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Vanhoucke T, Perima A, Zolfanelli L, Bruhns P, Broketa M. Deep learning enabled label-free microfluidic droplet classification for single cell functional assays. Front Bioeng Biotechnol 2024; 12:1468738. [PMID: 39359262 PMCID: PMC11445169 DOI: 10.3389/fbioe.2024.1468738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 08/30/2024] [Indexed: 10/04/2024] Open
Abstract
Droplet-based microfluidics techniques coupled to microscopy allow for the characterization of cells at the single-cell scale. However, such techniques generate substantial amounts of data and microscopy images that must be analyzed. Droplets on these images usually need to be classified depending on the number of cells they contain. This verification, when visually carried out by the experimenter image-per-image, is time-consuming and impractical for analysis of many assays or when an assay yields many putative droplets of interest. Machine learning models have already been developed to classify cell-containing droplets within microscopy images, but not in the context of assays in which non-cellular structures are present inside the droplet in addition to cells. Here we develop a deep learning model using the neural network ResNet-50 that can be applied to functional droplet-based microfluidic assays to classify droplets according to the number of cells they contain with >90% accuracy in a very short time. This model performs high accuracy classification of droplets containing both cells with non-cellular structures and cells alone and can accommodate several different cell types, for generalization to a broader array of droplet-based microfluidics applications.
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Affiliation(s)
- Thibault Vanhoucke
- Institut Pasteur, Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1222, Antibodies in Therapy and Pathology, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Angga Perima
- Institut Pasteur, Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1222, Antibodies in Therapy and Pathology, Paris, France
| | - Lorenzo Zolfanelli
- Institut Pasteur, Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1222, Antibodies in Therapy and Pathology, Paris, France
- Laboratoire de Colloides et Matériaux Divisés, École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris, Université Paris Sciences et Lettres, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 8231, Paris, France
| | - Pierre Bruhns
- Institut Pasteur, Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1222, Antibodies in Therapy and Pathology, Paris, France
- Paris Est Créteil University (UPEC), Assistance Publique-Hôpitaux de Paris (AP-HP), Henri Mondor Hospital, Fédération Hospitalo-Universitaire TRUE InnovaTive theRapy for immUne disordErs, Créteil, France
| | - Matteo Broketa
- Institut Pasteur, Université Paris Cité, Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1222, Antibodies in Therapy and Pathology, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
- Evexta Bio, Paris, France
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2
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Abu-Shmais AA, Vukovich MJ, Wasdin PT, Suresh YP, Marinov TM, Rush SA, Gillespie RA, Sankhala RS, Choe M, Joyce MG, Kanekiyo M, McLellan JS, Georgiev IS. Antibody sequence determinants of viral antigen specificity. mBio 2024:e0156024. [PMID: 39264172 DOI: 10.1128/mbio.01560-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/13/2024] [Indexed: 09/13/2024] Open
Abstract
Throughout life, humans experience repeated exposure to viral antigens through infection and vaccination, resulting in the generation of diverse, antigen-specific antibody repertoires. A paramount feature of antibodies that enables their critical contributions in counteracting recurrent and novel pathogens, and consequently fostering their utility as valuable targets for therapeutic and vaccine development, is the exquisite specificity displayed against their target antigens. Yet, there is still limited understanding of the determinants of antibody-antigen specificity, particularly as a function of antibody sequence. In recent years, experimental characterization of antibody repertoires has led to novel insights into fundamental properties of antibody sequences but has been largely decoupled from at-scale antigen specificity analysis. Here, using the LIBRA-seq technology, we generated a large data set mapping antibody sequence to antigen specificity for thousands of B cells, by screening the repertoires of a set of healthy individuals against 20 viral antigens representing diverse pathogens of biomedical significance. Analysis uncovered virus-specific patterns in variable gene usage, gene pairing, somatic hypermutation, as well as the presence of convergent antiviral signatures across multiple individuals, including the presence of public antibody clonotypes. Notably, our results showed that, for B-cell receptors originating from different individuals but leveraging an identical combination of heavy and light chain variable genes, there is a specific CDRH3 identity threshold above which B cells appear to exclusively share the same antigen specificity. This finding provides a quantifiable measure of the relationship between antibody sequence and antigen specificity and further defines experimentally grounded criteria for defining public antibody clonality.IMPORTANCEThe B-cell compartment of the humoral immune system plays a critical role in the generation of antibodies upon new and repeated pathogen exposure. This study provides an unprecedented level of detail on the molecular characteristics of antibody repertoires that are specific to each of the different target pathogens studied here and provides empirical evidence in support of a 70% CDRH3 amino acid identity threshold in pairs of B cells encoded by identical IGHV:IGL(K)V genes, as a means of defining public clonality and therefore predicting B-cell antigen specificity in different individuals. This is of exceptional importance when leveraging public clonality as a method to annotate B-cell receptor data otherwise lacking antigen specificity information. Understanding the fundamental rules of antibody-antigen interactions can lead to transformative new approaches for the development of antibody therapeutics and vaccines against current and emerging viruses.
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Affiliation(s)
- Alexandra A Abu-Shmais
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Matthew J Vukovich
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Perry T Wasdin
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yukthi P Suresh
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Toma M Marinov
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Scott A Rush
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Rajeshwer S Sankhala
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Misook Choe
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - M Gordon Joyce
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
- Program in Computational Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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3
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Autour A, Merten CA. Fluorescence-activated droplet sequencing (FAD-seq) directly provides sequences of screening hits in antibody discovery. Proc Natl Acad Sci U S A 2024; 121:e2405342121. [PMID: 39240970 PMCID: PMC11406258 DOI: 10.1073/pnas.2405342121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 08/04/2024] [Indexed: 09/08/2024] Open
Abstract
Droplet microfluidics has become a very powerful tool in high-throughput screening, including antibody discovery. Screens are usually carried out by physically sorting droplets hosting cells of the desired phenotype, breaking them, recovering the encapsulated cells, and sequencing the paired antibody light and heavy chain genes at the single-cell level. This series of multiple consecutive manipulation steps of rare screening hits is complex and challenging, resulting in a significant loss of clones with the desired phenotype or large fractions of cells with incomplete antibody information. Here, we present fluorescence-activated droplet sequencing, in which droplets showing the desired phenotype are selectively picoinjected with reagents for RT-PCR. Subsequently, light and heavy chain genes are natively paired, fused into a single-chain fragment variant format, and amplified before off-chip transfer and downstream nanopore sequencing. This workflow is sufficiently sensitive for obtaining different paired full-length antibody sequences from as little as five droplets, fulfilling the desired phenotype. Replacing physical sorting by specific sequencing overcomes a general bottleneck in droplet microfluidic screening and should be compatible with many more applications.
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Affiliation(s)
- Alexis Autour
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
- European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Christoph A Merten
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
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4
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Fischer K, Lulla A, So TY, Pereyra-Gerber P, Raybould MIJ, Kohler TN, Yam-Puc JC, Kaminski TS, Hughes R, Pyeatt GL, Leiss-Maier F, Brear P, Matheson NJ, Deane CM, Hyvönen M, Thaventhiran JED, Hollfelder F. Rapid discovery of monoclonal antibodies by microfluidics-enabled FACS of single pathogen-specific antibody-secreting cells. Nat Biotechnol 2024:10.1038/s41587-024-02346-5. [PMID: 39143416 DOI: 10.1038/s41587-024-02346-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/27/2024] [Indexed: 08/16/2024]
Abstract
Monoclonal antibodies are increasingly used to prevent and treat viral infections and are pivotal in pandemic response efforts. Antibody-secreting cells (ASCs; plasma cells and plasmablasts) are an excellent source of high-affinity antibodies with therapeutic potential. Current methods to study antigen-specific ASCs either have low throughput, require expensive and labor-intensive screening or are technically demanding and therefore not widely accessible. Here we present a straightforward technology for the rapid discovery of monoclonal antibodies from ASCs. Our approach combines microfluidic encapsulation of single cells into an antibody capture hydrogel with antigen bait sorting by conventional flow cytometry. With our technology, we screened millions of mouse and human ASCs and obtained monoclonal antibodies against severe acute respiratory syndrome coronavirus 2 with high affinity (<1 pM) and neutralizing capacity (<100 ng ml-1) in 2 weeks with a high hit rate (>85% of characterized antibodies bound the target). By facilitating access to the underexplored ASC compartment, the approach enables efficient antibody discovery and immunological studies into the generation of protective antibodies.
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Affiliation(s)
- Katrin Fischer
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Aleksei Lulla
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tsz Y So
- MRC Toxicology Unit, Gleeson Building, Cambridge, UK
| | - Pehuén Pereyra-Gerber
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
| | - Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | - Timo N Kohler
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Robert Hughes
- MRC Toxicology Unit, Gleeson Building, Cambridge, UK
| | | | | | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Nicholas J Matheson
- Cambridge Institute for Therapeutic Immunology and Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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5
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Yang Y, Vagin SI, Rieger B, Destgeer G. Fabrication of Crescent Shaped Microparticles for Particle Templated Droplet Formation. Macromol Rapid Commun 2024; 45:e2300721. [PMID: 38615246 DOI: 10.1002/marc.202300721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/08/2024] [Indexed: 04/15/2024]
Abstract
Crescent-shaped hydrogel microparticles are shown to template uniform volume aqueous droplets upon simple mixing with aqueous and oil media for various bioassays. This emerging "lab on a particle" technique requires hydrogel particles with tunable material properties and dimensions. The crescent shape of the particles is attained by aqueous two-phase separation of polymers followed by photopolymerization of the curable precursor. In this work, the phase separation of poly(ethylene glycol) diacrylate (PEGDA, Mw 700) and dextran (Mw 40 000) for tunable manufacturing of crescent-shaped particles is investigated. The particles' morphology is precisely tuned by following a phase diagram, varying the UV intensity, and adjusting the flow rates of various streams. The fabricated particles with variable dimensions encapsulate uniform aqueous droplets upon mixing with an oil phase. The particles are fluorescently labeled with red and blue emitting dyes at variable concentrations to produce six color-coded particles. The blue fluorescent dye shows a moderate response to the pH change. The fluorescently labeled particles are able to tolerate an extremely acidic solution (pH 1) but disintegrate within an extremely basic solution (pH 14). The particle-templated droplets are able to effectively retain the disintegrating particle and the fluorescent signal at pH 14.
