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Gattuso G, Lavoro A, Caltabiano R, Madonna G, Capone M, Ascierto PA, Falzone L, Libra M, Candido S. Methylation‑sensitive restriction enzyme‑ droplet digital PCR assay for the one‑step highly sensitive analysis of DNA methylation hotspots. Int J Mol Med 2024; 53:42. [PMID: 38488030 PMCID: PMC10998716 DOI: 10.3892/ijmm.2024.5366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/23/2023] [Indexed: 03/19/2024] Open
Abstract
DNA methylation is an epigenetic modification that plays a key role in several cellular processes mediating the fine regulation of gene expression. Aberrant DNA methylation is observed in a wide range of pathologies, including cancer. Since these DNA modifications are transferred to the cell progenies and are stable over the time, the analysis of DNA methylation status has been proposed for diagnostic and prognostic purposes in cancer. Currently, DNA bisulfite conversion is the gold standard method for the high‑throughput analysis of DNA methylation alterations. However, bisulfite treatment induces DNA fragmentation affecting its quality for the downstream analyses. In this field, it is mandatory to identify novel methods to overcome the limits of conventional approaches. In the present study, the Methylation‑Sensitive Restriction Enzyme‑droplet digital PCR (MSRE‑ddPCR) assay was developed as a novel sensitive method for the analysis of DNA methylation of short genomic regions, combining the MSRE assay with the high‑sensitivity ddPCR and using an exogenous methylation sequence as control. Setup and validation experiments were performed analyzing a methylation hotspot of the Solute Carrier Family 22 Member 17 in DNA samples derived from melanoma cell lines as well as from tissues and serum samples obtained from patients with melanoma and healthy controls. Compared with the standard MSRE approaches, the MSRE‑ddPCR assay is more appropriate for the analysis of DNA methylation (methDNA) in samples with low amounts of DNA (up to 0.651 ng) showing a greater sensitivity. These findings suggested the potential clinical application of MSRE‑ddPCR paving the way to the analysis of other methDNA hotspots in different tumors.
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Affiliation(s)
- Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Alessandro Lavoro
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Rosario Caltabiano
- Department of Medical and Surgical Sciences and Advanced Technologies 'G.F. Ingrassia', University of Catania, I‑95123 Catania, Italy
| | - Gabriele Madonna
- Melanoma Cancer Immunotherapy and Innovative Therapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, I‑80131 Naples, Italy
| | - Mariaelena Capone
- Melanoma Cancer Immunotherapy and Innovative Therapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, I‑80131 Naples, Italy
| | - Paolo Antonio Ascierto
- Melanoma Cancer Immunotherapy and Innovative Therapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, I‑80131 Naples, Italy
| | - Luca Falzone
- Epidemiology and Biostatistics Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, I‑80131 Naples, Italy
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
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Wang D, Trimbos KB, Gomes SIF, Jacquemyn H, Merckx VSFT. Metabarcoding read abundances of orchid mycorrhizal fungi are correlated to copy numbers estimated using ddPCR. New Phytol 2024; 242:1825-1834. [PMID: 37929750 DOI: 10.1111/nph.19385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/20/2023] [Indexed: 11/07/2023]
Abstract
Quantifying the abundances of fungi is key to understanding natural variation in mycorrhizal communities in relation to plant ecophysiology and environmental heterogeneity. High-throughput metabarcoding approaches have transformed our ability to characterize and compare complex mycorrhizal communities. However, it remains unclear how well metabarcoding read counts correlate with actual read abundances in the sample, potentially limiting their use as a proxy for species abundances. Here, we use droplet digital PCR (ddPCR) to evaluate the reliability of ITS2 metabarcoding data for quantitative assessments of mycorrhizal communities in the orchid species Neottia ovata sampled at multiple sites. We performed specific ddPCR assays for eight families of orchid mycorrhizal fungi and compared the results with read counts obtained from metabarcoding. Our results demonstrate a significant correlation between DNA copy numbers measured by ddPCR assays and metabarcoding read counts of major mycorrhizal partners of N. ovata, highlighting the usefulness of metabarcoding for quantifying the abundance of orchid mycorrhizal fungi. Yet, the levels of correlation between the two methods and the numbers of false zero values varied across fungal families, which warrants cautious evaluation of the reliability of low-abundance families. This study underscores the potential of metabarcoding data for more quantitative analyses of mycorrhizal communities and presents practical workflows for metabarcoding and ddPCR to achieve a more comprehensive understanding of orchid mycorrhizal communities.
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Affiliation(s)
- Deyi Wang
- Naturalis Biodiversity Center, 2332 AA, Leiden, the Netherlands
- Institute of Biology, Leiden University, 2333 BE, Leiden, the Netherlands
| | - Krijn B Trimbos
- Department of Environmental Biology, Institute of Environmental Sciences, 2333 CC, Leiden University, Leiden, the Netherlands
| | - Sofia I F Gomes
- Institute of Biology, Leiden University, 2333 BE, Leiden, the Netherlands
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, Heverlee, 3001, Leuven, Belgium
| | - Vincent S F T Merckx
- Naturalis Biodiversity Center, 2332 AA, Leiden, the Netherlands
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1098 XH, Amsterdam, the Netherlands
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Uchiyama S, Fukushima K, Katagiri S, Tsuchiya J, Kubo T, Chi S, Minami Y. Advancements in minimal residual disease detection: a practical approach using single-cell droplet PCR for comprehensive monitoring in hematological malignancy. Ther Adv Hematol 2024; 15:20406207241245510. [PMID: 38628436 PMCID: PMC11020714 DOI: 10.1177/20406207241245510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 03/20/2024] [Indexed: 04/19/2024] Open
Abstract
The identification of chromosomal abnormalities accompanied by copy number alterations is important for understanding tumor characteristics. Testing methodologies for copy number abnormality have limited sensitivity, resulting in their use only for the sample provided at the time of diagnosis or recurrence of malignancy, but not for the monitoring of minimal residual disease (MRD) during and after therapy. We developped the "DimShift" technology which enable to measure the copy number of target gene/chromosome in each cell, which is given by the single cell droplet PCR. Qualitative result of DimShift given by peripheral blood was perfectly concordant with that of bone marrow. These findings and performances are promising to be the new methodology for MRD detection in malignant diseases utilizing bone marrow as well as peripheral blood.
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Affiliation(s)
- Satoshi Uchiyama
- Department of Hematology, National Cancer Center East Hospital, Kashiwa, Japan
| | - Kentaro Fukushima
- Department of Hematology and Oncology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Seiichiro Katagiri
- Department of Hematology, Tokyo Medical University Hospital, Shinjuku City, Japan
| | - Junichi Tsuchiya
- Department of Research and Development, TL Genomics Inc., Koganei City, Japan
| | - Tomohiro Kubo
- Department of Research and Development, TL Genomics Inc., Koganei City, Japan
| | - SungGi Chi
- Department of Hematology, National Cancer Center East Hospital, Kashiwa, Japan
| | - Yosuke Minami
- Department of Hematology, National Cancer Center East Hospital, 2-7-1 Kashiwano-ha, Kashiwa, Chiba 277-8577, Japan
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Mao S, Lin Y, Qin X, Miao Y, Luo C, Luo C, Wang J, Huang X, Zhu H, Lai J, Chen J. Droplet digital PCR: An effective method for monitoring and prognostic evaluation of minimal residual disease in JMML. Br J Haematol 2024. [PMID: 38622924 DOI: 10.1111/bjh.19465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/25/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024]
Abstract
Juvenile myelomonocytic leukaemia (JMML) is a rare myeloproliferative neoplasm requiring haematopoietic stem cell transplantation (HSCT) for potential cure. Relapse poses a significant obstacle to JMML HSCT treatment, as the lack of effective minimal residual disease (MRD)-monitoring methods leads to delayed interventions. This retrospective study utilized the droplet digital PCR (ddPCR) technique, a highly sensitive nucleic acid detection and quantification technique, to monitor MRD in 32 JMML patients. The results demonstrated that ddPCR detected relapse manifestations earlier than traditional methods and uncovered molecular insights into JMML MRD dynamics. The findings emphasized a critical 1- to 3-month window post-HSCT for detecting molecular relapse, with 66.7% (8/12) of relapses occurring within this period. Slow MRD clearance post-HSCT was observed, as 65% (13/20) of non-relapse patients took over 6 months to achieve ddPCR-MRD negativity. Furthermore, bone marrow ddPCR-MRD levels at 1-month post-HSCT proved to be prognostically significant. Relapsed patients exhibited significantly elevated ddPCR-MRD levels at this time point (p = 0.026), with a cut-off of 0.465% effectively stratifying overall survival (p = 0.007), event-free survival (p = 0.035) and cumulative incidence of relapse (p = 0.035). In conclusion, this study underscored ddPCR's superiority in JMML MRD monitoring post-HSCT. It provided valuable insights into JMML MRD dynamics, offering guidance for the effective management of JMML.
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Affiliation(s)
- Shengqiao Mao
- Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuchen Lin
- Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xia Qin
- Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Miao
- Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Changying Luo
- Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chengjuan Luo
- Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jianmin Wang
- Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaohang Huang
- Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hua Zhu
- Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Junchen Lai
- Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Chen
- Department of Hematology and Oncology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Yang S, Wu S, Zhao F, Zhao Z, Shen X, Yu X, Zhang M, Wen F, Sun Z, Menghe B. Diversity Analysis of Intestinal Bifidobacteria in the Hohhot Population. Microorganisms 2024; 12:756. [PMID: 38674700 DOI: 10.3390/microorganisms12040756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 03/26/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
(1) Background: Bifidobacterium plays a pivotal role within the gut microbiota, significantly affecting host health through its abundance and composition in the intestine. Factors such as age, gender, and living environment exert considerable influence on the gut microbiota, yet scant attention has been directed towards understanding the specific effects of these factors on the Bifidobacterium population. Therefore, this study focused on 98 adult fecal samples to conduct absolute and relative quantitative analyses of bifidobacteria. (2) Methods: Using droplet digital PCR and the PacBio Sequel II sequencing platform, this study sought to determine the influence of various factors, including living environment, age, and BMI, on the absolute content and biodiversity of intestinal bifidobacteria. (3) Results: Quantitative results indicated that the bifidobacteria content in the intestinal tract ranged from 106 to 109 CFU/g. Notably, the number of bifidobacteria in the intestinal tract of the school population surpassed that of the off-campus population significantly (p = 0.003). Additionally, the group of young people exhibited a significantly higher count of bifidobacteria than the middle-aged and elderly groups (p = 0.041). The normal-weight group displayed a significantly higher bifidobacteria count than the obese group (p = 0.027). Further analysis of the relative abundance of bifidobacteria under different influencing factors revealed that the living environment emerged as the primary factor affecting the intestinal bifidobacteria structure (p = 0.046, R2 = 2.411). Moreover, the diversity of bifidobacteria in the intestinal tract of college students surpassed that in the out-of-school population (p = 0.034). This was characterized by a notable increase in 11 strains, including B. longum, B. bifidum, and B. pseudolongum, in the intestinal tract of college students, forming a more intricate intestinal bifidobacteria interaction network. (4) Conclusions: In summary, this study elucidated the principal factors affecting intestinal bifidobacteria and delineated their characteristics of intestinal bifidobacteria in diverse populations. By enriching the theory surrounding gut microbiota and health, this study provides essential data support for further investigations into the intricate dynamics of the gut microbiota.
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Affiliation(s)
- Shuying Yang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Su Wu
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Feiyan Zhao
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhixin Zhao
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xin Shen
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xia Yu
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Meng Zhang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Fang Wen
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zhihong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Bilige Menghe
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
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Liu C, He Z, Kong M, Jin D. Development of a duplex droplet digital PCR assay for the detection of Burkholderia cepacia complex and Stenotrophomonas maltophilia in bloodstream infections. Microbiol Spectr 2024; 12:e0356923. [PMID: 38411052 DOI: 10.1128/spectrum.03569-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/03/2024] [Indexed: 02/28/2024] Open
Abstract
Burkholderia cepacia complex (BCC) and Stenotrophomonas maltophilia are nosocomial pathogens that cause various infections and exhibit high resistance to multiple antimicrobial agents. In this study, we aimed to develop a duplex droplet digital PCR (ddPCR) assay for detecting BCC and S. maltophilia in bloodstream infections. We optimized the experimental conditions by setting the annealing temperature to 51°C and determining the optimal concentrations of primers and probes, as well as the thermal cycle numbers. The feasibility of the duplex ddPCR reaction system with the optimal conditions was established and verified through parallel reactions with reference strains of BCC and S. maltophilia. The specificity of the assay, tested with 33 reference strains, was found to be 100%. The duplex ddPCR assay demonstrated good repeatability and could detect as low as 5.35 copies/reaction of BCC and 7.67 copies/reaction of S. maltophilia. This level of sensitivity was consistent in the simulated blood and blood bottle samples. We compared nucleic acid extraction methods and found that the Chelex-100 boiling method and kit extraction method exhibited similar detection sensitivity, suggesting the potential application of the Chelex-100 boiling method in the ddPCR assay. In the clinical samples, the duplex ddPCR assay accurately detected BCC and S. maltophilia in 58 cases. In conclusion, our study successfully developed a duplex ddPCR assay that provides accurate and convenient detection of BCC and S. maltophilia in bloodstream infections.IMPORTANCEBurkholderia cepacia complex (BCC) and Stenotrophomonas maltophilia are implicated in a wide range of infections, including bloodstream infections (BSIs), pneumonia, and meningitis, and often exhibit high intrinsic resistance to multiple antimicrobial agents, limiting therapeutic options. The gold standard for diagnosing bloodstream infections remains blood culture. However, current blood culture detection and positivity rates do not meet the "rapid diagnosis" required for the diagnosis and treatment of critically ill patients with BSIs. The digital droplet PCR (ddPCR) method is a potentially more powerful tool in the diagnosis of BSIs compared to other molecular methods due to its greater sensitivity, specificity, accuracy, and reproducibility. In this study, a duplex ddPCR assay for the detection of BCC and S. maltophilia in BSIs was developed.
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Affiliation(s)
- Chunmei Liu
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ziqiang He
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mimi Kong
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dong Jin
- Department of Epidemiology, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Hebei Key Laboratory of Intractable Pathogens, Shijiazhuang Center for Disease Control and Prevention, Shijiazhuang, Hebei, China
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Wang H, Chen C, Xie M, Zhang Y, Chen B, Li Y, Jia W, Chen J, Zhou W. Research on quantitative detection technology of raccoon-derived ingredient adulteration in sausage products. Food Sci Nutr 2024; 12:2963-2972. [PMID: 38628186 PMCID: PMC11016427 DOI: 10.1002/fsn3.3976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/13/2023] [Accepted: 01/06/2024] [Indexed: 04/19/2024] Open
Abstract
This project presents a quantitative detection method to identify raccoon-derived ingredient adulteration in sausage products. The specific copy gene of the raccoon was selected as the target gene. According to the specificity of its primer and probe, the quantitative detection method of raccoon microdrops by droplet digital PCR was established. In addition, the accuracy of the proposed method was verified by artificially mixed samples, and the applicability of this method was tested based on the commercially available products. The experimental results indicate that the raccoon mass (M) and raccoon-extracted DNA concentration have a good linear relationship when the sample content is 5-100 mg, and there is also a significant linear relationship between DNA content and DNA copy number (C) with R 2 = .9982. Therefore, using DNA concentration as the median signal, the conversion equation between raw raccoon mass (M) and DNA copy number (C) could be obtained as follows: M = (C + 177.403)/16.954. The detection of artificially mixed samples and commercial samples shows that the method is accurate and suitable for quantitative adulteration detection of various sausage products in the market.
