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Fürstenau M, Giza A, Weiss J, Kleinert F, Robrecht S, Franzen F, Stumpf J, Langerbeins P, Al-Sawaf O, Simon F, Fink AM, Schneider C, Tausch E, Schetelig J, Dreger P, Böttcher S, Fischer K, Kreuzer KA, Ritgen M, Schilhabel A, Brüggemann M, Stilgenbauer S, Eichhorst B, Hallek M, Cramer P. Acalabrutinib, venetoclax, and obinutuzumab in relapsed/refractory CLL: final efficacy and ctDNA analysis of the CLL2-BAAG trial. Blood 2024; 144:272-282. [PMID: 38620072 DOI: 10.1182/blood.2023022730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/17/2024] Open
Abstract
ABSTRACT The phase 2 CLL2-BAAG trial tested the measurable residual disease (MRD)-guided triple combination of acalabrutinib, venetoclax, and obinutuzumab after optional bendamustine debulking in 45 patients with relapsed/refractory chronic lymphocytic leukemia (CLL). MRD was measured by flow cytometry (FCM; undetectable MRD <10-4) in peripheral blood (PB) and circulating tumor DNA (ctDNA) using digital droplet polymerase chain reaction of variable-diversity-joining (VDJ) rearrangements and CLL-related mutations in plasma. The median number of previous treatments was 1 (range, 1-4); 18 patients (40%) had received a Bruton tyrosine kinase inhibitor (BTKi) and/or venetoclax before inclusion, 14 of 44 (31.8%) had TP53 aberrations, and 34 (75.6%) had unmutated immunoglobulin heavy-chain variable region genes. With a median observation time of 36.3 months and all patients off-treatment for a median of 21.9 months, uMRD <10-4 in PB was achieved in 42 of the 45 patients (93.3%) at any time point, including 17 of 18 (94.4%) previously exposed to venetoclax/BTKi and 13 of 14 (92.9%) with TP53 aberrations. The estimated 3-year progression-free and overall survival rates were 85.0% and 93.8%, respectively. Overall, 585 paired FCM/ctDNA samples were analyzed and 18 MRD recurrences (5 with and 13 without clinical progression) occurred after the end of treatment. Twelve samples were first detected by ctDNA, 3 by FCM, and 3 synchronously. In conclusion, time-limited MRD-guided acalabrutinib, venetoclax, and obinutuzumab achieved deep remissions in almost all patients with relapsed/refractory CLL. The addition of ctDNA-based analyses to FCM MRD assessment seems to improve early detection of relapses. This trial was registered at www.clinicaltrials.gov as #NCT03787264.
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MESH Headings
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Sulfonamides/administration & dosage
- Sulfonamides/therapeutic use
- Aged
- Middle Aged
- Female
- Male
- Bridged Bicyclo Compounds, Heterocyclic/administration & dosage
- Bridged Bicyclo Compounds, Heterocyclic/therapeutic use
- Circulating Tumor DNA/genetics
- Circulating Tumor DNA/blood
- Pyrazines/administration & dosage
- Pyrazines/therapeutic use
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Aged, 80 and over
- Antibodies, Monoclonal, Humanized/administration & dosage
- Antibodies, Monoclonal, Humanized/therapeutic use
- Neoplasm, Residual
- Benzamides/administration & dosage
- Benzamides/therapeutic use
- Adult
- Recurrence
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Affiliation(s)
- Moritz Fürstenau
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
| | - Adam Giza
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
| | - Jonathan Weiss
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
| | - Fanni Kleinert
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
| | - Sandra Robrecht
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
| | - Fabian Franzen
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
| | - Janina Stumpf
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
| | - Petra Langerbeins
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
| | - Othman Al-Sawaf
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
| | - Florian Simon
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
| | - Anna-Maria Fink
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
| | - Christof Schneider
- Division of Chronic Lymphocytic Leukemia, Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Eugen Tausch
- Division of Chronic Lymphocytic Leukemia, Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Johannes Schetelig
- Department I of Internal Medicine, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Peter Dreger
- Department V of Internal Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Sebastian Böttcher
- Department III of Internal Medicine, University Hospital Rostock, Rostock, Germany
| | - Kirsten Fischer
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
| | - Karl-Anton Kreuzer
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
| | - Matthias Ritgen
