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Yoon S, Kilicarslan You D, Jeong U, Lee M, Kim E, Jeon TJ, Kim SM. Microfluidics in High-Throughput Drug Screening: Organ-on-a-Chip and C. elegans-Based Innovations. BIOSENSORS 2024; 14:55. [PMID: 38275308 PMCID: PMC10813408 DOI: 10.3390/bios14010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
The development of therapeutic interventions for diseases necessitates a crucial step known as drug screening, wherein potential substances with medicinal properties are rigorously evaluated. This process has undergone a transformative evolution, driven by the imperative need for more efficient, rapid, and high-throughput screening platforms. Among these, microfluidic systems have emerged as the epitome of efficiency, enabling the screening of drug candidates with unprecedented speed and minimal sample consumption. This review paper explores the cutting-edge landscape of microfluidic-based drug screening platforms, with a specific emphasis on two pioneering approaches: organ-on-a-chip and C. elegans-based chips. Organ-on-a-chip technology harnesses human-derived cells to recreate the physiological functions of human organs, offering an invaluable tool for assessing drug efficacy and toxicity. In parallel, C. elegans-based chips, boasting up to 60% genetic homology with humans and a remarkable affinity for microfluidic systems, have proven to be robust models for drug screening. Our comprehensive review endeavors to provide readers with a profound understanding of the fundamental principles, advantages, and challenges associated with these innovative drug screening platforms. We delve into the latest breakthroughs and practical applications in this burgeoning field, illuminating the pivotal role these platforms play in expediting drug discovery and development. Furthermore, we engage in a forward-looking discussion to delineate the future directions and untapped potential inherent in these transformative technologies. Through this review, we aim to contribute to the collective knowledge base in the realm of drug screening, providing valuable insights to researchers, clinicians, and stakeholders alike. We invite readers to embark on a journey into the realm of microfluidic-based drug screening platforms, fostering a deeper appreciation for their significance and promising avenues yet to be explored.
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Affiliation(s)
- Sunhee Yoon
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Dilara Kilicarslan You
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Uiechan Jeong
- Department of Mechanical Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Mina Lee
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Eunhye Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Tae-Joon Jeon
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
- Department of Biological Engineering, Inha University, Incheon 22212, Republic of Korea
- Biohybrid Systems Research Center (BSRC), Inha University, Incheon 22212, Republic of Korea
| | - Sun Min Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
- Department of Mechanical Engineering, Inha University, Incheon 22212, Republic of Korea
- Biohybrid Systems Research Center (BSRC), Inha University, Incheon 22212, Republic of Korea
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Wang Y, Goh B, Moorehead M, Hattrick-Simpers J, Couet A. High-Throughput Electrochemistry to Study Materials Degradation in Extreme Environments. Anal Chem 2022; 94:16528-16537. [DOI: 10.1021/acs.analchem.2c03325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Yafei Wang
- Department of Engineering Physics, University of Wisconsin−Madison, Madison, Wisconsin53715, United States
- School of Nuclear Science and Engineering, Shanghai Jiao Tong University, Shanghai200240, China
| | - Bonita Goh
- Department of Engineering Physics, University of Wisconsin−Madison, Madison, Wisconsin53715, United States
| | - Michael Moorehead
- Department of Engineering Physics, University of Wisconsin−Madison, Madison, Wisconsin53715, United States
| | - Jason Hattrick-Simpers
- Department of Materials Science & Engineering, University of Toronto, Toronto, OntarioM5S 3E4, Canada
| | - Adrien Couet
- Department of Engineering Physics, University of Wisconsin−Madison, Madison, Wisconsin53715, United States
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Lee Y, Chen Z, Lim W, Cho H, Park S. High-Throughput Screening of Anti-cancer Drugs Using a Microfluidic Spheroid Culture Device with a Concentration Gradient Generator. Curr Protoc 2022; 2:e529. [PMID: 36066205 DOI: 10.1002/cpz1.529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Tumor spheroid models are widely used for drug screening as in vitro models of the tumor microenvironment. There are various ways in which tumor spheroid models can be prepared, including the self-assembly of cells using low-adherent plates, micro-patterned plates, or hanging-drop plates. Recently, drug high-throughput screening (HTS) approaches have incorporated the use of these culture systems. These HTS culture systems, however, require complicated equipment, such as robot arms, detectors, and software for handling solutions and data processing. Here, we describe protocols that allow tumor spheroids to be tested with different concentrations of a drug in a parallel fashion using a microfluidic device that generates a gradient of anti-cancer drugs. This microfluidic spheroid culture device with a concentration gradient generator (μFSCD-CGG) enables the formation of 50 tumor spheroids and the testing of drugs at five different concentrations. First, we provide a protocol for the fabrication of the μFSCD-CGG, which has both a culture array in which tumor cells are injected and aggregate to form spheroids and a concentration gradient generator for drug testing. Second, we provide a protocol for tumor spheroid formation and HTS of anti-cancer drugs using the device. Finally, we provide a protocol for assessing the response of tumor spheroids at different drug concentrations. To address the needs of the pharmaceutical industry, this protocol can be used for various cell types, including stem cells, and the number of tumor spheroids and drug concentration ranges that can be tested in the μFSCD-CGG can be increased. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Fabrication of a microfluidic spheroid culture device with a concentration gradient generator (μFSCD-CGG) Basic Protocol 2: Seeding cells and formation of spheroids in the μFSCD-CGG Basic Protocol 3: Drug treatment and assessment of cell viability in the μFSCD-CGG.
