1
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Liu Z, Fan Y, Cui M, Wang X, Zhao P. Investigation of tumour environments through advancements in microtechnology and nanotechnology. Biomed Pharmacother 2024; 178:117230. [PMID: 39116787 DOI: 10.1016/j.biopha.2024.117230] [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: 06/05/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Cancer has a significant negative social and economic impact on both developed and developing countries. As a result, understanding the onset and progression of cancer is critical for developing therapies that can improve the well-being and health of individuals with cancer. With time, study has revealed, the tumor microenvironment has great influence on this process. Micro and nanoscale engineering techniques can be used to study the tumor microenvironment. Nanoscale and Microscale engineering use Novel technologies and designs with small dimensions to recreate the TME. Knowing how cancer cells interact with one another can help researchers develop therapeutic approaches that anticipate and counteract cancer cells' techniques for evading detection and fighting anti-cancer treatments, such as microfabrication techniques, microfluidic devices, nanosensors, and nanodevices used to study or recreate the tumor microenvironment. Nevertheless, a complicated action just like the growth and in cancer advancement, and their intensive association along the environment around it that has to be studied in more detail.
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Affiliation(s)
- Zhen Liu
- Department of Radiology, Shengjing Hospital of China Medical University, China
| | - Yan Fan
- Department of Pediatrics, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Mengyao Cui
- Department of Surgical Oncology, Breast Surgery, General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xu Wang
- Department of Surgical Oncology, Breast Surgery, General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Pengfei Zhao
- Department of Radiology, Shengjing Hospital of China Medical University, China.
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2
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Wang J, Liu X, Li J, Chen W. Digital Circulating Tumor Cells Quantification. Anal Chem 2024; 96:6881-6888. [PMID: 38659346 DOI: 10.1021/acs.analchem.3c02769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Circulating tumor cells (CTCs) are an emerging but vital biomarker for cancer management. An efficient methodology for accurately quantifying CTCs remains challenging due to their rareness. Here, we develop a digital CTC detection strategy using partitioning instead of enrichment to quantify CTCs. By utilizing the characteristics of droplet microfluidics that can rapidly generate a large number of parallel independent reactors, combined with Poisson distribution, we realize the quantification of CTCs in the blood directly. The limit of detection of our digital CTCs quantification assay is five cells per 5 mL of whole blood. By simultaneously detecting multiple genetic mutations, our approach achieves highly sensitive and specific detection of CTCs in peripheral blood from NSCLC patients (AUC = 1). Our digital platform offers a potential approach and strategy for the quantification of CTCs, which could contribute to the advancement of cancer medical management.
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Affiliation(s)
- Jidong Wang
- Medical Research Center, Huazhong University of Science and Technology Union Shenzhen Hospital, the Sixth Affiliated Hospital, Shenzhen University Medical School, Shenzhen University, Shenzhen 518052, People's Republic of China
| | - Xiaolei Liu
- School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, People's Republic of China
| | - Jiang Li
- Gynecology Department, Huazhong University of Science and Technology Union Shenzhen Hospital, the Sixth Affiliated Hospital, Shenzhen University Medical School, Shenzhen University, Shenzhen 518052, People's Republic of China
| | - Wenwen Chen
- School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen 518055, People's Republic of China
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3
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Jiang L, Guo K, Chen Y, Xiang N. Droplet Microfluidics for Current Cancer Research: From Single-Cell Analysis to 3D Cell Culture. ACS Biomater Sci Eng 2024; 10:1335-1354. [PMID: 38420753 DOI: 10.1021/acsbiomaterials.3c01866] [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: 03/02/2024]
Abstract
Cancer is the second leading cause of death worldwide. Differences in drug resistance and treatment response caused by the heterogeneity of cancer cells are the primary reasons for poor cancer therapy outcomes in patients. In addition, current in vitro anticancer drug-screening methods rely on two-dimensional monolayer-cultured cancer cells, which cannot accurately predict drug behavior in vivo. Therefore, a powerful tool to study the heterogeneity of cancer cells and produce effective in vitro tumor models is warranted to leverage cancer research. Droplet microfluidics has become a powerful platform for the single-cell analysis of cancer cells and three-dimensional cell culture of in vitro tumor spheroids. In this review, we discuss the use of droplet microfluidics in cancer research. Droplet microfluidic technologies, including single- or double-emulsion droplet generation and passive- or active-droplet manipulation, are concisely discussed. Recent advances in droplet microfluidics for single-cell analysis of cancer cells, circulating tumor cells, and scaffold-free/based 3D cell culture of tumor spheroids have been systematically introduced. Finally, the challenges that must be overcome for the further application of droplet microfluidics in cancer research are discussed.
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Affiliation(s)
- Lin Jiang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Kefan Guo
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Yao Chen
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
| | - Nan Xiang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing 211189, China
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4
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Zhang K, Xiang W, Liu J, Xie Z. Flexible droplet transportation and coalescence via controllable thermal fields. Anal Chim Acta 2023; 1277:341669. [PMID: 37604623 DOI: 10.1016/j.aca.2023.341669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/03/2023] [Accepted: 07/26/2023] [Indexed: 08/23/2023]
Abstract
Flexible droplet transportation and coalescence are significant for lots of applications such as material synthesis and analytical detection. Herein, we present an effective method for controllable droplet transportation and coalescence via thermal fields. The device used for droplet manipulation is composed of a glass substrate with indium tin oxide-made microheaers and a microchannel with two transport branches and a central chamber, and it's manipulated by sequentially powering the microheaters located at the bottom of microchannel. The fluid will be unevenly heated when the microheater is actuated, leading to the formation of thermal buoyancy convection and the decrease of interfacial tension of fluids. Subsequently, the microdroplets can be transported from the inlets of microchannel to the target position by the buoyancy flow-induced Stokes drag. And the droplet migration velocity can be flexibly adjusted by changing the voltage applied on the microheater. After being transported to the center of central chamber, the coalescence behaviors of microdroplets can be triggered if the microheater located at the bottom of central chamber is continuously actuated. The droplet coalescence is the combined effect of decreased fluid interfacial tension, the shortened droplet distance by buoyancy flow and the increased instability of droplet under the elevated temperature. The droplet coalescence efficiency is also related to the voltage of microheater, by increasing the voltage from 3.5 V to 7 V, the needed time for droplet coalescence dramatically decrease from 220s to 1.4 s. Finally, by the droplet coalescence-triggered calcium hydroxide precipitation reaction, we demonstrate the applicability of the droplet manipulation method on specific sample detection. Therefore, this approach used for droplet transportation and coalescence can be attractive for many droplet-based applications such as analytical detection.
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Affiliation(s)
- Kailiang Zhang
- College of Mechanical and Electrical Engineering, Northeast Forestry University, Harbin, 150001, PR China
| | - Wei Xiang
- College of Mechanical and Electrical Engineering, Northeast Forestry University, Harbin, 150001, PR China
| | - Jiuqing Liu
- College of Mechanical and Electrical Engineering, Northeast Forestry University, Harbin, 150001, PR China
| | - Zhijie Xie
- College of Mechanical and Electrical Engineering, Northeast Forestry University, Harbin, 150001, PR China.
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5
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Kim M, Panagiotakopoulou M, Chen C, Ruiz SB, Ganesh K, Tammela T, Heller DA. Micro-engineering and nano-engineering approaches to investigate tumour ecosystems. Nat Rev Cancer 2023; 23:581-599. [PMID: 37353679 PMCID: PMC10528361 DOI: 10.1038/s41568-023-00593-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/25/2023] [Indexed: 06/25/2023]
Abstract
The interactions among tumour cells, the tumour microenvironment (TME) and non-tumour tissues are of interest to many cancer researchers. Micro-engineering approaches and nanotechnologies are under extensive exploration for modelling these interactions and measuring them in situ and in vivo to investigate therapeutic vulnerabilities in cancer and extend a systemic view of tumour ecosystems. Here we highlight the greatest opportunities for improving the understanding of tumour ecosystems using microfluidic devices, bioprinting or organ-on-a-chip approaches. We also discuss the potential of nanosensors that can transmit information from within the TME or elsewhere in the body to address scientific and clinical questions about changes in chemical gradients, enzymatic activities, metabolic and immune profiles of the TME and circulating analytes. This Review aims to connect the cancer biology and engineering communities, presenting biomedical technologies that may expand the methodologies of the former, while inspiring the latter to develop approaches for interrogating cancer ecosystems.
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Affiliation(s)
- Mijin Kim
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | | | - Chen Chen
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, Sloan Kettering Institute, New York, NY, USA
| | - Stephen B Ruiz
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Karuna Ganesh
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Tuomas Tammela
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY, USA
| | - Daniel A Heller
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA.
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA.
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6
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Nie L, Zeng X, Hongbo L, Wang S, Lu Z, Yu R. Entropy-driven DNA circuit with two-stage strand displacement for elegant and robust detection of miRNA let-7a. Anal Chim Acta 2023; 1269:341392. [PMID: 37290851 DOI: 10.1016/j.aca.2023.341392] [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: 12/27/2022] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/10/2023]
Abstract
MicroRNAs (miRNAs) research in cancer diagnosis is expanding, on account of miRNAs were demonstrated to be key indicator of gene expression and hopeful candidates for biomarkers. In this study, a stable miRNA-let-7a fluorescent biosensor was successfully designed based on an exonuclease Ⅲ-assisted two-stage strand displacement reaction (SDR). First, an entropy-driven SDR containing a three-chain structure of the substrate is used in our designed biosensor, leading to reduce the reversibility of the target recycling process in each step. The target acts on the first stage to start the entropy-driven SDR, which generates the trigger used to stimulate the exonuclease Ⅲ-assisted SDR in the second stage. At the same time, we design a SDR one-step amplification strategy as a comparison. Expectly, this developed two-stage strand displacement system has a low detection limit of 25.0 pM as well as a broad detection range of 4 orders of magnitude, making it more sensitive than the SDR one-step sensor, whose detection limit is 0.8 nM. In addition, this sensor has high specificity across members of the miRNA family. Therefore, we can take advantage of this biosensor to promote miRNA research in cancer diagnosis sensing systems.
