1
|
Slavny P, Hegde M, Doerner A, Parthiban K, McCafferty J, Zielonka S, Hoet R. Advancements in mammalian display technology for therapeutic antibody development and beyond: current landscape, challenges, and future prospects. Front Immunol 2024; 15:1469329. [PMID: 39381002 PMCID: PMC11459229 DOI: 10.3389/fimmu.2024.1469329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 09/04/2024] [Indexed: 10/10/2024] Open
Abstract
The evolving development landscape of biotherapeutics and their growing complexity from simple antibodies into bi- and multi-specific molecules necessitates sophisticated discovery and engineering platforms. This review focuses on mammalian display technology as a potential solution to the pressing challenges in biotherapeutic development. We provide a comparative analysis with established methodologies, highlighting key aspects of mammalian display technology, including genetic engineering, construction of display libraries, and its pivotal role in hit selection and/or developability engineering. The review delves into the mechanisms underpinning developability-driven selection via mammalian display and their broader implications. Applications beyond antibody discovery are also explored, alongside advancements towards function-first screening technologies, precision genome engineering and AI/ML-enhanced libraries, situating them in the context of mammalian display. Overall, the review provides a comprehensive overview of the current mammalian display technology landscape, underscores the expansive potential of the technology for biotherapeutic development, addresses the critical challenges for the full realisation of this potential, and examines advances in related disciplines that might impact the future application of mammalian display technologies.
Collapse
Affiliation(s)
- Peter Slavny
- Discovery & Engineering Division, Iontas Ltd./FairJourney Biologics, Cambridge, United Kingdom
| | - Manjunath Hegde
- Technology Division, Iontas/FairJourney Biologics, Cambridge, United Kingdom
| | - Achim Doerner
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Kothai Parthiban
- Discovery & Engineering Division, Iontas Ltd./FairJourney Biologics, Cambridge, United Kingdom
| | - John McCafferty
- Maxion Therapeutics, Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Stefan Zielonka
- Antibody Discovery & Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Rene Hoet
- Technology Division, Iontas/FairJourney Biologics, Cambridge, United Kingdom
- Technology Division, FairJourney Biologics, Porto, Portugal
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Dortaj H, Amani AM, Tayebi L, Azarpira N, Ghasemi Toudeshkchouei M, Hassanpour-Dehnavi A, Karami N, Abbasi M, Najafian-Najafabadi A, Zarei Behjani Z, Vaez A. Droplet-based microfluidics: an efficient high-throughput portable system for cell encapsulation. J Microencapsul 2024; 41:479-501. [PMID: 39077800 DOI: 10.1080/02652048.2024.2382744] [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: 12/01/2023] [Accepted: 07/17/2024] [Indexed: 07/31/2024]
Abstract
One of the goals of tissue engineering and regenerative medicine is restoring primary living tissue function by manufacturing a 3D microenvironment. One of the main challenges is protecting implanted non-autologous cells or tissues from the host immune system. Cell encapsulation has emerged as a promising technique for this purpose. It involves entrapping cells in biocompatible and semi-permeable microcarriers made from natural or synthetic polymers that regulate the release of cellular secretions. In recent years, droplet-based microfluidic systems have emerged as powerful tools for cell encapsulation in tissue engineering and regenerative medicine. These systems offer precise control over droplet size, composition, and functionality, allowing for creating of microenvironments that closely mimic native tissue. Droplet-based microfluidic systems have extensive applications in biotechnology, medical diagnosis, and drug discovery. This review summarises the recent developments in droplet-based microfluidic systems and cell encapsulation techniques, as well as their applications, advantages, and challenges in biology and medicine. The integration of these technologies has the potential to revolutionise tissue engineering and regenerative medicine by providing a precise and controlled microenvironment for cell growth and differentiation. By overcoming the immune system's challenges and enabling the release of cellular secretions, these technologies hold great promise for the future of regenerative medicine.
Collapse
Affiliation(s)
- Hengameh Dortaj
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Mohammad Amani
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Lobat Tayebi
- Marquette University School of Dentistry, Milwaukee, WI, USA
| | - Negar Azarpira
- Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Ashraf Hassanpour-Dehnavi
- Tissue Engineering Lab, Department of Anatomical Sciences, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Neda Karami
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Milad Abbasi
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Atefeh Najafian-Najafabadi
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zeinab Zarei Behjani
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Vaez
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| |
Collapse
|
4
|
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.
Collapse
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
| | | | | |
Collapse
|
5
|
Chen HC, Ma Y, Cheng J, Chen YC. Advances in Single-Cell Techniques for Linking Phenotypes to Genotypes. CANCER HETEROGENEITY AND PLASTICITY 2024; 1:0004. [PMID: 39156821 PMCID: PMC11328949 DOI: 10.47248/chp2401010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Single-cell analysis has become an essential tool in modern biological research, providing unprecedented insights into cellular behavior and heterogeneity. By examining individual cells, this approach surpasses conventional population-based methods, revealing critical variations in cellular states, responses to environmental cues, and molecular signatures. In the context of cancer, with its diverse cell populations, single-cell analysis is critical for investigating tumor evolution, metastasis, and therapy resistance. Understanding the phenotype-genotype relationship at the single-cell level is crucial for deciphering the molecular mechanisms driving tumor development and progression. This review highlights innovative strategies for selective cell isolation based on desired phenotypes, including robotic aspiration, laser detachment, microraft arrays, optical traps, and droplet-based microfluidic systems. These advanced tools facilitate high-throughput single-cell phenotypic analysis and sorting, enabling the identification and characterization of specific cell subsets, thereby advancing therapeutic innovations in cancer and other diseases.
Collapse
Affiliation(s)
- Hsiao-Chun Chen
- UPMC Hillman Cancer Center, University of Pittsburgh, 5115 Centre Ave, Pittsburgh, PA 15232, USA
- Department of Computational and Systems Biology, University of Pittsburgh, 3420 Forbes Avenue, Pittsburgh, PA 15260, USA
| | - Yushu Ma
- UPMC Hillman Cancer Center, University of Pittsburgh, 5115 Centre Ave, Pittsburgh, PA 15232, USA
- Department of Computational and Systems Biology, University of Pittsburgh, 3420 Forbes Avenue, Pittsburgh, PA 15260, USA
| | - Jinxiong Cheng
- UPMC Hillman Cancer Center, University of Pittsburgh, 5115 Centre Ave, Pittsburgh, PA 15232, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, PA 15260, USA
| | - Yu-Chih Chen
- UPMC Hillman Cancer Center, University of Pittsburgh, 5115 Centre Ave, Pittsburgh, PA 15232, USA
- Department of Computational and Systems Biology, University of Pittsburgh, 3420 Forbes Avenue, Pittsburgh, PA 15260, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, 3700 O'Hara Street, Pittsburgh, PA 15260, USA
- CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh, 3420 Forbes Avenue, Pittsburgh, PA 15260, USA
| |
Collapse
|
6
|
Liu Y, Herr AE. DropBlot: single-cell western blotting of chemically fixed cancer cells. Nat Commun 2024; 15:5888. [PMID: 39003254 PMCID: PMC11246512 DOI: 10.1038/s41467-024-50046-0] [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: 09/04/2023] [Accepted: 06/27/2024] [Indexed: 07/15/2024] Open
Abstract
Archived patient-derived tissue specimens play a central role in understanding disease and developing therapies. To address specificity and sensitivity shortcomings of existing single-cell resolution proteoform analysis tools, we introduce a hybrid microfluidic platform (DropBlot) designed for proteoform analyses in chemically fixed single cells. DropBlot serially integrates droplet-based encapsulation and lysis of single fixed cells, with on-chip microwell-based antigen retrieval, with single-cell western blotting of target antigens. A water-in-oil droplet formulation withstands the harsh chemical (SDS, 6 M urea) and thermal conditions (98 °C, 1-2 hr) required for effective antigen retrieval, and supports analysis of retrieved protein targets by single-cell electrophoresis. We demonstrate protein-target retrieval from unfixed, paraformaldehyde-fixed (PFA), and methanol-fixed cells. Key protein targets (HER2, GAPDH, EpCAM, Vimentin) retrieved from PFA-fixed cells were resolved and immunoreactive. Relevant to biorepositories, DropBlot profiled targets retrieved from human-derived breast tumor specimens archived for six years, offering a workflow for single-cell protein-biomarker analysis of sparing biospecimens.
Collapse
Affiliation(s)
- Yang Liu
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA, 30602, USA.