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Affiliation(s)
- Yugyeong Lee
- Department of Biomedical Engineering, Sungkyunkwan University (SKKU), Suwon, Korea
| | - Zhenzhong Chen
- School of Mechanical Engineering, Sungkyunkwan University (SKKU), Suwon, Korea
| | - Wanyoung Lim
- Department of Biomedical Engineering, Sungkyunkwan University (SKKU), Suwon, Korea
| | - Hansang Cho
- Institute of Quantum Biophysics (IQB), Sungkyunkwan University (SKKU), Suwon, Korea
- Department of Biophysics, Sungkyunkwan University (SKKU), Suwon, Korea
- Department of Mechanical Engineering and Engineering Science, University of North Carolina at Charlotte, Charlotte, North Carolina
| | - Sungsu Park
- Department of Biomedical Engineering, Sungkyunkwan University (SKKU), Suwon, Korea
- School of Mechanical Engineering, Sungkyunkwan University (SKKU), Suwon, Korea
- Institute of Quantum Biophysics (IQB), Sungkyunkwan University (SKKU), Suwon, Korea
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University (SKKU), Suwon, Korea
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De Stefano P, Bianchi E, Dubini G. The impact of microfluidics in high-throughput drug-screening applications. BIOMICROFLUIDICS 2022; 16:031501. [PMID: 35646223 PMCID: PMC9142169 DOI: 10.1063/5.0087294] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/02/2022] [Indexed: 05/05/2023]
Abstract
Drug discovery is an expensive and lengthy process. Among the different phases, drug discovery and preclinical trials play an important role as only 5-10 of all drugs that begin preclinical tests proceed to clinical trials. Indeed, current high-throughput screening technologies are very expensive, as they are unable to dispense small liquid volumes in an accurate and quick way. Moreover, despite being simple and fast, drug screening assays are usually performed under static conditions, thus failing to recapitulate tissue-specific architecture and biomechanical cues present in vivo even in the case of 3D models. On the contrary, microfluidics might offer a more rapid and cost-effective alternative. Although considered incompatible with high-throughput systems for years, technological advancements have demonstrated how this gap is rapidly reducing. In this Review, we want to further outline the role of microfluidics in high-throughput drug screening applications by looking at the multiple strategies for cell seeding, compartmentalization, continuous flow, stimuli administration (e.g., drug gradients or shear stresses), and single-cell analyses.
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Affiliation(s)
- Paola De Stefano
- Laboratory of Biological Structure Mechanics, Department of Chemistry, Materials and Chemical Engineering “G. Natta,” Politecnico di Milano, Italy
| | - Elena Bianchi
- Laboratory of Biological Structure Mechanics, Department of Chemistry, Materials and Chemical Engineering “G. Natta,” Politecnico di Milano, Italy
| | - Gabriele Dubini
- Laboratory of Biological Structure Mechanics, Department of Chemistry, Materials and Chemical Engineering “G. Natta,” Politecnico di Milano, Italy
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Cecen B, Karavasili C, Nazir M, Bhusal A, Dogan E, Shahriyari F, Tamburaci S, Buyukoz M, Kozaci LD, Miri AK. Multi-Organs-on-Chips for Testing Small-Molecule Drugs: Challenges and Perspectives. Pharmaceutics 2021; 13:1657. [PMID: 34683950 PMCID: PMC8540732 DOI: 10.3390/pharmaceutics13101657] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/30/2021] [Accepted: 10/03/2021] [Indexed: 12/13/2022] Open
Abstract
Organ-on-a-chip technology has been used in testing small-molecule drugs for screening potential therapeutics and regulatory protocols. The technology is expected to boost the development of novel therapies and accelerate the discovery of drug combinations in the coming years. This has led to the development of multi-organ-on-a-chip (MOC) for recapitulating various organs involved in the drug-body interactions. In this review, we discuss the current MOCs used in screening small-molecule drugs and then focus on the dynamic process of drug absorption, distribution, metabolism, and excretion. We also address appropriate materials used for MOCs at low cost and scale-up capacity suitable for high-performance analysis of drugs and commercial high-throughput screening platforms.
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Affiliation(s)
- Berivan Cecen
- Department of Mechanical Engineering, Rowan University, Glassboro, NJ 08028, USA; (A.B.); (E.D.); (A.K.M.)
- Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Istinye University, Istanbul 34010, Turkey
| | - Christina Karavasili
- Department of Pharmaceutical Technology, School of Pharmacy, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
| | - Mubashir Nazir
- Department of Microbiology, Sher-i-Kashmir Institute of Medical Sciences, Srinagar 190011, India;
| | - Anant Bhusal
- Department of Mechanical Engineering, Rowan University, Glassboro, NJ 08028, USA; (A.B.); (E.D.); (A.K.M.)
| | - Elvan Dogan
- Department of Mechanical Engineering, Rowan University, Glassboro, NJ 08028, USA; (A.B.); (E.D.); (A.K.M.)
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Fatemeh Shahriyari
- Institute of Health Science, Department of Translational Medicine, Ankara Yildirim Beyazit University, Ankara 06800, Turkey;
| | - Sedef Tamburaci
- Izmir Institute of Technology, Graduate Program of Biotechnology and Bioengineering, Gulbahce Campus, Izmir 35430, Turkey;
- Izmir Institute of Technology, Department of Chemical Engineering, Gulbahce Campus, Izmir 35430, Turkey
| | - Melda Buyukoz
- Care of Elderly Program, Vocational School of Health Services, Izmir Democracy University, Izmir 35140, Turkey;
| | - Leyla Didem Kozaci
- Department of Medical Biochemistry, Faculty of Medicine, Ankara Yildirim Beyazit University, Ankara 06800, Turkey;
| | - Amir K. Miri
- Department of Mechanical Engineering, Rowan University, Glassboro, NJ 08028, USA; (A.B.); (E.D.); (A.K.M.)
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
- Department of Mechanical and Industrial Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
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Volpe C, Vadstein O, Andersen G, Andersen T. Nanocosm: a well plate photobioreactor for environmental and biotechnological studies. LAB ON A CHIP 2021; 21:2027-2039. [PMID: 34008610 DOI: 10.1039/d0lc01250e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytoplankton are key primary producers at the bottom of the aquatic food chain. They are a highly diverse group of organisms essential for the functioning of our ecosystems and because of their characteristics, their biomass is considered for various commercial applications. A full appreciation of their abundance, diversity and potential is only feasible by using systems that enable simultaneous testing of strains and/or variables in a fast and easy way. A major bottleneck is the lack of a cost-effective method with the capacity for complex experimental set-ups that enable fast and reproducible screening and analysis. In this study, we present nanocosm, a versatile LED-based micro-scale photobioreactor (PBR) that allows simultaneous testing of multiple variables such as temperature and light within the same plate. Every well can be independently controlled for intensity, temporal variation and light type (RGB, white, UV). We show that our systems guarantee homogeneous conditions because of controlled temperature and evaporation and adjustments for light crosstalk. By ensuring controlled environmental conditions the nanocosm is suitable for running factorial experimental designs where each well can be used as an independent micro-PBR. To validate culture performances, we assess well-to-well reproducibility and our results show minimal well-to-well variability for all the conditions tested. Possible modes of operation and application are discussed together with future development of the system.
