1
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Hein JB, Nguyen HT, Garvanska DH, Nasa I, Kruse T, Feng Y, Lopez Mendez B, Davey N, Kettenbach AN, Fordyce PM, Nilsson J. Phosphatase specificity principles uncovered by MRBLE:Dephos and global substrate identification. Mol Syst Biol 2023; 19:e11782. [PMID: 37916966 PMCID: PMC10698503 DOI: 10.15252/msb.202311782] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023] Open
Abstract
Phosphoprotein phosphatases (PPPs) regulate major signaling pathways, but the determinants of phosphatase specificity are poorly understood. This is because methods to investigate this at scale are lacking. Here, we develop a novel in vitro assay, MRBLE:Dephos, that allows multiplexing of dephosphorylation reactions to determine phosphatase preferences. Using MRBLE:Dephos, we establish amino acid preferences of the residues surrounding the dephosphorylation site for PP1 and PP2A-B55, which reveals common and unique preferences. To compare the MRBLE:Dephos results to cellular substrates, we focused on mitotic exit that requires extensive dephosphorylation by PP1 and PP2A-B55. We use specific inhibition of PP1 and PP2A-B55 in mitotic exit lysates coupled with phosphoproteomics to identify more than 2,000 regulated sites. Importantly, the sites dephosphorylated during mitotic exit reveal key signatures that are consistent with MRBLE:Dephos. Furthermore, integration of our phosphoproteomic data with mitotic interactomes of PP1 and PP2A-B55 provides insight into how binding of phosphatases to substrates shapes dephosphorylation. Collectively, we develop novel approaches to investigate protein phosphatases that provide insight into mitotic exit regulation.
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Affiliation(s)
- Jamin B Hein
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Department of BioengineeringStanford UniversityStanfordCAUSA
| | - Hieu T Nguyen
- Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Dimitriya H Garvanska
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Isha Nasa
- Department of BioengineeringStanford UniversityStanfordCAUSA
| | - Thomas Kruse
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Yinnian Feng
- Department of GeneticsStanford UniversityStanfordCAUSA
| | - Blanca Lopez Mendez
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Norman Davey
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
| | - Arminja N Kettenbach
- Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Polly M Fordyce
- Department of BioengineeringStanford UniversityStanfordCAUSA
- Department of GeneticsStanford UniversityStanfordCAUSA
- Sarafan ChEM‐HStanford UniversityStanfordCAUSA
- Chan Zuckerberg BiohubSan FranciscoCAUSA
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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2
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Ortiz-Perez A, Izquierdo-Lozano C, Meijers R, Grisoni F, Albertazzi L. Identification of fluorescently-barcoded nanoparticles using machine learning. NANOSCALE ADVANCES 2023; 5:2307-2317. [PMID: 37056621 PMCID: PMC10089084 DOI: 10.1039/d2na00648k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Barcoding of nano- and micro-particles allows distinguishing multiple targets at the same time within a complex mixture and is emerging as a powerful tool to increase the throughput of many assays. Fluorescent barcoding is one of the most used strategies, where microparticles are labeled with dyes and classified based on fluorescence color, intensity, or other features. Microparticles are ideal targets due to their relative ease of detection, manufacturing, and higher homogeneity. Barcoding is considerably more challenging in the case of nanoparticles (NPs), where their small size results in a lower signal and greater heterogeneity. This is a significant limitation since many bioassays require the use of nano-sized carriers. In this study, we introduce a machine-learning-assisted workflow to write, read, and classify barcoded PLGA-PEG NPs at a single-particle level. This procedure is based on the encapsulation of fluorescent markers without modifying their physicochemical properties (writing), the optimization of their confocal imaging (reading), and the implementation of a machine learning-based barcode reader (classification). We found nanoparticle heterogeneity as one of the main factors that challenges barcode separation, and that information extracted from the dyes' nanoscale confinement effects (such as Förster Resonance Energy Transfer, FRET) can aid barcode identification. Moreover, we provide a guide to reaching the optimal trade-off between the number of simultaneous barcodes and classification accuracy supporting the use of this workflow for a variety of bioassays.
