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Wachholz Junior D, Kubota LT. CRISPR-based electrochemical biosensors: an alternative for point-of-care diagnostics? Talanta 2024; 278:126467. [PMID: 38968657 DOI: 10.1016/j.talanta.2024.126467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/17/2024] [Accepted: 06/22/2024] [Indexed: 07/07/2024]
Abstract
The combination of CRISPR technology and electrochemical sensors has sparked a paradigm shift in the landscape of point-of-care (POC) diagnostics. This review explores the dynamic convergence between CRISPR and electrochemical sensing, elucidating their roles in rapid and precise biosensing platforms. CRISPR, renowned for its remarkable precision in genome editing and programmability capability, has found a novel application in conjunction with electrochemical sensors, promising highly sensitive and specific detection of nucleic acids and biomarkers associated with diverse diseases. This article navigates through fundamental principles, research developments, and applications of CRISPR-based electrochemical sensors, highlighting their potential to revolutionize healthcare accessibility and patient outcomes. In addition, some key points and challenges regarding applying CRISPR-powered electrochemical sensors in real POC settings are presented. By discussing recent advancements and challenges in this interdisciplinary field, this review evaluates the potential of these innovative sensors as an alternative for decentralized, rapid, and accurate POC testing, offering some insights into their applications across clinical scenarios and their impact on the future of diagnostics.
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Affiliation(s)
- Dagwin Wachholz Junior
- Department of Analytical Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), 13083-970, Brazil; National Institute of Science and Technology in Bioanalytic (INCTBio), Brazil
| | - Lauro Tatsuo Kubota
- Department of Analytical Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), 13083-970, Brazil; National Institute of Science and Technology in Bioanalytic (INCTBio), Brazil.
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2
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Iida T, Ando J, Yoshimura M, Makino A, Nakano M, Kogo Y, Shinoda H, Toyoda M, Noda T, Watanabe R. Portable wide-field femtoliter-chamber imaging system for point-of-care digital bioanalysis. iScience 2024; 27:110868. [PMID: 39310765 PMCID: PMC11416649 DOI: 10.1016/j.isci.2024.110868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 08/15/2024] [Accepted: 08/29/2024] [Indexed: 09/25/2024] Open
Abstract
Recently, digital bioanalysis using femtoliter (fL)-chamber arrays has significantly improved the sensitivity, accuracy, and throughput of conventional nucleic acid and antigen tests, with great potential for the diagnosis of infectious diseases and underlying disorders. However, the large size of conventional platforms with costly assay consumables for digital bioanalysis complicates its use in point-of-care testing (POCT). To solve these problems, in this study, we developed a wide-field fL-chamber imaging system (COWFISH2), a portable wide-field femtoliter-chamber imaging system (footprint: 14 × 22 cm), by redesigning various electronic controls and optical systems of COWFISH, accompanied by the development of low-cost and durable consumables for digital bioanalysis. As a proof of concept, the point-of-care digital bioanalysis was successfully performed in a hospital setting, using amplification-free multiplex digital RNA detection of SARS-CoV-2, influenza A virus, and influenza B virus. Collectively, COWFISH2 will facilitate versatile and convenient digital bioanalysis in POCT, contributing to the improvement of public health, including the prevention of infectious diseases.
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Affiliation(s)
- Tatsuya Iida
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Jun Ando
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Mami Yoshimura
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Asami Makino
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Masahiro Nakano
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Yasushi Kogo
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Hajime Shinoda
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Masashi Toyoda
- Tokyo Metropolitan Institute for Geriatrics and Gerontology, Tokyo, Japan
| | - Takeshi Noda
- Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Rikiya Watanabe
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
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3
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Qian X, Xu Q, Lyon CJ, Hu TY. CRISPR for companion diagnostics in low-resource settings. LAB ON A CHIP 2024. [PMID: 39268697 PMCID: PMC11393808 DOI: 10.1039/d4lc00340c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/17/2024]
Abstract
New point-of-care tests (POCTs), which are especially useful in low-resource settings, are needed to expand screening capacity for diseases that cause significant mortality: tuberculosis, multiple cancers, and emerging infectious diseases. Recently, clustered regularly interspaced short palindromic repeats (CRISPR)-based diagnostic (CRISPR-Dx) assays have emerged as powerful and versatile alternatives to traditional nucleic acid tests, revealing a strong potential to meet this need for new POCTs. In this review, we discuss CRISPR-Dx assay techniques that have been or could be applied to develop POCTs, including techniques for sample processing, target amplification, multiplex assay design, and signal readout. This review also describes current and potential applications for POCTs in disease diagnosis and includes future opportunities and challenges for such tests. These tests need to advance beyond initial assay development efforts to broadly meet criteria for use in low-resource settings.
