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Park J, Kadam PS, Atiyas Y, Chhay B, Tsourkas A, Eberwine JH, Issadore DA. High-Throughput Single-Cell, Single-Mitochondrial DNA Assay Using Hydrogel Droplet Microfluidics. Angew Chem Int Ed Engl 2024; 63:e202401544. [PMID: 38470412 DOI: 10.1002/anie.202401544] [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: 01/23/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/13/2024]
Abstract
There is growing interest in understanding the biological implications of single cell heterogeneity and heteroplasmy of mitochondrial DNA (mtDNA), but current methodologies for single-cell mtDNA analysis limit the scale of analysis to small cell populations. Although droplet microfluidics have increased the throughput of single-cell genomic, RNA, and protein analysis, their application to sub-cellular organelle analysis has remained a largely unsolved challenge. Here, we introduce an agarose-based droplet microfluidic approach for single-cell, single-mtDNA analysis, which allows simultaneous processing of hundreds of individual mtDNA molecules within >10,000 individual cells. Our microfluidic chip encapsulates individual cells in agarose beads, designed to have a sufficiently dense hydrogel network to retain mtDNA after lysis and provide a robust scaffold for subsequent multi-step processing and analysis. To mitigate the impact of the high viscosity of agarose required for mtDNA retention on the throughput of microfluidics, we developed a parallelized device, successfully achieving ~95 % mtDNA retention from single cells within our microbeads at >700,000 drops/minute. To demonstrate utility, we analyzed specific regions of the single-mtDNA using a multiplexed rolling circle amplification (RCA) assay. We demonstrated compatibility with both microscopy, for digital counting of individual RCA products, and flow cytometry for higher throughput analysis.
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Affiliation(s)
- Juhwan Park
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Parnika S Kadam
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Yasemin Atiyas
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Bonirath Chhay
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Andrew Tsourkas
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - James H Eberwine
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - David A Issadore
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
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2
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Park J, Kadam PS, Atiyas Y, Chhay B, Tsourkas A, Eberwine JH, Issadore DA. High-throughput single-cell, single-mitochondrial DNA assay using hydrogel droplet microfluidics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577854. [PMID: 38352577 PMCID: PMC10862758 DOI: 10.1101/2024.01.29.577854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
There is growing interest in understanding the biological implications of single cell heterogeneity and intracellular heteroplasmy of mtDNA, but current methodologies for single-cell mtDNA analysis limit the scale of analysis to small cell populations. Although droplet microfluidics have increased the throughput of single-cell genomic, RNA, and protein analysis, their application to sub-cellular organelle analysis has remained a largely unsolved challenge. Here, we introduce an agarose-based droplet microfluidic approach for single-cell, single-mtDNA analysis, which allows simultaneous processing of hundreds of individual mtDNA molecules within >10,000 individual cells. Our microfluidic chip encapsulates individual cells in agarose beads, designed to have a sufficiently dense hydrogel network to retain mtDNA after lysis and provide a robust scaffold for subsequent multi-step processing and analysis. To mitigate the impact of the high viscosity of agarose required for mtDNA retention on the throughput of microfluidics, we developed a parallelized device, successfully achieving ~95% mtDNA retention from single cells within our microbeads at >700,000 drops/minute. To demonstrate utility, we analyzed specific regions of the single mtDNA using a multiplexed rolling circle amplification (RCA) assay. We demonstrated compatibility with both microscopy, for digital counting of individual RCA products, and flow cytometry for higher throughput analysis.
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Wu X, Liu M, Niu J, Liu Q, Jiang X, Zheng Y, Qian Y, Zhang YM, Shen J, Liu Y. An in situ protonation-activated supramolecular self-assembly for selective suppression of tumor growth. Chem Sci 2023; 14:1724-1731. [PMID: 36819851 PMCID: PMC9930980 DOI: 10.1039/d2sc05652f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/09/2023] [Indexed: 01/18/2023] Open
Abstract
An in situ supramolecular self-assembly in the subcellular organelles could provide a new strategy to treat diseases. Herein, we report a protonation-activated in situ supramolecular self-assembly system in the lysosomes, which could destabilize the lysosome membrane, resulting in the selective suppression of cancer cells. In this system, pyridyl-functionalized tetraphenylethylene (TPE-Py) was protonated in the lysosomes of A549 lung cancer cells to form octahedron-like structures with cucurbit[8]uril (CB[8]), which impaired the integrity of the lysosome membrane, resulting in selective suppression of cancer cells. Moreover, its anticancer efficiency was also systematically evaluated in vivo, triggering the apoptosis of tumor tissues with ignorable effects on normal organs. Overall, the protonation-activated self-assembly in the lysosomes based on the host-guest complexation would provide a method for novel anti-cancer systems.
