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Fang W, Liu X, Maiga M, Cao W, Mu Y, Yan Q, Zhu Q. Digital PCR for Single-Cell Analysis. BIOSENSORS 2024; 14:64. [PMID: 38391982 PMCID: PMC10886679 DOI: 10.3390/bios14020064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024]
Abstract
Single-cell analysis provides an overwhelming strategy for revealing cellular heterogeneity and new perspectives for understanding the biological function and disease mechanism. Moreover, it promotes the basic and clinical research in many fields at a single-cell resolution. A digital polymerase chain reaction (dPCR) is an absolute quantitative analysis technology with high sensitivity and precision for DNA/RNA or protein. With the development of microfluidic technology, digital PCR has been used to achieve absolute quantification of single-cell gene expression and single-cell proteins. For single-cell specific-gene or -protein detection, digital PCR has shown great advantages. So, this review will introduce the significance and process of single-cell analysis, including single-cell isolation, single-cell lysis, and single-cell detection methods, mainly focusing on the microfluidic single-cell digital PCR technology and its biological application at a single-cell level. The challenges and opportunities for the development of single-cell digital PCR are also discussed.
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Affiliation(s)
- Weibo Fang
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
| | - Xudong Liu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
| | - Mariam Maiga
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
| | - Wenjian Cao
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
| | - Ying Mu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
| | - Qiang Yan
- Department of Hepatobiliary and Pancreatic Surgery, Huzhou Central Hospital, Huzhou Key Laboratory of Intelligent and Digital Precision Surgery, Department of General Surgery, Affiliated Huzhou Hospital, School of Medicine, Zhejiang University, Huzhou 313000, China
| | - Qiangyuan Zhu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, College of Control Science and Engineering, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou 310027, China; (W.F.); (X.L.); (M.M.); (W.C.); (Y.M.)
- Huzhou Institute of Zhejiang University, Huzhou 313002, China
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Liu CW, Tsutsui H. Sample-to-answer sensing technologies for nucleic acid preparation and detection in the field. SLAS Technol 2023; 28:302-323. [PMID: 37302751 DOI: 10.1016/j.slast.2023.06.002] [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: 03/23/2023] [Revised: 05/16/2023] [Accepted: 06/06/2023] [Indexed: 06/13/2023]
Abstract
Efficient sample preparation and accurate disease diagnosis under field conditions are of great importance for the early intervention of diseases in humans, animals, and plants. However, in-field preparation of high-quality nucleic acids from various specimens for downstream analyses, such as amplification and sequencing, is challenging. Thus, developing and adapting sample lysis and nucleic acid extraction protocols suitable for portable formats have drawn significant attention. Similarly, various nucleic acid amplification techniques and detection methods have also been explored. Combining these functions in an integrated platform has resulted in emergent sample-to-answer sensing systems that allow effective disease detection and analyses outside a laboratory. Such devices have a vast potential to improve healthcare in resource-limited settings, low-cost and distributed surveillance of diseases in food and agriculture industries, environmental monitoring, and defense against biological warfare and terrorism. This paper reviews recent advances in portable sample preparation technologies and facile detection methods that have been / or could be adopted into novel sample-to-answer devices. In addition, recent developments and challenges of commercial kits and devices targeting on-site diagnosis of various plant diseases are discussed.
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Affiliation(s)
- Chia-Wei Liu
- Department of Mechanical Engineering, University of California, Riverside, CA 92521, USA
| | - Hideaki Tsutsui
- Department of Mechanical Engineering, University of California, Riverside, CA 92521, USA; Department of Bioengineering, University of California, Riverside, CA 92521, USA.