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Affiliation(s)
- Lanxin Nie
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Xiaogang Zeng
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Li Hongbo
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China; Key Laboratory of Energy Catalysis and Conversion of Nanchang, Nanchang, 330022, PR China; State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China.
| | - Suqin Wang
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China
| | - Zhanghui Lu
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang, 330022, PR China; Key Laboratory of Energy Catalysis and Conversion of Nanchang, Nanchang, 330022, PR China.
| | - Ruqin Yu
- State Key Laboratory for Chemo/Biosensing and Chemometrics, Hunan University, Changsha, 410082, PR China
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7
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Huang Y, Sun L, Liu W, Yang L, Song Z, Ning X, Li W, Tan M, Yu Y, Li Z. Multiplex single-cell droplet PCR with machine learning for detection of high-risk human papillomaviruses. Anal Chim Acta 2023; 1252:341050. [PMID: 36935138 DOI: 10.1016/j.aca.2023.341050] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/12/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023]
Abstract
High-risk human papillomavirus (HPV) testing can significantly decline the incidence and mortality of cervical cancer. Microfluidic technology provides an effective method for accurate detection of high-risk HPV by utilizing multiplex single-cell droplet polymerase chain reaction (PCR). However, current strategies are limited by low-integration microfluidic chip, complex reagent system, expensive detection equipment and time-consuming droplet identification. Here, we developed a novel multiplex droplet PCR method that directly detected high-risk HPV sequences in single cells. A multiplex microfluidic chip integrating four flow-focusing structures was designed for one-step and parallel droplet preparation. Using single-cell droplet PCR, multi-target sequences were detected simultaneously based on a monochromatic fluorescence signal. We applied machine learning to automatically identify the large populations of single-cell droplets with 97% accuracy. HPV16, 18 and 45 sequences were sensitively detected without cross-contamination in mixed CaSki and Hela cells. The approach enables rapid and reliable detection of multi-target sequences in single cells, making it powerful for investigating cellular heterogeneity related to cancer diagnosis and treatment.
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Affiliation(s)
- Yizheng Huang
- State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China; College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Linjun Sun
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China; Beijing Key Laboratory of Semiconductor Neural Network Intelligent Sensing and Computing Technology, Beijing, 100083, China
| | - Wenwen Liu
- State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China
| | - Ling Yang
- State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China
| | - Zhigang Song
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China; State Key Laboratory of Superlattices and Microstructures, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China
| | - Xin Ning
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China; Beijing Key Laboratory of Semiconductor Neural Network Intelligent Sensing and Computing Technology, Beijing, 100083, China
| | - Weijun Li
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China; Beijing Key Laboratory of Semiconductor Neural Network Intelligent Sensing and Computing Technology, Beijing, 100083, China
| | - Manqing Tan
- State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China; College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yude Yu
- State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China; College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, 100101, China
| | - Zhao Li
- State Key Laboratory on Integrated Optoelectronics, Institute of Semiconductors, Chinese Academy of Sciences, Beijing, 100083, China; College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China; Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, 100101, China.
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8
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Hu Q, Hu F, Xu D, Zhang K. Numerical Analysis of Droplet Impacting on an Immiscible Liquid via Three-Phase Field Method. MICROMACHINES 2023; 14:mi14050951. [PMID: 37241573 DOI: 10.3390/mi14050951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/15/2023] [Accepted: 04/23/2023] [Indexed: 05/28/2023]
Abstract
In this work, we establish a two-dimensional axisymmetric simulation model to numerically study the impacting behaviors between oil droplets and an immiscible aqueous solution based on the three-phase field method. The numerical model is established by using the commercial software of COMSOL Multiphysics first and then validated by comparing the numerical results with the previous experimental study. The simulation results show that under the impact of oil droplets, a crater will form on the surface of the aqueous solution, which firstly expands and then collapses with the transfer and dissipation of kinetic energy of this three-phase system. As for the droplet, it flattens, spreads, stretches, or immerses on the crater surface and finally achieves an equilibrium state at the gas-liquid interface after experiencing several sinking-bouncing circles. The impacting velocity, fluid density, viscosity, interfacial tension, droplet size, and the property of non-Newtonian fluids all play important roles in the impact between oil droplets and aqueous solution. The conclusions can help to cognize the mechanism of droplet impact on an immiscible fluid and provide useful guidelines for those applications concerning droplet impact.
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Affiliation(s)
- Qingming Hu
- School of Mechtranoics Engineering, Qiqihar University, Qiqihaer 161006, China
- The Engineering Technology Research Center for Precision Manufacturing Equipment and Industrial Perception of Heilongjiang Province, Qiqihar University, Qiqihaer 161006, China
- The Collaborative Innovation Center for Intelligent Manufacturing Equipment Industrialization, Qiqihar University, Qiqihaer 161006, China
| | - Fengshi Hu
- School of Mechtranoics Engineering, Qiqihar University, Qiqihaer 161006, China
| | - Donghui Xu
- School of Mechtranoics Engineering, Qiqihar University, Qiqihaer 161006, China
| | - Kailiang Zhang
- College of Mechanical and Electrical Engineering, Northeast Forestry University, Harbin 150040, China
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9
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Ho V, Baker JR, Willison KR, Barnes PJ, Donnelly LE, Klug DR. Single cell quantification of microRNA from small numbers of non-invasively sampled primary human cells. Commun Biol 2023; 6:458. [PMID: 37100999 PMCID: PMC10133449 DOI: 10.1038/s42003-023-04845-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
Expression levels of microRNAs (miRNAs) in single cells are low and conventional miRNA detection methods require amplification that can be complex, time-consuming, costly and may bias results. Single cell microfluidic platforms have been developed; however, current approaches are unable to absolutely quantify single miRNA molecules expressed in single cells. Herein, we present an amplification-free sandwich hybridisation assay to detect single miRNA molecules in single cells using a microfluidic platform that optically traps and lyses individual cells. Absolute quantification of miR-21 and miR-34a molecules was achieved at a single cell level in human cell lines and validated using real-time qPCR. The sensitivity of the assay was demonstrated by quantifying single miRNA molecules in nasal epithelial cells and CD3+ T-cells, as well as nasal fluid collected non-invasively from healthy individuals. This platform requires ~50 cells or ~30 µL biofluid and can be extended for other miRNA targets therefore it could monitor miRNA levels in disease progression or clinical studies.
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Affiliation(s)
- Vanessa Ho
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Jonathan R Baker
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Keith R Willison
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
| | - Peter J Barnes
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Louise E Donnelly
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK.
| | - David R Klug
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
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10
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Nan L, Mao T, Shum HC. Self-synchronization of reinjected droplets for high-efficiency droplet pairing and merging. MICROSYSTEMS & NANOENGINEERING 2023; 9:24. [PMID: 36910256 PMCID: PMC9995457 DOI: 10.1038/s41378-023-00502-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/10/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Droplet merging serves as a powerful tool to add reagents to moving droplets for biological and chemical reactions. However, unsynchronized droplet pairing impedes high-efficiency merging. Here, we develop a microfluidic design for the self-synchronization of reinjected droplets. A periodic increase in the hydrodynamic resistance caused by droplet blocking a T-junction enables automatic pairing of droplets. After inducing spacing, the paired droplets merge downstream under an electric field. The blockage-based design can achieve a 100% synchronization efficiency even when the mismatch rate of droplet frequencies reaches 10%. Over 98% of the droplets can still be synchronized at nonuniform droplet sizes and fluctuating reinjection flow rates. Moreover, the droplet pairing ratio can be adjusted flexibly for on-demand sample addition. Using this system, we merge two groups of droplets encapsulating enzyme/substrate, demonstrating its capacity to conduct multi-step reactions. We also combine droplet sorting and merging to coencapsulate single cells and single beads, providing a basis for high-efficiency single-cell sequencing. We expect that this system can be integrated with other droplet manipulation systems for a broad range of chemical and biological applications.
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Affiliation(s)
- Lang Nan
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong China
| | - Tianjiao Mao
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Ho Cheung Shum
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong China
- Department of Mechanical Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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11
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Khariton M, McClune CJ, Brower KK, Klemm S, Sattely ES, Fordyce PM, Wang B. Alleviating Cell Lysate-Induced Inhibition to Enable RT-PCR from Single Cells in Picoliter-Volume Double Emulsion Droplets. Anal Chem 2023; 95:935-945. [PMID: 36598332 DOI: 10.1021/acs.analchem.2c03475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Microfluidic droplet assays enable single-cell polymerase chain reaction (PCR) and sequencing analyses at unprecedented scales, with most methods encapsulating cells within nanoliter-sized single emulsion droplets (water-in-oil). Encapsulating cells within picoliter double emulsion (DE) (water-in-oil-in-water) allows sorting droplets with commercially available fluorescence-activated cell sorter (FACS) machines, making it possible to isolate single cells based on phenotypes of interest for downstream analyses. However, sorting DE droplets with standard cytometers requires small droplets that can pass FACS nozzles. This poses challenges for molecular biology, as prior reports suggest that reverse transcription (RT) and PCR amplification cannot proceed efficiently at volumes below 1 nL due to cell lysate-induced inhibition. To overcome this limitation, we used a plate-based RT-PCR assay designed to mimic reactions in picoliter droplets to systematically quantify and ameliorate the inhibition. We find that RT-PCR is blocked by lysate-induced cleavage of nucleic acid probes and primers, which can be efficiently alleviated through heat lysis. We further show that the magnitude of inhibition depends on the cell type, but that RT-PCR can proceed in low-picoscale reaction volumes for most mouse and human cell lines tested. Finally, we demonstrate one-step RT-PCR from single cells in 20 pL DE droplets with fluorescence quantifiable via FACS. These results open up new avenues for improving picoscale droplet RT-PCR reactions and expanding microfluidic droplet-based single-cell analysis technologies.
