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Zhang J, Xue J, Luo N, Chen F, Chen B, Zhao Y. Microwell array chip-based single-cell analysis. LAB ON A CHIP 2023; 23:1066-1079. [PMID: 36625143 DOI: 10.1039/d2lc00667g] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Single-cell profiling is key to uncover the cellular heterogeneity and drives deep understanding of cell fate. In recent years, microfluidics has become an ideal tool for single-cell profiling owing to its benefits of high throughput and automation. Among various microfluidic platforms, microwell has the advantages of simple operation and easy integration with in situ analysis ability, making it an ideal technique for single-cell studies. Herein, recent advances of single-cell analysis based on microwell array chips are summarized. We first introduce the design and preparation of different microwell chips. Then microwell-based cell capture and lysis strategies are discussed. We finally focus on advanced microwell-based analysis of single-cell proteins, nucleic acids, and metabolites. The challenges and opportunities for the development of microwell-based single-cell analysis are also presented.
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Affiliation(s)
- Jin Zhang
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
| | - Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
| | - Ningfeng Luo
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
| | - Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
| | - Badong Chen
- Institute of Artificial Intelligence and Robotics and the College of Artificial Intelligence, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China.
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2
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A 4 × 4 Array of Complementary Split-Ring Resonators for Label-Free Dielectric Spectroscopy. CHEMOSENSORS 2021. [DOI: 10.3390/chemosensors9120348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this study, complementary split-ring resonator (CSRR) metamaterial structures are proposed for label-free dielectric spectroscopy of liquids in microplates. This novel combination of an array of sensors and microplates is readily scalable and thus offers a great potential for non-invasive, rapid, and label-free dielectric spectroscopy of liquids in large microplate arrays. The proposed array of sensors on a printed circuit board consists of a microstrip line coupled to four CSRRs in cascade with resonant frequencies ranging from 7 to 10 GHz, spaced around 1 GHz. The microwells were manufactured and bonded to the CSRR using polydimethylsiloxane, whose resonant frequency is dependent on a complex relative permittivity of the liquid loaded in the microwell. The individual microstrip lines with CSRRs were interconnected to the measurement equipment using two electronically controllable microwave switches, which enables microwave measurements of the 4 × 4 CSRR array using only a two-port measurement system. The 4 × 4 microwell sensor arrays were calibrated and evaluated using water-ethanol mixtures with different ethanol concentrations. The proposed measurement setup offers comparable results to ones obtained using a dielectric probe, confirming the potential of the planar sensor array for large-scale microplate experiments.
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3
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Manzoor AA, Romita L, Hwang DK. A review on microwell and microfluidic geometric array fabrication techniques and its potential applications in cellular studies. CAN J CHEM ENG 2020. [DOI: 10.1002/cjce.23875] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ahmad Ali Manzoor
- Department of Chemical Engineering Ryerson University Toronto Ontario Canada
- Keenan Research Centre for Biomedical Science St. Michael's Hospital Toronto Ontario Canada
- Institute for Biomedical Engineering Science and Technology (iBEST) A partnership between Ryerson University and St. Michael's Hospital Toronto Ontario Canada
| | - Lauren Romita
- Department of Chemical Engineering Ryerson University Toronto Ontario Canada
- Keenan Research Centre for Biomedical Science St. Michael's Hospital Toronto Ontario Canada
- Institute for Biomedical Engineering Science and Technology (iBEST) A partnership between Ryerson University and St. Michael's Hospital Toronto Ontario Canada
| | - Dae Kun Hwang
- Department of Chemical Engineering Ryerson University Toronto Ontario Canada
- Keenan Research Centre for Biomedical Science St. Michael's Hospital Toronto Ontario Canada
- Institute for Biomedical Engineering Science and Technology (iBEST) A partnership between Ryerson University and St. Michael's Hospital Toronto Ontario Canada
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4
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Stein D, Thom V, Hubbuch J. High throughput screening setup of a scale-down device for membrane chromatography-aggregate removal of monoclonal antibodies. Biotechnol Prog 2020; 36:e3055. [PMID: 32710474 DOI: 10.1002/btpr.3055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/18/2020] [Accepted: 07/23/2020] [Indexed: 11/07/2022]
Abstract
In biopharmaceutical process development, resin-based high throughput screening (HTS) is well known for overcoming experimental limitations by permitting automated parallel processing at miniaturized scale, which results in fast data generation and reduced feed consumption. For membrane adsorber (MA), HTS solutions have so far only been available to a partial extent. Three case studies were performed with the aim of aligning HTS applications for MAs with those established for column chromatography: Process parameter range determination, mechanistic modeling (MM), and scalability. In order to exploit the MA typically features, such as high mass transfer and easy scalability, for scalable high throughput process development, a scale-down device (SDD) for MA was developed. Its applicability is confirmed for a monoclonal antibody aggregate removal step. The first case study explores the experimental application of the SDD developed. It uses bind and elute mode and variations of pH and salt concentration to obtain process operation windows for ion-exchange MAs Sartobind® S and Q. In the second case study, we successfully developed a mechanistic model based on parameters obtained from the SDD-HTS setup. The results proved to validate the use of the SDD developed for parameter estimation and thus model-based process development. The third case study shows the transferability and scalability of data from the SDD-HTS setup using both a direct scale factor and MM. Both approaches show good applicability with a deviation below 20% in the prediction of 10% dynamic breakthrough capacity and reliable scale-up from 0.42 to 800 ml.
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Affiliation(s)
- Dominik Stein
- Sartorius Stedim Biotech GmbH, Goettingen, Germany.,Department of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Volkmar Thom
- Sartorius Stedim Biotech GmbH, Goettingen, Germany
| | - Jürgen Hubbuch
- Department of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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5
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Sreejith KR, Ooi CH, Jin J, Dao DV, Nguyen NT. Digital polymerase chain reaction technology - recent advances and future perspectives. LAB ON A CHIP 2018; 18:3717-3732. [PMID: 30402632 DOI: 10.1039/c8lc00990b] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Digital polymerase chain reaction (dPCR) technology has remained a "hot topic" in the last two decades due to its potential applications in cell biology, genetic engineering, and medical diagnostics. Various advanced techniques have been reported on sample dispersion, thermal cycling and output monitoring of digital PCR. However, a fully automated, low-cost and handheld digital PCR platform has not been reported in the literature. This paper attempts to critically evaluate the recent developments in techniques for sample dispersion, thermal cycling and output evaluation for dPCR. The techniques are discussed in terms of hardware simplicity, portability, cost-effectiveness and suitability for automation. The present paper also discusses the research gaps observed in each step of dPCR and concludes with possible improvements toward portable, low-cost and automatic digital PCR systems.