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Affiliation(s)
- Yimin Yang
- Control and Manipulation of Microscale Living Objects, Department of Electrical Engineering, TUM School of Computation, Information and Technology, TranslaTUM - Center for Translational Cancer Research, Technical University of Munich, Einsteinstraße 25, 81675, Munich, Germany
| | - Sergei I Vagin
- WACKER-Chair of Macromolecular Chemistry, Department of Chemistry, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Bernhard Rieger
- WACKER-Chair of Macromolecular Chemistry, Department of Chemistry, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Ghulam Destgeer
- Control and Manipulation of Microscale Living Objects, Department of Electrical Engineering, TUM School of Computation, Information and Technology, TranslaTUM - Center for Translational Cancer Research, Technical University of Munich, Einsteinstraße 25, 81675, Munich, Germany
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6
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Lu Z, Yuan Y, Han Q, Wang Y, Liang Q. Lab-on-a-chip: an advanced technology for the modernization of traditional Chinese medicine. Chin Med 2024; 19:80. [PMID: 38853247 PMCID: PMC11163804 DOI: 10.1186/s13020-024-00956-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 06/01/2024] [Indexed: 06/11/2024] Open
Abstract
Benefiting from the complex system composed of various constituents, medicament portions, species, and places of origin, traditional Chinese medicine (TCM) possesses numerous customizable and adaptable efficacies in clinical practice guided by its theories. However, these unique features are also present challenges in areas such as quality control, screening active ingredients, studying cell and organ pharmacology, and characterizing the compatibility between different Chinese medicines. Drawing inspiration from the holistic concept, an integrated strategy and pattern more aligned with TCM research emerges, necessitating the integration of novel technology into TCM modernization. The microfluidic chip serves as a powerful platform for integrating technologies in chemistry, biology, and biophysics. Microfluidics has given rise to innovative patterns like lab-on-a-chip and organoids-on-a-chip, effectively challenging the conventional research paradigms of TCM. This review provides a systematic summary of the nature and advanced utilization of microfluidic chips in TCM, focusing on quality control, active ingredient screening/separation, pharmaceutical analysis, and pharmacological/toxicological assays. Drawing on these remarkable references, the challenges, opportunities, and future trends of microfluidic chips in TCM are also comprehensively discussed, providing valuable insights into the development of TCM.
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Affiliation(s)
- Zenghui Lu
- Institute of Traditional Chinese Medicine-X, State Administration of Traditional Chinese Medicine Third-Level Laboratory of Traditional Chinese Medicine Chemistry, Modern Research Center for Traditional Chinese Medicine, Tsinghua University, Beijing, 100084, China
| | - Yue Yuan
- Beijing Key Laboratory of TCM Pharmacology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, 100730, China
| | - Qiang Han
- Institute of Traditional Chinese Medicine-X, State Administration of Traditional Chinese Medicine Third-Level Laboratory of Traditional Chinese Medicine Chemistry, Modern Research Center for Traditional Chinese Medicine, Tsinghua University, Beijing, 100084, China
| | - Yu Wang
- Institute of Traditional Chinese Medicine-X, State Administration of Traditional Chinese Medicine Third-Level Laboratory of Traditional Chinese Medicine Chemistry, Modern Research Center for Traditional Chinese Medicine, Tsinghua University, Beijing, 100084, China
| | - Qionglin Liang
- Institute of Traditional Chinese Medicine-X, State Administration of Traditional Chinese Medicine Third-Level Laboratory of Traditional Chinese Medicine Chemistry, Modern Research Center for Traditional Chinese Medicine, Tsinghua University, Beijing, 100084, China.
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Ahmadi F, Tran H, Letourneau N, Little SR, Fortin A, Moraitis AN, Shih SCC. An Automated Single-Cell Droplet-Digital Microfluidic Platform for Monoclonal Antibody Discovery. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308950. [PMID: 38441226 DOI: 10.1002/smll.202308950] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/30/2024] [Indexed: 06/27/2024]
Abstract
Monoclonal antibody (mAb) discovery plays a prominent role in diagnostic and therapeutic applications. Droplet microfluidics has become a standard technology for high-throughput screening of antibody-producing cells due to high droplet single-cell confinement frequency and rapid analysis and sorting of the cells of interest with their secreted mAbs. In this work, a new method is described for on-demand co-encapsulation of cells that eliminates the difficulties associated with washing in between consecutive steps inside the droplets and enables the washing and addition of fresh media. The new platform identifies hybridoma cells that are expressing antibodies of interest using antibody-characterization assays to find the best-performing or rare-cell antibody candidates.
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Affiliation(s)
- Fatemeh Ahmadi
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
| | - Hao Tran
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada
| | - Natasha Letourneau
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
| | - Samuel R Little
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
| | - Annie Fortin
- Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, Québec, H4P 2R2, Canada
| | - Anna N Moraitis
- Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, Québec, H4P 2R2, Canada
| | - Steve C C Shih
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
- Department of Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
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8
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Omidfar K, Kashanian S. A mini review on recent progress of microfluidic systems for antibody development. J Diabetes Metab Disord 2024; 23:323-331. [PMID: 38932846 PMCID: PMC11196548 DOI: 10.1007/s40200-024-01386-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/06/2024] [Indexed: 06/28/2024]
Abstract
Objectives Antibody is specific reagent that be utilized in various field of biomedical research. Monoclonal antibodies are mostly produced using two common techniques namely hybridoma and antibody engineering, which suffer from some limitations such as boring screening procedures, long production time, low efficacy and a degree of automation. To address these limitations, various microfluidics techniques have been developed for the antibody isolation and screening. Methods This study specifically investigates nearly recent reports published in peer-reviewed journals indexed in various databases including Web of Science, Scopus, PubMed, Google Scholar, and Science Direct. Results In this study, we identified a total of seventy papers from a pool of 130 articles. These papers focus on the application of three major groups of microfluidic platforms, namely valves, microwells, and droplets, in the development of antibodies using hybridoma method and phage display technology. We provide a summary of these applications and also discuss the key findings in this field. Additionally, we illustrate our discussion with several examples to enhance understanding. Conclusions Microfluidics has the potential to serve as a valuable tool in streamlining complex laboratory procedures involved in antibody discovery. However, it is important to note that microfluidics is limited to laboratory settings. Further enhancements are needed to address existing challenges and to make microfluidics a reliable, accurate, and cost-effective tool for antibody discovery.
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Affiliation(s)
- Kobra Omidfar
- Biosensor Research Center, Endocrinology and Metabolism Molecular–Cellular Sciences Institute, Tehran University of Medical Sciences, P.O. Box 14395/1179, Tehran, IR Iran
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sohiela Kashanian
- Faculty of Chemistry, Razi University, Kermanshah, 6714414971 Iran
- Nanobiotechnology Department, Faculty of Innovative Science and Technology, Razi University, Kermanshah, 6714414971 Iran
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Leal-Alves C, Deng Z, Kermeci N, Shih SCC. Integrating microfluidics and synthetic biology: advancements and diverse applications across organisms. LAB ON A CHIP 2024; 24:2834-2860. [PMID: 38712893 DOI: 10.1039/d3lc01090b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Synthetic biology is the design and modification of biological systems for specific functions, integrating several disciplines like engineering, genetics, and computer science. The field of synthetic biology is to understand biological processes within host organisms through the manipulation and regulation of their genetic pathways and the addition of biocontrol circuits to enhance their production capabilities. This pursuit serves to address global challenges spanning diverse domains that are difficult to tackle through conventional routes of production. Despite its impact, achieving precise, dynamic, and high-throughput manipulation of biological processes is still challenging. Microfluidics offers a solution to those challenges, enabling controlled fluid handling at the microscale, offering lower reagent consumption, faster analysis of biochemical reactions, automation, and high throughput screening. In this review, we diverge from conventional focus on automating the synthetic biology design-build-test-learn cycle, and instead, focus on microfluidic platforms and their role in advancing synthetic biology through its integration with host organisms - bacterial cells, yeast, fungi, animal cells - and cell-free systems. The review illustrates how microfluidic devices have been instrumental in understanding biological systems by showcasing microfluidics as an essential tool to create synthetic genetic circuits, pathways, and organisms within controlled environments. In conclusion, we show how microfluidics expedite synthetic biology applications across diverse domains including but not limited to personalized medicine, bioenergy, and agriculture.
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Affiliation(s)
- Chiara Leal-Alves
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada.
- Department of Electrical and Computer Engineering, Concordia University, 1515 Ste-Catherine St. W, Montréal, QC, H3G1M8 Canada
| | - Zhiyang Deng
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada.
- Department of Electrical and Computer Engineering, Concordia University, 1515 Ste-Catherine St. W, Montréal, QC, H3G1M8 Canada
| | - Natalia Kermeci
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada.
- Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada
| | - Steve C C Shih
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada.
- Department of Electrical and Computer Engineering, Concordia University, 1515 Ste-Catherine St. W, Montréal, QC, H3G1M8 Canada
- Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada
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10
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Zhu L, Cui X, Jiang L, Fang F, Liu B. Application and prospect of microfluidic devices for rapid assay of cell activities in the tumor microenvironment. BIOMICROFLUIDICS 2024; 18:031506. [PMID: 38899164 PMCID: PMC11185871 DOI: 10.1063/5.0206058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024]
Abstract
The global impact of cancer on human health has raised significant concern. In this context, the tumor microenvironment (TME) plays a pivotal role in the tumorigenesis and malignant progression. In order to enhance the accuracy and efficacy of therapeutic outcomes, there is an imminent requirement for in vitro models that can accurately replicate the intricate characteristics and constituents of TME. Microfluidic devices exhibit notable advantages in investigating the progression and treatment of tumors and have the potential to become a novel methodology for evaluating immune cell activities in TME and assist clinicians in assessing the prognosis of patients. In addition, it shows great advantages compared to traditional cell experiments. Therefore, the review first outlines the applications and advantages of microfluidic chips in facilitating tumor cell culture, constructing TME and investigating immune cell activities. Second, the roles of microfluidic devices in the analysis of circulating tumor cells, tumor prognosis, and drug screening have also been mentioned. Moreover, a forward-looking perspective is discussed, anticipating the widespread clinical adoption of microfluidic devices in the future.
