1
|
Bao K, Jiang X, Hu HM, Liu T, Zhang J. DEPICT-seq: Single-Cell Transcriptomic Analysis of Rare Cell Subsets Isolated via Nucleic Acid Cytometry. Anal Chem 2024. [PMID: 39287475 DOI: 10.1021/acs.analchem.4c03075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
The ability to dive deep into specific rare cell populations is critical for understanding tissue physiology and pathology across various biological domains. As single-cell RNA-seq flourishes, many newly discovered cell subtypes are defined by their transcriptomic markers. However, our ability to retrieve and analyze cells based on their nucleic acid markers remains underdeveloped. Here, we present Double Emulsion PCR-Initiated Cell sorting and Transcriptomic Sequencing (DEPICT-seq), a high-throughput droplet nucleic acid cytometry method that integrates batch cell fixation for cellular information preservation, double emulsion digital PCR-based cell sorting to target nucleic acid markers of interest, and in-depth full-length transcriptomic analyses at single-cell resolution. We utilize DEPICT-seq to isolate and characterize T cell receptor (TCR)-engineered T cells within a mixed population and also demonstrate a variation of the workflow by incorporating an RNase H-dependent PCR step to enrich full-length TCR sequences for paired single-cell TCR sequencing and transcriptomic profiling.
Collapse
Affiliation(s)
- Kaixuan Bao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Endocrinology and Metabolism, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | | | - Hong-Min Hu
- ImmuXell Biotech Ltd., Shanghai 201315, China
| | - Tiemin Liu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Department of Endocrinology and Metabolism, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
- School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia 010020, China
| | - Jingwei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200438, China
- Zhejiang Lab, Hangzhou, Zhejiang 311121, China
| |
Collapse
|
2
|
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
|
3
|
Sun G, Wu Y, Huang Z, Liu Y, Li J, Du G, Lv X, Liu L. Directed evolution of diacetylchitobiose deacetylase via high-throughput droplet sorting with a novel, bacteria-based biosensor. Biosens Bioelectron 2023; 219:114818. [PMID: 36327560 DOI: 10.1016/j.bios.2022.114818] [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: 08/23/2022] [Revised: 10/02/2022] [Accepted: 10/12/2022] [Indexed: 11/19/2022]
Abstract
Numerous biological disciplines rely on high-throughput cell sorting. Flow cytometry, the current gold standard, is capable of ultrahigh-throughput cell sorting, but measurements are primarily limited to cell size and surface marker. Droplet sorting technology is gaining increasing attention with the ability to provide an individual environment for the analysis of single-cell secretion. Although various droplet detecting methods, such as fluorescence, absorbance, mass spectrum, imaging analysis, have been developed for droplet sorting, it remains challenging to establish high-throughput sorting methods for numerous analytes. We aim to develop a high-throughput sorting system based on the glucosamine (GlcN) measurement for the directed evolution of diacetylchitobiose deacetylase (Dac), the key enzyme for GlcN production. To overcome the limitation that no high-throughput sorting system existed for GlcN, we designed a novel bacteria-based biosensor capable of converting GlcN to a positively correlated fluorescence signal. Through characterization and optimization, it was possible to detect GlcN in droplets for high-throughput droplet sorting. We recovered the best Dac mutant S60I/R157T/F168S after sorting ∼0.2 million Dac mutants; its activity was 48.6 ± 1.5 U/mL, which was 1.8-times that of our previously discovered Dac mutant R157T (27.2 ± 1.8 U/mL). This result successfully demonstrated the combination of high-throughput droplet sorting technology and a bacteria-based biosensor, which could facilitate the industrial production of GlcN and serve as a model for similar droplet sorting applications.
Collapse
Affiliation(s)
- Guoyun Sun
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Ziyang Huang
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China.
| |
Collapse
|
4
|
Bognár Z, de Jonge MI, Gyurcsányi RE. In situ silver nanoparticle coating of virions for quantification at single virus level. NANOSCALE 2022; 14:2296-2303. [PMID: 35081610 DOI: 10.1039/d1nr07607h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In situ labelling and encapsulation of biological entities, such as of single viruses, may provide a versatile approach to modulate their functionality and facilitate their detection at single particle level. Here, we introduce a novel virus metallization approach based on in situ coating of viruses in solution with silver nanoparticles (AgNP) in a two-step synthetic process, i.e. surface activation with a tannic acid - Sn(II) coordination complex, which subsequently induces silver ion (I) reduction. The metalic coating on the virus surface opens the opportunity for electrochemical quantification of the AgNP-tagged viruses by nano-impact electrochemistry on a microelectrode with single particle sensitivity, i.e. enable the detection of particles oherwise undetectable. We show that the silver coating of the virus particles impacting the electrode can be oxidized to produce distinct current peaks the frequency of which show a linear correlation with the virus count. The proof of the concept was done with inactivated Influenza A (H3N2) viruses resulting in their quantitation down to the femtomolar concentrations (ca. 5 × 107 particles per mL) using 50 s counting sequences.