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Affiliation(s)
- Xu Qian
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China.
| | - Qiang Xu
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China.
| | - Christopher J Lyon
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA.
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
| | - Tony Y Hu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA.
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave, New Orleans, LA, 70112, USA
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4
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Zhang L, Wang H, Yang S, Liu J, Li J, Lu Y, Cheng J, Xu Y. High-Throughput and Integrated CRISPR/Cas12a-Based Molecular Diagnosis Using a Deep Learning Enabled Microfluidic System. ACS NANO 2024; 18:24236-24251. [PMID: 39173188 DOI: 10.1021/acsnano.4c05734] [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: 08/24/2024]
Abstract
CRISPR/Cas-based molecular diagnosis demonstrates potent potential for sensitive and rapid pathogen detection, notably in SARS-CoV-2 diagnosis and mutation tracking. Yet, a major hurdle hindering widespread practical use is its restricted throughput, limited integration, and complex reagent preparation. Here, a system, microfluidic multiplate-based ultrahigh throughput analysis of SARS-CoV-2 variants of concern using CRISPR/Cas12a and nonextraction RT-LAMP (mutaSCAN), is proposed for rapid detection of SARS-CoV-2 and its variants with limited resource requirements. With the aid of the self-developed reagents and deep-learning enabled prototype device, our mutaSCAN system can detect SARS-CoV-2 in mock swab samples below 30 min as low as 250 copies/mL with the throughput up to 96 per round. Clinical specimens were tested with this system, the accuracy for routine and mutation testing (22 wildtype samples, 26 mutational samples) was 98% and 100%, respectively. No false-positive results were found for negative (n = 24) samples.
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Affiliation(s)
- Li Zhang
- School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China
| | - Huili Wang
- School of Biomedical Engineering, Tsinghua University, Beijing 100084, China
| | - Sheng Yang
- School of Biomedical Engineering, Tsinghua University, Beijing 100084, China
| | - Jiajia Liu
- CapitalBiotech Technology, Beijing 101111, China
| | - Jie Li
- CapitalBiotech Technology, Beijing 101111, China
| | - Ying Lu
- School of Biomedical Engineering, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102200, China
| | - Jing Cheng
- School of Biomedical Engineering, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102200, China
| | - Youchun Xu
- School of Biomedical Engineering, Tsinghua University, Beijing 100084, China
- National Engineering Research Center for Beijing Biochip Technology, Beijing 102200, China
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5
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Tanifuji Y, Tong G, Hiruta Y, Citterio D. Paper-based analytical device for point-of-care nucleic acid quantification combining CRISPR/Cas12a and a personal glucose meter. Analyst 2024. [PMID: 39171545 DOI: 10.1039/d4an00905c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Although CRISPR-based nucleic acid detection has great potential in point-of-care testing due to its simplicity, it has been rarely integrated into paper-based analytical devices (PADs), which are attractive platforms to simplify assays. This work introduces a CRISPR-assisted nucleic acid quantification approach integrated into a PAD with signal readout by a personal glucose meter (PGM). Retention of magnetic beads by filter paper and pre-deposition of all required reagents by freeze-drying stabilized with trehalose enabled the indirect quantification of human papilloma virus (HPV) DNA through a PGM readout without complicated user intervention and complex reagent handling. The calculated limit of detection was 57 pM, which is comparable with other amplification-free CRISPR-based assays detecting nucleic acids. The fully integrated device exhibited good storage stability for up to 4 weeks, suggesting its applicability toward practical point-of-care nucleic acid quantification.