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Affiliation(s)
- Linjing Zhu
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Xueling Cui
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Lingling Jiang
- Department of Oral Comprehensive Therapy, Hospital of Stomatology, Jilin University, Changchun, Jilin 130021, China
| | - Fang Fang
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, Jilin 130021, China
| | - Boyang Liu
- Author to whom correspondence should be addressed:
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11
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Verbist W, Breukers J, Sharma S, Rutten I, Gerstmans H, Coelmont L, Dal Dosso F, Dallmeier K, Lammertyn J. SeParate: multiway fluorescence-activated droplet sorting based on integration of serial and parallel triaging concepts. LAB ON A CHIP 2024; 24:2107-2121. [PMID: 38450543 DOI: 10.1039/d3lc01075a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Fluorescence-activated droplet sorting (FADS) has emerged as a versatile high-throughput sorting tool that is, unlike most fluorescence-activated cell sorting (FACS) platforms, capable of sorting droplet-compartmentalized cells, cell secretions, entire enzymatic reactions and more. Recently, multiplex FADS platforms have been developed for the sorting of multi-fluorophore populations towards different outlets in addition to the standard, more commonly used, 2-way FADS platform. These multiplex FADS platforms consist of either multiple 2-way junctions one after the other (i.e. serial sorters) or of one junction sorting droplets in more than 2 outlets (i.e. parallel sorters). In this work, we present SeParate, a novel platform based on integrating s̲e̲rial and p̲a̲r̲allel sorting principles for accura̲t̲e̲ multiplex droplet sorting that is able to mitigate limitations of current multiplex sorters. We show the SeParate platform and its capability in highly accurate 4-way sorting of a multi-fluorophore population into four subpopulations with the potential to expand to more. More specifically, the SeParate platform was thoroughly validated using mixed populations of fluorescent beads and picoinjected droplets, yielding sorting accuracies up to 100% and 99.9%, respectively. Finally, transfected HEK-293T cells were sorted employing two different optical setups, resulting in an accuracy up to 99.5%. SeParate's high accuracy for a diverse set of samples, including highly variable biological specimens, together with its scalability beyond the demonstrated 4-way sorting, warrants a broad applicability for multi-fluorophore studies in life sciences, environmental sciences and others.
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Affiliation(s)
- Wannes Verbist
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Jolien Breukers
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Sapna Sharma
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, KU Leuven, 3000 Leuven, Belgium
| | - Iene Rutten
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Lotte Coelmont
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, KU Leuven, 3000 Leuven, Belgium
| | - Francesco Dal Dosso
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
| | - Kai Dallmeier
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Molecular Vaccinology and Vaccine Discovery, KU Leuven, 3000 Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems - Biosensors Group, KU Leuven, Willem de Croylaan 42, Box 2428, 3001 Leuven, Belgium.
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12
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Hua X, Han K, Mandracchia B, Radmand A, Liu W, Kim H, Yuan Z, Ehrlich SM, Li K, Zheng C, Son J, Silva Trenkle AD, Kwong GA, Zhu C, Dahlman JE, Jia S. Light-field flow cytometry for high-resolution, volumetric and multiparametric 3D single-cell analysis. Nat Commun 2024; 15:1975. [PMID: 38438356 PMCID: PMC10912605 DOI: 10.1038/s41467-024-46250-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024] Open
Abstract
Imaging flow cytometry (IFC) combines flow cytometry and fluorescence microscopy to enable high-throughput, multiparametric single-cell analysis with rich spatial details. However, current IFC techniques remain limited in their ability to reveal subcellular information with a high 3D resolution, throughput, sensitivity, and instrumental simplicity. In this study, we introduce a light-field flow cytometer (LFC), an IFC system capable of high-content, single-shot, and multi-color acquisition of up to 5,750 cells per second with a near-diffraction-limited resolution of 400-600 nm in all three dimensions. The LFC system integrates optical, microfluidic, and computational strategies to facilitate the volumetric visualization of various 3D subcellular characteristics through convenient access to commonly used epi-fluorescence platforms. We demonstrate the effectiveness of LFC in assaying, analyzing, and enumerating intricate subcellular morphology, function, and heterogeneity using various phantoms and biological specimens. The advancement offered by the LFC system presents a promising methodological pathway for broad cell biological and translational discoveries, with the potential for widespread adoption in biomedical research.
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Affiliation(s)
- Xuanwen Hua
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Keyi Han
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Biagio Mandracchia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Afsane Radmand
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Chemical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Hyejin Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Zhou Yuan
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Samuel M Ehrlich
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kaitao Li
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Corey Zheng
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jeonghwan Son
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Aaron D Silva Trenkle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cheng Zhu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - James E Dahlman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA.
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13
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Zhao Y, Sun Y, Xie X, Liang Y, Cavalcanti-Adam EA, Feng W. Compact Micropatterned Chip Empowers Undisturbed and Programmable Drug Addition in High-Throughput Cell Screening. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2306814. [PMID: 37793694 DOI: 10.1002/adma.202306814] [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: 07/11/2023] [Revised: 09/15/2023] [Indexed: 10/06/2023]
Abstract
Simultaneously adding multiple drugs and other chemical reagents to individual droplets at specific time points presents a significant challenge, particularly when dealing with tiny droplets in high-throughput screening applications. In this study, a micropatterned polymer chip is developed as a miniaturized platform for light-induced programmable drug addition in cell-based screening. This chip incorporates a porous superhydrophobic polymer film with atom transfer radical polymerization reactivity, facilitating the efficient grafting of azobenzene methacrylate, a photoconformationally changeable group, onto the hydrophilic regions of polymer matrix at targeted locations and with precise densities. By employing light irradiation, the cyclodextrin-azobenzene host-guest complexes formed on the polymer chip can switch from an "associated" to a "dissociated" state, granting precise photochemical control over the supramolecular coding system and its surface patterning ability. Significantly, the exceptional spatial and temporal control offered by these chemical transitions empowers to utilize digital light processing systems for simultaneous regulation and release of cyclodextrin-bearing drugs across numerous droplets containing suspended or adhered cells. This approach minimizes mechanical disruption while achieving precise control over the timing of addition, dosage, and integration varieties of released drugs in high-throughput screening, all programmable to meet specific requirements.
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Affiliation(s)
- Yuanyi Zhao
- College of Polymer Science and Engineering, Sichuan University, Chengdu, 610065, China
| | - Yingxue Sun
- College of Polymer Science and Engineering, Sichuan University, Chengdu, 610065, China
| | - Xinjian Xie
- College of Polymer Science and Engineering, Sichuan University, Chengdu, 610065, China
| | - Yujia Liang
- College of Polymer Science and Engineering, Sichuan University, Chengdu, 610065, China
| | | | - Wenqian Feng
- College of Polymer Science and Engineering, Sichuan University, Chengdu, 610065, China
- State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
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14
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Autour A, Merten CA. Screening for drivers of SARS-CoV-2 uptake. Nat Biomed Eng 2024; 8:205-206. [PMID: 38158441 DOI: 10.1038/s41551-023-01170-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Affiliation(s)
- Alexis Autour
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Christoph A Merten
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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15
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Nan L, Zhang H, Weitz DA, Shum HC. Development and future of droplet microfluidics. LAB ON A CHIP 2024; 24:1135-1153. [PMID: 38165829 DOI: 10.1039/d3lc00729d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Over the past two decades, advances in droplet-based microfluidics have facilitated new approaches to process and analyze samples with unprecedented levels of precision and throughput. A wide variety of applications has been inspired across multiple disciplines ranging from materials science to biology. Understanding the dynamics of droplets enables optimization of microfluidic operations and design of new techniques tailored to emerging demands. In this review, we discuss the underlying physics behind high-throughput generation and manipulation of droplets. We also summarize the applications in droplet-derived materials and droplet-based lab-on-a-chip biotechnology. In addition, we offer perspectives on future directions to realize wider use of droplet microfluidics in industrial production and biomedical analyses.
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Affiliation(s)
- Lang Nan
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| | - Huidan Zhang
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
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16
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Schlotheuber LJ, Lüchtefeld I, Eyer K. Antibodies, repertoires and microdevices in antibody discovery and characterization. LAB ON A CHIP 2024; 24:1207-1225. [PMID: 38165819 PMCID: PMC10898418 DOI: 10.1039/d3lc00887h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/01/2023] [Indexed: 01/04/2024]
Abstract
Therapeutic antibodies are paramount in treating a wide range of diseases, particularly in auto-immunity, inflammation and cancer, and novel antibody candidates recognizing a vast array of novel antigens are needed to expand the usefulness and applications of these powerful molecules. Microdevices play an essential role in this challenging endeavor at various stages since many general requirements of the overall process overlap nicely with the general advantages of microfluidics. Therefore, microfluidic devices are rapidly taking over various steps in the process of new candidate isolation, such as antibody characterization and discovery workflows. Such technologies can allow for vast improvements in time-lines and incorporate conservative antibody stability and characterization assays, but most prominently screenings and functional characterization within integrated workflows due to high throughput and standardized workflows. First, we aim to provide an overview of the challenges of developing new therapeutic candidates, their repertoires and requirements. Afterward, this review focuses on the discovery of antibodies using microfluidic systems, technological aspects of micro devices and small-scale antibody protein characterization and selection, as well as their integration and implementation into antibody discovery workflows. We close with future developments in microfluidic detection and antibody isolation principles and the field in general.
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Affiliation(s)
- Luca Johannes Schlotheuber
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
| | - Ines Lüchtefeld
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
- ETH Laboratory for Tumor and Stem Cell Dynamics, Institute of Molecular Health Sciences, D-BIOL, ETH Zürich, 8093 Zürich, Switzerland
| | - Klaus Eyer
- ETH Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, 8093 Zürich, Switzerland.
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17
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Wang Z, Huang AS, Tang L, Wang J, Wang G. Microfluidic-assisted single-cell RNA sequencing facilitates the development of neutralizing monoclonal antibodies against SARS-CoV-2. LAB ON A CHIP 2024; 24:642-657. [PMID: 38165771 DOI: 10.1039/d3lc00749a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
As a class of antibodies that specifically bind to a virus and block its entry, neutralizing monoclonal antibodies (neutralizing mAbs) have been recognized as a top choice for combating COVID-19 due to their high specificity and efficacy in treating serious infections. Although conventional approaches for neutralizing mAb development have been optimized for decades, there is an urgent need for workflows with higher efficiency due to time-sensitive concerns, including the high mutation rate of SARS-CoV-2. One promising approach is the identification of neutralizing mAb candidates via single-cell RNA sequencing (RNA-seq), as each B cell has a unique transcript sequence corresponding to its secreted antibody. The state-of-the-art high-throughput single-cell sequencing technologies, which have been greatly facilitated by advances in microfluidics, have greatly accelerated the process of neutralizing mAb development. Here, we provide an overview of the general procedures for high-throughput single-cell RNA-seq enabled by breakthroughs in droplet microfluidics, introduce revolutionary approaches that combine single-cell RNA-seq to facilitate the development of neutralizing mAbs against SARS-CoV-2, and outline future steps that need to be taken to further improve development strategies for effective treatments against infectious diseases.