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| |
Collapse
|
7
|
Larsen DN, Kaczmarek JZ, Palarasah Y, Graversen JH, Højrup P. Epitope mapping of SARS-CoV-2 RBDs by hydroxyl radical protein footprinting reveals the importance of including negative antibody controls. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141011. [PMID: 38499233 DOI: 10.1016/j.bbapap.2024.141011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/01/2024] [Accepted: 03/11/2024] [Indexed: 03/20/2024]
Abstract
Understanding protein-protein interactions is crucial for drug design and investigating biological processes. Various techniques, such as CryoEM, X-ray spectroscopy, linear epitope mapping, and mass spectrometry-based methods, can be employed to map binding regions on proteins. Commonly used mass spectrometry-based techniques are cross-linking and hydrogen‑deuterium exchange (HDX). Another approach, hydroxyl radical protein footprinting (HRPF), identifies binding residues on proteins but faces challenges due to high initial costs and complex setups. This study introduces a generally applicable method using Fenton chemistry for epitope mapping in a standard mass spectrometry laboratory. It emphasizes the importance of controls, particularly the inclusion of a negative antibody control, not widely utilized in HRPF epitope mapping. Quantification by TMT labelling is introduced to reduce false positives, enabling direct comparison between sample conditions and biological triplicates. Additionally, six technical replicates were incorporated to enhance the depth of analysis. Observations on the receptor-binding domain (RBD) of SARS-CoV-2 Spike Protein, Alpha and Delta variants, revealed both binding and opening regions. Significantly changed peptides upon mixing with a negative control antibody suggested structural alterations or nonspecific binding induced by the antibody alone. Integration of negative control antibody experiments and high overlap between biological triplicates led to the exclusion of 40% of significantly changed regions. The final identified binding region correlated with existing literature on neutralizing antibodies against RBD. The presented method offers a straightforward implementation for HRPF analysis in a generic mass spectrometry-based laboratory. Enhanced data reliability was achieved through increased technical and biological replicates alongside negative antibody controls.
Collapse
Affiliation(s)
- Daniel Nyberg Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark; Ovodan Biotech A/S, Havnegade 36, DK-5000 Odense, Denmark
| | | | - Yaseelan Palarasah
- Department of Inflammation, Institute of Molecular Medicine, Faculty of Health and Medical Sciences, University of Southern Denmark, Odense, Denmark
| | - Jonas Heilskov Graversen
- Department of Inflammation, Institute of Molecular Medicine, Faculty of Health and Medical Sciences, University of Southern Denmark, Odense, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark; Ovodan Biotech A/S, Havnegade 36, DK-5000 Odense, Denmark.
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Moraes da Silva Junior S, Bento Ribeiro LE, Fruett F, Stiens J, Swart JW, Moshkalev S. A Novel Microfluidics Droplet-Based Interdigitated Ring-Shaped Electrode Sensor for Lab-on-a-Chip Applications. MICROMACHINES 2024; 15:672. [PMID: 38930642 PMCID: PMC11205656 DOI: 10.3390/mi15060672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024]
Abstract
This paper presents a comprehensive study focusing on the detection and characterization of droplets with volumes in the nanoliter range. Leveraging the precise control of minute liquid volumes, we introduced a novel spectroscopic on-chip microsensor equipped with integrated microfluidic channels for droplet generation, characterization, and sensing simultaneously. The microsensor, designed with interdigitated ring-shaped electrodes (IRSE) and seamlessly integrated with microfluidic channels, offers enhanced capacitance and impedance signal amplitudes, reproducibility, and reliability in droplet analysis. We were able to make analyses of droplet length in the range of 1.0-6.0 mm, velocity of 0.66-2.51 mm/s, and volume of 1.07 nL-113.46 nL. Experimental results demonstrated that the microsensor's performance is great in terms of droplet size, velocity, and length, with a significant signal amplitude of capacitance and impedance and real-time detection capabilities, thereby highlighting its potential for facilitating microcapsule reactions and enabling on-site real-time detection for chemical and biosensor analyses on-chip. This droplet-based microfluidics platform has great potential to be directly employed to promote advances in biomedical research, pharmaceuticals, drug discovery, food engineering, flow chemistry, and cosmetics.
Collapse
Affiliation(s)
- Salomão Moraes da Silva Junior
- Electronics & Informatics, Vrije Universiteit of Brussel, 1050 Brussels, Belgium
- Center for Semiconductor Components and Nanotechnologies, State University of Campinas, Campinas 13083-852, Brazil;
- School of Electrical and Computer Engineering, State University of Campinas, Campinas 13083-852, Brazil (J.W.S.)
- BioSense Institute, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Luiz Eduardo Bento Ribeiro
- School of Electrical and Computer Engineering, State University of Campinas, Campinas 13083-852, Brazil (J.W.S.)
| | - Fabiano Fruett
- School of Electrical and Computer Engineering, State University of Campinas, Campinas 13083-852, Brazil (J.W.S.)
| | - Johan Stiens
- Electronics & Informatics, Vrije Universiteit of Brussel, 1050 Brussels, Belgium
| | - Jacobus Willibrordus Swart
- School of Electrical and Computer Engineering, State University of Campinas, Campinas 13083-852, Brazil (J.W.S.)
| | - Stanislav Moshkalev
- Center for Semiconductor Components and Nanotechnologies, State University of Campinas, Campinas 13083-852, Brazil;
| |
Collapse
|
11
|
Shingai M, Iida S, Kawai N, Kawahara M, Sekiya T, Ohno M, Nomura N, Handabile C, Kawakita T, Omori R, Yamagishi J, Sano K, Ainai A, Suzuki T, Ohnishi K, Ito K, Kida H. Extraction of the CDRH3 sequence of the mouse antibody repertoire selected upon influenza virus infection by subtraction of the background antibody repertoire. J Virol 2024; 98:e0199523. [PMID: 38323813 PMCID: PMC10949447 DOI: 10.1128/jvi.01995-23] [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: 12/19/2023] [Accepted: 01/14/2024] [Indexed: 02/08/2024] Open
Abstract
Historically, antibody reactivity to pathogens and vaccine antigens has been evaluated using serological measurements of antigen-specific antibodies. However, it is difficult to evaluate all antibodies that contribute to various functions in a single assay, such as the measurement of the neutralizing antibody titer. Bulk antibody repertoire analysis using next-generation sequencing is a comprehensive method for analyzing the overall antibody response; however, it is unreliable for estimating antigen-specific antibodies due to individual variation. To address this issue, we propose a method to subtract the background signal from the repertoire of data of interest. In this study, we analyzed changes in antibody diversity and inferred the heavy-chain complementarity-determining region 3 (CDRH3) sequences of antibody clones that were selected upon influenza virus infection in a mouse model using bulk repertoire analysis. A decrease in the diversity of the antibody repertoire was observed upon viral infection, along with an increase in neutralizing antibody titers. Using kernel density estimation of sequences in a high-dimensional sequence space with background signal subtraction, we identified several clusters of CDRH3 sequences induced upon influenza virus infection. Most of these repertoires were detected more frequently in infected mice than in uninfected control mice, suggesting that infection-specific antibody sequences can be extracted using this method. Such an accurate extraction of antigen- or infection-specific repertoire information will be a useful tool for vaccine evaluation in the future. IMPORTANCE As specific interactions between antigens and cell-surface antibodies trigger the proliferation of B-cell clones, the frequency of each antibody sequence in the samples reflects the size of each clonal population. Nevertheless, it is extremely difficult to extract antigen-specific antibody sequences from the comprehensive bulk antibody sequences obtained from blood samples due to repertoire bias influenced by exposure to dietary antigens and other infectious agents. This issue can be addressed by subtracting the background noise from the post-immunization or post-infection repertoire data. In the present study, we propose a method to quantify repertoire data from comprehensive repertoire data. This method allowed subtraction of the background repertoire, resulting in more accurate extraction of expanded antibody repertoires upon influenza virus infection. This accurate extraction of antigen- or infection-specific repertoire information is a useful tool for vaccine evaluation.
Collapse
Affiliation(s)
- Masashi Shingai
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Vaccine Immunology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Sayaka Iida
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naoko Kawai
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mamiko Kawahara
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Toshiki Sekiya
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Marumi Ohno
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Naoki Nomura
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Chimuka Handabile
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Tomomi Kawakita
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Vaccine Immunology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ryosuke Omori
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Junya Yamagishi
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kaori Sano
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Ainai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuo Ohnishi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kimihito Ito
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroshi Kida
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| |
Collapse
|
12
|
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.
Collapse
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.
| |
Collapse
|
13
|
Wulandari DA, Tsuru K, Minamihata K, Wakabayashi R, Goto M, Kamiya N. A Functional Hydrogel Bead-Based High-Throughput Screening System for Mammalian Cells with Enhanced Secretion of Therapeutic Antibodies. ACS Biomater Sci Eng 2024; 10:628-636. [PMID: 38048166 DOI: 10.1021/acsbiomaterials.3c01386] [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] [Indexed: 12/06/2023]
Abstract
Droplet-based high-throughput screening systems are an emerging technology that provides a quick test to screen millions of cells with distinctive characteristics. Biopharmaceuticals, specifically therapeutic proteins, are produced by culturing cells that secrete heterologous recombinant proteins with different populations and expression levels; therefore, a technology to discriminate cells that produce more target proteins is needed. Here, we present a droplet-based microfluidic strategy for encapsulating, screening, and selecting target cells with redox-responsive hydrogel beads (HBs). As a proof-of-concept study, we demonstrate the enrichment of hybridoma cells with enhanced capability of antibody secretion using horseradish peroxidase (HRP)-catalyzed hydrogelation of tetra-thiolate poly(ethylene glycol); hybridoma cells were encapsulated in disulfide-bonded HBs. Recombinant protein G or protein M with a C-terminal cysteine residue was installed in the HBs via disulfide bonding to capture antibodies secreted from the cells. HBs were fluorescently stained by adding the protein L-HRP conjugate using a tyramide signal amplification system. HBs were then separated by fluorescence-activated droplet sorting and degraded by reducing the disulfide bonds to recover the target cells. Finally, we succeeded in the selection of hybridoma cells with enhanced antibody secretion, indicating the potential of this system in the therapeutic protein production.