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Affiliation(s)
- Ana Ortiz-Perez
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
| | - Cristina Izquierdo-Lozano
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
| | - Rens Meijers
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
| | - Francesca Grisoni
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
| | - Lorenzo Albertazzi
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology PO Box 513 5600 MB Eindhoven The Netherlands
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3
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Lee S, Lee W, Lee AC, Nam J, Lee J, Kim H, Jeong Y, Yeom H, Kim N, Song SW, Kwon S. I-LIFT (image-based laser-induced forward transfer) platform for manipulating encoded microparticles. BIOMICROFLUIDICS 2022; 16:061101. [PMID: 36483021 PMCID: PMC9726220 DOI: 10.1063/5.0131733] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Encoded microparticles have great potential in small-volume multiplexed assays. It is important to link the micro-level assays to the macro-level by indexing and manipulating the microparticles to enhance their versatility. There are technologies to actively manipulate the encoded microparticles, but none is capable of directly manipulating the encoded microparticles with homogeneous physical properties. Here, we report the image-based laser-induced forward transfer system for active manipulation of the graphically encoded microparticles. By demonstrating the direct retrieval of the microparticles of interest, we show that this system has the potential to expand the usage of encoded microparticles.
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Affiliation(s)
- Sumin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Wooseok Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Amos Chungwon Lee
- Bio-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Juhong Nam
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - JinYoung Lee
- Division of Engineering Science, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Hamin Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Yunjin Jeong
- Bio-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Huiran Yeom
- Bio-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Namphil Kim
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Seo Woo Song
- Bio-MAX Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunghoon Kwon
- Authors to whom correspondence should be addressed: and
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4
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A bead-based method for high-throughput mapping of the sequence- and force-dependence of T cell activation. Nat Methods 2022; 19:1295-1305. [PMID: 36064771 DOI: 10.1038/s41592-022-01592-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/21/2022] [Indexed: 11/08/2022]
Abstract
Adaptive immunity relies on T lymphocytes that use αβ T cell receptors (TCRs) to discriminate among peptides presented by major histocompatibility complex molecules (pMHCs). Identifying pMHCs capable of inducing robust T cell responses will not only enable a deeper understanding of the mechanisms governing immune responses but could also have broad applications in diagnosis and treatment. T cell recognition of sparse antigenic pMHCs in vivo relies on biomechanical forces. However, in vitro screening methods test potential pMHCs without force and often at high (nonphysiological) pMHC densities and thus fail to predict potent agonists in vivo. Here, we present a technology termed BATTLES (biomechanically assisted T cell triggering for large-scale exogenous-pMHC screening) that uses biomechanical force to initiate T cell triggering for peptides and cells in parallel. BATTLES displays candidate pMHCs on spectrally encoded beads composed of a thermo-responsive polymer capable of applying shear loads to T cells, facilitating exploration of the force- and sequence-dependent landscape of T cell responses. BATTLES can be used to explore basic T cell mechanobiology and T cell-based immunotherapies.
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5
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Cowell TW, Dobria A, Han HS. Simplified, Shear Induced Generation of Double Emulsions for Robust Compartmentalization during Single Genome Analysis. ACS APPLIED MATERIALS & INTERFACES 2022; 14:20528-20537. [PMID: 35502700 DOI: 10.1021/acsami.1c22692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Drop microfluidics has driven innovations for high throughput, low input analysis techniques such as single-cell RNA-seq. However, the instability of single emulsion (SE) drops occasionally causes significant merging during drop processing, limiting most applications to single-step reactions in drops. Here, we show that double emulsion (DE) drops address this critical limitation and completely prevent drop contents from mixing. DEs show excellent stability during thermal cycling. More importantly, DEs undergo rupture into the continuous phase instead of merging, preventing content mixing and eliminating unstable drops from the downstream analysis. Due to the lack of drop merging, the monodispersity of drops is maintained throughout a workflow, enabling the deterministic manipulation of drops downstream. We also developed a simple, one-layer DE drop maker compatible with simple surface treatment using a plasma cleaner. The device allows for the robust production of single-core DEs at a wide range of flow rates and better control over the shell thickness, both of which have been significant limitations of conventional two-layer devices. This approach makes the fabrication of DE devices much more accessible, facilitating its broader adoption. Finally, we show that DE droplets eliminate content mixing and maintain compartmentalization of single virus genomes during PCR-based amplification and barcoding, while SEs mixed contents due to merging. With their resistance to content mixing, DE drops have key advantages for multistep reactions in drops, which is limited in SEs due to merging and content mixing.