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Affiliation(s)
- Ziwei Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Amelia Siqi Huang
- Dalton Academy, The Affiliated High School of Peking University, Beijing, 100190, China
| | - Lingfang Tang
- Dalton Academy, The Affiliated High School of Peking University, Beijing, 100190, China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guanbo Wang
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
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18
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Sesta L, Pagnani A, Fernandez-de-Cossio-Diaz J, Uguzzoni G. Inference of annealed protein fitness landscapes with AnnealDCA. PLoS Comput Biol 2024; 20:e1011812. [PMID: 38377054 PMCID: PMC10878520 DOI: 10.1371/journal.pcbi.1011812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 01/08/2024] [Indexed: 02/22/2024] Open
Abstract
The design of proteins with specific tasks is a major challenge in molecular biology with important diagnostic and therapeutic applications. High-throughput screening methods have been developed to systematically evaluate protein activity, but only a small fraction of possible protein variants can be tested using these techniques. Computational models that explore the sequence space in-silico to identify the fittest molecules for a given function are needed to overcome this limitation. In this article, we propose AnnealDCA, a machine-learning framework to learn the protein fitness landscape from sequencing data derived from a broad range of experiments that use selection and sequencing to quantify protein activity. We demonstrate the effectiveness of our method by applying it to antibody Rep-Seq data of immunized mice and screening experiments, assessing the quality of the fitness landscape reconstructions. Our method can be applied to several experimental cases where a population of protein variants undergoes various rounds of selection and sequencing, without relying on the computation of variants enrichment ratios, and thus can be used even in cases of disjoint sequence samples.
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Affiliation(s)
- Luca Sesta
- Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy
| | - Andrea Pagnani
- Department of Applied Science and Technology, Politecnico di Torino, Torino, Italy
- Italian Institute for Genomic Medicine, Torino, Italy
- INFN, Sezione di Torino, Torino, Italy
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19
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Xu Y, Wu KC, Jiang W, Hou Y, Cheow LF, Lee VHF, Chen CH. Single-Cell Secretion Analysis via Microfluidic Cell Membrane Immunosorbent Assay for Immune Profiling. Anal Chem 2024; 96:49-58. [PMID: 38109488 DOI: 10.1021/acs.analchem.3c02562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Single-cell multiplexed phenotypic analysis expands the biomarkers for diagnosis, heralding a new era of precision medicine. Cell secretions are the primary measures of immune function, but single-cell screening remains challenging. Here, a novel cell membrane-based assay was developed using cholesterol-linked antibodies (CLAbs), integrating immunosorbent assays and droplet microfluidics to develop a flexible high-throughput single-cell secretion assay for multiplexed phenotyping. CLAb-grafted single cells were encapsulated in water-in-oil droplets to capture their own secretions. Subsequently, the cells were extracted from droplets for fluorescence labeling and screening. Multiple secretions and surface proteins were simultaneously measured from single cells by flow cytometry. To validate the approach, THP-1 cells, THP-1-derived M1 macrophages, and dendritic cells were assayed, indicating the differentiation efficiency of THP-1 cells under different chemical stimulations. Moreover, peripheral blood mononuclear cells from healthy donors under various stimuli showed varied active immune cell populations (6.62-47.14%). The peripheral blood mononuclear cells (PBMCs) of nasopharyngeal carcinoma patients were analyzed to identify a higher percentage of actively cytokine-secreted single cells in the basal state (2.82 ± 1.48%), compared with that in the health donors (0.70 ± 0.29%).
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Affiliation(s)
- Ying Xu
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong SAR 999077, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen Virtual University Park, Shenzhen 518057, China
| | - Ka-Chun Wu
- Department of Clinical Oncology, Queen Mary Hospital, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
- Laboratory for Synthetic Chemistry and Chemical Biology, Hong Kong Science and Technology Park, Hong Kong SAR 999077, China
| | - Wenxin Jiang
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong SAR 999077, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen Virtual University Park, Shenzhen 518057, China
| | - Yi Hou
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong SAR 999077, China
| | - Lih Feng Cheow
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore
| | - Victor Ho-Fun Lee
- Department of Clinical Oncology, Queen Mary Hospital, The University of Hong Kong, Pokfulam Road, Hong Kong SAR 999077, China
| | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong SAR 999077, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen Virtual University Park, Shenzhen 518057, China
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20
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Lashkaripour A, McIntyre DP, Calhoun SGK, Krauth K, Densmore DM, Fordyce PM. Design automation of microfluidic single and double emulsion droplets with machine learning. Nat Commun 2024; 15:83. [PMID: 38167827 PMCID: PMC10761910 DOI: 10.1038/s41467-023-44068-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
Droplet microfluidics enables kHz screening of picoliter samples at a fraction of the cost of other high-throughput approaches. However, generating stable droplets with desired characteristics typically requires labor-intensive empirical optimization of device designs and flow conditions that limit adoption to specialist labs. Here, we compile a comprehensive droplet dataset and use it to train machine learning models capable of accurately predicting device geometries and flow conditions required to generate stable aqueous-in-oil and oil-in-aqueous single and double emulsions from 15 to 250 μm at rates up to 12000 Hz for different fluids commonly used in life sciences. Blind predictions by our models for as-yet-unseen fluids, geometries, and device materials yield accurate results, establishing their generalizability. Finally, we generate an easy-to-use design automation tool that yield droplets within 3 μm (<8%) of the desired diameter, facilitating tailored droplet-based platforms and accelerating their utility in life sciences.
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Affiliation(s)
- Ali Lashkaripour
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
| | - David P McIntyre
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | | | - Karl Krauth
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Douglas M Densmore
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- Department of Electrical & Computer Engineering, Boston University, Boston, MA, USA
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Chan-Zuckerberg Biohub, San Francisco, CA, USA.
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA, USA.
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21
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Evers A, Krah S, Demir D, Gaa R, Elter D, Schroeter C, Zielonka S, Rasche N, Dotterweich J, Knuehl C, Doerner A. Engineering hydrophobicity and manufacturability for optimized biparatopic antibody-drug conjugates targeting c-MET. MAbs 2024; 16:2302386. [PMID: 38214660 DOI: 10.1080/19420862.2024.2302386] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/03/2024] [Indexed: 01/13/2024] Open
Abstract
Optimal combinations of paratopes assembled into a biparatopic antibody have the capacity to mediate high-grade target cross-linking on cell membranes, leading to degradation of the target, as well as antibody and payload delivery in the case of an antibody-drug conjugate (ADC). In the work presented here, molecular docking suggested a suitable paratope combination targeting c-MET, but hydrophobic patches in essential binding regions of one moiety necessitated engineering. In addition to rational design of HCDR2 and HCDR3 mutations, site-specific spiking libraries were generated and screened in yeast and mammalian surface display approaches. Comparative analyses revealed similar positions amendable for hydrophobicity reduction, with a broad combinatorial diversity obtained from library outputs. Optimized variants showed high stability, strongly reduced hydrophobicity, retained affinities supporting the desired functionality and enhanced producibility. The resulting biparatopic anti-c-MET ADCs were comparably active on c-MET expressing tumor cell lines as REGN5093 exatecan DAR6 ADC. Structural molecular modeling of paratope combinations for preferential inter-target binding combined with protein engineering for manufacturability yielded deep insights into the capabilities of rational and library approaches. The methodologies of in silico hydrophobicity identification and sequence optimization could serve as a blueprint for rapid development of optimal biparatopic ADCs targeting further tumor-associated antigens in the future.
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Affiliation(s)
- Andreas Evers
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Simon Krah
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Deniz Demir
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Ramona Gaa
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Desislava Elter
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | | | - Stefan Zielonka
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Nicolas Rasche
- ADC and Targeted Therapeutics, Merck Healthcare KGaA, Darmstadt, Germany
| | | | - Christine Knuehl
- Research Unit Oncology, Merck Healthcare KGaA, Darmstadt, Germany
| | - Achim Doerner
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
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22
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Wu Z, Sun L, Chen H, Zhao Y. Bioinspired Surfaces Derived from Acoustic Waves for On-Demand Droplet Manipulations. RESEARCH (WASHINGTON, D.C.) 2023; 6:0263. [PMID: 39290236 PMCID: PMC11407685 DOI: 10.34133/research.0263] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/13/2023] [Indexed: 09/19/2024]
Abstract
The controllable manipulation and transfer of droplets are fundamental in a wide range of chemical reactions and even life processes. Herein, we present a novel, universal, and straightforward acoustic approach to fabricating biomimetic surfaces for on-demand droplet manipulations like many natural creatures. Based on the capillary waves induced by surface acoustic waves, various polymer films could be deformed into pre-designed structures, such as parallel grooves and grid-like patterns. These structured and functionalized surfaces exhibit impressive ability in droplet transportation and water collection, respectively. Besides these static surfaces, the tunability of acoustics could also endow polymer surfaces with dynamic controllability for droplet manipulations, including programming wettability, mitigating droplet evaporation, and accelerating chemical reactions. Our approach is capable of achieving universal surface manufacturing and droplet manipulation simultaneously, which simplifies the fabrication process and eliminates the need for additional chemical modifications. Thus, we believe that our acoustic-derived surfaces and technologies could provide a unique perspective for various applications, including microreactor integration, biochemical reaction control, tissue engineering, and so on.
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Affiliation(s)
- Zhuhao Wu
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Lingyu Sun
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Hanxu Chen
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yuanjin Zhao
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China
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23
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Gaa R, Kumari K, Mayer HM, Yanakieva D, Tsai SP, Joshi S, Guenther R, Doerner A. An integrated mammalian library approach for optimization and enhanced microfluidics-assisted antibody hit discovery. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2023; 51:74-82. [PMID: 36762883 DOI: 10.1080/21691401.2023.2173219] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Recent years have seen the development of a variety of mammalian library approaches for display and secretion mode. Advantages include library approaches for engineering, preservation of precious immune repertoires and their repeated interrogation, as well as screening in final therapeutic format and host. Mammalian display approaches for antibody optimization exploit these advantages, necessitating the generation of large libraries but in turn enabling early screening for both manufacturability and target specificity. For suitable libraries, high antibody integration rates and resulting monoclonality need to be balanced - we present a solution for sufficient transmutability and acceptable monoclonality by applying an optimized ratio of coding to non-coding lentivirus. The recent advent of microfluidic-assisted hit discovery represents a perfect match to mammalian libraries in secretion mode, as the lower throughput fits well with the facile generation of libraries comprising a few million functional clones. In the presented work, Chinese Hamster Ovary cells were engineered to both express the target of interest and secrete antibodies in relevant formats, and specific clones were strongly enriched by high throughput screening for autocrine cellular binding. The powerful combination of mammalian secretion libraries and microfluidics-assisted hit discovery could reduce attrition rates and increase the probability to identify the best possible therapeutic antibody hits faster.