- Department II of Internal Medicine, University Hospital of Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Anke Schilhabel
- Department II of Internal Medicine, University Hospital of Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Monika Brüggemann
- Department II of Internal Medicine, University Hospital of Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stephan Stilgenbauer
- Division of Chronic Lymphocytic Leukemia, Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Barbara Eichhorst
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
| | - Michael Hallek
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
| | - Paula Cramer
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Chronic Lymphocytic Leukemia Study Group, University of Cologne, Cologne, Germany
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2
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Bonanno Ferraro G, Bonomo C, Brandtner D, Mancini P, Veneri C, Briancesco R, Coccia AM, Lucentini L, Suffredini E, Bongiorno D, Musso N, Stefani S, La Rosa G. Characterisation of microbial communities and quantification of antibiotic resistance genes in Italian wastewater treatment plants using 16S rRNA sequencing and digital PCR. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:173217. [PMID: 38750766 DOI: 10.1016/j.scitotenv.2024.173217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/19/2024]
Abstract
The spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in humans, animals and environment is a growing threat to public health. Wastewater treatment plants (WWTPs) are crucial in mitigating the risk of environmental contamination by effectively removing contaminants before discharge. However, the persistence of ARB and ARGs even after treatment is a challenge for the management of water system. To comprehensively assess antimicrobial resistance dynamics, we conducted a one-year monitoring study in three WWTPs in central Italy, both influents and effluents. We used seasonal sampling to analyze microbial communities by 16S rRNA, as well as to determine the prevalence and behaviour of major ARGs (sul1, tetA, blaTEM, blaOXA-48, blaCTX-M-1 group, blaKPC) and the class 1 Integron (int1). Predominant genera included in order: Arcobacter, Acinetobacter, Flavobacterium, Pseudarcobacter, Bacteroides, Aeromonas, Trichococcus, Cloacibacterium, Pseudomonas and Streptococcus. A higher diversity of bacterial communities was observed in the effluents compared to the influents. Within these communities, we also identified bacteria that may be associated with antibiotic resistance and pose a significant threat to human health. The mean concentrations (in gene copies per liter, gc/L) of ARGs and int1 in untreated wastewater (absolute abundance) were as follows: sul1 (4.1 × 109), tetA (5.2 × 108), blaTEM (1.1 × 108), blaOXA-48 (2.1 × 107), blaCTX-M-1 group (1.1 × 107), blaKPC (9.4 × 105), and int1 (5.5 × 109). The mean values in treated effluents showed reductions ranging from one to three log. However, after normalizing to the 16S rRNA gene (relative abundance), it was observed that in 37.5 % (42/112) of measurements, the relative abundance of ARGs increased in effluents compared to influents. Furthermore, correlations were identified between ARGs and bacterial genera including priority pathogens. This study improves our understanding of the dynamics of ARGs and provides insights to develop more effective strategies to reduce their spread, protecting public health and preserving the future efficacy of antibiotics.
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Affiliation(s)
- Giusy Bonanno Ferraro
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy; Department of Biomedical and Biotechnological Science, University of Catania, Italy
| | - Carmelo Bonomo
- Department of Biomedical and Biotechnological Science, University of Catania, Italy
| | - David Brandtner
- Departments of Infectious Disease, Istituto Superiore di Sanità, Rome, Italy
| | - Pamela Mancini
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - Carolina Veneri
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - Rossella Briancesco
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - Anna Maria Coccia
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - Luca Lucentini
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Dafne Bongiorno
- Department of Biomedical and Biotechnological Science, University of Catania, Italy
| | - Nicolò Musso
- Department of Biomedical and Biotechnological Science, University of Catania, Italy
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Science, University of Catania, Italy
| | - Giuseppina La Rosa
- National Center for Water Safety (CeNSia), Istituto Superiore di Sanità, Rome, Italy.