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Affiliation(s)
- Margarita Khariton
- Department of Bioengineering, Stanford University, Stanford, California94305, United States
| | - Conor J McClune
- Department of Chemical Engineering, Stanford University, Stanford, California94305, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, California94305, United States
| | - Kara K Brower
- Department of Bioengineering, Stanford University, Stanford, California94305, United States
| | - Sandy Klemm
- Department of Genetics, Stanford University, Stanford, California94305, United States
| | - Elizabeth S Sattely
- Department of Chemical Engineering, Stanford University, Stanford, California94305, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, California94305, United States
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, California94305, United States.,Department of Genetics, Stanford University, Stanford, California94305, United States.,ChEM-H Institute, Stanford University, Stanford, California94305, United States.,Chan Zuckerberg Biohub, San Francisco, California94110, United States
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, California94305, United States
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12
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Jiang L, Yang H, Cheng W, Ni Z, Xiang N. Droplet microfluidics for CTC-based liquid biopsy: a review. Analyst 2023; 148:203-221. [PMID: 36508171 DOI: 10.1039/d2an01747d] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Circulating tumor cells (CTCs) are important biomarkers of liquid biopsy. The number and heterogeneity of CTCs play an important role in cancer diagnosis and personalized medicine. However, owing to the low-abundance biomarkers of CTCs, conventional assays are only able to detect CTCs at the population level. Therefore, there is a pressing need for a highly sensitive method to analyze CTCs at the single-cell level. As an important branch of microfluidics, droplet microfluidics is a high-throughput and sensitive single-cell analysis platform for the quantitative detection and heterogeneity analysis of CTCs. In this review, we focus on the quantitative detection and heterogeneity analysis of CTCs using droplet microfluidics. Technologies that enable droplet microfluidics, particularly high-throughput droplet generation and high-efficiency droplet manipulation, are first discussed. Then, recent advances in detecting and analyzing CTCs using droplet microfluidics from the different aspects of nucleic acids, proteins, and metabolites are introduced. The purpose of this review is to provide guidance for the continued study of droplet microfluidics for CTC-based liquid biopsy.
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Affiliation(s)
- Lin Jiang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
| | - Hang Yang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
| | - Weiqi Cheng
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
| | - Zhonghua Ni
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
| | - Nan Xiang
- School of Mechanical Engineering, and Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, Southeast University, Nanjing, 211189, China.
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13
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Jiang Z, Shi H, Tang X, Qin J. Recent advances in droplet microfluidics for single-cell analysis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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14
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Sieskind R, Cortajarena AL, Manteca A. Cell-Free Production Systems in Droplet Microfluidics. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:91-127. [PMID: 37306704 DOI: 10.1007/10_2023_224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The use of cell-free production systems in droplet microfluidic devices has gained significant interest during the last decade. Encapsulating DNA replication, RNA transcription, and protein expression systems in water-in-oil drops allows for the interrogation of unique molecules and high-throughput screening of libraries of industrial and biomedical interest. Furthermore, the use of such systems in closed compartments enables the evaluation of various properties of novel synthetic or minimal cells. In this chapter, we review the latest advances in the usage of the cell-free macromolecule production toolbox in droplets, with a special emphasis on new on-chip technologies for the amplification, transcription, expression, screening, and directed evolution of biomolecules.
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Affiliation(s)
- Rémi Sieskind
- Institut Pasteur, Université de Paris, Unité d'Architecture et de Dynamique des Macromolécules Biologiques, Paris, France
| | - Aitziber L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Aitor Manteca
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain.
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15
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Ahmadi F, Simchi M, Perry JM, Frenette S, Benali H, Soucy JP, Massarweh G, Shih SCC. Integrating machine learning and digital microfluidics for screening experimental conditions. LAB ON A CHIP 2022; 23:81-91. [PMID: 36416045 DOI: 10.1039/d2lc00764a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Digital microfluidics (DMF) has the signatures of an ideal liquid handling platform - as shown through almost two decades of automated biological and chemical assays. However, in the current state of DMF, we are still limited by the number of parallel biological or chemical assays that can be performed on DMF. Here, we report a new approach that leverages design-of-experiment and numerical methodologies to accelerate experimental optimization on DMF. The integration of the one-factor-at-a-time (OFAT) experimental technique with machine learning algorithms provides a set of recommended optimal conditions without the need to perform a large set of experiments. We applied our approach towards optimizing the radiochemistry synthesis yield given the large number of variables that affect the yield. We believe that this work is the first to combine such techniques which can be readily applied to any other assays that contain many parameters and levels on DMF.
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Affiliation(s)
- Fatemeh Ahmadi
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada.
- PERFORM Centre, Concordia University, 7200 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
| | - Mohammad Simchi
- Department of Mechanical & Industrial Engineering, University of Toronto, 5 King's College Rd, Toronto, Ontario, M5S 3G8, Canada
| | - James M Perry
- PERFORM Centre, Concordia University, 7200 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
| | - Stephane Frenette
- PERFORM Centre, Concordia University, 7200 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
| | - Habib Benali
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada.
- PERFORM Centre, Concordia University, 7200 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
| | - Jean-Paul Soucy
- PERFORM Centre, Concordia University, 7200 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, 3801 University Street, Montréal, Québec, H3A 2B4, Canada
| | - Gassan Massarweh
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, 3801 University Street, Montréal, Québec, H3A 2B4, Canada
| | - Steve C C Shih
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada.
- PERFORM Centre, Concordia University, 7200 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
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16
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Liu Y, Wang S, Lyu M, Xie R, Guo W, He Y, Shi X, Wang Y, Qi J, Zhu Q, Zhang H, Luo T, Chen H, Zhu Y, Dong X, Li Z, Gu Y, Liu L, Xu X, Liu Y. Droplet Microfluidics Enables Tracing of Target Cells at the Single-Cell Transcriptome Resolution. Bioengineering (Basel) 2022; 9:674. [PMID: 36354585 PMCID: PMC9687293 DOI: 10.3390/bioengineering9110674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/10/2023] Open
Abstract
The rapid promotion of single-cell omics in various fields has begun to help solve many problems encountered in research, including precision medicine, prenatal diagnosis, and embryo development. Meanwhile, single-cell techniques are also constantly updated with increasing demand. For some specific target cells, the workflow from droplet screening to single-cell sequencing is a preferred option and should reduce the impact of operation steps, such as demulsification and cell recovery. We developed an all-in-droplet method integrating cell encapsulation, target sorting, droplet picoinjection, and single-cell transcriptome profiling on chips to achieve labor-saving monitoring of TCR-T cells. As a proof of concept, in this research, TCR-T cells were encapsulated, sorted, and performed single-cell transcriptome sequencing (scRNA-seq) by injecting reagents into droplets. It avoided the tedious operation of droplet breakage and re-encapsulation between droplet sorting and scRNA-seq. Moreover, convenient device operation will accelerate the progress of chip marketization. The strategy achieved an excellent recovery performance of single-cell transcriptome with a median gene number over 4000 and a cross-contamination rate of 8.2 ± 2%. Furthermore, this strategy allows us to develop a device with high integrability to monitor infused TCR-T cells, which will promote the development of adoptive T cell immunotherapy and their clinical application.
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Affiliation(s)
- Yang Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Shiyu Wang
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Menghua Lyu
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Run Xie
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Weijin Guo
- Department of Biomedical Engineering, Shantou University, Shantou 515063, China
| | - Ying He
- Department of Gynaecological Oncology, Cancer Hospital Chinese Academy of Medical Sciences, Shenzhen Center, Shenzhen 518116, China
| | - Xuyang Shi
- BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Wang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jingyu Qi
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Hui Zhang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Tao Luo
- Department of Mechanical & Electrical Engineering, Xiamen University, Xiamen 361101, China
| | - Huaying Chen
- School of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen, Shenzhen 518055, China
| | - Yonggang Zhu
- School of Mechanical Engineering and Automation, Harbin Institute of Technology, Shenzhen, Shenzhen 518055, China
| | - Xuan Dong
- BGI-Shenzhen, Shenzhen 518083, China
| | - Zida Li
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen 518060, China
| | - Ying Gu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Ya Liu
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen 518100, China
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17
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Thio SK, Park SY. A review of optoelectrowetting (OEW): from fundamentals to lab-on-a-smartphone (LOS) applications to environmental sensors. LAB ON A CHIP 2022; 22:3987-4006. [PMID: 35916120 DOI: 10.1039/d2lc00372d] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Electrowetting-on-dielectric (EWOD) has been extensively explored as an active-type technology for small-scale liquid handling due to its several unique advantages, including no requirement of mechanical components, low power consumption, and rapid response time. However, conventional EWOD devices are often accompanied with complex fabrication processes for patterning and wiring of 2D arrayed electrodes. Furthermore, their sandwich device configuration makes integration with other microfluidic components difficult. More recently, optoelectrowetting (OEW), a light-driven mechanism for effective droplet manipulation, has been proposed as an alternative approach to overcome these issues. By utilizing optical addressing on a photoconductive surface, OEW can dynamically control an electrowetting phenomenon without the need for complex control circuitry on a chip, while providing higher functionality and flexibility. Using commercially available spatial light modulators such as LCD displays and smartphones, millions of optical pixels are readily generated to modulate virtual electrodes for large-scale droplet manipulations in parallel on low-cost OEW devices. The benefits of the OEW mechanism have seen it being variously explored in its potential biological and biochemical applications. This review article presents the fundamentals of OEW, discusses its research progress and limitations, highlights various technological advances and innovations, and finally introduces the emergence of the OEW technology as portable smartphone-integrated environmental sensors.
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Affiliation(s)
- Si Kuan Thio
- Department of Mechanical Engineering, National University of Singapore, 9 Engineering Drive 1, 117575, Singapore
| | - Sung-Yong Park
- Department of Mechanical Engineering, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA.
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18
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Leonaviciene G, Mazutis L. RNA cytometry of single-cells using semi-permeable microcapsules. Nucleic Acids Res 2022; 51:e2. [PMID: 36268865 PMCID: PMC9841424 DOI: 10.1093/nar/gkac918] [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: 07/31/2022] [Revised: 09/23/2022] [Accepted: 10/07/2022] [Indexed: 01/29/2023] Open
Abstract
Analytical tools for gene expression profiling of individual cells are critical for studying complex biological systems. However, the techniques enabling rapid measurements of gene expression on thousands of single-cells are lacking. Here, we report a high-throughput RNA cytometry for digital profiling of single-cells isolated in liquid droplets enveloped by a thin semi-permeable membrane (microcapsules). Due to the selective permeability of the membrane, the desirable enzymes and reagents can be loaded, or replaced, in the microcapsule at any given step by simply changing the reaction buffer in which the microcapsules are dispersed. Therefore, complex molecular biology workflows can be readily adapted to conduct nucleic acid analysis on encapsulated mammalian cells, or other biological species. The microcapsules support sequential multi-step enzymatic reactions and remain intact under different biochemical conditions, freezing, thawing, and thermocycling. Combining microcapsules with conventional FACS provides a high-throughput approach for conducting RNA cytometry of individual cells based on their digital gene expression signature.
