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Li W, Zhang S, Dang S, Gao L, Li G, Cheng D, Jiang L, Huang T, Zhai J. Establishment of an A/T-Rich Specifically MGB Probe digital droplet PCR Assays Based on SNP for Brucella wild strains and vaccine strains. Diagn Microbiol Infect Dis 2024; 110:116432. [PMID: 39024932 DOI: 10.1016/j.diagmicrobio.2024.116432] [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: 03/27/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024]
Abstract
In recent years, immunization with the S2 live-attenuated vaccine has been recognized as the most economical and effective strategy for preventing brucellosis in Inner Mongolia, China. However, there are still challenges related to vaccine toxicity and the inability to distinguish between vaccine immunization and natural infection. Therefore, in this study, we developed a digital droplet polymerase chain reaction (ddPCR) assay based on single-nucleotide polymorphism (SNP) loci to identify wild Brucella strains and S2 vaccine strains. The assay demonstrated excellent linearity (R2> 0.99) with a lower detection limit of 10 copies/µL for both wild and vaccine strains. Additionally, the ddPCR assay outperformed the real-time fluorescent quantitative PCR (qPCR) assay in screening 50 clinical samples. We have established an effective and highly sensitive ddPCR assay for Brucella, providing an efficient method for detecting and differentiating wild strains of Brucella from the S2 vaccine strain.
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Affiliation(s)
- Wanyang Li
- Medical College, Inner Mongolia Minzu University, Tongliao 028000, China
| | - Shuai Zhang
- Medical College, Inner Mongolia Minzu University, Tongliao 028000, China
| | - Sheng Dang
- Keerqin District First People's Hospital, Tongliao 028000, China
| | - Lanzhu Gao
- Tongliao Infectious Disease Hospital, Tongliao 028000, China
| | - Guangchen Li
- Tongliao Infectious Disease Hospital, Tongliao 028000, China
| | - Dawei Cheng
- Beidahuang Industry Group General Hospital, Harbin 150000, China
| | - Longguang Jiang
- College of Chemistry, Fuzhou University, Fuzhou 350000, China
| | - Tianpeng Huang
- College of Public Health, Inner Mongolia Minzu University, Tongliao 028000, China; Brucellosis Prevention and Treatment Engineering Research Center of Inner Mongolia Autonomous Region, Tongliao 028000, China; Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Tongliao 028000, China
| | - Jingbo Zhai
- Medical College, Inner Mongolia Minzu University, Tongliao 028000, China; Brucellosis Prevention and Treatment Engineering Research Center of Inner Mongolia Autonomous Region, Tongliao 028000, China; Key Laboratory of Zoonose Prevention and Control at Universities of Inner Mongolia Autonomous Region, Tongliao 028000, China.
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2
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Gao Y, Zhang X, Wang X, Sun R, Li Y, Li J, Quan W, Yao Y, Hou Y, Li D, Sun Z. The clinical value of rapidly detecting urinary exosomal lncRNA RMRP in bladder cancer with an RT-RAA-CRISPR/Cas12a method. Clin Chim Acta 2024; 562:119855. [PMID: 38981565 DOI: 10.1016/j.cca.2024.119855] [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: 05/16/2024] [Revised: 06/25/2024] [Accepted: 07/05/2024] [Indexed: 07/11/2024]
Abstract
BACKGROUND AND AIMS Bladder cancer (BCa) is a highly aggressive malignancy of the urinary system. Timely detection is imperative for enhancing BCa patient prognosis. MATERIALS AND METHODS This study introduces a novel approach for detecting long non-coding RNA (lncRNA) Mitochondrial RNA Processing Endoribonuclease (RMRP) in urine exosomes from BCa patients using the reverse transcription recombinase-aided amplification (RT-RAA) and clustered regularly interspaced short palindromic repeats and associated Cas12a proteins (CRISPR/Cas12a) technique. Various statistical methods were used to evaluate its diagnostic value for BCa. RESULTS The specificity of urine exosomal RMRP detection for BCa diagnosis was enhanced by using RT-RAA combined with CRISPR/Cas12a. The testing process duration was reduced to 30 min, which supports rapid detection. Moreover, this approach allows the identification of target signals in real-time using blue light, facilitating immediate detection. In clinical sample analysis, this methodology exhibited a high level of diagnostic efficacy. This was evidenced by larger area under the curve values with receiver operating characteristic curve analysis compared with using traditional RT-qPCR methods, indicating superior diagnostic accuracy and sensitivity. Furthermore, the combined analysis of RMRP expression in urine exosomes detected by RT-RAA-CRISPR/Cas12a and NMP-22 expression may further enhance diagnostic accuracy. CONCLUSIONS The RT-RAA-CRISPR/Cas12a technology is a swift, sensitive, and uncomplicated method for nucleic acid detection. Because of its convenient and non-invasive sampling approach, user-friendly operation, and reproducibility, this technology is very promising for automated detection and holds favorable application possibilities within clinical environments.
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Affiliation(s)
- Yuting Gao
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Xueru Zhang
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Xuanlin Wang
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Ruixin Sun
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Yaran Li
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Jing Li
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Wenqiang Quan
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Yiwen Yao
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China
| | - Yanqiang Hou
- Department of Clinical Laboratory, Songjiang Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 201600, PR China.
| | - Dong Li
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China.
| | - Zujun Sun
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, PR China.
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3
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Whang K, Min J, Shin Y, Hwang I, Lee H, Kwak T, La JA, Kim S, Kim D, Lee LP, Kang T. Capillarity-Driven Enrichment and Hydrodynamic Trapping of Trace Nucleic Acids by Plasmonic Cavity Membrane for Rapid and Sensitive Detections. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2403896. [PMID: 38663435 DOI: 10.1002/adma.202403896] [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: 03/16/2024] [Revised: 04/22/2024] [Indexed: 05/03/2024]
Abstract
Small-reactor-based polymerase chain reaction (PCR) has attracted considerable attention. A significant number of tiny reactors must be prepared in parallel to capture, amplify, and accurately quantify few target genes in clinically relevant large volume, which, however, requires sophisticated microfabrication and longer sample-to-answer time. Here, single plasmonic cavity membrane is reported that not only enriches and captures few nucleic acids by taking advantage of both capillarity and hydrodynamic trapping but also quickly amplifies them for sensitive plasmonic detection. The plasmonic cavity membrane with few nanoliters in a void volume is fabricated by self-assembling gold nanorods with SiO2 tips. Simulations reveal that hydrodynamic stagnation between the SiO2 tips is mainly responsible for the trapping of the nucleic acid in the membrane. Finally, it is shown that the plasmonic cavity membrane is capable of enriching severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genes up to 20 000-fold within 1 min, amplifying within 3 min, and detecting the trace genes as low as a single copy µL-1. It is anticipated that this work not only expands the utility of PCR but also provides an innovative way of the enrichment and detection of trace biomolecules in a variety of point-of-care testing applications.
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Affiliation(s)
- Keumrai Whang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, South Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
| | - Junwon Min
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, South Korea
| | - Yonghee Shin
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, South Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
| | - Inhyeok Hwang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, South Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
| | - Hyunjoo Lee
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, South Korea
| | - Taejin Kwak
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, South Korea
| | - Ju A La
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, South Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
| | - Sungbong Kim
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
- Department of Chemistry, Military Academy, Seoul, 01805, South Korea
| | - Dongchoul Kim
- Department of Mechanical Engineering, Sogang University, Seoul, 04107, South Korea
| | - Luke P Lee
- Harvard Institute of Medicine, Harvard Medical School, Brigham and Women's Hospital, Harvard University, Boston, MA, 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwonsi, Gyeonggi-do, 16419, South Korea
| | - Taewook Kang
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, 04107, South Korea
- Institute of Integrated Biotechnology, Sogang University, Seoul, 04107, South Korea
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4
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Shuai J, Song S, Wang Z, Zeng R, Han X, Zhang X. MALDI-TOF nucleic acid mass spectrometry for simultaneously detection of fourteen porcine viruses and its application. J Virol Methods 2024; 329:114990. [PMID: 38925439 DOI: 10.1016/j.jviromet.2024.114990] [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: 02/27/2024] [Revised: 06/21/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND Mixed infections of multiple viruses significantly contribute to the prevalence of swine diseases, adversely affecting global livestock production and the economy. However, effectively monitoring multiple viruses and detecting mixed infection samples remains challenging. This study describes a method that combines single-base extension PCR with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to detect important porcine viruses. RESULTS Our approach accurately and simultaneously identified 14 porcine viruses, including porcine circovirus types 1-3, porcine bocaviruses groups 1-3, African swine fever virus, pseudorabies virus, porcine parvovirus, torque teno sus virus, swine influenza virus, porcine reproductive and respiratory syndrome virus, classical swine fever virus, and foot-and-mouth disease virus. The low limit of detection for multiplex identification ranges from 13.54 to 1.59 copies/μL. Inter- and intra-assay stability was found to be ≥98.3 %. In a comprehensive analysis of 114 samples, the assay exhibited overall agreement with qPCR results of 97.9 %. CONCLUSIONS The developed MALDI-TOF NAMS assay exhibits high sensitivity, specificity, and reliability in detecting and distinguishing a wide spectrum of porcine viruses in complex matrix samples. This underscores its potential as an efficient diagnostic tool for porcine-derived virus surveillance and swine disease control.
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Affiliation(s)
- Jiangbing Shuai
- Hangzhou Customs Technical Center, Hangzhou 311202, China; Zhejiang Academy of Science & Technology for Inspection & Quarantine, Hangzhou 310016, China
| | - Shiqi Song
- Zhejiang Digena Diagnostic Technology Co., Ltd., Hangzhou 311100, China
| | - Zhongcai Wang
- Hangzhou Customs Technical Center, Hangzhou 311202, China
| | - Ruoxue Zeng
- Hangzhou Customs Technical Center, Hangzhou 311202, China
| | - Xiao Han
- Zhejiang Academy of Science & Technology for Inspection & Quarantine, Hangzhou 310016, China
| | - Xiaofeng Zhang
- Hangzhou Customs Technical Center, Hangzhou 311202, China; Zhejiang Academy of Science & Technology for Inspection & Quarantine, Hangzhou 310016, China.
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5
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Chen K, He Y, Wang W, Yuan X, Carbone DP, Yang F. Development of new techniques and clinical applications of liquid biopsy in lung cancer management. Sci Bull (Beijing) 2024; 69:1556-1568. [PMID: 38641511 DOI: 10.1016/j.scib.2024.03.062] [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: 09/25/2023] [Revised: 12/12/2023] [Accepted: 01/17/2024] [Indexed: 04/21/2024]
Abstract
Lung cancer is an exceedingly malignant tumor reported as having the highest morbidity and mortality of any cancer worldwide, thus posing a great threat to global health. Despite the growing demand for precision medicine, current methods for early clinical detection, treatment and prognosis monitoring in lung cancer are hampered by certain bottlenecks. Studies have found that during the formation and development of a tumor, molecular substances carrying tumor-related genetic information can be released into body fluids. Liquid biopsy (LB), a method for detecting these tumor-related markers in body fluids, maybe a way to make progress in these bottlenecks. In recent years, LB technology has undergone rapid advancements. Therefore, this review will provide information on technical updates to LB and its potential clinical applications, evaluate its effectiveness for specific applications, discuss the existing limitations of LB, and present a look forward to possible future clinical applications. Specifically, this paper will introduce technical updates from the prospectives of engineering breakthroughs in the detection of membrane-based LB biomarkers and other improvements in sequencing technology. Additionally, it will summarize the latest applications of liquid biopsy for the early detection, diagnosis, treatment, and prognosis of lung cancer. We will present the interconnectedness of clinical and laboratory issues and the interplay of technology and application in LB today.
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Affiliation(s)
- Kezhong Chen
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China
| | - Yue He
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China
| | - Wenxiang Wang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China
| | - Xiaoqiu Yuan
- Peking University Health Science Center, Beijing 100191, China
| | - David P Carbone
- Thoracic Oncology Center, Ohio State University, Columbus 43026, USA.
| | - Fan Yang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Peking University People's Hospital Thoracic Oncology Institute & Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Beijing 100044, China.
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6
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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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7
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Wu Z, Yao Y, Li X, Cai H, Wang G, Yu W, Lou H, Chen Q, Zeng Z, Yu H, Xia J, Yu Y, Zhou H. Sensitive and rapid identification of pathogens by droplet digital PCR in a cohort of septic patients: a prospective diagnostic study. Infect Dis (Lond) 2024:1-12. [PMID: 38753988 DOI: 10.1080/23744235.2024.2354312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND There is a critical need for a rapid and sensitive pathogen detection method for septic patients. This study aimed to investigate the diagnostic efficacy of Digital droplet polymerase chain reaction (ddPCR) in identifying pathogens among suspected septic patients. METHODS We conducted a prospective pilot diagnostic study to clinically validate the multiplex ddPCR panel in diagnosing suspected septic patients. A total of 100 sepsis episodes of 89 patients were included in the study. RESULTS In comparison to blood culture, the ddPCR panel exhibited an overall sensitivity of 75.0% and a specificity of 69.7%, ddPCR yielded an additional detection rate of 17.0% for sepsis cases overall, with a turnaround time of 2.5 h. The sensitivity of ddPCR in the empirical antibiotic treatment and the non-empirical antibiotic treatment group were 78.6% versus 80.0% (p > 0.05). Antimicrobial resistance genes were identified in a total of 13 samples. Whenever ddPCR detected the genes beta-lactamase-Klebsiella pneumoniae carbapenemase (blaKPC) or beta-lactamase-New Delhi metallo (blaNDM), these findings corresponded to the cultivation of carbapenem-resistant gram-negative bacteria. Dynamic ddPCR monitoring revealed a consistent alignment between the quantitative ddPCR results and the trends observed in C-reactive protein and procalcitonin levels. CONCLUSIONS Compared to blood culture, ddPCR exhibited higher sensitivity for pathogen diagnosis in suspected septic patients, and it provided pathogen and drug resistance information in a shorter time. The quantitative results of ddPCR generally aligned with the trends seen in C-reactive protein and procalcitonin levels, indicating that ddPCR can serve as a dynamic monitoring tool for pathogen load in septic patients.