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3
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Villa C, Costa J, Mafra I. First nanoplate digital PCR method to trace allergenic foods: Improved sensitivity for the detection of sesame. Food Chem 2024; 444:138650. [PMID: 38330611 DOI: 10.1016/j.foodchem.2024.138650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Sesame (Sesamum indicum L.) is an important allergenic food whose presence can be the cause of severe allergic reactions in sensitised individuals. In this work, nanoplate digital PCR (ndPCR) was used to develop two methods to detect trace amounts of sesame in processed foods and compared with previously proposed real-time PCR assays. Two independent ndPCR approaches were successfully advanced, achieving sensitivities of 5 and 0.1 mg/kg of sesame in dough/biscuits, targeting the CO6b-1 and ITS regions, respectively. The sensitivity using both targets was improved by one order of magnitude comparing with real-time PCR and was not affected by food processing. CO6b-1 system was not influenced by food matrix, exhibiting similar performance regardless the use of complex matrix extracts or serial diluted DNA. Herein, ndPCR was proposed for the first time for the detection of allergenic foods with the advantage of providing better performance than real-time PCR regarding sensitivity and robustness.
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Affiliation(s)
- Caterina Villa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, Porto 4050-313, Portugal.
| | - Joana Costa
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, Porto 4050-313, Portugal
| | - Isabel Mafra
- REQUIMTE-LAQV, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, Porto 4050-313, Portugal
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Pyatnitskiy MA, Poverennaya EV. Transcript-Level Biomarkers of Early Lung Carcinogenesis in Bronchial Lesions. Cancers (Basel) 2024; 16:2260. [PMID: 38927965 PMCID: PMC11202239 DOI: 10.3390/cancers16122260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/09/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Premalignant lesions within the bronchial epithelium signify the initial phases of squamous cell lung carcinoma, posing challenges for detection via conventional methods. Instead of focusing solely on gene expression, in this study, we explore transcriptomic alterations linked to lesion progression, with an emphasis on protein-coding transcripts. We reanalyzed a publicly available RNA-Seq dataset on airway epithelial cells from 82 smokers with and without premalignant lesions. Transcript and gene abundance were quantified using kallisto, while differential expression and transcript usage analysis was performed utilizing sleuth and RATs packages. Functional characterization involved overrepresentation analysis via clusterProfiler, weighted coexpression network analysis (WGCNA), and network analysis via Enrichr-KG. We detected 5906 differentially expressed transcripts and 4626 genes, exhibiting significant enrichment within pathways associated with oxidative phosphorylation and mitochondrial function. Remarkably, transcript-level WGCNA revealed a single module correlated with dysplasia status, notably enriched in cilium-related biological processes. Notable hub transcripts included RABL2B (ENST00000395590), DNAH1 (ENST00000420323), EFHC1 (ENST00000635996), and VWA3A (ENST00000563389) along with transcription factors such as FOXJ1 and ZNF474 as potential regulators. Our findings underscore the value of transcript-level analysis in uncovering novel insights into premalignant bronchial lesion biology, including identification of potential biomarkers associated with early lung carcinogenesis.
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Affiliation(s)
- Mikhail A. Pyatnitskiy
- Institute of Biomedical Chemistry, Moscow 119121, Russia;
- National Research University Higher School of Economics, Moscow 101000, Russia
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5
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Houghton MJ, Balland E, Gartner MJ, Thomas BJ, Subbarao K, Williamson G. The flavonoid quercetin decreases ACE2 and TMPRSS2 expression but not SARS-CoV-2 infection in cultured human lung cells. Biofactors 2024. [PMID: 38886986 DOI: 10.1002/biof.2084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/11/2024] [Indexed: 06/20/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) binds to angiotensin-converting enzyme 2 (ACE2) on host cells, via its spike protein, and transmembrane protease, serine 2 (TMPRSS2) cleaves the spike-ACE2 complex to facilitate virus entry. As rate-limiting steps for virus entry, modulation of ACE2 and/or TMPRSS2 may decrease SARS-CoV-2 infectivity and COVID-19 severity. In silico modeling suggested the natural bioactive flavonoid quercetin can bind to ACE2 and a recent randomized clinical trial demonstrated that oral supplementation with quercetin increased COVID-19 recovery. A range of cultured human cells were assessed for co-expression of ACE2 and TMPRSS2. Immortalized Calu-3 lung cells, cultured and matured at an air-liquid interface (Calu-3-ALIs), were established as the most appropriate. Primary bronchial epithelial cells (PBECs) were obtained from healthy adult males (N = 6) and cultured under submerged conditions to corroborate the