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Abstract
We here present a micrometer-scale implementation of fluorescence in situ hybridization that we term μFISH. This μFISH implementation makes use of a non-contact scanning probe technology, namely, a microfluidic probe (MFP) that hydrodynamically shapes nanoliter volumes of liquid on a surface with micrometer resolution. By confining FISH probes at the tip of this microfabricated scanning probe, we locally exposed approximately 1000 selected MCF-7 cells of a monolayer to perform incubation of probes - the rate-limiting step in conventional FISH. This method is compatible with the standard workflow of conventional FISH, allows re-budgeting of the sample for various tests, and results in a ~ 15-fold reduction in probe consumption. The continuous flow of probes and shaping liquid on these selected cells resulted in a 120-fold reduction of the hybridization time compared with the standard protocol (3 min vs. 6 h) and efficient rinsing, thereby shortening the total FISH assay time for centromeric probes. We further demonstrated spatially multiplexed μFISH, enabling the use of spectrally equivalent probes for detailed and real-time analysis of a cell monolayer, which paves the way towards rapid and automated multiplexed FISH on standard cytological supports.
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Affiliation(s)
- D Huber
- IBM Research - Zurich, Säumerstrasse 4, 8803, Rüschlikon, Switzerland
| | - J Autebert
- IBM Research - Zurich, Säumerstrasse 4, 8803, Rüschlikon, Switzerland
| | - G V Kaigala
- IBM Research - Zurich, Säumerstrasse 4, 8803, Rüschlikon, Switzerland.
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Kashyap A, Autebert J, Delamarche E, Kaigala GV. Selective local lysis and sampling of live cells for nucleic acid analysis using a microfluidic probe. Sci Rep 2016; 6:29579. [PMID: 27411740 PMCID: PMC4944176 DOI: 10.1038/srep29579] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/23/2016] [Indexed: 01/18/2023] Open
Abstract
Heterogeneity is inherent to biology, thus it is imperative to realize methods capable of obtaining spatially-resolved genomic and transcriptomic profiles of heterogeneous biological samples. Here, we present a new method for local lysis of live adherent cells for nucleic acid analyses. This method addresses bottlenecks in current approaches, such as dilution of analytes, one-sample-one-test, and incompatibility to adherent cells. We make use of a scanning probe technology - a microfluidic probe - and implement hierarchical hydrodynamic flow confinement (hHFC) to localize multiple biochemicals on a biological substrate in a non-contact, non-destructive manner. hHFC enables rapid recovery of nucleic acids by coupling cell lysis and lysate collection. We locally lysed ~300 cells with chemical systems adapted for DNA or RNA and obtained lysates of ~70 cells/μL for DNA analysis and ~15 cells/μL for mRNA analysis. The lysates were introduced into PCR-based workflows for genomic and transcriptomic analysis. This strategy further enabled selective local lysis of subpopulations in a co-culture of MCF7 and MDA-MB-231 cells, validated by characteristic E-cadherin gene expression in individually extracted cell types. The developed strategy can be applied to study cell-cell, cell-matrix interactions locally, with implications in understanding growth, progression and drug response of a tumor.
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Affiliation(s)
- Aditya Kashyap
- IBM Research - Zurich, Säumerstrasse 4, 8803 Rüschlikon, Switzerland
| | - Julien Autebert
- IBM Research - Zurich, Säumerstrasse 4, 8803 Rüschlikon, Switzerland
| | | | - Govind V Kaigala
- IBM Research - Zurich, Säumerstrasse 4, 8803 Rüschlikon, Switzerland
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Abstract
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We
present a new methodology for efficient and high-quality patterning
of biological reagents for surface-based biological assays. The method
relies on hydrodynamically confined nanoliter volumes of reagents
to interact with the substrate at the micrometer-length scale. We
study the interplay between diffusion, advection, and surface chemistry
and present the design of a noncontact scanning microfluidic device
to efficiently present reagents on surfaces. By leveraging convective
flows, recirculation, and mixing of a processing liquid, this device
overcomes limitations of existing biopatterning approaches, such as
passive diffusion of analytes, uncontrolled wetting, and drying artifacts.