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Affiliation(s)
- Zhenping Wu
- Department of Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yake Yao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xi Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Hongliu Cai
- Department of Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guobin Wang
- Department of Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenqiao Yu
- Department of Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Lou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhu Zeng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hao Yu
- Pilot Gene Technology (Hangzhou) Co., Ltd, Hangzhou, China
| | - Jiang Xia
- Pilot Gene Technology (Hangzhou) Co., Ltd, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Disease, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hua Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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8
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Sivaganesan M, Willis JR, Diedrich A, Shanks OC. A fecal score approximation model for analysis of real-time quantitative PCR fecal source identification measurements. WATER RESEARCH 2024; 255:121482. [PMID: 38598887 DOI: 10.1016/j.watres.2024.121482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 04/12/2024]
Abstract
Numerous qPCR-based methods are available to estimate the concentration of fecal pollution sources in surface waters. However, qPCR fecal source identification data sets often include a high proportion of non-detections (reactions failing to attain a prespecified minimal signal intensity for detection) and measurements below the assay lower limit of quantification (minimal signal intensity required to estimate target concentration), making it challenging to interpret results in a quantitative manner while accounting for error. In response, a Bayesian statistic based Fecal Score (FS) approach was developed that estimates the weighted average concentration of a fecal source identification genetic marker across a defined group of samples, mathematically incorporating qPCR measurements from all samples. Yet, implementation is technically demanding and computationally intensive requiring specialized training, the use of expert software, and access to high performance computing. To address these limitations, this study reports a novel approximation model for FS determination based on a frequentist approach. The performance of the Bayesian and Frequentist models are compared using fecal source identification qPCR data representative of different 'censored' data scenarios from a recently published study focusing on the impact of stormwater discharge in urban streams. In addition, data set eligibility recommendations for the responsible use of these models are presented. Findings indicate that the Frequentist model can generate similar average concentrations and uncertainty estimates for FS, compared to the original Bayesian approach. The Frequentist model should make calculations less computationally and technically intensive, allowing for the development of easier to use data analysis tools for fecal source identification applications.
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Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Adam Diedrich
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA.
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9
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Hayden RT, Su Y, Tang L, Zhu H, Gu Z, Glasgow HL, Sam SS, Caliendo AM. Accuracy of quantitative viral secondary standards: a re-examination. J Clin Microbiol 2024; 62:e0166923. [PMID: 38380932 PMCID: PMC10935634 DOI: 10.1128/jcm.01669-23] [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: 12/14/2023] [Accepted: 01/24/2024] [Indexed: 02/22/2024] Open
Abstract
Interlaboratory agreement of viral load assays depends on the accuracy and uniformity of quantitative calibrators. Previous work demonstrated poor agreement of secondary cytomegalovirus (CMV) standards with nominal values. This study re-evaluated this issue among commercially produced secondary standards for both BK virus (BKV) and CMV, using digital polymerase chain reaction (dPCR) to compare the materials from three different manufacturers. Overall, standards showed an improved agreement compared to prior work, against nominal values in both log10 copies/mL and log10 international unit (IU)/mL, with bias from manufacturer-assigned nominal values of 0.0-0.9 log10 units (either copies or IU)/mL. Standards normalized to IU and those values assigned by dPCR rather than by real-time PCR (qPCR) showed better agreement with nominal values. The latter reinforces prior conclusions regarding the utility of using such methods for quantitative value assignment in reference materials. Quantitative standards have improved over the last several years, and the remaining bias from nominal values might be further reduced by universal implementation of dPCR methods for value assignment, normalized to IU. IMPORTANCE Interlaboratory agreement of viral load assays depends on accuracy and uniformity of quantitative calibrators. Previous work, published in JCM several years ago, demonstrated poor agreement of secondary cytomegalovirus (CMV) standards with nominal values. This study re-evaluated this issue among commercially produced secondary standards for both BK virus (BKV) and CMV, using digital polymerase chain reaction (dPCR) to compare the materials from three different manufacturers. Overall, standards showed an improved agreement compared to prior work, against nominal values, indicating a substantial improvement in the production of accurate secondary viral standards, while supporting the need for further work in this area and for the broad adaption of international unit (IU) as a reporting standard for quantitative viral load results.
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Affiliation(s)
- R. T. Hayden
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Y. Su
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - L. Tang
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - H. Zhu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Z. Gu
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - H. L. Glasgow
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - S. S. Sam
- Division of Infectious Diseases, Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - A. M. Caliendo
- Department of Medicine, Alpert Medical School of Brown University, Providence, Rhode Island, USA
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10
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Fu X, Sun J, Yu B, Ye Y, Sheng L, Ji J, Zheng J, Fan M, Shao J, Sun X. Investigating enzyme kinetics and fluorescence sensing strategy of CRISPR/Cas12a for foodborne pathogenic bacteria. Anal Chim Acta 2024; 1290:342203. [PMID: 38246741 DOI: 10.1016/j.aca.2024.342203] [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: 10/29/2023] [Revised: 12/10/2023] [Accepted: 01/01/2024] [Indexed: 01/23/2024]
Abstract
Foodborne pathogenic bacteria are widespread in various foods, whose cross-contamination and re-contamination are critical influences on food safety. Rapid, accurate, and sensitive detection of foodborne pathogenic bacteria remains a topic of concern. CRISPR/Cas12a can recognize double-stranded DNA directly, showing great potential in nucleic acid detection. However, few studies have investigated the cleavage properties of CRISPR/Cas12a. In this study, the trans-cleavage properties of LbCas12a and AsCas12a were investigated to construct the detection methods for foodborne pathogenic bacteria. The highly sensitive fluorescent strategies for foodborne pathogens were constructed by analyzing the cleavage rates and properties of substrates at different substrate concentrations. Cas12a was activated in the presence of foodborne pathogenic target sequence was present, resulting in the cleavage of a single-stranded reporter ssDNA co-labelled by fluorescein quencher and fluorescein. The sensitivity and specificity of the Cas12a fluorescent strategy was investigated with Salmonella and Staphylococcus aureus as examples. The results showed that AsCas12a was slightly more capable of trans-cleavage than LbCas12a. The detection limits of AsCas12a for Salmonella and Staphylococcus aureus were 24.9 CFU mL-1 and 1.50 CFU mL-1, respectively. In all the seven bacteria, Staphylococcus aureus and Salmonella were accurately discriminated. The study provided a basis for constructing and improving the CRISPR/Cas12a fluorescence strategies. The AsCas12a-based detection strategy is expected to be a promising method for field detection.
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Affiliation(s)
- XuRan Fu
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - JiaDi Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China.
| | - Bingqian Yu
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China
| | - Yongli Ye
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Lina Sheng
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jian Ji
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jiayu Zheng
- Product Quality Comprehensive Inspection and Testing Center, Baoying, Jiangsu, 225800, PR China
| | - Minghong Fan
- Product Quality Comprehensive Inspection and Testing Center, Baoying, Jiangsu, 225800, PR China
| | - Jingdong Shao
- Comprehensive Technology Center of Zhangjiagang Customs, Zhangjiagang, Jiangsu, 215600, PR China
| | - XiuLan Sun
- School of Food Science and Technology, International Joint Laboratory on Food Safety, Synergetic Innovation Center of Food Safety and Quality Control, Jiangnan University, Wuxi, Jiangsu, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China.
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11
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An N, Dou X, Yin N, Lu H, Zheng J, Liu X, Yang H, Zhu X, Xiao X. The Use of Digital PCR for the Diagnosis of Demodex Blepharitis. Curr Eye Res 2024; 49:33-38. [PMID: 37823373 DOI: 10.1080/02713683.2023.2265083] [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: 07/10/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
PURPOSE This was a pilot study to evaluate the efficacy of digital polymerase chain reaction detection of Demodex in eyelid margin swabs for the diagnosis of Demodex blepharitis. This study aims to explore the possibility of digital polymerase chain reaction detection to improve the diagnostic accuracy of Demodex blepharitis detection. METHODS Volunteers were prospectively recruited and classified by experienced doctors into suspected Demodex blepharitis or healthy controls using slit-lamp evaluation of the eyelid margin and an inquiry about symptoms. Three eyelashes from each eyelid were epilated from participants in each group for microscopic observation and mite counting. Then, swabs from the eyelid margins of each eye were collected after the eyelashes were epilated and stored at -80 °C for future DNA extraction and digital polymerase chain reaction detection. The positive or negative results of both methods were compared for diagnostic accuracy, and the Kappa value was also calculated to evaluate their consistency. RESULTS The accuracy of the digital polymerase chain reaction detection was 71.6% and that of the mite counting method was 75%. Their combined accuracy was improved to 77.3%. The Kappa value of the two methods was 0.505, indicating moderate consistency. CONCLUSION Digital polymerase chain reaction detection of Demodex from ocular surface swabs was painless and noninvasive and is a potentially accurate quantitative method available for diagnosing Demodex blepharitis. This method is also complementary to the conventional mite counting method, particularly when a sufficient number of eyelashes cannot be effectively epilated.
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Affiliation(s)
- Na An
- Shaanxi Provincial Clinical Research Center for Ophthalmic Diseases, Xi'an City First Hospital, Xi'an, China
- Shaanxi Key Laboratory of Ophthalmology, Shaanxi Institute of Ophthalmology, Xi'an, China
| | - Xiuhong Dou
- Shaanxi Key Laboratory of Ophthalmology, Shaanxi Institute of Ophthalmology, Xi'an, China
| | - Ni Yin
- Shaanxi Provincial Clinical Research Center for Ophthalmic Diseases, Xi'an City First Hospital, Xi'an, China
- Shaanxi Key Laboratory of Ophthalmology, Shaanxi Institute of Ophthalmology, Xi'an, China
| | - Haiqing Lu
- Shaanxi Provincial Clinical Research Center for Ophthalmic Diseases, Xi'an City First Hospital, Xi'an, China
- Shaanxi Key Laboratory of Ophthalmology, Shaanxi Institute of Ophthalmology, Xi'an, China
| | - Jie Zheng
- Clinical Research Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xianning Liu
- Shaanxi Provincial Clinical Research Center for Ophthalmic Diseases, Xi'an City First Hospital, Xi'an, China
- Shaanxi Key Laboratory of Ophthalmology, Shaanxi Institute of Ophthalmology, Xi'an, China
| | - Hua Yang
- Shaanxi Provincial Clinical Research Center for Ophthalmic Diseases, Xi'an City First Hospital, Xi'an, China
- Shaanxi Key Laboratory of Ophthalmology, Shaanxi Institute of Ophthalmology, Xi'an, China
| | - Xiuping Zhu
- Shaanxi Provincial Clinical Research Center for Ophthalmic Diseases, Xi'an City First Hospital, Xi'an, China
- Shaanxi Key Laboratory of Ophthalmology, Shaanxi Institute of Ophthalmology, Xi'an, China
| | - Xianghua Xiao
- Shaanxi Provincial Clinical Research Center for Ophthalmic Diseases, Xi'an City First Hospital, Xi'an, China
- Shaanxi Key Laboratory of Ophthalmology, Shaanxi Institute of Ophthalmology, Xi'an, China
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12
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Quan PL, Alvarez-Amador M, Jiang Y, Sauzade M, Brouzes E. Robust and rapid partitioning in thermoplastic. Analyst 2023; 149:100-107. [PMID: 37982399 PMCID: PMC10777811 DOI: 10.1039/d3an01869e] [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] [Indexed: 11/21/2023]
Abstract
Partitioning is the core technology supporting digital assays. It divides a sample into thousands of individual reactors prior to amplification and absolute quantification of target molecules. Thermoplastics are attractive materials for large scale manufacturing, however they have been seldomly used for fabricating partitioning arrays. Patitioning in thermoplastic devices has proven difficult due to the challenge of efficiently displacing the air trapped in the nanoliter structures during priming of thousands of chambers. Here, we report the design of an array of chambers made of thermoplastics where the progression of the liquid-air interface is controlled by capillary effects. Our device performs robust partitioning over a wide range of pressures and can be actuated at low pressure by a simple micropipette. Our thermoplastic device lays the foundation to cost-effective and instrument-free partitioning platforms, which could be deployed in low-resource settings.
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Affiliation(s)
- Phenix-Lan Quan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Maria Alvarez-Amador
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Yuhe Jiang
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Martin Sauzade
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA.
| | - Eric Brouzes
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, 11794, USA.