outcomes. Upon maturation or reaching 80% confluence, respectively, the Calu-3-ALIs and PBECs were treated with quercetin, and mRNA and protein expression were assessed by droplet digital PCR and ELISA, respectively. SARS-CoV-2 infectivity, and the effects of pre- and co-treatment with quercetin, was assessed by median tissue culture infectious dose assay. Quercetin dose-dependently decreased ACE2 and TMPRSS2 mRNA and protein in both Calu-3-ALIs and PBECs after 4 h, while TMPRSS2 remained suppressed in response to prolonged treatment with lower doses (twice daily for 3 days). Quercetin also acutely decreased ADAM17 mRNA, but not ACE, in Calu-3-ALIs, and this warrants further investigation. Calu-3-ALIs, but not PBECs, were successfully infected with SARS-CoV-2; however, quercetin had no antiviral effect, neither directly nor indirectly through downregulation of ACE2 and TMPRSS2. Calu-3-ALIs were reaffirmed to be an optimal cell model for research into the regulation of ACE2 and TMPRSS2, without the need for prior genetic modification, and will prove valuable in future coronavirus and respiratory infectious disease work. However, our data demonstrate that a significant decrease in the expression of ACE2 and TMPRSS2 by a promising prophylactic candidate may not translate to infection prevention.
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Affiliation(s)
- Michael James Houghton
- Department of Nutrition, Dietetics and Food, Monash University, BASE Facility, Notting Hill, VIC, Australia
- Victorian Heart Institute, Monash University, Victorian Heart Hospital, Clayton, VIC, Australia
| | - Eglantine Balland
- Department of Nutrition, Dietetics and Food, Monash University, BASE Facility, Notting Hill, VIC, Australia
- Monash Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Matthew James Gartner
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Belinda Jane Thomas
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Monash Lung and Sleep, Monash Health, Monash Medical Centre, Clayton, VIC, Australia
| | - Kanta Subbarao
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Gary Williamson
- Department of Nutrition, Dietetics and Food, Monash University, BASE Facility, Notting Hill, VIC, Australia
- Victorian Heart Institute, Monash University, Victorian Heart Hospital, Clayton, VIC, Australia
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Bardol T, Dujon AM, Taly V, Dunyach-Remy C, Lavigne JP, Costa-Silva B, Kurma K, Eslami-S Z, Cayrefourcq L, Canivet C, Muscari F, Bournet B, Alix-Panabières C. Early detection of pancreatic cancer by liquid biopsy "PANLIPSY": a french nation-wide study project. BMC Cancer 2024; 24:709. [PMID: 38853244 PMCID: PMC11163786 DOI: 10.1186/s12885-024-12463-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 05/31/2024] [Indexed: 06/11/2024] Open
Abstract
BACKGROUND Pancreatic cancer, predominantly characterized by ductal adenocarcinoma (PDAC) accounts for 90% of cases and is the fourth leading cause of cancer-related deaths globally. Its incidence is notably increasing. This poor prognosis is primarily due to late-stage diagnosis (approximately 70% to 80% of patients are diagnosed at an advanced stage), aggressive tumor biology, and low sensitivity to chemotherapy. Consequently, it is crucial to identify and develop a simple, feasible and reproducible blood-based signature (i.e., combination of biomarkers) for early detection of PDAC. METHODS The PANLIPSY study is a multi-center, non-interventional prospective clinical trial designed to achieve early detection of PDAC with high specificity and sensitivity, using a combinatorial approach in blood samples. These samples are collected from patients with resectable, borderline or locally advanced, and metastatic stage PDAC within the framework of the French Biological and Clinical Database for PDAC cohort (BACAP 2). All partners of the BACAP consortium are eligible to participate. The study will include 215 PDAC patients, plus 25 patients with benign pancreatic conditions from the PAncreatic Disease Cohort of TOuLouse (PACTOL) cohort, and 115 healthy controls, totaling 355 individuals. Circulating biomarkers will be collected in a total volume of 50 mL of blood, divided into one CellSave tube (10 mL), two CELL-FREE DNA BCT® preservative tubes (18 mL), and five EDTA tubes (22 mL in total). Samples preparation will adhere to the guidelines of the European Liquid Biopsy Society (ELBS). A unique feature of the study is the AI-based comparison of these complementary liquid biopsy biomarkers. Main end-points: i) to define a liquid biopsy signature that includes the most relevant circulating biomarkers, ii) to validate the multi-marker panel in an independent cohort of healthy controls and patients, with resectable PDAC, and iii) to establish a unique liquid biopsy biobank for PDAC study. DISCUSSION The PANLIPSY study is a unique prospective non-interventional clinical trial that brings together liquid biopsy experts. The aim is to develop a biological signature for the early detection of PDAC based on AI-assisted detection of circulating biomarkers in blood samples (CTCs, ctDNA, EVs, circulating immune system, circulating cell-free nucleosomes, proteins, and microbiota). TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT06128343 / NCT05824403. Registration dates: June 8,2023 and April 21, 2023.