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Cao Z, Ye Y, Li G, Zhang R, Dong S, Liu Y. Monolithically integrated microchannel plate functionalized with ZnO nanorods for fluorescence-enhanced digital polymerase chain reaction. Biosens Bioelectron 2022; 213:114499. [DOI: 10.1016/j.bios.2022.114499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/08/2022] [Accepted: 06/21/2022] [Indexed: 11/27/2022]
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Gao X, Li J, Li C, Zhang Z, Zhang W, Yao J, Guan M, Guo Z, Li C, Zhou L. High filling rate digital PCR through-hole array chip with double independent S-shaped flow channels. BIOMICROFLUIDICS 2020; 14:034109. [PMID: 32509051 PMCID: PMC7266645 DOI: 10.1063/5.0006374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/16/2020] [Indexed: 05/13/2023]
Abstract
Sample digital technology is a powerful method for absolute quantification of target molecules such as nucleic acids and proteins. The excellent sample stability and mass production capability has enabled the development of microwell array-based sample digitizing methods. However, in current microwell array chips, samples are loaded by the liquid scraping method, which requires complex manual operation and results in a low filling rate and limited hole filling uniformity. Here, we perform sample loading of a through-hole array chip by a microfluidics-driven method and design a double independent S-shaped flow channels sandwiched through-hole array chip. Because of the capillary force and capillary burst pressure, the sample flowing in the channel can be trapped into through-holes, but cannot flow through the other side. Via air flow and displacement of the remaining sample in the channel, the sample can be partitioned consistently, with zero surplus sample residue in the channel. We evaluated the actual performance of the sample-loading process: the chip enables 99.10% filling rate of 18 500 through-holes, with a grayscale coefficient of variation value of 6.03% determined from fluorescence images. In performing digital polymerase chain reaction on chip, the chip demonstrates good performance for the absolute quantification of target DNA. The simple and robust design of our chip, with excellent filling rate and microsample uniformity, indicates potential for use in a variety of sample digitization applications.
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Affiliation(s)
| | - Jinze Li
- CAS Key Laboratory of Bio-medical Diagnostics,
Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of
Sciences, Suzhou, Jiangsu 215163, People's Republic of
China
| | | | | | | | | | - Ming Guan
- Huashan Hospital, Fudan University,
Shanghai 200040, People's Republic of China
| | | | - Chao Li
- CAS Key Laboratory of Bio-medical Diagnostics,
Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of
Sciences, Suzhou, Jiangsu 215163, People's Republic of
China
| | - Lianqun Zhou
- Author to whom correspondence should be addressed:
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Pang B, Fu K, Liu Y, Ding X, Hu J, Wu W, Xu K, Song X, Wang J, Mu Y, Zhao C, Li J. Development of a self-priming PDMS/paper hybrid microfluidic chip using mixed-dye-loaded loop-mediated isothermal amplification assay for multiplex foodborne pathogens detection. Anal Chim Acta 2018; 1040:81-89. [DOI: 10.1016/j.aca.2018.07.024] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/03/2018] [Accepted: 07/10/2018] [Indexed: 11/26/2022]
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Sinha N, Subedi N, Tel J. Integrating Immunology and Microfluidics for Single Immune Cell Analysis. Front Immunol 2018; 9:2373. [PMID: 30459757 PMCID: PMC6232771 DOI: 10.3389/fimmu.2018.02373] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/24/2018] [Indexed: 12/16/2022] Open
Abstract
The field of immunoengineering aims to develop novel therapies and modern vaccines to manipulate and modulate the immune system and applies innovative technologies toward improved understanding of the immune system in health and disease. Microfluidics has proven to be an excellent technology for analytics in biology and chemistry. From simple microsystem chips to complex microfluidic designs, these platforms have witnessed an immense growth over the last decades with frequent emergence of new designs. Microfluidics provides a highly robust and precise tool which led to its widespread application in single-cell analysis of immune cells. Single-cell analysis allows scientists to account for the heterogeneous behavior of immune cells which often gets overshadowed when conventional bulk study methods are used. Application of single-cell analysis using microfluidics has facilitated the identification of several novel functional immune cell subsets, quantification of signaling molecules, and understanding of cellular communication and signaling pathways. Single-cell analysis research in combination with microfluidics has paved the way for the development of novel therapies, point-of-care diagnostics, and even more complex microfluidic platforms that aid in creating in vitro cellular microenvironments for applications in drug and toxicity screening. In this review, we provide a comprehensive overview on the integration of microsystems and microfluidics with immunology and focus on different designs developed to decode single immune cell behavior and cellular communication. We have categorized the microfluidic designs in three specific categories: microfluidic chips with cell traps, valve-based microfluidics, and droplet microfluidics that have facilitated the ongoing research in the field of immunology at single-cell level.