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Affiliation(s)
- Hui Wang
- Hebei Food Safety Key Laboratory, Key Laboratory of Special Food Supervision Technology for State Market Regulation, Hebei Engineering Research Center for Special Food Safety and HealthHebei Food Inspection and Research InstituteShijiazhuangChina
| | - Chen Chen
- Hebei Food Safety Key Laboratory, Key Laboratory of Special Food Supervision Technology for State Market Regulation, Hebei Engineering Research Center for Special Food Safety and HealthHebei Food Inspection and Research InstituteShijiazhuangChina
| | - Mengying Xie
- Hebei Food Safety Key Laboratory, Key Laboratory of Special Food Supervision Technology for State Market Regulation, Hebei Engineering Research Center for Special Food Safety and HealthHebei Food Inspection and Research InstituteShijiazhuangChina
| | - Yan Zhang
- Hebei Food Safety Key Laboratory, Key Laboratory of Special Food Supervision Technology for State Market Regulation, Hebei Engineering Research Center for Special Food Safety and HealthHebei Food Inspection and Research InstituteShijiazhuangChina
| | - Boxu Chen
- Hebei Food Safety Key Laboratory, Key Laboratory of Special Food Supervision Technology for State Market Regulation, Hebei Engineering Research Center for Special Food Safety and HealthHebei Food Inspection and Research InstituteShijiazhuangChina
| | - Yongyan Li
- Hebei Food Safety Key Laboratory, Key Laboratory of Special Food Supervision Technology for State Market Regulation, Hebei Engineering Research Center for Special Food Safety and HealthHebei Food Inspection and Research InstituteShijiazhuangChina
| | - Wenshen Jia
- Institute of Quality Standard and Testing TechnologyBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jia Chen
- College of Chemical TechnologyShijiazhuang UniversityShijiazhuangChina
| | - Wei Zhou
- Hebei Food Safety Key Laboratory, Key Laboratory of Special Food Supervision Technology for State Market Regulation, Hebei Engineering Research Center for Special Food Safety and HealthHebei Food Inspection and Research InstituteShijiazhuangChina
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Matsumoto S, Uchiumi T, Noda N, Ueyanagi Y, Hotta T, Kang D. Droplet digital polymerase chain reaction to measure heteroplasmic m.3243A>G mitochondrial mutations. Lab Med 2024; 55:227-233. [PMID: 37478467 PMCID: PMC10920975 DOI: 10.1093/labmed/lmad063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2023] Open
Abstract
OBJECTIVE Different mitochondrial DNA genotypes can coexist in a cell population as well as in a single cell, a condition known as heteroplasmy. Here, we accurately determined the heteroplasmy levels of the m.3243A>G mutation, which is the most frequently identified mutation in patients with mitochondrial diseases, using droplet digital polymerase chain reaction (ddPCR). METHODS The m.3243A>G heteroplasmy levels in artificial heteroplasmy controls mixed with various proportions of wild-type and mutant plasmids were measured using ddPCR, PCR-restriction fragment length polymorphism, and Sanger sequencing. The m.3243A>G heteroplasmy levels in DNA, extracted from the peripheral blood of patients with suspected mitochondrial disease and healthy subjects, were determined using ddPCR. RESULTS The accuracy of the ddPCR method was high. The lower limit of detection was 0.1%, which indicated its higher sensitivity compared with other methods. The m.3243A>G heteroplasmy levels in peripheral blood, measured using ddPCR, correlated inversely with age at the time of analysis. The m.3243A>G mutation may be overlooked in the peripheral blood-derived DNA of elderly people, as patients >60 years of age have heteroplasmy levels <10%, which is difficult to detect using methods other than the highly sensitive ddPCR. CONCLUSION ddPCR may be considered an accurate and sensitive method for measuring m.3243 A>G heteroplasmy levels of mitochondrial DNA.
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Affiliation(s)
- Shinya Matsumoto
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Takeshi Uchiumi
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Nozomi Noda
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Yasushi Ueyanagi
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Taeko Hotta
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Wei Y, Abbasi SMT, Mehmood N, Li L, Qu F, Cheng G, Hu D, Ho YP, Yuan W, Ho HP. Deep-qGFP: A Generalist Deep Learning Assisted Pipeline for Accurate Quantification of Green Fluorescent Protein Labeled Biological Samples in Microreactors. Small Methods 2024; 8:e2301293. [PMID: 38010980 DOI: 10.1002/smtd.202301293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/12/2023] [Indexed: 11/29/2023]
Abstract
Absolute quantification of biological samples provides precise numerical expression levels, enhancing accuracy, and performance for rare templates. Current methodologies, however, face challenges-flow cytometers are costly and complex, whereas fluorescence imaging, relying on software or manual counting, is time-consuming and error-prone. It is presented that Deep-qGFP, a deep learning-aided pipeline for the automated detection and classification of green fluorescent protein (GFP) labeled microreactors, enables real-time absolute quantification. This approach achieves an accuracy of 96.23% and accurately measures the sizes and occupancy status of microreactors using standard laboratory fluorescence microscopes, providing precise template concentrations. Deep-qGFP demonstrates remarkable speed, quantifying over 2000 microreactors across ten images in just 2.5 seconds, with a dynamic range of 56.52-1569.43 copies µL-1 . The method demonstrates impressive generalization capabilities, successfully applied to various GFP-labeling scenarios, including droplet-based, microwell-based, and agarose-based applications. Notably, Deep-qGFP is the first all-in-one image analysis algorithm successfully implemented in droplet digital polymerase chain reaction (PCR), microwell digital PCR, droplet single-cell sequencing, agarose digital PCR, and bacterial quantification, without requiring transfer learning, modifications, or retraining. This makes Deep-qGFP readily applicable in biomedical laboratories and holds potential for broader clinical applications.
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Affiliation(s)
- Yuanyuan Wei
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999 077, China
| | - Syed Muhammad Tariq Abbasi
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999 077, China
| | - Nawaz Mehmood
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999 077, China
| | - Luoquan Li
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999 077, China
| | - Fuyang Qu
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999 077, China
| | - Guangyao Cheng
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999 077, China
| | - Dehua Hu
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999 077, China
| | - Yi-Ping Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999 077, China
- Centre for Biomaterials, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999 077, China
- Hong Kong Branch of CAS Center for Excellence in Animal Evolution and Genetics, Shatin, Hong Kong SAR, 999 077, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Shatin, Hong Kong SAR, 999 077, China
| | - Wu Yuan
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999 077, China
| | - Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, 999 077, China
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Grossi I, Assoni C, Lorini L, Smussi D, Gurizzan C, Grisanti S, Paderno A, Mattavelli D, Piazza C, Pelisenco IA, De Petro G, Salvi A, Bossi P. Evaluation of DNA methylation levels of SEPT9 and SHOX2 in plasma of patients with head and neck squamous cell carcinoma using droplet digital PCR. Oncol Rep 2024; 51:52. [PMID: 38299234 PMCID: PMC10865173 DOI: 10.3892/or.2024.8711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/12/2023] [Indexed: 02/02/2024] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the seventh most commonly diagnosed cancer globally. HNSCC develops from the mucosa of the oral cavity, pharynx and larynx. Methylation levels of septin 9 (SEPT9) and short stature homeobox 2 (SHOX2) genes in circulating cell‑free DNA (ccfDNA) are considered epigenetic biomarkers and have shown predictive value in preliminary reports in HNSCC. Liquid biopsy is a non‑invasive procedure that collects tumor‑derived molecules, including ccfDNA. In the present study, a droplet digital PCR (ddPCR)‑based assay was developed to detect DNA methylation levels of circulating SEPT9 and SHOX2 in the plasma of patients with HNSCC. The assay was first set up using commercial methylated and unmethylated DNA. The dynamic changes in the methylation levels of SEPT9 and SHOX2 were then quantified in 20 patients with HNSCC during follow‑up. The results highlighted: i) The ability of the ddPCR‑based assay to detect very low copies of methylated molecules; ii) the significant decrease in SEPT9 and SHOX2 methylation levels in the plasma of patients with HNSCC at the first time points of follow‑up with respect to T0; iii) a different trend of longitudinally DNA methylation variations in small groups of stratified patients. The absolute and precise quantification of SEPT9 and SHOX2 methylation levels in HNSCC may be useful for studies with translational potential.
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Affiliation(s)
- Ilaria Grossi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Claudia Assoni
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Luigi Lorini
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Davide Smussi
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Cristina Gurizzan
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Salvatore Grisanti
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Alberto Paderno
- Unit of Otorhinolaryngology-Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Davide Mattavelli
- Unit of Otorhinolaryngology-Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Cesare Piazza
- Unit of Otorhinolaryngology-Head and Neck Surgery, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
| | - Iulia Andreea Pelisenco
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Giuseppina De Petro
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Alessandro Salvi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, I-25123 Brescia, Italy
| | - Paolo Bossi
- Unit of Medical Oncology, Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, ASST Spedali Civili of Brescia, University of Brescia, I-25123 Brescia, Italy
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11
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Sánchez-Carvajal JM, Vera-Salmoral E, Huerta B, Galán-Relaño Á, Ruedas-Torres I, Larenas-Muñoz F, Luque I, Carrasco L, Gómez-Laguna J. Droplet digital PCR as alternative to microbiological culture for Mycobacterium tuberculosis complex detection in bovine lymph node tissue samples. Front Cell Infect Microbiol 2024; 14:1349999. [PMID: 38469351 PMCID: PMC10925636 DOI: 10.3389/fcimb.2024.1349999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction Bovine tuberculosis (bTB) caused by Mycobacterium tuberculosis complex (MTC) remains a significant concern for public health. Direct real-time PCR and droplet digital PCR (ddPCR) are proposed as alternative tools to enhance diagnostic precision and efficiency. This study aims to assess the diagnostic performance of a ddPCR assay targeting IS6110 for the detection of MTC DNA in both microbiological culture and fresh lymph node (LN) tissue samples obtained from cattle, in comparison with the established reference standard, the microbiological culture followed by real-time PCR. Methods The fresh LNs (N=100) were collected each from a different cattle carcass at the slaughterhouse. The limit of detection of ddPCR-IS6110 was set to 101 copies per 20 μl reaction. Results DdPCR-IS6110 detected 44 out of 49 reference-standard positive samples and yielded negative results in 47 out of 51 reference-standard negative samples, resulting in adjusted sensitivity (Se) and specificity (Sp) of 90.76% [95% confidence interval (CI): 82.58 - 98.96%)], and 100% (95% CI: 100%) respectively. The estimated adjusted false negative rate (FNR) was 9.23% (95% CI: 1.04 - 17.42%) and the false positive rate (FPR) was 0% (95% CI: 0%). When directly applied from fresh bovine LN tissues, ddPCR-IS6110 identified 47 out of 49 reference-standard positive samples as ddPCR-IS6110-positive and 42 out of 51 reference-standard negative samples as ddPCR-IS6110-negative, resulting in adjusted Se and Sp values of 94.80% [95% (CI): 88.52 - 100%] and 100% (95% CI: 100%), respectively. The adjusted FNR was 5.20% (95% CI: 0 - 11.50%) and the FPR was 0% (95% CI: 0%). Noteworthy, ddPCR-IS6110 disclosed as positive 9 samples negative to reference-standard. Discussion DdPCR-IS6110 proved to be a rapid, highly sensitive, and specific diagnostic tool as an alternative to reference-standard method.
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Affiliation(s)
- José María Sánchez-Carvajal
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
| | - Eduardo Vera-Salmoral
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
- Department of Animal Health, Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes (ENZOEM), University of Córdoba, University of Córdoba, Córdoba, Spain
| | - Belén Huerta
- Department of Animal Health, Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes (ENZOEM), University of Córdoba, University of Córdoba, Córdoba, Spain
| | - Ángela Galán-Relaño
- Department of Animal Health, Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes (ENZOEM), University of Córdoba, University of Córdoba, Córdoba, Spain
| | - Inés Ruedas-Torres
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
- UK Health Security Agency (UKHSA), Salisbury, United Kingdom
| | - Fernanda Larenas-Muñoz
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
| | - Inmaculada Luque
- Department of Animal Health, Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes (ENZOEM), University of Córdoba, University of Córdoba, Córdoba, Spain
| | - Librado Carrasco
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
| | - Jaime Gómez-Laguna
- Department of Anatomy and Comparative Pathology and Toxicology, Pathology and Immunology Group (UCO-PIG), Unidad de Investigación Competitiva (UIC) Zoonosis y Enfermedades Emergentes ENZOEM, University of Córdoba, Córdoba, Spain
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12
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Park JW, Bae SJ, Yun JH, Kim S, Park M. Assessment of Genetic Stability in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes by Using Droplet Digital PCR. Int J Mol Sci 2024; 25:1101. [PMID: 38256178 PMCID: PMC10815998 DOI: 10.3390/ijms25021101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/04/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
Unintended genetic modifications that occur during the differentiation and proliferation of human induced pluripotent stem cells (hiPSCs) can lead to tumorigenicity. This is a crucial concern in the development of stem cell-based therapies to ensure the safety and efficacy of the final product. Moreover, conventional genetic stability testing methods are limited by low sensitivity, which is an issue that remains unsolved. In this study, we assessed the genetic stability of hiPSCs and hiPSC-derived cardiomyocytes using various testing methods, including karyotyping, CytoScanHD chip analysis, whole-exome sequencing, and targeted sequencing. Two specific genetic mutations in KMT2C and BCOR were selected from the 17 gene variants identified by whole-exome and targeted sequencing methods, which were validated using droplet digital PCR. The applicability of this approach to stem cell-based therapeutic products was further demonstrated with associated validation according to the International Council for Harmonisation (ICH) guidelines, including specificity, precision, robustness, and limit of detection. Our droplet digital PCR results showed high sensitivity and accuracy for quantitatively detecting gene mutations, whereas conventional qPCR could not avoid false positives. In conclusion, droplet digital PCR is a highly sensitive and precise method for assessing the expression of mutations with tumorigenic potential for the development of stem cell-based therapeutics.
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Affiliation(s)
| | | | | | | | - Misun Park
- Advanced Bioconvergence Product Research Division, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju-si 28159, Republic of Korea; (J.W.P.); (S.J.B.); (J.H.Y.); (S.K.)
