-cell gene expression and uniqueness of sequencing library preparation protocol for single-cell sequencing. However, there is lack of generic expression variation model for different scRNA-seq data sets. Hence, the objective of this study is to develop a gene expression variation model (GEVM), utilizing the relationship between coefficient of variation (CV) and average expression level to address the over-dispersion of single-cell data, and its corresponding statistical significance to quantify the variably expressed genes (VEGs). Results We have built a simulation framework that generated scRNA-seq data with different number of cells, model parameters, and variation levels. We implemented our GEVM and demonstrated the robustness by using a set of simulated scRNA-seq data under different conditions. We evaluated the regression robustness using root-mean-square error (RMSE) and assessed the parameter estimation process by varying initial model parameters that deviated from homogeneous cell population. We also applied the GEVM on real scRNA-seq data to test the performance under distinct cases. Conclusions In this paper, we proposed a gene expression variation model that can be used to determine significant variably expressed genes. Applying the model to the simulated single-cell data, we observed robust parameter estimation under different conditions with minimal root mean square errors. We also examined the model on two distinct scRNA-seq data sets using different single-cell protocols and determined the VEGs. Obtaining VEGs allowed us to observe possible subpopulations, providing further evidences of cell heterogeneity. With the GEVM, we can easily find out significant variably expressed genes in different scRNA-seq data sets.
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Affiliation(s)
- Hung-I Harry Chen
- Greehey Children`s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.,Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Yufang Jin
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Yufei Huang
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX, 78249, USA.
| | - Yidong Chen
- Greehey Children`s Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA. .,Department of Epidemiology and Biostatistics, The University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229, USA.
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54
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Single-cell multimodal profiling reveals cellular epigenetic heterogeneity. Nat Methods 2016; 13:833-6. [PMID: 27525975 DOI: 10.1038/nmeth.3961] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/08/2016] [Indexed: 12/21/2022]
Abstract
Sample heterogeneity often masks DNA methylation signatures in subpopulations of cells. Here, we present a method to genotype single cells while simultaneously interrogating gene expression and DNA methylation at multiple loci. We used this targeted multimodal approach, implemented on an automated, high-throughput microfluidic platform, to assess primary lung adenocarcinomas and human fibroblasts undergoing reprogramming by profiling epigenetic variation among cell types identified through genotyping and transcriptional analysis.
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55
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Nashimoto Y, Takahashi Y, Zhou Y, Ito H, Ida H, Ino K, Matsue T, Shiku H. Evaluation of mRNA Localization Using Double Barrel Scanning Ion Conductance Microscopy. ACS NANO 2016; 10:6915-6922. [PMID: 27399804 DOI: 10.1021/acsnano.6b02753] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Information regarding spatial mRNA localization in single cells is necessary for a better understanding of cellular functions in tissues. Here, we report a method for evaluating localization of mRNA in single cells using double-barrel scanning ion conductance microscopy (SICM). Two barrels in a nanopipette were filled with aqueous and organic electrolyte solutions and used for SICM and as an electrochemical syringe, respectively. We confirmed that the organic phase barrel could be used to collect cytosol from living cells, which is a minute but sufficient amount to assess cellular status using qPCR analysis. The water phase barrel could be used for SICM to image topography with subcellular resolution, which could be used to determine positions for analyzing mRNA expression. This system was able to evaluate mRNA localization in single cells. After puncturing the cellular membrane in a minimally invasive manner, using SICM imaging as a guide, we collected a small amount cytosol from different positions within a single cell and showed that mRNA expression depends on cellular position. In this study, we show that SICM imaging can be utilized for the analysis of mRNA localization in single cells. In addition, we fully automated the pipet movement in the XYZ-directions during the puncturing processes, making it applicable as a high-throughput system for collecting cytosol and analyzing mRNA localization.
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Affiliation(s)
| | - Yasufumi Takahashi
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST) , Saitama 332-0012, Japan
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56
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Rakszewska A, Stolper RJ, Kolasa AB, Piruska A, Huck WTS. Quantitative Single-Cell mRNA Analysis in Hydrogel Beads. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601969] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Agata Rakszewska
- Institute for Molecules and Materials; Radboud University Nijmegen; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Rosa J. Stolper
- Institute for Molecules and Materials; Radboud University Nijmegen; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Anna B. Kolasa
- Warsaw University of Life Sciences-SGGW; Nowoursynowska 166 ST 02-787 Warszawa Poland
| | - Aigars Piruska
- Institute for Molecules and Materials; Radboud University Nijmegen; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and Materials; Radboud University Nijmegen; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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57
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Rakszewska A, Stolper RJ, Kolasa AB, Piruska A, Huck WTS. Quantitative Single-Cell mRNA Analysis in Hydrogel Beads. Angew Chem Int Ed Engl 2016; 55:6698-701. [PMID: 27075637 DOI: 10.1002/anie.201601969] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Indexed: 01/05/2023]
Abstract
In recent years, technologies capable of analyzing single cells have emerged that are transforming many fields of biological research. Herein we report how DNA-functionalized hydrogel beads can serve as a matrix to capture mRNA from lysed single cells. mRNA quantification free of pre-amplification bias is ensured by using padlock probes and rolling circle amplification followed by hybridization with fluorescent probes. The number of transcripts in individual cells is assessed by simply counting fluorescent dots inside gel beads. The method extends the potential of existing techniques and provides a general platform for capturing molecules of interest from single cells.
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Affiliation(s)
- Agata Rakszewska
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Rosa J Stolper
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Anna B Kolasa
- Warsaw University of Life Sciences-SGGW, Nowoursynowska 166 ST, 02-787, Warszawa, Poland
| | - Aigars Piruska
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands.
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58
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Picoliter Well Array Chip-Based Digital Recombinase Polymerase Amplification for Absolute Quantification of Nucleic Acids. PLoS One 2016; 11:e0153359. [PMID: 27074005 PMCID: PMC4830604 DOI: 10.1371/journal.pone.0153359] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 03/29/2016] [Indexed: 11/28/2022] Open
Abstract
Absolute, precise quantification methods expand the scope of nucleic acids research and have many practical applications. Digital polymerase chain reaction (dPCR) is a powerful method for nucleic acid detection and absolute quantification. However, it requires thermal cycling and accurate temperature control, which are difficult in resource-limited conditions. Accordingly, isothermal methods, such as recombinase polymerase amplification (RPA), are more attractive. We developed a picoliter well array (PWA) chip with 27,000 consistently sized picoliter reactions (314 pL) for isothermal DNA quantification using digital RPA (dRPA) at 39°C. Sample loading using a scraping liquid blade was simple, fast, and required small reagent volumes (i.e., <20 μL). Passivating the chip surface using a methoxy-PEG-silane agent effectively eliminated cross-contamination during dRPA. Our creative optical design enabled wide-field fluorescence imaging in situ and both end-point and real-time analyses of picoliter wells in a 6-cm2 area. It was not necessary to use scan shooting and stitch serial small images together. Using this method, we quantified serial dilutions of a Listeria monocytogenes gDNA stock solution from 9 × 10-1 to 4 × 10-3 copies per well with an average error of less than 11% (N = 15). Overall dRPA-on-chip processing required less than 30 min, which was a 4-fold decrease compared to dPCR, requiring approximately 2 h. dRPA on the PWA chip provides a simple and highly sensitive method to quantify nucleic acids without thermal cycling or precise micropump/microvalve control. It has applications in fast field analysis and critical clinical diagnostics under resource-limited settings.
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59
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Kim J, Stockton AM, Jensen EC, Mathies RA. Pneumatically actuated microvalve circuits for programmable automation of chemical and biochemical analysis. LAB ON A CHIP 2016; 16:812-9. [PMID: 26864083 DOI: 10.1039/c5lc01397f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Programmable microfluidic platforms (PMPs) are enabling significant advances in the utility of microfluidics for chemical and biochemical analysis. Traditional microfluidic devices are analogous to application-specific devices--a new device is needed to implement each new chemical or biochemical assay. PMPs are analogous to digital electronic processors--all that is needed to implement a new assay is a change in the order of operations conducted by the device. In this review, we introduce PMPs based on normally-closed microvalves. We discuss recent applications of PMPs in diverse fields including genetic analysis, antibody-based biomarker analysis, and chemical analysis in planetary exploration. Prospects, challenges, and future concepts for this emerging technology will also be presented.
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Affiliation(s)
- Jungkyu Kim
- Department of Mechanical Engineering, Texas Tech University, Lubbock, TX, USA
| | - Amanda M Stockton
- Department of Chemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | - Richard A Mathies
- Department of Chemistry, University of California, Berkeley, CA 94720, USA.