Collapse
Affiliation(s)
- Diah Anggraini Wulandari
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kyosuke Tsuru
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kosuke Minamihata
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Rie Wakabayashi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Division of Biotechnology, Centre for Future Chemistry, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka 819-0395, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Division of Biotechnology, Centre for Future Chemistry, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka 819-0395, Japan
| |
Collapse
|
14
|
Zhong R, Sullivan M, Upreti N, Chen R, De Ganzó A, Yang K, Yang S, Jin K, He Y, Li K, Xia J, Ma Z, Lee LP, Konry T, Huang TJ. Cellular immunity analysis by a modular acoustofluidic platform: CIAMAP. SCIENCE ADVANCES 2023; 9:eadj9964. [PMID: 38134285 PMCID: PMC10745697 DOI: 10.1126/sciadv.adj9964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
The study of molecular mechanisms at the single-cell level holds immense potential for enhancing immunotherapy and understanding neuroinflammation and neurodegenerative diseases by identifying previously concealed pathways within a diverse range of paired cells. However, existing single-cell pairing platforms have limitations in low pairing efficiency, complex manual operation procedures, and single-use functionality. Here, we report a multiparametric cellular immunity analysis by a modular acoustofluidic platform: CIAMAP. This platform enables users to efficiently sort and collect effector-target (i.e., NK92-K562) cell pairs and monitor the real-time dynamics of immunological response formation. Furthermore, we conducted transcriptional and protein expression analyses to evaluate the pathways that mediate effector cytotoxicity toward target cells, as well as the synergistic effect of doxorubicin on the cellular immune response. Our CIAMAP can provide promising building blocks for high-throughput quantitative single-cell level coculture to understand intercellular communication while also empowering immunotherapy by precision analysis of immunological synapses.
Collapse
Affiliation(s)
- Ruoyu Zhong
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Matthew Sullivan
- Department of Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA 02115, USA
| | - Neil Upreti
- Biomedical Engineering Department, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Roy Chen
- Biomedical Engineering Department, Pratt School of Engineering, Duke University, Durham, NC 27708, USA
| | - Agustin De Ganzó
- Department of Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA 02115, USA
| | - Kaichun Yang
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Shujie Yang
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ke Jin
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Ye He
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Ke Li
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Jianping Xia
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Zhiteng Ma
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| | - Luke P. Lee
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720, USA
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Tania Konry
- Department of Pharmaceutical Sciences, Bouvé College of Health Sciences, Northeastern University, Boston, MA 02115, USA
| | - Tony Jun Huang
- Thomas Lord Department of Mechanical Engineering & Materials Science, Duke University, Durham, NC 27708, USA
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Yang G, Gao C, Chen D, Wang J, Huo X, Chen J. Multiplex fluorescence detection of single-cell droplet microfluidics and its application in quantifying protein expression levels. BIOMICROFLUIDICS 2023; 17:064106. [PMID: 38162228 PMCID: PMC10754627 DOI: 10.1063/5.0179121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024]
Abstract
This study presented a platform of multiplex fluorescence detection of single-cell droplet microfluidics with demonstrative applications in quantifying protein expression levels. The platform of multiplex fluorescence detection mainly included optical paths adopted from conventional microscopy enabling the generation of three optical spots from three laser sources for multiple fluorescence excitation and capture of multiple fluorescence signals by four photomultiplier tubes. As to platform characterization, microscopic images of three optical spots were obtained where clear Gaussian distributions of intensities without skewness confirmed the functionality of the scanning lens, while the controllable distances among three optical spots validated the functionality of fiber collimators and the reflector lens. As to demonstration, this platform was used to quantify single-cell protein expression within droplets where four-type protein expression of α-tubulin, Ras, c-Myc, and β-tubulin of CAL 27 (Ncell = 1921) vs WSU-HN6 (Ncell = 1881) were quantitatively estimated, which were (2.85 ± 0.72) × 105 vs (4.83 ± 1.58) × 105, (3.69 ± 1.41) × 104 vs (5.07 ± 2.13) × 104, (5.90 ± 1.45) × 104 vs (9.57 ± 2.85) × 104, and (3.84 ± 1.28) × 105 vs (3.30 ± 1.10) × 105, respectively. Neural pattern recognition was utilized for the classification of cell types, achieving successful rates of 69.0% (α-tubulin), 75.4% (Ras), 89.1% (c-Myc), 65.8% (β-tubulin), and 99.1% in combination, validating the capability of this platform of multiplex fluorescence detection to quantify various types of single-cell proteins, which could provide comprehensive evaluations on cell status.
Collapse
Affiliation(s)
| | | | | | - Junbo Wang
- Authors to whom correspondence should be addressed:; ; and
| | - Xiaoye Huo
- Authors to whom correspondence should be addressed:; ; and
| | - Jian Chen
- Authors to whom correspondence should be addressed:; ; and
| |
Collapse
|
17
|
Keitany GJ, Rubin BER, Garrett ME, Musa A, Tracy J, Liang Y, Ebert P, Moore AJ, Guan J, Eggers E, Lescano N, Brown R, Carbo A, Al-Asadi H, Ching T, Day A, Harris R, Linkem C, Popov D, Wilkins C, Li L, Wang J, Liu C, Chen L, Dines JN, Atyeo C, Alter G, Baldo L, Sherwood A, Howie B, Klinger M, Yusko E, Robins HS, Benzeno S, Gilbert AE. Multimodal, broadly neutralizing antibodies against SARS-CoV-2 identified by high-throughput native pairing of BCRs from bulk B cells. Cell Chem Biol 2023; 30:1377-1389.e8. [PMID: 37586370 PMCID: PMC10659930 DOI: 10.1016/j.chembiol.2023.07.011] [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: 09/20/2022] [Revised: 04/25/2023] [Accepted: 07/23/2023] [Indexed: 08/18/2023]
Abstract
TruAB Discovery is an approach that integrates cellular immunology, high-throughput immunosequencing, bioinformatics, and computational biology in order to discover naturally occurring human antibodies for prophylactic or therapeutic use. We adapted our previously described pairSEQ technology to pair B cell receptor heavy and light chains of SARS-CoV-2 spike protein-binding antibodies derived from enriched antigen-specific memory B cells and bulk antibody-secreting cells. We identified approximately 60,000 productive, in-frame, paired antibody sequences, from which 2,093 antibodies were selected for functional evaluation based on abundance, isotype and patterns of somatic hypermutation. The exceptionally diverse antibodies included RBD-binders with broad neutralizing activity against SARS-CoV-2 variants, and S2-binders with broad specificity against betacoronaviruses and the ability to block membrane fusion. A subset of these RBD- and S2-binding antibodies demonstrated robust protection against challenge in hamster and mouse models. This high-throughput approach can accelerate discovery of diverse, multifunctional antibodies against any target of interest.
Collapse
Affiliation(s)
| | | | | | - Andrea Musa
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Jeff Tracy
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Yu Liang
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Peter Ebert
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | - Erica Eggers
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | - Ryan Brown
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Adria Carbo
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | - Austin Day
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | | | | | - Lianqu Li
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | - Jiao Wang
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | - Chuanxin Liu
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | - Li Chen
- GenScript ProBio Biotech, Nanjing, Jiangsu Province, China
| | | | - Caroline Atyeo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Lance Baldo
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | - Bryan Howie
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Mark Klinger
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | - Erik Yusko
- Adaptive Biotechnologies, Seattle, WA 98109, USA
| | | | | | | |
Collapse
|
18
|
Tello JA, Jiang L, Zohar Y, Restifo LL. Drosophila CASK regulates brain size and neuronal morphogenesis, providing a genetic model of postnatal microcephaly suitable for drug discovery. Neural Dev 2023; 18:6. [PMID: 37805506 PMCID: PMC10559581 DOI: 10.1186/s13064-023-00174-y] [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: 08/20/2023] [Accepted: 09/08/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND CASK-related neurodevelopmental disorders are untreatable. Affected children show variable severity, with microcephaly, intellectual disability (ID), and short stature as common features. X-linked human CASK shows dosage sensitivity with haploinsufficiency in females. CASK protein has multiple domains, binding partners, and proposed functions at synapses and in the nucleus. Human and Drosophila CASK show high amino-acid-sequence similarity in all functional domains. Flies homozygous for a hypomorphic CASK mutation (∆18) have motor and cognitive deficits. A Drosophila genetic model of CASK-related disorders could have great scientific and translational value. METHODS We assessed the effects of CASK loss of function on morphological phenotypes in Drosophila using established genetic, histological, and primary neuronal culture approaches. NeuronMetrics software was used to quantify neurite-arbor morphology. Standard nonparametric statistics methods were supplemented by linear mixed effects modeling in some cases. Microfluidic devices of varied dimensions were fabricated and numerous fluid-flow parameters were used to induce oscillatory stress fields on CNS tissue. Dissociation into viable neurons and neurite outgrowth in vitro were assessed. RESULTS We demonstrated that ∆18 homozygous flies have small brains, small heads, and short bodies. When neurons from developing CASK-mutant CNS were cultured in vitro, they grew small neurite arbors with a distinctive, quantifiable "bushy" morphology that was significantly rescued by transgenic CASK+. As in humans, the bushy phenotype showed dosage-sensitive severity. To overcome the limitations of manual tissue trituration for neuronal culture, we optimized the design and operation of a microfluidic system for standardized, automated dissociation of CNS tissue into individual viable neurons. Neurons from CASK-mutant CNS dissociated in the microfluidic system recapitulate the bushy morphology. Moreover, for any given genotype, device-dissociated neurons grew larger arbors than did manually dissociated neurons. This automated dissociation method is also effective for rodent CNS. CONCLUSIONS These biological and engineering advances set the stage for drug discovery using the Drosophila model of CASK-related disorders. The bushy phenotype provides a cell-based assay for compound screening. Nearly a dozen genes encoding CASK-binding proteins or transcriptional targets also have brain-development mutant phenotypes, including ID. Hence, drugs that improve CASK phenotypes might also benefit children with disorders due to mutant CASK partners.