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Affiliation(s)
- Charlotte Volpe
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, N-7491, Trondheim, Norway.
| | - Olav Vadstein
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, N-7491, Trondheim, Norway.
| | | | - Tom Andersen
- Department of Biosciences, Section for Aquatic Biology and Toxicology (AQUA), University of Oslo, N-0316, Oslo, Norway
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Rodríguez-Martínez X, Pascual-San-José E, Campoy-Quiles M. Accelerating organic solar cell material's discovery: high-throughput screening and big data. ENERGY & ENVIRONMENTAL SCIENCE 2021; 14:3301-3322. [PMID: 34211582 PMCID: PMC8209551 DOI: 10.1039/d1ee00559f] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/20/2021] [Indexed: 05/27/2023]
Abstract
The discovery of novel high-performing materials such as non-fullerene acceptors and low band gap donor polymers underlines the steady increase of record efficiencies in organic solar cells witnessed during the past years. Nowadays, the resulting catalogue of organic photovoltaic materials is becoming unaffordably vast to be evaluated following classical experimentation methodologies: their requirements in terms of human workforce time and resources are prohibitively high, which slows momentum to the evolution of the organic photovoltaic technology. As a result, high-throughput experimental and computational methodologies are fostered to leverage their inherently high exploratory paces and accelerate novel materials discovery. In this review, we present some of the computational (pre)screening approaches performed prior to experimentation to select the most promising molecular candidates from the available materials libraries or, alternatively, generate molecules beyond human intuition. Then, we outline the main high-throuhgput experimental screening and characterization approaches with application in organic solar cells, namely those based on lateral parametric gradients (measuring-intensive) and on automated device prototyping (fabrication-intensive). In both cases, experimental datasets are generated at unbeatable paces, which notably enhance big data readiness. Herein, machine-learning algorithms find a rewarding application niche to retrieve quantitative structure-activity relationships and extract molecular design rationale, which are expected to keep the material's discovery pace up in organic photovoltaics.
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Affiliation(s)
| | | | - Mariano Campoy-Quiles
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC, Campus UAB 08193 Bellaterra Spain
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Hofmann T, Schmidt J, Ciesielski E, Becker S, Rysiok T, Schütte M, Toleikis L, Kolmar H, Doerner A. Intein mediated high throughput screening for bispecific antibodies. MAbs 2021; 12:1731938. [PMID: 32151188 PMCID: PMC7153837 DOI: 10.1080/19420862.2020.1731938] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Bispecific antibodies comprise extremely diverse architectures enabling complex modes of action, such as effector cell recruitment or conditional target modulation via dual targeting, not conveyed by monospecific antibodies. In recent years, research on bispecific therapeutics has substantially grown. However, evaluation of binding moiety combinations often leads to undesired prolonged development times. While high throughput screening for small molecules and classical antibodies has evolved into a mature discipline in the pharmaceutical industry, dual-targeting antibody screening methodologies lack the ability to fully evaluate the tremendous number of possible combinations and cover only a limited portion of the combinatorial screening space. Here, we propose a novel combinatorial screening approach for bispecific IgG-like antibodies to extenuate screening limitations in industrial scale, expanding the limiting screening space. Harnessing the ability of a protein trans-splicing reaction by the split intein Npu DnaE, antibody fragments were reconstituted within the hinge region in vitro. This method allows for fully automated, rapid one-pot antibody reconstitution, providing biological activity in several biochemical and functional assays. The technology presented here is suitable for automated functional and combinatorial high throughput screening of bispecific antibodies.
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Affiliation(s)
- Tim Hofmann
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.,Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Johannes Schmidt
- Compound Logistic & Bioassay Automation, Merck KGaA, Darmstadt, Germany
| | - Elke Ciesielski
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Stefan Becker
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Thomas Rysiok
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Mark Schütte
- Global Innovation and Alliance Management, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Lars Toleikis
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
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Di Girolamo S, Puorger C, Lipps G. Stable and selective permeable hydrogel microcapsules for high-throughput cell cultivation and enzymatic analysis. Microb Cell Fact 2020; 19:170. [PMID: 32854709 PMCID: PMC7451113 DOI: 10.1186/s12934-020-01427-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/17/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Miniaturization of biochemical reaction volumes within artificial microcompartments has been the key driver for directed evolution of several catalysts in the past two decades. Typically, single cells are co-compartmentalized within water-in-oil emulsion droplets with a fluorogenic substrate whose conversion allows identification of catalysts with improved performance. However, emulsion droplet-based technologies prevent cell proliferation to high density and preclude the feasibility of biochemical reactions that require the exchange of small molecule substrates. Here, we report on the development of a high-throughput screening method that addresses these shortcomings and that relies on a novel selective permeable polymer hydrogel microcapsule. RESULTS Hollow-core polyelectrolyte-coated chitosan alginate microcapsules (HC-PCAMs) with selective permeability were successfully constructed by jet break-up and layer-by-layer (LBL) technology. We showed that HC-PCAMs serve as miniaturized vessels for single cell encapsulation, enabling cell growth to high density and cell lysis to generate monoclonal cell lysate compartments suitable for high-throughput analysis using a large particle sorter (COPAS). The feasibility of using HC-PCAMs as reaction compartments which exchange small molecule substrates was demonstrated using the transpeptidation reaction catalyzed by the bond-forming enzyme sortase F from P. acnes. The polyelectrolyte shell surrounding microcapsules allowed a fluorescently labelled peptide substrate to enter the microcapsule and take part in the transpeptidation reaction catalyzed by the intracellularly expressed sortase enzyme retained within the capsule upon cell lysis. The specific retention of fluorescent transpeptidation products inside microcapsules enabled the sortase activity to be linked with a fluorescent readout and allowed clear separation of microcapsules expressing the wild type SrtF from those expressing the inactive variant. CONCLUSION A novel polymer hydrogel microcapsule-based method, which allows for high-throughput analysis based on encapsulation of single cells has been developed. The method has been validated for the transpeptidation activity of sortase enzymes and represents a powerful tool for screening of libraries of sortases, other bond-forming enzymes, as well as of binding affinities in directed evolution experiments. Moreover, selective permeable microcapsules encapsulating microcolonies provide a new and efficient means for preparing novel caged biocatalyst and biosensor agents.