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Affiliation(s)
- Thomas Bardol
- Laboratory of Rare Circulating Human Cells - Liquid Biopsy Lab, Institut Universitaire de Recherche Clinique (IURC), University Medical Center of Montpellier, 641, Avenue du Doyen Gaston Giraud, Cedex 5 34093, Montpellier, France.
- CREEC/CANECEV MIVEGEC (CREES), University of Montpellier, CNRS, Montpellier, IRD, France.
- European Liquid Biopsy Society (ELBS), Hamburg, Germany.
| | - Antoine M Dujon
- CREEC/CANECEV MIVEGEC (CREES), University of Montpellier, CNRS, Montpellier, IRD, France
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, Victoria, Australia
| | - Valerie Taly
- Équipe Labélisée Ligue Nationale Contre Le Cancer, Centre de Recherche Des Cordeliers, Université Paris Cité, UMR-S1138, CNRS SNC5096, Paris, France
- METHYS Dx, 67 Rue Saint-Jacques, Paris, France
| | - Catherine Dunyach-Remy
- Department of Microbiology and Hospital Hygiene Bacterial Virulence and Chronic Infections, University of Montpellier CHU Nîmes, INSERM U1047, Nîmes, France
| | - Jean-Philippe Lavigne
- Department of Microbiology and Hospital Hygiene Bacterial Virulence and Chronic Infections, University of Montpellier CHU Nîmes, INSERM U1047, Nîmes, France
| | - Bruno Costa-Silva
- Champalimaud Physiology and Cancer Programme, Champalimaud Foundation, 1400-038, Lisbon, Portugal
| | - Keerthi Kurma
- Laboratory of Rare Circulating Human Cells - Liquid Biopsy Lab, Institut Universitaire de Recherche Clinique (IURC), University Medical Center of Montpellier, 641, Avenue du Doyen Gaston Giraud, Cedex 5 34093, Montpellier, France
- CREEC/CANECEV MIVEGEC (CREES), University of Montpellier, CNRS, Montpellier, IRD, France
- European Liquid Biopsy Society (ELBS), Hamburg, Germany
| | - Zahra Eslami-S
- Laboratory of Rare Circulating Human Cells - Liquid Biopsy Lab, Institut Universitaire de Recherche Clinique (IURC), University Medical Center of Montpellier, 641, Avenue du Doyen Gaston Giraud, Cedex 5 34093, Montpellier, France
- CREEC/CANECEV MIVEGEC (CREES), University of Montpellier, CNRS, Montpellier, IRD, France
- European Liquid Biopsy Society (ELBS), Hamburg, Germany
| | - Laure Cayrefourcq
- Laboratory of Rare Circulating Human Cells - Liquid Biopsy Lab, Institut Universitaire de Recherche Clinique (IURC), University Medical Center of Montpellier, 641, Avenue du Doyen Gaston Giraud, Cedex 5 34093, Montpellier, France
- CREEC/CANECEV MIVEGEC (CREES), University of Montpellier, CNRS, Montpellier, IRD, France
- European Liquid Biopsy Society (ELBS), Hamburg, Germany
| | - Cindy Canivet
- Department of Gastroenterology and Pancreatology, CHU - Rangueil and the University of Toulouse, 1 Avenue Jean Poulhès, Cedex 9 50032, 31059, Toulouse, TSA, France
| | - Fabrice Muscari
- Digestive Surgery and Liver Transplantation Department, Toulouse University Hospital, Toulouse, France
| | - Barbara Bournet
- Department of Gastroenterology and Pancreatology, CHU - Rangueil and the University of Toulouse, 1 Avenue Jean Poulhès, Cedex 9 50032, 31059, Toulouse, TSA, France
| | - Catherine Alix-Panabières
- Laboratory of Rare Circulating Human Cells - Liquid Biopsy Lab, Institut Universitaire de Recherche Clinique (IURC), University Medical Center of Montpellier, 641, Avenue du Doyen Gaston Giraud, Cedex 5 34093, Montpellier, France.