Collapse
Affiliation(s)
- Judith A Tello
- Graduate Interdisciplinary Program in Neuroscience, University of Arizona, Tucson, AZ, 85721, USA
- Department of Neurology, University of Arizona Health Sciences, 1501 N. Campbell Ave, Tucson, AZ, 85724-5023, USA
- Present address: Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY, 10010, USA
| | - Linan Jiang
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, 85721, USA
| | - Yitshak Zohar
- Department of Aerospace and Mechanical Engineering, University of Arizona, Tucson, AZ, 85721, USA
- Department of Biomedical Engineering, University of Arizona, Tucson, AZ, 85721, USA
- BIO5 Interdisciplinary Research Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Linda L Restifo
- Graduate Interdisciplinary Program in Neuroscience, University of Arizona, Tucson, AZ, 85721, USA.
- Department of Neurology, University of Arizona Health Sciences, 1501 N. Campbell Ave, Tucson, AZ, 85724-5023, USA.
- BIO5 Interdisciplinary Research Institute, University of Arizona, Tucson, AZ, 85721, USA.
- Department of Cellular & Molecular Medicine, University of Arizona Health Sciences, Tucson, AZ, 85724, USA.
| |
Collapse
|
19
|
Liu Y, Herr AE. DropBlot: single-cell western blotting of chemically fixed cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.04.556277. [PMID: 37732260 PMCID: PMC10508777 DOI: 10.1101/2023.09.04.556277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
To further realize proteomics of archived tissues for translational research, we introduce a hybrid microfluidic platform for high-specificity, high-sensitivity protein detection from individual chemically fixed cells. To streamline processing-to-analysis workflows and minimize signal loss, DropBlot serially integrates sample preparation using droplet-based antigen retrieval from single fixed cells with unified analysis-on-a-chip comprising microwell-based antigen extraction followed by chip-based single-cell western blotting. A water-in-oil droplet formulation proves robust to the harsh chemical (SDS, 6M urea) and thermal conditions (98°C, 1-2 hr.) required for sufficient antigen retrieval, and the electromechanical conditions required for electrotransfer of retrieved antigen from microwell-encapsulated droplets to single-cell electrophoresis. Protein-target retrieval was demonstrated for unfixed, paraformaldehyde-(PFA), and methanol-fixed cells. We observed higher protein electrophoresis separation resolution from PFA-fixed cells with sufficient immunoreactivity confirmed for key targets (HER2, GAPDH, EpCAM, Vimentin) from both fixation chemistries. Multiple forms of EpCAM and Vimentin were detected, a hallmark strength of western-blot analysis. DropBlot of PFA-fixed human-derived breast tumor specimens (n = 5) showed antigen retrieval from cells archived frozen for 6 yrs. DropBlot could provide a precision integrated workflow for single-cell resolution protein-biomarker mining of precious biospecimen repositories.
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Monserrat Lopez D, Rottmann P, Puebla-Hellmann G, Drechsler U, Mayor M, Panke S, Fussenegger M, Lörtscher E. Direct electrification of silicon microfluidics for electric field applications. MICROSYSTEMS & NANOENGINEERING 2023; 9:81. [PMID: 37342556 PMCID: PMC10277806 DOI: 10.1038/s41378-023-00552-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/25/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023]
Abstract
Microfluidic systems are widely used in fundamental research and industrial applications due to their unique behavior, enhanced control, and manipulation opportunities of liquids in constrained geometries. In micrometer-sized channels, electric fields are efficient mechanisms for manipulating liquids, leading to deflection, injection, poration or electrochemical modification of cells and droplets. While PDMS-based microfluidic devices are used due to their inexpensive fabrication, they are limited in terms of electrode integration. Using silicon as the channel material, microfabrication techniques can be used to create nearby electrodes. Despite the advantages that silicon provides, its opacity has prevented its usage in most important microfluidic applications that need optical access. To overcome this barrier, silicon-on-insulator technology in microfluidics is introduced to create optical viewports and channel-interfacing electrodes. More specifically, the microfluidic channel walls are directly electrified via selective, nanoscale etching to introduce insulation segments inside the silicon device layer, thereby achieving the most homogeneous electric field distributions and lowest operation voltages feasible across microfluidic channels. These ideal electrostatic conditions enable a drastic energy reduction, as effectively shown via picoinjection and fluorescence-activated droplet sorting applications at voltages below 6 and 15 V, respectively, facilitating low-voltage electric field applications in next-generation microfluidics.
Collapse
Affiliation(s)
- Diego Monserrat Lopez
- IBM Research Europe - Zurich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Philipp Rottmann
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Gabriel Puebla-Hellmann
- IBM Research Europe - Zurich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
- University of Basel, Department of Chemistry, St. Johanns-Ring 19, CH-4056 Basel, Switzerland
| | - Ute Drechsler
- IBM Research Europe - Zurich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
| | - Marcel Mayor
- University of Basel, Department of Chemistry, St. Johanns-Ring 19, CH-4056 Basel, Switzerland
- Institute for Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), P. O. Box 3640, 76021 Karlsruhe, Germany
| | - Sven Panke
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Martin Fussenegger
- ETH Zürich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058 Basel, Switzerland
- University of Basel, Faculty of Life Science, Basel, Switzerland
| | - Emanuel Lörtscher
- IBM Research Europe - Zurich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
| |
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
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.
Collapse
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.
| |
Collapse
|
24
|
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.
Collapse
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.
| |
Collapse
|
25
|
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.
Collapse
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.
| |
Collapse
|
26
|
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.
Collapse
|
27
|
Zhuang S, Liu H, Inglis DW, Li M. Tuneable Cell-Laden Double-Emulsion Droplets for Enhanced Signal Detection. Anal Chem 2023; 95:2039-2046. [PMID: 36634052 DOI: 10.1021/acs.analchem.2c04697] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Water-in-oil-in-water (w/o/w) or double-emulsion (DE) droplets have been widely used for cellular assays at a single-cell level because of their stability and biocompatibility. The oil shell of w/o/w droplets plays the role of a semipermeable membrane that allows substances with low molecular weight (e.g., water) to travel through but restricts those with high molecular weight (e.g., fluorescent biomarkers). Therefore, the core of DEs can be manipulated using osmosis, resulting in the shrinking or swelling of the core. Water leaves the inner aqueous phase to the outer phase via the oil shell when the osmotic pressure of the outer phase is higher than that in the inner phase, causing the shrinkage of DEs and vice versa. These processes can be achieved by transferring the DEs to hypertonic or hypotonic solutions. Manipulation of the core size of DEs can be beneficial to cellular assays. First, due to the selectivity of the oil shell of DEs, the concentration of biomarkers in the core increases when the inner aqueous phase is shrunk, resulting in the enhancement of biosignals. We demonstrate this by encapsulating the Bgl3 enzyme-secreting yeast with a substrate that displays fluorescence after hydrolyzation. In a second application, a single GFP-tagged yeast cell was encapsulated in DEs. After swelling the core of DEs, we observe that the larger core of DEs promotes cell growth compared to those with the smaller cores, leading to more intracellular proteins (green-fluorescent protein) for screening. These osmotic manipulations provide new tools for droplet-based biochemistry.
Collapse
Affiliation(s)
- Siyuan Zhuang
- School of Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Hangrui Liu
- Department of Physics and Astronomy, Macquarie University, Sydney, New South Wales 2109, Australia
| | - David W Inglis
- School of Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Ming Li
- School of Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, New South Wales 2109, Australia
| |
Collapse
|
28
|
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]
|
29
|
Lapizco-Encinas BH, Zhang YV. Microfluidic systems in clinical diagnosis. Electrophoresis 2023; 44:217-245. [PMID: 35977346 DOI: 10.1002/elps.202200150] [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: 06/08/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 02/01/2023]
Abstract
The use of microfluidic devices is highly attractive in the field of biomedical and clinical assessments, as their portability and fast response time have become crucial in providing opportune therapeutic treatments to patients. The applications of microfluidics in clinical diagnosis and point-of-care devices are continuously growing. The present review article discusses three main fields where miniaturized devices are successfully employed in clinical applications. The quantification of ions, sugars, and small metabolites is examined considering the analysis of bodily fluids samples and the quantification of this type of analytes employing real-time wearable devices. The discussion covers the level of maturity that the devices have reached as well as cost-effectiveness. The analysis of proteins with clinical relevance is presented and organized by the function of the proteins. The last section covers devices that can perform single-cell metabolomic and proteomic assessments. Each section discusses several strategically selected recent reports on microfluidic devices successfully employed for clinical assessments, to provide the reader with a wide overview of the plethora of novel systems and microdevices developed in the last 5 years. In each section, the novel aspects and main contributions of each reviewed report are highlighted. Finally, the conclusions and future outlook section present a summary and speculate on the future direction of the field of miniaturized devices for clinical applications.