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13
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Pacini A, Paredes F, Heckel S, Ibarra G, Petreli MV, Perez M, Agnella Y, Piskulic L, Allasia MB, Caprile L, Colaneri A, Sesma J. Ready for new waves: optimizing SARS-CoV-2 variants monitoring in pooled samples with droplet digital PCR. Front Public Health 2024; 11:1340420. [PMID: 38298257 PMCID: PMC10829044 DOI: 10.3389/fpubh.2023.1340420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024] Open
Abstract
Introduction The declaration of the end of the Public Health Emergency for COVID-19 on May 11th, 2023, has shifted the global focus led by WHO and CDC towards monitoring the evolution of SARS-CoV-2. Augmenting these international endeavors with local initiatives becomes crucial to not only track the emergence of new variants but also to understand their spread. We present a cost-effective digital PCR-based pooled sample testing methodology tailored for early variant surveillance. Methods Using 1200 retrospective SARS-CoV-2 positive samples, either negative or positive for Delta or Omicron, we assessed the sensitivity and specificity of our detection strategy employing commercial TaqMan variant probes in a 1:9 ratio of variant-positive to variant-negative samples. Results The study achieved 100% sensitivity and 99% specificity in 10-sample pools, with an Area Under the Curve (AUC) exceeding 0.998 in ROC curves, using distinct commercial TaqMan variant probes. Discussion The employment of two separate TaqMan probes for both Delta and Omicron establishes dual validation routes, emphasizing the method's robustness. Although we used known samples to model realistic emergence scenarios of the Delta and Omicron variants, our main objective is to demonstrate the versatility of this strategy to identify future variant appearances. The utilization of two divergent variants and distinct probes for each confirms the method's independence from specific variants and probes. This flexibility ensures it can be tailored to recognize any subsequent variant emergence, given the availability of its sequence and a specific probe. Consequently, our approach stands as a robust tool for tracking and managing any new variant outbreak, reinforcing our global readiness against possible future SARS-CoV-2 waves.
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Affiliation(s)
- Antonella Pacini
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario, CONICET, Rosario, Argentina
| | - Franco Paredes
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, Argentina
| | - Sofia Heckel
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario, CONICET, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, Argentina
| | - Guadalupe Ibarra
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, Argentina
| | - Maria Victoria Petreli
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas de Rosario, Universidad Nacional de Rosario, Rosario, Argentina
| | - Marilina Perez
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
| | - Yanina Agnella
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Facultad de Ciencias Veterinarias, Universidad Nacional de Rosario, Casilda, Argentina
| | - Laura Piskulic
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Maria Belen Allasia
- Área Estadística y Procesamiento de Datos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Luis Caprile
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
| | - Alejandro Colaneri
- Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Juliana Sesma
- Molecular Biology Department, Hospital Provincial de Rosario, Rosario, Argentina
- Instituto de Inmunología Clínica y Experimental de Rosario, CONICET, Rosario, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de Rosario, Rosario, Argentina
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14
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Blay E, Hardyman E, Morovic W. PCR-based analytics of gene therapies using adeno-associated virus vectors: Considerations for cGMP method development. Mol Ther Methods Clin Dev 2023; 31:101132. [PMID: 37964893 PMCID: PMC10641278 DOI: 10.1016/j.omtm.2023.101132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
The field of gene therapy has evolved and improved so that today the treatment of thousands of genetic diseases is now possible. An integral aspect of the drug development process is generating analytical methods to be used throughout clinical and commercial manufacturing. Enumeration and identification assays using genetic testing are critical to ensure the safety, efficacy, and stability of many active pharmaceutical ingredients. While nucleic acid-based methods are already reliable and rapid, there are unique biological, technological, and regulatory aspects in gene therapies that must be considered. This review surveys aspects of method development and validation using nucleic acid-based testing of gene therapies by focusing on adeno-associated virus (AAV) vectors and their co-transfection factors. Key differences between quantitative PCR and droplet digital technologies are discussed to show how improvements can be made while still adhering to regulatory guidance. Example validation parameters for AAV genome titers are described to demonstrate the scope of analytical development. Finally, several areas for improving analytical testing are presented to inspire future innovation, including next-generation sequencing and artificial intelligence. Reviewing the broad characteristics of gene therapy assessment serves as an introduction for new researchers, while clarifying processes for professionals already involved in pharmaceutical manufacturing.
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Affiliation(s)
- Emmanuel Blay
- Gene & Cell Therapy, PPD GMP Laboratories, Part of ThermoFisher Scientific, Middleton, WI, USA
| | - Elaine Hardyman
- Gene & Cell Therapy, PPD GMP Laboratories, Part of ThermoFisher Scientific, Middleton, WI, USA
| | - Wesley Morovic
- Gene & Cell Therapy, PPD GMP Laboratories, Part of ThermoFisher Scientific, Middleton, WI, USA
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15
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Caneparo V, Rinaldi C, Ferrante D, Ravanini P, Lo Cigno I, Cavalieri S, Gariglio M, Borgogna C. Longitudinal monitoring of SARS-CoV-2 viral load in self-collected saliva from health care workers during breakthrough infections to spare working days. Microbiol Spectr 2023; 11:e0255523. [PMID: 37982633 PMCID: PMC10714835 DOI: 10.1128/spectrum.02555-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/03/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Real-time quantitative PCR (RT-qPCR) on nasopharyngeal swabs (NPS) has been used as the standard method for detecting and monitoring SARS-CoV-2 infection during the pandemic. However, NPS collection often causes discomfort and poses a higher risk of transmission to health care workers (HCW). Furthermore, RT-qPCR only provides relative quantification and does not allow distinguishing those samples with residual, no longer active infection, whereas droplet digital PCR (ddPCR) allows for precise quantification of viral load, offering greater sensitivity and reproducibility. This study highlights the effectiveness of using self-collected saliva as a convenient and reliable sampling method. By utilizing ddPCR to measure the SARS-CoV-2 viral load in saliva samples, individuals with low or undetectable viral loads can be quickly identified. This approach is particularly advantageous for surveillance programs targeting HCW, as it enables the early identification and release of uninfected personnel, minimizing lost workdays. Additionally, analyzing viral load in saliva samples by ddPCR is valuable in determining virus shedding duration across different SARS-CoV-2 variants, informing transmission and disease control. Finally, testing saliva could overcome the detection of historic cases due to prolonged RNA swabbing past-infection and the unnecessary exclusion of those individuals from the workplace.
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Affiliation(s)
- Valeria Caneparo
- CAAD-Center for Translational Research on Autoimmune and Allergic Disease, University of Piemonte Orientale, Novara, Italy
| | - Carmela Rinaldi
- Aging Project, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
- Education and Research area, Health Professions Direction, Maggiore Della Carità Hospital, Novara, Italy
| | - Daniela Ferrante
- Medical Statistics, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Paolo Ravanini
- Unit of Microbiology and Virology, Department of Laboratory Medicine, "Maggiore della Carità" Hospital, Novara, Italy
| | - Irene Lo Cigno
- Virology Unit, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Silvia Cavalieri
- Occupational Health Unit, Specialist Medical and Oncological Department, "Maggiore della Carità" University - Hospital, Novara, Italy
| | - Marisa Gariglio
- Virology Unit, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Cinzia Borgogna
- Virology Unit, Department of Translational Medicine, University of Piemonte Orientale, Novara, Italy
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16
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Haqshenas G, Garland SM, Balgovind P, Cornall A, Danielewski J, Molano M, Machalek DA, Murray G. Development of a touchdown droplet digital PCR assay for the detection and quantitation of human papillomavirus 16 and 18 from self-collected anal samples. Microbiol Spectr 2023; 11:e0183623. [PMID: 37962350 PMCID: PMC10714734 DOI: 10.1128/spectrum.01836-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 10/09/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE The quantity of the human papillomavirus (HPV) is associated with disease outcome. We designed an accurate and precise digital PCR assay for quantitating HPV in anal samples, a sample type that is typically problematic due to the presence of PCR inhibitors.
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Affiliation(s)
- Gholamreza Haqshenas
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Suzanne M. Garland
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Prisha Balgovind
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Alyssa Cornall
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Jennifer Danielewski
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Monica Molano
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
| | - Dorothy A. Machalek
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
- The Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia
| | - Gerald Murray
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Women’s Infectious Diseases, The Royal Women’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
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17
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Sun W, Zhou C, Peng C, Yang R, Li M, Geng J, Zhou J, Chen L, Li W. Diagnostic value of plasma circular RNA based on droplet digital polymerase chain reaction in lung adenocarcinoma. Lab Med 2023:lmad101. [PMID: 38048812 DOI: 10.1093/labmed/lmad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Plasma circular (circ)RNAs detected by droplet digital polymerase chain reaction (ddPCR) may be ideal markers for liquid biopsy. However, ddPCR detection of circRNAs in plasma for diagnosis of lung adenocarcinoma has been rarely reported. METHODS An RNA sequencing analysis was performed in plasma from patients with early lung adenocarcinoma and healthy individuals. Droplet digital PCR was used to verify the differentially expressed genes. RESULTS The copy numbers of circle RNALZIC (circLZIC)and circle RNACEP350 (circCEP350) in the plasma of lung adenocarcinoma patients were significantly higher than in plasma of healthy people, and the copy numbers in postoperative plasma of the same patients were significantly lower than those in preoperative plasma. CircLZIC and circCEP350 alone and in combination had diagnostic value in lung adenocarcinoma and early lung adenocarcinoma. CircLZIC and circCEP350 had more binding sites with multiple microRNAs. Their target genes were enriched in several signaling pathways. CONCLUSION The copy numbers of circLZIC and circCEP350 were higher in plasma of lung adenocarcinoma patients than in plasma of healthy controls, significantly correlated with tumor size and TNM stage, and closely related to the occurrence and development of tumors. These circRNAs may serve as molecular markers for the diagnosis of lung adenocarcinoma.
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Affiliation(s)
- Wanying Sun
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Center for Clinical Medicine of Respiratory Disease (Tumor) in Anhui, Bengbu, China
- Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu, China
| | - Changming Zhou
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Center for Clinical Medicine of Respiratory Disease (Tumor) in Anhui, Bengbu, China
- Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu, China
| | - Caiqiu Peng
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Center for Clinical Medicine of Respiratory Disease (Tumor) in Anhui, Bengbu, China
- Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu, China
| | - Ran Yang
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Center for Clinical Medicine of Respiratory Disease (Tumor) in Anhui, Bengbu, China
- Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu, China
| | - Mengting Li
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Center for Clinical Medicine of Respiratory Disease (Tumor) in Anhui, Bengbu, China
- Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu, China
| | - Jian Geng
- Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu, China
| | - Jihong Zhou
- Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu, China
| | - Liang Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wei Li
- Department of Respiratory Disease, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
- Center for Clinical Medicine of Respiratory Disease (Tumor) in Anhui, Bengbu, China
- Provincial Key Laboratory of Respiratory Disease in Anhui, Bengbu, China
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18
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Tian Y, Fan Z, Zhang X, Xu L, Cao Y, Pan Z, Mo Y, Gao Y, Zheng S, Huang J, Zou H, Duan Z, Li H, Ren F. CRISPR/Cas13a-Assisted accurate and portable hepatitis D virus RNA detection. Emerg Microbes Infect 2023; 12:2276337. [PMID: 37882492 PMCID: PMC10796118 DOI: 10.1080/22221751.2023.2276337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/23/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND & AIMS Hepatitis delta virus (HDV) infection accelerates the progression of chronic hepatitis B virus (HBV) infection, posing a large economic and health burden to patients. At present, there remains a lack of accurate and portable detection methods for HDV RNA. Here, we aim to establish a convenient, rapid, highly sensitive and specific method to detect HDV RNA using CRISPR-Cas13a technology. METHODS We established fluorescence (F) and lateral flow strip (L) assays based on CRISPR-Cas13a combined with RT-PCR and RT-RAA for HDV RNA detection, respectively. we conducted a cohort study of 144 patients with HDV-IgG positive to evaluate the CRISPR-Cas13a diagnostic performance for identifying HDV in clinical samples, compared to RT-qPCR and RT-ddPCR. RESULTS For synthetic HDV RNA plasmids, the sensitivity of RT-PCR-CRISPR-based fluorescence assays was 1 copy/μL, higher than that of RT-qPCR (10 copies/μL) and RT-ddPCR (10 copies/μL); for HDV RNA-positive samples, the sensitivity of RT-RAA-CRISPR-based fluorescence and lateral flow strip assays was 10 copies/μL, as low as that of RT-qPCR and RT-ddPCR, and the assay took only approximately 85 min. Additionally, the positivity rates of anti-HDV IgG-positive samples detected by the RT-qPCR, RT-ddPCR, RT-PCR-CRISPR fluorescence and RT-RAA-CRISPR lateral flow strip methods were 66.7% (96/144), 76.4% (110/144), 81.9% (118/144), and 72.2% (104/144), respectively. CONCLUSIONS We developed a highly sensitive and specific, as well as a portable and easy CRISPR-based assay for the detection of HDV RNA, which could be a prospective measure for monitoring the development of HDV infection and evaluating the therapeutic effect.
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Affiliation(s)
- Yuan Tian
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Zihao Fan
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Xiangying Zhang
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Ling Xu
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Yaling Cao
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Zhenzhen Pan
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Yinkang Mo
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Yao Gao
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Sujun Zheng
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Jing Huang
- Department of Infection Control, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Huaibin Zou
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Zhongping Duan
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Hao Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
| | - Feng Ren
- Beijing Institute of Hepatology, Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
- Beijing Youan Hospital, Capital Medical University, Beijing, People’s Republic of China
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19
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Voegel TM, McGonigal P, Nelson LM, Úrbez-Torres JR. Health Status of Ready-to-Plant Grapevine Nursery Material in Canada Regarding Crown Gall and Description of the First Allorhizobium vitis Strain OP-G1 Isolated from British Columbia. Plant Dis 2023; 107:3666-3673. [PMID: 37436214 DOI: 10.1094/pdis-05-23-0901-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Crown gall disease of grapevines caused by Allorhizobium vitis causes significant damage to vineyards in cold-climate viticulture areas such as Canada and the northern United States. Introduction of the disease into vineyards occurs mainly through planting of infected but asymptomatic nursery material. Because A. vitis is not a regulated pest for import into Canada, no information on the health status of nursery material destined for import into Canada has previously been collected. This study evaluated the health status of ready-to-plant nursery material from domestic and international nurseries in regard to crown gall by determining the abundance of A. vitis in different plant sections via Droplet Digital PCR technology. In addition, different rootstocks from one nursery were compared. Results showed that A. vitis was present in planting material from all nurseries tested. The bacteria were nonuniformly distributed in dormant nursery material, and there was no difference in abundance between the rootstocks tested. In addition, the first A. vitis strain OP-G1 isolated from galls in British Columbia is described. Results showed that a minimum of 5,000 bacterial OP-G1 cells were needed for symptom expression, suggesting that the initiation of symptom development is not based on presence of bacteria in nursery material alone; a minimum threshold is needed, and environmental conditions need to be met.