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Affiliation(s)
- Yohei Tanifuji
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
| | - Guodong Tong
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
| | - Yuki Hiruta
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
| | - Daniel Citterio
- Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
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Wang Q, Heo W, Choi S, Jang W, Lim CS, Jung HI. Hand-held all-in-one (HAO) self-test kit for rapid and on-site detection of SARS-CoV-2 with colorimetric LAMP. LAB ON A CHIP 2024; 24:3265-3275. [PMID: 38847067 DOI: 10.1039/d4lc00199k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Throughout the COVID-19 pandemic, individuals potentially infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were forcibly recalled to local or central hospitals, where the diagnostic results were obtained a couple of days after the liquid biopsies were subjected to conventional polymerase chain reaction (PCR). This slow output of such a complex and time-consuming laboratory procedure hindered its widespread application. To overcome the limitations associated with such a centralized diagnostic system, we developed a hand-held and all-in-one type test kit in which the analytical results can be obtained in only 30 min. The test kit consists of three major steps for on-site SARS-CoV-2 RNA detection: 1) virus lysis by heat, 2) RNA enrichment by membrane, and 3) real-time detection by colorimetric loop-mediated isothermal amplification (c-LAMP). The proposed device operates in a sample-to-answer format, is fully automated, and reduces dependence on traditional laboratory settings, facilitating large-scale population screening.
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Affiliation(s)
- Qingyang Wang
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Woong Heo
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Seoyeon Choi
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
- The DABOM Inc., Seoul, 03722, Republic of Korea
| | - Woongsik Jang
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Chae Seung Lim
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, 02841, Republic of Korea
| | - Hyo-Il Jung
- Department of Mechanical Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
- The DABOM Inc., Seoul, 03722, Republic of Korea
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7
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Zhang L, Zhang S, Floer C, Kantubuktha SAR, Velasco MJGR, Friend J. Surface Acoustic Wave-Driven Enhancement of Enzyme-Linked Immunosorbent Assays: ELISAW. Anal Chem 2024; 96:9676-9683. [PMID: 38813952 PMCID: PMC11170557 DOI: 10.1021/acs.analchem.4c01615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
Enzyme-linked immunosorbent assays (ELISAs) are widely used in biology and clinical diagnosis. Relying on antigen-antibody interaction through diffusion, the standard ELISA protocol can be time-consuming, preventing its use in rapid diagnostics. We present a time-saving and more sensitive ELISA without changing the standard setup and protocol, using surface acoustic waves (SAWs) to enhance performance. Each step of the assay, from the initial antibody binding onto the walls of the well plate to the target analyte molecules' binding for detection─except, notably, for the blocking step─is improved principally via acoustic streaming-driven advection. Using SAWs, the time required for one step of an example ELISA is reduced from 60 to 15 min to achieve the same binding amount. By extending the duration of SAW exposure to 20 min, the sensitivity can be significantly improved over the 60 min, 35 °C ELISA without SAWs. It is also possible to confer beneficial improvements to bead-based ELISA by combining it with SAWs to further reduce the time required for binding to 2 min. By significantly increasing the speed of ELISA, its utility may be improved for a wide range of point-of-care diagnostics applications.