Collapse
Affiliation(s)
- Blanca H Lapizco-Encinas
- Microscale Bioseparations Laboratory and Biomedical Engineering Department, Rochester Institute of Technology, Rochester, New York, USA
| | - Yan Victoria Zhang
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| |
Collapse
|
30
|
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.
Collapse
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
| | | |
Collapse
|
31
|
Li B, Ma X, Cheng J, Tian T, Guo J, Wang Y, Pang L. Droplets microfluidics platform-A tool for single cell research. Front Bioeng Biotechnol 2023; 11:1121870. [PMID: 37152651 PMCID: PMC10154550 DOI: 10.3389/fbioe.2023.1121870] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
Cells are the most basic structural and functional units of living organisms. Studies of cell growth, differentiation, apoptosis, and cell-cell interactions can help scientists understand the mysteries of living systems. However, there is considerable heterogeneity among cells. Great differences between individuals can be found even within the same cell cluster. Cell heterogeneity can only be clearly expressed and distinguished at the level of single cells. The development of droplet microfluidics technology opens up a new chapter for single-cell analysis. Microfluidic chips can produce many nanoscale monodisperse droplets, which can be used as small isolated micro-laboratories for various high-throughput, precise single-cell analyses. Moreover, gel droplets with good biocompatibility can be used in single-cell cultures and coupled with biomolecules for various downstream analyses of cellular metabolites. The droplets are also maneuverable; through physical and chemical forces, droplets can be divided, fused, and sorted to realize single-cell screening and other related studies. This review describes the channel design, droplet generation, and control technology of droplet microfluidics and gives a detailed overview of the application of droplet microfluidics in single-cell culture, single-cell screening, single-cell detection, and other aspects. Moreover, we provide a recent review of the application of droplet microfluidics in tumor single-cell immunoassays, describe in detail the advantages of microfluidics in tumor research, and predict the development of droplet microfluidics at the single-cell level.
Collapse
Affiliation(s)
- Bixuan Li
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| | - Xi Ma
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| | - Jianghong Cheng
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| | - Tian Tian
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| | - Jiao Guo
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| | - Yang Wang
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
- *Correspondence: Yang Wang,
| | - Long Pang
- Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, Xi’an, China
- School of Basic Medicine, Xi’an Medical University, Xi’an, China
| |
Collapse
|
32
|
Diao Z, Kan L, Zhao Y, Yang H, Song J, Wang C, Liu Y, Zhang F, Xu T, Chen R, Ji Y, Wang X, Jing X, Xu J, Li Y, Ma B. Artificial intelligence-assisted automatic and index-based microbial single-cell sorting system for One-Cell-One-Tube. MLIFE 2022; 1:448-459. [PMID: 38818483 PMCID: PMC10989846 DOI: 10.1002/mlf2.12047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 06/01/2024]
Abstract
Identification, sorting, and sequencing of individual cells directly from in situ samples have great potential for in-depth analysis of the structure and function of microbiomes. In this work, based on an artificial intelligence (AI)-assisted object detection model for cell phenotype screening and a cross-interface contact method for single-cell exporting, we developed an automatic and index-based system called EasySort AUTO, where individual microbial cells are sorted and then packaged in a microdroplet and automatically exported in a precisely indexed, "One-Cell-One-Tube" manner. The target cell is automatically identified based on an AI-assisted object detection model and then mobilized via an optical tweezer for sorting. Then, a cross-interface contact microfluidic printing method that we developed enables the automated transfer of cells from the chip to the tube, which leads to coupling with subsequent single-cell culture or sequencing. The efficiency of the system for single-cell printing is >93%. The throughput of the system for single-cell printing is ~120 cells/h. Moreover, >80% of single cells of both yeast and Escherichia coli are culturable, suggesting the superior preservation of cell viability during sorting. Finally, AI-assisted object detection supports automated sorting of target cells with high accuracy from mixed yeast samples, which was validated by downstream single-cell proliferation assays. The automation, index maintenance, and vitality preservation of EasySort AUTO suggest its excellent application potential for single-cell sorting.
Collapse
Affiliation(s)
- Zhidian Diao
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Single‐Cell Center, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Lingyan Kan
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Single‐Cell Center, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Yilong Zhao
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Single‐Cell Center, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Huaibo Yang
- Qingdao Single‐Cell Biotechnology Co. Ltd.QingdaoChina
| | - Jingyun Song
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Single‐Cell Center, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Chen Wang
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Single‐Cell Center, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Yang Liu
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Single‐Cell Center, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Fengli Zhang
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Single‐Cell Center, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Teng Xu
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Single‐Cell Center, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Rongze Chen
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Single‐Cell Center, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Yuetong Ji
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Single‐Cell Center, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- Qingdao Single‐Cell Biotechnology Co. Ltd.QingdaoChina
| | - Xixian Wang
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Single‐Cell Center, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Xiaoyan Jing
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Single‐Cell Center, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Jian Xu
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Single‐Cell Center, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Yuandong Li
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Single‐Cell Center, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| | - Bo Ma
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Single‐Cell Center, Qingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoChina
- University of Chinese Academy of SciencesBeijingChina
- Shandong Energy InstituteQingdaoChina
- Qingdao New Energy Shandong LaboratoryQingdaoChina
| |
Collapse
|
33
|
Utharala R, Grab A, Vafaizadeh V, Peschke N, Ballinger M, Turei D, Tuechler N, Ma W, Ivanova O, Ortiz AG, Saez-Rodriguez J, Merten CA. A microfluidic Braille valve platform for on-demand production, combinatorial screening and sorting of chemically distinct droplets. Nat Protoc 2022; 17:2920-2965. [PMID: 36261631 DOI: 10.1038/s41596-022-00740-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 06/16/2022] [Indexed: 11/09/2022]
Abstract
Droplet microfluidics is a powerful tool for a variety of biological applications including single-cell genetics, antibody discovery and directed evolution. All these applications make use of genetic libraries, illustrating the difficulty of generating chemically distinct droplets for screening applications. This protocol describes our Braille Display valving platform for on-demand generation of droplets with different chemical contents (16 different reagents and combinations thereof), as well as sorting droplets with different chemical properties, on the basis of fluorescence signals. The Braille Display platform is compact, versatile and cost efficient (only ~US$1,000 on top of a standard droplet microfluidics setup). The procedure includes manufacturing of microfluidic chips, assembly of custom hardware, co-encapsulation of cells and drugs into droplets, fluorescence detection of readout signals and data analysis using shared, freely available LabVIEW and Python packages. As a first application, we demonstrate the complete workflow for screening cancer cell drug sensitivities toward 74 conditions. Furthermore, we describe here an assay enabling the normalization of the observed drug sensitivity to the number of cancer cells per droplet, which additionally increases the robustness of the system. As a second application, we also demonstrate the sorting of droplets according to enzymatic activity. The drug screening application can be completed within 2 d; droplet sorting takes ~1 d; and all preparatory steps for manufacturing molds, chips and setting up the Braille controller can be accomplished within 1 week.
Collapse
Affiliation(s)
- Ramesh Utharala
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Anna Grab
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Clinical Cooperation Unit Molecular Hematology/Oncology, DKFZ Heidelberg and Translational Myeloma Research Group, Department of Internal Medicine V, University Hospital, Heidelberg, Germany
| | - Vida Vafaizadeh
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Nicolas Peschke
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martine Ballinger
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Denes Turei
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | - Nadine Tuechler
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Wenwei Ma
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Olga Ivanova
- Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
| | | | - Julio Saez-Rodriguez
- Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Heidelberg University, Heidelberg, Germany
- Faculty of Medicine, Joint Research Centre for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, Aachen, Germany
| | - Christoph A Merten
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| |
Collapse
|
34
|
Samlali K, Alves CL, Jezernik M, Shih SCC. Droplet digital microfluidic system for screening filamentous fungi based on enzymatic activity. MICROSYSTEMS & NANOENGINEERING 2022; 8:123. [PMID: 36438986 PMCID: PMC9681769 DOI: 10.1038/s41378-022-00456-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/24/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Fungal cell-wall-degrading enzymes have great utility in the agricultural and food industries. These cell-wall-degrading enzymes are known to have functions that can help defend against pathogenic organisms. The existing methods used to discover these enzymes are not well adapted to fungi culture and morphology, which prevents the proper evaluation of these enzymes. We report the first droplet-based microfluidic method capable of long-term incubation and low-voltage conditions to sort filamentous fungi inside nanoliter-sized droplets. The new method was characterized and validated in solid-phase media based on colloidal chitin such that the incubation of single spores in droplets was possible over multiple days (2-4 days) and could be sorted without droplet breakage. With long-term culture, we examined the activity of cell-wall-degrading enzymes produced by fungi during solid-state droplet fermentation using three highly sensitive fluorescein-based substrates. We also used the low-voltage droplet sorter to select clones with highly active cell-wall-degrading enzymes, such as chitinases, β-glucanases, and β-N-acetylgalactosaminidases, from a filamentous fungi droplet library that had been incubated for >4 days. The new system is portable, affordable for any laboratory, and user-friendly compared to classical droplet-based microfluidic systems. We propose that this system will be useful for the growing number of scientists interested in fungal microbiology who are seeking high-throughput methods to incubate and sort a large library of fungal cells.