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Cancer Center, Stony Brook School of Medicine, Stony Brook, NY 11794, USA
- Institute for Engineering Driven Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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13
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Ju DU, Park D, Kim IH, Kim S, Yoo HM. Development of Human Rhinovirus RNA Reference Material Using Digital PCR. Genes (Basel) 2023; 14:2210. [PMID: 38137032 PMCID: PMC10742479 DOI: 10.3390/genes14122210] [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: 10/03/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
The human rhinovirus (RV) is a positive-stranded RNA virus that causes respiratory tract diseases affecting both the upper and lower halves of the respiratory system. RV enhances its replication by concentrating RNA synthesis within a modified host membrane in an intracellular compartment. RV infections often occur alongside infections caused by other respiratory viruses, and the RV virus may remain asymptomatic for extended periods. Alongside qualitative detection, it is essential to accurately quantify RV RNA from clinical samples to explore the relationships between RV viral load, infections caused by the virus, and the resulting symptoms observed in patients. A reference material (RM) is required for quality evaluation, the performance evaluation of molecular diagnostic products, and evaluation of antiviral agents in the laboratory. The preparation process for the RM involves creating an RV RNA mixture by combining RV viral RNA with RNA storage solution and matrix. The resulting RV RNA mixture is scaled up to a volume of 25 mL, then dispensed at 100 µL per vial and stored at -80 °C. The process of measuring the stability and homogeneity of RV RMs was conducted by employing reverse transcription droplet digital polymerase chain reaction (RT-ddPCR). Digital PCR is useful for the analysis of standards and can help to improve measurement compatibility: it represents the equivalence of a series of outcomes for reference materials and samples being analyzed when a few measurement procedures are employed, enabling objective comparisons between quantitative findings obtained through various experiments. The number of copies value represents a measured result of approximately 1.6 × 105 copies/μL. The RM has about an 11% bottle-to-bottle homogeneity and shows stable results for 1 week at temperatures of 4 °C and -20 °C and for 12 months at a temperature of -80 °C. The developed RM can enhance the dependability of RV molecular tests by providing a precise reference value for the absolute copy number of a viral target gene. Additionally, it can serve as a reference for diverse studies.
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Affiliation(s)
- Dong U Ju
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- School of Biomedical Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Dongju Park
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Il-Hwan Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
| | - Seil Kim
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
| | - Hee Min Yoo
- Biometrology Group, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Republic of Korea
- Department of Precision Measurement, University of Science & Technology (UST), Daejeon 34113, Republic of Korea
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14
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Shi Q, Li J, Liu C, Zhai X, Chen L, Zhang Y, Feng D, Zhang R, Li J, Ling S, Zheng L, Luo Y, Liu Y. Fluorescence-coded logarithmic-dilution digital droplet PCR for ultrawide-dynamic-range nucleic acid quantification. Biosens Bioelectron 2023; 241:115702. [PMID: 37751652 DOI: 10.1016/j.bios.2023.115702] [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: 07/01/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/28/2023]
Abstract
Digital PCR (dPCR) is considered the next generation of nucleic acid detection for its ability of absolute quantification and high sensitivity. However, when compared to the current gold standard, quantitative PCR (qPCR), dPCR is falling behind by several orders of magnitude in dynamic range, which limits its clinical applicability. Here we present fluorescence-coded logarithmic-dilution digital droplet PCR (Flodd-PCR) that features a dynamic range across 7 orders of magnitude, over 2 orders higher than conventional dPCR (4-5 log range) and approaching that of qPCR (7-8 log range). Flodd-PCR realizes such a wide dynamic range by dividing ∼20,000 droplets into 4 groups, each featuring a unique dilution factor of the loaded DNA template and thus a shifted dynamic range. This is achieved by a microfluidic chip that performs multi-step serial dilution (20-925 folds) and droplet generation. The post-PCR droplets can be clustered in silico based on their dilution indicator fluorescence and analyzed independently. Experimentally, Flodd-PCR can detect 4-20,000,000 copies/μL (cp./μL) of the synthetic human papillomavirus (HPV) DNA and outperforms standard dPCR when analyzing clinical HPV samples. Furthermore, Flodd-PCR can be implemented with existing dPCR system set-up with minimal adjustment, and therefore will also have wide practicality in different applications which conventional dPCR has already demonstrated.
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Affiliation(s)
- Qingyuan Shi
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China; School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jie Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Chunchen Liu
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China; Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xuanpei Zhai
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Long Chen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Ye Zhang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China; Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Dezhi Feng
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Rong Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jian Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Shengjie Ling
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China; Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Yuan Luo
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China.
| | - Yifan Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China; Shanghai Clinical Research and Trial Center, Shanghai, 201210, China.
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15
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Edwards RL, Takach JE, McAndrew MJ, Menteer J, Lestz RM, Whitman D, Baxter-Lowe LA. Next generation multiplexing for digital PCR using a novel melt-based hairpin probe design. Front Genet 2023; 14:1272964. [PMID: 38028620 PMCID: PMC10667681 DOI: 10.3389/fgene.2023.1272964] [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: 08/04/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Digital PCR (dPCR) is a powerful tool for research and diagnostic applications that require absolute quantification of target molecules or detection of rare events, but the number of nucleic acid targets that can be distinguished within an assay has limited its usefulness. For most dPCR systems, one target is detected per optical channel and the total number of targets is limited by the number of optical channels on the platform. Higher-order multiplexing has the potential to dramatically increase the usefulness of dPCR, especially in scenarios with limited sample. Other potential benefits of multiplexing include lower cost, additional information generated by more probes, and higher throughput. To address this unmet need, we developed a novel melt-based hairpin probe design to provide a robust option for multiplexing digital PCR. A prototype multiplex digital PCR (mdPCR) assay using three melt-based hairpin probes per optical channel in a 16-well microfluidic digital PCR platform accurately distinguished and quantified 12 nucleic acid targets per well. For samples with 10,000 human genome equivalents, the probe-specific ranges for limit of blank were 0.00%-0.13%, and those for analytical limit of detection were 0.00%-0.20%. Inter-laboratory reproducibility was excellent (r 2 = 0.997). Importantly, this novel melt-based hairpin probe design has potential to achieve multiplexing beyond the 12 targets/well of this prototype assay. This easy-to-use mdPCR technology with excellent performance characteristics has the potential to revolutionize the use of digital PCR in research and diagnostic settings.
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Affiliation(s)
- Rebecca L. Edwards
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | | | | | - Jondavid Menteer
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Division of Cardiology, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Rachel M. Lestz
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Division of Nephrology, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Douglas Whitman
- Luminex Corporation, A Diasorin Company, Austin, TX, United States
| | - Lee Ann Baxter-Lowe
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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16
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Ozono Y, Kawakami H, Uchiyama N, Hatada H, Ogawa S. Current status and issues in genomic analysis using EUS-FNA/FNB specimens in hepatobiliary-pancreatic cancers. J Gastroenterol 2023; 58:1081-1093. [PMID: 37698719 PMCID: PMC10590314 DOI: 10.1007/s00535-023-02037-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
Comprehensive genomic profiling based on next-generation sequencing has recently been used to provide precision medicine for various advanced cancers. Endoscopic ultrasound (EUS)-guided fine-needle aspiration (EUS-FNA) and EUS-guided fine-needle biopsy (EUS-FNB) play essential roles in the diagnosis of abdominal masses, mainly pancreatic cancers. In recent years, CGP analysis using EUS-FNA/FNB specimens for hepatobiliary-pancreatic cancers has increased; however, the success rate of CGP analysis is not clinically satisfactory, and many issues need to be resolved to improve the success rate of CGP analysis. In this article, we review the transition from EUS-FNA to FNB, compare each test, and discuss the current status and issues in genomic analysis of hepatobiliary-pancreatic cancers using EUS-FNA/FNB specimens.
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Affiliation(s)
- Yoshinori Ozono
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan
| | - Hiroshi Kawakami
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan.
| | - Naomi Uchiyama
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan
| | - Hiroshi Hatada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan
| | - Souichiro Ogawa
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki, 889-1692, Japan
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17
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Calabrese S, Markl AM, Neugebauer M, Krauth SJ, Borst N, von Stetten F, Lehnert M. Reporter emission multiplexing in digital PCRs (REM-dPCRs): direct quantification of multiple target sequences per detection channel by population specific reporters. Analyst 2023; 148:5243-5254. [PMID: 37727114 DOI: 10.1039/d3an00191a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Digital PCRs (dPCRs) are widely used methods for the detection and quantification of rare abundant sequences relevant to fields such as liquid biopsy or oncology. In order to increase the information content and save valuable sample materials, there is a significant need for digital multiplexing methods that are easy to establish, analyse, and interpret, and ideally allow the usage of existing lab equipment. Herein, we present a novel reporter emission multiplexing approach for the digital PCR method (REM-dPCR), which meets these requirements. It further increases the multiplexing capacity of commercial dPCR devices. For example, we present a stepwise increase in multiplexing degrees from a monochrome two-plex assay in one detection channel to a six-plex REM-dPCR assay in a three-color dPCR device for KRAS/BRAF single nucleotide polymorphism (SNP) target sequences. The guidelines for the REM-dPCR design are presented, and the process from duplex to six-plex assay establishment, taking into account the target sequence-dependent effects on assay performance, is discussed. Furthermore, the assay-specific, sensitive and precise quantification of different fractions of KRAS mutant and wild-type DNA sequences in different ratios is demonstrated. To increase the device capacitance and the degree of multiplexing, the REM-dPCR uses the advantage of n target-independent reporter molecules in combination with target sequence-specific mediator probes. Different reporter types are labelled with fluorophores of different signal intensities but not necessarily different emission spectra. This leads to the generation of n independent single-positive populations in the dataspace, created by k detection channels, whereby n > k and n ≥ 2. By usage of target-independent but population-specific reporter types, a fixed set of six optimized signalling molecules could be defined. This reporter set enables the robust generation and precise differentiation of multiple fluorescence signals in dPCRs and can be transferred to new target panels. The set which enables stable signal generation and differentiation in a specified device would allow easy transfer to new target panels.
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Affiliation(s)
| | - Anja M Markl
- Hahn-Schickard, 79110 Freiburg, Germany.
- Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Maximilian Neugebauer
- Hahn-Schickard, 79110 Freiburg, Germany.
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany
| | - Stefanie J Krauth
- School of Biodiversity, One Health, and Veterinary Medicine, University of Glasgow, Glasgow, UK
- School of Health and Wellbeing, General Practice and Primary Care, University of Glasgow, Glasgow, UK
| | - Nadine Borst
- Hahn-Schickard, 79110 Freiburg, Germany.
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany
| | - Felix von Stetten
- Hahn-Schickard, 79110 Freiburg, Germany.
- Laboratory for MEMS Applications, IMTEK-Department of Microsystems Engineering, University of Freiburg, 79110 Freiburg, Germany
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18
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Verlicchi A, Canale M, Chiadini E, Cravero P, Urbini M, Andrikou K, Pasini L, Flospergher M, Burgio MA, Crinò L, Ulivi P, Delmonte A. The Clinical Significance of Circulating Tumor DNA for Minimal Residual Disease Identification in Early-Stage Non-Small Cell Lung Cancer. Life (Basel) 2023; 13:1915. [PMID: 37763318 PMCID: PMC10532754 DOI: 10.3390/life13091915] [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: 07/07/2023] [Revised: 08/18/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Lung cancer (LC) is the deadliest malignancy worldwide. In an operable stage I-III patient setting, the detection of minimal residual disease (MRD) after curative treatment could identify patients at higher risk of relapse. In this context, the study of circulating tumor DNA (ctDNA) is emerging as a useful tool to identify patients who could benefit from an adjuvant treatment, and patients who could avoid adverse events related to a more aggressive clinical management. On the other hand, ctDNA profiling presents technical, biological and standardization challenges before entering clinical practice as a decisional tool. In this paper, we review the latest advances regarding the role of ctDNA in identifying MRD and in predicting patients' prognosis, with a particular focus on clinical trials investigating the potential of ctDNA, the technical challenges to address and the biological parameters that influence the MRD detection.
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Affiliation(s)
- Alberto Verlicchi
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Matteo Canale
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Elisa Chiadini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Paola Cravero
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Milena Urbini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Kalliopi Andrikou
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Luigi Pasini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Michele Flospergher
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Marco Angelo Burgio
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Lucio Crinò
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
| | - Paola Ulivi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (E.C.); (M.U.); (L.P.); (P.U.)
| | - Angelo Delmonte
- Medical Oncology Department, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (A.V.); (P.C.); (K.A.); (M.F.); (M.A.B.); (L.C.); (A.D.)
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19
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Liu DD, Muliaditan D, Viswanathan R, Cui X, Cheow LF. Melt-Encoded-Tags for Expanded Optical Readout in Digital PCR (METEOR-dPCR) Enables Highly Multiplexed Quantitative Gene Panel Profiling. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301630. [PMID: 37485651 PMCID: PMC10520687 DOI: 10.1002/advs.202301630] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/27/2023] [Indexed: 07/25/2023]
Abstract
Digital PCR (dPCR) is an important tool for precise nucleic acid quantification in clinical setting, but the limited multiplexing capability restricts its applications for quantitative gene panel profiling. Here, this work describes melt-encoded-tags for expanded optical readout in digital PCR (METEOR-dPCR), a simple two-step assay that enables simultaneous quantification of a large panel of arbitrary genes in a dPCR platform. Target genes are quantitatively converted into DNA tags with unique melting temperatures through a ligation approach. These tags are then counted and distinguished by their melt-curve profiles on a dPCR platform. A multiplexing capacity of M^N, where M is the number of resolvable melting temperature and N is the number of fluorescence channel, can be achieved. This work validates METEOR-dPCR with simultaneous DNA copy number profiling of 60 targets using dPCR in cancer cells, and demonstrates its sensitivity for estimating tumor fraction in mixed tumor and normal DNA samples. The rapid, quantitative, and highly multiplexed METEOR-dPCR assay will have wide appeal for many clinical applications.