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Affiliation(s)
- Lei Zhang
- Medically
Advanced Devices Laboratory, Center for Medical Devices, Department
of Mechanical and Aerospace Engineering, Jacobs School of Engineering,
and the Department of Medicine, School of Medicine, University of California San Diego, 9500 Gilman Drive MC0411, La Jolla, California 92093, United States
| | - Shuai Zhang
- Medically
Advanced Devices Laboratory, Center for Medical Devices, Department
of Mechanical and Aerospace Engineering, Jacobs School of Engineering,
and the Department of Medicine, School of Medicine, University of California San Diego, 9500 Gilman Drive MC0411, La Jolla, California 92093, United States
| | - Cécile Floer
- Medically
Advanced Devices Laboratory, Center for Medical Devices, Department
of Mechanical and Aerospace Engineering, Jacobs School of Engineering,
and the Department of Medicine, School of Medicine, University of California San Diego, 9500 Gilman Drive MC0411, La Jolla, California 92093, United States
- Université
de Lorraine, Centre national de la recherche
scientifique (CNRS), Institut Jean Lamour, F-54000 Nancy, France
| | - Sreeya Anjana Raj Kantubuktha
- Medically
Advanced Devices Laboratory, Center for Medical Devices, Department
of Mechanical and Aerospace Engineering, Jacobs School of Engineering,
and the Department of Medicine, School of Medicine, University of California San Diego, 9500 Gilman Drive MC0411, La Jolla, California 92093, United States
- Materials
Science and Engineering Program, University
of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - María José González Ruiz Velasco
- Medically
Advanced Devices Laboratory, Center for Medical Devices, Department
of Mechanical and Aerospace Engineering, Jacobs School of Engineering,
and the Department of Medicine, School of Medicine, University of California San Diego, 9500 Gilman Drive MC0411, La Jolla, California 92093, United States
- Materials
Science and Engineering Program, University
of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - James Friend
- Medically
Advanced Devices Laboratory, Center for Medical Devices, Department
of Mechanical and Aerospace Engineering, Jacobs School of Engineering,
and the Department of Medicine, School of Medicine, University of California San Diego, 9500 Gilman Drive MC0411, La Jolla, California 92093, United States
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8
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Ando J, Murai K, Mori M, Michiyuki T, Iida T, Makino A, Shinoda H, Watanabe R. Exploring fluoropolymers for fabrication of femtoliter chamber arrays used in digital bioanalysis. Sci Rep 2024; 14:11442. [PMID: 38769440 PMCID: PMC11106263 DOI: 10.1038/s41598-024-61726-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 05/08/2024] [Indexed: 05/22/2024] Open
Abstract
The global supply of fluoropolymers and fluorinated solvents is decreasing due to environmental concerns regarding polyfluoroalkyl substances. CYTOP has been used for decades primarily as a component of a femtoliter chamber array for digital bioanalysis; however, its supply has recently become scarce, increasing the urgency of fabricating a femtoliter chamber array using alternative materials. In this study, we investigated the feasibility of fabricating a femtoliter chamber array using four types of fluoropolymers in stable supply as candidate substitutes and verified their applicability for digital bioanalysis. Among these candidates, Fluorine Sealant emerged as a viable option for fabricating femtoliter chamber arrays using a conventional photolithography process. To validate its efficacy, we performed various digital bioanalysis using FP-A-based chamber arrays with model enzymes such as CRISPR-Cas, horseradish peroxidase, and β-galactosidase. The results demonstrated the similar performance to that of CYTOP, highlighting the broader utility of FP-A in digital bioanalysis. Our findings underscore the potential of FP-A to enhance the versatility of digital bioanalysis and foster the ongoing advancement of innovative diagnostic technologies.
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Affiliation(s)
- Jun Ando
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan.
| | - Kazue Murai
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Makiko Mori
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Tomoe Michiyuki
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Tatsuya Iida
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Asami Makino
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Hajime Shinoda
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan
| | - Rikiya Watanabe
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Saitama, Japan.