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Affiliation(s)
- Greta Leonaviciene
- Institute of Biotechnology, Life Sciences Centre, Vilnius University, 7 Sauletekio av., Vilnius, LT-10257, Lithuania
| | - Linas Mazutis
- To whom correspondence should be addressed. Tel: +370 5 2234356;
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19
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Recent advances in integrated microfluidics for liquid biopsies and future directions. Biosens Bioelectron 2022; 217:114715. [PMID: 36174359 DOI: 10.1016/j.bios.2022.114715] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 07/20/2022] [Accepted: 09/09/2022] [Indexed: 12/12/2022]
Abstract
Liquid biopsies have piqued the interest of researchers as a new tumor diagnosis technique due to their unique benefits of non-invasiveness, sensitivity, and convenience. Recent advances in microfluidic technology have integrated separation, purification, and detection, allowing for high-throughput, high-sensitivity, and high-controllability detection of specific biomarkers in liquid biopsies. With the increasing demand for tumor detection and individualized treatment, new challenges are emerging for the ever-improving microfluidic technology. The state-of-the-art microfluidic design and fabrications have been reviewed in this manuscript, and how this technology can be applied to liquid biopsies from the point of view of the detection process. The primary discussion objectives are circulating tumor cells (CTCs), exosomes, and circulating nucleic acid (ctDNA). Furthermore, the challenges and future direction of microfluidic technology in detecting liquid biomarkers have been discussed.
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20
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Khosla NK, Lesinski JM, Colombo M, Bezinge L, deMello AJ, Richards DA. Simplifying the complex: accessible microfluidic solutions for contemporary processes within in vitro diagnostics. LAB ON A CHIP 2022; 22:3340-3360. [PMID: 35984715 PMCID: PMC9469643 DOI: 10.1039/d2lc00609j] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/15/2022] [Indexed: 05/02/2023]
Abstract
In vitro diagnostics (IVDs) form the cornerstone of modern medicine. They are routinely employed throughout the entire treatment pathway, from initial diagnosis through to prognosis, treatment planning, and post-treatment surveillance. Given the proven links between high quality diagnostic testing and overall health, ensuring broad access to IVDs has long been a focus of both researchers and medical professionals. Unfortunately, the current diagnostic paradigm relies heavily on centralized laboratories, complex and expensive equipment, and highly trained personnel. It is commonly assumed that this level of complexity is required to achieve the performance necessary for sensitive and specific disease diagnosis, and that making something affordable and accessible entails significant compromises in test performance. However, recent work in the field of microfluidics is challenging this notion. By exploiting the unique features of microfluidic systems, researchers have been able to create progressively simple devices that can perform increasingly complex diagnostic assays. This review details how microfluidic technologies are disrupting the status quo, and facilitating the development of simple, affordable, and accessible integrated IVDs. Importantly, we discuss the advantages and limitations of various approaches, and highlight the remaining challenges within the field.
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Affiliation(s)
- Nathan K Khosla
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
| | - Jake M Lesinski
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
| | - Monika Colombo
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
| | - Léonard Bezinge
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
| | - Andrew J deMello
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
| | - Daniel A Richards
- Institute for Chemical and Bioengineering, ETH Zürich, Vladimir Prelog Weg 1, Zürich, 8093, Switzerland.
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21
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Qu F, Zhao L, Li L, Zhao S, Yang M, Yu J, Ho YP. Thermo-Induced Coalescence of Dual Cores in Double Emulsions for Single-Cell RT-PCR. Anal Chem 2022; 94:11670-11678. [PMID: 35968810 DOI: 10.1021/acs.analchem.2c02294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-cell reverse-transcription polymerase chain reaction (RT-PCR) has shown significant promise for transcriptional profiling of heterogeneous cells. However, currently developed microfluidic droplet-based methodologies for single-cell RT-PCR often require complex chip design to accommodate the associated multistep processes as well as customized detection platforms for high-throughput analysis. Herein, we proposed a dual-core double emulsion (DE)-based method to streamline the single-cell RT-PCR through thermo-induced coalescence of the dual cores. The dual-core DEs were produced by pairing two water-in-oil single emulsions containing a single-cell/lysis buffer and RT-PCR mix, respectively. After complete lysis of single cells in one of the cores, the dual-core DEs were merged by gentle heating, made possible by the optimized glycerol concentration present in the cores. Upon the coalescence of dual cores, the alkaline lysis buffer present in the core of the cell lysate was neutralized by the reaction buffer presented in the RT-PCR core, allowing TaqMan assay-based RT-PCR to occur effectively within the DEs. To demonstrate the potential of this streamlined dual-core platform, AKR1B10-positive A549 cells and AKR1B10-negative HEK293 cells were investigated via the TaqMan assay. Subsequently, specific transcript of AKR1B10 was readily available for quantitative profiling at the single-cell level using a commercially available flow cytometer in a high-throughput manner.
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Affiliation(s)
- Fuyang Qu
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China
| | - Liuyang Zhao
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Luoquan Li
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China
| | - Shirui Zhao
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China
| | - Mo Yang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR 999077, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yi-Ping Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China.,Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China.,The Ministry of Education Key Laboratory of Regeneration Medicine, Shatin, New Territories, Hong Kong SAR 999077, China.,Centre for Novel Biomaterials, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR 999077, China
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22
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Calhoun SGK, Brower KK, Suja VC, Kim G, Wang N, McCully AL, Kusumaatmaja H, Fuller GG, Fordyce PM. Systematic characterization of effect of flow rates and buffer compositions on double emulsion droplet volumes and stability. LAB ON A CHIP 2022; 22:2315-2330. [PMID: 35593127 PMCID: PMC9195911 DOI: 10.1039/d2lc00229a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
Double emulsion droplets (DEs) are water/oil/water droplets that can be sorted via fluorescence-activated cell sorting (FACS), allowing for new opportunities in high-throughput cellular analysis, enzymatic screening, and synthetic biology. These applications require stable, uniform droplets with predictable microreactor volumes. However, predicting DE droplet size, shell thickness, and stability as a function of flow rate has remained challenging for monodisperse single core droplets and those containing biologically-relevant buffers, which influence bulk and interfacial properties. As a result, developing novel DE-based bioassays has typically required extensive initial optimization of flow rates to find conditions that produce stable droplets of the desired size and shell thickness. To address this challenge, we conducted systematic size parameterization quantifying how differences in flow rates and buffer properties (viscosity and interfacial tension at water/oil interfaces) alter droplet size and stability, across 6 inner aqueous buffers used across applications such as cellular lysis, microbial growth, and drug delivery, quantifying the size and shell thickness of >22 000 droplets overall. We restricted our study to stable single core droplets generated in a 2-step dripping-dripping formation regime in a straightforward PDMS device. Using data from 138 unique conditions (flow rates and buffer composition), we also demonstrated that a recent physically-derived size law of Wang et al. can accurately predict double emulsion shell thickness for >95% of observations. Finally, we validated the utility of this size law by using it to accurately predict droplet sizes for a novel bioassay that requires encapsulating growth media for bacteria in droplets. This work has the potential to enable new screening-based biological applications by simplifying novel DE bioassay development.
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Affiliation(s)
- Suzanne G K Calhoun
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Kara K Brower
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
| | - Vineeth Chandran Suja
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- School of Engineering and Applied Sciences, Harvard University, MA - 01234, USA
| | - Gaeun Kim
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
| | - Ningning Wang
- School of Energy & Power Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Alexandra L McCully
- Department of Civil & Environmental Engineering, Stanford University, Stanford, CA 94305, USA
| | | | - Gerald G Fuller
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
- ChEM-H Institute, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg BioHub, San Francisco, CA 94158, USA
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23
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Pourabed A, Chakkumpulakkal Puthan Veettil T, Devendran C, Nair P, Wood BR, Alan T. A star shaped acoustofluidic mixer enhances rapid malaria diagnostics via cell lysis and whole blood homogenisation in 2 seconds. LAB ON A CHIP 2022; 22:1829-1840. [PMID: 35380576 DOI: 10.1039/d2lc00195k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Malaria is a life-threatening disease caused by a parasite, which can be transmitted to humans through bites of infected female Anopheles mosquitoes. This disease plagues a significant population of the world, necessitating the need for better diagnostic platforms to enhance the detection sensitivity, whilst reducing processing times, sample volumes and cost. A critical step in achieving improved detection is the effective lysis of blood samples. Here, we propose the use of an acoustically actuated microfluidic mixer for enhanced blood cell lysis. Guided by numerical simulations, we experimentally demonstrate that the device is capable of lysing a 20× dilution of isolated red blood cells (RBCs) with an efficiency of ∼95% within 350 ms (0.1 mL). Further, experimental results show that the device can effectively lyse whole blood irrespective of its dilution factor. Compared to the conventional method of using water, this platform is capable of releasing a larger quantity of haemoglobin into plasma, increasing the efficiency without the need for lysis reagents. The lysis efficiency was validated with malaria infected whole blood samples, resulting in an improved sensitivity as compared to the unlysed infected samples. Partial least squares-regression (PLS-R) analysis exhibits cross-validated R2 values of 0.959 and 0.98 from unlysed and device lysed spectral datasets, respectively. Critically, as expected, the root mean square error of cross validation (RMSECV) value was significantly reduced in the acoustically lysed datasets (RMSECV of 0.97), indicating the improved quantification of parasitic infections compared to unlysed datasets (RMSECV of 1.48). High lysis efficiency and ultrafast processing of very small sample volumes makes the combined acoustofluidic/spectroscopic approach extremely attractive for point-of-care blood diagnosis, especially for detection of neonatal and congenital malaria in babies, for whom a heel prick is often the only option for blood collection.