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Affiliation(s)
- Dong Dong Liu
- Institute for Health Innovation and TechnologyNational University of SingaporeSingapore117599Singapore
| | - Daniel Muliaditan
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
- Genome institute of SingaporeAgency for ScienceTechnology and ResearchSingapore138672Singapore
| | - Ramya Viswanathan
- Institute for Health Innovation and TechnologyNational University of SingaporeSingapore117599Singapore
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
| | - Xu Cui
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
| | - Lih Feng Cheow
- Institute for Health Innovation and TechnologyNational University of SingaporeSingapore117599Singapore
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
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20
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Flütsch S, Wiestner F, Butticaz L, Moor D, Stölting KN. Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp. BMC Genomics 2023; 24:375. [PMID: 37403035 DOI: 10.1186/s12864-023-09429-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND Vibrio spp. are a diverse group of ecologically important marine bacteria responsible for several foodborne outbreaks of gastroenteritis around the world. Their detection and characterization are moving away from conventional culture-based methods towards next generation sequencing (NGS)-based approaches. However, genomic methods are relative in nature and suffer from technical biases arising from library preparation and sequencing. Here, we introduce a quantitative NGS-based method that enables the quantitation of Vibrio spp. at the limit of quantification (LOQ) through artificial DNA standards and their absolute quantification via digital PCR (dPCR). RESULTS We developed six DNA standards, called Vibrio-Sequins, together with optimized TaqMan assays for their quantification in individually sequenced DNA libraries via dPCR. To enable Vibrio-Sequin quantification, we validated three duplex dPCR methods to quantify the six targets. LOQs were ranging from 20 to 120 cp/µl for the six standards, whereas the limit of detection (LOD) was ~ 10 cp/µl for all six assays. Subsequently, a quantitative genomics approach was applied to quantify Vibrio-DNA in a pooled DNA mixture derived from several Vibrio species in a proof-of-concept study, demonstrating the increased power of our quantitative genomic pipeline through the coupling of NGS and dPCR. CONCLUSIONS We significantly advance existing quantitative (meta)genomic methods by ensuring metrological traceability of NGS-based DNA quantification. Our method represents a useful tool for future metagenomic studies aiming at quantifying microbial DNA in an absolute manner. The inclusion of dPCR into sequencing-based methods supports the development of statistical approaches for the estimation of measurement uncertainties (MU) for NGS, which is still in its infancy.
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Affiliation(s)
- Sabrina Flütsch
- Swiss Federal Institute of Metrology METAS, Lindenweg 50, Bern-Wabern, 3003, Switzerland.
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland.
| | - Fabian Wiestner
- Swiss Federal Institute of Metrology METAS, Lindenweg 50, Bern-Wabern, 3003, Switzerland
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland
| | - Lisa Butticaz
- Federal Food Safety and Veterinary Office FSVO, Schwarzenburgstrasse 165, Bern-Köniz, 3003, Switzerland
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland
| | - Dominik Moor
- Federal Food Safety and Veterinary Office FSVO, Schwarzenburgstrasse 165, Bern-Köniz, 3003, Switzerland
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland
| | - Kai N Stölting
- Swiss Federal Institute of Metrology METAS, Lindenweg 50, Bern-Wabern, 3003, Switzerland.
- Swiss Federal Institute of Metrology METAS, Campus Liebefeld, Schwarzenburgstrasse 165, Bern-Köniz, 3097, Switzerland.
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21
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Huang Z, Lyon CJ, Wang J, Lu S, Hu TY. CRISPR Assays for Disease Diagnosis: Progress to and Barriers Remaining for Clinical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301697. [PMID: 37162202 PMCID: PMC10369298 DOI: 10.1002/advs.202301697] [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: 03/18/2023] [Revised: 04/24/2023] [Indexed: 05/11/2023]
Abstract
Numerous groups have employed the special properties of CRISPR/Cas systems to develop platforms that have broad potential applications for sensitive and specific detection of nucleic acid (NA) targets. However, few of these approaches have progressed to commercial or clinical applications. This review summarizes the properties of known CRISPR/Cas systems and their applications, challenges associated with the development of such assays, and opportunities to improve their performance or address unmet assay needs using nano-/micro-technology platforms. These include rapid and efficient sample preparation, integrated single-tube, amplification-free, quantifiable, multiplex, and non-NA assays. Finally, this review discusses the current outlook for such assays, including remaining barriers for clinical or point-of-care applications and their commercial development.
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Affiliation(s)
- Zhen Huang
- National Clinical Research Center for Infectious DiseasesShenzhen Third People's HospitalSouthern University of Science and Technology29 Bulan RoadShenzhenGuangdong518112China
- Center for Cellular and Molecular DiagnosticsTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
- Department of Biochemistry and Molecular BiologyTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
| | - Christopher J. Lyon
- Center for Cellular and Molecular DiagnosticsTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
- Department of Biochemistry and Molecular BiologyTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
| | - Jin Wang
- Tolo Biotechnology Company Limited333 Guiping RoadShanghai200233China
| | - Shuihua Lu
- National Clinical Research Center for Infectious DiseasesShenzhen Third People's HospitalSouthern University of Science and Technology29 Bulan RoadShenzhenGuangdong518112China
| | - Tony Y. Hu
- Center for Cellular and Molecular DiagnosticsTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
- Department of Biochemistry and Molecular BiologyTulane University School of Medicine1430 Tulane AveNew OrleansLA70112USA
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22
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Li X, Lin YL, Shao JK, Wu XJ, Li X, Yao H, Shi FL, Li LS, Zhang WG, Chang ZY, Chai NL, Wang YL, Linghu EQ. Plasma exosomal hsa_circ_0079439 as a novel biomarker for early detection of gastric cancer. World J Gastroenterol 2023; 29:3482-3496. [PMID: 37389236 PMCID: PMC10303519 DOI: 10.3748/wjg.v29.i22.3482] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/04/2023] [Accepted: 05/11/2023] [Indexed: 06/06/2023] Open
Abstract
BACKGROUND Due to the poor prognosis of gastric cancer (GC), early detection methods are urgently needed. Plasma exosomal circular RNAs (circRNAs) have been suggested as novel biomarkers for GC.
AIM To identify a novel biomarker for early detection of GC.
METHODS Healthy donors (HDs) and GC patients diagnosed by pathology were recruited. Nine GC patients and three HDs were selected for exosomal whole-transcriptome RNA sequencing. The expression profiles of circRNAs were analyzed by bioinformatics methods and validated by droplet digital polymerase chain reaction. The expression levels and area under receiver operating characteristic curve values of plasma exosomal circRNAs and standard serum biomarkers were used to compare their diagnostic efficiency.
RESULTS There were 303 participants, including 240 GC patients and 63 HDs, involved in the study. The expression levels of exosomal hsa_circ_0079439 were significantly higher in GC patients than in HDs (P < 0.0001). However, the levels of standard serum biomarkers were similar between the two groups. The area under the curve value of exosomal hsa_circ_0079439 was higher than those of standard biomarkers, including carcinoembryonic antigen, carbohydrate antigen (CA)19-9, CA72-4, alpha-fetoprotein, and CA125 (0.8595 vs 0.5862, 0.5660, 0.5360, 0.5082, and 0.5018, respectively). The expression levels of exosomal hsa_circ_0079439 were significantly decreased after treatment (P < 0.05). Moreover, the expression levels of exosomal hsa_circ_0079439 were obviously higher in early GC (EGC) patients than in HDs (P < 0.0001).
CONCLUSION Our results suggest that plasma exosomal hsa_circ_0079439 is upregulated in GC patients. Moreover, the levels of exosomal hsa_circ_0079439 could distinguish EGC and advanced GC patients from HDs. Therefore, plasma exosomal hsa_circ_0079439 might be a potential biomarker for the diagnosis of GC during both the early and late stages.
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Affiliation(s)
- Xiao Li
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
- Medical School of Chinese PLA, Beijing 100853, China
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - Yan-Li Lin
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - Jia-Kang Shao
- Medical School of Chinese PLA, Beijing 100853, China
| | - Xiao-Jie Wu
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - Xiang Li
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - He Yao
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - Fa-Liang Shi
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - Long-Song Li
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
- Medical School of Chinese PLA, Beijing 100853, China
| | - Wen-Gang Zhang
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
- Medical School of Chinese PLA, Beijing 100853, China
| | | | - Ning-Li Chai
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
| | - You-Liang Wang
- Beijing Institute of Biotechnology, Beijing 100071, China
| | - En-Qiang Linghu
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853, China
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23
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Dong T, Wang M, Liu J, Ma P, Pang S, Liu W, Liu A. Diagnostics and analysis of SARS-CoV-2: current status, recent advances, challenges and perspectives. Chem Sci 2023; 14:6149-6206. [PMID: 37325147 PMCID: PMC10266450 DOI: 10.1039/d2sc06665c] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/03/2023] [Indexed: 06/17/2023] Open
Abstract
The disastrous spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has induced severe public healthcare issues and weakened the global economy significantly. Although SARS-CoV-2 infection is not as fatal as the initial outbreak, many infected victims suffer from long COVID. Therefore, rapid and large-scale testing is critical in managing patients and alleviating its transmission. Herein, we review the recent advances in techniques to detect SARS-CoV-2. The sensing principles are detailed together with their application domains and analytical performances. In addition, the advantages and limits of each method are discussed and analyzed. Besides molecular diagnostics and antigen and antibody tests, we also review neutralizing antibodies and emerging SARS-CoV-2 variants. Further, the characteristics of the mutational locations in the different variants with epidemiological features are summarized. Finally, the challenges and possible strategies are prospected to develop new assays to meet different diagnostic needs. Thus, this comprehensive and systematic review of SARS-CoV-2 detection technologies may provide insightful guidance and direction for developing tools for the diagnosis and analysis of SARS-CoV-2 to support public healthcare and effective long-term pandemic management and control.
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Affiliation(s)
- Tao Dong
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
- School of Pharmacy, Medical College, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Mingyang Wang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Junchong Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Pengxin Ma
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Shuang Pang
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
| | - Wanjian Liu
- Qingdao Hightop Biotech Co., Ltd 369 Hedong Road, Hi-tech Industrial Development Zone Qingdao 266112 China
| | - Aihua Liu
- Institute for Chemical Biology & Biosensing, College of Life Sciences, Qingdao University 308 Ningxia Road Qingdao 266071 China
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Abstract
There has been a recent surge of advances in biomolecular assays based on the measurement of discrete molecular targets as opposed to signals averaged across molecular ensembles. Many of these "digital" assay designs derive from now-mature technologies involving single-molecule imaging and microfluidics and provide an assortment of new modalities to quantify nucleic acids and proteins in biospecimens such as blood and tissue homogenates. A primary new benefit is the robust detection of trace analytes at attomolar to femtomolar concentrations for which many ensemble assays cannot distinguish signals above noise levels. In addition, multiple biomolecules can be differentiated within a mixture using optical barcodes, with much faster and simpler readouts compared with sequencing methods. In ideal digital assays, signals should, in theory, further represent absolute molecular counts, rather than relative levels, eliminating the need for calibration standards that are the mainstay of typical assays. Several digital assay platforms have now been commercialized but challenges hinder the adoption and diversification of these new formats, as there are broad needs to balance sensitivity and dynamic range of detection, increase analyte multiplexing, improve sample throughput, and reduce cost. Our lab and others have developed technologies to address these challenges by redesigning molecular probes and labels, improving molecular transport within detection focal volumes, and applying solution-based readout methods in flow.This Account describes the principles, formats, and design constraints of digital biomolecular assays that apply optical labels toward the goal of simple and routine target counting that may ultimately approach absolute readout standards. The primary challenges can be understood from fundamental concepts in thermodynamics and kinetics of association reactions, mass transport, and discrete statistics. Major advances include (1) new inorganic nanocrystal probes for more robust counting compared with dyes, (2) diverse molecular amplification tools that endow attachment of numerous labels to single targets, (3) specialized surfaces with patterned features for electromagnetic coupling to labels for signal amplification, (4) surface capture enhancement methods to concentrate targets through disruption of diffusion depletion zones, and (5) flow counting in which analytes are rapidly counted in solution without pull-down to a surface. Further progress and integration of these tools for biomolecular counting could improve the precision of laboratory measurements in life sciences research and benefit clinical diagnostic assays for low abundance biomarkers in limiting biospecimen volumes that are out of reach of traditional ensemble-level bioassays.
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Affiliation(s)
- Chia-Wei Kuo
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Andrew M Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Materials Science & Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, Urbana, Illinois 61801, United States
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25
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Rong N, Chen K, Shao J, Ouyang Q, Luo C. A 3D Scalable Chamber-Array Chip for Digital LAMP. Anal Chem 2023; 95:7830-7838. [PMID: 37115526 DOI: 10.1021/acs.analchem.2c05288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
As an absolute quantification method at the single-molecule level, digital PCR (dPCR) offers the highest accuracy. In this work, we developed a 3D scalable chamber-array chip that multiplied the number of partitions by stacking chamber-array layers and realized digital loop-mediated isothermal amplification to quantify DNA molecules. It greatly increases the number of partitions to improve the performance of dPCR without increasing the chip size, the operation workflow complicity, and operation time. For the three-chamber-array-layer chip which contains 200,000 reactors of a 0.125 nL volume, it has been proved that the reagent filling and partition were finished within 3 min, and the whole detection could be finished within 1 h. The method demonstrated that it could be scalable to a six-chamber-array layer, which contains 400,000 reactors without increasing the size of the chip and the complication of filling/partition workflow but only takes an additional hour for scanning. Due to its potential for high throughput, low cost, and simple operation, our device may significantly expand the clinical application range of dPCR.