- CREEC/CANECEV MIVEGEC (CREES), University of Montpellier, CNRS, Montpellier, IRD, France.
- European Liquid Biopsy Society (ELBS), Hamburg, Germany.
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7
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Gao N, Huo Y, Yu D, Cheng F, Wang T, Zhang X, Zhang L, Hu W, Li J, Yuan P, Liu J, Wang Y, Yan J. Evaluation of reverse transcription yield of RNA standards and forensic samples based on droplet digital PCR. Biochem Biophys Res Commun 2024; 711:149909. [PMID: 38615573 DOI: 10.1016/j.bbrc.2024.149909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
RNA analysis has shown great value in forensic science, such as body fluids and tissue identification, postmortem interval estimation, biological age prediction, etc. Currently, most RNA follow-up experiments involve reverse transcription (RT) procedures. It has been shown that the RT step is variable and has a greater impact on subsequent data analysis, especially for forensic trace samples. However, the pattern of variation between different RNA template inputs and complementary DNA (cDNA) yield is unclear. In this study, a series of 2-fold gradient dilutions of RNA standards (1 μg/μL - 0.24 ng/μL) and forensic samples (including blood samples, saliva samples, bloodstains, and saliva stains) were reverse-transcribed using EasyQuick RT MasterMix. The obtained cDNA was quantified by droplet digital PCR (ddPCR) to assess the RT yield of the ACTB gene. The results showed that the 125 ng RNA template had the highest RT yield in a 10 μL RT reaction system with the selected kit. For all stain samples, the RT yield improved as the amount of RNA template input increased since RNA quantities were below 125 ng. As many commercialized reverse transcription kits using different kinds of enzymes are available for forensic RNA research, we recommend that systematic experiments should be performed in advance to determine the amount of RNA input at the optimum RT yield when using any kit for reverse transcription experiments.
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Affiliation(s)
- Niu Gao
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Yumei Huo
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Daijing Yu
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Feng Cheng
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Tian Wang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Xiaomeng Zhang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Liwei Zhang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Wenjing Hu
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Piao Yuan
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China.
| | - Yan Wang
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China; Clinical Biobank Center, Medical Innovation Research Division of Chinese, PLA General Hospital, Beijing, China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, No. 55 Wenhua Street, Yuci District, Jinzhong, Shanxi, China; Shanxi Key Laboratory of Forensic Medicine, Yuci District, Jinzhong, Shanxi, China.
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8
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Bonilla DA, Orozco CA, Forero DA, Odriozola A. Techniques, procedures, and applications in host genetic analysis. ADVANCES IN GENETICS 2024; 111:1-79. [PMID: 38908897 DOI: 10.1016/bs.adgen.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
This chapter overviews genetic techniques' fundamentals and methodological features, including different approaches, analyses, and applications that have contributed to advancing health and disease. The aim is to describe laboratory methodologies and analyses employed to understand the genetic landscape of different biological contexts, from conventional techniques to cutting-edge technologies. Besides describing detailed aspects of the polymerase chain reaction (PCR) and derived types as one of the principles for many novel techniques, we also discuss microarray analysis, next-generation sequencing, and genome editing technologies such as transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems. These techniques study several phenotypes, ranging from autoimmune disorders to viral diseases. The significance of integrating diverse genetic methodologies and tools to understand host genetics comprehensively and addressing the ethical, legal, and social implications (ELSI) associated with using genetic information is highlighted. Overall, the methods, procedures, and applications in host genetic analysis provided in this chapter furnish researchers and practitioners with a roadmap for navigating the dynamic landscape of host-genome interactions.