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60
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Liu S, Gong H, Wang Y, Wang L. Label-free electrochemical nucleic acid biosensing by tandem polymerization and cleavage-mediated cascade target recycling and DNAzyme amplification. Biosens Bioelectron 2016; 77:818-23. [DOI: 10.1016/j.bios.2015.10.056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 10/18/2015] [Accepted: 10/19/2015] [Indexed: 12/12/2022]
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61
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Ezra E, Maor I, Bavli D, Shalom I, Levy G, Prill S, Jaeger MS, Nahmias Y. Microprocessor-based integration of microfluidic control for the implementation of automated sensor monitoring and multithreaded optimization algorithms. Biomed Microdevices 2016; 17:82. [PMID: 26227212 DOI: 10.1007/s10544-015-9989-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Microfluidic applications range from combinatorial synthesis to high throughput screening, with platforms integrating analog perfusion components, digitally controlled micro-valves and a range of sensors that demand a variety of communication protocols. Currently, discrete control units are used to regulate and monitor each component, resulting in scattered control interfaces that limit data integration and synchronization. Here, we present a microprocessor-based control unit, utilizing the MS Gadgeteer open framework that integrates all aspects of microfluidics through a high-current electronic circuit that supports and synchronizes digital and analog signals for perfusion components, pressure elements, and arbitrary sensor communication protocols using a plug-and-play interface. The control unit supports an integrated touch screen and TCP/IP interface that provides local and remote control of flow and data acquisition. To establish the ability of our control unit to integrate and synchronize complex microfluidic circuits we developed an equi-pressure combinatorial mixer. We demonstrate the generation of complex perfusion sequences, allowing the automated sampling, washing, and calibrating of an electrochemical lactate sensor continuously monitoring hepatocyte viability following exposure to the pesticide rotenone. Importantly, integration of an optical sensor allowed us to implement automated optimization protocols that require different computational challenges including: prioritized data structures in a genetic algorithm, distributed computational efforts in multiple-hill climbing searches and real-time realization of probabilistic models in simulated annealing. Our system offers a comprehensive solution for establishing optimization protocols and perfusion sequences in complex microfluidic circuits.
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Affiliation(s)
- Elishai Ezra
- Grass Center for Bioengineering, The Hebrew University of Jerusalem, Edmond J. Safra Campus, 91904, Jerusalem, Israel
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Affiliation(s)
- Sanjin Hosic
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| | - Shashi K. Murthy
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, USA
| | - Abigail N. Koppes
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
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63
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SUN HAO, LI ZHANDONG, TAO JIANGUO. INTEGRATED 3D MULTI-PHYSICAL SIMULATION OF A MICROFLUIDIC SYSTEM USING FINITE ELEMENT ANALYSIS. J MECH MED BIOL 2015. [DOI: 10.1142/s0219519415400436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Microfluidics technology has emerged as an attractive approach in physics, chemistry and biomedical science by providing increased analytical accuracy, sensitivity and efficiency in minimized systems. Numerical simulation can improve theoretical understanding, reduce prototyping consumption, and speed up development. In this paper, we setup a 3D model of an integrated microfluidic system and study the multi-physical dynamics of the system via the finite element method (FEM). The fluid–structure interaction (FSI) of fluid and an immobilized single cell within the cell trapping component, and the on-chip thermodynamics have been analyzed. The velocity magnitude and streamline of flow field, the distribution of von Mises stress and Tresca stress on the FSI interface have been studied. In addition, the on-chip heat transfer performance and temperature distribution in the heating zone have been evaluated and analyzed respectively. The presented approach is capable of optimizing microfluidic design, and revealing the complicated mechanism of multi-physical fields. Therefore, it holds the potential for improving microfluidics application in fundamental research and clinical settings.
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Affiliation(s)
- HAO SUN
- School of Mechatronics Engineering Harbin Institute of Technology Harbin 150001, Heilongjiang, P. R. China
| | - ZHANDONG LI
- School of Mechatronics Engineering Harbin Institute of Technology Harbin 150001, Heilongjiang, P. R. China
| | - JIANGUO TAO
- School of Mechatronics Engineering Harbin Institute of Technology Harbin 150001, Heilongjiang, P. R. China
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64
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Cell type specific gene expression analysis of prostate needle biopsies resolves tumor tissue heterogeneity. Oncotarget 2015; 6:1302-14. [PMID: 25514598 PMCID: PMC4359234 DOI: 10.18632/oncotarget.2744] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/11/2014] [Indexed: 12/21/2022] Open
Abstract
A lack of cell surface markers for the specific identification, isolation and subsequent analysis of living prostate tumor cells hampers progress in the field. Specific characterization of tumor cells and their microenvironment in a multi-parameter molecular assay could significantly improve prognostic accuracy for the heterogeneous prostate tumor tissue. Novel functionalized gold-nano particles allow fluorescence-based detection of absolute mRNA expression levels in living cells by fluorescent activated flow cytometry (FACS). We use of this technique to separate prostate tumor and benign cells in human prostate needle biopsies based on the expression levels of the tumor marker alpha-methylacyl-CoA racemase (AMACR). We combined RNA and protein detection of living cells by FACS to gate for epithelial cell adhesion molecule (EPCAM) positive tumor and benign cells, EPCAM/CD45 double negative mesenchymal cells and CD45 positive infiltrating lymphocytes. EPCAM positive epithelial cells were further sub-gated into AMACR high and low expressing cells. Two hundred cells from each population and several biopsies from the same patient were analyzed using a multiplexed gene expression profile to generate a cell type resolved profile of the specimen. This technique provides the basis for the clinical evaluation of cell type resolved gene expression profiles as pre-therapeutic prognostic markers for prostate cancer.
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65
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Ong SG, Huber BC, Lee WH, Kodo K, Ebert AD, Ma Y, Nguyen PK, Diecke S, Chen WY, Wu JC. Microfluidic Single-Cell Analysis of Transplanted Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes After Acute Myocardial Infarction. Circulation 2015; 132:762-771. [PMID: 26304668 DOI: 10.1161/circulationaha.114.015231] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Human induced pluripotent stem cells (iPSCs) are attractive candidates for therapeutic use, with the potential to replace deficient cells and to improve functional recovery in injury or disease settings. Here, we test the hypothesis that human iPSC-derived cardiomyocytes (iPSC-CMs) can secrete cytokines as a molecular basis to attenuate adverse cardiac remodeling after myocardial infarction. METHODS AND RESULTS Human iPSCs were generated from skin fibroblasts and differentiated in vitro with a small molecule-based protocol. Troponin(+) iPSC-CMs were confirmed by immunohistochemistry, quantitative polymerase chain reaction, fluorescence-activated cell sorting, and electrophysiological measurements. Afterward, 2×10(6) iPSC-CMs derived from a cell line transduced with a vector expressing firefly luciferase and green fluorescent protein were transplanted into adult NOD/SCID mice with acute left anterior descending artery ligation. Control animals received PBS injection. Bioluminescence imaging showed limited engraftment on transplantation into ischemic myocardium. However, magnetic resonance imaging of animals transplanted with iPSC-CMs showed significant functional improvement and attenuated cardiac remodeling compared with PBS-treated control animals. To understand the underlying molecular mechanism, microfluidic single-cell profiling of harvested iPSC-CMs, laser capture microdissection of host myocardium, and in vitro ischemia stimulation were used to demonstrate that the iPSC-CMs could release significant levels of proangiogenic and antiapoptotic factors in the ischemic microenvironment. CONCLUSIONS Transplantation of human iPSC-CMs into an acute mouse myocardial infarction model can improve left ventricular function and attenuate cardiac remodeling. Because of limited engraftment, most of the effects are possibly explained by paracrine activity of these cells.