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Affiliation(s)
- Nan Rong
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Kaiyue Chen
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
| | - Jiqi Shao
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Qi Ouyang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
| | - Chunxiong Luo
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
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Chen M, Xue J, Sang Y, Jiang W, He W, Hong S, Lv W, Xiao H, Liu R. Highly sensitive droplet digital PCR for detection of RET fusion in papillary thyroid cancer. BMC Cancer 2023; 23:363. [PMID: 37081420 PMCID: PMC10120194 DOI: 10.1186/s12885-023-10852-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/15/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Thyroid cancer is the most frequent malignancy of the endocrine system, of which papillary thyroid cancer (PTC) is the predominant form with a rapid increasing incidence worldwide. Rearranged during transfection (RET) fusions are common genetic drivers of PTC and the potent RET inhibitor selpercatinib has been recently approved for treating advanced or metastatic RET fusion-positive thyroid cancer. In this study we aimed to develop a droplet digital PCR (ddPCR) system to accurately detect RET fusion in PTC samples. METHODS The frequency and distribution of RET fusions in PTC were analyzed using genomic data of 402 PTC patients in The Cancer Genome Atlas (TCGA) database. To establish the ddPCR system for detecting CCDC6::RET fusion, a plasmid containing CCDC6::RET infusion fragment was constructed as standard template, the annealing temperature and concentrations of primers and probe were optimized. The analytical performance of ddPCR and quantitative reverse transcription PCR (qRT-PCR) were assessed in standard templates and tissue samples from 112 PTC patients. Sanger sequencing was performed in all the RET fusion-positive samples identified by ddPCR. RESULTS RET fusions were observed in 25 (6.2%) of the 402 TCGA samples, and 15 (60%) of the RET fusion-positive patients had the CCDC6::RET fusion. Compared with qRT-PCR, the ddPCR method showed a lower limit of detection (128.0 and 430.7 copies/reaction for ddPCR and qRT-PCR, respectively). When applying the two methods to 112 tissue samples of PTC, eleven (9.8%) CCDC6::RET fusion-positive samples were detected by qRT-PCR, while ddPCR identified 4 additional positive samples (15/112, 13.4%). All the CCDC6::RET fusion-positive cases identified by ddPCR were confirmed by Sanger sequencing except for one case with 0.14 copies/uL of the fusion. CONCLUSION The accurate and sensitive ddPCR method reported here is powerful to detection CCDC6::RET fusion in PTC samples, application of this method would benefit more RET fusion-positive patients in the clinic.
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Affiliation(s)
- Mengke Chen
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Junyu Xue
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Ye Sang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Wenting Jiang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Weiman He
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Shubin Hong
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Weiming Lv
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Haipeng Xiao
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China.
| | - Rengyun Liu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China.
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Chiho M, Ono Y, Hayashi A, Takahashi K, Taniue K, Kakisaka R, Mori M, Ishii T, Sato H, Okada T, Kawabata H, Goto T, Tamamura N, Omori Y, Takahashi K, Katanuma A, Karasaki H, Liss AS, Mizukami Y. Multiplex digital PCR assay to detect multiple KRAS and GNAS mutations associated with pancreatic carcinogenesis from minimal specimen amounts. J Mol Diagn 2023; 25:367-377. [PMID: 36965665 DOI: 10.1016/j.jmoldx.2023.02.007] [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: 03/08/2022] [Revised: 02/14/2023] [Accepted: 02/24/2023] [Indexed: 03/27/2023] Open
Abstract
Digital PCR (dPCR) allows for highly sensitive quantification of low-frequency mutations and facilitates early detection of cancer. However, low throughput targeting of single hotspots in dPCR hinders variant specification when multiple probes are used. Here we developed a dPCR method to simultaneously identify major variants related to pancreatic carcinogenesis. Using a 2-D plot of droplet fluorescence under the optimized concentration of two fluorescent probe pools, we determined the absolute quantification of different KRAS and GNAS variants. Successful detection of the multiple driver mutations was verified in 24 surgically resected tumor samples from 19 patients and 22 FNA samples from patients with pancreatic ductal adenocarcinoma. Precise quantification of the variant allele frequency was optimized using template DNA at a concentration as low as 1-10 ng. Furthermore, amplicons targeting multiple hotspots were successfully enriched with fewer false positives using high-fidelity polymerase, allowing for the detection of various KRAS and GNAS mutations with high probability in small cell/tissue specimens. Using this target enrichment, mutations at a rate of 90% in small residual tissues, such as the FNA needle flush and microscopic lesions in resected specimens, have successfully been identified. The proposed method allows for low-cost and accurate detection of driver mutations to diagnose cancers, even with minimal tissue collection.
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Affiliation(s)
- Maeda Chiho
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan; Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan.
| | - Akihiro Hayashi
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Kenji Takahashi
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Kenzui Taniue
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan; Isotope Science Center, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Rika Kakisaka
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Miyuki Mori
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Takahiro Ishii
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Hiroki Sato
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan; Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Tetsuhiro Okada
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Hidemasa Kawabata
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Takuma Goto
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Nobue Tamamura
- Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
| | - Yuko Omori
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan; Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Kuniyuki Takahashi
- Center for Gastroenterology, Teine Keijinkai Hospital, Sapporo, 006-0811, Japan
| | - Akio Katanuma
- Center for Gastroenterology, Teine Keijinkai Hospital, Sapporo, 006-0811, Japan
| | - Hidenori Karasaki
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan
| | - Andrew Scott Liss
- Division of Gastrointestinal and Oncologic Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114
| | - Yusuke Mizukami
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, 065-0033, Japan; Department of Medicine, Asahikawa Medical University, Asahikawa, 078-8510, Japan
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Primary Quantitative Reference Standards for Viral Nucleic Acids Should Be Developed Using Digital Polymerase Chain Reaction Instead of Consensus Testing. J Clin Microbiol 2023; 61:e0133822. [PMID: 36475837 PMCID: PMC9879095 DOI: 10.1128/jcm.01338-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Yang H, Yu J, Jin L, Zhao Y, Gao Q, Shi C, Ye L, Li D, Yu H, Xu Y. A deep learning based method for automatic analysis of high-throughput droplet digital PCR images. Analyst 2023; 148:239-247. [PMID: 36511172 DOI: 10.1039/d2an01631a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Droplet digital PCR (ddPCR) is a technique for absolute quantification of nucleic acid molecules and is widely used in biomedical research and clinical diagnosis. ddPCR partitions the reaction solution containing target molecules into a large number of independent microdroplets for amplification and performs quantitative analysis of target molecules by calculating the proportion of positive droplets by the principle of Poisson distribution. Accurate recognition of positive droplets in ddPCR images is of great importance to guarantee the accuracy of target nucleic acid quantitative analysis. However, hand-designed operators are sensitive to interference and have disadvantages such as low contrast, uneven illumination, low sample copy number, and noise, and their accuracy and robustness still need to be improved. Herein, we developed a deep learning-based high-throughput ddPCR droplet detection framework for robust and accurate ddPCR image analysis, and the experimental results show that our method achieves excellent performance in the recognition of positive droplets (99.71%) within a limited time. By combining the Hough transform and a convolutional neural network (CNN), our novel method can automatically filter out invalid droplets that are difficult to be identified by local or global encoding methods and realize high-precision localization and classification of droplets in ddPCR images under variable exposure, contrast, and uneven illumination conditions without the need for image pre-processing and normalization processes.
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Affiliation(s)
- Haixu Yang
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China. .,Binjiang Institute of Zhejiang University, Hangzhou, 310053, China
| | - Jiahui Yu
- Binjiang Institute of Zhejiang University, Hangzhou, 310053, China
| | - Luhong Jin
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China.
| | - Yunpeng Zhao
- ZJU-Bioer Technology Research & Development Center, Hangzhou Bioer Technology, Hangzhou, 310053, China
| | - Qi Gao
- ZJU-Bioer Technology Research & Development Center, Hangzhou Bioer Technology, Hangzhou, 310053, China
| | - Changrong Shi
- ZJU-Bioer Technology Research & Development Center, Hangzhou Bioer Technology, Hangzhou, 310053, China
| | - Lei Ye
- ZJU-Bioer Technology Research & Development Center, Hangzhou Bioer Technology, Hangzhou, 310053, China
| | - Dong Li
- ZJU-Bioer Technology Research & Development Center, Hangzhou Bioer Technology, Hangzhou, 310053, China
| | - Hai Yu
- ZJU-Bioer Technology Research & Development Center, Hangzhou Bioer Technology, Hangzhou, 310053, China
| | - Yingke Xu
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, 310027, China. .,Binjiang Institute of Zhejiang University, Hangzhou, 310053, China.,Department of Endocrinology, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Children's Health, Hangzhou, 310051, China
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Wang D, Liu E, Liu H, Jin X, Niu C, Gao Y, Su X. A droplet digital PCR assay for detection and quantification of Verticillium nonalfalfae and V. albo-atrum. Front Cell Infect Microbiol 2023; 12:1110684. [PMID: 36710974 PMCID: PMC9874294 DOI: 10.3389/fcimb.2022.1110684] [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: 11/29/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
Verticillium nonalfalfae and V. albo-atrum are notorious pathogenic fungi that cause a destructive vascular disease called Verticillium wilt worldwide. Thus, timely and quantitative monitoring of fungal progression is highly desirable for early diagnosis and risk assessment. In this study, we developed a droplet digital polymerase chain reaction (ddPCR) assay to detect and quantify V. nonalfalfae and V. albo-atrum. The performance of this assay was validated in comparison with that of a quantitative real-time polymerase chain reaction (qPCR) assay. The standard curve analysis of the ddPCR assay showed good linearity. The ddPCR assay indicated similar detection sensitivity to that of qPCR on pure genomic DNA, while it enhanced the positive rate for low-abundance fungi, especially in alfalfa stems. Receiver operating characteristic analysis revealed that ddPCR provided superior diagnostic performance on field tissues compared to qPCR, and the area under curve values were 0.94 and 0.90 for alfalfa roots and stems, respectively. Additionally, the quantitative results of the two methods were highly concordant (roots: R2 = 0.91; stems: R2 = 0.76); however, the concentrations determined by ddPCR were generally higher than those determined by qPCR. This discrepancy was potentially caused by differing amplification efficiencies for qPCR between cultured and field samples. Furthermore, the ddPCR assays appreciably improved quantitative precision, as reflected by lower coefficients of variation. Overall, the ddPCR method enables sensitive detection and accurate quantification of V. nonalfalfae and V. albo-atrum, providing a valuable tool for evaluating disease progression and enacting effective disease control.
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Affiliation(s)
- Di Wang
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Enliang Liu
- 2Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Haiyang Liu
- 3Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xi Jin
- 4Hebei Technology Innovation Center for Green Management of Soil-Borne Diseases, Baoding University, Hebei, China
| | - Chunyan Niu
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yunhua Gao
- 1Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China,*Correspondence: Yunhua Gao, ; Xiaofeng Su,
| | - Xiaofeng Su
- 5Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China,*Correspondence: Yunhua Gao, ; Xiaofeng Su,
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Park JH, Myung JK, Lee SJ, Kim H, Kim S, Lee SB, Jang H, Jang WI, Park S, Yang H, Shim S, Kim MJ. ABCA1-Mediated EMT Promotes Papillary Thyroid Cancer Malignancy through the ERK/Fra-1/ZEB1 Pathway. Cells 2023; 12:cells12020274. [PMID: 36672209 PMCID: PMC9857273 DOI: 10.3390/cells12020274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/29/2022] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Papillary thyroid cancer (PTC) is the most prevalent histological type of thyroid cancer (TC) worldwide. Although tumor metastasis occurs in regional lymph nodes, distant metastasis (DM) may also occur. Radioactive iodine (RAI) therapy is an effective treatment for TC; however, resistance to RAI occurs in patients with DM. Therefore, in this study, we investigated the efficacy of DM-related biomarkers as therapeutic targets for PTC therapy. ABCA1 expression was higher in aggressive BCPAP cells than in other PTC cells in terms of migration and invasion capacity. The knockdown of ABCA1 substantially decreased the expression of the epithelial-mesenchymal transition (EMT) marker, N-cadherin, and EMT regulator (ZEB1), resulting in suppressed migration and invasion of BCPAP cells. ABCA1 knockdown also reduced ERK activity and Fra-1 expression, which correlated with the effects of an ERK inhibitor or siRNA-mediated inhibition of ERK or Fra-1 expression. Furthermore, ABCA1-knocked-down BCPAP cells suppressed cell migration and invasion by reducing Fra-1 recruitment to Zeb1 promoter; lung metastasis was not observed in mice injected with ABCA1-knocked-down cells. Overall, our findings suggest that ABCA1 regulates lung metastasis in TC cells.