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Affiliation(s)
- Diego A Bonilla
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain; Research Division, Dynamical Business & Science Society-DBSS International SAS, Bogotá, Colombia.
| | - Carlos A Orozco
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología de Colombia, Bogotá, Colombia
| | - Diego A Forero
- School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Adrián Odriozola
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
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9
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Boeri M, Signoroni S, Ciniselli CM, Gariboldi M, Zanutto S, Rausa E, Segale M, Zanghì A, Ricci MT, Verderio P, Sozzi G, Vitellaro M. Detection of (pre)cancerous colorectal lesions in Lynch syndrome patients by microsatellite instability liquid biopsy. Cancer Gene Ther 2024; 31:842-850. [PMID: 38332046 PMCID: PMC11192631 DOI: 10.1038/s41417-023-00721-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 02/10/2024]
Abstract
Lynch syndrome (LS) is an inherited condition characterized by an increased risk of developing cancer, in particular colorectal cancer (CRC). Microsatellite instability (MSI) is the main feature of (pre)cancerous lesions occurring in LS patients. Close endoscopic surveillance is the only option available to reduce CRC morbidity and mortality. However, it may fail to intercept interval cancers and patients' compliance to such an invasive procedure may decrease over the years. The development of a minimally invasive test able to detect (pre)cancerous colorectal lesions, could thus help tailor surveillance programs in LS patients. Taking advantage of an endoscopic surveillance program, we retrospectively assessed the instability of five microsatellites (BAT26, BAT25, NR24, NR21, and Mono27) in liquid biopsies collected at baseline and possibly at two further endoscopic rounds. For this purpose, we tested a new multiplex drop-off digital polymerase chain reaction (dPCR) assay, reaching mutant allele frequencies (MAFs) as low as 0.01%. Overall, 78 plasma samples at the three time-points from 18 patients with baseline (pre)cancerous lesions and 18 controls were available for molecular analysis. At baseline, the MAFs of BAT26, BAT25 and NR24 were significantly higher in samples of patients with lesions but did not differ with respect to the grade of dysplasia or any other clinico-pathological characteristics. When all markers were combined to determine MSI in blood, this test was able to discriminate lesion-bearing patients with an AUC of 0.80 (95%CI: 0.66; 0.94).
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Affiliation(s)
- Mattia Boeri
- Epigenomics and Biomarkers of Solid Tumors Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Stefano Signoroni
- Unit of Hereditary Digestive Tract Tumors, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
| | - Chiara Maura Ciniselli
- Bioinformatics and Biostatistics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Manuela Gariboldi
- Molecular Epigenomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Susanna Zanutto
- Molecular Epigenomics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Emanuele Rausa
- Unit of Hereditary Digestive Tract Tumors, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Miriam Segale
- Epigenomics and Biomarkers of Solid Tumors Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Anna Zanghì
- Epigenomics and Biomarkers of Solid Tumors Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maria Teresa Ricci
- Unit of Hereditary Digestive Tract Tumors, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Verderio
- Bioinformatics and Biostatistics Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Gabriella Sozzi
- Epigenomics and Biomarkers of Solid Tumors Unit, Experimental Oncology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marco Vitellaro
- Unit of Hereditary Digestive Tract Tumors, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Colorectal Surgery Division, Department of Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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10
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Huggett JF, O'Sullivan DM, Cowen S, Cleveland MH, Davies K, Harris K, Moran-Gilad J, Winter A, Braybrook J, Messenger M. Ensuring accuracy in the development and application of nucleic acid amplification tests (NAATs) for infectious disease. Mol Aspects Med 2024; 97:101275. [PMID: 38772082 DOI: 10.1016/j.mam.2024.101275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/29/2024] [Accepted: 04/22/2024] [Indexed: 05/23/2024]
Abstract