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Affiliation(s)
- Sang-Ging Ong
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA.,Depts of Medicine and Radiology, Stanford University School of Medicine, Stanford, CA.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA
| | - Bruno C Huber
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA.,Depts of Medicine and Radiology, Stanford University School of Medicine, Stanford, CA.,Ludwig-Maximilians-University, Medical Department I, Campus Grosshadern, Munich, Germany
| | - Won Hee Lee
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA.,Depts of Medicine and Radiology, Stanford University School of Medicine, Stanford, CA
| | - Kazuki Kodo
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA.,Depts of Medicine and Radiology, Stanford University School of Medicine, Stanford, CA
| | - Antje D Ebert
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA.,Depts of Medicine and Radiology, Stanford University School of Medicine, Stanford, CA
| | - Yu Ma
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA.,Depts of Medicine and Radiology, Stanford University School of Medicine, Stanford, CA
| | - Patricia K Nguyen
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA.,Depts of Medicine and Radiology, Stanford University School of Medicine, Stanford, CA
| | - Sebastian Diecke
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA.,Depts of Medicine and Radiology, Stanford University School of Medicine, Stanford, CA
| | - Wen-Yi Chen
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA.,Depts of Medicine and Radiology, Stanford University School of Medicine, Stanford, CA
| | - Joseph C Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA.,Depts of Medicine and Radiology, Stanford University School of Medicine, Stanford, CA.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA
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Chandran Y, Kang NY, Park SJ, Husen Alamudi S, Kim JY, Sahu S, Su D, Lee J, Vendrell M, Chang YT. A highly selective fluorescent probe for direct detection and isolation of mouse embryonic stem cells. Bioorg Med Chem Lett 2015; 25:4862-4865. [PMID: 26115574 PMCID: PMC4613884 DOI: 10.1016/j.bmcl.2015.06.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 02/06/2023]
Abstract
Stem cell research has gathered immense attention in the past decade due to the remarkable ability of stem cells for self-renewal and tissue-specific differentiation. Despite having numerous advancements in stem cell isolation and manipulation techniques, there is a need for highly reliable probes for the specific detection of live stem cells. Herein we developed a new fluorescence probe (CDy9) with high selectivity for mouse embryonic stem cells. CDy9 allows the detection and isolation of intact stem cells with marginal impact on their function and capabilities.
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Affiliation(s)
- Yogeswari Chandran
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research, 11 Biopolis Way, #02-02 Helios, Singapore 138667, Singapore
| | - Nam-Young Kang
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research, 11 Biopolis Way, #02-02 Helios, Singapore 138667, Singapore
| | - Sung-Jin Park
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research, 11 Biopolis Way, #02-02 Helios, Singapore 138667, Singapore
| | - Samira Husen Alamudi
- Department of Chemistry & MedChem Program, Life Sciences Institute, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Jun-Young Kim
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research, 11 Biopolis Way, #02-02 Helios, Singapore 138667, Singapore
| | - Srikanta Sahu
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research, 11 Biopolis Way, #02-02 Helios, Singapore 138667, Singapore
| | - Dongdong Su
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research, 11 Biopolis Way, #02-02 Helios, Singapore 138667, Singapore
| | - Jungyeol Lee
- Department of Chemistry & MedChem Program, Life Sciences Institute, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Marc Vendrell
- MRC Centre for Inflammation Research, The University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, United Kingdom.
| | - Young-Tae Chang
- Singapore Bioimaging Consortium, Agency for Science, Technology and Research, 11 Biopolis Way, #02-02 Helios, Singapore 138667, Singapore; Department of Chemistry & MedChem Program, Life Sciences Institute, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore.
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[Heterogeneity of hematopoietic stem cell]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2015; 36:878-82. [PMID: 26477773 PMCID: PMC7364952 DOI: 10.3760/cma.j.issn.0253-2727.2015.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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68
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Bi X, Adriani G, Xu Y, Chakrabortty S, Pastorin G, Ho HK, Ang WH, Chan Y. Gene Detection in Complex Biological Media Using Semiconductor Nanorods within an Integrated Microfluidic Device. Anal Chem 2015; 87:10292-8. [PMID: 26382664 DOI: 10.1021/acs.analchem.5b01942] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The salient optical properties of highly luminescent semiconductor nanocrystals render them ideal fluorophores for clinical diagnostics, therapeutics, and highly sensitive biochip applications. Microfluidic systems allow miniaturization and integration of multiple biochemical processes in a single device and do not require sophisticated diagnostic tools. Herein, we describe a microfluidic system that integrates RNA extraction, reverse transcription to cDNA, amplification and detection within one integrated device to detect histidine decarboxylase (HDC) gene directly from human white blood cells samples. When anisotropic semiconductor nanorods (NRs) were used as the fluorescent probes, the detection limit was found to be 0.4 ng of total RNA, which was much lower than that obtained using spherical quantum dots (QDs) or organic dyes. This was attributed to the large action cross-section of NRs and their high probability of target capture in a pull-down detection scheme. The combination of large scale integrated microfluidics with highly fluorescent semiconductor NRs may find widespread utility in point-of-care devices and multitarget diagnostics.
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Affiliation(s)
- Xinyan Bi
- Department of Chemistry, National University of Singapore , 3 Science Drive 3, Singapore 117543, Singapore
| | - Giulia Adriani
- Department of Chemistry, National University of Singapore , 3 Science Drive 3, Singapore 117543, Singapore
| | - Yang Xu
- Institute of Materials Research & Engineering A*STAR , 3 Research Link, Singapore 117602, Singapore
| | - Sabyasachi Chakrabortty
- Department of Chemistry, National University of Singapore , 3 Science Drive 3, Singapore 117543, Singapore
| | - Giorgia Pastorin
- Department of Pharmacy, National University of Singapore , 18 Science Drive 4, Singapore 117543, Singapore
| | - Han Kiat Ho
- Department of Pharmacy, National University of Singapore , 18 Science Drive 4, Singapore 117543, Singapore
| | - Wee Han Ang
- Department of Chemistry, National University of Singapore , 3 Science Drive 3, Singapore 117543, Singapore
| | - Yinthai Chan
- Department of Chemistry, National University of Singapore , 3 Science Drive 3, Singapore 117543, Singapore.,Institute of Materials Research & Engineering A*STAR , 3 Research Link, Singapore 117602, Singapore
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69
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Fujii T, Matsuda S, Tejedor ML, Esaki T, Sakane I, Mizuno H, Tsuyama N, Masujima T. Direct metabolomics for plant cells by live single-cell mass spectrometry. Nat Protoc 2015. [PMID: 26313480 DOI: 10.1038/nprot.2015-084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Live single-cell mass spectrometry (live MS) provides a mass spectrum that shows thousands of metabolite peaks from a single live plant cell within minutes. By using an optical microscope, a cell is chosen for analysis and a metal-coated nanospray microcapillary tip is used to remove the cell's contents. After adding a microliter of ionization solvent to the opposite end of the tip, the trapped contents are directly fed into the mass spectrometer by applying a high voltage between the tip and the inlet port of the spectrometer to induce nanospray ionization. Proteins are not detected because of insufficient sensitivity. Metabolite peaks are identified by exact mass or tandem mass spectrometry (MS/MS) analysis, and isomers can be separated by combining live MS with ion-mobility separation. By using this approach, spectra can be acquired in 10 min. In combination with metabolic maps and/or molecular databases, the data can be annotated into metabolic pathways; the data analysis takes 30 min to 4 h, depending on the MS/MS data availability from databases. This method enables the analysis of a number of metabolites from a single cell with rapid sampling at sub-attomolar-level sensitivity.
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Affiliation(s)
- Takashi Fujii
- Laboratory for Molecular Medicine and Devices, Graduated School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
- Laboratory for Single Cell Mass Spectrometry, Quantitative Biology Center, RIKEN, Suita, Osaka, Japan
| | - Shuichi Matsuda
- Laboratory for Molecular Medicine and Devices, Graduated School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
- Laboratory for Single Cell Mass Spectrometry, Quantitative Biology Center, RIKEN, Suita, Osaka, Japan
| | - Mónica Lorenzo Tejedor
- Laboratory for Molecular Medicine and Devices, Graduated School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Tsuyoshi Esaki
- Laboratory for Single Cell Mass Spectrometry, Quantitative Biology Center, RIKEN, Suita, Osaka, Japan
| | - Iwao Sakane
- Laboratory for Single Cell Mass Spectrometry, Quantitative Biology Center, RIKEN, Suita, Osaka, Japan
| | - Hajime Mizuno
- Laboratory for Molecular Medicine and Devices, Graduated School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
- Laboratory for Single Cell Mass Spectrometry, Quantitative Biology Center, RIKEN, Suita, Osaka, Japan
| | - Naohiro Tsuyama
- Laboratory for Molecular Medicine and Devices, Graduated School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
- Laboratory for Single Cell Mass Spectrometry, Quantitative Biology Center, RIKEN, Suita, Osaka, Japan
| | - Tsutomu Masujima
- Laboratory for Molecular Medicine and Devices, Graduated School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
- Laboratory for Single Cell Mass Spectrometry, Quantitative Biology Center, RIKEN, Suita, Osaka, Japan
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70
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Fujii T, Matsuda S, Tejedor ML, Esaki T, Sakane I, Mizuno H, Tsuyama N, Masujima T. Direct metabolomics for plant cells by live single-cell mass spectrometry. Nat Protoc 2015; 10:1445-56. [DOI: 10.1038/nprot.2015.084] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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71
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Sun Z, Lawson DA, Sinclair E, Wang CY, Lai MD, Hetts SW, Higashida RT, Dowd CF, Halbach VV, Werb Z, Su H, Cooke DL. Endovascular biopsy: Strategy for analyzing gene expression profiles of individual endothelial cells obtained from human vessels ✩. ACTA ACUST UNITED AC 2015; 7:157-165. [PMID: 26989654 PMCID: PMC4792280 DOI: 10.1016/j.btre.2015.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The combination of guide wire sampling, FACS and high throughput microfluidic single-cell quantitative RT-PCR, is an effective strategy for analyzing molecular changes of ECs in vascular lesions. Although heterogeneous, the ECs in normal iliac artery fall into two classes.