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9
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Zhang J, Li Z, Guo C, Guan X, Avery L, Banach D, Liu C. Intrinsic RNA Targeting Triggers Indiscriminate DNase Activity of CRISPR-Cas12a. Angew Chem Int Ed Engl 2024; 63:e202403123. [PMID: 38516796 PMCID: PMC11073899 DOI: 10.1002/anie.202403123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/23/2024]
Abstract
The CRISPR-Cas12a system has emerged as a powerful tool for next-generation nucleic acid-based molecular diagnostics. However, it has long been believed to be effective only on DNA targets. Here, we investigate the intrinsic RNA-enabled trans-cleavage activity of AsCas12a and LbCas12a and discover that they can be directly activated by full-size RNA targets, although LbCas12a exhibits weaker trans-cleavage activity than AsCas12a on both single-stranded DNA and RNA substrates. Remarkably, we find that the RNA-activated Cas12a possesses higher specificity in recognizing mutated target sequences compared to DNA activation. Based on these findings, we develop the "Universal Nuclease for Identification of Virus Empowered by RNA-Sensing" (UNIVERSE) assay for nucleic acid testing. We incorporate a T7 transcription step into this assay, thereby eliminating the requirement for a protospacer adjacent motif (PAM) sequence in the target. Additionally, we successfully detect multiple PAM-less targets in HIV clinical samples that are undetectable by the conventional Cas12a assay based on double-stranded DNA activation, demonstrating unrestricted target selection with the UNIVERSE assay. We further validate the clinical utility of the UNIVERSE assay by testing both HIV RNA and HPV 16 DNA in clinical samples. We envision that the intrinsic RNA targeting capability may bring a paradigm shift in Cas12a-based nucleic acid detection and further enhance the understanding of CRISPR-Cas biochemistry.
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Affiliation(s)
- Jiongyu Zhang
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Ziyue Li
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Chong Guo
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Xin Guan
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
- Department of Biomedical Engineering, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Lori Avery
- Department of Pathology and Laboratory Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - David Banach
- Department of Medicine, Division of Infectious Diseases, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
| | - Changchun Liu
- Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, Connecticut 06030, United States
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10
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Xiu L, Li H, Hu Q, Zhang Y, Chen SB, Wang C, Zhou XN, Chen JH, Yin K. A versatile microfluidic platform for malaria infection screening and Plasmodium species genotyping. EBioMedicine 2023; 98:104898. [PMID: 38029461 PMCID: PMC10697993 DOI: 10.1016/j.ebiom.2023.104898] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Malaria, a widespread parasitic disease caused by Plasmodium species, remains a significant global health concern. Rapid and accurate detection, as well as species genotyping, are critical for effective malaria control. METHODS We have developed a Flexible, Robust, Equipment-free Microfluidic (FREM) platform, which integrates recombinase polymerase amplification (RPA) and clustered regularly interspaced short palindromic repeats (CRISPR)-based detection, enabling simultaneous malaria infection screening and Plasmodium species genotyping. The microfluidic chip enabled the parallel detection of multiple Plasmodium species, each amplified by universal RPA primers and genotyped by specific crRNAs. The inclusion of a sucrose solution effectively created spatial separation between the RPA and CRISPR assays within a one-pot system, effectively resolving compatibility issues. FINDINGS Clinical assessment of DNA extracts from patients with suspected malaria demonstrates the FREM platform's superior sensitivity (98.41%) and specificity (92.86%), yielding consistent results with PCR-sequencing for malaria detection, which achieved a positive predictive agreement of 98.41% and a negative predictive agreement of 92.86%. Additionally, the accuracy of species genotyping was validated through concordance rates of 90.91% between the FREM platform and PCR-sequencing. INTERPRETATION The FREM platform offers a promising solution for point-of-care malaria screening and Plasmodium species genotyping. It highlights the possibility of improving malaria control efforts and expanding its applicability to address other infectious diseases. FUNDING This work was financially supported by International Joint Laboratory on Tropical Diseases Control in Greater Mekong Subregion, National Natural Science Foundation of China, the Natural Science Foundation of Shanghai, Bill & Melinda Gates Foundation and National Research and Development Plan of China.