Collapse
Affiliation(s)
- Zsófia Bognár
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary.
- MTA-BME Lendület Chemical Nanosensors Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Marien I de Jonge
- Section Paediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Center for Infectious Diseases, Radboud University Medical Center, Philips van Leydenlaan 15, 6525 EX Nijmegen, The Netherlands
| | - Róbert E Gyurcsányi
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary.
- MTA-BME Lendület Chemical Nanosensors Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME Computation Driven Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| |
Collapse
|
5
|
Hatori MN, Modavi C, Xu P, Weisgerber D, Abate AR. Dual-layered hydrogels allow complete genome recovery with nucleic acid cytometry. Biotechnol J 2022; 17:e2100483. [PMID: 35088927 PMCID: PMC9208836 DOI: 10.1002/biot.202100483] [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: 09/06/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/09/2022]
Abstract
Targeting specific cells for sequencing is important for applications in cancer, microbiology, and infectious disease. Nucleic acid cytometry is a powerful approach for accomplishing this because it allows specific cells to be isolated based on sequence biomarkers that are otherwise impossible to detect. However, existing methods require specialized microfluidic devices, limiting adoption. Here, we describe a modified workflow that uses particle-templated emulsification and flow cytometry to conduct the essential steps of cell detection and sorting normally accomplished by microfluidics. Our microfluidic-free workflow allows facile isolation and sequencing of cells, viruses, and nucleic acids and thus provides a powerful enrichment approach for targeted sequencing applications. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Makiko N Hatori
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Cyrus Modavi
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Peng Xu
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Daniel Weisgerber
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, CA, 94158, USA.,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| |
Collapse
|
6
|
Van Lent J, Breukers J, Ven K, Ampofo L, Horta S, Pollet F, Imbrechts M, Geukens N, Vanhoorelbeke K, Declerck P, Lammertyn J. Miniaturized single-cell technologies for monoclonal antibody discovery. LAB ON A CHIP 2021; 21:3627-3654. [PMID: 34505611 DOI: 10.1039/d1lc00243k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antibodies (Abs) are among the most important class of biologicals, showcasing a high therapeutic and diagnostic value. In the global therapeutic Ab market, fully-human monoclonal Abs (FH-mAbs) are flourishing thanks to their low immunogenicity and high specificity. The rapidly emerging field of single-cell technologies has paved the way to efficiently discover mAbs by facilitating a fast screening of the antigen (Ag)-specificity and functionality of Abs expressed by B cells. This review summarizes the principles and challenges of the four key concepts to discover mAbs using these technologies, being confinement of single cells using either droplet microfluidics or microstructure arrays, identification of the cells of interest, retrieval of those cells and single-cell sequence determination required for mAb production. This review reveals the enormous potential for mix-and-matching of the above-mentioned strategies, which is illustrated by the plethora of established, highly integrated devices. Lastly, an outlook is given on the many opportunities and challenges that still lie ahead to fully exploit miniaturized single-cell technologies for mAb discovery.
Collapse
Affiliation(s)
- Julie Van Lent
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Jolien Breukers
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Karen Ven
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Louanne Ampofo
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
| | - Sara Horta
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk 8500, Belgium
| | - Francesca Pollet
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| | - Maya Imbrechts
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Nick Geukens
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Karen Vanhoorelbeke
- Laboratory for Thrombosis Research, IRF Life Sciences, KU Leuven Campus Kulak Kortrijk, Kortrijk 8500, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Paul Declerck
- Laboratory for Therapeutic and Diagnostic Antibodies, KU Leuven, Leuven 3000, Belgium
- PharmAbs, The KU Leuven Antibody Center, KU Leuven, Leuven 3000, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Leuven 3001, Belgium.
| |
Collapse
|
7
|
Sun C, Liu L, Vasudevan HN, Chang KC, Abate AR. Accurate Bulk Quantitation of Droplet Digital Polymerase Chain Reaction. Anal Chem 2021; 93:9974-9979. [PMID: 34252272 PMCID: PMC8829825 DOI: 10.1021/acs.analchem.1c00877] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Droplet digital PCR
provides superior accuracy for nucleic acid
quantitation. The requirement of microfluidics to generate and analyze
the emulsions, however, is a barrier to its adoption, particularly
in low resource settings or clinical laboratories. Here, we report
a novel method to prepare ddPCR droplets by vortexing and readout
of the results by bulk analysis of recovered amplicons. We demonstrate
the approach by accurately quantitating SARS-CoV-2 sequences using
entirely bulk processing and no microfluidics. Our approach for quantitating
reactions should extend to all digital assays that generate amplicons,
including digital PCR and LAMP conducted in droplets, microchambers,
or nanoliter wells. More broadly, our approach combines important
attributes of ddPCR, including enhanced accuracy and robustness to
inhibition, with the high-volume sample processing ability of quantitative
PCR.