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Affiliation(s)
- Ramona Gaa
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Kavita Kumari
- Discovery Biology, Syngene International, Phase-IV, Bangalore, India
| | - Hannah Melina Mayer
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Desislava Yanakieva
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Shang-Pu Tsai
- Protein Engineering and Antibody Technologies, EMD Serono, Billerica, MA, USA
| | - Saurabh Joshi
- Discovery Biology, Syngene International, Phase-IV, Bangalore, India
| | - Ralf Guenther
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany
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24
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Diao Z, Wang X, Zhang J, Ge A, Xu T, Kan L, Li Y, Ji Y, Jing X, Xu J, Ma B. Optical-based microbubble for on-demand droplet release from static droplet array (SDA) for dispensing one droplet into one tube. Biosens Bioelectron 2023; 240:115639. [PMID: 37660461 DOI: 10.1016/j.bios.2023.115639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023]
Abstract
Static droplet array (SDA) is a pivotal tool for high-capacity screening assays, yet extraction and collection the target droplets that contain unique analytes or cells from the SDA remains one major technical bottleneck that limits its broader application. Here we present an optical-based on-demand droplet release (OODR) system by incorporating a 1064 nm laser-responsive indium tin oxide (ITO) layer into a chamber array-based droplet microfluidic chip. By focusing the 1064 nm laser onto the ITO layer, microbubbles can be created via local heating to selectively push-out the droplets from the chamber. Then the released droplet is readily exported in a one-droplet-one-tube (ODOT) manner by the inherent capillary force into pipette tip. Releasing of the droplets containing fluorescein sodium demonstrated ∼100% successful rate (9 out of 6400 droplets were successfully released) and low residual (only ∼5% of the droplet volume remains in the chamber). White or fluorescence image-based releasing of single-cell-droplets directly after cell loading or multi-cells-droplets derived from on-chip single-cell cultivation for both E. coli and yeast cells further demonstrated the wide applicability of OODR. The present system is user-friendly and has the potential to be applied in various high-throughput screening assays, including single molecule/cell analysis, drug screening, and phenotype-based cell sorting.
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Affiliation(s)
- Zhidian Diao
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Xixian Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Jiaping Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Anle Ge
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Teng Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Lingyan Kan
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Yuandong Li
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Yuetong Ji
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Qingdao Single-Cell Biotech., Co., Ltd., Qingdao, China
| | - Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China.
| | - Bo Ma
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China.
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25
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Zhou Y, He M, Zhang H, Liu B, Sun C, Han Z, Duan X. Pinch-off droplet generator using microscale gigahertz acoustics. LAB ON A CHIP 2023; 23:4860-4867. [PMID: 37867322 DOI: 10.1039/d3lc00515a] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
The generation and dispensing of microdroplets is a vital process in various fields such as biomedicine, medical diagnosis and chemistry. However, most methods still require the structures of nozzles or microchannels to assist droplet generation, which leads to limitations on system flexibility and restrictions on the size range of the generated droplets. In this paper, we propose a nozzle-free acoustic-based method for generating droplets using a gigahertz (GHz) bulk acoustic wave (BAW). Unlike most of the acoustofluidic approaches, the proposed method produces the droplet by pinching-off the liquid column generated by the acoustic body force at the oil-water interface. Benefitting from the focused acoustic energy and small footprint of the device, four orders of magnitude (ranging from 2 μm to 1800 μm) of droplet size could be produced by controlling the working time and power of the device. We also demonstrated cell encapsulation in the droplet and a high cell viability was achieved. The proposed acoustic-based droplet generation method exhibits capacity for generating droplets with a wide size range, versatility toward different viscosities, as well as biocompatibility for handling viable samples, which shows potential in miniaturization and scalability.
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Affiliation(s)
- Yangchao Zhou
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Meihang He
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Haitao Zhang
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Bohua Liu
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Chongling Sun
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Ziyu Han
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
| | - Xuexin Duan
- State Key Laboratory of Precision Measuring Technology and Instruments, College of Precision Instruments and Opto-electronics Engineering, Tianjin University, Tianjin 300072, China
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26
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Schweizer L. Drug Intelligence Science (DIS®): Pioneering a high-resolution translational platform to enhance the probability of success for drug discovery and development. Drug Discov Today 2023; 28:103795. [PMID: 37805064 DOI: 10.1016/j.drudis.2023.103795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/26/2023] [Accepted: 10/02/2023] [Indexed: 10/09/2023]
Abstract
Translational research has a crucial role in bridging the gap between basic biology discoveries and their clinical applications. Deep scientific understanding and advanced technology platforms are both crucial for translational research. Here, I describe a novel integrated Drug Intelligence Science (DIS®) translational platform that combines single cell technology with artificial intelligence (AI) and machine learning (ML) to gain insights into high-resolution cell biology, thus enabling the discovery of disease-relevant targets, high-quality drug candidates, and predictive biomarkers. The innovative DIS® approach has the potential to provide unprecedented mechanistic understanding of human diseases and enable in-depth pharmacological profiling of drug candidates to increase the probability of success (POS) in drug discovery and development.
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Affiliation(s)
- Liang Schweizer
- HiFiBiO Therapeutics, 237 Putnam Avenue, Cambridge, MA 02139, USA.
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27
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Ormundo LF, Barreto CT, Tsuruta LR. Development of Therapeutic Monoclonal Antibodies for Emerging Arbovirus Infections. Viruses 2023; 15:2177. [PMID: 38005854 PMCID: PMC10675117 DOI: 10.3390/v15112177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Antibody-based passive immunotherapy has been used effectively in the treatment and prophylaxis of infectious diseases. Outbreaks of emerging viral infections from arthropod-borne viruses (arboviruses) represent a global public health problem due to their rapid spread, urging measures and the treatment of infected individuals to combat them. Preparedness in advances in developing antivirals and relevant epidemiological studies protect us from damage and losses. Immunotherapy based on monoclonal antibodies (mAbs) has been shown to be very specific in combating infectious diseases and various other illnesses. Recent advances in mAb discovery techniques have allowed the development and approval of a wide number of therapeutic mAbs. This review focuses on the technological approaches available to select neutralizing mAbs for emerging arbovirus infections and the next-generation strategies to obtain highly effective and potent mAbs. The characteristics of mAbs developed as prophylactic and therapeutic antiviral agents for dengue, Zika, chikungunya, West Nile and tick-borne encephalitis virus are presented, as well as the protective effect demonstrated in animal model studies.
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Affiliation(s)
- Leonardo F. Ormundo
- Biopharmaceuticals Laboratory, Instituto Butantan, São Paulo 05503-900, Brazil; (L.F.O.); (C.T.B.)
- The Interunits Graduate Program in Biotechnology, University of São Paulo, São Paulo 05503-900, Brazil
| | - Carolina T. Barreto
- Biopharmaceuticals Laboratory, Instituto Butantan, São Paulo 05503-900, Brazil; (L.F.O.); (C.T.B.)
- The Interunits Graduate Program in Biotechnology, University of São Paulo, São Paulo 05503-900, Brazil
| | - Lilian R. Tsuruta
- Biopharmaceuticals Laboratory, Instituto Butantan, São Paulo 05503-900, Brazil; (L.F.O.); (C.T.B.)
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28
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Hou Y, Yao H, Lin JM. Recent advancements in single-cell metabolic analysis for pharmacological research. J Pharm Anal 2023; 13:1102-1116. [PMID: 38024859 PMCID: PMC10658044 DOI: 10.1016/j.jpha.2023.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 12/01/2023] Open
Abstract
Cellular heterogeneity is crucial for understanding tissue biology and disease pathophysiology. Pharmacological research is being advanced by single-cell metabolic analysis, which offers a technique to identify variations in RNA, proteins, metabolites, and drug molecules in cells. In this review, the recent advancement of single-cell metabolic analysis techniques and their applications in drug metabolism and drug response are summarized. High-precision and controlled single-cell isolation and manipulation are provided by microfluidics-based methods, such as droplet microfluidics, microchamber, open microfluidic probe, and digital microfluidics. They are used in tandem with variety of detection techniques, including optical imaging, Raman spectroscopy, electrochemical detection, RNA sequencing, and mass spectrometry, to evaluate single-cell metabolic changes in response to drug administration. The advantages and disadvantages of different techniques are discussed along with the challenges and future directions for single-cell analysis. These techniques are employed in pharmaceutical analysis for studying drug response and resistance pathway, therapeutic targets discovery, and in vitro disease model evaluation.
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Affiliation(s)
- Ying Hou
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Hongren Yao
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Jin-Ming Lin
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
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29
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Dufossez R, Krafft MP, Ursuegui S, Mosser M, Mouftakhir S, Pernod K, Chaubet G, Ryckelynck M, Wagner A. Microfluidic Droplet Stabilization via SPAAC Promoted Antibody Conjugation at the Water/Oil Interface. ACS APPLIED MATERIALS & INTERFACES 2023; 15:45498-45505. [PMID: 37704020 DOI: 10.1021/acsami.3c10655] [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: 09/15/2023]
Abstract
Droplet-based microfluidics is leading the development of miniaturized, rapid, and sensitive version of enzyme-linked immunosorbent assays (ELISAs), a central method for protein detection. These assays involve the use of a functionalized surface able to selectively capture the desired analyte. Using the droplet's oil water interface as a capture surface requires designing custom-perfluorinated fluorosurfactants bearing azide-containing polar groups, which spontaneously react when forming the droplet with strain-alkyne-functionalized antibodies solubilized in the aqueous phase. In this article, we present our research on the influence of the structure of surfactant's hydrophilic heads on the efficiency of SPAAC functionalization and on the effect of this antibody grafting process on droplet stability. We have shown that while short linkers lead to high grafting efficiency, long linkers lead to high stability, and that an intermediate size is required to balance both parameters. In the described family of surfactants, the optimal structure proved to be a PEG4 linker connecting a polar di-azide head and a per-fluoropolyether tail (Krytox). We also found that grafting an increasing amount of antibody, thus increasing interface coverage, increases droplet stability. It thus appears that such a bi-partite system with a reactive fluoro-surfactant in the oil phase and reactive antibody counterpart in the aqueous phase gives access in situ to novel surfactant construct providing unexplored interface structures and droplet functionality.
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Affiliation(s)
- Robin Dufossez
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Marie-Pierre Krafft
- Institut Charles Sadron (CNRS), University of Strasbourg, 67034 Strasbourg, France
| | - Sylvain Ursuegui
- MicroOmix, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Michel Mosser
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Safae Mouftakhir
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
- CNRS, Architecture et Réactivité de l'ARN (UPR 9002), University of Strasbourg, 67000 Strasbourg, France
| | - Ketty Pernod
- MicroOmix, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Michael Ryckelynck
- CNRS, Architecture et Réactivité de l'ARN (UPR 9002), University of Strasbourg, 67000 Strasbourg, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
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30
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Esene JE, Nasman PR, Miner DS, Nordin GP, Woolley AT. High-performance microchip electrophoresis separations of preterm birth biomarkers using 3D printed microfluidic devices. J Chromatogr A 2023; 1706:464242. [PMID: 37595419 PMCID: PMC10473225 DOI: 10.1016/j.chroma.2023.464242] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/20/2023]
Abstract
We employed digital light processing-stereolithography 3D printing to create microfluidic devices with different designs for microchip electrophoresis (µCE). Short or long straight channel, and two- or four-turn serpentine channel microfluidic devices with separation channel lengths of 1.3, 3.1, 3.0, and 4.7 cm, respectively, all with a cross injector design, were fabricated. We measured current as a function of time and voltage to determine a separation time window and conditions for the onset of Joule heating in these designs. Separations in these devices were evaluated by performing µCE and measuring theoretical plate counts for electric field strengths near and above the onset of Joule heating, with fluorescently labeled glycine and phenylalanine as model analytes. We further demonstrated µCE of peptides and proteins related to preterm birth risk, showing increased peak capacity and resolution compared to previous results with 3D printed microdevices. These results mark an important step forward in the use of 3D printed microfluidic devices for rapid bioanalysis by µCE.