We demonstrate the deposition of analytes, showing a 2- to 5-fold
increase in deposition rate together with a 10-fold reduction in analyte
consumption while ensuring less than 6% variation in pattern homogeneity
on a standard biological substrate. In addition, we demonstrate the
recirculation of a processing liquid using a microfluidic probe (MFP)
in the context of a surface assay for (i) probing 12 independent areas
with a single microliter of processing liquid and (ii) processing
a 2 mm2 surface to create 170 antibody spots of 50 ×
100 μm2 area using 1.6 μL of liquid. We observe
high pattern quality, conservative usage of reagents, micrometer precision
of localization and convection-enhanced fast deposition. Such a device
and method may facilitate quantitative biological assays and spur
the development of the next generation of protein microarrays.
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Affiliation(s)
- Julien Autebert
- IBM Research-Zurich , Säumerstrasse 4, 8803 Rüschlikon, Switzerland
| | - Julien F Cors
- IBM Research-Zurich , Säumerstrasse 4, 8803 Rüschlikon, Switzerland
| | - David P Taylor
- IBM Research-Zurich , Säumerstrasse 4, 8803 Rüschlikon, Switzerland
| | - Govind V Kaigala
- IBM Research-Zurich , Säumerstrasse 4, 8803 Rüschlikon, Switzerland
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Autebert J, Coudert B, Champ J, Saias L, Guneri ET, Lebofsky R, Bidard FC, Pierga JY, Farace F, Descroix S, Malaquin L, Viovy JL. High purity microfluidic sorting and analysis of circulating tumor cells: towards routine mutation detection. Lab Chip 2015; 15:2090-101. [PMID: 25815443 DOI: 10.1039/c5lc00104h] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A new generation of the Ephesia cell capture technology optimized for CTC capture and genetic analysis is presented, characterized in depth and compared with the CellSearch system as a reference. This technology uses magnetic particles bearing tumour-cell specific EpCAM antibodies, self-assembled in a regular array in a microfluidic flow cell. 48,000 high aspect-ratio columns are generated using a magnetic field in a high throughput (>3 ml h(-1)) device and act as sieves to specifically capture the cells of interest through antibody-antigen interactions. Using this device optimized for CTC capture and analysis, we demonstrated the capture of epithelial cells with capture efficiency above 90% for concentrations as low as a few cells per ml. We showed the high specificity of capture with only 0.26% of non-epithelial cells captured for concentrations above 10 million cells per ml. We investigated the capture behavior of cells in the device, and correlated the cell attachment rate with the EpCAM expression on the cell membranes for six different cell lines. We developed and characterized a two-step blood processing method to allow for rapid processing of 10 ml blood tubes in less than 4 hours, and showed a capture rate of 70% for as low as 25 cells spiked in 10 ml blood tubes, with less than 100 contaminating hematopoietic cells. Using this device and procedure, we validated our system on patient samples using an automated cell immunostaining procedure and a semi-automated cell counting method. Our device captured CTCs in 75% of metastatic prostate cancer patients and 80% of metastatic breast cancer patients, and showed similar or better results than the CellSearch device in 10 out of 13 samples. Finally, we demonstrated the possibility of detecting cancer-related PIK3CA gene mutation in 20 cells captured in the chip with a good correlation between the cell count and the quantitation value Cq of the post-capture qPCR.
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Affiliation(s)
- Julien Autebert
- Institut Curie, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, PSL Research University, Unité Mixte de Recherche 168, 75005 Paris, France.