Purpose To develop a strategy of achieving targeted collection of endothelial cells (ECs) by endovascular methods and analyzing the gene expression profiles of collected single ECs. Methods and results 134 ECs and 37 leukocytes were collected from four patients' intra-iliac artery endovascular guide wires by fluorescence activated cell sorting (FACS) and analyzed by single-cell quantitative RT-PCR for expression profile of 48 genes. Compared to CD45+ leukocytes, the ECs expressed higher levels (p < 0.05) of EC surface markers used on FACS and other EC related genes. The gene expression profile showed that these isolated ECs fell into two clusters, A and B, that differentially expressed 19 genes related to angiogenesis, inflammation and extracellular matrix remodeling, with cluster B ECs have demonstrating similarities to senescent or aging ECs. Conclusion Combination of endovascular device sampling, FACS and single-cell quantitative RT-PCR is a feasible method for analyzing EC gene expression profile in vascular lesions.
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Affiliation(s)
- Zhengda Sun
- Division of Neurointerventional Radiology, Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, USA
| | - Devon A Lawson
- Department of Anatomy, University of California, San Francisco, CA, USA
| | - Elizabeth Sinclair
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Chih-Yang Wang
- Department of Anatomy, University of California, San Francisco, CA, USA; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ming-Derg Lai
- Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Steven W Hetts
- Division of Neurointerventional Radiology, Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, USA
| | - Randall T Higashida
- Division of Neurointerventional Radiology, Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, USA
| | - Christopher F Dowd
- Division of Neurointerventional Radiology, Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, USA
| | - Van V Halbach
- Division of Neurointerventional Radiology, Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, USA
| | - Zena Werb
- Department of Anatomy, University of California, San Francisco, CA, USA
| | - Hua Su
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA
| | - Daniel L Cooke
- Division of Neurointerventional Radiology, Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA, USA
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72
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Get to Understand More from Single-Cells: Current Studies of Microfluidic-Based Techniques for Single-Cell Analysis. Int J Mol Sci 2015. [PMID: 26213918 PMCID: PMC4581168 DOI: 10.3390/ijms160816763] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
This review describes the microfluidic techniques developed for the analysis of a single cell. The characteristics of microfluidic (e.g., little sample amount required, high-throughput performance) make this tool suitable to answer and to solve biological questions of interest about a single cell. This review aims to introduce microfluidic related techniques for the isolation, trapping and manipulation of a single cell. The major approaches for detection in single-cell analysis are introduced; the applications of single-cell analysis are then summarized. The review concludes with discussions of the future directions and opportunities of microfluidic systems applied in analysis of a single cell.
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73
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Walsh MT, Hsiao AP, Lee HS, Liu Z, Huang X. Capture and enumeration of mRNA transcripts from single cells using a microfluidic device. LAB ON A CHIP 2015; 15:2968-2980. [PMID: 26040942 DOI: 10.1039/c5lc00445d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Accurate measurement of RNA transcripts from single cells will enable the precise classification of cell types and characterization of the heterogeneity in cell populations that play key roles in normal cellular physiology and diseases. As a step towards this end, we have developed a microfluidic device and methods for automatic hydrodynamic capture of single mammalian cells and subsequent immobilization and digital counting of polyadenylated mRNA molecules released from the individual cells. Using single-molecule fluorescence imaging, we have demonstrated that polyadenylated mRNA molecules from single HeLa cells can be captured within minutes by hybridization to polydeoxyribothymidine oligonucleotides covalently attached on the glass surface in the device. The total mRNA molecule counts in the individual HeLa cells are found to vary significantly from one another. Our technology opens up the possibility of direct digital enumeration of RNA transcripts from single cells with single-molecule sensitivity using a single integrated microfluidic device.
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Affiliation(s)
- Matthew T Walsh
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
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74
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Sikorski DJ, Caron NJ, VanInsberghe M, Zahn H, Eaves CJ, Piret JM, Hansen CL. Clonal analysis of individual human embryonic stem cell differentiation patterns in microfluidic cultures. Biotechnol J 2015; 10:1546-54. [PMID: 26059045 DOI: 10.1002/biot.201500035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/04/2015] [Accepted: 06/05/2015] [Indexed: 01/23/2023]
Abstract
Heterogeneity in the clonal outputs of individual human embryonic stem cells (hESCs) confounds analysis of their properties in studies of bulk populations and how to manipulate them for clinical applications. To circumvent this problem we developed a microfluidic device that supports the robust generation of colonies derived from single ESCs. This microfluidic system contains 160 individually addressable chambers equipped for perfusion culture of individual hESCs that could be shown to match the growth rates, marker expression and colony morphologies obtained in conventional cultures. Use of this microfluidic device to analyze the clonal growth kinetics of multiple individual hESCs induced to differentiation revealed variable shifts in the growth rate, area per cell and expression of OCT4 in the progeny of individual hESCs. Interestingly, low OCT4 expression, a slower growth rate and low nuclear to cytoplasmic ratios were found to be correlated responses. This study demonstrates how microfluidic systems can be used to enable large scale live-cell imaging of isolated hESCs exposed to changing culture conditions, to examine how different aspects of their variable responses are correlated.
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Affiliation(s)
- Darek J Sikorski
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada.,Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Nicolas J Caron
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Michael VanInsberghe
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
| | - Hans Zahn
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada
| | - Connie J Eaves
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - James M Piret
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Carl L Hansen
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC, Canada. .,Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada.
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75
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Affiliation(s)
- Hu Zhang
- School of Chemical Engineering; University of Adelaide; Adelaide Australia
| | - Xiaolin Cui
- School of Chemical Engineering; University of Adelaide; Adelaide Australia
| | - Jingxiu Bi
- School of Chemical Engineering; University of Adelaide; Adelaide Australia
| | - Sheng Dai
- School of Chemical Engineering; University of Adelaide; Adelaide Australia
| | - Haitao Ye
- School of Engineering and Applied Science; Aston University; Birmingham United Kingdom
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76
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Korem Y, Szekely P, Hart Y, Sheftel H, Hausser J, Mayo A, Rothenberg ME, Kalisky T, Alon U. Geometry of the Gene Expression Space of Individual Cells. PLoS Comput Biol 2015; 11:e1004224. [PMID: 26161936 PMCID: PMC4498931 DOI: 10.1371/journal.pcbi.1004224] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 03/04/2015] [Indexed: 12/14/2022] Open
Abstract
There is a revolution in the ability to analyze gene expression of single cells in a tissue. To understand this data we must comprehend how cells are distributed in a high-dimensional gene expression space. One open question is whether cell types form discrete clusters or whether gene expression forms a continuum of states. If such a continuum exists, what is its geometry? Recent theory on evolutionary trade-offs suggests that cells that need to perform multiple tasks are arranged in a polygon or polyhedron (line, triangle, tetrahedron and so on, generally called polytopes) in gene expression space, whose vertices are the expression profiles optimal for each task. Here, we analyze single-cell data from human and mouse tissues profiled using a variety of single-cell technologies. We fit the data to shapes with different numbers of vertices, compute their statistical significance, and infer their tasks. We find cases in which single cells fill out a continuum of expression states within a polyhedron. This occurs in intestinal progenitor cells, which fill out a tetrahedron in gene expression space. The four vertices of this tetrahedron are each enriched with genes for a specific task related to stemness and early differentiation. A polyhedral continuum of states is also found in spleen dendritic cells, known to perform multiple immune tasks: cells fill out a tetrahedron whose vertices correspond to key tasks related to maturation, pathogen sensing and communication with lymphocytes. A mixture of continuum-like distributions and discrete clusters is found in other cell types, including bone marrow and differentiated intestinal crypt cells. This approach can be used to understand the geometry and biological tasks of a wide range of single-cell datasets. The present results suggest that the concept of cell type may be expanded. In addition to discreet clusters in gene-expression space, we suggest a new possibility: a continuum of states within a polyhedron, in which the vertices represent specialists at key tasks. In the past, biological experiments usually pooled together millions of cells, masking the differences between individual cells. Current technology takes a big step forward by measuring gene expression from individual cells. Interpreting this data is challenging because we need to understand how cells are arranged in a high dimensional gene expression space. Here we test recent theory that suggests that cells facing multiple tasks should be arranged in simple low dimensional polygons or polyhedra (generally called polytopes). The vertices of the polytopes are gene expression profiles optimal for each of the tasks. We find evidence for such simplicity in a variety of tissues—spleen, bone marrow, intestine—analyzed by different single-cell technologies. We find that cells are distributed inside polytopes, such as tetrahedrons or four-dimensional simplexes, with cells closest to each vertex responsible for a different key task. For example, intestinal progenitor cells that give rise to the other cell types show a continuous distribution in a tetrahedron whose vertices correspond to several key sub-tasks. Immune dendritic cells likewise are continuously distributed between key immune tasks. This approach of testing whether data falls in polytopes may be useful for interpreting a variety of single-cell datasets in terms of biological tasks.