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Affiliation(s)
- Xuan Wu
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University Wenzhou Zhejiang 325035 China .,University of the Chinese Academy of Sciences Wenzhou Institute Wenzhou Zhejiang 325035 China
| | - Ming Liu
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University Wenzhou Zhejiang 325035 China
| | - Jie Niu
- Department of Chemistry, State Key Laboratory of Elemento Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University Tianjin 300071 China
| | - Qian Liu
- University of the Chinese Academy of Sciences Wenzhou InstituteWenzhouZhejiang 325035China
| | - Xin Jiang
- Department of Urology, Xiangya Hospital, Central South UniversityChangsha 410008China
| | - Yujing Zheng
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University Wenzhou Zhejiang 325035 China
| | - Yuna Qian
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University Wenzhou Zhejiang 325035 China .,University of the Chinese Academy of Sciences Wenzhou Institute Wenzhou Zhejiang 325035 China
| | - Ying-Ming Zhang
- Department of Chemistry, State Key Laboratory of Elemento Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University Tianjin 300071 China
| | - Jianliang Shen
- School of Ophthalmology & Optometry, School of Biomedical Engineering, Wenzhou Medical University Wenzhou Zhejiang 325035 China .,University of the Chinese Academy of Sciences Wenzhou Institute Wenzhou Zhejiang 325035 China
| | - Yu Liu
- Department of Chemistry, State Key Laboratory of Elemento Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University Tianjin 300071 China
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Chantipmanee N, Xu Y. Toward nanofluidics‐based mass spectrometry for exploring the unknown complex and heterogenous subcellular worlds. VIEW 2022. [DOI: 10.1002/viw.20220036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Nattapong Chantipmanee
- Department of Chemical Engineering Graduate School of Engineering Osaka Metropolitan University Sakai Japan
| | - Yan Xu
- Department of Chemical Engineering Graduate School of Engineering Osaka Metropolitan University Sakai Japan
- Japan Science and Technology Agency (JST) PRESTO Kawaguchi Japan
- Japan Science and Technology Agency (JST) CREST Kawaguchi Japan
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Chantipmanee N, Xu Y. Nanofluidics for chemical and biological dynamics in solution at the single molecular level. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Morales RTT, Ko J. Future of Digital Assays to Resolve Clinical Heterogeneity of Single Extracellular Vesicles. ACS NANO 2022; 16:11619-11645. [PMID: 35904433 PMCID: PMC10174080 DOI: 10.1021/acsnano.2c04337] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Extracellular vesicles (EVs) are complex lipid membrane vehicles with variable expressions of molecular cargo, composed of diverse subpopulations that participate in the intercellular signaling of biological responses in disease. EV-based liquid biopsies demonstrate invaluable clinical potential for overhauling current practices of disease management. Yet, EV heterogeneity is a major needle-in-a-haystack challenge to translate their use into clinical practice. In this review, existing digital assays will be discussed to analyze EVs at a single vesicle resolution, and future opportunities to optimize the throughput, multiplexing, and sensitivity of current digital EV assays will be highlighted. Furthermore, this review will outline the challenges and opportunities that impact the clinical translation of single EV technologies for disease diagnostics and treatment monitoring.
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Affiliation(s)
- Renee-Tyler T Morales
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jina Ko
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Amor M, Faivre D, Corvisier J, Tharaud M, Busigny V, Komeili A, Guyot F. Defining Local Chemical Conditions in Magnetosomes of Magnetotactic Bacteria. J Phys Chem B 2022; 126:2677-2687. [PMID: 35362974 PMCID: PMC9098202 DOI: 10.1021/acs.jpcb.2c00752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Defining chemical properties of intracellular organelles is necessary to determine their function(s) as well as understand and mimic the reactions they host. However, the small size of bacterial and archaeal microorganisms often prevents defining local intracellular chemical conditions in a similar way to what has been established for eukaryotic organelles. This work proposes to use magnetite (Fe3O4) nanocrystals contained in magnetosome organelles of magnetotactic bacteria as reporters of elemental composition, pH, and redox potential of a hypothetical environment at the site of formation of intracellular magnetite. This methodology requires combining recent single-cell mass spectrometry measurements together with elemental composition of magnetite in trace and minor elements. It enables a quantitative characterization of chemical disequilibria of 30 chemical elements between the intracellular and external media of magnetotactic bacteria, revealing strong transfers of elements with active influx or efflux processes that translate into elemental accumulation (Mo, Se, and Sn) or depletion (Sr and Bi) in the bacterial internal medium of up to seven orders of magnitude relative to the extracellular medium. Using this concept, we show that chemical conditions in magnetosomes are compatible with a pH of 7.5-9.5 and a redox potential of -0.25 to -0.6 V.