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Affiliation(s)
- Kamalalayam Rajan Sreejith
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, 4111 Queensland, Australia.
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Veses-Garcia M, Antypas H, Löffler S, Brauner A, Andersson-Svahn H, Richter-Dahlfors A. Rapid Phenotypic Antibiotic Susceptibility Testing of Uropathogens Using Optical Signal Analysis on the Nanowell Slide. Front Microbiol 2018; 9:1530. [PMID: 30042754 PMCID: PMC6048231 DOI: 10.3389/fmicb.2018.01530] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 06/20/2018] [Indexed: 01/30/2023] Open
Abstract
Achieving fast antimicrobial susceptibility results is a primary goal in the fight against antimicrobial resistance. Standard antibiotic susceptibility testing (AST) takes, however, at least a day from patient sample to susceptibility profile. Here, we developed and clinically validated a rapid phenotypic AST based on a miniaturized nanotiter plate, the nanowell slide, that holds 672 wells in a 500 nl format for bacterial cultivation. The multitude of nanowells allows multiplexing with a panel of six antibiotics relevant for urinary tract infections. Inclusion of seven concentrations per antibiotic plus technical replicates enabled us to determine a precise minimum inhibitory concentration for 70 clinical uropathogenic Escherichia coli isolates. By combining optical recordings of bacterial growth with an algorithm for optical signal analysis, we calculated Tlag, the point of transition from lag to exponential phase, in each nanoculture. Algorithm-assisted analysis determined antibiotic susceptibility as early as 3 h 40 min. In comparison to standard disk diffusion assays, the nanowell AST showed a total categorical agreement of 97.9% with 2.6% major errors and 0% very major errors for all isolate-antibiotic combination tested. Taking advantage of the optical compatibility of the nanowell slide, we performed microscopy to illustrate its potential in defining susceptibility profiles based on bacterial morphotyping. The excellent clinical performance of the nanowell AST, combined with a short detection time, morphotyping, and the very low consumption of reagents clearly show the advantage of this phenotypic AST as a diagnostic tool in a clinical setting.
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Affiliation(s)
- Marta Veses-Garcia
- Swedish Medical Nanoscience Center, Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Haris Antypas
- Swedish Medical Nanoscience Center, Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Susanne Löffler
- Swedish Medical Nanoscience Center, Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Annelie Brauner
- Department of Microbiology, Tumor and Cell Biology, Division of Clinical Microbiology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Helene Andersson-Svahn
- Division of Proteomics and Nanobiotechnology, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Agneta Richter-Dahlfors
- Swedish Medical Nanoscience Center, Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
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7
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Antypas H, Veses-Garcia M, Weibull E, Andersson-Svahn H, Richter-Dahlfors A. A universal platform for selection and high-resolution phenotypic screening of bacterial mutants using the nanowell slide. LAB ON A CHIP 2018; 18:1767-1777. [PMID: 29781496 PMCID: PMC5996734 DOI: 10.1039/c8lc00190a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/07/2018] [Indexed: 06/08/2023]
Abstract
The Petri dish and microtiter plate are the golden standard for selection and screening of bacteria in microbiological research. To improve on the limited resolution and throughput of these methods, we developed a universal, user-friendly platform for selection and high-resolution phenotypic screening based on the nanowell slide. This miniaturized platform has an optimal ratio between throughput and assay complexity, holding 672 nanowells of 500 nl each. As monoclonality is essential in bacterial genetics, we used FACS to inoculate each nanowell with a single bacterium in 15 min. We further extended the protocol to select and sort only bacteria of interest from a mixed culture. We demonstrated this by isolating single transposon mutants generated by a custom-made transposon with dual selection for GFP fluorescence and kanamycin resistance. Optical compatibility of the nanowell slide enabled phenotypic screening of sorted mutants by spectrophotometric recording during incubation. By processing the absorbance data with our custom algorithm, a phenotypic screen for growth-associated mutations was performed. Alternatively, by processing fluorescence data, we detected metabolism-associated mutations, exemplified by a screen for β-galactosidase activity. Besides spectrophotometry, optical compatibility enabled us to perform microscopic analysis directly in the nanowells to screen for mutants with altered morphologies. Despite the miniaturized format, easy transition from nano- to macroscale cultures allowed retrieval of bacterial mutants for downstream genetic analysis, demonstrated here by a cloning-free single-primer PCR protocol. Taken together, our FACS-linked nanowell slide replaces manual selection of mutants on agar plates, and enables combined selection and phenotypic screening in a one-step process. The versatility of the nanowell slide, and the modular workflow built on mainstream technologies, makes our universal platform widely applicable in microbiological research.
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Affiliation(s)
- H. Antypas
- Swedish Medical Nanoscience Center
, Department of Neuroscience
, Karolinska Institutet
,
Stockholm
, Sweden
.
| | - M. Veses-Garcia
- Swedish Medical Nanoscience Center
, Department of Neuroscience
, Karolinska Institutet
,
Stockholm
, Sweden
.
| | - E. Weibull
- Division of Proteomics and Nanobiotechnology
, Science for Life Laboratory
, KTH-Royal Institute of Technology
,
Stockholm
, Sweden
| | - H. Andersson-Svahn
- Division of Proteomics and Nanobiotechnology
, Science for Life Laboratory
, KTH-Royal Institute of Technology
,
Stockholm
, Sweden
| | - A. Richter-Dahlfors
- Swedish Medical Nanoscience Center
, Department of Neuroscience
, Karolinska Institutet
,
Stockholm
, Sweden
.
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8
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Wang C, Liu W, Wei Q, Ren L, Tan M, Yu Y. A novel dual-well array chip for efficiently trapping single-cell in large isolated micro-well without complicated accessory equipment. BIOMICROFLUIDICS 2018; 12:034103. [PMID: 29774084 PMCID: PMC5938174 DOI: 10.1063/1.5030203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/20/2018] [Indexed: 06/08/2023]
Abstract
Conventional cell-sized well arrays have advantages of high occupancy, simple operation, and low cost for capturing single-cells. However, they have insufficient space for including reagents required for cell treatment or analysis, which restricts the wide application of cell-sized well arrays as a single-cell research tool alone. Here, we present a novel dual-well array chip, which integrates capture-wells (20 μm in diameter) with reaction-wells (100 μm in diameter) and describe a flow method for convenient single-cell analysis requiring neither complicated infra-structure nor high expenditure, while enabling highly efficient single cell trapping (75.8%) with only 11.3% multi-cells. Briefly, the cells are first loaded into the dual-wells by gravity and then multi-cells in the reaction-wells are washed out by phosphate buffer saline. Next, biochemical reagents are loaded into reaction-wells using the scraping method and the chip is packed as a sandwich structure. We thereby successfully measured intracellular β-galactosidase activity of K562 cells at the single-cell level. We also used computational simulations to illustrate the working principle of dual-well structure and found out a relationship between the wall shear stress distribution and the aspect ratio of the dual-well array chip which provides theoretical guidance for designing multi-wells chip for convenient single-cell analysis. Our work produced the first dual-well chip that can simultaneously provide a high occupancy rate for single cells and sufficient space for reagents, as well as being low in cost and simple to operate. We believe that the feasibility and convenience of our method will enhance its use as a practical single-cell research tool.