Collapse
Affiliation(s)
- Kenza Samlali
- Department of Electrical and Computer Engineering, Concordia University, Montréal, QC Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC Canada
| | - Chiara Leal Alves
- Department of Electrical and Computer Engineering, Concordia University, Montréal, QC Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC Canada
| | - Mara Jezernik
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON Canada
| | - Steve C. C. Shih
- Department of Electrical and Computer Engineering, Concordia University, Montréal, QC Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC Canada
- Department of Biology, Concordia University, Montréal, QC Canada
| |
Collapse
|
35
|
Kolmar L, Autour A, Ma X, Vergier B, Eduati F, Merten CA. Technological and computational advances driving high-throughput oncology. Trends Cell Biol 2022; 32:947-961. [PMID: 35577671 DOI: 10.1016/j.tcb.2022.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/11/2022] [Accepted: 04/20/2022] [Indexed: 01/21/2023]
Abstract
Engineering and computational advances have opened many new avenues in cancer research, particularly when being exploited in interdisciplinary approaches. For example, the combination of microfluidics, novel sequencing technologies, and computational analyses has been crucial to enable single-cell assays, giving a detailed picture of tumor heterogeneity for the very first time. In a similar way, these 'tech' disciplines have been elementary for generating large data sets in multidimensional cancer 'omics' approaches, cell-cell interaction screens, 3D tumor models, and tissue level analyses. In this review we summarize the most important technology and computational developments that have been or will be instrumental for transitioning classical cancer research to a large data-driven, high-throughput, high-content discipline across all biological scales.
Collapse
Affiliation(s)
- Leonie Kolmar
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Alexis Autour
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Xiaoli Ma
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Blandine Vergier
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Federica Eduati
- Department of Biomedical Engineering, Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands; Institute for Complex Molecular Systems, Eindhoven University of Technology, 5612 AZ Eindhoven, The Netherlands.
| | - Christoph A Merten
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| |
Collapse
|
36
|
Iyer V, Yang Z, Ko J, Weissleder R, Issadore D. Advancing microfluidic diagnostic chips into clinical use: a review of current challenges and opportunities. LAB ON A CHIP 2022; 22:3110-3121. [PMID: 35674283 PMCID: PMC9798730 DOI: 10.1039/d2lc00024e] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Microfluidic diagnostic (μDX) technologies miniaturize sensors and actuators to the length-scales that are relevant to biology: the micrometer scale to interact with cells and the nanometer scale to interrogate biology's molecular machinery. This miniaturization allows measurements of biomarkers of disease (cells, nanoscale vesicles, molecules) in clinical samples that are not detectable using conventional technologies. There has been steady progress in the field over the last three decades, and a recent burst of activity catalyzed by the COVID-19 pandemic. In this time, an impressive and ever-growing set of technologies have been successfully validated in their ability to measure biomarkers in clinical samples, such as blood and urine, with sensitivity and specificity not possible using conventional tests. Despite our field's many accomplishments to date, very few of these technologies have been successfully commercialized and brought to clinical use where they can fulfill their promise to improve medical care. In this paper, we identify three major technological trends in our field that we believe will allow the next generation of μDx to have a major impact on the practice of medicine, and which present major opportunities for those entering the field from outside disciplines: 1. the combination of next generation, highly multiplexed μDx technologies with machine learning to allow complex patterns of multiple biomarkers to be decoded to inform clinical decision points, for which conventional biomarkers do not necessarily exist. 2. The use of micro/nano devices to overcome the limits of binding affinity in complex backgrounds in both the detection of sparse soluble proteins and nucleic acids in blood and rare circulating extracellular vesicles. 3. A suite of recent technologies that obviate the manual pre-processing and post-processing of samples before they are measured on a μDX chip. Additionally, we discuss economic and regulatory challenges that have stymied μDx translation to the clinic, and highlight strategies for successfully navigating this challenging space.
Collapse
Affiliation(s)
- Vasant Iyer
- Electrical and Systems Engineering Department, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - Zijian Yang
- Mechanical Engineering Department, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jina Ko
- Bioengineering Department, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital/Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts, USA
| | - David Issadore
- Electrical and Systems Engineering Department, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
- Bioengineering Department, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
37
|
Sun J, Lo HTJ, Fan L, Yiu TL, Shakoor A, Li G, Lee WYW, Sun D. High-efficiency quantitative control of mitochondrial transfer based on droplet microfluidics and its application on muscle regeneration. SCIENCE ADVANCES 2022; 8:eabp9245. [PMID: 35977014 PMCID: PMC9385153 DOI: 10.1126/sciadv.abp9245] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/01/2022] [Indexed: 05/31/2023]
Abstract
Mitochondrial transfer is a spontaneous process to restore damaged cells in various pathological conditions. The transfer of mitochondria to cell therapy products before their administration can enhance therapeutic outcomes. However, the low efficiency of previously reported methods limits their clinical application. Here, we developed a droplet microfluidics-based mitochondrial transfer technique that can achieve high-efficiency and high-throughput quantitative mitochondrial transfer to single cells. Because mitochondria are essential for muscles, myoblast cells and a muscle injury model were used as a proof-of-concept model to evaluate the proposed technique. In vitro and in vivo experiments demonstrated that C2C12 cells with 31 transferred mitochondria had significant improvements in cellular functions compared to those with 0, 8, and 14 transferred mitochondria and also had better therapeutic effects on muscle regeneration. The proposed technique can considerably promote the clinical application of mitochondrial transfer, with optimized cell function improvements, for the cell therapy of mitochondria-related diseases.
Collapse
Affiliation(s)
- Jiayu Sun
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Hiu Tung Jessica Lo
- Department of Orthopaedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Stem Cells and Regenerative Medicine Laboratory, Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Lei Fan
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Tsz Lam Yiu
- Department of Orthopaedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Stem Cells and Regenerative Medicine Laboratory, Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Adnan Shakoor
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Gang Li
- Department of Orthopaedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Stem Cells and Regenerative Medicine Laboratory, Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Wayne Y. W. Lee
- Department of Orthopaedics and Traumatology, Faculty of Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Stem Cells and Regenerative Medicine Laboratory, Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
- SH Ho Scoliosis Research Laboratory, Joint Scoliosis Research Centre of the Chinese University of Hong Kong and Nanjing University, Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Dong Sun
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Centre for Robotics and Automation, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| |
Collapse
|
38
|
Zheng G, Gu F, Cui Y, Lu L, Hu X, Wang L, Wang Y. A microfluidic droplet array demonstrating high-throughput screening in individual lipid-producing microalgae. Anal Chim Acta 2022; 1227:340322. [DOI: 10.1016/j.aca.2022.340322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 08/17/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022]
|
39
|
Miwa H, Dimatteo R, de Rutte J, Ghosh R, Di Carlo D. Single-cell sorting based on secreted products for functionally defined cell therapies. MICROSYSTEMS & NANOENGINEERING 2022; 8:84. [PMID: 35874174 PMCID: PMC9303846 DOI: 10.1038/s41378-022-00422-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/18/2022] [Accepted: 06/13/2022] [Indexed: 05/13/2023]
Abstract
Cell therapies have emerged as a promising new class of "living" therapeutics over the last decade and have been particularly successful for treating hematological malignancies. Increasingly, cellular therapeutics are being developed with the aim of treating almost any disease, from solid tumors and autoimmune disorders to fibrosis, neurodegenerative disorders and even aging itself. However, their therapeutic potential has remained limited due to the fundamental differences in how molecular and cellular therapies function. While the structure of a molecular therapeutic is directly linked to biological function, cells with the same genetic blueprint can have vastly different functional properties (e.g., secretion, proliferation, cell killing, migration). Although there exists a vast array of analytical and preparative separation approaches for molecules, the functional differences among cells are exacerbated by a lack of functional potency-based sorting approaches. In this context, we describe the need for next-generation single-cell profiling microtechnologies that allow the direct evaluation and sorting of single cells based on functional properties, with a focus on secreted molecules, which are critical for the in vivo efficacy of current cell therapies. We first define three critical processes for single-cell secretion-based profiling technology: (1) partitioning individual cells into uniform compartments; (2) accumulating secretions and labeling via reporter molecules; and (3) measuring the signal associated with the reporter and, if sorting, triggering a sorting event based on these reporter signals. We summarize recent academic and commercial technologies for functional single-cell analysis in addition to sorting and industrial applications of these technologies. These approaches fall into three categories: microchamber, microfluidic droplet, and lab-on-a-particle technologies. Finally, we outline a number of unmet needs in terms of the discovery, design and manufacturing of cellular therapeutics and how the next generation of single-cell functional screening technologies could allow the realization of robust cellular therapeutics for all patients.