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Affiliation(s)
- Salvatore Di Girolamo
- University of Applied Sciences and Arts Northwestern Switzerland, Institute for Chemistry and Bioanalytics, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Chasper Puorger
- University of Applied Sciences and Arts Northwestern Switzerland, Institute for Chemistry and Bioanalytics, Hofackerstrasse 30, 4132, Muttenz, Switzerland
| | - Georg Lipps
- University of Applied Sciences and Arts Northwestern Switzerland, Institute for Chemistry and Bioanalytics, Hofackerstrasse 30, 4132, Muttenz, Switzerland.
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FACS-Based Functional Protein Screening via Microfluidic Co-encapsulation of Yeast Secretor and Mammalian Reporter Cells. Sci Rep 2020; 10:10182. [PMID: 32576855 PMCID: PMC7311539 DOI: 10.1038/s41598-020-66927-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 05/20/2020] [Indexed: 12/22/2022] Open
Abstract
In this study, we present a straightforward approach for functional cell-based screening by co-encapsulation of secretor yeast cells and reporter mammalian cells in millions of individual agarose-containing microdroplets. Our system is compatible with ultra-high-throughput selection utilizing standard fluorescence-activated cell sorters (FACS) without need of extensive adaptation and optimization. In a model study we co-encapsulated murine interleukin 3 (mIL-3)-secreting S. cerevisiae cells with murine Ba/F3 reporter cells, which express green fluorescent protein (GFP) upon stimulation with mIL-3, and could observe specific and robust induction of fluorescence signal compared to a control with yeast cells secreting a non-functional mIL-3 mutant. We demonstrate the successful enrichment of activating mIL-3 wt-secreting yeast cells from a 1:10,000 dilution in cells expressing the inactive cytokine variant by two consecutive cycles of co-encapsulation and FACS. This indicates the suitability of the presented strategy for functional screening of high-diversity yeast-based libraries and demonstrates its potential for the efficient isolation of clones secreting bioactive recombinant proteins.
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Ma J, Bair E, Motsinger-Reif A. Nonlinear Dose-Response Modeling of High-Throughput Screening Data Using an Evolutionary Algorithm. Dose Response 2020; 18:1559325820926734. [PMID: 32547333 PMCID: PMC7249578 DOI: 10.1177/1559325820926734] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/13/2020] [Accepted: 04/17/2020] [Indexed: 11/17/2022] Open
Abstract
Nonlinear dose-response relationships exist extensively in the cellular, biochemical, and physiologic processes that are affected by varying levels of biological, chemical, or radiation stress. Modeling such responses is a crucial component of toxicity testing and chemical screening. Traditional model fitting methods such as nonlinear least squares (NLS) are very sensitive to initial parameter values and often had convergence failure. The use of evolutionary algorithms (EAs) has been proposed to address many of the limitations of traditional approaches, but previous methods have been limited in the types of models they can fit. Therefore, we propose the use of an EA for dose-response modeling for a range of potential response model functional forms. This new method can not only fit the most commonly used nonlinear dose-response models (eg, exponential models and 3-, 4-, and 5-parameter logistic models) but also select the best model if no model assumption is made, which is especially useful in the case of high-throughput curve fitting. Compared with NLS, the new method provides stable and robust solutions without sensitivity to initial values.
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Affiliation(s)
- Jun Ma
- Bioinformatics Research Center, North Carolina State University, Durham, NC, USA.,Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
| | | | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, USA
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13
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Xu JG, Huang MS, Wang HF, Fang Q. Forming a Large-Scale Droplet Array in a Microcage Array Chip for High-Throughput Screening. Anal Chem 2019; 91:10757-10763. [DOI: 10.1021/acs.analchem.9b02288] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jin-Gang Xu
- Institute of Analytical Chemistry, Department of Chemistry and Center for Chemistry of Novel & High-Performance Materials, Zhejiang University, Hangzhou, 310058, China
| | - Meng-Shi Huang
- Institute of Analytical Chemistry, Department of Chemistry and Center for Chemistry of Novel & High-Performance Materials, Zhejiang University, Hangzhou, 310058, China
| | - Hui-Feng Wang
- Institute of Analytical Chemistry, Department of Chemistry and Center for Chemistry of Novel & High-Performance Materials, Zhejiang University, Hangzhou, 310058, China
| | - Qun Fang
- Institute of Analytical Chemistry, Department of Chemistry and Center for Chemistry of Novel & High-Performance Materials, Zhejiang University, Hangzhou, 310058, China
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A Microfluidic Spheroid Culture Device with a Concentration Gradient Generator for High-Throughput Screening of Drug Efficacy. Molecules 2018; 23:molecules23123355. [PMID: 30567363 PMCID: PMC6321514 DOI: 10.3390/molecules23123355] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 12/11/2022] Open
Abstract
Three-dimensional (3D) cell culture is considered more clinically relevant in mimicking the structural and physiological conditions of tumors in vivo compared to two-dimensional cell cultures. In recent years, high-throughput screening (HTS) in 3D cell arrays has been extensively used for drug discovery because of its usability and applicability. Herein, we developed a microfluidic spheroid culture device (μFSCD) with a concentration gradient generator (CGG) that enabled cells to form spheroids and grow in the presence of cancer drug gradients. The device is composed of concave microwells with several serpentine micro-channels which generate a concentration gradient. Once the colon cancer cells (HCT116) formed a single spheroid (approximately 120 μm in diameter) in each microwell, spheroids were perfused in the presence of the cancer drug gradient irinotecan for three days. The number of spheroids, roundness, and cell viability, were inversely proportional to the drug concentration. These results suggest that the μFSCD with a CGG has the potential to become an HTS platform for screening the efficacy of cancer drugs.