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Affiliation(s)
| | | | | | | | | | - Yude Yu
- Author to whom correspondence should be addressed: . Tel.: 86-10-82304979
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9
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Popova AA, Demir K, Hartanto TG, Schmitt E, Levkin PA. Droplet-microarray on superhydrophobic–superhydrophilic patterns for high-throughput live cell screenings. RSC Adv 2016. [DOI: 10.1039/c6ra06011k] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Droplet-microarray platform based on superhydrophobic–superhydrophilic patterning allows for miniaturized high throughput drug and transfection screenings of live cells in separated nanoliter droplets.
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Affiliation(s)
- Anna A. Popova
- Karlsruhe Institute of Technology
- Institute of Toxicology and Genetics
- 76344 Eggenstein-Leopoldshafen
- Germany
| | - Konstantin Demir
- Karlsruhe Institute of Technology
- Institute of Toxicology and Genetics
- 76344 Eggenstein-Leopoldshafen
- Germany
| | - Titus Genisius Hartanto
- Karlsruhe Institute of Technology
- Institute of Toxicology and Genetics
- 76344 Eggenstein-Leopoldshafen
- Germany
| | - Eric Schmitt
- Karlsruhe Institute of Technology
- Institute of Toxicology and Genetics
- 76344 Eggenstein-Leopoldshafen
- Germany
| | - Pavel A. Levkin
- Karlsruhe Institute of Technology
- Institute of Toxicology and Genetics
- 76344 Eggenstein-Leopoldshafen
- Germany
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10
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Popova AA, Schillo SM, Demir K, Ueda E, Nesterov-Mueller A, Levkin PA. Droplet-Array (DA) Sandwich Chip: A Versatile Platform for High-Throughput Cell Screening Based on Superhydrophobic-Superhydrophilic Micropatterning. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:5217-5222. [PMID: 26255809 DOI: 10.1002/adma.201502115] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 06/30/2015] [Indexed: 06/04/2023]
Abstract
A droplet-array (DA) sandwich chip is a miniaturized platform for cell-based high-throughput screening. It is based on sandwiching of a glass slide with a preprinted library and a superhydrophobic-superhydrophilic pattern, which consists of thousands of simultaneously formed microdroplets containing cells. The DA sandwich chip allows for one-step cell seeding, simultaneous initiation of screening, and 1000 times less reagent consumption than a regular 96-well plate.
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Affiliation(s)
- Anna A Popova
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Sebastian M Schillo
- Karlsruhe Institute of Technology, Institute of Microstructure Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Konstantin Demir
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Erica Ueda
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - A Nesterov-Mueller
- Karlsruhe Institute of Technology, Institute of Microstructure Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Pavel A Levkin
- Karlsruhe Institute of Technology, Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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Digital Microfluidics for Manipulation and Analysis of a Single Cell. Int J Mol Sci 2015; 16:22319-32. [PMID: 26389890 PMCID: PMC4613310 DOI: 10.3390/ijms160922319] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 08/12/2015] [Accepted: 08/18/2015] [Indexed: 12/31/2022] Open
Abstract
The basic structural and functional unit of a living organism is a single cell. To understand the variability and to improve the biomedical requirement of a single cell, its analysis has become a key technique in biological and biomedical research. With a physical boundary of microchannels and microstructures, single cells are efficiently captured and analyzed, whereas electric forces sort and position single cells. Various microfluidic techniques have been exploited to manipulate single cells through hydrodynamic and electric forces. Digital microfluidics (DMF), the manipulation of individual droplets holding minute reagents and cells of interest by electric forces, has received more attention recently. Because of ease of fabrication, compactness and prospective automation, DMF has become a powerful approach for biological application. We review recent developments of various microfluidic chips for analysis of a single cell and for efficient genetic screening. In addition, perspectives to develop analysis of single cells based on DMF and emerging functionality with high throughput are discussed.
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12
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Boitard L, Cottinet D, Bremond N, Baudry J, Bibette J. Growing microbes in millifluidic droplets. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400089] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Laurent Boitard
- Laboratoire de Colloïdes et Matériaux Divisés; UMR CBI 8231, ESPCI ParisTech, 10 rue Vauquelin; Paris France
| | - Denis Cottinet
- Laboratoire de Colloïdes et Matériaux Divisés; UMR CBI 8231, ESPCI ParisTech, 10 rue Vauquelin; Paris France
| | - Nicolas Bremond
- Laboratoire de Colloïdes et Matériaux Divisés; UMR CBI 8231, ESPCI ParisTech, 10 rue Vauquelin; Paris France
| | - Jean Baudry
- Laboratoire de Colloïdes et Matériaux Divisés; UMR CBI 8231, ESPCI ParisTech, 10 rue Vauquelin; Paris France
| | - Jérôme Bibette
- Laboratoire de Colloïdes et Matériaux Divisés; UMR CBI 8231, ESPCI ParisTech, 10 rue Vauquelin; Paris France
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Abstract
Unprecedented access to the biology of single cells is now feasible, enabled by recent technological advancements that allow us to manipulate and measure sparse samples and achieve a new level of resolution in space and time. This review focuses on advances in tools to study single cells for specific areas of biology. We examine both mature and nascent techniques to study single cells at the genomics, transcriptomics, and proteomics level. In addition, we provide an overview of tools that are well suited for following biological responses to defined perturbations with single-cell resolution. Techniques to analyze and manipulate single cells through soluble and chemical ligands, the microenvironment, and cell-cell interactions are provided. For each of these topics, we highlight the biological motivation, applications, methods, recent advances, and opportunities for improvement. The toolbox presented in this review can function as a starting point for the design of single-cell experiments.