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Affiliation(s)
- Nidhi Sinha
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Nikita Subedi
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Jurjen Tel
- Laboratory of Immunoengineering, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
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Campbell JM, Balhoff JB, Landwehr GM, Rahman SM, Vaithiyanathan M, Melvin AT. Microfluidic and Paper-Based Devices for Disease Detection and Diagnostic Research. Int J Mol Sci 2018; 19:E2731. [PMID: 30213089 PMCID: PMC6164778 DOI: 10.3390/ijms19092731] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 12/12/2022] Open
Abstract
Recent developments in microfluidic devices, nanoparticle chemistry, fluorescent microscopy, and biochemical techniques such as genetic identification and antibody capture have provided easier and more sensitive platforms for detecting and diagnosing diseases as well as providing new fundamental insight into disease progression. These advancements have led to the development of new technology and assays capable of easy and early detection of pathogenicity as well as the enhancement of the drug discovery and development pipeline. While some studies have focused on treatment, many of these technologies have found initial success in laboratories as a precursor for clinical applications. This review highlights the current and future progress of microfluidic techniques geared toward the timely and inexpensive diagnosis of disease including technologies aimed at high-throughput single cell analysis for drug development. It also summarizes novel microfluidic approaches to characterize fundamental cellular behavior and heterogeneity.
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Affiliation(s)
- Joshua M Campbell
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Joseph B Balhoff
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Grant M Landwehr
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
| | - Sharif M Rahman
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
| | | | - Adam T Melvin
- Cain Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA 70803, USA.
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Liu W, Warden A, Sun J, Shen G, Ding X. Simultaneous detection of multiple HPV DNA via bottom-well microfluidic chip within an infra-red PCR platform. BIOMICROFLUIDICS 2018; 12:024109. [PMID: 29576839 PMCID: PMC5851781 DOI: 10.1063/1.5023652] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/06/2018] [Indexed: 05/26/2023]
Abstract
Portable Polymerase Chain Reaction (PCR) devices combined with microfluidic chips or lateral flow stripes have shown great potential in the field of point-of-need testing (PoNT) as they only require a small volume of patient sample and are capable of presenting results in a short time. However, the detection for multiple targets in this field leaves much to be desired. Herein, we introduce a novel PCR platform by integrating a bottom-well microfluidic chip with an infra-red (IR) excited temperature control method and fluorescence co-detection of three PCR products. Microfluidic chips are utilized to partition different samples into individual bottom-wells. The oil phase in the main channel contains multi-walled carbon nanotubes which were used as a heat transfer medium that absorbs energy from the IR-light-emitting diode (LED) and transfers heat to the water phase below. Cyclical rapid heating and cooling necessary for PCR are achieved by alternative power switching of the IR-LED and Universal Serial Bus (USB) mini-fan with a pulse width modulation scheme. This design of the IR-LED PCR platform is economic, compact, and fully portable, making it a promising application in the field of PoNT. The bottom-well microfluidic chip and IR-LED PCR platform were combined to fulfill a three-stage thermal cycling PCR for 40 cycles within 90 min for Human Papilloma Virus (HPV) detection. The PCR fluorescent signal was successfully captured at the end of each cycle. The technique introduced here has broad applications in nucleic acid amplification and PoNT devices.
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Affiliation(s)
| | | | | | | | - Xianting Ding
- Author to whom correspondence should be addressed: . Tel.: +86-21-62932274
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Zhang L, Ding B, Chen Q, Feng Q, Lin L, Sun J. Point-of-care-testing of nucleic acids by microfluidics. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.07.013] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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Basha IHK, Ho ETW, Yousuff CM, Hamid NHB. Towards Multiplex Molecular Diagnosis-A Review of Microfluidic Genomics Technologies. MICROMACHINES 2017; 8:E266. [PMID: 30400456 PMCID: PMC6190060 DOI: 10.3390/mi8090266] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/30/2017] [Accepted: 07/16/2017] [Indexed: 12/21/2022]
Abstract
Highly sensitive and specific pathogen diagnosis is essential for correct and timely treatment of infectious diseases, especially virulent strains, in people. Point-of-care pathogen diagnosis can be a tremendous help in managing disease outbreaks as well as in routine healthcare settings. Infectious pathogens can be identified with high specificity using molecular methods. A plethora of microfluidic innovations in recent years have now made it increasingly feasible to develop portable, robust, accurate, and sensitive genomic diagnostic devices for deployment at the point of care. However, improving processing time, multiplexed detection, sensitivity and limit of detection, specificity, and ease of deployment in resource-limited settings are ongoing challenges. This review outlines recent techniques in microfluidic genomic diagnosis and devices with a focus on integrating them into a lab on a chip that will lead towards the development of multiplexed point-of-care devices of high sensitivity and specificity.
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Affiliation(s)
- Ismail Hussain Kamal Basha
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Eric Tatt Wei Ho
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Caffiyar Mohamed Yousuff
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
| | - Nor Hisham Bin Hamid
- Department of Electrical and Electronic Engineering, Universiti Teknologi PETRONAS, 32610 Seri Iskandar, Perak Darul Ridzuan, Malaysia.
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