Collapse
Affiliation(s)
- Chen Sun
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Leqian Liu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Harish N Vasudevan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States.,Department of Radiation Oncology, University of California San Francisco, San Francisco, California 94158, United States
| | - Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States.,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California 94158, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| |
Collapse
|
8
|
Abstract
![]()
Targeted
sequencing enables sensitive and cost-effective analysis
by focusing resources on molecules of interest. Existing methods,
however, are limited in enrichment power and target capture length.
Here, we present a novel method that uses compound nucleic acid cytometry
to achieve million-fold enrichments of molecules >10 kbp in length
using minimal prior target information. We demonstrate the approach
by sequencing HIV proviruses in infected individuals. Our method is
useful for rare target sequencing in research and clinical applications,
including for identifying cancer-associated mutations or sequencing
viruses infecting cells.
Collapse
Affiliation(s)
- Chen Sun
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States.,California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, California 94158, United States.,Chan Zuckerberg Biohub, San Francisco, California 94158, United States
| |
Collapse
|
9
|
Sun C, Liu L, Vasudevan HN, Chang KC, Abate AR. Accurate bulk quantitation of droplet digital PCR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.13.424628. [PMID: 33469578 PMCID: PMC7814815 DOI: 10.1101/2021.01.13.424628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Droplet digital PCR provides superior accuracy in nucleic acid quantitation. The requirement of microfluidics to generate and analyze the emulsions, however, is a barrier to its adoption, particularly in low resource or clinical settings. Here, we report a novel method to prepare ddPCR droplets by vortexing and readout the results by bulk analysis of recovered amplicons. We demonstrate the approach by accurately quantitating SARS-CoV-2 sequences using entirely bulk processing and no microfluidics. Our approach for quantitating reactions should extend to all digital assays that generate amplicons, including digital PCR and LAMP conducted in droplets, microchambers, or nanoliter wells. More broadly, our approach combines important attributes of ddPCR, including enhanced accuracy and robustness to inhibition, with the high-volume sample processing ability of quantitative PCR.
Collapse
Affiliation(s)
- Chen Sun
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Leqian Liu
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Harish N. Vasudevan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kai-Chun Chang
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Adam R. Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
- California Institute for Quantitative Biosciences, University of California San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| |
Collapse
|
10
|
Brower KK, Carswell-Crumpton C, Klemm S, Cruz B, Kim G, Calhoun SGK, Nichols L, Fordyce PM. Double emulsion flow cytometry with high-throughput single droplet isolation and nucleic acid recovery. LAB ON A CHIP 2020; 20:2062-2074. [PMID: 32417874 PMCID: PMC7670282 DOI: 10.1039/d0lc00261e] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Droplet microfluidics has made large impacts in diverse areas such as enzyme evolution, chemical product screening, polymer engineering, and single-cell analysis. However, while droplet reactions have become increasingly sophisticated, phenotyping droplets by a fluorescent signal and sorting them to isolate individual variants-of-interest at high-throughput remains challenging. Here, we present sdDE-FACS (s[combining low line]ingle d[combining low line]roplet D[combining low line]ouble E[combining low line]mulsion-FACS), a new method that uses a standard flow cytometer to phenotype, select, and isolate individual double emulsion droplets of interest. Using a 130 μm nozzle at high sort frequency (12-14 kHz), we demonstrate detection of droplet fluorescence signals with a dynamic range spanning 5 orders of magnitude and robust post-sort recovery of intact double emulsion (DE) droplets using 2 commercially-available FACS instruments. We report the first demonstration of single double emulsion droplet isolation with post-sort recovery efficiencies >70%, equivalent to the capabilities of single-cell FACS. Finally, we establish complete downstream recovery of nucleic acids from single, sorted double emulsion droplets via qPCR with little to no cross-contamination. sdDE-FACS marries the full power of droplet microfluidics with flow cytometry to enable a variety of new droplet assays, including rare variant isolation and multiparameter single-cell analysis.
Collapse
Affiliation(s)
- Kara K Brower
- Department of Bioengineering, Stanford University, Stanford, California, USA.