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Kucerova J, Svobodova Z, Knotek P, Palarcik J, Vlcek M, Kincl M, Horak D, Autebert J, Viovy JL, Bilkova Z. PEGylation of magnetic poly(glycidyl methacrylate) microparticles for microfluidic bioassays. Materials Science and Engineering: C 2014; 40:308-15. [DOI: 10.1016/j.msec.2014.04.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/15/2014] [Accepted: 04/03/2014] [Indexed: 11/25/2022]
Affiliation(s)
- Jana Kucerova
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 53210 Pardubice, Czech Republic
| | - Zuzana Svobodova
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 53210 Pardubice, Czech Republic
| | - Petr Knotek
- Joint Laboratory of Solid State Chemistry of IMC and University of Pardubice, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 53210 Pardubice, Czech Republic
| | - Jiri Palarcik
- Institute of Environmental and Chemical Engineering, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 53210 Pardubice, Czech Republic
| | - Milan Vlcek
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovsky Sq. 2, 16206 Prague 6, Czech Republic
| | - Miloslav Kincl
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovsky Sq. 2, 16206 Prague 6, Czech Republic
| | - Daniel Horak
- Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovsky Sq. 2, 16206 Prague 6, Czech Republic
| | - Julien Autebert
- Macromolecules and Microsystems in Biology and Medicine, Institute Curie, UMR 168, 26 Rue d'Ulm, 75005 Paris, France
| | - Jean-Louis Viovy
- Macromolecules and Microsystems in Biology and Medicine, Institute Curie, UMR 168, 26 Rue d'Ulm, 75005 Paris, France
| | - Zuzana Bilkova
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 53210 Pardubice, Czech Republic.
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Autebert J, Kashyap A, Lovchik RD, Delamarche E, Kaigala GV. Hierarchical hydrodynamic flow confinement: efficient use and retrieval of chemicals for microscale chemistry on surfaces. Langmuir 2014; 30:3640-5. [PMID: 24625080 PMCID: PMC4213896 DOI: 10.1021/la500875m] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We devised, implemented, and tested a new concept for efficient local surface chemistry that we call hierarchical hydrodynamic flow confinement (hierarchical HFC). This concept leverages the hydrodynamic shaping of multiple layers of liquid to address challenges inherent to microscale surface chemistry, such as minimal dilution, economical consumption of reagent, and fast liquid switching. We illustrate two modes of hierarchical HFC, nested and pinched, by locally denaturing and recovering a 26 bp DNA with as little as 2% dilution and by efficiently patterning an antibody on a surface, with a 5 μm resolution and a 100-fold decrease of reagent consumption compared to microcontact printing. In addition, valveless switching between nanoliter volumes of liquids was achieved within 20 ms. We believe hierarchical HFC will have broad utility for chemistry on surfaces at the microscale.
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Svobodova Z, Kucerova J, Autebert J, Horak D, Bruckova L, Viovy JL, Bilkova Z. Application of an improved magnetic immunosorbent in an Ephesia chip designed for circulating tumor cell capture. Electrophoresis 2013; 35:323-9. [DOI: 10.1002/elps.201300196] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 05/31/2013] [Accepted: 06/01/2013] [Indexed: 01/09/2023]
Affiliation(s)
- Zuzana Svobodova
- Department of Biological and Biochemical Sciences; Faculty of Chemical Technology, University of Pardubice; Pardubice Czech Republic
| | - Jana Kucerova
- Department of Biological and Biochemical Sciences; Faculty of Chemical Technology, University of Pardubice; Pardubice Czech Republic
| | - Julien Autebert
- Macromolecules and Microsystems in Biology and Medicine; Institute Curie; Paris France
| | - Daniel Horak
- Institute of Macromolecular Chemistry; Academy of Sciences of the Czech Republic; Prague Czech Republic
| | - Lenka Bruckova
- Department of Biological and Biochemical Sciences; Faculty of Chemical Technology, University of Pardubice; Pardubice Czech Republic
| | - Jean-Louis Viovy
- Macromolecules and Microsystems in Biology and Medicine; Institute Curie; Paris France
| | - Zuzana Bilkova
- Department of Biological and Biochemical Sciences; Faculty of Chemical Technology, University of Pardubice; Pardubice Czech Republic