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Construction of a versatile expression library for all human single-pass transmembrane proteins for receptor pairings by high throughput screening. J Biotechnol 2017; 260:18-30. [PMID: 28867483 DOI: 10.1016/j.jbiotec.2017.08.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/28/2017] [Accepted: 08/28/2017] [Indexed: 12/19/2022]
Abstract
Interactions between protein ligands and receptors play crucial roles in cell-cell signalling. Most of the human cell surface receptors have been identified in the post-Human Genome Project era but many of their corresponding ligands remain unknown. To facilitate the pairing of orphan receptors, 2762 sequences encoding all human single-pass transmembrane proteins were selected for inclusion into a mammalian-cell expression library. This expression library, consisting of all the individual extracellular domains (ECDs), was constructed as a Fab fusion for each protein. In this format, individual ECD can be produced as a soluble protein or displayed on cell surface, depending on the applied heavy-chain Fab configuration. The unique design of the Fab fusion concept used in the library led to not only superior success rate of protein production, but also versatile applications in various high-throughput screening paradigms including protein-protein binding assays as well as cell binding assays, which were not possible for any other existing expression libraries. The protein library was screened against human coagulation factor VIIa (FVIIa), an approved therapeutic for the treatment of hemophilia, for binding partners by AlphaScreen and ForteBio assays. Two previously known physiological ligands of FVIIa, tissue factor (TF) and endothelial protein C receptor (EPCR) were identified by both assays. The cell surface displayed library was screened against V-domain Ig suppressor of T-cell activation (VISTA), an important immune-checkpoint regulator. Immunoglobulin superfamily member 11 (IgSF11), a potential target for cancer immunotherapy, was identified as a new and previously undescribed binding partner for VISTA. The specificity of the binding was confirmed and validated by both fluorescence-activated cell sorting (FACS) and surface plasmon resonance (SPR) assays in different experimental setups.
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16
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Kim CM, Kim GM. 1600 Parallel Microchamber Microfluidic Device for Fast Sample Array Preparation Using the Immiscibility of Two Liquids. MICROMACHINES 2017. [PMCID: PMC6190353 DOI: 10.3390/mi8030063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
| | - Gyu Man Kim
- Correspondence: ; Tel.: +82-53-950-7570; Fax: +82-53-950-6550
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17
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Tong Z, Ivask A, Guo K, McCormick S, Lombi E, Priest C, Voelcker NH. Crossed flow microfluidics for high throughput screening of bioactive chemical-cell interactions. LAB ON A CHIP 2017; 17:501-510. [PMID: 28074962 DOI: 10.1039/c6lc01261b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This paper describes the use of crossed laminar flow microfluidics for the selective capture of multiple cell types on-chip aiming for high throughput screening of various cell treatment compounds. Parallel laminar streams containing different cell types were perfused and captured on a cell adhesion protein-functionalized reaction area. Thereafter, parallel streams containing cell treatment solutions were delivered orthogonally over the captured cells. Multiple cell types and a range of cell treatment conditions could therefore be assessed in a single experiment. We were also able to sort mixed cell populations via antibody array clusters, and to further deliver treatments to subpopulations of cells. Moreover, using solutions with different tonicities, we successfully demonstrated the incorporation of a live/dead cell viability assessment on-chip for a direct read out assay following the treatments. This crossed laminar flow microfluidics for generation of a cell-based assay could therefore offer an interesting platform for high throughput screening of potential drug candidates, nanoparticle toxicity testing, or other cellular and molecular interventions.
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Affiliation(s)
- Ziqiu Tong
- Future Industry Institute, University of South Australia, Mawson Lakes, SA 5095, Australia.
| | - Angela Ivask
- Future Industry Institute, University of South Australia, Mawson Lakes, SA 5095, Australia.
| | - Keying Guo
- Future Industry Institute, University of South Australia, Mawson Lakes, SA 5095, Australia.
| | - Scott McCormick
- Future Industry Institute, University of South Australia, Mawson Lakes, SA 5095, Australia.
| | - Enzo Lombi
- Future Industry Institute, University of South Australia, Mawson Lakes, SA 5095, Australia.
| | - Craig Priest
- Future Industry Institute, University of South Australia, Mawson Lakes, SA 5095, Australia.
| | - Nicolas H Voelcker
- Future Industry Institute, University of South Australia, Mawson Lakes, SA 5095, Australia.
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18
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Ostromohov N, Bercovici M, Kaigala GV. Delivery of minimally dispersed liquid interfaces for sequential surface chemistry. LAB ON A CHIP 2016; 16:3015-23. [PMID: 27354032 DOI: 10.1039/c6lc00473c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We present a method for sequential delivery of reagents to a reaction site with minimal dispersion of their interfaces. Using segmented flow to encapsulate the reagents as droplets, the dispersion between reagent plugs remains confined in a limited volume, while being transmitted to the reaction surface. In close proximity to the target surface, we use a passive array of microstructures for removal of the oil phase such that the original reagent sequence is reconstructed, and only the aqueous phase reaches the reaction surface. We provide a detailed analysis of the conditions under which the method can be applied and demonstrate maintaining a transition time of 560 ms between reagents transported to a reaction site over a distance of 60 cm. We implemented the method using a vertical microfluidic probe on an open surface, allowing contact-free interaction with biological samples, and demonstrated two examples of assays implemented using the method: measurements of receptor-ligand reaction kinetics and of the fluorescence response of immobilized GFP to local variations in pH. We believe that the method can be useful for studying the dynamic response of cells and proteins to various stimuli, as well as for highly automated multi-step assays.
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Affiliation(s)
- N Ostromohov
- Faculty of Mechanical Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel. and IBM Research-Zurich, Saeumerstrasse 4, CH-8803 Rueschlikon, Switzerland.
| | - M Bercovici
- Faculty of Mechanical Engineering, Technion - Israel Institute of Technology, Haifa 3200003, Israel.
| | - G V Kaigala
- IBM Research-Zurich, Saeumerstrasse 4, CH-8803 Rueschlikon, Switzerland.
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19
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Brown DR, Samsa LA, Qian L, Liu J. Advances in the Study of Heart Development and Disease Using Zebrafish. J Cardiovasc Dev Dis 2016; 3. [PMID: 27335817 PMCID: PMC4913704 DOI: 10.3390/jcdd3020013] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Animal models of cardiovascular disease are key players in the translational medicine pipeline used to define the conserved genetic and molecular basis of disease. Congenital heart diseases (CHDs) are the most common type of human birth defect and feature structural abnormalities that arise during cardiac development and maturation. The zebrafish, Danio rerio, is a valuable vertebrate model organism, offering advantages over traditional mammalian models. These advantages include the rapid, stereotyped and external development of transparent embryos produced in large numbers from inexpensively housed adults, vast capacity for genetic manipulation, and amenability to high-throughput screening. With the help of modern genetics and a sequenced genome, zebrafish have led to insights in cardiovascular diseases ranging from CHDs to arrhythmia and cardiomyopathy. Here, we discuss the utility of zebrafish as a model system and summarize zebrafish cardiac morphogenesis with emphasis on parallels to human heart diseases. Additionally, we discuss the specific tools and experimental platforms utilized in the zebrafish model including forward screens, functional characterization of candidate genes, and high throughput applications.