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Affiliation(s)
- Joule E Esene
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Parker R Nasman
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
| | - Dallin S Miner
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT, 84602, USA
| | - Gregory P Nordin
- Department of Electrical and Computer Engineering, Brigham Young University, Provo, UT, 84602, USA
| | - Adam T Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA.
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31
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Huang S, Wu J, Zheng L, Long Y, Chen J, Li J, Dai B, Lin F, Zhuang S, Zhang D. 3D free-assembly modular microfluidics inspired by movable type printing. MICROSYSTEMS & NANOENGINEERING 2023; 9:111. [PMID: 37705925 PMCID: PMC10495351 DOI: 10.1038/s41378-023-00585-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 09/15/2023]
Abstract
Reconfigurable modular microfluidics presents an opportunity for flexibly constructing prototypes of advanced microfluidic systems. Nevertheless, the strategy of directly integrating modules cannot easily fulfill the requirements of common applications, e.g., the incorporation of materials with biochemical compatibility and optical transparency and the execution of small batch production of disposable chips for laboratory trials and initial tests. Here, we propose a manufacturing scheme inspired by the movable type printing technique to realize 3D free-assembly modular microfluidics. Double-layer 3D microfluidic structures can be produced by replicating the assembled molds. A library of modularized molds is presented for flow control, droplet generation and manipulation and cell trapping and coculture. In addition, a variety of modularized attachments, including valves, light sources and microscopic cameras, have been developed with the capability to be mounted onto chips on demand. Microfluidic systems, including those for concentration gradient generation, droplet-based microfluidics, cell trapping and drug screening, are demonstrated. This scheme enables rapid prototyping of microfluidic systems and construction of on-chip research platforms, with the intent of achieving high efficiency of proof-of-concept tests and small batch manufacturing.
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Affiliation(s)
- Shaoqi Huang
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Jiandong Wu
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | - Lulu Zheng
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Yan Long
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Junyi Chen
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Jianlang Li
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Bo Dai
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Francis Lin
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, MB R3T 2N2 Canada
| | - Songlin Zhuang
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
| | - Dawei Zhang
- Engineering Research Center of Optical Instrument and System, the Ministry of Education, Shanghai Key Laboratory of Modern Optical System, University of Shanghai for Science and Technology, Shanghai, 200093 China
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32
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Liu Z, Chen S, Wu J. Advances in ultrahigh-throughput screening technologies for protein evolution. Trends Biotechnol 2023; 41:1168-1181. [PMID: 37088569 DOI: 10.1016/j.tibtech.2023.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/28/2023] [Accepted: 03/14/2023] [Indexed: 04/25/2023]
Abstract
Inspired by natural evolution, directed evolution randomly mutates the gene of interest through artificial evolution conditions with variants being screened for the required properties. Directed evolution is vital to the enhancement of protein properties and comprises the construction of libraries with considerable diversity as well as screening methods with sufficient efficiency as key steps. Owing to the various characteristics of proteins, specific methods are urgently needed for library screening, which is one of the main limiting factors in accelerating evolution. This review initially organizes the principles of ultrahigh-throughput screening from the perspective of protein properties. It then provides a comprehensive introduction to the latest progress and future trends in ultrahigh-throughput screening technologies for directed evolution.
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Affiliation(s)
- Zhanzhi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China; International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, Jiangsu Province, China.
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33
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Asrat S, Devlin JC, Vecchione A, Klotz B, Setliff I, Srivastava D, Limnander A, Rafique A, Adler C, Porter S, Murphy AJ, Atwal GS, Sleeman MA, Lim WK, Orengo JM. TRAPnSeq allows high-throughput profiling of antigen-specific antibody-secreting cells. CELL REPORTS METHODS 2023; 3:100522. [PMID: 37533642 PMCID: PMC10391570 DOI: 10.1016/j.crmeth.2023.100522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/06/2023] [Accepted: 06/15/2023] [Indexed: 08/04/2023]
Abstract
Following activation by cognate antigen, B cells undergo fine-tuning of their antigen receptors and may ultimately differentiate into antibody-secreting cells (ASCs). While antigen-specific B cells that express surface receptors (B cell receptors [BCRs]) can be readily cloned and sequenced following flow sorting, antigen-specific ASCs that lack surface BCRs cannot be easily profiled. Here, we report an approach, TRAPnSeq (antigen specificity mapping through immunoglobulin [Ig] secretion TRAP and Sequencing), that allows capture of secreted antibodies on the surface of ASCs, which in turn enables high-throughput screening of single ASCs against large antigen panels. This approach incorporates flow cytometry, standard microfluidic platforms, and DNA-barcoding technologies to characterize antigen-specific ASCs through single-cell V(D)J, RNA, and antigen barcode sequencing. We show the utility of TRAPnSeq by profiling antigen-specific IgG and IgE ASCs from both mice and humans and highlight its capacity to accelerate therapeutic antibody discovery from ASCs.
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Affiliation(s)
| | | | | | - Brian Klotz
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Ian Setliff
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | | | | | | | | | | | | | | | | | - Wei Keat Lim
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
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34
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Vitalis C, Wenzel T. Leveraging interactions in microfluidic droplets for enhanced biotechnology screens. Curr Opin Biotechnol 2023; 82:102966. [PMID: 37390513 DOI: 10.1016/j.copbio.2023.102966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 07/02/2023]
Abstract
Microfluidic droplet screens serve as an innovative platform for high-throughput biotechnology, enabling significant advancements in discovery, product optimization, and analysis. This review sheds light on the emerging trends of interaction assays in microfluidic droplets, underscoring the unique suitability of droplets for these applications. Encompassing a diverse range of biological entities such as antibodies, enzymes, DNA, RNA, various microbial and mammalian cell types, drugs, and other molecules, these assays demonstrate their versatility and scope. Recent methodological breakthroughs have escalated these screens to novel scales of bioanalysis and biotechnological product design. Moreover, we highlight pioneering advancements that extend droplet-based screens into new domains: cargo delivery within human bodies, application of synthetic gene circuits in natural environments, 3D printing, and the development of droplet structures responsive to environmental signals. The potential of this field is profound and only set to increase.
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Affiliation(s)
- Carolus Vitalis
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul 7820244, Santiago, Chile
| | - Tobias Wenzel
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul 7820244, Santiago, Chile.
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35
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Panwar J, Utharala R, Fennelly L, Frenzel D, Merten CA. iSort enables automated complex microfluidic droplet sorting in an effort to democratize technology. CELL REPORTS METHODS 2023; 3:100478. [PMID: 37323570 PMCID: PMC10261925 DOI: 10.1016/j.crmeth.2023.100478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/24/2023] [Accepted: 04/18/2023] [Indexed: 06/17/2023]
Abstract
Fluorescence-activated droplet sorting (FADS) is a widely used microfluidic technique for high-throughput screening. However, it requires highly trained specialists to determine optimal sorting parameters, and this results in a large combinatorial space that is challenging to optimize systematically. Additionally, it is currently challenging to track every single droplet within a screen, leading to compromised sorting and "hidden" false-positive events. To overcome these limitations, we have developed a setup in which the droplet frequency, spacing, and trajectory at the sorting junction are monitored in real time using impedance analysis. The resulting data are used to continuously optimize all parameters automatically and to counteract perturbations, resulting in higher throughput, higher reproducibility, increased robustness, and a beginner-friendly character. We believe this provides a missing piece for the spreading of phenotypic single-cell analysis methods, similar to what we have seen for single-cell genomics platforms.
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Affiliation(s)
- Jatin Panwar
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Ramesh Utharala
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Laura Fennelly
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Daniel Frenzel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Christoph A. Merten
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
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36
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Zhang L, Parvin R, Chen M, Hu D, Fan Q, Ye F. High-throughput microfluidic droplets in biomolecular analytical system: A review. Biosens Bioelectron 2023; 228:115213. [PMID: 36906989 DOI: 10.1016/j.bios.2023.115213] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Droplet microfluidic technology has revolutionized biomolecular analytical research, as it has the capability to reserve the genotype-to-phenotype linkage and assist for revealing the heterogeneity. Massive and uniform picolitre droplets feature dividing solution to the level that single cell and single molecule in each droplet can be visualized, barcoded, and analyzed. Then, the droplet assays can unfold intensive genomic data, offer high sensitivity, and screen and sort from a large number of combinations or phenotypes. Based on these unique advantages, this review focuses on up-to-date research concerning diverse screening applications utilizing droplet microfluidic technology. The emerging progress of droplet microfluidic technology is first introduced, including efficient and scaling-up in droplets encapsulation, and prevalent batch operations. Then the new implementations of droplet-based digital detection assays and single-cell muti-omics sequencing are briefly examined, along with related applications such as drug susceptibility testing, multiplexing for cancer subtype identification, interactions of virus-to-host, and multimodal and spatiotemporal analysis. Meanwhile, we specialize in droplet-based large-scale combinational screening regarding desired phenotypes, with an emphasis on sorting for immune cells, antibodies, enzymatic properties, and proteins produced by directed evolution methods. Finally, some challenges, deployment and future perspective of droplet microfluidics technology in practice are also discussed.
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Affiliation(s)
- Lexiang Zhang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Rokshana Parvin
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Mingshuo Chen
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Dingmeng Hu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China
| | - Qihui Fan
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Fangfu Ye
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou, Zhejiang, 325000, China; Zhejiang Engineering Research Center for Tissue Repair Materials, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325000, China; Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
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37
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Jiang J, Yang G, Ma F. Fluorescence coupling strategies in fluorescence-activated droplet sorting (FADS) for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Biotechnol Adv 2023; 66:108173. [PMID: 37169102 DOI: 10.1016/j.biotechadv.2023.108173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/17/2023] [Accepted: 05/06/2023] [Indexed: 05/13/2023]
Abstract
Fluorescence-activated droplet sorting (FADS) has emerged as a powerful tool for ultrahigh-throughput screening of enzymes, metabolites, and antibodies. Fluorescence coupling strategies (FCSs) are key to the development of new FADS methods through their coupling of analyte properties such as concentration, activities, and affinity with fluorescence signals. Over the last decade, a series of FCSs have been developed, greatly expanding applications of FADS. Here, we review recent advances in FCS for different analyte types, providing a critical comparison of the available FCSs and further classification into four categories according to their principles. We also summarize successful FADS applications employing FCSs in enzymes, metabolites, and antibodies. Further, we outline possible future developments in this area.