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Affiliation(s)
- Yael Korem
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Pablo Szekely
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yuval Hart
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hila Sheftel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jean Hausser
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Avi Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michael E. Rothenberg
- Department of Medicine, Division of Gastroenterology and Hepatology, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, United States of America
| | - Tomer Kalisky
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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77
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Nakae Y, Oka Y, Fujiki F, Morimoto S, Kamiya T, Takashima S, Nakata J, Nishida S, Nakajima H, Hosen N, Tsuboi A, Kyo T, Oji Y, Mizuguchi K, Kumanogoh A, Sugiyama H. Two distinct effector memory cell populations of WT1 (Wilms' tumor gene 1)-specific cytotoxic T lymphocytes in acute myeloid leukemia patients. Cancer Immunol Immunother 2015; 64:791-804. [PMID: 25835542 PMCID: PMC11028643 DOI: 10.1007/s00262-015-1683-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 03/14/2015] [Indexed: 10/23/2022]
Abstract
Wilms' tumor gene 1 (WT1) protein is a promising tumor-associated antigen for cancer immunotherapy. We have been performing WT1 peptide vaccination with good clinical responses in over 750 patients with leukemia or solid cancers. In this study, we generated single-cell gene-expression profiles of the effector memory (EM) subset of WT1-specific cytotoxic T lymphocytes (CTLs) in peripheral blood of nine acute myeloid leukemia patients treated with WT1 peptide vaccine, in order to discriminate responders (WT1 mRNA levels in peripheral blood decreased to undetectable levels, decreased but stayed at abnormal levels, were stable at undetectable levels, or remained unchanged from the initial abnormal levels more than 6 months after WT1 vaccination) from non-responders (leukemic blast cells and/or WT1 mRNA levels increased relative to the initial state within 6 months of WT1 vaccination) prior to WT1 vaccination. Cluster and principal component analyses performed using 83 genes did not discriminate between responders and non-responders prior to WT1 vaccination. However, these analyses revealed that EM subset of WT1-specific CTLs could be divided into two groups: the "activated" and "quiescent" states; in responders, EM subset of the CTLs shifted to the "quiescent" state, whereas in non-responders, those shifted to the "activated" state following WT1 vaccination. These results demonstrate for the first time the existence of two distinct EM states, each of which was characteristic of responders or non-responders, of WT1-specific CTLs in AML patients, and raises the possibility of using advanced gene-expression profile analysis to clearly discriminate between responders and non-responders prior to WT1 vaccination.
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MESH Headings
- Adult
- Aged
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Cancer Vaccines/immunology
- Cancer Vaccines/therapeutic use
- Female
- Gene Expression Profiling
- Humans
- Immunologic Memory/immunology
- Immunotherapy/methods
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/therapy
- Male
- Middle Aged
- Principal Component Analysis
- RNA, Messenger/blood
- RNA, Messenger/genetics
- T-Lymphocytes, Cytotoxic/cytology
- T-Lymphocytes, Cytotoxic/immunology
- Vaccines, Subunit/immunology
- Vaccines, Subunit/therapeutic use
- WT1 Proteins/genetics
- WT1 Proteins/immunology
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Affiliation(s)
- Yoshiki Nakae
- Departments of Respiratory Medicine, Allergy and Rheumatic Diseases, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Yoshihiro Oka
- Departments of Respiratory Medicine, Allergy and Rheumatic Diseases, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 Japan
- Department of Cancer Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 Japan
- Department of Immunopathology, Immunology Frontier Research Center (World Premier International Research Center), Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Fumihiro Fujiki
- Department of Cancer Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Soyoko Morimoto
- Department of Cancer Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Toshio Kamiya
- Department of Functional Diagnostic Science, Graduate School of Medicine, Osaka University, 1-7 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Satoshi Takashima
- Departments of Respiratory Medicine, Allergy and Rheumatic Diseases, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Jun Nakata
- Department of Cancer Immunotherapy, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Sumiyuki Nishida
- Departments of Respiratory Medicine, Allergy and Rheumatic Diseases, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Hiroko Nakajima
- Department of Cancer Immunology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Naoki Hosen
- Department of Cancer Stem Cell Biology, Graduate School of Medicine, Osaka University, 1-7 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Akihiro Tsuboi
- Department of Cancer Immunotherapy, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Taiichi Kyo
- Department of Hematology, Hiroshima Red Cross and Atomic Bomb Survivor Hospital, 1-9-6 Sendamachi, Nakaku, Hiroshima-City, Hiroshima 730-0052 Japan
| | - Yusuke Oji
- Department of Cancer Stem Cell Biology, Graduate School of Medicine, Osaka University, 1-7 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Kenji Mizuguchi
- National Institute of Biomedical Innovation, 7-6-8 Saitoasagi, Ibaraki, Osaka 567-0085 Japan
| | - Atsushi Kumanogoh
- Departments of Respiratory Medicine, Allergy and Rheumatic Diseases, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871 Japan
- Department of Immunopathology, Immunology Frontier Research Center (World Premier International Research Center), Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Haruo Sugiyama
- Department of Functional Diagnostic Science, Graduate School of Medicine, Osaka University, 1-7 Yamadaoka, Suita, Osaka 565-0871 Japan
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78
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Printing 2-dimentional droplet array for single-cell reverse transcription quantitative PCR assay with a microfluidic robot. Sci Rep 2015; 5:9551. [PMID: 25828383 PMCID: PMC4381353 DOI: 10.1038/srep09551] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/10/2015] [Indexed: 12/31/2022] Open
Abstract
This paper describes a nanoliter droplet array-based single-cell reverse transcription quantitative PCR (RT-qPCR) assay method for quantifying gene expression in individual cells. By sequentially printing nanoliter-scale droplets on microchip using a microfluidic robot, all liquid-handling operations including cell encapsulation, lysis, reverse transcription, and quantitative PCR with real-time fluorescence detection, can be automatically achieved. The inhibition effect of cell suspension buffer on RT-PCR assay was comprehensively studied to achieve high-sensitivity gene quantification. The present system was applied in the quantitative measurement of expression level of mir-122 in single Huh-7 cells. A wide distribution of mir-122 expression in single cells from 3061 copies/cell to 79998 copies/cell was observed, showing a high level of cell heterogeneity. With the advantages of full-automation in liquid-handling, simple system structure, and flexibility in achieving multi-step operations, the present method provides a novel liquid-handling mode for single cell gene expression analysis, and has significant potentials in transcriptional identification and rare cell analysis.
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79
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Chapman AR, He Z, Lu S, Yong J, Tan L, Tang F, Xie XS. Single cell transcriptome amplification with MALBAC. PLoS One 2015; 10:e0120889. [PMID: 25822772 PMCID: PMC4378937 DOI: 10.1371/journal.pone.0120889] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/27/2015] [Indexed: 12/21/2022] Open
Abstract
Recently, Multiple Annealing and Looping-Based Amplification Cycles (MALBAC) has been developed for whole genome amplification of an individual cell, relying on quasilinear instead of exponential amplification to achieve high coverage. Here we adapt MALBAC for single-cell transcriptome amplification, which gives consistently high detection efficiency, accuracy and reproducibility. With this newly developed technique, we successfully amplified and sequenced single cells from 3 germ layers from mouse embryos in the early gastrulation stage, and examined the epithelial-mesenchymal transition (EMT) program among cells in the mesoderm layer on a single-cell level.