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Affiliation(s)
- Amir Pourabed
- Department of Mechanical and Aerospace Engineering, Monash University, Melbourne, VIC, Australia.
| | | | - Citsabehsan Devendran
- Department of Mechanical and Aerospace Engineering, Monash University, Melbourne, VIC, Australia.
| | - Prasanna Nair
- Department of Mechanical and Aerospace Engineering, Monash University, Melbourne, VIC, Australia.
- Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Bayden R Wood
- Monash Centre for Biospectroscopy, Department of Chemistry, Monash University, Melbourne, VIC, Australia.
| | - Tuncay Alan
- Department of Mechanical and Aerospace Engineering, Monash University, Melbourne, VIC, Australia.
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24
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Shang L, Ye F, Li M, Zhao Y. Spatial confinement toward creating artificial living systems. Chem Soc Rev 2022; 51:4075-4093. [PMID: 35502858 DOI: 10.1039/d1cs01025e] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lifeforms are regulated by many physicochemical factors, and these factors could be controlled to play a role in the construction of artificial living systems. Among these factors, spatial confinement is an important one, which mediates biological behaviors at multiscale levels and participates in the biomanufacturing processes accordingly. This review describes how spatial confinement, as a fundamental biological phenomenon, provides cues for the construction of artificial living systems. Current knowledge about the role of spatial confinement in mediating individual cell behavior, collective cellular behavior, and tissue-level behavior are categorized. Endeavors on the synthesis of biomacromolecules, artificial cells, engineered tissues, and organoids in spatially confined bioreactors are then emphasized. After that, we discuss the cutting-edge applications of spatially confined artificial living systems in biomedical fields. Finally, we conclude by assessing the remaining challenges and future trends in the context of fundamental science, technical improvement, and practical applications.
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Affiliation(s)
- Luoran Shang
- Department of Rheumatology and Immunology, Institute of Translational Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008, China. .,Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, and the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China
| | - Fangfu Ye
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. .,Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health); Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China.
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
| | - Yuanjin Zhao
- Department of Rheumatology and Immunology, Institute of Translational Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008, China. .,Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health); Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China.
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25
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Chen JJ, Lin ZH. Fabrication of an Oscillating Thermocycler to Analyze the Canine Distemper Virus by Utilizing Reverse Transcription Polymerase Chain Reaction. MICROMACHINES 2022; 13:mi13040600. [PMID: 35457905 PMCID: PMC9026093 DOI: 10.3390/mi13040600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/29/2022] [Accepted: 04/11/2022] [Indexed: 02/04/2023]
Abstract
The reverse transcription-polymerase chain reaction (RT-PCR) has been utilized as an effective tool to diagnose the infectious diseases of viruses. In the present work, the oscillating thermocycler is fabricated and performed to carry out the one-step RT-PCR process successfully. The ribonucleic acid (RNA) mixture is pipetted into the fixed sample volume inside an aluminum reaction block. The sample oscillates the pathway onto the linear motion control system and through the specific RT-PCR heating zones with individual homemade thermal control modules. The present oscillating thermocycler combines the merits of the chamber type and the CF type systems. Before PCR, the reaction chamber moves to the low-temperature zone to complete the RT stage and synthesize the complementary deoxyribonucleic acid (DNA). Next, the low-temperature zone is regulated to the annealing zone. Furthermore, the reactive sample is moved back and forth among three isothermal zones to complete PCR. No extra heating zone is required for the RT stage. The total length of the moving displacement of the chamber is within 100 mm. The miniaturization of the oscillating thermocycler can be expected. In our oscillatory device, the denaturation zone located between the annealing and extension zones is suggested as the appropriate arrangement of the heating blocks. Heat management without thermal cross-talk is easy. Finally, an improved oscillating device is demonstrated to execute the RT-PCR process directly, utilized to amplify the canine distemper virus templates successfully, which could be well applied to a low-cost DNA analysis system in the future.
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26
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Abreu CM, Costa-Silva B, Reis RL, Kundu SC, Caballero D. Microfluidic platforms for extracellular vesicle isolation, analysis and therapy in cancer. LAB ON A CHIP 2022; 22:1093-1125. [PMID: 35253032 DOI: 10.1039/d2lc00006g] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Extracellular vesicles (EVs) are small lipidic particles packed with proteins, DNA, messenger RNA and microRNAs of their cell of origin that act as critical players in cell-cell communication. These vesicles have been identified as pivotal mediators in cancer progression and the formation of metastatic niches. Hence, their isolation and analysis from circulating biofluids is envisioned as the next big thing in the field of liquid biopsies for early non-invasive diagnosis and patient follow-up. Despite the promise, current benchtop isolation strategies are not compatible with point-of-care testing in a clinical setting. Microfluidic platforms are disruptive technologies capable of recovering, analyzing, and quantifying EVs within clinical samples with limited volume, in a high-throughput manner with elevated sensitivity and multiplexing capabilities. Moreover, they can also be employed for the controlled production of synthetic EVs and effective drug loading to produce EV-based therapies. In this review, we explore the use of microfluidic platforms for the isolation, characterization, and quantification of EVs in cancer, and compare these platforms with the conventional methodologies. We also highlight the state-of-the-art in microfluidic approaches for EV-based cancer therapeutics. Finally, we analyze the currently active or recently completed clinical trials involving EVs for cancer diagnosis, treatment or therapy monitoring and examine the future of EV-based point-of-care testing platforms in the clinic and EV-based therapy production by the industry.
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Affiliation(s)
- Catarina M Abreu
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark-Parque da Ciência e Tecnologia, Barco, 4805-017, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Bruno Costa-Silva
- Champalimaud Physiology and Cancer Programme, Champalimaud Foundation, Av. Brasília, 1400-038, Lisbon, Portugal
| | - Rui L Reis
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark-Parque da Ciência e Tecnologia, Barco, 4805-017, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Subhas C Kundu
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark-Parque da Ciência e Tecnologia, Barco, 4805-017, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - David Caballero
- 3B's Research Group, I3Bs - Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, AvePark-Parque da Ciência e Tecnologia, Barco, 4805-017, Guimarães, Portugal.
- ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
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27
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Liu Y, Li R, Zhang L, Guo S. Nanomaterial-Based Immunocapture Platforms for the Recognition, Isolation, and Detection of Circulating Tumor Cells. Front Bioeng Biotechnol 2022; 10:850241. [PMID: 35360401 PMCID: PMC8964261 DOI: 10.3389/fbioe.2022.850241] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/18/2022] [Indexed: 01/10/2023] Open
Abstract
Circulating tumor cells (CTCs) are a type of cancer cells that circulate in the peripheral blood after breaking away from solid tumors and are essential for the establishment of distant metastasis. Up to 90% of cancer-related deaths are caused by metastatic cancer. As a new type of liquid biopsy, detecting and analyzing CTCs will provide insightful information for cancer diagnosis, especially the in-time disease status, which would avoid some flaws and limitations of invasive tissue biopsy. However, due to the extremely low levels of CTCs among a large number of hematologic cells, choosing immunocapture platforms for CTC detection and isolation will achieve good performance with high purity, selectivity, and viability. These properties are directly associated with precise downstream analysis of CTC profiling. Recently, inspired by the nanoscale interactions of cells in the tissue microenvironment, platforms based on nanomaterials have been widely explored to efficiently enrich and sensitively detect CTCs. In this review, various immunocapture platforms based on different nanomaterials for efficient isolation and sensitive detection of CTCs are outlined and discussed. First, the design principles of immunoaffinity nanomaterials are introduced in detail. Second, the immunocapture and release of platforms based on nanomaterials ranging from nanoparticles, nanostructured substrates, and immunoaffinity microfluidic chips are summarized. Third, recent advances in single-cell release and analysis of CTCs are introduced. Finally, some perspectives and challenges are provided in future trends of CTC studies.
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Affiliation(s)
- Yichao Liu
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Rui Li
- Xinjiang Key Laboratory of Solid State Physics and Devices, Xinjiang University, Urumqi, China
| | - Lingling Zhang
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- *Correspondence: Lingling Zhang, ; Shishang Guo,
| | - Shishang Guo
- Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
- *Correspondence: Lingling Zhang, ; Shishang Guo,
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28
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Chakraborty S, Luchena C, Elton JJ, Schilling MP, Reischl M, Roux M, Levkin PA, Popova AA. "Cells-to-cDNA on Chip": Phenotypic Assessment and Gene Expression Analysis from Live Cells in Nanoliter Volumes Using Droplet Microarrays. Adv Healthc Mater 2022; 11:e2102493. [PMID: 35285171 DOI: 10.1002/adhm.202102493] [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: 11/15/2021] [Revised: 02/08/2022] [Indexed: 11/11/2022]
Abstract
In vitro cell-based experiments are particularly important in fundamental biological research. Microscopy-based readouts to identify cellular changes in response to various stimuli are a popular choice, but gene expression analysis is essential to delineate the underlying molecular dynamics in cells. However, cell-based experiments often suffer from interexperimental variation, especially while using different readout methods. Therefore, establishment of platforms that allow for cell screening, along with parallel investigations of morphological features, as well as gene expression levels, is crucial. The droplet microarray (DMA) platform enables cell screening in hundreds of nanoliter droplets. In this study, a "Cells-to-cDNA on Chip" method is developed enabling on-chip mRNA isolation from live cells and conversion to cDNA in individual droplets of 200 nL. This novel method works efficiently to obtain cDNA from different cell numbers, down to single cell per droplet. This is the first established miniaturized on-chip strategy that enables the entire course of cell screening, phenotypic microscopy-based assessments along with mRNA isolation and its conversion to cDNA for gene expression analysis by real-time PCR on an open DMA platform. The principle demonstrated in this study sets a beginning for myriad of possible applications to obtain detailed information about the molecular dynamics in cultured cells.