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Affiliation(s)
- Thomas W Cowell
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Mathews Ave., Urbana, Illinois 61801, United States
| | - Andrew Dobria
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Ave., Urbana, Illinois 61801, United States
| | - Hee-Sun Han
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Mathews Ave., Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr., Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, 405 North Mathews Ave., Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, 600 S Mathews Ave., Urbana, Illinois 61801, United States
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6
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Zhao X, Kolawole EM, Chan W, Feng Y, Yang X, Gee MH, Jude KM, Sibener LV, Fordyce PM, Germain RN, Evavold BD, Garcia KC. Tuning T cell receptor sensitivity through catch bond engineering. Science 2022; 376:eabl5282. [PMID: 35389803 PMCID: PMC9513562 DOI: 10.1126/science.abl5282] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Adoptive cell therapy using engineered T cell receptors (TCRs) is a promising approach for targeting cancer antigens, but tumor-reactive TCRs are often weakly responsive to their target ligands, peptide-major histocompatibility complexes (pMHCs). Affinity-matured TCRs can enhance the efficacy of TCR-T cell therapy but can also cross-react with off-target antigens, resulting in organ immunopathology. We developed an alternative strategy to isolate TCR mutants that exhibited high activation signals coupled with low-affinity pMHC binding through the acquisition of catch bonds. Engineered analogs of a tumor antigen MAGE-A3-specific TCR maintained physiological affinities while exhibiting enhanced target killing potency and undetectable cross-reactivity, compared with a high-affinity clinically tested TCR that exhibited lethal cross-reactivity with a cardiac antigen. Catch bond engineering is a biophysically based strategy to tune high-sensitivity TCRs for T cell therapy with reduced potential for adverse cross-reactivity.
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Affiliation(s)
- Xiang Zhao
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elizabeth M Kolawole
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Waipan Chan
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yinnian Feng
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Xinbo Yang
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marvin H Gee
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin M Jude
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Leah V Sibener
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Polly M Fordyce
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,ChEM-H Institute, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg BioHub, San Francisco, CA 94158, USA
| | - Ronald N Germain
- Lymphocyte Biology Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brian D Evavold
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - K Christopher Garcia
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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7
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Zhang J, Shu S, Guan X, Yang N. Lattice Boltzmann simulation of drop splitting in a fractal tree-like microchannel. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2021.117277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Jang AS, Praveen Kumar PP, Lim DK. Attomolar Sensitive Magnetic Microparticles and a Surface-Enhanced Raman Scattering-Based Assay for Detecting SARS-CoV-2 Nucleic Acid Targets. ACS APPLIED MATERIALS & INTERFACES 2022; 14:138-149. [PMID: 34914369 PMCID: PMC8691452 DOI: 10.1021/acsami.1c17028] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/05/2021] [Indexed: 05/09/2023]
Abstract
Highly sensitive, reliable assays with strong multiplexing capability for detecting nucleic acid targets are significantly important for diagnosing various diseases, particularly severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The nanomaterial-based assay platforms suffer from several critical issues such as non-specific binding and highly false-positive results. In this paper, to overcome such limitations, we reported sensitive and remarkably reproducible magnetic microparticles (MMPs) and a surface-enhanced Raman scattering (SERS)-based assay using stable silver nanoparticle clusters for detecting viral nucleic acids. The MMP-SERS-based assay exhibited a sensitivity of 1.0 fM, which is superior to the MMP-fluorescence-based assay. In addition, in the presence of anisotropic Ag nanostructures (nanostars and triangular nanoplates), the assay exhibited greatly enhanced sensitivity (10 aM) and excellent signal reproducibility. This assay platform intrinsically eliminated the non-specific binding that occurs in the target detection step, and the controlled formation of stable silver nanoparticle clusters in solution enabled the remarkable reproducibility of the results. These findings indicate that this assay can be employed for future practical bioanalytical applications.