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Affiliation(s)
- Alec R. Chapman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, United States of America
- Graduate program in Biophysics, Harvard University, Cambridge, MA, 02138, United States of America
| | - Zi He
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, United States of America
| | - Sijia Lu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, United States of America
| | - Jun Yong
- Biodynamics Optical Imaging Center, School of Life Sciences, Peking University, Beijing, China
| | - Longzhi Tan
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, United States of America
| | - Fuchou Tang
- Biodynamics Optical Imaging Center, School of Life Sciences, Peking University, Beijing, China
| | - X. Sunney Xie
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, United States of America
- * E-mail:
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80
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Abstract
This protocol details a method for measuring the DNA methylation state of multiple target sites in single cells, otherwise known as single-cell restriction analysis of methylation (SCRAM). The basic steps include isolating and lysing single cells, digesting genomic DNA with a methylation-sensitive restriction endonuclease (MSRE) and amplification of multiple targets by two rounds of PCR to determine the methylation status of target sites. The method can reliably and accurately detect the methylation status of multiple target sites in each single cell, and it can be completed in a relatively short time (<2 d) at low cost. Consequently, the method may be preferable over whole-genome methods in applications requiring highly reliable and cost-effective coverage of specific target sites in all cells from a sample and in cases when the DNA methylation states of single CpG sites are representative of the methylation status of corresponding regions of interest.
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81
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Lee WH, Nguyen P, Hu S, Liang G, Ong SG, Han L, Sanchez-Freire V, Lee AS, Vasanawala M, Segall G, Wu JC. Variable activation of the DNA damage response pathways in patients undergoing single-photon emission computed tomography myocardial perfusion imaging. Circ Cardiovasc Imaging 2015; 8:e002851. [PMID: 25609688 DOI: 10.1161/circimaging.114.002851] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Although single-photon emission computed tomography myocardial perfusion imaging (SPECT MPI) has improved the diagnosis and risk stratification of patients with suspected coronary artery disease, it remains a primary source of low-dose radiation exposure for cardiac patients. To determine the biological effects of low-dose radiation from SPECT MPI, we measured the activation of the DNA damage response pathways using quantitative flow cytometry and single-cell gene expression profiling. METHODS AND RESULTS Blood samples were collected from patients before and after SPECT MPI (n=63). Overall, analysis of all recruited patients showed no marked differences in the phosphorylation of proteins (H2AX, protein 53, and ataxia telangiectasia mutated) after SPECT. The majority of patients also had either downregulated or unchanged expression in DNA damage response genes at both 24 and 48 hours post-SPECT. Interestingly, a small subset of patients with increased phosphorylation had significant upregulation of genes associated with DNA damage, whereas those with no changes in phosphorylation had significant downregulation or no difference, suggesting that some patients may potentially be more sensitive to low-dose radiation exposure. CONCLUSIONS Our findings showed that SPECT MPI resulted in a variable activation of the DNA damage response pathways. Although only a small subset of patients had increased protein phosphorylation and elevated gene expression postimaging, continued care should be taken to reduce radiation exposure to both the patients and operators.
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Affiliation(s)
- Won Hee Lee
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, CA.,Department of Radiology, Molecular Imaging Program, Stanford University School of Medicine, Stanford, CA.,Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
| | - Patricia Nguyen
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, CA.,Department of Radiology, Molecular Imaging Program, Stanford University School of Medicine, Stanford, CA.,Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA.,Veterans Administration Palo Alto, Palo Alto, CA
| | - Shijun Hu
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, CA.,Department of Radiology, Molecular Imaging Program, Stanford University School of Medicine, Stanford, CA
| | - Grace Liang
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA.,Veterans Administration Palo Alto, Palo Alto, CA
| | - Sang-Ging Ong
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, CA.,Department of Radiology, Molecular Imaging Program, Stanford University School of Medicine, Stanford, CA
| | - Leng Han
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, CA.,Department of Radiology, Molecular Imaging Program, Stanford University School of Medicine, Stanford, CA
| | - Veronica Sanchez-Freire
- Department of Radiology, Molecular Imaging Program, Stanford University School of Medicine, Stanford, CA
| | - Andrew S Lee
- Department of Radiology, Molecular Imaging Program, Stanford University School of Medicine, Stanford, CA
| | | | | | - Joseph C Wu
- Department of Medicine, Division of Cardiology, Stanford University School of Medicine, Stanford, CA.,Department of Radiology, Molecular Imaging Program, Stanford University School of Medicine, Stanford, CA.,Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA
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82
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Durruthy-Durruthy R, Gottlieb A, Heller S. 3D computational reconstruction of tissues with hollow spherical morphologies using single-cell gene expression data. Nat Protoc 2015; 10:459-474. [PMID: 25675210 PMCID: PMC4523134 DOI: 10.1038/nprot.2015.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Single-cell gene expression analysis has contributed to a better understanding of the transcriptional heterogeneity in a variety of model systems, including those used in research in developmental, cancer and stem cell biology. Nowadays, technological advances facilitate the generation of large gene expression data sets in high-throughput format. Strategies are needed to pertinently visualize this information in a tissue structure-related context, so as to improve data analysis and aid the drawing of meaningful conclusions. Here we describe an approach that uses spatial properties of the tissue source to enable the reconstruction of hollow sphere-shaped tissues and organs from single-cell gene expression data in 3D space. To demonstrate our method, we used cells of the mouse otocyst and the renal vesicle as examples. This protocol presents a straightforward computational expression analysis workflow, and it is implemented on the MATLAB and R statistical computing and graphics software platforms. Hands-on time for typical experiments can be <1 h using a standard desktop PC or Mac.
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Affiliation(s)
- Robert Durruthy-Durruthy
- Department of Otolaryngology - Head & Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Assaf Gottlieb
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stefan Heller
- Department of Otolaryngology - Head & Neck Surgery, Stanford University School of Medicine, Stanford, CA 94305, USA
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83
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Fan HC, Fu GK, Fodor SPA. Expression profiling. Combinatorial labeling of single cells for gene expression cytometry. Science 2015; 347:1258367. [PMID: 25657253 DOI: 10.1126/science.1258367] [Citation(s) in RCA: 302] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present a technically simple approach for gene expression cytometry combining next-generation sequencing with stochastic barcoding of single cells. A combinatorial library of beads bearing cell- and molecular-barcoding capture probes is used to uniquely label transcripts and reconstruct the digital gene expression profile of thousands of individual cells in a single experiment without the need for robotics or automation. We applied the technology to dissect the human hematopoietic system and to characterize heterogeneous response to in vitro stimulation. High sensitivity is demonstrated by detection of low-abundance transcripts and rare cells. Under current implementation, the technique can analyze a few thousand cells simultaneously and can readily scale to 10,000s or 100,000s of cells.
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Affiliation(s)
- H Christina Fan
- Cellular Research, Inc., 3183 Porter Drive, Palo Alto, CA 94304, USA
| | - Glenn K Fu
- Cellular Research, Inc., 3183 Porter Drive, Palo Alto, CA 94304, USA
| | - Stephen P A Fodor
- Cellular Research, Inc., 3183 Porter Drive, Palo Alto, CA 94304, USA.
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84
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Zhou H, Zhao L, Zhang X. In-Channel Printing-Device Opening Assay for Micropatterning Multiple Cells and Gene Analysis. Anal Chem 2015; 87:2048-53. [DOI: 10.1021/ac504823s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Hao Zhou
- Research Center for Bioengineering
and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 10083, P. R. China
| | - Liang Zhao
- Research Center for Bioengineering
and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 10083, P. R. China
| | - Xueji Zhang
- Research Center for Bioengineering
and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 10083, P. R. China
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85
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Li G, Plonowska K, Kuppusamy R, Sturzu A, Wu SM. Identification of cardiovascular lineage descendants at single-cell resolution. Development 2015; 142:846-57. [PMID: 25633351 DOI: 10.1242/dev.116897] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The transcriptional profiles of cardiac cells derived from murine embryos and from mouse embryonic stem cells (mESCs) have primarily been studied within a cell population. However, the characterization of gene expression in these cells at a single-cell level might demonstrate unique variations that cannot be appreciated within a cell pool. In this study, we aimed to establish a single-cell quantitative PCR platform and perform side-by-side comparison between cardiac progenitor cells (CPCs) and cardiomyocytes (CMs) derived from mESCs and mouse embryos. We first generated a reference map for cardiovascular single cells through quantifying lineage-defining genes for CPCs, CMs, smooth muscle cells (SMCs), endothelial cells (EDCs), fibroblasts and mESCs. This panel was then applied against single embryonic day 10.5 heart cells to demonstrate its ability to identify each endocardial cell and chamber-specific CM. In addition, we compared the gene expression profile of embryo- and mESC-derived CPCs and CMs at different developmental stages and showed that mESC-derived CMs are phenotypically similar to embryo-derived CMs up to the neonatal stage. Furthermore, we showed that single-cell expression assays coupled with time-lapse microscopy can resolve the identity and the lineage relationships between progenies of single cultured CPCs. With this approach, we found that mESC-derived Nkx2-5(+) CPCs preferentially become SMCs or CMs, whereas single embryo-derived Nkx2-5(+) CPCs represent two phenotypically distinct subpopulations that can become either EDCs or CMs. These results demonstrate that multiplex gene expression analysis in single cells is a powerful tool for examining the unique behaviors of individual embryo- or mESC-derived cardiac cells.