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Affiliation(s)
- Daniel R. Brown
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.R.B.); (L.Q.)
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Leigh Ann Samsa
- Department of Cell Biology and Physiology; University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Li Qian
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.R.B.); (L.Q.)
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jiandong Liu
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (D.R.B.); (L.Q.)
- McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Correspondence: ; Tel.: +1-919-962-0326; Fax: +1-919- 843-2063
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20
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Ripoll-Rozada J, García-Cazorla Y, Getino M, Machón C, Sanabria-Ríos D, de la Cruz F, Cabezón E, Arechaga I. Type IV traffic ATPase TrwD as molecular target to inhibit bacterial conjugation. Mol Microbiol 2016; 100:912-21. [PMID: 26915347 DOI: 10.1111/mmi.13359] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Bacterial conjugation is the main mechanism responsible for the dissemination of antibiotic resistance genes. Hence, the search for specific conjugation inhibitors is paramount in the fight against the spread of these genes. In this pursuit, unsaturated fatty acids have been found to specifically inhibit bacterial conjugation. Despite the growing interest on these compounds, their mode of action and their specific target remain unknown. Here, we identified TrwD, a Type IV secretion traffic ATPase, as the molecular target for fatty acid-mediated inhibition of conjugation. Moreover, 2-alkynoic fatty acids, which are also potent inhibitors of bacterial conjugation, are also powerful inhibitors of the ATPase activity of TrwD. Characterization of the kinetic parameters of ATPase inhibition has led us to identify the catalytic mechanism by which fatty acids exert their activity. These results open a new avenue for the rational design of inhibitors of bacterial conjugation in the fight against the dissemination of antibiotic resistance genes.
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Affiliation(s)
- Jorge Ripoll-Rozada
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Yolanda García-Cazorla
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - María Getino
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Cristina Machón
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - David Sanabria-Ríos
- Inter American University of Puerto Rico-Metropolitan Campus, Faculty of Science and Technology, San Juan, Puerto Rico
| | - Fernando de la Cruz
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Elena Cabezón
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Ignacio Arechaga
- Departamento de Biología Molecular and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
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21
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Zimmermann S, Gretzinger S, Scheeder C, Schwab ML, Oelmeier SA, Osberghaus A, Gottwald E, Hubbuch J. High-throughput cell quantification assays for use in cell purification development - enabling technologies for cell production. Biotechnol J 2016; 11:676-86. [DOI: 10.1002/biot.201500577] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/24/2015] [Accepted: 01/22/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Sarah Zimmermann
- Karlsruhe Institute of Technology (KIT), Institute of Process Engineering in Life Science, Section IV: Biomolecular Separation Engineering (MAB); Karlsruhe Germany
| | - Sarah Gretzinger
- Karlsruhe Institute of Technology (KIT), Institute of Process Engineering in Life Science, Section IV: Biomolecular Separation Engineering (MAB); Karlsruhe Germany
| | - Christian Scheeder
- Karlsruhe Institute of Technology (KIT), Institute of Process Engineering in Life Science, Section IV: Biomolecular Separation Engineering (MAB); Karlsruhe Germany
| | - Marie-Luise Schwab
- Karlsruhe Institute of Technology (KIT), Institute of Process Engineering in Life Science, Section IV: Biomolecular Separation Engineering (MAB); Karlsruhe Germany
- DIARECT AG, Department of Quality Assurance and Quality Control; Freiburg Germany
| | - Stefan A. Oelmeier
- Karlsruhe Institute of Technology (KIT), Institute of Process Engineering in Life Science, Section IV: Biomolecular Separation Engineering (MAB); Karlsruhe Germany
- Boehringer Ingelheim Pharma GmbH & Co. KG, Global Bioprocess & Pharmaceutical Development; Biberach Germany
| | - Anna Osberghaus
- Karlsruhe Institute of Technology (KIT), Institute of Process Engineering in Life Science, Section IV: Biomolecular Separation Engineering (MAB); Karlsruhe Germany
| | - Eric Gottwald
- Karlsruhe Institute of Technology (KIT), Institute for Biological Interfaces (IBG 5); Eggenstein-Leopoldshafen Germany
| | - Jürgen Hubbuch
- Karlsruhe Institute of Technology (KIT), Institute of Process Engineering in Life Science, Section IV: Biomolecular Separation Engineering (MAB); Karlsruhe Germany
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22
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Microfluidics for cell-based high throughput screening platforms - A review. Anal Chim Acta 2015; 903:36-50. [PMID: 26709297 DOI: 10.1016/j.aca.2015.11.023] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 10/04/2015] [Accepted: 11/14/2015] [Indexed: 01/09/2023]
Abstract
In the last decades, the basic techniques of microfluidics for the study of cells such as cell culture, cell separation, and cell lysis, have been well developed. Based on cell handling techniques, microfluidics has been widely applied in the field of PCR (Polymerase Chain Reaction), immunoassays, organ-on-chip, stem cell research, and analysis and identification of circulating tumor cells. As a major step in drug discovery, high-throughput screening allows rapid analysis of thousands of chemical, biochemical, genetic or pharmacological tests in parallel. In this review, we summarize the application of microfluidics in cell-based high throughput screening. The screening methods mentioned in this paper include approaches using the perfusion flow mode, the droplet mode, and the microarray mode. We also discuss the future development of microfluidic based high throughput screening platform for drug discovery.