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Real-time quantification of protein expression and translocation at individual cell resolution using imaging-dish-based live cell array. Anal Bioanal Chem 2014; 406:7085-101. [PMID: 25258284 DOI: 10.1007/s00216-014-8157-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 08/19/2014] [Accepted: 09/02/2014] [Indexed: 01/19/2023]
Abstract
Cell populations represent intrinsically heterogeneous systems with a high level of spatiotemporal complexity. Monitoring and understanding cell-to-cell diversity is essential for the research and application of intra- and interpopulation variations. Optical analysis of live cells is challenging since both adherent and nonadherent cells change their spatial location. However, most currently available single-cell techniques do not facilitate treatment and monitoring of the same live cells over time throughout multistep experiments. An imaging-dish-based live cell array (ID-LCA) has been developed and produced for cell handling, culturing, and imaging of numerous live cells. The dish is composed of an array of pico scale cavities-pico wells (PWs) embossed on its glass bottom. Cells are seeded, cultured, treated, and spatiotemporally measured on the ID-LCA, while each cell or small group of cells are locally constrained in the PWs. Finally, predefined cells can be retrieved for further evaluation. Various types of ID-LCAs were used in this proof-of-principle work, to demonstrate on-ID-LCA transfection of fluorescently tagged chimeric proteins, as well as the detection and kinetic analysis of their induced translocation. High variability was evident within cell populations with regard to protein expression levels as well as the extent and dynamics of protein redistribution. The association of these parameters with cell morphology and functional parameters was examined. Both the new methodology and the device facilitate research of the translocation process at individual cell resolution within large populations and thus, can potentially be used in high-throughput fashion.
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15
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Bacterial nanoscale cultures for phenotypic multiplexed antibiotic susceptibility testing. J Clin Microbiol 2014; 52:3310-7. [PMID: 24989602 DOI: 10.1128/jcm.01161-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
An optimal antimicrobial drug regimen is the key to successful clinical outcomes of bacterial infections. To direct the choice of antibiotic, access to fast and precise antibiotic susceptibility profiling of the infecting bacteria is critical. We have developed a high-throughput nanowell antibiotic susceptibility testing (AST) device for direct, multiplexed analysis. By processing in real time the optical recordings of nanoscale cultures of reference and clinical uropathogenic Escherichia coli strains with a mathematical algorithm, the time point when growth shifts from lag phase to early logarithmic phase (Tlag) was identified for each of the several hundreds of cultures tested. Based on Tlag, the MIC could be defined within 4 h. Heatmap presentation of data from this high-throughput analysis allowed multiple resistance patterns to be differentiated at a glance. With a possibility to enhance multiplexing capacity, this device serves as a high-throughput diagnostic tool that rapidly aids clinicians in prescribing the optimal antibiotic therapy.
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16
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Ultrasound-Induced Cell–Cell Interaction Studies in a Multi-Well Microplate. MICROMACHINES 2014. [DOI: 10.3390/mi5010027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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17
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Ankam S, Teo BKK, Kukumberg M, Yim EKF. High throughput screening to investigate the interaction of stem cells with their extracellular microenvironment. Organogenesis 2013; 9:128-42. [PMID: 23899508 PMCID: PMC3896583 DOI: 10.4161/org.25425] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/19/2013] [Accepted: 06/15/2013] [Indexed: 02/06/2023] Open
Abstract
Stem cells in vivo are housed within a functional microenvironment termed the "stem cell niche." As the niche components can modulate stem cell behaviors like proliferation, migration and differentiation, evaluating these components would be important to determine the most optimal platform for their maintenance or differentiation. In this review, we have discussed methods and technologies that have aided in the development of high throughput screening assays for stem cell research, including enabling technologies such as the well-established multiwell/microwell plates and robotic spotting, and emerging technologies like microfluidics, micro-contact printing and lithography. We also discuss the studies that utilized high throughput screening platform to investigate stem cell response to extracellular matrix, topography, biomaterials and stiffness gradients in the stem cell niche. The combination of the aforementioned techniques could lay the foundation for new perspectives in further development of high throughput technology and stem cell research.
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Affiliation(s)
- Soneela Ankam
- Department of Bioengineering; National University of Singapore; Singapore
- Duke-NUS Graduate Medical School; Singapore
| | - Benjamin KK Teo
- Department of Bioengineering; National University of Singapore; Singapore
- Mechanobiology Institute Singapore; National University of Singapore; Singapore
| | - Marek Kukumberg
- Mechanobiology Institute Singapore; National University of Singapore; Singapore
| | - Evelyn KF Yim
- Department of Bioengineering; National University of Singapore; Singapore
- Mechanobiology Institute Singapore; National University of Singapore; Singapore
- Department of Surgery; National University of Singapore; Singapore
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Sott K, Eriksson E, Petelenz E, Goksör M. Optical systems for single cell analyses. Expert Opin Drug Discov 2013; 3:1323-44. [PMID: 23496168 DOI: 10.1517/17460441.3.11.1323] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Data extracted from a population of cells represent the average response from all cells within the population. Even when the cells are genetically identical, cell-to-cell variations and genetic noise can make the cells respond in completely different ways. To understand the mechanisms behind the behaviour of a population, the cells must also be analysed on an individual basis. OBJECTIVE This review highlights the use of optical manipulation, microfluidics and advanced fluorescence imaging techniques for the acquisition of single cell data. CONCLUSION By implementation of these three techniques, it is possible to achieve a deeper insight into the principles underlying cellular functioning and a more thorough understanding of the phenomena often observed in cell populations, thus facilitating research in drug discovery.
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Affiliation(s)
- Kristin Sott
- Postdoctoral fellow University of Gothenburg, Department of Physics, SE-41296, Gothenburg, Sweden
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19
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Weibull E, Matsui S, Sakai M, Andersson Svahn H, Ohashi T. Microfluidic device for generating a stepwise concentration gradient on a microwell slide for cell analysis. BIOMICROFLUIDICS 2013; 7:64115. [PMID: 24396549 PMCID: PMC3874052 DOI: 10.1063/1.4846435] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 11/28/2013] [Indexed: 05/04/2023]
Abstract
Understanding biomolecular gradients and their role in biological processes is essential for fully comprehending the underlying mechanisms of cells in living tissue. Conventional in vitro gradient-generating methods are unpredictable and difficult to characterize, owing to temporal and spatial fluctuations. The field of microfluidics enables complex user-defined gradients to be generated based on a detailed understanding of fluidic behavior at the μm-scale. By using microfluidic gradients created by flow, it is possible to develop rapid and dynamic stepwise concentration gradients. However, cells exposed to stepwise gradients can be perturbed by signals from neighboring cells exposed to another concentration. Hence, there is a need for a device that generates a stepwise gradient at discrete and isolated locations. Here, we present a microfluidic device for generating a stepwise concentration gradient, which utilizes a microwell slide's pre-defined compartmentalized structure to physically separate different reagent concentrations. The gradient was generated due to flow resistance in the microchannel configuration of the device, which was designed using hydraulic analogy and theoretically verified by computational fluidic dynamics simulations. The device had two reagent channels and two dilutant channels, leading to eight chambers, each containing 4 microwells. A dose-dependency assay was performed using bovine aortic endothelial cells treated with saponin. High reproducibility between experiments was confirmed by evaluating the number of living cells in a live-dead assay. Our device generates a fully mixed fluid profile using a simple microchannel configuration and could be used in various gradient studies, e.g., screening for cytostatics or antibiotics.