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Affiliation(s)
- Leshan Xiu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China.
| | - Huimin Li
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Qinqin Hu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Yuqian Zhang
- Department of Surgery, Division of Surgery Research, Mayo Clinic, Rochester, MN, 55905, USA; Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Shen-Bo Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, World Health Organization (WHO) Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China
| | - Chenxi Wang
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China
| | - Xiao-Nong Zhou
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, World Health Organization (WHO) Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China; Hainan Tropical Diseases Research Center (Hainan Sub-Center, Chinese Center for Tropical Diseases Research), Haikou, 571199, China
| | - Jun-Hu Chen
- National Institute of Parasitic Diseases, Chinese Center for Diseases Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission of the People's Republic of China (NHC) Key Laboratory of Parasite and Vector Biology, World Health Organization (WHO) Collaborating Center for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China; Hainan Tropical Diseases Research Center (Hainan Sub-Center, Chinese Center for Tropical Diseases Research), Haikou, 571199, China.
| | - Kun Yin
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China; One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, 200025, China.
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11
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Romero Deza AA, Schaumburg F, Berli CLA. Valveless On-Chip Aliquoting for Molecular Diagnosis. MICROMACHINES 2023; 14:1425. [PMID: 37512736 PMCID: PMC10386703 DOI: 10.3390/mi14071425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/09/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]
Abstract
The detection of nucleic acids as specific markers of infectious diseases is commonly implemented in molecular biology laboratories. The translation of these benchtop assays to a lab-on-a-chip format demands huge efforts of integration and automation. The present work is motivated by a strong requirement often posed by molecular assays that combine isothermal amplification and CRISPR/Cas-based detection: after amplification, a 2-8 microliter aliquot of the reaction products must be taken for the subsequent reaction. In order to fulfill this technical problem, we have designed and prototyped a microfluidic device that is able to meter and aliquot in the required range during the stepped assay. The operation is achieved by integrating a porous material that retains the desired amount of liquid after removing the excess reaction products, an innovative solution that avoids valving and external actuation. The prototypes were calibrated and experimentally tested to demonstrate the overall performance (general fluidics, metering, aliquoting, mixing and reaction). The proposed aliquoting method is fully compatible with additional functions, such as sample concentration or reagent storage, and could be further employed in alternative applications beyond molecular diagnosis.
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Affiliation(s)
| | - Federico Schaumburg
- Predio CCT CONICET Santa Fe, INTEC (Universidad Nacional del Litoral-CONICET), RN 168, Santa Fe 3000, Argentina
| | - Claudio L A Berli
- Predio CCT CONICET Santa Fe, INTEC (Universidad Nacional del Litoral-CONICET), RN 168, Santa Fe 3000, Argentina
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Iida T, Shinoda H, Watanabe R. SATORI: Amplification-free digital RNA detection method for the diagnosis of viral infections. Biophys Physicobiol 2023; 20:e200031. [PMID: 38124795 PMCID: PMC10728625 DOI: 10.2142/biophysico.bppb-v20.0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/10/2023] [Indexed: 12/23/2023] Open
Abstract
With the recent global outbreak of COVID-19, there is an urgent need to establish a versatile diagnostic method for viral infections. Gene amplification test or antigen test are widely used to diagnose viral infections; however, these methods generally have technical drawbacks either in terms of sensitivity, accuracy, or throughput. To address this issue, we recently developed an amplification-free digital RNA detection method (SATORI), which can identify and detect viral genes at the single-molecule level in approximately 9 min, satisfying almost all detection performance requirements for the diagnosis of viral infections. In addition, we also developed practical platforms for SATORI, such as an automated platform (opn-SATORI) and a low-cost compact fluorescence imaging system (COWFISH), with the aim of application in clinical settings. Our latest technologies can be inherently applied to diagnose a variety of RNA viral infections, such as COVID-19 and Influenza A/B, and therefore, we expect that SATORI will be established as a versatile platform for point-of-care testing of a wide range of infectious diseases, thus contributing to the prevention of future epidemics. This article is an extended version of the Japanese article published in the SEIBUTSU BUTSURI Vol. 63, p. 115-118 (2023).
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Affiliation(s)
- Tatsuya Iida
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Saitama 351-0198, Japan
| | - Hajime Shinoda
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Saitama 351-0198, Japan
| | - Rikiya Watanabe
- Molecular Physiology Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Saitama 351-0198, Japan
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