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23
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Rosa F, Sales KC, Cunha BR, Couto A, Lopes MB, Calado CRC. A comprehensive high-throughput FTIR spectroscopy-based method for evaluating the transfection event: estimating the transfection efficiency and extracting associated metabolic responses. Anal Bioanal Chem 2015; 407:8097-108. [PMID: 26329279 DOI: 10.1007/s00216-015-8983-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/29/2015] [Accepted: 08/14/2015] [Indexed: 12/11/2022]
Abstract
Reporter genes are routinely used in every laboratory for molecular and cellular biology for studying heterologous gene expression and general cellular biological mechanisms, such as transfection processes. Although well characterized and broadly implemented, reporter genes present serious limitations, either by involving time-consuming procedures or by presenting possible side effects on the expression of the heterologous gene or even in the general cellular metabolism. Fourier transform mid-infrared (FT-MIR) spectroscopy was evaluated to simultaneously analyze in a rapid (minutes) and high-throughput mode (using 96-wells microplates), the transfection efficiency, and the effect of the transfection process on the host cell biochemical composition and metabolism. Semi-adherent HEK and adherent AGS cell lines, transfected with the plasmid pVAX-GFP using Lipofectamine, were used as model systems. Good partial least squares (PLS) models were built to estimate the transfection efficiency, either considering each cell line independently (R (2) ≥ 0.92; RMSECV ≤ 2 %) or simultaneously considering both cell lines (R (2) = 0.90; RMSECV = 2 %). Additionally, the effect of the transfection process on the HEK cell biochemical and metabolic features could be evaluated directly from the FT-IR spectra. Due to the high sensitivity of the technique, it was also possible to discriminate the effect of the transfection process from the transfection reagent on KEK cells, e.g., by the analysis of spectral biomarkers and biochemical and metabolic features. The present results are far beyond what any reporter gene assay or other specific probe can offer for these purposes.
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Affiliation(s)
- Filipa Rosa
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Kevin C Sales
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Bernardo R Cunha
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Andreia Couto
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Marta B Lopes
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal.,Instituto de Telecomunicações, Instituto Superior Técnico, 1049-001, Lisbon, Portugal
| | - Cecília R C Calado
- Instituto Superior de Engenharia de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007, Lisbon, Portugal.
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24
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Keßler M, Rottbauer W, Just S. Recent progress in the use of zebrafish for novel cardiac drug discovery. Expert Opin Drug Discov 2015; 10:1231-41. [PMID: 26294375 DOI: 10.1517/17460441.2015.1078788] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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25
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Janzen WP. Screening technologies for small molecule discovery: the state of the art. ACTA ACUST UNITED AC 2015; 21:1162-70. [PMID: 25237860 DOI: 10.1016/j.chembiol.2014.07.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/14/2014] [Accepted: 07/16/2014] [Indexed: 01/24/2023]
Abstract
Screening, high-throughput screening, and ultra-high-throughput screening are all really just points on a spectrum that represent differing applications of the same process: the creation of biologically relevant assays that are relevant, reproducible, reliable, and robust. Whether the discovery program is developing a pharmaceutical, an academic probe, cosmetics, pesticides, or a toxicity monitoring assay, the development of a screen focuses on generating a method that will reliably deliver reproducible results over a period of weeks, months, or years and that will generate consistent results for every test along the way. This review provides both historical perspective on how this unique scientific discipline evolved and commentary on the current state of the art technologies and techniques.
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Affiliation(s)
- William P Janzen
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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26
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Hattori K, Sugiura S, Kanamori T. Pressure-Driven Microfluidic Perfusion Culture Device for Integrated Dose-Response Assays. ACTA ACUST UNITED AC 2013; 18:437-45. [DOI: 10.1177/2211068213503155] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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27
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An inexpensive high-throughput nuclear magnetic resonance tube cleaning apparatus. Anal Biochem 2011; 416:234-6. [DOI: 10.1016/j.ab.2011.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 05/09/2011] [Indexed: 11/23/2022]
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28
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Gradinaru CC, Marushchak DO, Samim M, Krull UJ. Fluorescence anisotropy: from single molecules to live cells. Analyst 2010; 135:452-9. [PMID: 20174695 DOI: 10.1039/b920242k] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The polarization of light emitted by fluorescent probes is an easily accessible physical quantity that is related to a multitude of molecular parameters including conformation, orientation, size and the nanoscale environment conditions, such as dynamic viscosity and temperature. In analytical biochemistry and analytical chemistry applied to biological problems, fluorescence anisotropy is widely used for measuring the folding state of proteins and nucleic acids, and the affinity constant of ligands through titration experiments. The emphasis of this review is on new multi-parameter single-molecule detection schemes and their bioanalytical applications, and on the use of ensemble polarization assays to study binding and conformational dynamics of proteins and aptamers and for high-throughput discovery of small-molecule drugs.
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Affiliation(s)
- Claudiu C Gradinaru
- Department of Physics, Institute for Optical Sciences, University of Toronto, Toronto, Canada.
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29
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Keeney TR, Bock C, Gold L, Kraemer S, Lollo B, Nikrad M, Stanton M, Stewart A, Vaught JD, Walker JJ. Automation of the SomaLogic Proteomics Assay: A Platform for Biomarker Discovery. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.jala.2009.05.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
At SomaLogic, we have embarked on an ambitious program of clinical studies using a novel aptamerbased proteomics technology to discover biomarkers and develop new tools to diagnose, understand, and treat human disease. As part of this program, we designed and implemented an automated assay for its highly multiplexed proteomics discovery platform. The performance of the automated assay was validated in a study that compared the automated assay to the specifications of an established manual method. Results showed that the automated method performed to the required specifications, and that the automation system improved the efficiency, productivity, and economics of our biomarker discovery program.
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Affiliation(s)
| | | | - Larry Gold
- SomaLogic, Boulder, CO
- University of Colorado, Boulder, CO
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Ostroff R, Foreman T, Keeney TR, Stratford S, Walker JJ, Zichi D. The stability of the circulating human proteome to variations in sample collection and handling procedures measured with an aptamer-based proteomics array. J Proteomics 2009; 73:649-66. [PMID: 19755178 DOI: 10.1016/j.jprot.2009.09.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Revised: 09/04/2009] [Accepted: 09/08/2009] [Indexed: 10/20/2022]
Abstract
Blood-based protein biomarkers hold great promise to advance medicine with applications that detect and diagnose diseases and aid in their treatment. We are developing such applications with our proteomics technology that combines high-content with low limits of detection. Biomarker discovery relies heavily on archived blood sample collections. Blood is dynamic and changes with different sampling procedures potentially confounding biomarker studies. In order to better understand the effects of sampling procedures on the circulating proteome, we studied three sample collection variables commonly encountered in archived sample sets. These variables included (1) three different sample tube types, PPT plasma, SST serum, and Red Top serum, (2) the time from venipuncture to centrifugation, and (3) the time from centrifugation to freezing. We profiled 498 proteins for each of 240 samples and compared the results by ANOVA. The results found no significant variation in the measurements for most proteins (approximately 99%) when the two sample processing times tested were 2h or less, regardless of sample tube type. Even at the longest timepoints, 20 h, approximately 82% of the proteins, on average for the three collection tube types, showed no significant change. These results are encouraging for proteomic biomarker discovery.