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Affiliation(s)
- Emilie Weibull
- Division of Proteomics and Nanobiotechnology, Science for Life Laboratory, KTH-Royal Institute of Technology, 171 65 Stockholm, Sweden
| | - Shunsuke Matsui
- Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Manabu Sakai
- Graduate School of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8628, Japan
| | - Helene Andersson Svahn
- Division of Proteomics and Nanobiotechnology, Science for Life Laboratory, KTH-Royal Institute of Technology, 171 65 Stockholm, Sweden
| | - Toshiro Ohashi
- Faculty of Engineering, Hokkaido University, Sapporo Hokkaido 060-8628, Japan
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20
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Abstract
Powerful methods in molecular biology are abundant; however, in many fields including hematology, stem cell biology, tissue engineering, and cancer biology, data from tools and assays that analyze the average signals from many cells may not yield the desired result because the cells of interest may be in the minority-their behavior masked by the majority-or because the dynamics of the populations of interest are offset in time. Accurate characterization of samples with high cellular heterogeneity may only be achieved by analyzing single cells. In this chapter, we discuss the rationale for performing analyses on individual cells in more depth, cover the fields of study in which single-cell behavior is yielding new insights into biological and clinical questions, and speculate on how single-cell analysis will be critical in the future.
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Affiliation(s)
- Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles, CA, USA.
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21
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Abstract
In order to better understand cellular processes and behavior, a controlled way of studying high numbers of single cells and their clone formation is greatly needed. This chapter describes a microwell plate with 672 wells in a standard array/slide format, applied for single-cell culture and analysis. Single cells can be seeded into each well of the plate (1) manually or (2) automatically using a sorting flow cytometer, followed by week-long culture and detection of cell growth, protein expression, etc. The glass/silicon plate is compatible with most standard instrumentation to facilitate easy handling and enable use of the plate for single-cell analysis in most laboratory settings.
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Affiliation(s)
- Sara Lindström
- Department of Cell and Molecular Biology, Science For Life Laboratory, Karolinska Institute, Stockholm, Sweden.
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22
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Abstract
Ultrasonic manipulation has emerged as a simple and powerful tool for trapping, aggregation, and separation of cells. During the last decade, an increasing amount of applications in the microscale format has been demonstrated, of which the most important is acoustophoresis (continuous acoustic cell or particle separation). Traditionally, the technology has proven to be suitable for treatment of high-density cell and particle suspensions, where large cell and particle numbers are handled simultaneously. In this chapter, we describe how ultrasound can be combined with microfluidics and microplates for particle and cell manipulation approaching the single-cell level. We demonstrate different cell handling methods with the purpose to select, trap, aggregate, and position individual cells in microdevices based on multifrequency ultrasonic actuation, and we discuss applications of the technology involving immune cell interaction studies.
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Affiliation(s)
- Martin Wiklund
- Department of Biomedical and X-Ray Physics, Royal Institute of Technology, Stockholm, Sweden.
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23
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A silicon-glass microwell platform for high-resolution imaging and high-content screening with single cell resolution. Biomed Microdevices 2011; 13:683-93. [DOI: 10.1007/s10544-011-9538-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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24
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Demming S, Sommer B, Llobera A, Rasch D, Krull R, Büttgenbach S. Disposable parallel poly(dimethylsiloxane) microbioreactor with integrated readout grid for germination screening of Aspergillus ochraceus. BIOMICROFLUIDICS 2011; 5:14104. [PMID: 21423594 PMCID: PMC3060924 DOI: 10.1063/1.3553004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2010] [Accepted: 12/24/2010] [Indexed: 05/07/2023]
Abstract
In this work a disposable, parallel microbioreactor (MBR) suitable for screening in batch or continuous mode is presented. The reactor consists of five parallel microchambers made of poly(dimethylsiloxane) bonded to a glass substrate. A grid structure is engraved on each chamber, allowing subsequent morphology imaging. Measurements are recorded over the entire cultivation period with constant parameters, namely, position and focus in the z-axis. The microdevice may be used for either parallel, uni- or multiparametric screening, and overcomes the drawback of gridless microwell plates which require expensive equipment such as an inverted microscope with an automatic stage. To validate the scalability from laboratory scale to microscale, and thus the cultivation protocol in the MBR, the germination of fungal spores (A. ochraceus) is evaluated for two different key magnitudes (pH and temperature) and compared to the results obtained from conventional laboratory scale systems (flasks and agar plates). Information on germination capacity with regard to interspecies' variability allows for optimization of industrial processes as optimal pH and temperature matched to the mesoscopic cultivation systems. The germination conditions therefore remain unaffected inside the MBR, while providing the following advantages: (i) dramatic reduction of medium consumption, (ii) submerged cultivation with constant oxygen supply, (iii) assured low cost and disposability, and (iv) possibility of a continuous cultivation mode.