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Affiliation(s)
- Guang Li
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karolina Plonowska
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rajarajan Kuppusamy
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Anthony Sturzu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA Cardiovascular Medicine Division, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sean M Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA Cardiovascular Medicine Division, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA Child Health Research Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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86
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Development and validation of a 48-target analytical method for high-throughput monitoring of genetically modified organisms. Sci Rep 2015; 5:7616. [PMID: 25556930 PMCID: PMC5154595 DOI: 10.1038/srep07616] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 12/03/2014] [Indexed: 12/12/2022] Open
Abstract
The rapid increase in the number of genetically modified (GM) varieties has led to a demand for high-throughput methods to detect genetically modified organisms (GMOs). We describe a new dynamic array-based high throughput method to simultaneously detect 48 targets in 48 samples on a Fludigm system. The test targets included species-specific genes, common screening elements, most of the Chinese-approved GM events, and several unapproved events. The 48 TaqMan assays successfully amplified products from both single-event samples and complex samples with a GMO DNA amount of 0.05 ng, and displayed high specificity. To improve the sensitivity of detection, a preamplification step for 48 pooled targets was added to enrich the amount of template before performing dynamic chip assays. This dynamic chip-based method allowed the synchronous high-throughput detection of multiple targets in multiple samples. Thus, it represents an efficient, qualitative method for GMO multi-detection.
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87
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Abstract
Droplet microfluidics may soon change the paradigm of performing chemical analyses and related instrumentation.
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Affiliation(s)
- Evgenia Yu Basova
- Masaryk University
- CEITEC, Central European Institute Technology
- Brno
- Czech Republic
| | - Frantisek Foret
- Masaryk University
- CEITEC, Central European Institute Technology
- Brno
- Czech Republic
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic
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88
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Sun H, Olsen T, Zhu J, Tao J, Ponnaiya B, Amundson SA, Brenner DJ, Lin Q. A Bead-Based Microfluidic Approach to Integrated Single-Cell Gene Expression Analysis by Quantitative RT-PCR. RSC Adv 2015; 5:4886-4893. [PMID: 25883782 DOI: 10.1039/c4ra13356k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Gene expression analysis at the single-cell level is critical to understanding variations among cells in heterogeneous populations. Microfluidic reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is well suited to gene expression assays of single cells. We present a microfluidic approach that integrates all functional steps for RT-qPCR of a single cell, including isolation and lysis of the cell, as well as purification, reverse transcription and quantitative real-time PCR of messenger RNA in the cell lysate. In this approach, all reactions in the multi-step assay of a single lysed cell can be completed on microbeads, thereby simplifying the design, fabrication and operation of the microfluidic device, as well as facilitating the minimization of sample loss or contamination. In the microfluidic device, a single cell is isolated and lysed; mRNA in the cell lysate is then analyzed by RT-qPCR using primers immobilized on microbeads in a single microchamber whose temperature is controlled in closed loop via an integrated heater and temperature sensor. The utility of the approach was demonstrated by the analysis of the effects of the drug (methyl methanesulfonate, MMS) on the induction of the cyclin-dependent kinase inhibitor 1a (CDKN1A) in single human cancer cells (MCF-7), demonstrating the potential of our approach for efficient, integrated single-cell RT-qPCR for gene expression analysis.
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Affiliation(s)
- Hao Sun
- Department of Mechatronics Engineering, Harbin Institute of Technology, Harbin, Heilongjiang, China ; Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Tim Olsen
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Jing Zhu
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Jianguo Tao
- Department of Mechatronics Engineering, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Brian Ponnaiya
- Center for Radiological Research, Columbia University, New York, NY, USA
| | - Sally A Amundson
- Department of Radiation Oncology, Columbia University, New York, NY, USA
| | - David J Brenner
- Center for Radiological Research, Columbia University, New York, NY, USA ; Department of Radiation Oncology, Columbia University, New York, NY, USA
| | - Qiao Lin
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
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89
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Multiplex, Quantitative, Reverse Transcription PCR Detection of Influenza Viruses Using Droplet Microfluidic Technology. MICROMACHINES 2014. [DOI: 10.3390/mi6010063] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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90
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O’Connor JE, Herrera G, Martínez-Romero A, de Oyanguren FS, Díaz L, Gomes A, Balaguer S, Callaghan RC. Systems Biology and immune aging. Immunol Lett 2014; 162:334-45. [DOI: 10.1016/j.imlet.2014.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
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91
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Bheda P, Schneider R. Epigenetics reloaded: the single-cell revolution. Trends Cell Biol 2014; 24:712-23. [PMID: 25283892 DOI: 10.1016/j.tcb.2014.08.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/27/2014] [Accepted: 08/28/2014] [Indexed: 01/15/2023]
Abstract
Mechanistically, how epigenetic states are inherited through cellular divisions remains an important open question in the chromatin field and beyond. Defining the heritability of epigenetic states and the underlying chromatin-based mechanisms within a population of cells is complicated due to cell heterogeneity combined with varying levels of stability of these states; thus, efforts must be focused toward single-cell analyses. The approaches presented here constitute the forefront of epigenetics research at the single-cell level using classic and innovative methods to dissect epigenetics mechanisms from the limited material available in a single cell. This review further outlines exciting future avenues of research to address the significance of epigenetic heterogeneity and the contributions of microfluidics technologies to single-cell isolation and analysis.
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Affiliation(s)
- Poonam Bheda
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104/Inserm U964/Université de Strasbourg, 67400 Illkirch, France
| | - Robert Schneider
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104/Inserm U964/Université de Strasbourg, 67400 Illkirch, France.
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92
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O'Connor JE, Herrera G, Martínez-Romero A, Oyanguren FSD, Díaz L, Gomes A, Balaguer S, Callaghan RC. WITHDRAWN: Systems Biology and Immune Aging. Immunol Lett 2014:S0165-2478(14)00197-7. [PMID: 25251659 DOI: 10.1016/j.imlet.2014.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
Abstract
The Publisher regrets that this article is an accidental duplication of anarticle that has already been published, http://dx.doi.org/10.1016/j.imlet.2014.09.009. The duplicate article has therefore been withdrawn.
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Affiliation(s)
- José-Enrique O'Connor
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain.
| | - Guadalupe Herrera
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Alicia Martínez-Romero
- Cytometry Technological Service, Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Francisco Sala-de Oyanguren
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Laura Díaz
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Angela Gomes
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Susana Balaguer
- Laboratory of Translational Cytomics, Joint Research Unit, The University of Valencia and Principe Felipe Research Center, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
| | - Robert C Callaghan
- Department of Pathology, Faculty of Medicine, The University of Valencia, Valencia, Spain; Cytometry Laboratory, Incliva Foundation, Clinical University Hospital, The University of Valencia, Valencia, Spain
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93
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Riahi R, Long M, Yang Y, Dean Z, Zhang DD, Slepian MJ, Wong PK. Single cell gene expression analysis in injury-induced collective cell migration. Integr Biol (Camb) 2014; 6:192-202. [PMID: 24336811 DOI: 10.1039/c3ib40095f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Collective cell behavior in response to mechanical injury is central to various regenerative and pathological processes. Using a double-stranded locked nucleic acid probe for monitoring real-time intracellular gene expression, we examined the spatiotemporal response of epithelial cells during injury-induced collective migration and compared to the blocker assay with minimal injury as control. We showed that cells ∼150 μm from the wound edge exhibit a gradient in response to mechanical injury, expressing different genes depending on the wounding process. While release of contact inhibition is sufficient to trigger the migratory behavior, cell injury additionally induces reactive oxygen species, Nrf2 protein, and stress response genes, including heat shock protein 70 and heme oxygenase-1, in a spatiotemporal manner. Furthermore, we show that Nrf2 has an inhibitory role in injury-induced epithelial-mesenchymal transition, suggesting a potential autoregulatory mechanism in injury-induced response. Taken together, our single-cell gene expression analyses reveal modular cell responses to mechanical injury, manipulation of which may afford novel strategies for tissue repair and prevention of tumor invasion in the future.