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Affiliation(s)
- Ah Seong Jang
- KU-KIST Graduate School of Converging Science and
Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul
02841, Republic of Korea
| | | | - Dong-Kwon Lim
- KU-KIST Graduate School of Converging Science and
Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul
02841, Republic of Korea
- Department of Integrative Energy Engineering, College
of Engineering, Korea University, 145 Anam-ro, Seongbuk-gu,
Seoul 02841, Republic of Korea
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9
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Hein J, Cyert MS, Fordyce PM. MRBLE-pep Measurements Reveal Accurate Binding Affinities for B56, a PP2A Regulatory Subunit. ACS MEASUREMENT SCIENCE AU 2021; 1:56-64. [PMID: 35128539 PMCID: PMC8809670 DOI: 10.1021/acsmeasuresciau.1c00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Signal transduction pathways rely on dynamic interactions between protein globular domains and short linear motifs (SLiMs). The weak affinities of these interactions are essential to allow fast rewiring of signaling pathways and downstream responses but also pose technical challenges for interaction detection and measurement. We recently developed a technique (MRBLE-pep) that leverages spectrally encoded hydrogel beads to measure binding affinities between a single protein of interest and 48 different peptide sequences in a single small volume. In prior work, we applied it to map the binding specificity landscape between calcineurin and the PxIxIT SLiM (Nguyen, H. Q. et al. Elife 2019, 8). Here, using peptide sequences known to bind the PP2A regulatory subunit B56α, we systematically compare affinities measured by MRBLE-pep or isothermal calorimetry (ITC) and confirm that MRBLE-pep accurately quantifies relative affinity over a wide dynamic range while using a fraction of the material required for traditional methods such as ITC.
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Affiliation(s)
- Jamin
B. Hein
- Department
of Biology, Stanford University, Stanford, California 94305, United States
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- The
Novo Nordisk Foundation Center for Protein Research, Faculty of Health
and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - Martha S. Cyert
- Department
of Biology, Stanford University, Stanford, California 94305, United States
| | - Polly M. Fordyce
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Department
of Genetics, Stanford University, Stanford, California 94305, United States
- ChEM-H
Institute, Stanford University, Stanford, California 94305, United States
- Chan
Zuckerberg
Biohub, San Francisco, California 94110, United States
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10
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Liu P, Jonkheijm P, Terstappen LWMM, Stevens M. Magnetic Particles for CTC Enrichment. Cancers (Basel) 2020; 12:cancers12123525. [PMID: 33255978 PMCID: PMC7760229 DOI: 10.3390/cancers12123525] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary For the enrichment of very rare cells, such as Circulating Tumor Cells (CTCs), immunomagnetic enrichment is frequently used. For this purpose, magnetic nanoparticles (MNPs) coated with specific antibodies directed against cancer cells are used. In this review, we look at the properties such a particle needs to have in order to be used successfully, and describe the different methods used in the production of such a particle as well as the methods for their separation. Additionally, an overview is given of the antibodies that could potentially be used for this purpose. Abstract Here, we review the characteristics and synthesis of magnetic nanoparticles (MNPs) and place these in the context of their usage in the immunomagnetic enrichment of Circulating Tumor Cells (CTCs). The importance of the different characteristics is explained, the need for a very specific enrichment is emphasized and different (commercial) magnetic separation techniques are shown. As the specificity of an MNP is in a large part dependent on the antibody coated onto the particle, different strategies in the coupling of specific antibodies as well as an overview of the available antibodies is given.
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Affiliation(s)
- Peng Liu
- Department of Medical Cell BioPhysics, University of Twente, 7522 NB Enschede, The Netherlnds; (P.L.); (L.W.M.M.T.)
- Department of Molecular Nanofabrication, University of Twente, 7522 NB Enschede, The Netherlands;
| | - Pascal Jonkheijm
- Department of Molecular Nanofabrication, University of Twente, 7522 NB Enschede, The Netherlands;
| | - Leon W. M. M. Terstappen
- Department of Medical Cell BioPhysics, University of Twente, 7522 NB Enschede, The Netherlnds; (P.L.); (L.W.M.M.T.)
| | - Michiel Stevens
- Department of Medical Cell BioPhysics, University of Twente, 7522 NB Enschede, The Netherlnds; (P.L.); (L.W.M.M.T.)
- Correspondence: ; Tel.: +31-53-489-4101
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