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25
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Khorshidi MA, Vanherberghen B, Kowalewski JM, Garrod KR, Lindström S, Andersson-Svahn H, Brismar H, Cahalan MD, Önfelt B. Analysis of transient migration behavior of natural killer cells imaged in situ and in vitro. Integr Biol (Camb) 2011; 3:770-8. [DOI: 10.1039/c1ib00007a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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26
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Demming S, Vila-Planas J, Aliasghar Zadeh S, Edlich A, Franco-Lara E, Radespiel R, Büttgenbach S, Llobera A. Poly(dimethylsiloxane) photonic microbioreactors based on segmented waveguides for local absorbance measurement. Electrophoresis 2010; 32:431-9. [PMID: 21298669 DOI: 10.1002/elps.201000482] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 11/03/2010] [Accepted: 11/09/2010] [Indexed: 11/09/2022]
Abstract
We present the development of microbioreactors (MBRs) based on poly(dimethylsiloxane) (PDMS) segmented waveguides (SWG) for local absorbance measurements. Two different MBRs were studied, either using symmetric or asymmetric SWG (being defined as MBR-S and MBR-A, respectively). Their optical and fluidic performances were numerically analyzed, showing robustness from an optical point of view and distinct fluid flow profile. The optical characterization was done in two steps. Initially, the experimental limit of detection (LOD) and the sensitivity were determined for two different analytes (fluorescein and methylorange). With both systems, a similar limit of detection for both analytes was obtained, being in the micromolar level. Their sensitivities were 20.2±0.3 (×10⁻³) A.U./μM and 5.5±0.2 (×10⁻³) A.U./μM for fluorescein and methylorange, respectively. Once validated its applicability for local absorbance measurements, a continuous cultivation of Saccharomyces cerevisiae was done to test the viability of the proposed systems for photonic MBRs. Concretely, the cell growth was locally monitored inside the MBR during 33 h. Spectral analysis showed that the determination of the culture parameters were wavelength dependant, with a growth rate of 0.39±0.02 h⁻¹ and a doubling time of 1.65±0.09 h at an optimal wavelength of 469.9±0.3 nm. Besides the easy and monolithic integration of the SWG into poly(dimethylsiloxane) microfluidic systems, the results presented here are very promising for the application in any disposable photonic lab-on-a-chip systems used for online analysis or photonic MBRs.
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Affiliation(s)
- Stefanie Demming
- Institut für Mikrotechnik, Technische Universität Braunschweig, Braunschweig, Germany
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27
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Lindström S, Andersson-Svahn H. Overview of single-cell analyses: microdevices and applications. LAB ON A CHIP 2010; 10:3363-72. [PMID: 20967379 DOI: 10.1039/c0lc00150c] [Citation(s) in RCA: 169] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Numerous microdevices developed for single-cell analyses have been presented in the last decades. Practical usefulness in biological and clinical settings has become an important focus during the development and implementation of new structures and assays. Single-cell analysis has been applied in intracellular research, gene- and protein content and expression, PCR, cell culture and division, clone formation, differentiation, morphology, lysis, separation, sorting, cytotoxicity and fluorescence screens, antibody secretion, etc. as discussed here along with brief descriptions of the technical devices used for the studies, e.g. well-, trap-, pattern-, and droplet-based structures. This review aims to serve as an overview of available techniques for single-cell analysis by describing the different biological single-cell assays that have been performed to date and how each individual application requires a particular device design.
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Affiliation(s)
- Sara Lindström
- Department of Cell and Molecular Biology, Karolinska Institute, Box 285, SE-171 77 Stockholm, Sweden.
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28
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Vanherberghen B, Manneberg O, Christakou A, Frisk T, Ohlin M, Hertz HM, Önfelt B, Wiklund M. Ultrasound-controlled cell aggregation in a multi-well chip. LAB ON A CHIP 2010; 10:2727-32. [PMID: 20820481 DOI: 10.1039/c004707d] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
We demonstrate a microplate platform for parallelized manipulation of particles or cells by frequency-modulated ultrasound. The device, consisting of a silicon-glass microchip and a single ultrasonic transducer, enables aggregation, positioning and high-resolution microscopy of cells distributed in an array of 100 microwells centered on the microchip. We characterize the system in terms of temperature control, aggregation and positioning efficiency, and cell viability. We use time-lapse imaging to show that cells continuously exposed to ultrasound are able to divide and remain viable for at least 12 hours inside the device. Thus, the device can be used to induce and maintain aggregation in a parallelized fashion, facilitating long-term microscopy studies of, e.g., cell-cell interactions.
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Affiliation(s)
- Bruno Vanherberghen
- Department of Applied Physics, Royal Institute of Technology, AlbaNova University Center, SE-106 91, Stockholm, Sweden
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29
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Liu C, Liu J, Gao D, Ding M, Lin JM. Fabrication of Microwell Arrays Based on Two-Dimensional Ordered Polystyrene Microspheres for High-Throughput Single-Cell Analysis. Anal Chem 2010; 82:9418-24. [DOI: 10.1021/ac102094r] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Chuansen Liu
- The Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jiangjiang Liu
- The Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Dan Gao
- The Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Mingyu Ding
- The Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jin-Ming Lin
- The Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
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30
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Ibarlucea B, Fernandez-Rosas E, Vila-Planas J, Demming S, Nogues C, Plaza JA, Büttgenbach S, Llobera A. Cell screening using disposable photonic lab on a chip systems. Anal Chem 2010; 82:4246-51. [PMID: 20411976 DOI: 10.1021/ac100590z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A low-cost photonic lab on a chip with three different working regimes for cell screening is presented. The proposed system is able to perform scattering, scattering + absorption, and absorption measurements without any modification. Opposite to the standard flow cytometers, in this proposed configuration, a single 30 ms scan allows to obtain information regarding the cell optical properties. An additional novelty is that the whole spectrum is obtained and analyzed, being then possible to determine for each regime which is the optimal working wavelength that would provide the best performance in terms of sensitivity and limit of detection (LOD). Experimental results have provided with an LOD of 54.9 +/- 0.7 cells (in the scattering regime using unlabeled cells), 53 +/- 1 cells (in the scattering + absorption regime using labeled cells), and 105 +/- 4 cells (in the absorption regime using labeled cells). Finally, the system has also been used for measuring the dead/live cell ratio, obtaining LODs between 7.6 +/- 0.4% and 6.7 +/- 0.3%, depending on the working regime used.