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Affiliation(s)
- Tanja M Voegel
- Department of Biology, Okanagan Campus, University of British Columbia, Kelowna, BC V1V 1V7, Canada
| | - Portiaa McGonigal
- Department of Biology, Okanagan Campus, University of British Columbia, Kelowna, BC V1V 1V7, Canada
| | - Louise M Nelson
- Department of Biology, Okanagan Campus, University of British Columbia, Kelowna, BC V1V 1V7, Canada
| | - José R Úrbez-Torres
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, BC V0H 1Z0, Canada
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20
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Kitagawa S, Ichihara S, Omori Y, Maeda C, Ono Y, Tahara M, Furukawa T, Muraoka S, Miyakawa H. Branch-duct Intraductal Papillary Mucinous Neoplasm with Rapidly Developing Intracystic Xanthogranulomatous Nodules. Intern Med 2023; 62:3489-3494. [PMID: 37062735 PMCID: PMC10749811 DOI: 10.2169/internalmedicine.0862-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/26/2023] [Indexed: 04/18/2023] Open
Abstract
We herein report a case of a branch-duct intraductal papillary mucinous neoplasm (IPMN) with rapidly developing intracystic xanthogranulomatous nodules. A unilocular cystic lesion without a mural nodule was found in the pancreatic tail of a 69-year-old man. Ten months later, multiple mural nodules emerged unexpectedly within the cyst, and the patient underwent distal pancreatectomy. Based on immunohistochemical studies and a molecular analysis, we diagnosed him with branch-duct IPMN of the gastric immunophenotype. Fragility of the pancreatic duct mucosa and consequent exposure of the wall to pancreatic juice might have caused marked granulation nodule formation in the cyst lumen.
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Affiliation(s)
- Sho Kitagawa
- Department of Gastroenterology, Sapporo Kosei General Hospital, Japan
| | - Shin Ichihara
- Department of Surgical Pathology, Sapporo Kosei General Hospital, Japan
| | - Yuko Omori
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Japan
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Japan
| | - Chiho Maeda
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Japan
| | - Yusuke Ono
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Japan
| | - Munenori Tahara
- Department of Surgery, Sapporo Kosei General Hospital, Japan
| | - Toru Furukawa
- Department of Investigative Pathology, Tohoku University Graduate School of Medicine, Japan
| | - Shunji Muraoka
- Department of Surgical Pathology, Sapporo Kosei General Hospital, Japan
| | - Hiroyuki Miyakawa
- Department of Gastroenterology, Sapporo Kosei General Hospital, Japan
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21
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Brokāne A, Bajo-Santos C, Zayakin P, Belovs A, Jansons J, Lietuvietis V, Martens-Uzunova ES, Jenster GW, Linē A. Validation of potential RNA biomarkers for prostate cancer diagnosis and monitoring in plasma and urinary extracellular vesicles. Front Mol Biosci 2023; 10:1279854. [PMID: 38099195 PMCID: PMC10720733 DOI: 10.3389/fmolb.2023.1279854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023] Open
Abstract
Introduction: Prostate cancer (PCa), one of the most prevalent malignancies affecting men worldwide, presents significant challenges in terms of early detection, risk stratification, and active surveillance. In recent years, liquid biopsies have emerged as a promising non-invasive approach to complement or even replace traditional tissue biopsies. Extracellular vesicles (EVs), nanosized membranous structures released by various cells into body fluids, have gained substantial attention as a source of cancer biomarkers due to their ability to encapsulate and transport a wide range of biological molecules, including RNA. In this study, we aimed to validate 15 potential RNA biomarkers, identified in a previous EV RNA sequencing study, using droplet digital PCR. Methods: The candidate biomarkers were tested in plasma and urinary EVs collected before and after radical prostatectomy from 30 PCa patients and their diagnostic potential was evaluated in a test cohort consisting of 20 benign prostate hyperplasia (BPH) and 20 PCa patients' plasma and urinary EVs. Next, the results were validated in an independent cohort of plasma EVs from 31 PCa and 31 BPH patients. Results: We found that the levels of NKX3-1 (p = 0.0008) in plasma EVs, and tRF-Phe-GAA-3b (p < 0.0001) tRF-Lys-CTT-5c (p < 0.0327), piR-28004 (p = 0.0081) and miR-375-3p (p < 0.0001) in urinary EVs significantly decreased after radical prostatectomy suggesting that the main tissue source of these RNAs is prostate and/or PCa. Two mRNA biomarkers-GLO1 and NKX3-1 showed promising diagnostic potential in distinguishing between PCa and BPH with AUC of 0.68 and 0.82, respectively, in the test cohort and AUC of 0.73 and 0.65, respectively, in the validation cohort, when tested in plasma EVs. Combining these markers in a biomarker model yielded AUC of 0.85 and 0.71 in the test and validation cohorts, respectively. Although the PSA levels in the blood could not distinguish PCa from BPH in our cohort, adding PSA to the mRNA biomarker model increased AUC from 0.71 to 0.76. Conclusion: This study identified two novel EV-enclosed RNA biomarkers-NKX3-1 and GLO1-for the detection of PCa, and highlights the complementary nature of GLO1, NKX3-1 and PSA as combined biomarkers in liquid biopsies of PCa.
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Affiliation(s)
- Agnese Brokāne
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | | | | | - Guido W. Jenster
- Department of Urology, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Aija Linē
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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22
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Ma XY, Shao ZL, Yu XP, Wang ZL. A Droplet Digital PCR-Based Approach for Quantitative Analysis of the Adulteration of Atlantic Salmon with Rainbow Trout. Foods 2023; 12:4309. [PMID: 38231780 DOI: 10.3390/foods12234309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 01/19/2024] Open
Abstract
Low-cost fish species are often used to adulterate or substitute for Atlantic salmon products, posing a serious threat to market order and public health. Hence, reliable techniques are urgently needed to detect Atlantic salmon adulteration. In this study, a precise method for identifying and quantifying adulterated Atlantic salmon with rainbow trout based on droplet digital PCR (ddPCR) testing was developed. Species-specific primers and probes were designed targeting the single-copy nuclear gene myoglobin of two salmonids. A quantitative formula for calculating the mass fraction of adulterated Atlantic salmon with rainbow trout was established based on a one-step conversion strategy, in which the DNA copy number ratios were directly transformed to meat mass fractions by introducing a fixed constant (the transfer coefficient). The dynamic range of the established ddPCR method was from 1% to 90%, with a limit of detection (LOD) of 0.2% and a limit of quantification (LOQ) of 0.8% for rainbow trout in Atlantic salmon, respectively. The quantification method demonstrated an acceptable level of repeatability and reproducibility, as the values of the relative standard deviation (RSD) for the tested meat mixtures with the known fractions were all less than 5%. Thermal and freezing treatments, as well as adding food additives within the recommended dosage limits, had no significant effect on the quantification accuracy. The method was successfully applied to detect rainbow trout adulteration in commercial raw and processed Atlantic salmon products. In comparison to real-time quantitative PCR (qPCR) testing, the established ddPCR method exhibited a higher level of stability and accuracy. Overall, the ddPCR-based quantitative method exhibited high levels of accuracy, stability, sensitivity, and practicability, suitable for applications in the routine surveillance and quality assurance of salmon products.
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Affiliation(s)
- Xiao-Yu Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhu-Long Shao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xiao-Ping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zheng-Liang Wang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection and Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
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23
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Carrasco R, Ingelmo-Torres M, Trullas R, Roldán FL, Rodríguez-Carunchio L, Juez L, Sureda J, Alcaraz A, Mengual L, Izquierdo L. Tumor-Agnostic Circulating Tumor DNA Testing for Monitoring Muscle-Invasive Bladder Cancer. Int J Mol Sci 2023; 24:16578. [PMID: 38068899 PMCID: PMC10706140 DOI: 10.3390/ijms242316578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023] Open
Abstract
Circulating tumor DNA (ctDNA) has recently emerged as a real-time prognostic and predictive biomarker for monitoring cancer patients. Here, we aimed to ascertain whether tumor-agnostic ctDNA testing would be a feasible strategy to monitor disease progression and therapeutic response in muscle-invasive bladder cancer (MIBC) patients after radical cystectomy (RC). Forty-two MIBC patients who underwent RC were prospectively included. Blood samples from these patients were collected at different follow-up time points. Two specific mutations (TERT c.1-124C>T and ATM c.1236-2A>T) were analyzed in the patients' plasma samples by droplet digital PCR to determine their ctDNA status. During a median follow-up of 21 months, 24% of patients progressed in a median of six months. ctDNA status was identified as a prognostic biomarker of tumor progression before RC and 4 and 12 months later (HR 6.774, HR 3.673, and HR 30.865, respectively; p < 0.05). Lastly, dynamic changes in ctDNA status between baseline and four months later were significantly associated with patient outcomes (p = 0.045). In conclusion, longitudinal ctDNA analysis using a tumor-agnostic approach is a potential tool for monitoring MIBC patients after RC. The implementation of this testing in a clinical setting could improve disease management and patients' outcomes.
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Affiliation(s)
- Raquel Carrasco
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
- Genètica i Tumors Urològics, Fundació de Recerca Clinic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 08036 Barcelona, Spain
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Mercedes Ingelmo-Torres
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
- Genètica i Tumors Urològics, Fundació de Recerca Clinic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 08036 Barcelona, Spain
| | - Ramón Trullas
- Unitat de Neurobiologia, Institut d’Investigacions Biomèdiques de Barcelona (IIBB/CSIC/IDIBAPS), 08036 Barcelona, Spain;
| | - Fiorella L. Roldán
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
- Genètica i Tumors Urològics, Fundació de Recerca Clinic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 08036 Barcelona, Spain
| | | | - Lourdes Juez
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
| | - Joan Sureda
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
| | - Antonio Alcaraz
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
- Genètica i Tumors Urològics, Fundació de Recerca Clinic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 08036 Barcelona, Spain
| | - Lourdes Mengual
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
- Genètica i Tumors Urològics, Fundació de Recerca Clinic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 08036 Barcelona, Spain
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), 08036 Barcelona, Spain
| | - Laura Izquierdo
- Laboratori i Servei d’Urologia, Hospital Clinic de Barcelona, 08036 Barcelona, Spain; (R.C.); (M.I.-T.); (F.L.R.); (L.J.); (J.S.); (A.A.); (L.I.)
- Genètica i Tumors Urològics, Fundació de Recerca Clinic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), 08036 Barcelona, Spain
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24
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Faaborg L, Andersen RF, Wen SW, Thomsen CB, Raunkilde L, Hansen TF, Jensen LH, Steffensen KD, Jakobsen A. Prognostic impact of early ctDNA dynamics during chemotherapy of metastatic cancer. Future Oncol 2023; 19:2361-2367. [PMID: 37965794 DOI: 10.2217/fon-2023-0111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023] Open
Abstract
Aim: Clinical utility of the dynamics of ctDNA is sparse. This study aimed at evaluating the prognostic impact of early ctDNA dynamics in patients with metastatic cancer treated with chemotherapy. Materials & methods: The ctDNA dynamics were evaluated in 595 patients with metastatic cancer using droplet digital PCR. Results: Patients with an increase in ctDNA after one treatment cycle (n = 73; 12.2%) had an overall survival of 5.6 months compared with 8.6 months in patients with stable or decreasing ctDNA (n = 328; 55.1%) and 21.0 months in patients with undetectable ctDNA (p < 0.001; hazard ratio: 0.47; 95% CI: 0.41-0.53). Conclusion: Early ctDNA dynamics hold important prognostic information and have great implications for evaluation with the perspective of a more individualized treatment strategy.
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Affiliation(s)
- Louise Faaborg
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, Odense C, 5000, Denmark
| | - Rikke Fredslund Andersen
- Department of Biochemistry & Immunology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
| | - Sara Wc Wen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, Odense C, 5000, Denmark
| | - Caroline B Thomsen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
| | - Louise Raunkilde
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, Odense C, 5000, Denmark
| | - Torben Frøstrup Hansen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, Odense C, 5000, Denmark
| | - Lars Henrik Jensen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
| | - Karina Dahl Steffensen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, Odense C, 5000, Denmark
- Center for Shared Decision Making, Lillebælt Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
| | - Anders Jakobsen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, Beriderbakken 4, Vejle, 7100, Denmark
- Department of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, Odense C, 5000, Denmark
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25
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Lawaju BR, Yan G, Whitworth J. Development of a Droplet Digital PCR Assay for Detection and Quantification of Stubby Root Nematode, Paratrichodorus allius, in Soil. Plant Dis 2023; 107:3344-3353. [PMID: 37115564 DOI: 10.1094/pdis-03-23-0439-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The stubby root nematode Paratrichodorus allius is an important plant-parasitic nematode species within the Trichodoridae family. It can directly harm the plants by feeding on the roots or indirectly by transmitting Tobacco rattle virus. These nematodes are mostly diagnosed either by traditional microscopic methods or a polymerase chain reaction (PCR)-based method. Droplet digital PCR (ddPCR) is a novel PCR technique which is sensitive and precise in quantifying DNA templates of the test samples. In this study, we developed a ddPCR assay to detect and quantify P. allius in soil. The specificity and sensitivity of the assay was first determined using P. allius nematode DNA or DNA from sterilized soil artificially inoculated with P. allius, and the assay was used to quantify P. allius populations in field soils. The assay did not detect nematodes other than P. allius, thus showing high specificity. It was able to detect P. allius equivalent to a 0.01 and 0.02 portion of a single nematode in soil DNA and nematode DNA extracts, respectively. Highly linear relationships between DNA copy numbers from ddPCR and serial dilutions of known concentrations were observed with DNA from P. allius nematodes (R2 = 0.9842) and from artificially infested soil (R2 = 0.9464). The P. allius populations from field soils determined by ddPCR were highly correlated with traditional microscopic counts (R2 = 0.7963). To our knowledge, this is the first report of applying ddPCR to detect and quantify stubby root nematode in soil. The results of this study support the potentiality of a ddPCR assay as a new research tool in diagnostics of plant-parasitic nematodes.
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Affiliation(s)
- Bisho Ram Lawaju
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Guiping Yan
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108
| | - Jonathan Whitworth
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID 83210
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26
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Meng Y, Jiang N, Xie Y, Wei Y, Wang C, Tian M, Xue M, Xu C, Li Y, Liu W, Fan Y, Zhou Y. Development of a droplet digital PCR assay for the sensitive detection of iridovirus in Andrias davidianus. J Fish Dis 2023; 46:1249-1256. [PMID: 37535813 DOI: 10.1111/jfd.13844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/20/2023] [Accepted: 07/22/2023] [Indexed: 08/05/2023]
Abstract
Chinese giant salamander iridovirus (GSIV) is the first known and causative viral pathogen in Andrias davidianus. Developing a sensitive, accurate and specific assay to detect GSIV in samples is essential to prevent the further spread of the pathogen. In this study, we established a droplet digital PCR (ddPCR) assay that targeted the mcp gene of GSIV, enabling rapid and quantitative detection of the virus. We determined that the optimal annealing temperature, primer concentration and probe concentration were 57.1°C, 50 nM and 500 nM, respectively. We analysed the specificity and sensitivity of the ddPCR assay and found that five common aquatic animal viruses, including Cyprinid herpesvirus 2 (CyHV-2), infectious spleen and kidney necrosis virus (ISKNV), Koi herpesvirus (KHV) and Carp Edema Virus (CEV) displayed negative results based on this GSIV ddPCR assay. The assay can detect GSIV with the lowest detection limit of 3.7 copies per reaction. To evaluate the sensitivity and accuracy of the ddPCR assay, we tested different infected tissue samples with both the ddPCR and TaqMan real-time PCR assays. Our results showed that the ddPCR assay detected GSIV in all samples with 100% positivity, while the TaqMan real-time PCR assay detected GSIV in only 82.1% of samples. The established ddPCR method provided several advantages in detecting GISV, including high sensitivity, high precision and absolute quantification, making it a powerful tool for detection of possible and potential GSIV infection, even in samples with low viral load.