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Affiliation(s)
- Jingjie Jiang
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Guangyu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fuqiang Ma
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
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38
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Segaliny AI, Jayaraman J, Chen X, Chong J, Luxon R, Fung A, Fu Q, Jiang X, Rivera R, Ma X, Ren C, Zimak J, Hedde PN, Shang Y, Wu G, Zhao W. A high throughput bispecific antibody discovery pipeline. Commun Biol 2023; 6:380. [PMID: 37029216 PMCID: PMC10082157 DOI: 10.1038/s42003-023-04746-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/22/2023] [Indexed: 04/09/2023] Open
Abstract
Bispecific antibodies (BsAbs) represent an emerging class of immunotherapy, but inefficiency in the current discovery has limited their broad clinical availability. Here we report a high throughput, agnostic, single-cell-based functional screening pipeline, comprising molecular and cell engineering for efficient generation of BsAb library cells, followed by functional interrogation at the single-cell level to identify and sort positive clones and downstream sequence identification and functionality characterization. Using a CD19xCD3 bispecific T cell engager (BiTE) as a model, we demonstrate that our single-cell platform possesses a high throughput screening efficiency of up to one and a half million variant library cells per run and can isolate rare functional clones at a low abundance of 0.008%. Using a complex CD19xCD3 BiTE-expressing cell library with approximately 22,300 unique variants comprising combinatorially varied scFvs, connecting linkers and VL/VH orientations, we have identified 98 unique clones, including extremely rare ones (~ 0.001% abundance). We also discovered BiTEs that exhibit novel properties and insights to design variable preferences for functionality. We expect our single-cell platform to not only increase the discovery efficiency of new immunotherapeutics, but also enable identifying generalizable design principles based on an in-depth understanding of the inter-relationships between sequence, structure, and function.
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Affiliation(s)
| | - Jayapriya Jayaraman
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
| | - Xiaoming Chen
- Amberstone Biosciences, Inc., Irvine, CA, 92618, USA
| | | | - Ryan Luxon
- Amberstone Biosciences, Inc., Irvine, CA, 92618, USA
| | - Audrey Fung
- Amberstone Biosciences, Inc., Irvine, CA, 92618, USA
| | - Qiwei Fu
- Amberstone Biosciences, Inc., Irvine, CA, 92618, USA
| | - Xianzhi Jiang
- Amberstone Biosciences, Inc., Irvine, CA, 92618, USA
| | | | - Xiaoya Ma
- Amberstone Biosciences, Inc., Irvine, CA, 92618, USA
| | - Ci Ren
- Amberstone Biosciences, Inc., Irvine, CA, 92618, USA
| | - Jan Zimak
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Per Niklas Hedde
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA
| | - Yonglei Shang
- Amberstone Biosciences, Inc., Irvine, CA, 92618, USA
| | - George Wu
- Amberstone Biosciences, Inc., Irvine, CA, 92618, USA.
| | - Weian Zhao
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA.
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA.
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA.
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA.
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
- Institute for Immunology, University of California, Irvine, Irvine, CA, 92697, USA.
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39
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Sun G, Qu L, Azi F, Liu Y, Li J, Lv X, Du G, Chen J, Chen CH, Liu L. Recent progress in high-throughput droplet screening and sorting for bioanalysis. Biosens Bioelectron 2023; 225:115107. [PMID: 36731396 DOI: 10.1016/j.bios.2023.115107] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/09/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
Owing to its ability to isolate single cells and perform high-throughput sorting, droplet sorting has been widely applied in several research fields. Compared with flow cytometry, droplet allows the encapsulation of single cells for cell secretion or lysate analysis. With the rapid development of this technology in the past decade, various droplet sorting devices with high throughput and accuracy have been developed. A droplet sorter with the highest sorting throughput of 30,000 droplets per second was developed in 2015. Since then, increased attention has been paid to expanding the possibilities of droplet sorting technology and strengthening its advantages over flow cytometry. This review aimed to summarize the recent progress in droplet sorting technology from the perspectives of device design, detection signal, actuating force, and applications. Technical details for improving droplet sorting through various approaches are introduced and discussed. Finally, we discuss the current limitations of droplet sorting for single-cell studies along with the existing gap between the laboratory and industry and provide our insights for future development of droplet sorters.
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Affiliation(s)
- Guoyun Sun
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Lisha Qu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Fidelis Azi
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology GTIIT, Shantou, Guangdong, 515063, China
| | - Yanfeng Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Chia-Hung Chen
- Department of Biomedical Engineering, College of Engineering, City University of Hong Kong, Hong Kong, China.
| | - Long Liu
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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40
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Zhong J, Liang M, Tang Q, Ai Y. Selectable encapsulated cell quantity in droplets via label-free electrical screening and impedance-activated sorting. Mater Today Bio 2023; 19:100594. [PMID: 36910274 PMCID: PMC9999206 DOI: 10.1016/j.mtbio.2023.100594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Single-cell encapsulation in droplets has become a powerful tool in immunotherapy, medicine discovery, and single-cell analysis, thanks to its capability for cell confinement in picoliter volumes. However, the purity and throughput of single-cell droplets are limited by random encapsulation process, which resuts in a majority of empty and multi-cells droplets. Herein we introduce the first label-free selectable cell quantity encapsulation in droplets sorting system to overcome this problem. The system utilizes a simple and reliable electrical impedance based screening (98.9% of accuracy) integrated with biocompatible acoustic sorting to select single-cell droplets, achieving 90.3% of efficiency and up to 200 Hz of throughput, by removing multi-cells (∼60% of rejection) and empty droplets (∼90% of rejection). We demonstrate the use of the droplet sorting to improve the throughput of single-cell encapsulation by ∼9-fold compared to the conventional random encapsulation process.
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Affiliation(s)
- Jianwei Zhong
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Minhui Liang
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Qiang Tang
- Jiangsu Provincial Engineering Research Center for Biomedical Materials and Advanced Medical Devices, Faculty of Mechanical and Material Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Ye Ai
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
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41
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Dufossez R, Ursuegui S, Baudrey S, Pernod K, Mouftakhir S, Oulad-Abdelghani M, Mosser M, Chaubet G, Ryckelynck M, Wagner A. Droplet Surface Immunoassay by Relocation (D-SIRe) for High-Throughput Analysis of Cytosolic Proteins at the Single-Cell Level. Anal Chem 2023; 95:4470-4478. [PMID: 36821722 DOI: 10.1021/acs.analchem.2c05168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Enzyme-linked immunosorbent assay (ELISA) is a central analytic method in biological science for the detection of proteins. Introduction of droplet-based microfluidics allowed the development of miniaturized, less-consuming, and more sensitive ELISA assays by coencapsulating the biological sample and antibody-functionalized particles. We report herein an alternative in-droplet immunoassay format, which avoids the use of particles. It exploits the oil/aqueous-phase interface as a protein capture and detection surface. This is achieved using tailored perfluorinated surfactants bearing azide-functionalized PEG-based polar headgroups, which spontaneously react when meeting at the droplet formation site, with strained alkyne-functionalized antibodies solubilized in the water phase. The resulting antibody-functionalized inner surface can then be used to capture a target protein. This surface capture process leads to concomitant relocation at the surface of a labeled detection antibody and in turn to a drastic change in the shape of the fluorescence signal from a convex shape (not captured) to a characteristic concave shape (captured). This novel droplet surface immunoassay by fluorescence relocation (D-SIRe) proved to be fast and sensitive at 2.3 attomoles of analyte per droplet. It was further demonstrated to allow detection of cytosolic proteins at the single bacteria level.
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Affiliation(s)
- Robin Dufossez
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Sylvain Ursuegui
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Stephanie Baudrey
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67000 Strasbourg, France
| | - Ketty Pernod
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Safae Mouftakhir
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Mustapha Oulad-Abdelghani
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Michel Mosser
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, 67000 Strasbourg, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
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42
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Jacková B, Mottet G, Rudiuk S, Morel M, Baigl D. DNA-Encoded Immunoassay in Picoliter Drops: A Minimal Cell-Free Approach. Adv Biol (Weinh) 2023; 7:e2200266. [PMID: 36750732 DOI: 10.1002/adbi.202200266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/21/2022] [Indexed: 02/09/2023]
Abstract
Immunoassays have emerged as indispensable bioanalytical tools but necessitate long preliminary steps for the selection, production, and purification of the antibody(ies) to be used. Here is explored the paradigm shift of creating a rapid and purification-free assay in picoliter drops where the antibody is expressed from coding DNA and its binding to antigens concomitantly characterized in situ. Efficient synthesis in bulk of various functional variable domains of heavy-chain only antibodies (VHH) using reconstituted cell-free expression media, including an anti-green fluorescent protein VHH, is shown first. A microfluidic device is then used to generate monodisperse drops (30 pL) containing all the assay components, including a capture scaffold, onto which the accumulation of VHH:antigen produces a specific fluorescent signal. This allows to assess, in parallel or sequentially at high throughput (500 Hz), the VHH-antigen binding and its specificity in less than 3 h, directly from a VHH-coding DNA, for multiple VHH sequences, various antigens and down to DNA concentrations as low as 12 plasmids per drop. It is anticipated that the ultraminiaturized format, robustness, and programmability of this novel cell-free immunoassay concept will constitute valuable assets in fields as diverse as antibody discovery, point-of-care diagnostics, synthetic biology, and/or bioanalytical assays.
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Affiliation(s)
- Barbara Jacková
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, 75005, France
- Large Molecules Research Platform, Sanofi, Vitry-sur-Seine, 94400, France
| | - Guillaume Mottet
- Large Molecules Research Platform, Sanofi, Vitry-sur-Seine, 94400, France
| | - Sergii Rudiuk
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, 75005, France
| | - Mathieu Morel
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, 75005, France
| | - Damien Baigl
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, Paris, 75005, France
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43
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Cedillo-Alcantar DF, Rodriguez-Moncayo R, Maravillas-Montero JL, Garcia-Cordero JL. On-Chip Analysis of Protein Secretion from Single Cells Using Microbead Biosensors. ACS Sens 2023; 8:655-664. [PMID: 36710459 DOI: 10.1021/acssensors.2c02148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The profiling of the effector functions of single immune cells─including cytokine secretion─can lead to a deeper understanding of how the immune system operates and to potential diagnostics and therapeutical applications. Here, we report a microfluidic device that pairs single cells and antibody-functionalized microbeads in hydrodynamic traps to quantitate cytokine secretion. The device contains 1008 microchambers, each with a volume of ∼500 pL, divided into six different sections individually addressed to deliver an equal number of chemical stimuli. Integrating microvalves allowed us to isolate cell/bead pairs, preventing cross-contamination with factors secreted by adjacent cells. We implemented a fluorescence sandwich immunoassay on the biosensing microbeads with a limit of detection of 9 pg/mL and were able to detect interleukin-8 (IL-8) secreted by single blood-derived human monocytes in response to different concentrations of LPS. Finally, our platform allowed us to observe a significant decrease in the number of IL-8-secreting monocytes when paracrine signaling becomes disrupted. Overall, our platform could have a variety of applications for which the analysis of cellular function heterogeneity is necessary, such as cancer research, antibody discovery, or rare cell screening.