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Affiliation(s)
- Bergoi Ibarlucea
- Centre Nacional de Microelectrònica (IMB-CNM, CSIC), Barcelona, Spain
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31
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Pla-Roca M, Leulmi RF, Djambazian H, Sundararajan S, Juncker D. Addressable nanowell arrays formed using reversibly sealable hybrid elastomer-metal stencils. Anal Chem 2010; 82:3848-55. [PMID: 20377190 DOI: 10.1021/ac100335d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
There are two major array formats used in life science research and biomedical analysis. The first is the microwell plate format with millimeter-sized wells each with microliter capacity addressed individually and repeatedly during experiments. The second is the microarray format with micrometer-sized spots that are patterned initially but not addressable individually thereafter. Here, we present an addressable nanoliter-well plate with micrometer sized wells that combines the advantages of the two array formats. The nanowells are formed by reversibly sealing a steel stencil featuring an array of micrometer-scale openings to an optically transparent substrate. The nanowells have a capacity of approximately 1 nL, are approximately 140 microm in diameter, and are arrayed at a density of 1600 wells cm(-2). A soft polymer is patterned photolithographically around each opening so as to form a microgasket for pressure sensitive, liquid tight, and reversible sealing to any type of smooth substrate, either hydrophilic or hydrophobic. The rigidity of the steel prevents the distortion that occurs in soft, all-polymeric stencils and permits accurate registration across the entire array, which in turn allows for repeated, individual addressing of wells using an inkjet spotter. The stencils are used to pattern cells, make protein microarrays, and create nanowells on surfaces to study reverse transfection by first spotting plasmids encoding fluorescent proteins into the wells, seeding cells, and monitoring the transfection of the cells in real time using time-lapse imaging. The hybrid elastomer-metal stencils (HEMSs) are versatile and useful for multiplexed analysis of drugs, biomolecules, and cells with microarray density.
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Affiliation(s)
- Mateu Pla-Roca
- Biomedical Engineering Department, McGill University, Montreal, Quebec, Canada H3A 1A4
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32
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Lindström S, Andersson-Svahn H. Miniaturization of biological assays -- overview on microwell devices for single-cell analyses. Biochim Biophys Acta Gen Subj 2010; 1810:308-16. [PMID: 20451582 DOI: 10.1016/j.bbagen.2010.04.009] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 04/07/2010] [Accepted: 04/16/2010] [Indexed: 01/08/2023]
Abstract
BACKGROUND Today, cells are commonly analyzed in ensembles, i.e. thousands of cells per sample, yielding results on the average response of the cells. However, cellular heterogeneity implies the importance of studying how individual cells respond, one by one, in order to learn more about drug targeting and cellular behavior. SCOPE OF REVIEW This review discusses general aspects on miniaturization of biological assays and in particular summarizes single-cell assays in microwell formats. A range of microwell-based chips are discussed with regard to their well characteristics, cell handling, choice of material etc. along with available detection systems for single-cell studies. History and trends in microsystem technology, various commonly used materials for device fabrication, and conventional methods for single-cell analysis are also discussed, before a closing section with a detailed example from our research in the field. MAJOR CONCLUSIONS A range of miniaturized and microwell devices have shown useful for studying individual cells. GENERAL SIGNIFICANCE In vitro assays offering low volume sampling and rapid analysis in a high-throughput manner are of great interest in a wide range of single-cell applications. Size compatibility between a cell and micron-sized tools has encouraged the field of micro- and nanotechnologies to move into areas such as life sciences and molecular biology. To test as many compounds as possible against a given amount of patient sample requires miniaturized tools where low volume sampling is sufficient for accurate results and on which a high number of experiments per cm(2) can be performed. This article is part of a Special Issue entitled Nanotechnologies - Emerging Applications in Biomedicine.
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Affiliation(s)
- Sara Lindström
- Division of Nanobiotechnology, School of Biotechnology,Albanova University Center, Royal Institute of Technology, Stockholm, Sweden.
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33
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Anderson K, Cooper JM, Haswell SJ, Marshall D, Yin H, Zhang X. Microfluidic-based measurements of cytochrome P450 enzyme activity of primary mammalian hepatocytes. Analyst 2010; 135:1282-7. [PMID: 20401410 DOI: 10.1039/c0an00031k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A microfluidic-based system was developed for the in situ monitoring of the 7-ethoxyresorufin O-dealkylation (EROD) activity of primary rat hepatocytes by measuring the fluorescent intensity of both cells and their surrounding media. The microfluidic chip was designed to allow the cell suspension and test reagent to be introduced in a layer-by-layer flow format, thereby resulting in a short mixing time by diffusion. A good linear relationship was obtained between the resorufin concentration up to 30 microM and fluorescent intensity over the chip's circular chamber area. The EROD activity was determined with 3-methylcholanthrene (3-MC)-induced hepatocytes. The inhibition effect of alpha-naphthoflavone was also examined on EROD activity resulting in an IC(50) value of 12.98 microM.
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Affiliation(s)
- Keith Anderson
- LGC Limited, Queens Road, Teddington, Middlesex TW11 0LY, UK
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34
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Lindström S, Mori K, Ohashi T, Andersson-Svahn H. A microwell array device with integrated microfluidic components for enhanced single-cell analysis. Electrophoresis 2010; 30:4166-71. [PMID: 19938185 DOI: 10.1002/elps.200900572] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Increasing awareness of the importance of cell heterogeneity in many biological and medical contexts is prompting increasing interest in systems that allow single-cell analysis rather than conventional bulk analysis (which provides average values for variables of interest from large numbers of cells). Recently, we presented a microwell chip for long-term, high-throughput single-cell analysis. The chip has proved to be useful for purposes such as screening individual cancer and stem cells for protein/gene markers. However, liquids in the wells can only be added or changed by manually rinsing the chip, or parts of it. This procedure has several well-known drawbacks--including risks of cross-contamination, large dead volumes and laboriousness--but there have been few previous attempts to integrate liquid rinsing/switching channels in "ready-to-use" systems for single-cell analysis. Here we present a microwell system designed (using flow simulations) for single-cell analysis with integrated microfluidic components (microchannels, magnetically driven micropumps and reservoirs) for supplying the cell culture wells with reagents, or rinsing, thus facilitating controlled, directed liquid handling. It can be used totally independently, since tubing is not essential. The practical utility of the integrated system has been demonstrated by culturing endothelial cells in the microwells, and successfully applying live-cell Calcein AM staining. Systems such as this combining high-density microwell chips with microfluidic components have great potential in numerous screening applications, such as exploring the important, but frequently undetected, heterogeneity in drug responses among individual cells.
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Affiliation(s)
- Sara Lindström
- Division of Nanobiotechnology, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden.