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Affiliation(s)
- Shraddha Chakraborty
- Institute of Biological and Chemical Systems‐Functional Molecular Systems Karlsruhe Institute of Technology Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
| | - Charlotte Luchena
- Institute of Biological and Chemical Systems‐Functional Molecular Systems Karlsruhe Institute of Technology Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
| | - Jonathan J. Elton
- Institute of Biological and Chemical Systems‐Functional Molecular Systems Karlsruhe Institute of Technology Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
| | - Marcel P. Schilling
- Institute for Automation and Applied Informatics Karlsruhe Institute of Technology Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
| | - Markus Reischl
- Institute for Automation and Applied Informatics Karlsruhe Institute of Technology Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
| | - Margaux Roux
- Cellenion SASU Bioserra 2, 60 avenue Rockefeller Lyon 69008 France
| | - Pavel A. Levkin
- Institute of Biological and Chemical Systems‐Functional Molecular Systems Karlsruhe Institute of Technology Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
- Institute of Organic Chemistry Karlsruhe Institute of Technology Fritz‐Haber Weg 6 Karlsruhe 76131 Germany
| | - Anna A. Popova
- Institute of Biological and Chemical Systems‐Functional Molecular Systems Karlsruhe Institute of Technology Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
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29
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Jing W, Han HS. Inertial Self-Assembly Dynamics of Interacting Droplet Ensembles in Microfluidic Flows. Anal Chem 2022; 94:3978-3986. [PMID: 35195992 DOI: 10.1021/acs.analchem.1c05116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The multiphase flow of droplets is widespread and used for both biological and nonbiological applications alike. However, the ensemble interactions of such systems are inherently nonlinear and complex, compounded by interfacial effects, making it a difficult many-body problem. In comparison, the self-assembly dynamics of solid particles in flow have long been studied and exploited in the field of inertial microfluidics. Here, we report novel self-assembly dynamics of liquid drops in microfluidic channels that contrast starkly with the established paradigm of inertial microfluidics, which stipulates that higher inertia leads to better spatial ordering. Instead, we find that ordering can be negatively correlated with inertia, while Dean flow can achieve long-range spatial periodicity on length scales at least 3 orders of magnitude greater than the drop diameter. Experimentally, we decouple droplet generation from ordering, enabling independent and systematic variation of key parameters, especially in ranges practical to droplet microfluidics. We find the inertia-dependent emergence of preferred drop separations and show that surfactant effects can influence the longitudinal ordering of multidrop arrays. The dynamics we describe have immediate utility to droplet microfluidics, where the ability to order drops is key to the streamlined integration of on-chip incubation with deterministic drop manipulation downstream─two important functions for biological assays. To this end, we demonstrate the use of passive inertial drop self-assembly to combine a delay line with picoinjection. These results not only present a largely unexplored direction for inertial microfluidics but also show the practical benefit of its unification with the versatile field of droplet microfluidics.
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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 W. Gregory Dr, Urbana, Illinois 61801, United States
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30
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Liu D, Sun M, Zhang J, Hu R, Fu W, Xuanyuan T, Liu W. Single-cell droplet microfluidics for biomedical applications. Analyst 2022; 147:2294-2316. [DOI: 10.1039/d1an02321g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review focuses on the recent advances in the fundamentals of single-cell droplet microfluidics and its applications in biomedicine, providing insights into design and establishment of single-cell microsystems and their further performance.
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Affiliation(s)
- Dan Liu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Meilin Sun
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Jinwei Zhang
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Rui Hu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Wenzhu Fu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Tingting Xuanyuan
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Wenming Liu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
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31
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Amirifar L, Besanjideh M, Nasiri R, Shamloo A, Nasrollahi F, de Barros NR, Davoodi E, Erdem A, Mahmoodi M, Hosseini V, Montazerian H, Jahangiry J, Darabi MA, Haghniaz R, Dokmeci MR, Annabi N, Ahadian S, Khademhosseini A. Droplet-based microfluidics in biomedical applications. Biofabrication 2021; 14. [PMID: 34781274 DOI: 10.1088/1758-5090/ac39a9] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/15/2021] [Indexed: 11/11/2022]
Abstract
Droplet-based microfluidic systems have been employed to manipulate discrete fluid volumes with immiscible phases. Creating the fluid droplets at microscale has led to a paradigm shift in mixing, sorting, encapsulation, sensing, and designing high throughput devices for biomedical applications. Droplet microfluidics has opened many opportunities in microparticle synthesis, molecular detection, diagnostics, drug delivery, and cell biology. In the present review, we first introduce standard methods for droplet generation (i.e., passive and active methods) and discuss the latest examples of emulsification and particle synthesis approaches enabled by microfluidic platforms. Then, the applications of droplet-based microfluidics in different biomedical applications are detailed. Finally, a general overview of the latest trends along with the perspectives and future potentials in the field are provided.
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Affiliation(s)
- Leyla Amirifar
- Mechanical Engineering, Sharif University of Technology, Tehran, Iran, Tehran, 11365-11155, Iran (the Islamic Republic of)
| | - Mohsen Besanjideh
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Tehran, 11365-11155, Iran (the Islamic Republic of)
| | - Rohollah Nasiri
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Tehran, 11365-11155, Iran (the Islamic Republic of)
| | - Amir Shamloo
- Department of Mechanical Engineering, Sharif University of Technology, Tehran, Tehran, 11365-11155, Iran (the Islamic Republic of)
| | | | - Natan Roberto de Barros
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, Los Angeles, 90024, UNITED STATES
| | - Elham Davoodi
- Bioengineering, University of California - Los Angeles, Los Angeles, Los Angeles, 90095, UNITED STATES
| | - Ahmet Erdem
- Bioengineering, University of California - Los Angeles, Los Angeles, Los Angeles, 90095, UNITED STATES
| | | | - Vahid Hosseini
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, Los Angeles, 90024, UNITED STATES
| | - Hossein Montazerian
- Bioengineering, University of California - Los Angeles, Los Angeles, Los Angeles, 90095, UNITED STATES
| | - Jamileh Jahangiry
- University of California - Los Angeles, Los Angeles, Los Angeles, 90095, UNITED STATES
| | | | - Reihaneh Haghniaz
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, Los Angeles, 90024, UNITED STATES
| | - Mehmet R Dokmeci
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, Los Angeles, 90024, UNITED STATES
| | - Nasim Annabi
- Chemical Engineering, UCLA, Los Angeles, Los Angeles, California, 90095, UNITED STATES
| | - Samad Ahadian
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, Los Angeles, 90024, UNITED STATES
| | - Ali Khademhosseini
- Terasaki Institute for Biomedical Innovation (TIBI), Los Angeles, Los Angeles, 90024, UNITED STATES
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32
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Hu B, Ye S, Chen D, Xie B, Hu R, Qiao Y, Yu Y, Yu H, Zheng X, Lan Y, Du W. Tunable and Contamination-Free Injection with Microfluidics by Stepinjection. Anal Chem 2021; 93:13112-13117. [PMID: 34546041 DOI: 10.1021/acs.analchem.1c02721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Droplet microfluidics with picoinjection provides significant advantages to multistep reactions and screenings. The T-junction design for picoinjection is convenient in adding picoliter reagents into passing droplets to initiate reactions. However, conventional picoinjectors face difficulties in eliminating cross-contamination between droplets, preventing them from widespread use in sensitive biological and molecular assays. Here, we introduce stepinjection, which uses a T-junction with a stepped channel design to elevate the diffusional buffer zone into the main channel and consequently increases the pressure difference between droplets and the inlet of the injection channel. To demonstrate the stepinjector's ability to perform contamination-sensitive enzymatic assays, we inject casein fluorescein isothiocyanate (FITC-casein) into a mixture of savinase and savinase-free (labeled with a red fluorescent dye) droplets. We observe no cross-contamination using stepinjection but find a severe cross-talk using an optimal picoinjection design. We envision that the simple, tunable, and reliable stepinjector can be easily integrated in various droplet processing devices, and facilitate various biomedical and biochemical applications including multiplex digital PCR, single-cell sequencing, and enzymatic screening.
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Affiliation(s)
- Beiyu Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China.,State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shun Ye
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Biomedical Engineering Department, College of Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Dongwei Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bingliang Xie
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ran Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuxin Qiao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanghuan Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haiyan Yu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xu Zheng
- State Key Laboratory of Nonlinear Mechanics, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China
| | - Ying Lan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 100049, China.,State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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33
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Li C, Gong Y, Wang X, Xu J, Ma B. Integrated Addressable Dynamic Droplet Array (aDDA) as Sub-Nanoliter Reactors for High-Coverage Genome Sequencing of Single Yeast Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2100325. [PMID: 34296526 DOI: 10.1002/smll.202100325] [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: 01/18/2021] [Revised: 06/25/2021] [Indexed: 06/13/2023]
Abstract
An addressable dynamic droplet array (aDDA) is presented that combines the advantages of static droplet arrays and continuous-flow droplet platforms. Modular fabrication is employed to create a self-contained integrated aDDA. All the sample preparation steps, including single-cell isolation, cell lysis, amplification, and product retrieval, are performed in sequence within a sub-nanoliter (≈300 pL) droplet. Sequencing-based validation suggests that aDDA reduces the amplification bias of multiple displacement amplification (MDA) and elevates the percentage of one-yeast-cell genome recovery to 91%, as compared to the average of 26% using conventional, 20 µL volume MDA reactions. Thus, aDDA is a valuable addition to the toolbox for high-genome-coverage sequencing of single microbial cells.
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Affiliation(s)
- Chunyu Li
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, China
| | - Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, China
| | - Xixian Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, China
| | - Bo Ma
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, China
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34
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Shi N, Mohibullah M, Easley CJ. Active Flow Control and Dynamic Analysis in Droplet Microfluidics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:133-153. [PMID: 33979546 PMCID: PMC8956363 DOI: 10.1146/annurev-anchem-122120-042627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Droplet-based microfluidics has emerged as an important subfield within the microfluidic and general analytical communities. Indeed, several unique applications such as digital assay readout and single-cell sequencing now have commercial systems based on droplet microfluidics. Yet there remains room for this research area to grow. To date, most analytical readouts are optical in nature, relatively few studies have integrated sample preparation, and passive means for droplet formation and manipulation have dominated the field. Analytical scientists continue to expand capabilities by developing droplet-compatible method adaptations, for example, by interfacing to mass spectrometers or automating droplet sampling for temporally resolved analysis. In this review, we highlight recently developed fluidic control techniques and unique integrations of analytical methodology with droplet microfluidics-focusing on automation and the connections to analog/digital domains-and we conclude by offering a perspective on current challenges and future applications.