Collapse
Affiliation(s)
- Hiromi Miwa
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
| | - Robert Dimatteo
- Department of Chemical and Biomolecular Engineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
| | - Joseph de Rutte
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
- Partillion Bioscience, Los Angeles, CA 90095 USA
| | - Rajesh Ghosh
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
- Department of Mechanical and Aerospace Engineering, University of California - Los Angeles, Los Angeles, CA 90095 USA
- California NanoSystems Institute (CNSI), University of California - Los Angeles, Los Angeles, CA 90095 USA
| |
Collapse
|
40
|
Szittner Z, Péter B, Kurunczi S, Székács I, Horváth R. Functional blood cell analysis by label-free biosensors and single-cell technologies. Adv Colloid Interface Sci 2022; 308:102727. [DOI: 10.1016/j.cis.2022.102727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/25/2022] [Accepted: 06/27/2022] [Indexed: 11/01/2022]
|
41
|
Lin WN, Tay MZ, Wong JXE, Lee CY, Fong SW, Wang CI, Ng LFP, Renia L, Chen CH, Cheow LF. Rapid microfluidic platform for screening and enrichment of cells secreting virus neutralizing antibodies. LAB ON A CHIP 2022; 22:2578-2589. [PMID: 35694804 DOI: 10.1039/d2lc00018k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
As part of the body's immune response, antibodies (Abs) have the ability to neutralize pathogenic viruses to prevent infection. To screen for neutralizing Abs (nAbs) from the immune repertoire, multiple screening techniques have been developed. However, conventional methods have a trade-off between screening throughput and the ability to screen for nAbs via their functional efficacy. Although droplet microfluidic platforms have the ability to bridge this disparity, the majority of such reported platforms still rely on Ab-binding assays as a proxy for function, which results in irrelevant hits. Herein, we report the multi-module Droplet-based Platform for Effective Antibody RetrievaL (DROP-PEARL) platform, which can achieve high-throughput enrichment of Ab-secreting cells (ASCs) based on the neutralizing activity of secreted nAbs against the a target virus. In this study, in-droplet Chikungunya virus (CHIKV) infection of host cells and neutralization was demonstrated via sequential delivery of viruses and host cells via picoinjection. In addition, we demonstrate the ability of the sorting system to accurately discriminate and isolate uninfected droplets from a mixed population of droplets at a rate of 150 000 cells per hour. As a proof of concept, a single-cell neutralization assay was performed on two populations of cells (nAb-producing and non-Ab producing cells), and up to 2.75-fold enrichment of ASCs was demonstrated. Finally, we demonstrated that DROP-PEARL is able to achieve similar enrichment for low frequency (∼2%) functional nAb-producing cells in a background of excess cells secreting irrelevant antibodies, highlighting its potential prospect as a first round enrichment platform for functional ASCs. We envision that the DROP-PEARL platform could potentially be used to accelerate the discovery of nAbs against other pathogenic viral targets, and we believe it will be a useful in the ongoing fight against biological threats.
Collapse
Affiliation(s)
- Weikang Nicholas Lin
- Department of Biomedical Engineering, National University of Singapore, Singapore.
| | - Matthew Zirui Tay
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Joel Xu En Wong
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Siew-Wai Fong
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
| | | | - Lisa Fong Poh Ng
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National Institute of Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Laurent Renia
- A*STAR Infectious Diseases Labs, Agency for Science, Technology and Research (A*STAR), Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Chia-Hung Chen
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering, National University of Singapore, Singapore.
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong
- Institute for Health Innovation & Technology (iHealthtech), Singapore
| |
Collapse
|
42
|
Li Y, Li P, Ke Y, Yu X, Yu W, Wen K, Shen J, Wang Z. A rare monoclonal antibody discovery based on indirect competitive screening of a single hapten-specific rabbit antibody secreting cell. Analyst 2022; 147:2942-2952. [PMID: 35674177 DOI: 10.1039/d2an00678b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A rare antibody that is able to tolerate physio-chemical factors is preferred and highly demanded in diagnosis and therapy. Rabbit monoclonal antibodies (RmAbs) are distinguished owing to their high affinity and stability. However, the efficiency and availability of traditional methods for RmAb discovery are limited, particularly for small molecules. Here, we present an indirect competitive screening method in nanowells, named CSMN, for single rabbit antibody-secreting cells (ASCs) selection with 20.6 h and propose an efficient platform for RmAb production against small molecules within 5.8 days for the first time. Chloramphenicol (CAP) as an antibacterial agent poses a great threat to public health. We applied CSMN to select CAP-specific ASCs and produced one high-affinity RmAb, surprisingly showed extremely halophilic properties with an IC50 of 0.08 ng mL-1 in the saturated salt solution, which has not yet been seen for other antibodies. The molecular dynamic simulation showed that the negatively charged surface improved the stability of the RmAb structure with additional disulfide bonds compared with mouse antibodies. Moreover, the reduced solvent accessible surface area of the binding pocket increased the interactions of RmAb with CAP in a saturated salt solution. Furthermore, RmAb was used to develop an immunoassay for the detection of CAP in real biological samples with simple pretreatment, shorter assay time, and higher sensitivity. The results demonstrated that the practical and efficient CSMN is suitable for rare RmAb discovery against small molecules.
Collapse
Affiliation(s)
- Yuan Li
- College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China.
| | - Peipei Li
- College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China.
| | - Yuebin Ke
- Key Laboratory of Molecular Epidemiology of Shenzhen, Shenzhen Center for Disease Control and Prevention, 518000 Shenzhen, China
| | - Xuezhi Yu
- College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China.
| | - Wenbo Yu
- College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China.
| | - Kai Wen
- College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China.
| | - Jianzhong Shen
- College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China.
| | - Zhanhui Wang
- College of Veterinary Medicine, China Agricultural University, Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, Beijing Laboratory for Food Quality and Safety, 100193 Beijing, People's Republic of China.
| |
Collapse
|
43
|
Abstract
Microfluidics has enabled a new era of cellular and molecular assays due to the small length scales, parallelization, and the modularity of various analysis and actuation functions. Droplet microfluidics, in particular, has been instrumental in providing new tools for biology with its ability to quickly and reproducibly generate drops that act as individual reactors. A notable beneficiary of this technology has been single-cell RNA sequencing, which has revealed new heterogeneities and interactions for the fundamental unit of life. However, viruses far surpass the diversity of cellular life, affect the dynamics of all ecosystems, and are a chronic source of global health crises. Despite their impact on the world, high-throughput and high-resolution viral profiling has been difficult, with conventional methods being limited to population-level averaging, large sample volumes, and few cultivable hosts. Consequently, most viruses have not been identified and studied. Droplet microfluidics holds the potential to address many of these limitations and offers new levels of sensitivity and throughput for virology. This Feature highlights recent efforts that have applied droplet microfluidics to the detection and study of viruses, including for diagnostics, virus-host interactions, and cell-independent virus assays. In combination with traditional virology methods, droplet microfluidics should prove a potent tool toward achieving a better understanding of the most abundant biological species on Earth.
Collapse
Affiliation(s)
- Wenyang Jing
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hee-Sun Han
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| |
Collapse
|
44
|
De Stefano P, Bianchi E, Dubini G. The impact of microfluidics in high-throughput drug-screening applications. BIOMICROFLUIDICS 2022; 16:031501. [PMID: 35646223 PMCID: PMC9142169 DOI: 10.1063/5.0087294] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 05/02/2022] [Indexed: 05/05/2023]
Abstract
Drug discovery is an expensive and lengthy process. Among the different phases, drug discovery and preclinical trials play an important role as only 5-10 of all drugs that begin preclinical tests proceed to clinical trials. Indeed, current high-throughput screening technologies are very expensive, as they are unable to dispense small liquid volumes in an accurate and quick way. Moreover, despite being simple and fast, drug screening assays are usually performed under static conditions, thus failing to recapitulate tissue-specific architecture and biomechanical cues present in vivo even in the case of 3D models. On the contrary, microfluidics might offer a more rapid and cost-effective alternative. Although considered incompatible with high-throughput systems for years, technological advancements have demonstrated how this gap is rapidly reducing. In this Review, we want to further outline the role of microfluidics in high-throughput drug screening applications by looking at the multiple strategies for cell seeding, compartmentalization, continuous flow, stimuli administration (e.g., drug gradients or shear stresses), and single-cell analyses.