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Affiliation(s)
- Reza Riahi
- Department of Aerospace and Mechanical Engineering, The University of Arizona, Tucson, Arizona 85721, USA.
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94
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Thompson AM, Paguirigan AL, Kreutz JE, Radich JP, Chiu DT. Microfluidics for single-cell genetic analysis. LAB ON A CHIP 2014; 14:3135-42. [PMID: 24789374 PMCID: PMC4117719 DOI: 10.1039/c4lc00175c] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The ability to correlate single-cell genetic information to cellular phenotypes will provide the kind of detailed insight into human physiology and disease pathways that is not possible to infer from bulk cell analysis. Microfluidic technologies are attractive for single-cell manipulation due to precise handling and low risk of contamination. Additionally, microfluidic single-cell techniques can allow for high-throughput and detailed genetic analyses that increase accuracy and decrease reagent cost compared to bulk techniques. Incorporating these microfluidic platforms into research and clinical laboratory workflows can fill an unmet need in biology, delivering the highly accurate, highly informative data necessary to develop new therapies and monitor patient outcomes. In this perspective, we describe the current and potential future uses of microfluidics at all stages of single-cell genetic analysis, including cell enrichment and capture, single-cell compartmentalization and manipulation, and detection and analyses.
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Affiliation(s)
- A M Thompson
- Department of Chemistry, University of Washington, Seattle, WA, USA.
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95
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Tomaiuolo G. Biomechanical properties of red blood cells in health and disease towards microfluidics. BIOMICROFLUIDICS 2014; 8:051501. [PMID: 25332724 PMCID: PMC4189537 DOI: 10.1063/1.4895755] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/03/2014] [Indexed: 05/04/2023]
Abstract
Red blood cells (RBCs) possess a unique capacity for undergoing cellular deformation to navigate across various human microcirculation vessels, enabling them to pass through capillaries that are smaller than their diameter and to carry out their role as gas carriers between blood and tissues. Since there is growing evidence that red blood cell deformability is impaired in some pathological conditions, measurement of RBC deformability has been the focus of numerous studies over the past decades. Nevertheless, reports on healthy and pathological RBCs are currently limited and, in many cases, are not expressed in terms of well-defined cell membrane parameters such as elasticity and viscosity. Hence, it is often difficult to integrate these results into the basic understanding of RBC behaviour, as well as into clinical applications. The aim of this review is to summarize currently available reports on RBC deformability and to highlight its association with various human diseases such as hereditary disorders (e.g., spherocytosis, elliptocytosis, ovalocytosis, and stomatocytosis), metabolic disorders (e.g., diabetes, hypercholesterolemia, obesity), adenosine triphosphate-induced membrane changes, oxidative stress, and paroxysmal nocturnal hemoglobinuria. Microfluidic techniques have been identified as the key to develop state-of-the-art dynamic experimental models for elucidating the significance of RBC membrane alterations in pathological conditions and the role that such alterations play in the microvasculature flow dynamics.
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Affiliation(s)
- Giovanna Tomaiuolo
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, Università di Napoli Federico II , Piazzale Tecchio 80, Napoli 80125, Italy and CEINGE Biotecnologie Avanzate , Via Gaetano Salvatore 486, Napoli 80145, Italy
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96
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Salehi-Reyhani A, Burgin E, Ces O, Willison KR, Klug DR. Addressable droplet microarrays for single cell protein analysis. Analyst 2014; 139:5367-74. [DOI: 10.1039/c4an01208a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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97
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Zhang K, Han X, Li Y, Li SY, Zu Y, Wang Z, Qin L. Hand-held and integrated single-cell pipettes. J Am Chem Soc 2014; 136:10858-61. [PMID: 25036187 PMCID: PMC4133013 DOI: 10.1021/ja5053279] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
Successful single-cell isolation is a primary step for subsequent
chemical and biological analyses of single cells. Conventional single-cell
isolation methods often encounter operational complexity, limited
efficiency, deterioration of cell viability, incompetence in the isolation
of a single-cell into nanoliter liquid, and/or inability to select
single adherent cells with specific phenotypes. Here, we develop a
hand-held single-cell pipet (hSCP) that is rapid, operationally simple,
highly efficient, and inexpensive for unbiased isolation of single
viable suspended cells directly from submicroliter cell suspensions
into nanoliter droplets without the assistance of any additional equipment.
An integrated SCP (iSCP) has also been developed for selective isolation
of single suspended and adherent cells according to the fluorescence
imaging and morphological features. The isolated single cells can
be conveniently transferred into standard 96-/384-well plates, Petri
dishes, or vials for cloning, PCR, and other single-cell biochemical
assays.
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Affiliation(s)
- Kai Zhang
- Department of Nanomedicine, Houston Methodist Research Institute , Houston, Texas 77030, United States
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98
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Avesar J, Arye TB, Levenberg S. Frontier microfluidic techniques for short and long-term single cell analysis. LAB ON A CHIP 2014; 14:2161-7. [PMID: 24671389 DOI: 10.1039/c4lc00013g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Here, we review the frontier microfluidic techniques for single cell analysis (SCA), which is important for research of many biological systems. Microfluidics provides high-throughput, high-resolution experiments at low cost and reagent use, making it especially useful for single cell analysis. Recent advancements in the field have made SCA more feasible, improving device throughput and resolution, adding capabilities, and combining different functions to bring forth new assays. Developments in incubation have allowed for long-term cell tracking assays to be performed with single cell resolution. The ability of systems to provide chemical isolation or prolonged growth of adherent cells is also discussed.
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Affiliation(s)
- Jonathan Avesar
- Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel 32000.
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99
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Mikheikin A, Olsen A, Leslie K, Mishra B, Gimzewski J, Reed J. Atomic force microscopic detection enabling multiplexed low-cycle-number quantitative polymerase chain reaction for biomarker assays. Anal Chem 2014; 86:6180-3. [PMID: 24918650 PMCID: PMC4082389 DOI: 10.1021/ac500896k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 06/11/2014] [Indexed: 02/06/2023]
Abstract
Quantitative polymerase chain reaction is the current "golden standard" for quantification of nucleic acids; however, its utility is constrained by an inability to easily and reliably detect multiple targets in a single reaction. We have successfully overcome this problem with a novel combination of two widely used approaches: target-specific multiplex amplification with 15 cycles of polymerase chain reaction (PCR), followed by single-molecule detection of amplicons with atomic force microscopy (AFM). In test experiments comparing the relative expression of ten transcripts in two different human total RNA samples, we find good agreement between our single reaction, multiplexed PCR/AFM data, and data from 20 individual singleplex quantitative PCR reactions. This technique can be applied to virtually any analytical problem requiring sensitive measurement concentrations of multiple nucleic acid targets.
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Affiliation(s)
- Andrey Mikheikin
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Anita Olsen
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Kevin Leslie
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Bud Mishra
- Departments
of Computer Science and Mathematics, Courant Institute of Mathematical
Sciences, New York University, New York, New York 10012, United States
| | - James
K. Gimzewski
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los
Angeles, California 90095, United States
- California
NanoSystems Institute (CNSI) at University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jason Reed
- Department
of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
- VCU
Massey Cancer Center, Richmond, Virginia 23298, United States
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Trombetta JJ, Gennert D, Lu D, Satija R, Shalek AK, Regev A. Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing. ACTA ACUST UNITED AC 2014; 107:4.22.1-4.22.17. [PMID: 24984854 DOI: 10.1002/0471142727.mb0422s107] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
For the past several decades, due to technical limitations, the field of transcriptomics has focused on population-level measurements that can mask significant differences between individual cells. With the advent of single-cell RNA-Seq, it is now possible to profile the responses of individual cells at unprecedented depth and thereby uncover, transcriptome-wide, the heterogeneity that exists within these populations. This unit describes a method that merges several important technologies to produce, in high-throughput, single-cell RNA-Seq libraries. Complementary DNA (cDNA) is made from full-length mRNA transcripts using a reverse transcriptase that has terminal transferase activity. This, when combined with a second "template-switch" primer, allows for cDNAs to be constructed that have two universal priming sequences. Following preamplification from these common sequences, Nextera XT is used to prepare a pool of 96 uniquely indexed samples ready for Illumina sequencing.
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