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Affiliation(s)
- Nan Shi
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA;
| | - Md Mohibullah
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA;
| | - Christopher J Easley
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA;
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35
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Chen S, Zhao J, Xu C, Sakharov IY, Zhao S. Absolute Quantification of MicroRNAs in a Single Cell with Chemiluminescence Detection Based on Rolling Circle Amplification on a Microchip Platform. Anal Chem 2021; 93:9218-9225. [PMID: 34128642 DOI: 10.1021/acs.analchem.1c01463] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The absolute quantification of miRNAs in a single cell allows to better understand the heterogeneity of cells and the relationship between miRNAs and diseases. However, seldom methods for miRNA quantification in a single cell have been reported because the miRNA content in a single cell is very low. Herein, an ultrasensitive chemiluminescence assay strategy based on rolling circle amplification (RCA) on a microchip platform was proposed for the absolute quantification of miRNAs in a single cell. In this strategy, a ring probe with specificity was designed and synthesized, which could perform RCA for target miRNAs to improve the sensitivity and satisfy the need of absolute quantification of miRNAs in a single cell. The 20 liver cancer cells (HepG2) and 20 normal liver cells (HL-7702) were analyzed using this method; it is found that the miRNA-21 contents varied among cells, and miRNA-21 was overexpressed in HepG2 cells. Compared with traditional methods, the proposed strategy has many advantages such as low cost, simple operation, short analysis time, good specificity, and lower probability of false positives. This method is expected to be one of the powerful tools for the absolute quantification of miRNAs in a single cell.
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Affiliation(s)
- Shengyu Chen
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China
| | - Jingjin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China
| | - Chunhuan Xu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China
| | - Ivan Yu Sakharov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory, Bldg.1, Moscow 119991, Russia
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, Guilin 541004, China
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36
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Ma Z, Zhao H, Shi L, Yu D, Guo X. Automatic medium exchange for micro-volume cell samples based on dielectrophoresis. Electrophoresis 2021; 42:1507-1515. [PMID: 33990980 DOI: 10.1002/elps.202000195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 03/27/2021] [Accepted: 04/20/2021] [Indexed: 11/06/2022]
Abstract
Cell medium exchange is a crucial step for life science and medicine. However, conventional cell medium exchange methods, including centrifuging and filtering, show limited ability for micro-volume cell samples such as circulating tumor cell (CTC) and circulating fetal cell (CFC). In this paper, we proposed an automatic medium exchange method for micro-volume cell samples based on dielectrophoresis (DEP) in microfluidic chip. Fresh medium and cell suspension were introduced into the microfluidic channel as the laminar flow. Plane stair-shaped interdigital electrodes were employed to drive the cells from the cell suspension to fresh media directly by DEP force. Additionally, we characterized and optimized the cell medium exchange according to both the theory and experiments. In the end, we achieved a 96.9% harvest rate of medium exchange for 0.3 μL samples containing micro-volume cells. For implementing an automatic continuous cell medium exchange, the proposed method can be integrated into the automatic cell processing system conveniently. Furthermore, the proposed method is a great candidate in micro-volume cell analysis and processing, cell electroporation, single cell sequencing, and other scenarios.
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Affiliation(s)
- Zhouyang Ma
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
| | - Hongwang Zhao
- School of Automobile and Traffic Engineering, Guilin University of Aerospace Technology, Guilin, Guangxi, P. R. China
| | - Liujia Shi
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, P. R. China
| | - Duli Yu
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China.,Beijing Advance Innovation Center for Soft Matter Science and Engineering, Beijing, P. R. China
| | - Xiaoliang Guo
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, P. R. China
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37
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Review of Microfluidic Methods for Cellular Lysis. MICROMACHINES 2021; 12:mi12050498. [PMID: 33925101 PMCID: PMC8145176 DOI: 10.3390/mi12050498] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/18/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023]
Abstract
Cell lysis is a process in which the outer cell membrane is broken to release intracellular constituents in a way that important information about the DNA or RNA of an organism can be obtained. This article is a thorough review of reported methods for the achievement of effective cellular boundaries disintegration, together with their technological peculiarities and instrumental requirements. The different approaches are summarized in six categories: chemical, mechanical, electrical methods, thermal, laser, and other lysis methods. Based on the results derived from each of the investigated reports, we outline the advantages and disadvantages of those techniques. Although the choice of a suitable method is highly dependent on the particular requirements of the specific scientific problem, we conclude with a concise table where the benefits of every approach are compared, based on criteria such as cost, efficiency, and difficulty.
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38
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Ma J, Tran G, Wan AMD, Young EWK, Kumacheva E, Iscove NN, Zandstra PW. Microdroplet-based one-step RT-PCR for ultrahigh throughput single-cell multiplex gene expression analysis and rare cell detection. Sci Rep 2021; 11:6777. [PMID: 33762663 PMCID: PMC7990930 DOI: 10.1038/s41598-021-86087-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/10/2021] [Indexed: 01/31/2023] Open
Abstract
Gene expression analysis of individual cells enables characterization of heterogeneous and rare cell populations, yet widespread implementation of existing single-cell gene analysis techniques has been hindered due to limitations in scale, ease, and cost. Here, we present a novel microdroplet-based, one-step reverse-transcriptase polymerase chain reaction (RT-PCR) platform and demonstrate the detection of three targets simultaneously in over 100,000 single cells in a single experiment with a rapid read-out. Our customized reagent cocktail incorporates the bacteriophage T7 gene 2.5 protein to overcome cell lysate-mediated inhibition and allows for one-step RT-PCR of single cells encapsulated in nanoliter droplets. Fluorescent signals indicative of gene expressions are analyzed using a probabilistic deconvolution method to account for ambient RNA and cell doublets and produce single-cell gene signature profiles, as well as predict cell frequencies within heterogeneous samples. We also developed a simulation model to guide experimental design and optimize the accuracy and precision of the assay. Using mixtures of in vitro transcripts and murine cell lines, we demonstrated the detection of single RNA molecules and rare cell populations at a frequency of 0.1%. This low cost, sensitive, and adaptable technique will provide an accessible platform for high throughput single-cell analysis and enable a wide range of research and clinical applications.
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Affiliation(s)
- Jennifer Ma
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
| | - Gary Tran
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Alwin M D Wan
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, M5S 3G8, Canada
| | - Edmond W K Young
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, M5S 3G8, Canada
| | - Eugenia Kumacheva
- Institute of Biomedical Engineering, University of Toronto, Toronto, ON, M5S 3G9, Canada
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, ON, M5S 3G8, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6, Canada
| | - Norman N Iscove
- Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Peter W Zandstra
- School of Biomedical Engineering, University of British Columbia, 2222 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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39
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Loveday EK, Zath GK, Bikos DA, Jay ZJ, Chang CB. Screening of Additive Formulations Enables Off-Chip Drop Reverse Transcription Quantitative Polymerase Chain Reaction of Single Influenza A Virus Genomes. Anal Chem 2021; 93:4365-4373. [PMID: 33635052 PMCID: PMC10016143 DOI: 10.1021/acs.analchem.0c03455] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The miniaturization of polymerase chain reaction (PCR) using drop-based microfluidics allows for amplification of single nucleic acids in aqueous picoliter-sized drops. Accurate data collection during PCR requires that drops remain stable to coalescence during thermocycling and drop contents are retained. Following systematic testing of known PCR additives, we identified an optimized formulation of 1% w/v Tween-20, 0.8 μg/μL bovine serum albumin, 1 M betaine in the aqueous phase, and 3 wt % (w/w) of the polyethylene glycol-perfluoropolyether2 surfactant in the oil phase of 50 μm diameter drops that maintains drop stability and prevents dye transport. This formulation enables a method we call off-chip drop reverse transcription quantitative PCR (OCD RT-qPCR) in which drops are thermocycled in a qPCR machine and sampled at various cycle numbers "off-chip", or outside of a microfluidic chip. qPCR amplification curves constructed from hundreds of individual drops using OCD RT-qPCR and imaged using epifluorescence microscopy correlate with amplification curves of ≈300,000 drops thermocycled using a qPCR machine. To demonstrate the utility of OCD RT-qPCR, influenza A virus (IAV) RNA was detected down to a single viral genome copy per drop, or 0.320 cpd. This work was extended to perform multiplexed detection of IAV M gene RNA and cellular β-actin DNA in drops, and direct amplification of IAV genomes from infected cells without a separate RNA extraction step. The optimized additive formulation and the OCD-qPCR method allow for drop-based RT-qPCR without complex devices and demonstrate the ability to quantify individual or rare nucleic acid species within drops with minimal processing.
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Affiliation(s)
- Emma Kate Loveday
- Center for Biofilm Engineering and the Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana 59717, United States
| | - Geoffrey K Zath
- Center for Biofilm Engineering and the Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana 59717, United States
| | - Dimitri A Bikos
- Center for Biofilm Engineering and the Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana 59717, United States
| | - Zackary J Jay
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Connie B Chang
- Center for Biofilm Engineering and the Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana 59717, United States
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40
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Affiliation(s)
- Keke Hu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Tho D. K. Nguyen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Stefania Rabasco
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Pieter E. Oomen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
- ParaMedir B.V., 1e Energieweg 13, 9301 LK Roden, The Netherlands
| | - Andrew G. Ewing
- Department of Chemistry and Molecular Biology, University of Gothenburg, Kemivägen 10, 41296 Gothenburg, Sweden
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41
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Cavett V, Paegel BM. Multiplexed Enzyme Activity-Based Probe Display via Hybridization. ACS COMBINATORIAL SCIENCE 2020; 22:579-585. [PMID: 32803953 DOI: 10.1021/acscombsci.0c00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Emulsions offer the means to miniaturize and parallelize high-throughput screening but require a robust method to localize activity-based fluorescent probes in each droplet. Multiplexing probes in droplets is impractical, though highly desirable for identifying library members that possess very specific activity. Here, we present multiplexed probe immobilization on library beads for emulsion screening. During library bead preparation, we quantitated ∼106 primers per bead by fluorescence in situ hybridization, however emulsion PCR yielded only ∼103 gene copies per bead. We leveraged the unextended bead-bound primers to hybridize complementary probe-oligonucleotide heteroconjugates to the library beads. The probe-hybridized bead libraries were then used to program emulsion in vitro transcription/translation reactions and analyzed by FACS to perform multiplexed activity-based screening of trypsin and chymotrypsin mutant libraries for novel proteolytic specificity. The approach's modularity should permit a high degree of probe multiplexing and appears extensible to other enzyme classes and library types.