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Affiliation(s)
- Diana F Cedillo-Alcantar
- Laboratory of Microtechnologies for Biomedicine, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Monterrey 66628, Nuevo León Mexico
| | - Roberto Rodriguez-Moncayo
- Laboratory of Microtechnologies for Biomedicine, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Monterrey 66628, Nuevo León Mexico
| | - Jose L Maravillas-Montero
- Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico
| | - Jose L Garcia-Cordero
- Laboratory of Microtechnologies for Biomedicine, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Monterrey 66628, Nuevo León Mexico.,Roche Institute for Translational Bioengineering (ITB), Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel 4058, Switzerland
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44
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Zhou Y, Yu Z, Wu M, Lan Y, Jia C, Zhao J. Single-cell sorting using integrated pneumatic valve droplet microfluidic chip. Talanta 2023. [DOI: 10.1016/j.talanta.2022.124044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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45
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Design and construction of a microfluidics workstation for high-throughput multi-wavelength fluorescence and transmittance activated droplet analysis and sorting. Nat Protoc 2023; 18:1090-1136. [PMID: 36707723 DOI: 10.1038/s41596-022-00796-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/09/2022] [Indexed: 01/28/2023]
Abstract
Droplet microfluidics has revolutionized quantitative high-throughput bioassays and screening, especially in the field of single-cell analysis where applications include cell characterization, antibody discovery and directed evolution. However, droplet microfluidic platforms capable of phenotypic, fluorescence-based readouts and sorting are still mostly found in specialized labs, because their setup is complex. Complementary to conventional FACS, microfluidic droplet sorters allow the screening of cell libraries for secreted factors, or even for the effects of secreted or surface-displayed factors on a second cell type. Furthermore, they also enable PCR-activated droplet sorting for the isolation of genetic material harboring specific markers. In this protocol, we provide a detailed step-by-step guide for the construction of a high-throughput droplet analyzer and sorter, which can be accomplished in ~45 working hours by nonspecialists. The resulting instrument is equipped with three lasers to excite the fluorophores in droplets and photosensors that acquire fluorescence signals in the blue (425-465 nm), green (505-545 nm) and red (580-630 nm) spectrum. This instrument also allows transmittance-activated droplet sorting by analyzing the brightfield light intensity transmitting through the droplets. The setup is validated by sorting droplets containing fluorescent beads at 200 Hz with 99.4% accuracy. We show results from an experiment where droplets hosting single cells were sorted on the basis of increased matrix metalloprotease activity as an application of our workstation in single-cell molecular biology, e.g., to analyze molecular determinants of cancer metastasis.
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46
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Gaa R, Ji Q, Doerner A. Antibody-Secreting Cell Isolation from Different Species for Microfluidic Antibody Hit Discovery. Methods Mol Biol 2023; 2681:313-325. [PMID: 37405655 DOI: 10.1007/978-1-0716-3279-6_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
The recent advent of microfluidic-assisted antibody hit discovery as standard methodology accelerated pharmaceutical research. While work on compatible recombinant antibody library approaches is ongoing, the major source of antibody-secreting cells (ASCs) remains to be primary B cells of mostly rodent origin. As fainting viability and secretion rates can lead to false-negative screening results, careful preparation of these cells is an essential prerequisite for successful hit discovery. We here describe procedures to enrich plasma cells from relevant tissues of mice and rats and plasmablasts from human blood donations. Although freshly prepared ASCs yield the most robust results, suitable freezing and thawing protocols to preserve the viability and antibody secretory function can circumvent extensive process time and allow transferring of samples between laboratories. An optimized procedure is described to yield similar secretion rates after prolonged storage when compared to freshly prepared cells. Finally, the identification of ASC-containing samples can increase the probability of success of droplet-based microfluidics-two methods for pre- or in-droplet staining are described. In summary, the preparative methods described herein can facilitate robust and successful microfluidic antibody hit discovery.
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Affiliation(s)
- Ramona Gaa
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Qingyong Ji
- Protein Engineering and Antibody Technologies, EMD Serono, Billerica, MA, USA
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany.
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47
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Pal A, Kaswan K, Barman SR, Lin YZ, Chung JH, Sharma MK, Liu KL, Chen BH, Wu CC, Lee S, Choi D, Lin ZH. Microfluidic nanodevices for drug sensing and screening applications. Biosens Bioelectron 2023; 219:114783. [PMID: 36257116 PMCID: PMC9533638 DOI: 10.1016/j.bios.2022.114783] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 09/18/2022] [Accepted: 10/01/2022] [Indexed: 11/03/2022]
Abstract
The outbreak of pandemics (e.g., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 in 2019), influenza A viruses (H1N1 in 2009), etc.), and worldwide spike in the aging population have created unprecedented urgency for developing new drugs to improve disease treatment. As a result, extensive efforts have been made to design novel techniques for efficient drug monitoring and screening, which form the backbone of drug development. Compared to traditional techniques, microfluidics-based platforms have emerged as promising alternatives for high-throughput drug screening due to their inherent miniaturization characteristics, low sample consumption, integration, and compatibility with diverse analytical strategies. Moreover, the microfluidic-based models utilizing human cells to produce in-vitro biomimetics of the human body pave new ways to predict more accurate drug effects in humans. This review provides a comprehensive summary of different microfluidics-based drug sensing and screening strategies and briefly discusses their advantages. Most importantly, an in-depth outlook of the commonly used detection techniques integrated with microfluidic chips for highly sensitive drug screening is provided. Then, the influence of critical parameters such as sensing materials and microfluidic platform geometries on screening performance is summarized. This review also outlines the recent applications of microfluidic approaches for screening therapeutic and illicit drugs. Moreover, the current challenges and the future perspective of this research field is elaborately highlighted, which we believe will contribute immensely towards significant achievements in all aspects of drug development.
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Affiliation(s)
- Arnab Pal
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan; International Intercollegiate PhD Program, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Kuldeep Kaswan
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan; International Intercollegiate PhD Program, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Snigdha Roy Barman
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan; International Intercollegiate PhD Program, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Yu-Zih Lin
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Jun-Hsuan Chung
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Manish Kumar Sharma
- Department of Materials Science and Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Kuei-Lin Liu
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Bo-Huan Chen
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan; International Intercollegiate PhD Program, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, 333, Taiwan
| | - Chih-Cheng Wu
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan; Center of Quality Management, National Taiwan University Hospital, Hsinchu Branch, Hsinchu, 30059, Taiwan; College of Medicine, National Taiwan University, Taipei, 10051, Taiwan; Institute of Cellular and System Medicine, National Health Research Institute, Zhunan, 35053, Taiwan
| | - Sangmin Lee
- School of Mechanical Engineering, Chung-Ang University, Seoul, 06974, South Korea.
| | - Dongwhi Choi
- Department of Mechanical Engineering (Integrated Engineering Program), Kyung Hee University, Gyeonggi, 17104, South Korea.
| | - Zong-Hong Lin
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan; International Intercollegiate PhD Program, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan; Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, 30013, Taiwan; Department of Mechanical Engineering (Integrated Engineering Program), Kyung Hee University, Gyeonggi, 17104, South Korea.
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48
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Jiang Z, Shi H, Tang X, Qin J. Recent advances in droplet microfluidics for single-cell analysis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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49
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Gaa R, Mayer HM, Noack D, Doerner A. Efficient Microfluidic Downstream Processes for Rapid Antibody Hit Confirmation. Methods Mol Biol 2023; 2681:327-341. [PMID: 37405656 DOI: 10.1007/978-1-0716-3279-6_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
Microfluidics has been recently applied to better understand the spatial and temporal progression of the immune response in several species, for tool and biotherapeutic production cell line development and rapid antibody hit discovery. Several technologies have emerged that allow interrogation of large diversities of antibody-secreting cells in defined compartments such as picoliter droplets or nanopens. Mostly primary cells of immunized rodents but also recombinant mammalian libraries are screened for specific binding or directly for the desired function. While post-microfluidic downstream processes appear as standard steps, they represent considerable and interdependent challenges that can lead to high attrition rates even if original selections had been successful. In addition to next-generation sequencing recently described in depth elsewhere, this report aims at in detail explanations of exemplary droplet-based sorting followed by single-cell antibody gene PCR recovery and reproduction or single-cell sub-cultivation for crude supernatant confirmatory studies.
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Affiliation(s)
- Ramona Gaa
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Hannah Melina Mayer
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Daniela Noack
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck Healthcare KGaA, Darmstadt, Germany.
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50
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Gaa R, Mayer HM, Noack D, Kumari K, Guenther R, Tsai SP, Ji Q, Doerner A. Mammalian display to secretion switchable libraries for antibody preselection and high throughput functional screening. MAbs 2023; 15:2251190. [PMID: 37646089 PMCID: PMC10469430 DOI: 10.1080/19420862.2023.2251190] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/10/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023] Open
Abstract
Recently, there has been a co-evolution of mammalian libraries and diverse microfluidic approaches for therapeutic antibody hit discovery. Mammalian libraries enable the preservation of full immune repertoires, produce hit candidates in final format and facilitate broad combinatorial bispecific antibody screening, while several available microfluidic methodologies offer opportunities for rapid high-content screens. Here, we report proof-of-concept studies exploring the potential of combining microfluidic technologies with mammalian libraries for antibody discovery. First, antibody secretion, target co-expression and integration of appropriate reporter cell lines enabled the selection of in-trans acting agonistic bispecific antibodies. Second, a functional screen for internalization was established and comparison of autocrine versus co-encapsulation setups highlighted the advantages of an autocrine one cell approach. Third, synchronization of antibody-secreting cells prior to microfluidic screens reduced assay variability. Furthermore, a display to secretion switchable system was developed and applied for pre-enrichment of antibody clones with high manufacturability in conjunction with subsequent screening for functional properties. These case studies demonstrate the system's feasibility and may serve as basis for further development of integrated workflows combining manufacturability sorting and functional screens for the identification of optimal therapeutic antibody candidates.
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Affiliation(s)
- Ramona Gaa
- NBE Technologies, Merck KGaA, Darmstadt, Germany
| | | | | | - Kavita Kumari
- Discovery Biology, Syngene International, Bangalore, India
| | | | | | - Qingyong Ji
- NBE Technologies, EMD Serono, Billerica, MA, USA
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