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Affiliation(s)
- Yan Meng
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Nan Jiang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Yixing Xie
- Zhangjiajie Giant salamander National Nature Reserve Affairs Center, Zhangjiajie, China
| | - Ying Wei
- Zhangjiajie Giant salamander National Nature Reserve Affairs Center, Zhangjiajie, China
| | - Cheng Wang
- Zhangjiajie Giant salamander National Nature Reserve Affairs Center, Zhangjiajie, China
| | - Mingzhu Tian
- Zhangjiajie Giant salamander National Nature Reserve Affairs Center, Zhangjiajie, China
| | - Mingyang Xue
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Chen Xu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Yiqun Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Wenzhi Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Yuding Fan
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Yong Zhou
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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Wood ML, Neumann R, Roy P, Nair V, Royle NJ. Characterization of integrated Marek's disease virus genomes supports a model of integration by homology-directed recombination and telomere-loop-driven excision. J Virol 2023; 97:e0071623. [PMID: 37737586 PMCID: PMC10617522 DOI: 10.1128/jvi.00716-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/03/2023] [Indexed: 09/23/2023] Open
Abstract
IMPORTANCE Marek's disease virus (MDV) is a ubiquitous chicken pathogen that inflicts a large economic burden on the poultry industry, despite worldwide vaccination programs. MDV is only partially controlled by available vaccines, and the virus retains the ability to replicate and spread between vaccinated birds. Following an initial infection, MDV enters a latent state and integrates into host telomeres and this may be a prerequisite for malignant transformation, which is usually fatal. To understand the mechanism that underlies the dynamic relationship between integrated-latent and reactivated MDV, we have characterized integrated MDV (iMDV) genomes and their associated telomeres. This revealed a single orientation among iMDV genomes and the loss of some terminal sequences that is consistent with integration by homology-directed recombination and excision via a telomere-loop-mediated process.
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Affiliation(s)
- Michael L. Wood
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Rita Neumann
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Poornima Roy
- Viral Oncogenesis Group, The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Venugopal Nair
- Viral Oncogenesis Group, The Pirbright Institute, Pirbright, Surrey, United Kingdom
| | - Nicola J. Royle
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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Rashid SA, Nazakat R, Muhamad Robat R, Ismail R, Suppiah J, Rajendran K, Raj Louis Masalamany ASS, Muhamad Hendri NA, Mohamad N, Khairul Hasni NA, Suib FA, Nik Hassan NMN, Pahrol MA, Shaharudin R. Droplet digital PCR application for the detection of SARS-CoV-2 in air sample. Front Public Health 2023; 11:1208348. [PMID: 37965510 PMCID: PMC10641526 DOI: 10.3389/fpubh.2023.1208348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/09/2023] [Indexed: 11/16/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) may transmit through airborne route particularly when the aerosol particles remain in enclosed spaces with inadequate ventilation. There has been no standard recommended method of determining the virus in air due to limitations in pre-analytical and technical aspects. Furthermore, the presence of low virus loads in air samples could result in false negatives. Our study aims to explore the feasibility of detecting SARS-CoV-2 ribonucleic acid (RNA) in air samples using droplet digital polymerase chain reaction (ddPCR). Active and passive air sampling was conducted between December 2021 and February 2022 with the presence of COVID-19 confirmed cases in two hospitals and a quarantine center in Klang Valley, Malaysia. SARS-CoV-2 RNA in air was detected and quantified using ddPCR and real-time reverse transcriptase-polymerase chain reaction (RT-PCR). The comparability of two different digital PCR platforms (QX200 and QIAcuity) to RT-PCR were also investigated. Additionally negative staining transmission electron microscopy was performed to visualize virus ultrastructure. Detection rates of SARS-CoV-2 in air samples using ddPCR were higher compared to RT-PCR, which were 15.2% (22/145) and 3.4% (5/145), respectively. The sensitivity and specificity of ddPCR was 100 and 87%, respectively. After excluding 17 negative samples (50%) by both QX200 and QIAcuity, 15% samples (5/34) were found to be positive both ddPCR and dPCR. There were 23.5% (8/34) samples that were detected positive by ddPCR but negative by dPCR. In contrast, there were 11.7% (4/34) samples that were detected positive by dPCR but negative by ddPCR. The SARS-CoV-2 detection method by ddPCR is precise and has a high sensitivity for viral RNA detection. It could provide advances in determining low viral titter in air samples to reduce false negative reports, which could complement detection by RT-PCR.
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Affiliation(s)
- Siti Aishah Rashid
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Raheel Nazakat
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Rosnawati Muhamad Robat
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Rohaida Ismail
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Jeyanthi Suppiah
- Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Kamesh Rajendran
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - A. S. Santhana Raj Louis Masalamany
- Special Resource Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Nur Afrina Muhamad Hendri
- Special Resource Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Nadia Mohamad
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Nurul Amalina Khairul Hasni
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Fatin Amirah Suib
- Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Nik Muhamad Nizam Nik Hassan
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Muhammad Alfatih Pahrol
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
| | - Rafiza Shaharudin
- Environmental Health Research Centre, Institute for Medical Research, National Institutes of Health, Ministry of Health Malaysia, Shah Alam, Selangor, Malaysia
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Geiger L, Orsi G, Cseh T, Gombos K, Illés Z, Czéh B. Circulating microRNAs correlate with structural and functional MRI parameters in patients with multiple sclerosis. Front Mol Neurosci 2023; 16:1173212. [PMID: 37881368 PMCID: PMC10597671 DOI: 10.3389/fnmol.2023.1173212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/21/2023] [Indexed: 10/27/2023] Open
Abstract
Introduction Circulating microRNAs are promising biomarkers for multiple sclerosis (MS). Our aim was to correlate serum microRNA levels with various magnetic resonance imaging (MRI) parameters. Methods We recruited 50 MS patients and measured cervical spine and cerebral white matter lesions together with regional brain volumes. Microstructural changes in the white matter were investigated with diffusion tensor imaging. Magnetic resonance spectroscopy was performed to measure cerebral metabolites. Functional connectivity within the default mode network was examined with resting-state functional MRI. On the day of the MRI measurements, we collected serum samples and carried out quantitative analysis of ten pre-selected microRNAs using droplet digital PCR. Results Serum level of miR-143.3p could differentiate between MS subtypes and had lower levels in progressive MS types. We found significant associations between microRNA levels and MRI measures: (1) higher miR-92a.3p and miR-486.5p levels were associated with greater total white matter lesion volumes within the cervical spine, (2) decreased miR-142.5p levels was associated with reduced total creatinine concentration and (3) miR-92a.3p, miR-142.5p and miR-486.5p levels were associated with functional connectivity strengths between specific nodes of the default mode network. Specifically, we found a negative association between miR-92a.3p and miR-486.5p levels and connectivity strength between the lateral temporal cortex and posterior inferior parietal lobule, and a positive association between miR-142.5p level and connectivity strength between the retrosplenial cortex and temporal pole. However, miRNA levels were not associated with regional brain volumes. Conclusion We provide here further evidence that circulating microRNAs may show correlation with both structural and functional neuroimaging outcomes in patients with MS.
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Affiliation(s)
- Lili Geiger
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Gergely Orsi
- HUN-REN-PTE Clinical Neuroscience MR Research Group, Eötvös Loránd Research Network, Pécs, Hungary
- Department of Neurology, Medical School, University of Pécs, Pécs, Hungary
- Pécs Diagnostic Centre, Pécs, Hungary
| | - Tamás Cseh
- Department of Neurology, Medical School, University of Pécs, Pécs, Hungary
| | - Katalin Gombos
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Zsolt Illés
- Department of Neurology, Medical School, University of Pécs, Pécs, Hungary
- Department of Neurology, Odense University Hospital, Odense, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Boldizsár Czéh
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
- Szentágothai Research Centre, University of Pécs, Pécs, Hungary
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30
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Wang W, Al-Hajj M, Alavi AS. Detection and quantification of integrated vector copy number by multiplex droplet digital PCR in dual-transduced CAR T cells. Mol Ther Methods Clin Dev 2023; 30:403-410. [PMID: 37622159 PMCID: PMC10445099 DOI: 10.1016/j.omtm.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 07/12/2023] [Indexed: 08/26/2023]
Abstract
The success of chimeric antigen receptor (CAR) T cell therapies in refractory hematologic malignancies has prompted investigation of their efficacy in solid tumors. AUTO6NG is a dual-transduced GD2-targeting CAR that encodes distinct modules designed to enhance T cell activity in relapsed/refractory neuroblastoma. The ability to detect and precisely quantify vector copy number (VCN) for each integrated vector is essential for assessing the effect of each module on T cell tumor infiltration, persistence, and clinical activity. Droplet digital PCR (ddPCR) enables accurate, sensitive, and absolute quantification of specific nucleic acid sequences. Compared to standard detection of two targets, multiplex ddPCR assays allow simultaneous detection of up to four targets by selective modulation of signal amplitude while retaining the ability to quantify the target. We have developed a multiplex assay based on the two-channel system for simultaneous detection and quantification of three targets in AUTO6NG CAR T cells. The assay was highly specific, sensitive, accurate, and reproducible across time and samples. No differences were observed in measuring VCN between standard duplex and multiplex assays. Our results demonstrate that ddPCR is an accurate and cost-effective method for simultaneous detection of multiple targets in genomic DNA derived from engineered CAR T cells.
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Affiliation(s)
- Wei Wang
- Autolus Therapeutics, The MediaWorks, 191 Wood Lane, W12 7FP London, UK
| | - Muhammad Al-Hajj
- Autolus Therapeutics, The MediaWorks, 191 Wood Lane, W12 7FP London, UK
| | - Alireza S. Alavi
- Autolus Therapeutics, The MediaWorks, 191 Wood Lane, W12 7FP London, UK
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31
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Chen J, Li D, Xu Y, Li Z, Ma S, Liu X, Yuan Y, Zhang C, Fu Q, Shi H. Establishment and application of multiplex droplet digital polymerase chain reaction assay for bovine enterovirus, bovine coronavirus, and bovine rotavirus. Front Vet Sci 2023; 10:1157900. [PMID: 37771940 PMCID: PMC10523346 DOI: 10.3389/fvets.2023.1157900] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 08/30/2023] [Indexed: 09/30/2023] Open
Abstract
Bovine enterovirus (BEV), bovine coronavirus (BCoV), and bovine rotavirus (BRV) are still the major worldwide concerns in the health care of cattle, causing serious economic losses in the livestock industry. It is urgent to establish specific and sensitive methods to detect viruses for the early control of diseases. Droplet digital PCR (ddPCR) has been proposed to effectively detect viral particles, and it does not involve Ct values or standard curves. In this study, we designed specific primers and probes, based on conserved regions of viral genomes, to optimize protocols for a dual ddPCR assay for detecting BCoV and BRV and a multiplex ddPCR assay for BEV, BCoV, and BRV. Sensitivity assays revealed that the lower limit of detection for qPCR was 1,000 copies/μL and for ddPCR for BEV, BCoV, and BRV, 2.7 copies/μL, 1 copy/μL and 2.4 copies/μL, respectively. Studying 82 samples collected from diarrheal calves on a farm, our dual ddPCR method detected BCoV, BRV, and co-infection at rates of 18.29%, 14.63%, and 6.1%, respectively. In contrast, conventional qPCR methods detected BCoV, BRV, and co-infection at rates of 10.98%, 12.2%, and 3.66%, respectively. On the other hand, studying 68 samples from another farm, qPCR detected BCoV, BRV, BEV, and co-infection of BCoV and BEV at rates of 14.49%, 1.45%, 5.80%, and 1.45%, respectively. Our multiplex ddPCR method detected BCoV, BRV, BEV, co-infection of BCoV and BEV, and co-infection of BRV and BEV. at rates of 14.49%, 2.9%, 8.7%, 2.9%, and 1.45%, respectively. Studying 93 samples from another farm, qPCR detected BCoV, BRV, BEV, and co-infection of BCoV and BEV was detected at rates of 5.38%, 1.08%, 18.28%, and 1.08%, respectively. Co-infection of BCoV, BRV, BEV, BCoV, and BEV, and co-infection of BRV and BEV, were detected by multiplex ddPCR methods at rates of 5.38%, 2.15%, 20.45%, 1.08%, and 1.08%, respectively. These results indicated that our optimized dual and multiplex ddPCR methods were more effective than conventional qPCR assays to detect these viral infections.
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Affiliation(s)
- Junzhen Chen
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Dan Li
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
- Tecon Biology Co., Ltd., Ürümqi, China
| | - Yafang Xu
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Zeyu Li
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Siqi Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Xinyi Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Yuanyuan Yuan
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Chengyuan Zhang
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Qiang Fu
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
| | - Huijun Shi
- College of Veterinary Medicine, Xinjiang Agricultural University, Ürümqi, China
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Souto S, Olveira JG, López-Vázquez C, Bandín I, Dopazo CP. Designing and Validation of a Droplet Digital PCR Procedure for Diagnosis and Accurate Quantification of Nervous Necrosis Virus in the Mediterranean Area. Pathogens 2023; 12:1155. [PMID: 37764963 PMCID: PMC10536565 DOI: 10.3390/pathogens12091155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The viral nervous necrosis virus (VNNV) is the causative agent of an important disease affecting fish species cultured worldwide. Early and accurate diagnosis is, at present, the most effective control and prevention tool, and molecular techniques have been strongly introduced and accepted by official organizations. Among those, real-time quantitative polymerase chain reaction (rt-qPCR) is nowadays displacing other molecular techniques. However, another PCR-based technology, droplet digital PCR (ddPCR), is on the increase. It has many advantages over qPCR, such as higher sensitivity and more reliability of the quantification. Therefore, we decided to design and validate a protocol for the diagnosis and quantification of SJ and RG type VNNV using reverse transcription-ddPCR (RT-ddPCR). We obtained an extremely low limit of detection, 10- to 100-fold lower than with RT-qPCR. Quantification by RT-ddPCR, with a dynamic range of 6.8-6.8 × 104 (SJ type) or 1.04 × 101-1.04 × 105 (RG type) cps/rctn, was more reliable than with RT-qPCR. The procedure was tested and validated in field samples, providing high clinical sensitivity and negative predictive values. In conclusion, we propose this method to substitute RT-qPCR protocols because it exceeds the expectations of qPCR in the diagnosis and quantification of VNNV.
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Affiliation(s)
| | | | | | | | - Carlos P. Dopazo
- Instituto de Acuicultura, Department of Microbiology, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain; (S.S.); (J.G.O.); (C.L.-V.); (I.B.)