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Affiliation(s)
- Matthieu Amor
- Aix-Marseille Université, CEA, CNRS, BIAM, 13108 Saint-Paul-lez-Durance, France.,Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, United States
| | - Damien Faivre
- Aix-Marseille Université, CEA, CNRS, BIAM, 13108 Saint-Paul-lez-Durance, France
| | - Jérôme Corvisier
- Mines ParisTech, PSL Research University, Centre de Géosciences, 35 rue Saint Honoré, Fontainebleau Cedex 77305, France
| | - Mickaël Tharaud
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris F-75005, France
| | - Vincent Busigny
- Université de Paris, Institut de Physique du Globe de Paris, CNRS, Paris F-75005, France.,Institut Universitaire de France, Paris 75005, France
| | - Arash Komeili
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3200, United States
| | - François Guyot
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d'Histoire Naturelle, Sorbonne Université, UMR 7590 CNRS, 61 rue Buffon, 75005 Paris, France
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Siedlik MJ, Issadore D. Pico-washing: simultaneous liquid addition and removal for continuous-flow washing of microdroplets. MICROSYSTEMS & NANOENGINEERING 2022; 8:46. [PMID: 35498338 PMCID: PMC9050730 DOI: 10.1038/s41378-022-00381-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/02/2022] [Accepted: 03/07/2022] [Indexed: 05/19/2023]
Abstract
Droplet microfluidics is based on a toolbox of several established unit operations, including droplet generation, incubation, mixing, pico-injection, and sorting. In the last two decades, the development of droplet microfluidic systems, which incorporate these multiple unit operations into a workflow, has demonstrated unique capabilities in fields ranging from single-cell transcriptomic analyses to materials optimization. One unit operation that is sorely underdeveloped in droplet microfluidics is washing, exchange of the fluid in a droplet with a different fluid. Here, we demonstrate what we name the "pico-washer," a unit operation capable of simultaneously adding fluid to and removing fluid from droplets in flow while requiring only a small footprint on a microfluidic chip. We describe the fabrication strategy, device architecture, and process parameters required for stable operation of this technology, which is capable of operating with kHz droplet throughput. Furthermore, we provide an image processing workflow to characterize the washing process with microsecond and micrometer resolution. Finally, we demonstrate the potential for integrated droplet workflows by arranging two of these unit operations in series with a droplet generator, describe a design rule for stable operation of the pico-washer when integrated into a system, and validate this design rule experimentally. We anticipate that this technology will contribute to continued development of the droplet microfluidics toolbox and the realization of novel droplet-based, multistep biological and chemical assays.
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Affiliation(s)
- Michael J. Siedlik
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 United States
| | - David Issadore
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 United States
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA 19104 United States
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9
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Zhao H, Zhang Y, Chen Y, Ho NRY, Sundah NR, Natalia A, Liu Y, Miow QH, Wang Y, Tambyah PA, Ong CWM, Shao H. Accessible detection of SARS-CoV-2 through molecular nanostructures and automated microfluidics. Biosens Bioelectron 2021; 194:113629. [PMID: 34534949 PMCID: PMC8435073 DOI: 10.1016/j.bios.2021.113629] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/16/2021] [Accepted: 09/10/2021] [Indexed: 11/15/2022]
Abstract
Accurate and accessible nucleic acid diagnostics is critical to reducing the spread of COVID-19 and resuming socioeconomic activities. Here, we present an integrated platform for the direct detection of SARS-CoV-2 RNA targets near patients. Termed electrochemical system integrating reconfigurable enzyme-DNA nanostructures (eSIREN), the technology leverages responsive molecular nanostructures and automated microfluidics to seamlessly transduce target-induced molecular activation into an enhanced electrochemical signal. Through responsive enzyme-DNA nanostructures, the technology establishes a molecular circuitry that directly recognizes specific RNA targets and catalytically enhances signaling; only upon target hybridization, the molecular nanostructures activate to liberate strong enzymatic activity and initiate cascading reactions. Through automated microfluidics, the system coordinates and interfaces the molecular circuitry with embedded electronics; its pressure actuation and liquid-guiding structures improve not only analytical performance but also automated implementation. The developed platform establishes a detection limit of 7 copies of RNA target per μl, operates against the complex biological background of native patient samples, and is completed in <20 min at room temperature. When clinically evaluated, the technology demonstrates accurate detection in extracted RNA samples and direct swab lysates to diagnose COVID-19 patients.
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Affiliation(s)
- Haitao Zhao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore
| | - Yan Zhang
- Institute for Health Innovation & Technology, National University of Singapore, Singapore; Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore
| | - Yuan Chen
- Institute for Health Innovation & Technology, National University of Singapore, Singapore; Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore
| | - Nicholas R Y Ho
- Institute for Health Innovation & Technology, National University of Singapore, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
| | - Noah R Sundah
- Institute for Health Innovation & Technology, National University of Singapore, Singapore; Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore
| | - Auginia Natalia
- Institute for Health Innovation & Technology, National University of Singapore, Singapore; Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore
| | - Yu Liu
- Institute for Health Innovation & Technology, National University of Singapore, Singapore; Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore
| | - Qing Hao Miow
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yu Wang
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Paul A Tambyah
- Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Infectious Diseases, Department of Medicine, National University Hospital, Singapore
| | - Catherine W M Ong
- Institute for Health Innovation & Technology, National University of Singapore, Singapore; Infectious Diseases Translational Research Programme, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Infectious Diseases, Department of Medicine, National University Hospital, Singapore
| | - Huilin Shao
- Institute for Health Innovation & Technology, National University of Singapore, Singapore; Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore; Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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