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35
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Chemical and biological single cell analysis. Curr Opin Biotechnol 2010; 21:12-20. [DOI: 10.1016/j.copbio.2010.01.007] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Accepted: 01/09/2010] [Indexed: 11/20/2022]
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36
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LINDSTRÖM S, ILES A, PERSSON J, HOSSEINKHANI H, HOSSEINKHANI M, KHADEMHOSSEINI A, LINDSTRÖM H, Andersson-SVAHN H. Nanoporous Titania Coating of Microwell Chips for Stem Cell Culture and Analysis. ACTA ACUST UNITED AC 2010. [DOI: 10.1299/jbse.5.272] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Sara LINDSTRÖM
- Division of Nanobiotechnology, Royal Institute of Technology
| | | | - Johanna PERSSON
- Division of Nanobiotechnology, Royal Institute of Technology
| | | | - Mohsen HOSSEINKHANI
- Kyoto University Hospital, Dept of Cardiovascular Medicine
- Harvard-MIT, Division of Health Science and Technology
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37
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Lindström S, Hammond M, Brismar H, Andersson-Svahn H, Ahmadian A. PCR amplification and genetic analysis in a microwell cell culturing chip. LAB ON A CHIP 2009; 9:3465-71. [PMID: 20024024 DOI: 10.1039/b912596e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
We have previously described a microwell chip designed for high throughput, long-term single-cell culturing and clonal analysis in individual wells providing a controlled way of studying high numbers of individual adherent or non-adherent cells. Here we present a method for the genetic analysis of cells cultured on-chip by PCR and minisequencing, demonstrated using two human adherent cell lines: one wild type and one with a single-base mutation in the p53 gene. Five wild type or mutated cells were seeded per well (in a defined set of wells, each holding 500 nL of culture medium) in a 672-microwell chip. The cell chip was incubated overnight, or cultured for up to five days, depending on the desired colony size, after which the cells were lysed and subjected to PCR directly in the wells. PCR products were detected, in the wells, using a biotinylated primer and a fluorescently labelled primer, allowing the products to be captured on streptavidin-coated magnetic beads and detected by a fluorescence microscope. In addition, to enable genetic analysis by minisequencing, the double-stranded PCR products were denatured and the immobilized strands were kept in the wells by applying a magnetic field from the bottom of the wells while the wells were washed, a minisequencing reaction mixture was added, and after incubation in appropriate conditions the expected genotypes were detected in the investigated microwells, simultaneously, by an array scanner. We anticipate that the technique could be used in mutation frequency screening, providing the ability to correlate cells' proliferative heterogeneity to their genetic heterogeneity, in hundreds of samples simultaneously. The presented method of single-cell culture and DNA amplification thus offers a potentially powerful alternative to single-cell PCR, with advantageous robustness and sensitivity.
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Affiliation(s)
- Sara Lindström
- Division of Nanobiotechnology, School of Biotechnology, AlbaNova University Center, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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38
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Lindström S, Eriksson M, Vazin T, Sandberg J, Lundeberg J, Frisén J, Andersson-Svahn H. High-density microwell chip for culture and analysis of stem cells. PLoS One 2009; 4:e6997. [PMID: 19750008 PMCID: PMC2736590 DOI: 10.1371/journal.pone.0006997] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Accepted: 08/19/2009] [Indexed: 11/25/2022] Open
Abstract
With recent findings on the role of reprogramming factors on stem cells, in vitro screening assays for studying (de)-differentiation is of great interest. We developed a miniaturized stem cell screening chip that is easily accessible and provides means of rapidly studying thousands of individual stem/progenitor cell samples, using low reagent volumes. For example, screening of 700,000 substances would take less than two days, using this platform combined with a conventional bio-imaging system. The microwell chip has standard slide format and consists of 672 wells in total. Each well holds 500 nl, a volume small enough to drastically decrease reagent costs but large enough to allow utilization of standard laboratory equipment. Results presented here include weeklong culturing and differentiation assays of mouse embryonic stem cells, mouse adult neural stem cells, and human embryonic stem cells. The possibility to either maintain the cells as stem/progenitor cells or to study cell differentiation of stem/progenitor cells over time is demonstrated. Clonality is critical for stem cell research, and was accomplished in the microwell chips by isolation and clonal analysis of single mouse embryonic stem cells using flow cytometric cell-sorting. Protocols for practical handling of the microwell chips are presented, describing a rapid and user-friendly method for the simultaneous study of thousands of stem cell cultures in small microwells. This microwell chip has high potential for a wide range of applications, for example directed differentiation assays and screening of reprogramming factors, opening up considerable opportunities in the stem cell field.
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Affiliation(s)
- Sara Lindström
- Division of Nanobiotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
| | - Malin Eriksson
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Tandis Vazin
- Division of Gene Technology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
- Cellular Neurobiology Research Branch, National Institute on Drug Abuse, National Institutes of Health, Department of Health and Human Services, Baltimore, Maryland, United States of America
| | - Julia Sandberg
- Division of Gene Technology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
| | - Joakim Lundeberg
- Division of Gene Technology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Helene Andersson-Svahn
- Division of Nanobiotechnology, AlbaNova University Center, Royal Institute of Technology, Stockholm, Sweden
- * E-mail:
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Engineering and characterization of a bispecific HER2 x EGFR-binding affibody molecule. Biotechnol Appl Biochem 2009; 54:121-31. [PMID: 19492986 DOI: 10.1042/ba20090096] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
HER2 (human epidermal-growth-factor receptor-2; ErbB2) and EGFR (epidermal-growth-factor receptor) are overexpressed in various forms of cancer, and the co-expression of both HER2 and EGFR has been reported in a number of studies. The simultaneous targeting of HER2 and EGFR has been discussed as a strategy with which to potentially increase efficiency and selectivity in molecular imaging and therapy of certain cancers. In an effort to generate a molecule capable of bispecifically targeting HER2 and EGFR, a gene fragment encoding a bivalent HER2-binding affibody molecule was genetically fused in-frame with a bivalent EGFR-binding affibody molecule via a (G4S)3 [(Gly4-Ser)3]-encoding gene fragment. The encoded 30 kDa affibody construct (ZHER2)2-(G4S)3-(ZEGFR)2, with potential for bs (bispecific) binding to HER2 and EGFR, was expressed in Escherichia coli and characterized in terms of its binding capabilities. The retained ability to bind HER2 and EGFR separately was demonstrated using both biosensor technology and flow-cytometric analysis, the latter using HER2- and EGFR-overexpressing cells. Furthermore, simultaneous binding to HER2 and EGFR was demonstrated in: (i) a sandwich format employing real-time biospecific interaction analysis where the bs affibody molecule bound immobilized EGFR and soluble HER2; (ii) immunofluorescence microscopy, where the bs affibody molecule bound EGFR-overexpressing cells and soluble HER2; and (iii) a cell-cell interaction analysis where the bs affibody molecule bound HER2-overexpressing SKBR-3 cells and EGFR-overexpressing A-431 cells. This is, to our knowledge, the first reported bs affinity protein with potential ability for the simultaneous targeting of HER2 and EGFR. The potential future use of this and similar constructs, capable of bs targeting of receptors to increase the efficacy and selectivity in imaging and therapy, is discussed.
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