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Affiliation(s)
- Rachel Ostroff
- SomaLogic, 2945 Wilderness Place, Boulder, CO 80301, USA
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31
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Taufer M, Armen R, Chen J, Teller P, Brooks C. Computational multiscale modeling in protein--ligand docking. ACTA ACUST UNITED AC 2009; 28:58-69. [PMID: 19349252 DOI: 10.1109/memb.2009.931789] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In biological systems, the binding of small molecule ligands to proteins is a crucial process for almost every aspect of biochemistry and molecular biology. Enzymes are proteins that function by catalyzing specific biochemical reactions that convert reactants into products. Complex organisms are typically composed of cells in which thousands of enzymes participate in complex and interconnected biochemical pathways. Some enzymes serve as sequential steps in specific pathways (such as energy metabolism), while others function to regulate entire pathways and cellular functions [1]. Small molecule ligands can be designed to bind to a specific enzyme and inhibit the biochemical reaction. Inhibiting the activity of key enzymes may result in the entire biochemical pathways being turned on or off [2], [3]. Many small molecule drugs marketed today function in this generic way as enzyme inhibitors. If research identifies a specific enzyme as being crucial to the progress of disease, then this enzyme may be targeted with an inhibitor, which may slow down or reverse the progress of disease. In this way, enzymes are targeted from specific pathogens (e.g., virus, bacteria, fungi) for infectious diseases [4], [5], and human enzymes are targeted for noninfectious diseases such as cardiovascular disease, cancer, diabetes, and neurodegenerative diseases [6].
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Affiliation(s)
- Michela Taufer
- Department of Computer and Information Sciences, University of Delaware, Newark, 19716, USA.
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32
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Hattori K, Sugiura S, Kanamori T. Generation of arbitrary monotonic concentration profiles by a serial dilution microfluidic network composed of microchannels with a high fluidic-resistance ratio. LAB ON A CHIP 2009; 9:1763-72. [PMID: 19495461 DOI: 10.1039/b816995k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
This paper reports a serial dilution microfluidic network composed of microchannels with a high fluidic-resistance ratio for generating linear concentration profiles as well as logarithmic concentration profiles spanning 3 and 6 orders of magnitude. The microfluidic networks were composed of thin fluidic-resistance microchannels with 160 to 730 microm(2) cross-sectional areas and thick diffusion-mixing microchannels with 3,600 to 17,000 microm(2) cross-sectional areas, and were fabricated from polydimethylsiloxane by multilayer photolithography and replica molding. We proposed a design algorithm of the microfluidic network for an arbitrary monotonic concentration profile by means of a hydrodynamic calculation. Because of the high fluidic-resistance ratio of the fluidic-resistance microchannels to the diffusion-mixing microchannels, appropriate geometry and dimensions of the fluidic-resistance microchannels allowed us to obtain desired concentration profiles. The fabricated microfluidic network was compact, occupying a 8 x 18 to 21.0 x 13.5 mm(2) area on the microchip. Both the linear and the logarithmic concentration profiles were successfully generated with the error less than 15% for the linear concentration profile, 22% and 35% for the logarithmic concentration profiles of 3 and 6 orders of magnitude, respectively. The generated linear concentration profiles of the small molecule, calcein, were independent of the flow rate within the range of 0.009 to 0.23 microL/min. The concentration profiles of the large molecules, dextrans, depended on the flow rate and molecular weight. The required residence time of large molecules in the diffusion-mixing microchannel was correlated with dimensionless diffusion time, Fick number, and was discussed based on the scaling law. These compact, stable serial dilution microfluidic networks are expected to be applied to various integrated on-chip analyses.
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Affiliation(s)
- Koji Hattori
- Research Center of Advanced Bionics, National Institute of Advanced Industrial Science and Technology (AIST), Central 5th, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
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Hong J, Edel JB, deMello AJ. Micro- and nanofluidic systems for high-throughput biological screening. Drug Discov Today 2008; 14:134-46. [PMID: 18983933 DOI: 10.1016/j.drudis.2008.10.001] [Citation(s) in RCA: 165] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Revised: 09/30/2008] [Accepted: 10/06/2008] [Indexed: 01/09/2023]
Abstract
High-throughput screening (HTS) is a method of scientific experimentation widely used in drug discovery and relevant to the fields of biology. The development of micro- and nanofluidic systems for use in the biological sciences has been driven by a range of fundamental attributes that accompany miniaturization and massively parallel experimentation. We review recent advances in both arraying strategies based on nano/microfluidics and novel nano/microfluidic devices with high analytical throughput rates.
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Affiliation(s)
- Jongin Hong
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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Kahakeaw D, Reetz M. A Cell-Based Adrenaline Assay for Automated High-Throughput Activity Screening of Epoxide Hydrolases. Chem Asian J 2008; 3:233-8. [DOI: 10.1002/asia.200700325] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Harbers M. The current status of cDNA cloning. Genomics 2008; 91:232-42. [PMID: 18222633 DOI: 10.1016/j.ygeno.2007.11.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 11/10/2007] [Accepted: 11/17/2007] [Indexed: 11/19/2022]
Abstract
The cloning of cDNAs, copies of cellular RNA, is one of the classical technologies in molecular biology. Over the past 30 years cDNA cloning technologies have been improved to enable the cloning of large cDNA collections, which are fundamental to today's understanding of the utilization of genetic information. With the discovery of noncoding RNAs, additional new approaches to the cloning of short RNAs have been developed. However, with the realization that much larger portions of genomes are transcribed than anticipated from genome annotations, cDNA cloning faces new challenges to uncover rare transcripts and to make the corresponding cDNAs available for functional studies. This review provides an overview on the current status of cDNA cloning and possibilities for the discovery and characterization of new RNA families.
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Affiliation(s)
- Matthias Harbers
- DNAFORM, Inc., Leading Venture Plaza 2, 75-1 Ono-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0046, Japan.
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