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Affiliation(s)
- Ji-Hye Park
- Laboratory of Radiation Exposure & Therapeutics, National Radiation Emergency Medical Center, Korea Institute of Radiological & Medical Science, Seoul 01812, Republic of Korea
- OPTOLANE Technologies Inc., Seongnam 13494, Republic of Korea
| | - Jae-Kyung Myung
- Laboratory of Radiation Exposure & Therapeutics, National Radiation Emergency Medical Center, Korea Institute of Radiological & Medical Science, Seoul 01812, Republic of Korea
- Department of Pathology, College of Medicine, Hanyang University, Seoul 01812, Republic of Korea
| | - Sun-Joo Lee
- Laboratory of Experimental Pathology, Departments of Pathology, Korea Institute of Radiological & Medical Science, Seoul 01812, Republic of Korea
| | - Hyewon Kim
- Laboratory of Experimental Pathology, Departments of Pathology, Korea Institute of Radiological & Medical Science, Seoul 01812, Republic of Korea
| | - Soyeon Kim
- Laboratory of Radiation Exposure & Therapeutics, National Radiation Emergency Medical Center, Korea Institute of Radiological & Medical Science, Seoul 01812, Republic of Korea
| | - Seung-Bum Lee
- Laboratory of Radiation Exposure & Therapeutics, National Radiation Emergency Medical Center, Korea Institute of Radiological & Medical Science, Seoul 01812, Republic of Korea
| | - Hyosun Jang
- Laboratory of Radiation Exposure & Therapeutics, National Radiation Emergency Medical Center, Korea Institute of Radiological & Medical Science, Seoul 01812, Republic of Korea
| | - Won-Il Jang
- Laboratory of Radiation Exposure & Therapeutics, National Radiation Emergency Medical Center, Korea Institute of Radiological & Medical Science, Seoul 01812, Republic of Korea
- Laboratory of Experimental Pathology, Departments of Pathology, Korea Institute of Radiological & Medical Science, Seoul 01812, Republic of Korea
| | - Sunhoo Park
- Laboratory of Radiation Exposure & Therapeutics, National Radiation Emergency Medical Center, Korea Institute of Radiological & Medical Science, Seoul 01812, Republic of Korea
- Laboratory of Experimental Pathology, Departments of Pathology, Korea Institute of Radiological & Medical Science, Seoul 01812, Republic of Korea
| | - Hyunwon Yang
- Biohealth Convergence, Seoul Women’s University, Seoul 01812, Republic of Korea
| | - Sehwan Shim
- Laboratory of Radiation Exposure & Therapeutics, National Radiation Emergency Medical Center, Korea Institute of Radiological & Medical Science, Seoul 01812, Republic of Korea
- Correspondence: (S.S.); (M.-J.K.); Tel.: +82-2-3399-5875 (S.S.); Fax: +82-2-3399-5870 (S.S.)
| | - Min-Jung Kim
- Laboratory of Radiation Exposure & Therapeutics, National Radiation Emergency Medical Center, Korea Institute of Radiological & Medical Science, Seoul 01812, Republic of Korea
- Correspondence: (S.S.); (M.-J.K.); Tel.: +82-2-3399-5875 (S.S.); Fax: +82-2-3399-5870 (S.S.)
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Drandi D, Ferrante M, Borriero M, Ferrero S. MYD88 L265P Mutation Detection by ddPCR: Recommendations for Screening and Minimal Residual Disease Monitoring : ddPCR for Highly Sensitive Detection of MYD88 L265P Mutation. Methods Mol Biol 2023; 2621:57-72. [PMID: 37041440 DOI: 10.1007/978-1-0716-2950-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
MYD88L265P is a gain-of-function mutation, arising from the missense alteration c.794T>C, that frequently occurs in B-cell malignancies such as Waldenstrom macroglobulinemia and less frequently in IgM monoclonal gammopathy of undetermined significance (IgM-MGUS) or other lymphomas. MYD88L265P has been recognized as a relevant diagnostic flag, but also as a valid prognostic and predictive biomarker, as well as an investigated therapeutic target. Up until now, allele-specific quantitative PCR (ASqPCR) has been widely used for MYD88L265P detection providing a higher level of sensitivity than Sanger sequencing. However, the recently developed droplet digital PCR (ddPCR) shows a deeper sensitivity, compared to ASqPCR, that is necessary for screening low infiltrated samples. Actually, ddPCR could represent an improvement in daily laboratory practice since it allows mutation detection in unselected tumor cells, allowing to bypass the time-consuming and costly B-cell selection procedure. ddPCR accuracy has been recently proved to be suitable also for mutation detection in "liquid biopsy" samples that might be used as a noninvasive and patient-friendly alternative to bone marrow aspiration especially during the disease monitoring. The relevance of MYD88L265P, both in daily management of patients and in prospective clinical trials investigating the efficacy of novel agents, makes crucial to find a sensitive, accurate, and reliable molecular technique for mutation detection. Here, we propose a protocol for MYD88L265P detection by ddPCR.
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Affiliation(s)
- Daniela Drandi
- Department of Molecular Biotechnology and Health Sciences, Hematology Division, University of Torino, Torino, Italy.
| | - Martina Ferrante
- Department of Molecular Biotechnology and Health Sciences, Hematology Division, University of Torino, Torino, Italy
| | - Michela Borriero
- Department of Molecular Biotechnology and Health Sciences, Hematology Division, University of Torino, Torino, Italy
| | - Simone Ferrero
- Department of Molecular Biotechnology and Health Sciences, Hematology Division, University of Torino, Torino, Italy
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Loskyll M, Podbiel D, Guber A, Hoffmann J. Partitioning and subsampling statistics in compartment-based quantification methods. PLoS One 2023; 18:e0285784. [PMID: 37186607 PMCID: PMC10184943 DOI: 10.1371/journal.pone.0285784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/01/2023] [Indexed: 05/17/2023] Open
Abstract
The precision of compartment-based quantification methods is subject to multiple effects, of which partitioning and subsampling play a major role. Partitioning is the process of aliquoting the sample liquid and consequently the contained target molecules, whereas subsampling denotes the fact that usually only a portion of a sample is analyzed. In this work, we present a detailed statistical description comprising the effects of partitioning and subsampling on the relative uncertainty of the test result. We show that the state-of-the-art binomial model does not provide accurate results for the level of subsampling present when analyzing the nucleic acid content of single specific cells. Hence, in this work we address partitioning and subsampling effects separately and subsequently combine them to derive the relative uncertainty of a test system and compare it for single cell content analysis and body fluid analysis. In point-of-care test systems the area for partitioning and detection is usually limited, which means that a trade-off between the number of partitions (related to a partitioning uncertainty) and the amount of analyzed volume (related to a subsampling uncertainty) might be inevitable. In case of low target concentration, the subsampling uncertainty is dominant whereas for high target concentration, the partitioning uncertainty increases, and a larger number of partitions is beneficial to minimize the combined uncertainty. We show, that by minimizing the subsampling uncertainty in the test system, the quantification uncertainty of low target concentrations in single cell content analysis is much smaller than in body fluid analysis. In summary, the work provides the methodological basis for a profound statistical evaluation of partitioning and subsampling effects in compartment-based quantification methods and paves the way towards an improved design of future digital quantification devices for highly accurate molecular diagnostic analysis at the point-of-care.
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Affiliation(s)
- Manuel Loskyll
- Advanced Technologies and Microsystems, Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Renningen, Baden-Württemberg, Germany
| | - Daniel Podbiel
- Advanced Technologies and Microsystems, Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Renningen, Baden-Württemberg, Germany
| | - Andreas Guber
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Baden-Württemberg, Germany
- BioMEMS Consulting, Karlsruhe, Baden-Württemberg, Germany
| | - Jochen Hoffmann
- Advanced Technologies and Microsystems, Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Renningen, Baden-Württemberg, Germany
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Ciurea SO, Kothari A, Sana S, Al Malki MM. The mythological chimera and new era of relapse prediction post-transplant. Blood Rev 2023; 57:100997. [PMID: 35961800 DOI: 10.1016/j.blre.2022.100997] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/13/2022] [Accepted: 07/21/2022] [Indexed: 01/28/2023]
Abstract
Allogeneic hemopoietic stem cell transplantation is the treatment of choice for high-risk or relapsed acute leukemia. However, unfortunately, relapse post-transplant continues to be the most common cause of treatment failure with 20-80% of patients relapsing based on disease risk and status at transplant. Advances in molecular profiling of different hematological malignancies have enabled us to monitor low level disease before and after transplant and develop a more personalized approach to the management of these disease including early detection post-transplant. While, in general, detectable disease by morphology remains the gold standard to diagnosing relapse, multiple approaches have allowed detection of cancer cells earlier, using peripheral blood-based methods with sensitivities as high as 1:106, together called minimal/measurable residual disease (MRD) detection. However, a in significant number of patients with acute leukemia where no such molecular markers exist it remains challenging to detect early relapse. In such patients who receive transplantation, chimerism monitoring remains the only option. An increase in mixed chimerism in post allogeneic HCT patients has been correlated with relapse in multiple studies. However, chimerism monitoring, while commonly accepted as a tool for assessing engraftment, has not been routinely used for relapse detection, at least in part because of the lack of standardized, high sensitivity, reliable methods for chimerism detection. In this paper, we review the various methods employed for MRD and chimerism detection post-transplant and discuss future trends in MRD and chimerism monitoring from the viewpoint of the practicing transplant physician.
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Affiliation(s)
- Stefan O Ciurea
- University of California Irvine, Orange, CA, United States of America.
| | | | - Sean Sana
- CareDx Inc., Brisbane, CA, United States of America
| | - Monzr M Al Malki
- City of Hope National Medical Center, Duarte, CA, United States of America
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Shum EY, Lai JH, Li S, Lee HG, Soliman J, Raol VK, Lee CK, Fodor SP, Fan HC. Next-Generation Digital Polymerase Chain Reaction: High-Dynamic-Range Single-Molecule DNA Counting via Ultrapartitioning. Anal Chem 2022; 94:17868-17876. [PMID: 36508568 PMCID: PMC9798378 DOI: 10.1021/acs.analchem.2c03649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Digital PCR (dPCR) was first conceived for single-molecule quantitation. However, current dPCR systems often require DNA templates to share partitions due to limited partitioning capacities. Here, we introduce UltraPCR, a next-generation dPCR system where DNA counting is performed in a single-molecule regimen through a 6-log dynamic range using a swift and parallelized workflow. Each UltraPCR reaction is divided into >30 million partitions without microfluidics to achieve single template occupancy. Combined with a unique emulsion chemistry, partitions are optically clear, enabling the use of a three-dimensional imaging technique to rapidly detect DNA-positive partitions. Single-molecule occupancy also allows for more straightforward multiplex assay development due to the absence of partition-specific competition. As a proof of concept, we developed a 222-plex UltraPCR assay and demonstrated its potential use as a rapid, low-cost screening assay for noninvasive prenatal testing for as low as 4% trisomy fraction samples with high precision, accuracy, and reproducibility.
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Shao Z, Zhu J, Wei Y, Jin J, Zheng Y, Liu J, Zhang R, Sun R, Hu B. Pathogen load and species monitored by droplet digital PCR in patients with bloodstream infections: A prospective case series study. BMC Infect Dis 2022; 22:771. [PMID: 36195855 PMCID: PMC9531393 DOI: 10.1186/s12879-022-07751-2] [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: 05/28/2022] [Revised: 08/31/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022] Open
Abstract
Background and objectives: Bloodstream infection (BSI) is a life-threatening condition in critically ill patients, but pathogen quantification techniques during treatment are laborious. This study aimed to explore the impact of monitoring pathogen DNA load changes and polymicrobial infection in blood by droplet digital polymerase chain reaction (ddPCR) on the prognosis of patients with BSIs. Methods This prospective case series study was conducted in the general intensive care unit of the Zhejiang Provincial People’s Hospital and included patients with BSIs from May 2020 to January 2021. Pathogens DNA load and presence of polymicrobial BSIs were dynamically monitored by ddPCR. Results Sixteen patients with BSIs proven by blood culture were recruited (87.5% men; mean age, 69.3 ± 13.7 years). All pathogens identified by blood culture were Gram-negative bacteria, among which seven were multidrug-resistant strains. The 28-day mortality rate was 62.5%. Compared to the 28-day survivors, the non-survivors were older (P = 0.04), had higher pathogen DNA load on the second (day 3–4) and third (day 6–7) ddPCR assay (P < 0.01 in both cases). In addition, the changes of pathogen DNA load in the 28-day survivors had a downward trend in the first three ddPCR assay, whereas stable load or an upward trend was observed in the 28-day non-survivors. Moreover, the number of pathogen species in patients with BSIs in the 28-day survivors decreased during the period of effective antibiotic treatment. Conclusion The changes of pathogen DNA load and species monitored in blood by ddPCR may be used to determine antibiotic efficacy and make a more accurate prognostic assessment in patients with BSIs. Supplementary information The online version contains supplementary material available at 10.1186/s12879-022-07751-2.
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Affiliation(s)
- Ziqiang Shao
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Shangtang Road 158, 310014, Hangzhou, Zhejiang, China
| | - Jingwen Zhu
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Shangtang Road 158, 310014, Hangzhou, Zhejiang, China
| | - Yanyan Wei
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Shangtang Road 158, 310014, Hangzhou, Zhejiang, China
| | - Jun Jin
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Shangtang Road 158, 310014, Hangzhou, Zhejiang, China
| | - Yang Zheng
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Shangtang Road 158, 310014, Hangzhou, Zhejiang, China
| | - Jingquan Liu
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Shangtang Road 158, 310014, Hangzhou, Zhejiang, China
| | - Run Zhang
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Shangtang Road 158, 310014, Hangzhou, Zhejiang, China
| | - Renhua Sun
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Shangtang Road 158, 310014, Hangzhou, Zhejiang, China
| | - Bangchuan Hu
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Shangtang Road 158, 310014, Hangzhou, Zhejiang, China.