Collapse
Affiliation(s)
- Paola De Stefano
- Laboratory of Biological Structure Mechanics, Department of Chemistry, Materials and Chemical Engineering “G. Natta,” Politecnico di Milano, Italy
| | - Elena Bianchi
- Laboratory of Biological Structure Mechanics, Department of Chemistry, Materials and Chemical Engineering “G. Natta,” Politecnico di Milano, Italy
| | - Gabriele Dubini
- Laboratory of Biological Structure Mechanics, Department of Chemistry, Materials and Chemical Engineering “G. Natta,” Politecnico di Milano, Italy
| |
Collapse
|
45
|
Sun H, Hu N, Wang J. Application of Microfluidic Technology in Antibody Screening. Biotechnol J 2022; 17:e2100623. [PMID: 35481726 DOI: 10.1002/biot.202100623] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/13/2022] [Accepted: 04/23/2022] [Indexed: 11/07/2022]
Abstract
Specific antibodies are widely used in the biomedical field. Current screening methods for specific antibodies mainly involve hybridoma technology and antibody engineering techniques. However, these technologies suffer from tedious screening processes, long preparation periods, high costs, low efficiency, and a degree of automation, which have become a bottleneck for the screening of specific antibodies. To overcome these difficulties, microfluidics has been developed as a promising technology for high-throughput screening and high purity of antibody. In this review, we provide an overview of the recent advances in microfluidic applications for specific antibody screening. In particular, hybridoma technology and four antibody engineering techniques (including phage display, single B cell antibody screening, antibody expression, and cell-free protein synthesis) based on microfluidics have been introduced, challenges, and the future outlook of these technologies are also discussed. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Heng Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Ning Hu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| | - Jianhua Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China
| |
Collapse
|
46
|
Hata M, Suzuki M, Yasukawa T. Selective retrieval of antibody-secreting hybridomas in cell arrays based on the dielectrophoresis. Biosens Bioelectron 2022; 209:114250. [PMID: 35395585 DOI: 10.1016/j.bios.2022.114250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 11/02/2022]
Abstract
A cascade of the formation of cell arrays, the discrimination of cells secreting specific molecules, and the selective retrieval of cells has been developed to harvest antibody-secreting hybridomas in heterogeneous cell populations simply and rapidly. The microwell array device consisted of three-dimensional microband electrodes by assembling both upper and lower substrates perpendicularly. Arrays of hybridomas secreting specific antibodies were prepared by aligning hybridomas in each microwell based on the attractive force of positive dielectrophoresis (p-DEP). Antibody secreted by the hybridomas in the microwells was recognized by the antigen immobilized on the microwells or the membrane surfaces of hybridomas to discriminate hybridomas with the secretion ability. Thereafter, a repulsive force of negative dielectrophoresis (n-DEP) was applied to release the target hybridomas from the microwell array. To harvest the target hybridoma, AC signals could be modulated in the n-DEP frequency region and applied to a pair of microband electrodes located above and below each microwell containing target hybridoma. Thus, the cell-based array system described in this study allowed selective retrieval of single target hybridomas by merely switching from p-DEP to n-DEP after selecting the antibody-secreting hybridomas trapped in each microwell. The development of this high-affinity device could be useful to recover hybridomas producing antibodies in large populations of cells rapidly and effectively.
Collapse
Affiliation(s)
- Misaki Hata
- Graduate School of Science, University of Hyogo, 3-2-1, Kouto, Kamigori, Ako, Hyogo, 678-1297, Japan
| | - Masato Suzuki
- Graduate School of Science, University of Hyogo, 3-2-1, Kouto, Kamigori, Ako, Hyogo, 678-1297, Japan
| | - Tomoyuki Yasukawa
- Graduate School of Science, University of Hyogo, 3-2-1, Kouto, Kamigori, Ako, Hyogo, 678-1297, Japan.
| |
Collapse
|
47
|
Xie H, Ding X. The Intriguing Landscape of Single-Cell Protein Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105932. [PMID: 35199955 PMCID: PMC9036017 DOI: 10.1002/advs.202105932] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Indexed: 05/15/2023]
Abstract
Profiling protein expression at single-cell resolution is essential for fundamental biological research (such as cell differentiation and tumor microenvironmental examination) and clinical precision medicine where only a limited number of primary cells are permitted. With the recent advances in engineering, chemistry, and biology, single-cell protein analysis methods are developed rapidly, which enable high-throughput and multiplexed protein measurements in thousands of individual cells. In combination with single cell RNA sequencing and mass spectrometry, single-cell multi-omics analysis can simultaneously measure multiple modalities including mRNAs, proteins, and metabolites in single cells, and obtain a more comprehensive exploration of cellular signaling processes, such as DNA modifications, chromatin accessibility, protein abundance, and gene perturbation. Here, the recent progress and applications of single-cell protein analysis technologies in the last decade are summarized. Current limitations, challenges, and possible future directions in this field are also discussed.
Collapse
Affiliation(s)
- Haiyang Xie
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| |
Collapse
|
48
|
Toppi A, Dufva M. Accessible, fast and easy fabrication of hydrophilic-in-hydrophobic microdroplet arrays. PLoS One 2022; 17:e0263282. [PMID: 35213568 PMCID: PMC8880433 DOI: 10.1371/journal.pone.0263282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 01/16/2022] [Indexed: 11/18/2022] Open
Abstract
Microdroplet arrays (MDAs) are powerful tools for digital immunoassays, high-throughput screening and single cell analysis. However, MDAs are usually produced with cleanroom processes, which are associated with high costs and low availability. Furthermore, in order to obtain robust and stable MDAs based on hydrophilic spots surrounded by a hydrophobic background, the chemistry must be strictly controlled, which is challenging using shared equipment. Here, we developed a new method to fabricate MDA substrates independently from the cleanroom. A small and low-cost in-house built system to collimate the light source was assembled for photopatterning a negative resist, and spots with diameters down to 4 μm were obtained, with only 3% to 5% spot-to-spot variation across the same sample and high batch-to-batch reproducibility. The use of a negative photoresist enabled the formation of a hydrophobic coating in solution which yielded high-quality MDAs. The feasibility for carrying out digital assays was demonstrated by measuring anti-Tau antibody in sample buffers containing bovine serum albumin, with no noticeable surface fouling. The reported, robust, cost-effective, and fast process could hence lower the threshold to fabricate and use MDAs for digital immunoassays and other microcompartmentalization-based applications.
Collapse
Affiliation(s)
- Arianna Toppi
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Martin Dufva
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
| |
Collapse
|
49
|
Taylor D, Verdon N, Lomax P, Allen RJ, Titmuss S. Tracking the stochastic growth of bacterial populations in microfluidic droplets. Phys Biol 2022; 19:026003. [PMID: 35042205 PMCID: PMC7613235 DOI: 10.1088/1478-3975/ac4c9b] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 01/18/2022] [Indexed: 11/11/2022]
Abstract
Bacterial growth in microfluidic droplets is relevant in biotechnology, in microbial ecology, and in understanding stochastic population dynamics in small populations. However, it has proved challenging to automate measurement of absolute bacterial numbers within droplets, forcing the use of proxy measures for population size. Here we present a microfluidic device and imaging protocol that allows high-resolution imaging of thousands of droplets, such that individual bacteria stay in the focal plane and can be counted automatically. Using this approach, we track the stochastic growth of hundreds of replicateEscherichia colipopulations within droplets. We find that, for early times, the statistics of the growth trajectories obey the predictions of the Bellman-Harris model, in which there is no inheritance of division time. Our approach should allow further testing of models for stochastic growth dynamics, as well as contributing to broader applications of droplet-based bacterial culture.
Collapse
Affiliation(s)
- Daniel Taylor
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Nia Verdon
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Peter Lomax
- Scottish Microelectronics Centre, Alexander Crum Brown Road, King's Buildings, Edinburgh, EH9 3FF, United Kingdom
| | - Rosalind J Allen
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Simon Titmuss
- School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| |
Collapse
|
50
|
Broketa M, Bruhns P. Single-Cell Technologies for the Study of Antibody-Secreting Cells. Front Immunol 2022; 12:821729. [PMID: 35173713 PMCID: PMC8841722 DOI: 10.3389/fimmu.2021.821729] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/29/2021] [Indexed: 01/05/2023] Open
Abstract
Antibody-secreting cells (ASC), plasmablasts and plasma cells, are terminally differentiated B cells responsible for large-scale production and secretion of antibodies. ASC are derived from activated B cells, which may differentiate extrafollicularly or form germinal center (GC) reactions within secondary lymphoid organs. ASC therefore consist of short-lived, poorly matured plasmablasts that generally secrete lower-affinity antibodies, or long-lived, highly matured plasma cells that generally secrete higher-affinity antibodies. The ASC population is responsible for producing an immediate humoral B cell response, the polyclonal antibody repertoire, as well as in parallel building effective humoral memory and immunity, or potentially driving pathology in the case of autoimmunity. ASC are phenotypically and transcriptionally distinct from other B cells and further distinguishable by morphology, varied lifespans, and anatomical localization. Single cell analyses are required to interrogate the functional and transcriptional diversity of ASC and their secreted antibody repertoire and understand the contribution of individual ASC responses to the polyclonal humoral response. Here we summarize the current and emerging functional and molecular techniques for high-throughput characterization of ASC with single cell resolution, including flow and mass cytometry, spot-based and microfluidic-based assays, focusing on functional approaches of the secreted antibodies: specificity, affinity, and secretion rate.
Collapse
Affiliation(s)
- Matteo Broketa
- Institut Pasteur, Université de Paris, INSERM UMR 1222, Unit of Antibodies in Therapy and Pathology, Paris, France
- Sorbonne Université, Collège doctoral, Paris, France
| | - Pierre Bruhns
- Institut Pasteur, Université de Paris, INSERM UMR 1222, Unit of Antibodies in Therapy and Pathology, Paris, France
| |
Collapse
|