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Sayour NV, Tóth VÉ, Nagy RN, Vörös I, Gergely TG, Onódi Z, Nagy N, Bödör C, Váradi B, Ruppert M, Radovits T, Bleckwedel F, Zelarayán LC, Pacher P, Ágg B, Görbe A, Ferdinandy P, Varga ZV. Droplet Digital PCR Is a Novel Screening Method Identifying Potential Cardiac G-Protein-Coupled Receptors as Candidate Pharmacological Targets in a Rat Model of Pressure-Overload-Induced Cardiac Dysfunction. Int J Mol Sci 2023; 24:13826. [PMID: 37762130 PMCID: PMC10531061 DOI: 10.3390/ijms241813826] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The identification of novel drug targets is needed to improve the outcomes of heart failure (HF). G-protein-coupled receptors (GPCRs) represent the largest family of targets for already approved drugs, thus providing an opportunity for drug repurposing. Here, we aimed (i) to investigate the differential expressions of 288 cardiac GPCRs via droplet digital PCR (ddPCR) and bulk RNA sequencing (RNAseq) in a rat model of left ventricular pressure-overload; (ii) to compare RNAseq findings with those of ddPCR; and (iii) to screen and test for novel, translatable GPCR drug targets in HF. Male Wistar rats subjected to transverse aortic constriction (TAC, n = 5) showed significant systolic dysfunction vs. sham operated animals (SHAM, n = 5) via echocardiography. In TAC vs. SHAM hearts, RNAseq identified 69, and ddPCR identified 27 significantly differentially expressed GPCR mRNAs, 8 of which were identified using both methods, thus showing a correlation between the two methods. Of these, Prostaglandin-F2α-receptor (Ptgfr) was further investigated and localized on cardiomyocytes and fibroblasts in murine hearts via RNA-Scope. Antagonizing Ptgfr via AL-8810 reverted angiotensin-II-induced cardiomyocyte hypertrophy in vitro. In conclusion, using ddPCR as a novel screening method, we were able to identify GPCR targets in HF. We also show that the antagonism of Ptgfr could be a novel target in HF by alleviating cardiomyocyte hypertrophy.
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Affiliation(s)
- Nabil V. Sayour
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- HCEMM-SU Cardiometabolic Immunology Research Group, 1085 Budapest, Hungary
- MTA-SE Momentum Cardio-Oncology and Cardioimmunology Research Group, Semmelweis University, 1085 Budapest, Hungary
| | - Viktória É. Tóth
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- HCEMM-SU Cardiometabolic Immunology Research Group, 1085 Budapest, Hungary
- MTA-SE Momentum Cardio-Oncology and Cardioimmunology Research Group, Semmelweis University, 1085 Budapest, Hungary
| | - Regina N. Nagy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
| | - Imre Vörös
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- HCEMM-SU Cardiometabolic Immunology Research Group, 1085 Budapest, Hungary
- MTA-SE Momentum Cardio-Oncology and Cardioimmunology Research Group, Semmelweis University, 1085 Budapest, Hungary
| | - Tamás G. Gergely
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- HCEMM-SU Cardiometabolic Immunology Research Group, 1085 Budapest, Hungary
- MTA-SE Momentum Cardio-Oncology and Cardioimmunology Research Group, Semmelweis University, 1085 Budapest, Hungary
| | - Zsófia Onódi
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- HCEMM-SU Cardiometabolic Immunology Research Group, 1085 Budapest, Hungary
- MTA-SE Momentum Cardio-Oncology and Cardioimmunology Research Group, Semmelweis University, 1085 Budapest, Hungary
| | - Noémi Nagy
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary
| | - Csaba Bödör
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary
| | - Barnabás Váradi
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- HCEMM-SU Cardiometabolic Immunology Research Group, 1085 Budapest, Hungary
| | - Mihály Ruppert
- Heart and Vascular Center, Semmelweis University, 1085 Budapest, Hungary
| | - Tamás Radovits
- Heart and Vascular Center, Semmelweis University, 1085 Budapest, Hungary
| | - Federico Bleckwedel
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen (UMG), 37075 Göttingen, Germany
- German Center for Cardiovascular Research (DZHK) Partner Site, 37075 Goettingen, Germany
| | - Laura C. Zelarayán
- Institute of Pharmacology and Toxicology, University Medical Center Goettingen (UMG), 37075 Göttingen, Germany
- German Center for Cardiovascular Research (DZHK) Partner Site, 37075 Goettingen, Germany
| | - Pal Pacher
- Laboratory of Cardiovascular Physiology and Tissue Injury, National Institute on Alcohol Abuse and Alcoholism, National Institute of Health, Rockville, MD 20852, USA
| | - Bence Ágg
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary
- Pharmahungary Group, 6720 Szeged, Hungary
| | - Anikó Görbe
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- Pharmahungary Group, 6720 Szeged, Hungary
| | - Péter Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- MTA-SE System Pharmacology Research Group, Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary
- Pharmahungary Group, 6720 Szeged, Hungary
| | - Zoltán V. Varga
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, 1085 Budapest, Hungary; (N.V.S.)
- HCEMM-SU Cardiometabolic Immunology Research Group, 1085 Budapest, Hungary
- MTA-SE Momentum Cardio-Oncology and Cardioimmunology Research Group, Semmelweis University, 1085 Budapest, Hungary
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Tournayre O, Wolfe R, McCurdy-Adams H, Chabot AA, Lougheed SC. A species-specific digital PCR assay for the endangered blue racer ( Coluber constrictor foxii) in Canada. Genome 2023; 66:251-260. [PMID: 37270848 DOI: 10.1139/gen-2023-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The only population of the endangered blue racer (Coluber constrictor foxii) in Canada occurs on Pelee Island, Ontario. The species is threatened by multiple factors, including habitat degradation and loss, road mortality, persecution, and potentially predation. We designed and evaluated the performance of an environmental DNA droplet digital PCR assay that can be used for multiple facets of conservation of this species. We tested the assay in silico and in vitro using DNA of blue racers and co-occurring snake species and estimated the LOD and LOQ using synthetic DNA. As wild turkey predation has been suggested to negatively affect racers, we tested the assay on eight wild turkey faecal samples. Our assay is specific, can detect the target species at very low levels of concentration (0.002 copies/µL), and can accurately quantify copy numbers ≥ 0.26 copies/µL. We detected no racer DNA in any wild turkey faecal sample. More faecal samples collected at strategic locations during snake peak activity on Pelee Island would enable a more thorough assessment of the possibility of turkey predation. Our assay should be effective for other environmental samples and can be used for investigating other factors negatively affecting blue racers, for example, helping to quantify blue racer habitat suitability and site occupancy.
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Affiliation(s)
- Orianne Tournayre
- Biology Department, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Ryan Wolfe
- Natural Resource Solutions Inc., Waterloo, ON N2L 3X2, Canada
| | | | - Amy A Chabot
- African Lion Safari, Cambridge, ON N1R 5S2, Canada
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Hepsenoglu YE, Ersahan S. Is XP-endo Finisher a better treatment option for its efficacy against intracanal bacteria for post-treatment apical periodontitis cases than EndoActivator? AUST ENDOD J 2023; 49 Suppl 1:399-412. [PMID: 37026533 DOI: 10.1111/aej.12756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/01/2023] [Accepted: 03/21/2023] [Indexed: 04/08/2023]
Abstract
To investigate the efficacy of the supplementary use of a rotary agitation method [XP-endo Finisher (XPF)] and sonically-activated irrigation [EndoActivator (EA)], using droplet digital PCR (ddPCR) on reducing the bacterial load in previously root canal treated teeth with apical periodontitis. Twenty patients with post-treatment apical periodontitis were allocated into two groups according to the irrigation activation method used: XPF and EA group. Total bacterial loads, as well as the amount of Enterococcus faecalis (E. faecalis) were determined before (S1) and after (S2) chemomechanical preparation, and after final irrigation activation (S3) by means of ddPCR. The bacterial copy numbers were compared between groups using the Friedman test (Nonparametric Repeated Measures ANOVA). When the groups were examined in terms of gender, age, number of root canals, periapical index score, sterility control total bacteria (SCTB), S1- and S2-total bacteria copy number, it was found that there was no statistical difference between the XPF group and the EA group (p > 0.05). Subsequent activation (S3) resulted in a significant microbial reduction in both XPF and EA groups, both of which reduced significantly more bacteria than chemomechanical instrumentation (S2) (p < 0.0001). On the contrary, S3-total bacteria copy number of the EA group was lower than the XPF group (p < 0.0147). There was no statistical difference between the XPF group and the EA group in terms of E. faecalis copy number (p > 0.05). Although both the XPF and the EA optimised the antibacterial efficiency of chemomechanical preparation in previously root canal-treated teeth with apical periodontitis, a lower total bacterial copy number was achieved with the EA application than the XPF application.
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Affiliation(s)
- Yelda Erdem Hepsenoglu
- Department of Endodontics, Faculty of Dentistry, Istanbul Medipol University, Istanbul, Turkey
| | - Seyda Ersahan
- Department of Endodontics, Faculty of Dentistry, Istanbul Medipol University, Istanbul, Turkey
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Mu Y, Rivera J, McManus DP, Weerakoon KG, Ross AG, Olveda RM, Gordon CA, You H, Jones MK, Cai P. Comparative assessment of the SjSAP4-incorporated gold immunochromatographic assay for the diagnosis of human schistosomiasis japonica. Front Public Health 2023; 11:1249637. [PMID: 37736084 PMCID: PMC10509475 DOI: 10.3389/fpubh.2023.1249637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 08/17/2023] [Indexed: 09/23/2023] Open
Abstract
Background Schistosomiasis, a disease caused by parasites of the genus Schistosoma, remains a global public health threat. This study aimed to validate the diagnostic performance of a recently developed gold immunochromatographic assay (GICA) for the detection of S. japonicum infection in a rural endemic area of the Philippines. Methods Human clinical samples were collected from 412 subjects living in Laoang and Palapag municipalities, Northern Samar, the Philippines. The presence of Schistosoma-specific antibodies in serum samples was tested with the SjSAP4-incorporated GICA strips and the results were converted to fully quantitative data by introducing an R value. The performance of the established GICA was further compared with other diagnostic tools, including the Kato-Katz (KK) technique, point-of-care circulating cathodic antigen (POC-CCA), droplet digital (dd) PCR, and enzyme-linked immunosorbent assays (ELISAs). Results The developed GICA strip was able to detect KK positive individuals with a sensitivity of 83.3% and absolute specificity. When calibrated with the highly sensitive faecal ddPCR assay, the immunochromatographic assay displayed an accuracy of 60.7%. Globally, the GICA assay showed a high concordance with the SjSAP4-ELISA assay. The schistosomiasis positivity rate determined by the GICA test was similar to those obtained with the SjSAP4-ELISA assay and the ddPCR assay performed on serum samples (SR_ddPCR), and was 2.3 times higher than obtained with the KK method. Conclusion The study further confirms that the developed GICA is a valuable diagnostic tool for detecting light S. japonicum infections and implies that this point-of-care assay is a viable solution for surveying endemic areas of low-intensity schistosomiasis and identifying high-priority endemic areas for targeted interventions.
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Affiliation(s)
- Yi Mu
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jonas Rivera
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Donald P. McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Kosala G. Weerakoon
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Allen G. Ross
- Rural Health and Medical Research Institute, Charles Sturt University, Orange, NSW, Australia
| | - Remigio M. Olveda
- Department of Immunology, Research Institute for Tropical Medicine, Manila, Philippines
| | - Catherine A. Gordon
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Public Health, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Hong You
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Veterinary Science, The University of Queensland, Brisbane, QLD, Australia
| | - Malcolm K. Jones
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Veterinary Science, The University of Queensland, Brisbane, QLD, Australia
| | - Pengfei Cai
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
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Feng J, Cui X, Du B, Zhao H, Feng Y, Cui J, Yan C, Gan L, Fan Z, Fu T, Xu Z, Yu Z, Zhang R, Du S, Tian Z, Zhang Q, Xue G, Yuan J. Detection and Quantification of Klebsiella pneumoniae in Fecal Samples Using Digital Droplet PCR in Comparison with Real-Time PCR. Microbiol Spectr 2023; 11:e0424922. [PMID: 37306605 PMCID: PMC10433836 DOI: 10.1128/spectrum.04249-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/18/2023] [Indexed: 06/13/2023] Open
Abstract
This study aimed to develop a rapid and sensitive droplet digital PCR (ddPCR) assay for the specific detection of Klebsiella pneumoniae in fecal samples, and to evaluate its application in the clinic by comparison with real-time PCR assay and conventional microbial culture. Specific primers and a probe targeting the K. pneumoniae hemolysin (khe) gene were designed. Thirteen other pathogens were used to evaluate the specificity of the primers and probe. A recombinant plasmid containing the khe gene was constructed and used to assess the sensitivity, repeatability, and reproducibility of the ddPCR. Clinical fecal samples (n = 103) were collected and tested by the ddPCR, real-time PCR, and conventional microbial culture methods. The detection limit of ddPCR for K. pneumoniae was 1.1 copies/μL, about a 10-fold increase in sensitivity compared with real-time PCR. The ddPCR was negative for the 13 pathogens other than K. pneumoniae, confirming its high specificity. Clinical fecal samples gave a higher rate of positivity in the K. pneumoniae ddPCR assay than in analysis by real-time PCR or conventional culture. ddPCR also showed less inhibition by the inhibitor in fecal sample than real-time PCR. Thus, we established a sensitive and effective ddPCR-based assay method for K. pneumoniae. It could be a useful tool for K. pneumoniae detection in feces and may serve as a reliable method to identify causal pathogens and help guide treatment decisions. IMPORTANCE Klebsiella pneumoniae can cause a range of illnesses and has a high colonization rate in the human gut, making it crucial to develop an efficient method for detecting K. pneumoniae in fecal samples.
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Affiliation(s)
- Junxia Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Xiaohu Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Bing Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Hanqing Zhao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jinghua Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zheng Fan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Tongtong Fu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziying Xu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zihui Yu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shuheng Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziyan Tian
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Qun Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Guanhua Xue
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jing Yuan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
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Tumpach C, Rhodes A, Kim Y, Ong J, Liu H, Chibo D, Druce J, Williamson D, Hoh R, Deeks SG, Yukl SA, Roche M, Lewin SR, Telwatte S. Adaptation of Droplet Digital PCR-Based HIV Transcription Profiling to Digital PCR and Association of HIV Transcription and Total or Intact HIV DNA. Viruses 2023; 15:1606. [PMID: 37515292 PMCID: PMC10384802 DOI: 10.3390/v15071606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
In most people living with HIV (PLWH) on effective antiretroviral therapy (ART), cell-associated viral transcripts are readily detectable in CD4+ T cells despite the absence of viremia. Quantification of HIV RNA species provides insights into the transcriptional activity of proviruses that persist in cells and tissues throughout the body during ART ('HIV reservoir'). One such technique for HIV RNA quantitation, 'HIV transcription profiling', developed in the Yukl laboratory, measures a series of HIV RNA species using droplet digital PCR. To take advantage of advances in digital (d)PCR, we adapted the 'HIV transcription profiling' technique to Qiagen's dPCR platform (QIAcuity) and compared its performance to droplet digital (dd)PCR (Bio-Rad QX200 system). Using RNA standards, the two technologies were tested in parallel and assessed for multiple parameters including sensitivity, specificity, linearity, and intra- and inter-assay variability. The newly validated dPCR assays were then applied to samples from PLWH to determine HIV transcriptional activity relative to HIV reservoir size. We report that HIV transcriptional profiling was readily adapted to dPCR and assays performed similarly to ddPCR, with no differences in assay characteristics. We applied these assays in a cohort of 23 PLWH and found that HIV reservoir size, based on genetically intact proviral DNA, does not predict HIV transcriptional activity. In contrast, levels of total DNA correlated with levels of most HIV transcripts (initiated, proximally and distally elongated, unspliced, and completed, but not multiply spliced), suggesting that a considerable proportion of HIV transcripts likely originate from defective proviruses. These findings may have implications for measuring and assessing curative strategies and clinical trial outcomes.