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Wu H, Cao X, Meng Y, Richards D, Wu J, Ye Z, deMello AJ. DropCRISPR: A LAMP-Cas12a based digital method for ultrasensitive detection of nucleic acid. Biosens Bioelectron 2022; 211:114377. [DOI: 10.1016/j.bios.2022.114377] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 12/26/2022]
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Wang D, Jiao X, Jia H, Cheng S, Jin X, Wang Y, Gao Y, Su X. Detection and quantification of Verticillium dahliae and V. longisporum by droplet digital PCR versus quantitative real-time PCR. Front Cell Infect Microbiol 2022; 12:995705. [PMID: 36072220 PMCID: PMC9441566 DOI: 10.3389/fcimb.2022.995705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
Vascular wilt, caused by Verticillium dahliae and V. longisporum, limits the quality and yield of agricultural crops. Although quantitative real-time PCR (qPCR) has greatly improved the diagnosis of these two pathogens over traditional, time-consuming isolation methods, the relatively poor detection sensitivity and high measurement bias for traceable matrix-rich samples need to be improved. Here, we thus developed a droplet digital PCR (ddPCR) assay for accurate, sensitive detection and quantification of V. dahliae and V. longisporum. We compared the analytical and diagnostic performance in detail of ddPCR and the corresponding qPCR assay against the genomic DNA (gDNA) of the two fungi from cultures and field samples. In our study, the species specificity, quantification linearity, analytical sensitivity, and measurement viability of the two methods were analyzed. The results indicated that ddPCR using field samples enhanced diagnostic sensitivity, decreased quantification bias, and indicated less susceptibility to inhibitors compared with qPCR. Although ddPCR was as sensitive as qPCR when using gDNA from cultures of V. dahliae and V. longisporum, its detection rates using field samples were much higher than those of qPCR, potentially due to the inhibition from residual matrix in the extracts. The results showed that digital PCR is more sensitive and accurate than qPCR for quantifying trace amounts of V. dahliae and V. longisporum and can facilitate management practices to limit or prevent their prevalence.
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Affiliation(s)
- Di Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Xinya Jiao
- College of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Haijiang Jia
- Raw Material Technology Center of Guangxi Tobacco, Nanning, China
| | - Shumei Cheng
- College of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Xi Jin
- Hebei Technology Innovation Center for Green Management of Soil-Borne Diseases, Baoding University, Hebei, China
| | - Youhua Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
- *Correspondence: Xiaofeng Su, ; Yunhua Gao,
| | - Xiaofeng Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Xiaofeng Su, ; Yunhua Gao,
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Wei Y, An X, Cao Q, Che N, Xue Y, Deng H, Wang Q, Zhou R. Lentiviral vector–based xenograft tumors as candidate reference materials for detection of HER2-low breast cancer. Front Oncol 2022; 12:955943. [PMID: 36052254 PMCID: PMC9425432 DOI: 10.3389/fonc.2022.955943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/14/2022] [Indexed: 12/09/2022] Open
Abstract
The human epidermal growth factor receptor 2 (HER2) is an important biomarker that plays a pivotal role in therapeutic decision-making for patients with breast cancer (BC). Patients with HER2-low BC can benefit from new HER2 targeted therapy. For ensuring the accurate and reproducible detection of HER2-low cancer, reliable reference materials are required for monitoring the sensitivity and specificity of detection assays. Herein, a lentiviral vector was used to transduce the HER2 gene into MDA-MB-231 cells that exhibited low HER2 density, and the cells were characterized by droplet digital PCR to accurately determine the copy number variation. Then, the formalin-fixed paraffin-embedded (FFPE) samples from xenografts were prepared and evaluated for suitability as candidate reference materials by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). The FFPE reference materials were selected on the basis of IHC score of 2+ and negative FISH result to meet the requirement for HER2-low BC detection. Furthermore, the FFPE reference materials exhibited typical histological structures that resembled the clinical BC specimens. These novel FFPE reference materials displayed the high stability and homogeneity, and they were produced in high quantity. In summary, we generated high-quality reference materials for internal quality control and proficiency testing in HER2-low detection.
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Affiliation(s)
- Yali Wei
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, The Third Clinical Medical College of Capital Medical University, Beijing, China
| | - Xu An
- Department of Clinical Laboratory, Tongzhou Maternal and Child Health Hospital of Beijing, Beijing, China
| | - Qinmei Cao
- Department of Clinical Laboratory, China-Japan Friendship Hospital, Clinical Medical College of Capital Medical University, Beijing, China
| | - Nanying Che
- Department of Pathology, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yuanyuan Xue
- Ministry of Education (MOE) Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haiteng Deng
- Ministry of Education (MOE) Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qingtao Wang
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, The Third Clinical Medical College of Capital Medical University, Beijing, China
- *Correspondence: Qingtao Wang, ; Rui Zhou,
| | - Rui Zhou
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, The Third Clinical Medical College of Capital Medical University, Beijing, China
- *Correspondence: Qingtao Wang, ; Rui Zhou,
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Yu Z, Xu L, Lyu W, Shen F. Parallel multistep digital analysis SlipChip demonstrated with the quantification of nucleic acid by digital LAMP-CRISPR. LAB ON A CHIP 2022; 22:2954-2961. [PMID: 35696983 DOI: 10.1039/d2lc00284a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Digital biological analysis compartmentalizes targets of interest, such as nucleic acids, proteins, and cells, to a single event level and performs detection and further investigation. Microfluidic-based digital biological analysis methods, including digital PCR, digital protein analysis, and digital cell analysis, have demonstrated superior advantages in research applications and clinical diagnostics. However, most of the methods are still based on a one-step "divide and detect" strategy, and it is challenging for these methods to perform further parallel manipulation of reaction partitions to achieve "divide, manipulate, and analyze" capabilities. Here, we present a parallel multistep digital analysis (PAMDA) SlipChip for the parallel multistep manipulation of a large number of droplets for digital biological analysis, demonstrated by the quantification of SARS-CoV-2 nucleic acids by a two-step digital isothermal amplification combined with clustered regularly interspaced short palindromic repeats (CRISPR). This PAMDA SlipChip utilizes a "chain-of-pearl" channel with a self-partitioning droplet formation mechanism that does not require the precise alignment of microfeatures for fluidic loading as the traditional SlipChip design. This device can first generate 2400 3.2 nanoliter droplets to perform digital loop-mediated isothermal amplification (LAMP) and then deliver reagents containing Cas12a protein and crRNA to each individual partition in parallel to simultaneously initiate digital CRISPR detection by a simple multistep slipping operation. This PAMDA SlipChip not only provides a promising tool to perform digital CRISPR with a flexible assay and workflow design but can also be applied for a broad range of applications in digital biological analysis that require multistep manipulation of partitions in parallel.
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Affiliation(s)
- Ziqing Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, China.
| | - Lei Xu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, China.
- MineBio Technology LLC, 333 Gui Ping Road, Shanghai, 200233, China
| | - Weiyuan Lyu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, China.
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, China.
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Zhang H, Laššáková S, Yan Z, Wang X, Šenkyřík P, Gaňová M, Chang H, Korabecna M, Neuzil P. Digital polymerase chain reaction duplexing method in a single fluorescence channel. Anal Chim Acta 2022; 1238:340243. [DOI: 10.1016/j.aca.2022.340243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/24/2022]
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Dobre EG, Constantin C, Neagu M. Skin Cancer Research Goes Digital: Looking for Biomarkers within the Droplets. J Pers Med 2022; 12:jpm12071136. [PMID: 35887633 PMCID: PMC9323323 DOI: 10.3390/jpm12071136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 12/24/2022] Open
Abstract
Skin cancer, which includes the most frequent malignant non-melanoma carcinomas (basal cell carcinoma, BCC, and squamous cell carcinoma, SCC), along with the difficult to treat cutaneous melanoma (CM), pose important worldwide issues for the health care system. Despite the improved anti-cancer armamentarium and the latest scientific achievements, many skin cancer patients fail to respond to therapies, due to the remarkable heterogeneity of cutaneous tumors, calling for even more sophisticated biomarker discovery and patient monitoring approaches. Droplet digital polymerase chain reaction (ddPCR), a robust method for detecting and quantifying low-abundance nucleic acids, has recently emerged as a powerful technology for skin cancer analysis in tissue and liquid biopsies (LBs). The ddPCR method, being capable of analyzing various biological samples, has proved to be efficient in studying variations in gene sequences, including copy number variations (CNVs) and point mutations, DNA methylation, circulatory miRNome, and transcriptome dynamics. Moreover, ddPCR can be designed as a dynamic platform for individualized cancer detection and monitoring therapy efficacy. Here, we present the latest scientific studies applying ddPCR in dermato-oncology, highlighting the potential of this technology for skin cancer biomarker discovery and validation in the context of personalized medicine. The benefits and challenges associated with ddPCR implementation in the clinical setting, mainly when analyzing LBs, are also discussed.
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Affiliation(s)
- Elena-Georgiana Dobre
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Correspondence:
| | - Carolina Constantin
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Monica Neagu
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
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Le Duff Y, Gärtner K, Busby EJ, Dalzini A, Danaviah S, Fuentes JLJ, Giaquinto C, Huggett JF, Hurley M, Marcellin AG, Muñoz-Fernández MÁ, O’Sullivan DM, Persaud D, Powell L, Rigsby P, Rossi P, de Rossi A, Siems L, Smit T, Watters SA, Almond N, Nastouli E. Assessing the Variability of Cell-Associated HIV DNA Quantification through a Multicenter Collaborative Study. Microbiol Spectr 2022; 10:e0024322. [PMID: 35658711 PMCID: PMC9241949 DOI: 10.1128/spectrum.00243-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
Reliable and accurate quantification of cell-associated HIV DNA (CA HIV DNA) is critical for early infant diagnosis, clinical management of patients under therapy, and to inform new therapeutics efficacy. The present study assessed the variability of CA HIV DNA quantification obtained from various assays and the value of using reference materials to help harmonize the measurements. Using a common set of reagents, our multicenter collaborative study highlights significant variability of CA HIV DNA quantification and lower limit of quantification across assays. The quantification of CA HIV DNA from a panel of infected PBMCs can be harmonized through cross-subtype normalization but assay calibration with the commonly used 8E5 cell line failed to reduce quantification variability between assays, demonstrating the requirement to thoroughly evaluate reference material candidates to help improve the comparability of CA HIV DNA diagnostic assay performance. IMPORTANCE Despite a global effort, HIV remains a major public health burden with an estimated 1.5 million new infections occurring in 2020. HIV DNA is an important viral marker, and its monitoring plays a critical role in the fight against HIV: supporting diagnosis in infants and underpinning clinical management of patients under therapy. Our study demonstrates that HIV DNA measurement of the same samples can vary significantly from one laboratory to another, due to heterogeneity in the assay, protocol, and reagents used. We show that when carefully selected, reference materials can reduce measurement variability and harmonize HIV DNA quantification across laboratories, which will help contribute to improved diagnosis and clinical management of patients living with HIV.
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Affiliation(s)
- Yann Le Duff
- Division of Infectious Disease Diagnostics, Centre for AIDS Reagent, National Institute for Biological Standards and Control, South Mimms, United Kingdom
| | - Kathleen Gärtner
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Eloise J. Busby
- National Measurement Laboratory, LGC group Teddington, Middlesex, United Kingdom
| | - Annalisa Dalzini
- Section of Oncology and Immunology, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
| | | | - José Luis Jiménez Fuentes
- Instituto Investigación Sanitaria Gregorio Marañón, Laboratorio InmunoBiología Molecular and Spanish HIV HGM BioBank, Madrid, Spain
| | - Carlo Giaquinto
- Department for Woman’s and Child’s Health, University of Padova, Padua, Italy
| | - Jim F. Huggett
- National Measurement Laboratory, LGC group Teddington, Middlesex, United Kingdom
| | - Matthew Hurley
- Division of Infectious Disease Diagnostics, Centre for AIDS Reagent, National Institute for Biological Standards and Control, South Mimms, United Kingdom
| | - Anne-Geneviève Marcellin
- Sorbonne Université, INSERM, Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP), Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpêtrière Hospital, Department of Virology, Paris, France
| | - María Ángeles Muñoz-Fernández
- Instituto Investigación Sanitaria Gregorio Marañón, Laboratorio InmunoBiología Molecular and Spanish HIV HGM BioBank, Madrid, Spain
| | - Denise M. O’Sullivan
- National Measurement Laboratory, LGC group Teddington, Middlesex, United Kingdom
| | - Deborah Persaud
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Laura Powell
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Peter Rigsby
- Division of Analytical Biological Sciences, National Institute for Biological Standards and Control, South Mimms, United Kingdom
| | - Paolo Rossi
- Department of Pediatrics, University of Rome Tor Vergata, Rome, Italy
| | - Anita de Rossi
- Section of Oncology and Immunology, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Lilly Siems
- The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Theresa Smit
- Africa Health Research Institute, Durban, South Africa
| | - Sarah A. Watters
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Neil Almond
- Division of Infectious Disease Diagnostics, Centre for AIDS Reagent, National Institute for Biological Standards and Control, South Mimms, United Kingdom
| | - Eleni Nastouli
- Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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Schwinghammer C, Koopmann J, Chitadze G, Karawajew L, Brüggemann M, Eckert C. Droplet Digital PCR: A New View on Minimal Residual Disease Quantification in Acute Lymphoblastic Leukemia. J Mol Diagn 2022; 24:856-866. [PMID: 35691569 DOI: 10.1016/j.jmoldx.2022.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 03/05/2022] [Accepted: 04/06/2022] [Indexed: 11/27/2022] Open
Abstract
Real-time quantitative PCR (qPCR) using immunoglobulin/T-cell receptor gene rearrangements has been used as the gold standard for minimal residual disease (MRD) monitoring in acute lymphoblastic leukemia (ALL) for >20 years. Recently, new PCR-based technologies have emerged, such as droplet digital PCR (ddPCR), which could offer several methodologic advances for MRD monitoring. In the current work, qPCR and ddPCR were compared in an unbiased blinded prospective study (n = 88 measurements) and in a retrospective study with selected critical low positive samples (n = 65 measurements). The former included flow cytometry (Flow; n = 31 measurements) as a third MRD detection method. Published guidelines (qPCR) and the latest, revised evaluation criteria (ie, ddPCR, Flow) have been applied for data analysis. The prospective study shows that ddPCR outperforms qPCR with a significantly better quantitative limit of detection and sensitivity. The number of critical MRD estimates below quantitative limit was reduced by sixfold and by threefold in the retrospective and prospective cohorts, respectively. Furthermore, the concordance of quantitative values between ddPCR and Flow was higher than between ddPCR and qPCR, probably because ddPCR and Flow are absolute quantification methods independent of the diagnostic sample, unlike qPCR. In summary, our data highlight the advantages of ddPCR as a more precise and sensitive technology that could be used to refine response monitoring in ALL.