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Affiliation(s)
- Valerie Cavett
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92617, United States
| | - Brian M. Paegel
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92617, United States
- Departments of Chemistry & Biomedical Engineering, University of California, Irvine, California 92617, United States
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42
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Mutafopulos K, Lu PJ, Garry R, Spink P, Weitz DA. Selective cell encapsulation, lysis, pico-injection and size-controlled droplet generation using traveling surface acoustic waves in a microfluidic device. LAB ON A CHIP 2020; 20:3914-3921. [PMID: 32966482 DOI: 10.1039/d0lc00723d] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We generate droplets in a microfluidic device using a traveling surface acoustic wave (TSAW), and control droplet size by adjusting TSAW power and duration. We combine droplet production and fluorescence detection to selectively-encapsulate cells and beads; with this active method, the overwhelming majority of single particles or cells are encapsulated individually into droplets, contrasting the Poisson distribution of encapsulation number that governs traditional, passive microfluidic encapsulation. In addition, we lyse cells before selective encapsulation, and pico-inject new materials into existing droplets.
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Affiliation(s)
- Kirk Mutafopulos
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.
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43
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Clark IC, Delley CL, Sun C, Thakur R, Stott SL, Thaploo S, Li Z, Quintana FJ, Abate AR. Targeted Single-Cell RNA and DNA Sequencing With Fluorescence-Activated Droplet Merger. Anal Chem 2020; 92:14616-14623. [PMID: 33049138 PMCID: PMC8182774 DOI: 10.1021/acs.analchem.0c03059] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Analyzing every cell in a diverse sample provides insight into population-level heterogeneity, but abundant cell types dominate the analysis and rarer populations are scarcely represented in the data. To focus on specific cell types, the current paradigm is to physically isolate subsets of interest prior to analysis; however, it remains difficult to isolate and then single-cell sequence such populations because of compounding losses. Here, we describe an alternative approach that selectively merges cells with reagents to achieve enzymatic reactions without having to physically isolate cells. We apply this technique to perform single-cell transcriptome and genome sequencing of specific cell subsets. Our method for analyzing heterogeneous populations obviates the need for pre- or post-enrichment and simplifies single-cell workflows, making it useful for other applications in single-cell biology, combinatorial chemical synthesis, and drug screening.
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Affiliation(s)
- Iain C Clark
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Cyrille L Delley
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Chen Sun
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Rohan Thakur
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Shannon L Stott
- Center for Engineering in Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Shravan Thaploo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Zhaorong Li
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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44
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Li J, Weng X, Mo F, Han M, Li H. Superparamagnetic Nanostructures Coupled with an Entropy-Driven DNA Circuit for Elegant and Robust Photoelectrochemical Biosensing. Anal Chem 2020; 92:15145-15151. [DOI: 10.1021/acs.analchem.0c03580] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jing Li
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Xuan Weng
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Fan Mo
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Min Han
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, PR China
| | - Hongbo Li
- School of Chemistry and Chemical Engineering, Yancheng Institute of Technology, Yancheng 224051, PR China
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45
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Zhuang J, Huo Q, Yang F, Xie N. Perspectives on the Role of Histone Modification in Breast Cancer Progression and the Advanced Technological Tools to Study Epigenetic Determinants of Metastasis. Front Genet 2020; 11:603552. [PMID: 33193750 PMCID: PMC7658393 DOI: 10.3389/fgene.2020.603552] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022] Open
Abstract
Metastasis is a complex process that involved in various genetic and epigenetic alterations during the progression of breast cancer. Recent evidences have indicated that the mutation in the genome sequence may not be the key factor for increasing metastatic potential. Epigenetic changes were revealed to be important for metastatic phenotypes transition with the development in understanding the epigenetic basis of breast cancer. Herein, we aim to present the potential epigenetic drivers that induce dysregulation of genes related to breast tumor growth and metastasis, with a particular focus on histone modification including histone acetylation and methylation. The pervasive role of major histone modification enzymes in cancer metastasis such as histone acetyltransferases (HAT), histone deacetylases (HDACs), DNA methyltransferases (DNMTs), and so on are demonstrated and further discussed. In addition, we summarize the recent advances of next-generation sequencing technologies and microfluidic-based devices for enhancing the study of epigenomic landscapes of breast cancer. This feature also introduces several important biotechnologists for identifying robust epigenetic biomarkers and enabling the translation of epigenetic analyses to the clinic. In summary, a comprehensive understanding of epigenetic determinants in metastasis will offer new insights of breast cancer progression and can be achieved in the near future with the development of innovative epigenomic mapping tools.
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Affiliation(s)
- Jialang Zhuang
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qin Huo
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Fan Yang
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Ni Xie
- Biobank, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
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46
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High-throughput screening for high-efficiency small-molecule biosynthesis. Metab Eng 2020; 63:102-125. [PMID: 33017684 DOI: 10.1016/j.ymben.2020.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/14/2023]
Abstract
Systems metabolic engineering faces the formidable task of rewiring microbial metabolism to cost-effectively generate high-value molecules from a variety of inexpensive feedstocks for many different applications. Because these cellular systems are still too complex to model accurately, vast collections of engineered organism variants must be systematically created and evaluated through an enormous trial-and-error process in order to identify a manufacturing-ready strain. The high-throughput screening of strains to optimize their scalable manufacturing potential requires execution of many carefully controlled, parallel, miniature fermentations, followed by high-precision analysis of the resulting complex mixtures. This review discusses strategies for the design of high-throughput, small-scale fermentation models to predict improved strain performance at large commercial scale. Established and promising approaches from industrial and academic groups are presented for both cell culture and analysis, with primary focus on microplate- and microfluidics-based screening systems.
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47
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Zhu H, Zhang H, Ni S, Korabečná M, Yobas L, Neuzil P. The vision of point-of-care PCR tests for the COVID-19 pandemic and beyond. Trends Analyt Chem 2020; 130:115984. [PMID: 32834243 PMCID: PMC7369599 DOI: 10.1016/j.trac.2020.115984] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Infectious diseases, such as the most recent case of coronavirus disease 2019, have brought the prospect of point-of-care (POC) diagnostic tests into the spotlight. A rapid, accurate, low-cost, and easy-to-use test in the field could stop epidemics before they develop into full-blown pandemics. Unfortunately, despite all the advances, it still does not exist. Here, we critically review the limited number of prototypes demonstrated to date that is based on a polymerase chain reaction (PCR) and has come close to fulfill this vision. We summarize the requirements for the POC-PCR tests and then go on to discuss the PCR product-detection methods, the integration of their functional components, the potential applications, and other practical issues related to the implementation of lab-on-a-chip technologies. We conclude our review with a discussion of the latest findings on nucleic acid-based diagnosis.
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Affiliation(s)
- Hanliang Zhu
- Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072 Shaanxi, PR China
| | - Haoqing Zhang
- Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072 Shaanxi, PR China
| | - Sheng Ni
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, S.A.R., PR China
| | - Marie Korabečná
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine, Charles University and General University Hospital in Prague, Albertov 4, Prague 2, Czech Republic
| | - Levent Yobas
- Department of Electronic and Computer Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, S.A.R., PR China,Corresponding author
| | - Pavel Neuzil
- Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072 Shaanxi, PR China,CEITEC Brno University of Technology, Purkyňova 123, 612 00 Brno, Czech Republic,Faculty of Electrical Engineering and Communications, Brno University of Technology, Technická 3058/10, 616 00 Brno, Czech Republic,Corresponding author. Department of Microsystem Engineering, School of Mechanical Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072 Shaanxi, PR China
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48
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Bae J, Ju J, Kim D, Kim T. Double-Sided Microwells with a Stepped Through-Hole Membrane for High-Throughput Microbial Assays. Anal Chem 2020; 92:9501-9510. [PMID: 32571023 DOI: 10.1021/acs.analchem.0c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To improve the throughput of microwell arrays for identifying immense cellular diversities even at a single-bacteria level, further miniaturization or densification of the microwells has been an obvious breakthrough. However, controlling millions of nanoliter samples or more at the microscale remains technologically difficult and has been spatially restricted to a single open side of the microwells. Here we employed a stepped through-hole membrane to utilize the bottom as well as top side of a high-density nanoliter microwell array, thus improving spatial efficiency. The stepped structure shows additional effectiveness for handling several millions of nanoliter bacterial samples in the overall perspectives of controllability, throughput, simplicity, versatility, and automation by using novel methods for three representative procedures in bacterial assays: partitioning cells, manipulating the chemical environment, and extracting selected cells. As a potential application, we show proof-of-concept isolation of rare cells in a mixed ratio of 1 to around 106 using a single chip. Our device can be further applied to various biological studies pertaining to synthetic biology, drug screening, mutagenesis, and single-cell heterogeneity.
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Affiliation(s)
- Juyeol Bae
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Janghyun Ju
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Dahyun Kim
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
| | - Taesung Kim
- Department of Mechanical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea.,Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulsan 44919, Republic of Korea
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49
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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.
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Affiliation(s)
- Kara K Brower
- Department of Bioengineering, Stanford University, Stanford, California, USA.
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50
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Xu Y, Doonan SR, Ordog T, Bailey RC. Translational Opportunities for Microfluidic Technologies to Enable Precision Epigenomics. Anal Chem 2020; 92:7989-7997. [PMID: 32496751 DOI: 10.1021/acs.analchem.0c01288] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Personalizing health care by taking genetic, environmental, and lifestyle factors into account is central to modern medicine. The crucial and pervasive roles epigenetic factors play in shaping gene-environment interactions are now well recognized. However, identifying robust epigenetic biomarkers and translating them to clinical tests has been difficult due in part to limitations of available platforms to detect epigenetic features genome-wide (epigenomic assays). This Feature introduces several important prospects for precision epigenomics, highlights capabilities and limitations of current laboratory technologies, and emphasizes opportunities for microfluidic tools to facilitate translation of epigenetic analyses to the clinic, with a particular focus on methods to profile gene-associated histone modifications and their impacts on chromatin structure and gene expression.
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Affiliation(s)
- Yi Xu
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Steven R Doonan
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Tamas Ordog
- Epigenomics Program, Center for Individualized Medicine, Department of Physiology and Biomedical Engineering, and Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Ryan C Bailey
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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