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Affiliation(s)
- Carolin Tumpach
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Ajantha Rhodes
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Youry Kim
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Jesslyn Ong
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Haoming Liu
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Doris Chibo
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Julian Druce
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
| | - Deborah Williamson
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
- Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
- Walter and Eliza Hall Institute, Melbourne 3052, Australia
| | - Rebecca Hoh
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Steven G. Deeks
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Steven A. Yukl
- Department of Medicine, University of California San Francisco (UCSF), San Francisco, CA 94143, USA
- San Francisco Veteran Affairs Medical Center, San Francisco, CA 94121, USA
| | - Michael Roche
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
- Infectious and Inflammatory Diseases Theme, School of Health and Biomedical Sciences, RMIT University, Melbourne 3000, Australia
| | - Sharon R. Lewin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne 3004, Australia
| | - Sushama Telwatte
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne 3000, Australia
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Zhang J, Lai C, Shentu X, Hao P, Pang K, Yu X. Establishment of a Rapid Detection Method for Yeast-like Symbionts in Brown Planthopper Based on Droplet Digital PCR Technology. Int J Mol Sci 2023; 24:11071. [PMID: 37446249 DOI: 10.3390/ijms241311071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/26/2023] [Accepted: 07/02/2023] [Indexed: 07/15/2023] Open
Abstract
The brown planthopper Nilaparvata lugens (Stål) (BPH) is a typical monophagous sucking rice pest. Over the course of their evolution, BPH and its symbionts have established an interdependent and mutually beneficial relationship, with the symbionts being important to the growth, development, reproduction, and variation in virulence of BPH. Yeast-like symbionts (YLS), harbored in the abdomen fat body cells of BPH, are vital to the growth and reproduction of the host. In recent research, the symbionts in BPH have mainly been detected using blood cell counting, PCR, real-time quantitative PCR, and other methods. These methods are vulnerable to external interference, cumbersome, time consuming and laborious. Droplet digital PCR (ddPCR) does not need a standard curve, can achieve absolute quantification, does not rely on Cq values, and is more useful for analyzing copy number variation, gene mutations, and relative gene expression. A rapid detection method for the YLS of BPH based on ddPCR was established and optimized in this study. The results showed that the method's limits of detection for the two species of YLS (Ascomycetes symbionts and Pichia guilliermondii) were 1.3 copies/μL and 1.2 copies/μL, respectively. The coefficient of variation of the sample repetition was less than 5%; therefore, the ddPCR method established in this study had good sensitivity, specificity, and repeatability. It can be used to detect the YLS of BPH rapidly and accurately.
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Affiliation(s)
- Jun Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Modern Science and Technology, China Jiliang University, Hangzhou 310018, China
| | - Chengling Lai
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Modern Science and Technology, China Jiliang University, Hangzhou 310018, China
| | - Xuping Shentu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Modern Science and Technology, China Jiliang University, Hangzhou 310018, China
| | - Peiying Hao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Modern Science and Technology, China Jiliang University, Hangzhou 310018, China
| | - Kun Pang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Modern Science and Technology, China Jiliang University, Hangzhou 310018, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Modern Science and Technology, China Jiliang University, Hangzhou 310018, China
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Weerarathne P, Sanders TL, Kao YF, Cotey SR, Place JD, Fairbanks WS, Miller CA, Reichard MV. HIGH PREVALENCE OF CYTAUXZOON FELIS IN BOBCATS (LYNX RUFUS) ACROSS OKLAHOMA AND OCCURRENCE IN WEST TEXAS, USA. J Wildl Dis 2023; 59:432-441. [PMID: 37270185 DOI: 10.7589/jwd-d-22-00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/10/2023] [Indexed: 06/05/2023]
Abstract
Cytauxzoonosis is a fatal tick-borne disease in domestic cats caused by infection with the apicomplexan Cytauxzoon felis. Bobcats are the natural wild-vertebrate reservoirs for C. felis, and infections are typically subclinical and chronic in this species. The present study was done to determine the prevalence and geographic distribution of C. felis infection in wild bobcats from Oklahoma and the occurrence in northwestern Texas. Tongue samples from 360 bobcats were collected from 53 counties in Oklahoma and 13 samples from three counties in Texas. For DNA extracted from each tongue sample, a probe-based droplet digital PCR assay was performed targeting the C. felis mitochondrial gene cytochrome c oxidase subunit III (cox3). Prevalence of C. felis infection was calculated for each county sampled, and data from individual counties were combined according to geographic regions and compared using chi-square tests. Overall prevalence of C. felis in bobcats from Oklahoma was 80.0% (95% confidence interval [CI], 75.6-83.8). The prevalence of infection was >90% for bobcats from central, northeastern, south-central, and southeastern regions of Oklahoma, but <68% for bobcats from northwestern and southwestern regions. Bobcats from central counties in Oklahoma were 25.693 times more likely to be infected with C. felis compared to all other bobcats sampled from the state. Higher prevalence estimates of C. felis in bobcats appeared to be in counties where known tick vectors are most common. Occurrence of C. felis in bobcats from northwestern Texas was 30.8% (95% CI, 12.4%-58.0%) based on 13 samples. Results of this study support the utilization of bobcats as sentinel animals to identify geographic areas with risk of C. felis infection to domestic cats.
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Affiliation(s)
- Pabasara Weerarathne
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Tiana L Sanders
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Yun-Fan Kao
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Stacy R Cotey
- College of Forest Resources and Environmental Science, Michigan Tech University, Houghton, Michigan 49931, USA
| | - Joshua D Place
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - W Sue Fairbanks
- Department of Natural Resources Ecology and Management, Division of Agricultural Science and Natural Resources, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Craig A Miller
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Mason V Reichard
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma 74078, USA
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Shinde M, Lavania M, Rawal J, Chavan N, Shinde P. Evaluation of droplet digital qRT-PCR (dd qRT-PCR) for quantification of SARS CoV-2 RNA in stool and urine specimens of COVID-19 patients. Front Med (Lausanne) 2023; 10:1148688. [PMID: 37469662 PMCID: PMC10352106 DOI: 10.3389/fmed.2023.1148688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/09/2023] [Indexed: 07/21/2023] Open
Abstract
Introduction There have been a few reports of viral load detection in stool and urine samples of patients with coronavirus disease 2019 (COVID-19), and the transmission of the virus through faecal oral route. For clinical diagnosis and treatment, the widely used reverse transcription-polymerase chain reaction (qRT-PCR) method has some limitations. Methods The aim of our study to assess the presence and concentration of SARS CoV-2 RNA in stool and urine samples from COVID-19 patients with mild, moderate, and severe disease, we compared a traditional qRT-PCR approach with a ddPCR. ddPCR and qRT-PCR-based target gene analysis were performed on 107 COVID-19-confirmed patients paired samples (N1 and N2). The MagMax magnetic beads base method was used to isolate RNA. Real-time qRT-PCR and dd PCR were performed on all patients. Results and Discussion The average cycle threshold (Ct) of qRT-PCR was highly correlated with the average copy number of 327.10 copies/l analyzed in ddPCR. In ddPCR, urine samples showed 27.1% positivity while for stool it was 100%. Conclusion This study's findings not only show that SARS CoV-2 is present in urine and faeces, but also suggest that low concentrations of the viral target ddPCR make it easier to identify positive samples and help resolve for cases of inconclusive diagnosis.
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Zhang S, Chen X, Lin Z, Tan Y, Liang B, Pan Y, Huang M, Su B, Hu X, Xu Y, Li Q. Quantification of Isoniazid-Heteroresistant Mycobacterium tuberculosis Using Droplet Digital PCR. J Clin Microbiol 2023; 61:e0188422. [PMID: 37195177 PMCID: PMC10281145 DOI: 10.1128/jcm.01884-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/04/2023] [Indexed: 05/18/2023] Open
Abstract
The quantitative detection of drug-resistance mutations in Mycobacterium tuberculosis (MTB) is critical for determining the drug resistance status of a sample. We developed a drop-off droplet digital PCR (ddPCR) assay targeting all major isoniazid (INH)-resistant mutations. The ddPCR assay consisted of three reactions: reaction A detects mutations at katG S315; reaction B detects inhA promoter mutations; and reaction C detects ahpC promoter mutations. All reactions could quantify 1%-50% of mutants in the presence of the wild-type, ranging from 100 to 50,000 copies/reaction. Clinical evaluation with 338 clinical isolates yielded clinical sensitivity of 94.5% (95% confidence interval [CI] = 89.1%-97.3%) and clinical specificity of 97.6% (95% CI = 94.6%-99.0%) compared with the traditional drug susceptibility testing (DST). Further clinical evaluation using 194 nucleic acid-positive MTB sputum samples revealed clinical sensitivity of 87.8% (95% CI = 75.8%-94.3%) and clinical specificity of 96.5% (95% CI = 92.2%-98.5%) in comparison with DST. All the mutant and heteroresistant samples detected by the ddPCR assay but susceptible by DST were confirmed by combined molecular assays, including Sanger sequencing, mutant-enriched Sanger sequencing and a commercial melting curve analysis-based assay. Finally, the ddPCR assay was used to monitor longitudinally the INH-resistance status and the bacterial load in nine patients undergoing treatment. Overall, the developed ddPCR assay could be an indispensable tool for quantification of INH-resistant mutations in MTB and bacterial loads in patients.
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Affiliation(s)
- Siqi Zhang
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xiaohong Chen
- The Pulmonary Hospital of Fuzhou in Fujian Province, Fuzhou, Fujian, China
| | - Zhonghui Lin
- The Pulmonary Hospital of Fuzhou in Fujian Province, Fuzhou, Fujian, China
| | - Yaoju Tan
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, China
| | - Bin Liang
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yuying Pan
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Mingxiang Huang
- The Pulmonary Hospital of Fuzhou in Fujian Province, Fuzhou, Fujian, China
| | - Biyi Su
- Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou, China
| | - Xiaoman Hu
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, China
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Abdullah O, Fall A, Forman M, Howard C, Klein E, Mostafa HH. Respiratory Adenovirus Quantification with a Droplet Digital Polymerase Chain Reaction (ddPCR) Assay. Microbiol Spectr 2023; 11:e0026923. [PMID: 37070988 PMCID: PMC10269445 DOI: 10.1128/spectrum.00269-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/31/2023] [Indexed: 04/19/2023] Open
Abstract
Human adenoviruses (HAdVs) are double-stranded DNA viruses that can cause a wide spectrum of disease, including respiratory infections. Little is known about the value of respiratory HAdV quantification and its correlation with disease severity. In this study, we developed a quantitative HAdV droplet digital PCR (ddPCR) assay to study the association between viral loads, circulating types, and clinical outcomes. Remnant respiratory specimens positive for HAdV after the standard of care testing were collected from December 2020 to April 2022. A total of 129 samples were tested by a ddPCR method. Typing was performed using Nanopore sequencing of the hexon gene hypervariable region. Clinical chart reviews were performed to correlate the viral loads with the disease severity. The ddPCR assay showed an analytical sensitivity and a lower limit of quantification below 100 copies/mL. Of 129 positive clinical samples, 100 were quantified by ddPCR, 7 were too concentrated to be quantified, and 22 were negative. Of the 22 false negatives, only 3 were successfully typed; however, 99 of the 107 positive samples had a characterized genotype. The main HAdV types identified in this cohort were C1 (49.5%) followed by C2 (34.3%). No significant difference in HAdV loads was noted between patients who were admitted, those who required supplemental oxygen, and outpatients or between different HAdV types. HAdV ddPCR is a reliable absolute quantification approach for HAdV from respiratory samples. HAdV loads at initial presentation does not appear to differ between patients who require hospitalization versus outpatients. IMPORTANCE Measuring viral load using droplet digital PCR (ddPCR) is an absolute quantification approach that can facilitate comparability between different laboratories. This approach could prove valuable in studies that focus on the clinical utility of quantification. In this study, we evaluate a human adenovirus (HAdV) ddPCR assay and study the relationship between viral loads and outcomes after HAdV respiratory infections.
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Affiliation(s)
- Omar Abdullah
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Amary Fall
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Michael Forman
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Craig Howard
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
| | - Eili Klein
- Department of Emergency Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Center for Disease Dynamics, Economics, and Policy, Washington, DC, USA
| | - Heba H. Mostafa
- Johns Hopkins School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland, USA
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Cutarelli A, De Falco F, Cuccaro B, Milićević V, Kureljušić B, Bojkovski J, Cerino P, Perillo A, Marica R, Catoi C, Roperto S. Prevalence and genotype distribution of caprine papillomavirus in peripheral blood of healthy goats in farms from three European countries. Front Vet Sci 2023; 10:1213150. [PMID: 37396991 PMCID: PMC10310300 DOI: 10.3389/fvets.2023.1213150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/01/2023] [Indexed: 07/04/2023] Open
Abstract
Caprine papillomaviruses (ChPVs, Capra hircus papillomaviruses) were detected and quantified for the first time using droplet digital polymerase chain reaction (ddPCR) in blood samples of 374 clinically healthy goats from farms located in Italy, Romania, and Serbia. Overall, ddPCR revealed ChPV DNA in 78 of the 374 examined samples, indicating that ~21% of the goats harbored circulating papillomavirus DNA. In particular, in Italian goat farms, ChPV genotypes were detected and quantified in 58 of 157 blood samples (~37%), 11 of 117 samples from Serbian farms (~9.4%), and 9 of 100 from Romanian blood samples (9%). Blood samples from Italian goat farms showed a high prevalence of ChPV1, which was detected in 45 samples (28.6%). The ChPV2 genotype was detected in 13 samples (~8.3%). Therefore, significant differences in prevalence and genotype distributions were observed. On Serbian and Romanian farms, no significant differences were observed in the genotype prevalence of ChPVs. Molecular findings are consistent with ChPV prevalence, characterized by a territorial distribution similar to that of papillomaviruses in other mammalian species. Furthermore, this study showed that ddPCR is a very sensitive and accurate assay for ChPV detection and quantification. The ddPCR may be the molecular diagnostic tool of choice, ultimately providing useful insights into the molecular epidemiology and field surveillance of ChPV.