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Recent Advances in Droplet-based Microfluidic Technologies for Biochemistry and Molecular Biology. MICROMACHINES 2019; 10:mi10060412. [PMID: 31226819 PMCID: PMC6631694 DOI: 10.3390/mi10060412] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/16/2019] [Accepted: 06/18/2019] [Indexed: 12/16/2022]
Abstract
Recently, droplet-based microfluidic systems have been widely used in various biochemical and molecular biological assays. Since this platform technique allows manipulation of large amounts of data and also provides absolute accuracy in comparison to conventional bioanalytical approaches, over the last decade a range of basic biochemical and molecular biological operations have been transferred to drop-based microfluidic formats. In this review, we introduce recent advances and examples of droplet-based microfluidic techniques that have been applied in biochemistry and molecular biology research including genomics, proteomics and cellomics. Their advantages and weaknesses in various applications are also comprehensively discussed here. The purpose of this review is to provide a new point of view and current status in droplet-based microfluidics to biochemists and molecular biologists. We hope that this review will accelerate communications between researchers who are working in droplet-based microfluidics, biochemistry and molecular biology.
Collapse
|
12
|
Abstract
![]()
The compartmentalization of reactions
in monodispersed droplets
is valuable for applications across biology. However, the requirement
of microfluidics to partition the sample into monodispersed droplets
is a significant barrier that impedes implementation. Here, we introduce
particle-templated emulsification, a method to encapsulate samples
in monodispersed emulsions without microfluidics. By vortexing a mixture
of hydrogel particles and sample solution, we encapsulate the sample
in monodispersed emulsions that are useful for most droplet applications.
We illustrate the method with ddPCR and single cell culture. The ability
to encapsulate samples in monodispersed droplets without microfluidics
should facilitate the implementation of compartmentalized reactions
in biology.
Collapse
Affiliation(s)
- Makiko N Hatori
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences , University of California , San Francisco , California 94158 , United States
| | - Samuel C Kim
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences , University of California , San Francisco , California 94158 , United States
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences , University of California , San Francisco , California 94158 , United States.,Chan Zuckerberg Biohub , San Francisco , California 94158 , United States
| |
Collapse
|
13
|
Murphy TW, Zhang Q, Naler LB, Ma S, Lu C. Recent advances in the use of microfluidic technologies for single cell analysis. Analyst 2017; 143:60-80. [PMID: 29170786 PMCID: PMC5839671 DOI: 10.1039/c7an01346a] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The inherent heterogeneity in cell populations has become of great interest and importance as analytical techniques have improved over the past decades. With the advent of personalized medicine, understanding the impact of this heterogeneity has become an important challenge for the research community. Many different microfluidic approaches with varying levels of throughput and resolution exist to study single cell activity. In this review, we take a broad view of the recent microfluidic developments in single cell analysis based on microwell, microchamber, and droplet platforms. We cover physical, chemical, and molecular biology approaches for cellular and molecular analysis including newly emerging genome-wide analysis.
Collapse
Affiliation(s)
- Travis W Murphy
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA.
| | | | | | | | | |
Collapse
|
14
|
Clark IC, Abate AR. Finding a helix in a haystack: nucleic acid cytometry with droplet microfluidics. LAB ON A CHIP 2017; 17:2032-2045. [PMID: 28540956 PMCID: PMC6005652 DOI: 10.1039/c7lc00241f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nucleic acids encode the information of life, programming cellular functions and dictating many biological outcomes. Differentiating between cells based on their nucleic acid programs is, thus, a powerful way to unravel the genetic bases of many phenotypes. This is especially important considering that most cells exist in heterogeneous populations, requiring them to be isolated before they can be studied. Existing flow cytometry techniques, however, are unable to reliably recover specific cells based on nucleic acid content. Nucleic acid cytometry is a new field built on droplet microfluidics that allows robust identification, sorting, and sequencing of cells based on specific nucleic acid biomarkers. This review highlights applications that immediately benefit from the approach, biological questions that can be addressed for the first time with it, and considerations for building successful workflows.
Collapse
Affiliation(s)
- Iain C Clark
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.
| | | |
Collapse
|
15
|
Haliburton JR, Kim SC, Clark IC, Sperling RA, Weitz DA, Abate AR. Efficient extraction of oil from droplet microfluidic emulsions. BIOMICROFLUIDICS 2017; 11:034111. [PMID: 28611871 PMCID: PMC5438281 DOI: 10.1063/1.4984035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/10/2017] [Indexed: 06/07/2023]
Abstract
Droplet microfluidic techniques can perform large numbers of single molecule and cell reactions but often require controlled, periodic flow to merge, split, and sort droplets. Here, we describe a simple method to convert aperiodic flows into periodic ones. Using an oil extraction module, we efficiently remove oil from emulsions to readjust the droplet volume fraction, velocity, and packing, producing periodic flows. The extractor acts as a universal adaptor to connect microfluidic modules that do not operate under identical flow conditions, such as droplet generators, incubators, and merger devices.
Collapse
Affiliation(s)
| | - S C Kim
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, California 94158, USA
| | - I C Clark
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, California 94158, USA
| | - R A Sperling
- Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - D A Weitz
- Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | | |
Collapse
|