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Horák D, Svobodová Z, Autebert J, Coudert B, Plichta Z, Královec K, Bílková Z, Viovy JL. Albumin-coated monodisperse magnetic poly(glycidyl methacrylate) microspheres with immobilized antibodies: application to the capture of epithelial cancer cells. J Biomed Mater Res A 2012; 101:23-32. [PMID: 22767416 DOI: 10.1002/jbm.a.34297] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 05/16/2012] [Accepted: 05/22/2012] [Indexed: 11/07/2022]
Abstract
Monodisperse (4 μm) macroporous crosslinked poly(glycidyl methacrylate) (PGMA) microspheres for use in microfluidic immunomagnetic cell sorting, with a specific application to the capture of circulating tumor cells (CTCs), were prepared by multistep swelling polymerization in the presence of cyclohexyl acetate porogen and hydrolyzed and ammonolyzed. Iron oxide was then precipitated in the microspheres to render them magnetic. Repeated precipitation made possible to raise the iron oxide content to more than 30 wt %. To minimize nonspecific adsorption of the microspheres in a microchannel and of cells on the microspheres, they were coated with albumin crosslinked with glutaraldehyde. Antibodies of epithelial cell adhesion molecule (anti-EpCAM) were then immobilized on the albumin-coated magnetic microspheres using the carbodiimide method. Capture of breast cancer MCF7 cells as a model of CTCs by the microspheres with immobilized anti-EpCAM IgG was performed in a batch experiment. Finally, MCF7 cells were captured by the anti-EpCAM-immobilized albumin-coated magnetic microspheres in an Ephesia chip. A very good rejection of lymphocytes was achieved. Thus, albumin-coated monodisperse magnetic PGMA microspheres with immobilized anti-EpCAM seem to be promising for capture of CTCs in a microfluidic device.
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Affiliation(s)
- Daniel Horák
- Department of Polymer Particles, Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic.
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Autebert J, Coudert B, Bidard FC, Pierga JY, Descroix S, Malaquin L, Viovy JL. Microfluidic: An innovative tool for efficient cell sorting. Methods 2012; 57:297-307. [DOI: 10.1016/j.ymeth.2012.07.002] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 06/13/2012] [Accepted: 07/02/2012] [Indexed: 01/16/2023] Open
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Saias L, Autebert J, Malaquin L, Viovy JL. Design, modeling and characterization of microfluidic architectures for high flow rate, small footprint microfluidic systems. Lab Chip 2011; 11:822-32. [PMID: 21240403 DOI: 10.1039/c0lc00304b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We propose a strategy for optimizing distribution of flow in a microfluidic chamber for microreactor, lateral flow assay and immunocapture applications. It is aimed at maximizing flow throughput, while keeping footprint, cell thickness, and shear stress in the distribution channels at a minimum, and offering a uniform flow field along the whole analysis chamber. In order to minimize footprint, the traditional tree-like or "rhombus" design, in which distribution microchannels undergo a series of splittings into two subchannels with equal lengths and widths, was replaced by a design in which subchannel lengths are unequal, and widths are analytically adapted within the Hele-Shaw approximation, in order to keep the flow resistance uniform along all flow paths. The design was validated by hydrodynamic flow simulation using COMSOL finite element software. Simulations show that, if the channel is too narrow, the Hele-Shaw approximation loses accuracy, and the flow velocity in the chamber can fluctuate by up to 20%. We thus used COMSOL simulation to fine-tune the channel parameters, and obtained a fluctuation of flow velocity across the whole chamber below 10%. The design was then implemented into a PDMS device, and flow profiles were measured experimentally using particle tracking. Finally, we show that this system can be applied to cell sorting in self-assembling magnetic arrays, increasing flow throughput by a factor 100 as compared to earlier reported designs.
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Affiliation(s)
- Laure Saias
- Macromolecules and Microsystems in Biology and Medicine, Institut Curie, Centre National de Recherche Scientifique, Université Pierre et Marie Curie, UMR 168, 75005 Paris, France
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