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Affiliation(s)
- Anna Cutarelli
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici, Italy
| | - Francesca De Falco
- Dipartimento di Medicina Veterinaria e delle Produzioni Animali, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Bianca Cuccaro
- Dipartimento di Medicina Veterinaria e delle Produzioni Animali, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Vesna Milićević
- Institute of Veterinary Medicine of Serbia, Belgrade, Serbia
| | | | - Jovan Bojkovski
- Faculty of Veterinary Medicine, Department for Ruminants and Swine disease, Belgrade, Serbia
| | - Pellegrino Cerino
- Dipartimento di Sanità pubblica, Università degli Studi di Napoli Federico II, Napoli, Italy
| | - Antonella Perillo
- Medicina di Precisione e Rigenerativa e Area Jonica, Università degli Studi di Bari “Aldo Moro”, Bari, Italy
| | - Raluca Marica
- Pathology Department, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Cornel Catoi
- Pathology Department, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Sante Roperto
- Dipartimento di Medicina Veterinaria e delle Produzioni Animali, Università degli Studi di Napoli Federico II, Napoli, Italy
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Yang J, Xu H, Ke Z, Kan N, Zheng E, Qiu Y, Huang M. Absolute quantification of viable Vibrio cholerae in seawater samples using multiplex droplet digital PCR combined with propidium monoazide. Front Microbiol 2023; 14:1149981. [PMID: 37362935 PMCID: PMC10288211 DOI: 10.3389/fmicb.2023.1149981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Toxigenic Vibrio cholerae serogroup O1 and O139 are the pathogens responsible for the global cholera epidemic. V. cholerae can settle in the water and spread via the fecal-oral route. Rapid and accurate monitoring of live V. cholerae in environmental water has become an important strategy to prevent and control cholera transmission. Conventional plate counting is widely used to detect viable bacteria but requires time and effort. Methods This study aims to develop a new assay that combines triplex droplet digital PCR (ddPCR) with propidium monoazide (PMA) treatment for quantitatively detecting live V. cholerae O1/O139 and cholera enterotoxin. Specific primers and probes were designed according to the conserved regions of gene rfb O1, rfb O139, and ctxA. The amplification procedures and PMA treatment conditions were optimized. The specificity, sensitivity, and ability of PMA-ddPCR to detect viable bacteria-derived DNA were evaluated in simulated seawater samples. Results and Discussion The results revealed that the optimal primer concentrations of rfb O1, rfb O139, and ctxA were 1 μM, while the concentrations of the three probes were 0.25, 0.25, and 0.4 μM, respectively. The best annealing temperature was 58°C to obtain the most accurate results. The optimal strategy for distinguishing dead and live bacteria from PMA treatment was incubation at the concentration of 20 μM for 15 min, followed by exposure to a 650-W halogen lamp for 20 min. In pure culture solutions, the limit of detection (LODs) of V. cholerae O1 and O139, and ctxA were 127.91, 120.23 CFU/mL, and 1.5 copies/reaction in PMA-triplex ddPCR, respectively, while the LODs of the three targets were 150.66, 147.57 CFU/mL, and 2 copies/reaction in seawater samples. The PMA-ddPCR sensitivity was about 10 times higher than that of PMA-qPCR. When detecting spiked seawater samples with live bacterial concentrations of 1.53 × 102 and 1.53 × 105 CFU/mL, the assay presented a higher sensitivity (100%, 16/16) than qPCR (50.00%, 8/16) and a perfect specificity (100%, 9/9). These results indicate that the developed PMA-triplex ddPCR is superior to the qPCR regarding sensitivity and specificity and can be used to rapidly detect viable toxigenic V. cholerae O1 and O139 in suspicious seawater samples.
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Affiliation(s)
- Jinsong Yang
- Fujian Center for Disease Control and Prevention, Fuzhou, China
- Fujian Provincial Key Laboratory of Zoonosis Research, Fuzhou, China
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Haibin Xu
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Zili Ke
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Naipeng Kan
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Enhui Zheng
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Yufeng Qiu
- Fujian Center for Disease Control and Prevention, Fuzhou, China
| | - Mengying Huang
- Fujian Center for Disease Control and Prevention, Fuzhou, China
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Chatterton S, Schwinghamer TD, Pagé A, Davidson RB, Harding MW, Banniza S. Inoculum dose-disease response relationships for the pea root rot pathogen, Aphanomyces euteiches, are dependent on soil type and other pathogens. Front Plant Sci 2023; 14:1115420. [PMID: 37235016 PMCID: PMC10205554 DOI: 10.3389/fpls.2023.1115420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 04/03/2023] [Indexed: 05/28/2023]
Abstract
The oomycete pathogen, Aphanomyces euteiches, was implicated for the first time in pea and lentil root rot in Saskatchewan and Alberta in 2012 and 2013. Subsequent surveys from 2014 to 2017 revealed that Aphanomyces root rot (ARR) was widespread across the Canadian prairies. The absence of effective chemical, biological, and cultural controls and lack of genetic resistance leave only one management option: avoidance. The objectives of this study were to relate oospore levels in autoclaved and non-autoclaved soils to ARR severity across soil types from the vast prairie landscape and to determine the relationship of measured DNA quantity of A. euteiches using droplet digital PCR or quantitative PCR to the initial oospore inoculum dose in soils. These objectives support a future end goal of creating a rapid assessment method capable of categorizing root rot risk in field soil samples to aid producers with pulse crop field selection decisions. The ARR severity to oospore dose relationship was statistically significantly affected by the soil type and location from which soils were collected and did not show a linear relationship. For most soil types, ARR did not develop at oospore levels below 100/g soil, but severity rose above this level, confirming a threshold level of 100 oospores/g soil for disease development. For most soil types, ARR severity was significantly higher in non-autoclaved compared to autoclaved treatments, demonstrating the role that other pathogens play in increasing disease severity. There was a significant linear relationship between DNA concentrations measured in soil and oospore inoculum concentration, although the strength of the relationship was better for some soil types, and in some soil types, DNA measurement results underestimated the number of oospores. This research is important for developing a root rot risk assessment system for the Canadian prairies based on soil inoculum quantification, following field validation of soil quantification and relationship to root rot disease severity.
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Affiliation(s)
- Syama Chatterton
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Timothy D. Schwinghamer
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Antoine Pagé
- Aquatic and Crop Resource Development, National Research Council Canada, Montreal, QC, Canada
| | | | - Michael W. Harding
- Plant and Bee Health Surveillance, Alberta Ministry of Agriculture and Irrigation, Brooks, AB, Canada
| | - Sabine Banniza
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
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Stepien N, Senfter D, Furtner J, Haberler C, Dorfer C, Czech T, Lötsch-Gojo D, Mayr L, Hedrich C, Baumgartner A, Aliotti-Lippolis M, Schned H, Holler J, Bruckner K, Slavc I, Azizi AA, Peyrl A, Müllauer L, Madlener S, Gojo J. Proof-of-Concept for Liquid Biopsy Disease Monitoring of MYC-Amplified Group 3 Medulloblastoma by Droplet Digital PCR. Cancers (Basel) 2023; 15:2525. [PMID: 37173990 PMCID: PMC10177279 DOI: 10.3390/cancers15092525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Liquid biopsy diagnostic methods are an emerging complementary tool to imaging and pathology techniques across various cancer types. However, there is still no established method for the detection of molecular alterations and disease monitoring in MB, the most common malignant CNS tumor in the pediatric population. In the presented study, we investigated droplet digital polymerase chain reaction (ddPCR) as a highly sensitive method for the detection of MYC amplification in bodily fluids of group 3 MB patients. METHODS We identified a cohort of five MYC-amplified MBs by methylation array and FISH. Predesigned and wet-lab validated probes for ddPCR were used to establish the detection method and were validated in two MYC-amplified MB cell lines as well as tumor tissue of the MYC-amplified cohort. Finally, a total of 49 longitudinal CSF samples were analyzed at multiple timepoints during the course of the disease. RESULTS Detection of MYC amplification by ddPCR in CSF showed a sensitivity and specificity of 90% and 100%, respectively. We observed a steep increase in amplification rate (AR) at disease progression in 3/5 cases. ddPCR was proven to be more sensitive than cytology for the detection of residual disease. In contrast to CSF, MYC amplification was not detectable by ddPCR in blood samples. CONCLUSIONS ddPCR proves to be a sensitive and specific method for the detection of MYC amplification in the CSF of MB patients. These results warrant implementation of liquid biopsy in future prospective clinical trials to validate the potential for improved diagnosis, disease staging and monitoring.
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Affiliation(s)
- Natalia Stepien
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Daniel Senfter
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Julia Furtner
- Division of Neuroradiology and Musculoskeletal Radiology, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1090 Vienna, Austria
- Research Center for Medical Image Analysis and Artificial Intelligence (MIAAI), Faculty of Medicine and Dentistry, Danube Private University, 3500 Krems-Stein, Austria
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Christian Dorfer
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Thomas Czech
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Daniela Lötsch-Gojo
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Lisa Mayr
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Cora Hedrich
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Alicia Baumgartner
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Maria Aliotti-Lippolis
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Hannah Schned
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Johannes Holler
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Katharina Bruckner
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Amedeo A. Azizi
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Andreas Peyrl
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Leonhard Müllauer
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
| | - Sibylle Madlener
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
| | - Johannes Gojo
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics and Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (N.S.); (S.M.)
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Hwang HS, Lo CM, Murphy M, Grudda T, Gallagher N, Luo CH, Robinson ML, Mirza A, Conte M, Conte A, Zhou R, Vergara C, Brooke CB, Pekosz A, Mostafa HH, Manabe YC, Thio CL, Balagopal A. Characterizing SARS-CoV-2 Transcription of Subgenomic and Genomic RNAs During Early Human Infection Using Multiplexed Droplet Digital Polymerase Chain Reaction. J Infect Dis 2023; 227:981-992. [PMID: 36468309 PMCID: PMC10319975 DOI: 10.1093/infdis/jiac472] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/20/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission requires understanding SARS-CoV-2 replication dynamics. METHODS We developed a multiplexed droplet digital polymerase chain reaction (ddPCR) assay to quantify SARS-CoV-2 subgenomic RNAs (sgRNAs), which are only produced during active viral replication, and discriminate them from genomic RNAs (gRNAs). We applied the assay to specimens from 144 people with single nasopharyngeal samples and 27 people with >1 sample. Results were compared to quantitative PCR (qPCR) and viral culture. RESULTS sgRNAs were quantifiable across a range of qPCR cycle threshold (Ct) values and correlated with Ct values. The ratio sgRNA:gRNA was stable across a wide range of Ct values, whereas adjusted amounts of N sgRNA to a human housekeeping gene declined with higher Ct values. Adjusted sgRNA and gRNA amounts were quantifiable in culture-negative samples, although levels were significantly lower than in culture-positive samples. Daily testing of 6 persons revealed that sgRNA is concordant with culture results during the first week of infection but may be discordant with culture later in infection. sgRNA:gRNA is constant during infection despite changes in viral culture. CONCLUSIONS Ct values from qPCR correlate with active viral replication. More work is needed to understand why some cultures are negative despite presence of sgRNA.
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Affiliation(s)
- Hyon S Hwang
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Che-Min Lo
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael Murphy
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Tanner Grudda
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Nicholas Gallagher
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chun Huai Luo
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matthew L Robinson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Agha Mirza
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Madison Conte
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Abigail Conte
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Ruifeng Zhou
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Candelaria Vergara
- Department of Microbiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Christopher B Brooke
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yukari C Manabe
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Chloe L Thio
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Ashwin Balagopal
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Hu G, Huang K, Zhou W, Wang R, Zhao W, Zou H, Li W, Wu S, Li M, Wang G. Comparison of droplet digital PCR and real-time quantitative PCR for quantitative detection of the parasitic ciliate Ichthyophthirius multifiliis in the water environment. J Fish Dis 2023; 46:357-367. [PMID: 36606558 DOI: 10.1111/jfd.13749] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Ichthyophthiriasis, caused by the parasitic ciliate Ichthyophthirius multifiliis (Ich), is considered one of the most harmful diseases affecting freshwater fish globally. It can cause mass mortalities of fish in intensive farming systems. In such systems, it is thus necessary to detect and quantify the number of Ich in the water so that control measures can be implemented before Ichthyophthiriasis breaks out. In recent years, molecular diagnostic methods have become increasingly important in aquaculture. Real-time quantitative polymerase chain reaction (qPCR) and droplet digital polymerase chain reaction (ddPCR) have become robust assays for detecting pathogens. In this study, a set of specific primers and a TaqMan-minor groove binder probe targeting the small-subunit rDNA (SSU rDNA) of Ich were developed. They were used in qPCR and ddPCR assays to compare the performance of these two different methods in quantitatively detecting Ich. After optimizing the reaction conditions, both qPCR and ddPCR assays were found to have high linearity and quantitative correlations for standard plasmid DNA. When used for the detection of Ich eDNA in water samples, the qPCR assay had a wider detection range, making it a suitable method to screen for the prevalence of Ichthyophthiriasis. However, the ddPCR approach had higher sensitivity, which would help provide advance notice of the disease in complex water environmental samples.
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Affiliation(s)
- Guangran Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ke Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Weitian Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Runqiu Wang
- Hubei Key Laboratory of Three Gorges Project for Conservation of Fishes, Chinese Sturgeon Research Institute, China Three Gorges Corporation, Yichang, China
| | - Weishan Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hong Zou
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Wenxiang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Shangong Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Ming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guitang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Wan L, Ma J, Gong X, Li Q, Wang Y, Wei H, Wang J, Xiao Z, Mi Y. Droplet digital polymerase chain reaction improves the detection of BCR-ABL1 kinase domain mutation in Philadelphia chromosome-positive acute lymphoblastic leukemia. Int J Lab Hematol 2023. [PMID: 36990968 DOI: 10.1111/ijlh.14069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
INTRODUCTION Sanger sequencing (SS) is the most frequently used method for detecting ABL1 kinase domain (KD) mutations in patients with Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ ALL). However, it cannot detect low levels of mutation. Recently, droplet digital polymerase chain reaction (ddPCR) has been developed as a sensitive technique for detecting mutations in hematological neoplasms. The aim of our study was to explore the value of ddPCR in detecting ABL1 KD mutations. METHODS We compared the results of SS and ddPCR in detecting ABL1 KD mutations in a consecutive cohort of 65 adolescent and adult patients with Ph+ ALL treated with intensive multiagent chemotherapy plus TKIs. RESULTS At diagnosis, SS and ddPCR identified 1 (1.5%) and 26 (40%) out of 65 patients with positive ABL1 KD mutations, respectively. Patients with T315I mutations detected by ddPCR at diagnosis all developed SS-detectable T315I mutations during treatment with first- or second-generation TKIs, and non-T315I mutations detected by ddPCR at diagnosis displayed a limited prognostic impact. CONCLUSION Our study demonstrates that ddPCR is a highly sensitive and accurate mutation detection method and the presence of T315I mutations before treatment shows prognostic significance in the context of first- or second-generation TKIs.
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Affiliation(s)
- Li Wan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jiao Ma
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Xiaoyuan Gong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Qinghua Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Ying Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Hui Wei
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Jianxiang Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Zhijian Xiao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Yingchang Mi
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
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