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Affiliation(s)
- Claudia Schwinghammer
- Department of Paediatric Oncology/Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Johannes Koopmann
- Department of Haematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Guranda Chitadze
- Department of Haematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Leonid Karawajew
- Department of Paediatric Oncology/Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Monika Brüggemann
- Department of Haematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Cornelia Eckert
- Department of Paediatric Oncology/Haematology, Charité-Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany.
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Xiao M, Tian F, Liu X, Zhou Q, Pan J, Luo Z, Yang M, Yi C. Virus Detection: From State-of-the-Art Laboratories to Smartphone-Based Point-of-Care Testing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105904. [PMID: 35393791 PMCID: PMC9110880 DOI: 10.1002/advs.202105904] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/27/2022] [Indexed: 05/07/2023]
Abstract
Infectious virus outbreaks pose a significant challenge to public healthcare systems. Early and accurate virus diagnosis is critical to prevent the spread of the virus, especially when no specific vaccine or effective medicine is available. In clinics, the most commonly used viral detection methods are molecular techniques that involve the measurement of nucleic acids or proteins biomarkers. However, most clinic-based methods require complex infrastructure and expensive equipment, which are not suitable for low-resource settings. Over the past years, smartphone-based point-of-care testing (POCT) has rapidly emerged as a potential alternative to laboratory-based clinical diagnosis. This review summarizes the latest development of virus detection. First, laboratory-based and POCT-based viral diagnostic techniques are compared, both of which rely on immunosensing and nucleic acid detection. Then, various smartphone-based POCT diagnostic techniques, including optical biosensors, electrochemical biosensors, and other types of biosensors are discussed. Moreover, this review covers the development of smartphone-based POCT diagnostics for various viruses including COVID-19, Ebola, influenza, Zika, HIV, et al. Finally, the prospects and challenges of smartphone-based POCT diagnostics are discussed. It is believed that this review will aid researchers better understand the current challenges and prospects for achieving the ultimate goal of containing disease-causing viruses worldwide.
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Affiliation(s)
- Meng Xiao
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical EngineeringShenzhen Campus of Sun Yat‐Sen UniversityShenzhen518107P. R. China
| | - Feng Tian
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHunghomHong Kong999077P. R. China
| | - Xin Liu
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical EngineeringShenzhen Campus of Sun Yat‐Sen UniversityShenzhen518107P. R. China
| | - Qiaoqiao Zhou
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical EngineeringShenzhen Campus of Sun Yat‐Sen UniversityShenzhen518107P. R. China
| | - Jiangfei Pan
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical EngineeringShenzhen Campus of Sun Yat‐Sen UniversityShenzhen518107P. R. China
| | - Zhaofan Luo
- Department of Clinical LaboratoryThe Seventh Affiliated Hospital of Sun Yat‐Sen UniversityShenzhen518107P. R. China
| | - Mo Yang
- Department of Biomedical EngineeringThe Hong Kong Polytechnic UniversityHunghomHong Kong999077P. R. China
| | - Changqing Yi
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical EngineeringShenzhen Campus of Sun Yat‐Sen UniversityShenzhen518107P. R. China
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Digital Droplet-PCR for Quantification of Viable Campylobacter jejuni and Campylobacter coli in Chicken Meat Rinses. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12115315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The EU commission established Regulation (2017/1495) in 2017 to reduce Campylobacter on chicken skin and to decrease the number of human cases of campylobacteriosis attributable to the consumption of poultry meat. A Process Hygiene Criterion based on colony-forming unit data was set to a maximum of 1000 CFU Campylobacter spp. per gram chicken neck skin at slaughterhouses. Confronted with stressors, including cold, oxidative stress or antibiotic treatment, live cells may enter into a viable but non-cultivable state (VBNC) and lose the ability to grow, in reference to the plate count ISO 10272-2:2017 method, but still possess the potential to recover and cause infections under favorable conditions. In this study, a droplet digital PCR combined with the intercalating dye propidium monoazide (PMA) was established for quantification of C. coli and C. jejuni in chicken meat rinses. The PMA was used to inactivate DNA from dead cells in this technique. This method was successfully validated against the reference method according to ISO 16140-2:2016 for accuracy and relative trueness. Additionally, it presented a 100% selectivity for Campylobacter jejuni and C. coli. Moreover, the technical measurement uncertainty was determined according to ISO 19036:2019, and the applicability of ddPCR for quantifying C. coli and C. jejuni in chicken meat rinses was investigated on naturally contaminated samples from slaughterhouses and supermarkets. Results obtained from this study demonstrated a strong correlation to qPCR as well as the classical microbiological reference method.
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Lambrescu I, Popa A, Manole E, Ceafalan LC, Gaina G. Application of Droplet Digital PCR Technology in Muscular Dystrophies Research. Int J Mol Sci 2022; 23:ijms23094802. [PMID: 35563191 PMCID: PMC9099497 DOI: 10.3390/ijms23094802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 11/25/2022] Open
Abstract
Although they are considered rare disorders, muscular dystrophies have a strong impact on people’s health. Increased disease severity with age, frequently accompanied by the loss of ability to walk in some people, and the lack of treatment, have directed the researchers towards the development of more effective therapeutic strategies aimed to improve the quality of life and life expectancy, slow down the progression, and delay the onset or convert a severe phenotype into a milder one. Improved understanding of the complex pathology of these diseases together with the tremendous advances in molecular biology technologies has led to personalized therapeutic procedures. Different approaches that are currently under extensive investigation require more efficient, sensitive, and less invasive methods. Due to its remarkable analytical sensitivity, droplet digital PCR has become a promising tool for accurate measurement of biomarkers that monitor disease progression and quantification of various therapeutic efficiency and can be considered a tool for non-invasive prenatal diagnosis and newborn screening. Here, we summarize the recent applications of droplet digital PCR in muscular dystrophy research and discuss the factors that should be considered to get the best performance with this technology.
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Affiliation(s)
- Ioana Lambrescu
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Cell Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Alexandra Popa
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Animal Production and Public Health, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 050097 Bucharest, Romania
| | - Emilia Manole
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Laura Cristina Ceafalan
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Department of Cell Biology and Histology, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Gisela Gaina
- Laboratory of Cell Biology, Neuroscience and Experimental Myology, Victor Babes National Institute of Pathology, 050096 Bucharest, Romania; (I.L.); (A.P.); (E.M.); (L.C.C.)
- Correspondence: ; Tel.: +40-21-319-2732
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Tjensvoll K, Lapin M, Gilje B, Garresori H, Oltedal S, Forthun RB, Molven A, Rozenholc Y, Nordgård O. Novel hybridization- and tag-based error-corrected method for sensitive ctDNA mutation detection using ion semiconductor sequencing. Sci Rep 2022; 12:5816. [PMID: 35388068 PMCID: PMC8986848 DOI: 10.1038/s41598-022-09698-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/24/2022] [Indexed: 11/08/2022] Open
Abstract
Circulating tumor DNA (ctDNA) analysis has emerged as a clinically useful tool for cancer diagnostics and treatment monitoring. However, ctDNA detection is complicated by low DNA concentrations and technical challenges. Here we describe our newly developed sensitive method for ctDNA detection on the Ion Torrent sequencing platform, which we call HYbridization- and Tag-based Error-Corrected sequencing (HYTEC-seq). This method combines hybridization-based capture with molecular tags, and the novel variant caller PlasmaMutationDetector2 to eliminate background errors. We describe the validation of HYTEC-seq using control samples with known mutations, demonstrating an analytical sensitivity down to 0.1% at > 99.99% specificity. Furthermore, to demonstrate the utility of this method in a clinical setting, we analyzed plasma samples from 44 patients with advanced pancreatic cancer, revealing mutations in 57% of the patients at allele frequencies as low as 0.23%.
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Affiliation(s)
- Kjersti Tjensvoll
- Department of Hematology and Oncology, Laboratory for Molecular Biology, Stavanger University Hospital, 4068, Stavanger, Norway.
| | - Morten Lapin
- Department of Hematology and Oncology, Laboratory for Molecular Biology, Stavanger University Hospital, 4068, Stavanger, Norway
| | - Bjørnar Gilje
- Department of Hematology and Oncology, Laboratory for Molecular Biology, Stavanger University Hospital, 4068, Stavanger, Norway
| | - Herish Garresori
- Department of Hematology and Oncology, Laboratory for Molecular Biology, Stavanger University Hospital, 4068, Stavanger, Norway
| | - Satu Oltedal
- Department of Hematology and Oncology, Laboratory for Molecular Biology, Stavanger University Hospital, 4068, Stavanger, Norway
| | - Rakel Brendsdal Forthun
- Department of Medical Genetics, Haukeland University Hospital, 5020, Bergen, Norway
- Department of Internal Medicine, Hematology Section, Haukeland University Hospital, 5020, Bergen, Norway
| | - Anders Molven
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, 5020, Bergen, Norway
- Department of Pathology, Haukeland University Hospital, 5021, Bergen, Norway
| | - Yves Rozenholc
- BioSTM UR 7537, Faculté de Pharmacie de Paris, Université Paris Citè, 75006, Paris, France
| | - Oddmund Nordgård
- Department of Hematology and Oncology, Laboratory for Molecular Biology, Stavanger University Hospital, 4068, Stavanger, Norway
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De Brun ML, Cosme B, Petersen M, Alvarez I, Folgueras-Flatschart A, Flatschart R, Panei CJ, Puentes R. Development of a droplet digital PCR assay for quantification of the proviral load of bovine leukemia virus. J Vet Diagn Invest 2022; 34:439-447. [PMID: 35369822 PMCID: PMC9254064 DOI: 10.1177/10406387221085581] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Droplet digital PCR (ddPCR) is a highly sensitive tool developed for the detection and quantification of short-sequence variants—a tool that offers unparalleled precision enabling measurement of smaller-fold changes. We describe here the use of ddPCR for the detection of Bovine leukemia virus (BLV) DNA provirus. Serum samples and whole blood from experimentally infected sheep and naturally infected cattle were analyzed through ddPCR to detect the BLV gp51 gene, and then compared with serologic and molecular tests. The ddPCR assay was significantly more accurate and sensitive than AGID, ELISA, nested PCR, and quantitative PCR. The limit of detection of ddPCR was 3.3 copies/µL, detecting positive experimentally infected sheep beginning at 6 d post-infection. The ddPCR methodology offers a promising tool for evaluating the BLV proviral load, particularly for the detection of low viral loads.
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Affiliation(s)
- María L. De Brun
- Instituto de Patobiología, Unidad de Microbiología, Facultad de Veterinaria–Universidad de la República, Montevideo, Uruguay
| | - Bruno Cosme
- Instituto Nacional de Metrología, Calidad y Tecnología (Inmetro), Rio de Janeiro, Brazil
| | - Marcos Petersen
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Virología e Innovaciones Tecnológicas (IVIT), Buenos Aires, Argentina
| | - Irene Alvarez
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Virología e Innovaciones Tecnológicas (IVIT), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | - Roberto Flatschart
- Instituto Nacional de Metrología, Calidad y Tecnología (Inmetro), Rio de Janeiro, Brazil
| | - Carlos Javier Panei
- Laboratorio de Virología, Facultad de Ciencias Veterinarias, Universidad Nacional de la Plata (FCV-UNLP), La Plata, Argentina
| | - Rodrigo Puentes
- Instituto de Patobiología, Unidad de Microbiología, Facultad de Veterinaria–Universidad de la República, Montevideo, Uruguay
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