Diagnostic tests were heralded as crucial during the Coronavirus disease (COVID-19) pandemic with most of the key methods using bioanalytical approaches that detected larger molecules (RNA, protein antigens or antibodies) rather than conventional clinical biochemical techniques. Nucleic Acid Amplification Tests (NAATs), like the Polymerase Chain Reaction (PCR), and other molecular methods, like sequencing (that often work in combination with NAATs), were essential to the diagnosis and management during COVID-19. This was exemplified both early in the pandemic but also later on, following the emergence of new genetic SARS-CoV-2 variants. The 100 day mission to respond to future pandemic threats highlights the need for effective diagnostics, therapeutics and vaccines. Of the three, diagnostics represents the first opportunity to manage infectious diseases while also being the most poorly supported in terms of the infrastructure needed to demonstrate effectiveness. Where performance targets exist, they are not well served by consensus on how to demonstrate they are being met; this includes analytical factors such as limit of detection (LOD) false positive results as well as how to approach clinical evaluation. The selection of gold standards or use of epidemiological factors such as predictive value, reference ranges or clinical thresholds are seldom correctly considered. The attention placed on molecular diagnostic tests during COVID-19 illustrates important considerations and assumptions on the use of these methods for infectious disease diagnosis and beyond. In this manuscript, we discuss state-of-the-art approaches to diagnostic evaluation and explore how they may be better tailored to diagnostic techniques like NAATs to maximise the impact of these highly versatile bioanalytical tools, both generally and during future outbreaks.
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Affiliation(s)
- Jim F Huggett
- National Measurement Laboratory (NML), LGC, Queens Road, Teddington, TW11 0LY, Middlesex, UK; School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK.
| | - Denise M O'Sullivan
- National Measurement Laboratory (NML), LGC, Queens Road, Teddington, TW11 0LY, Middlesex, UK; School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK
| | - Simon Cowen
- National Measurement Laboratory (NML), LGC, Queens Road, Teddington, TW11 0LY, Middlesex, UK
| | - Megan H Cleveland
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
| | - Kerrie Davies
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust/University of Leeds, UK; NIHR Leeds MedTech In Vitro Diagnostic Cooperative, University of Leeds, UK; NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals and University of Leeds, UK
| | - Kathryn Harris
- Department of Virology, NHS East and South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - Jacob Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Amanda Winter
- The Newcastle Upon Tyne Hospitals NHS Foundation Trust, North East Innovation Laboratory, The Biosphere, Drayman's Way, Newcastle Upon Tyne, NE4 5BX, UK
| | - Julian Braybrook
- National Measurement Laboratory (NML), LGC, Queens Road, Teddington, TW11 0LY, Middlesex, UK
| | - Michael Messenger
- FIND, Campus Biotech, Chemin des Mines 9, 1202 Geneva, Switzerland; School of Medicine and Health, University of Leeds Worsley Building, University of Leeds, Woodhouse, Leeds LS2 9JT, UK; British In Vitro Diagnostic Association (BIVDA), 299 Oxford St, London, W1C 2DZ, UK
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11
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Li C, Kang N, Ye S, Huang W, Wang X, Wang C, Li Y, Liu YF, Lan Y, Ma L, Zhao Y, Han Y, Fu J, Shen D, Dong L, Du W. All-In-One OsciDrop Digital PCR System for Automated and Highly Multiplexed Molecular Diagnostics. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309557. [PMID: 38516754 DOI: 10.1002/advs.202309557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/29/2024] [Indexed: 03/23/2024]
Abstract
Digital PCR (dPCR) holds immense potential for precisely detecting nucleic acid markers essential for personalized medicine. However, its broader application is hindered by high consumable costs, complex procedures, and restricted multiplexing capabilities. To address these challenges, an all-in-one dPCR system is introduced that eliminates the need for microfabricated chips, offering fully automated operations and enhanced multiplexing capabilities. Using this innovative oscillation-induced droplet generation technique, OsciDrop, this system supports a comprehensive dPCR workflow, including precise liquid handling, pipette-based droplet printing, in situ thermocycling, multicolor fluorescence imaging, and machine learning-driven analysis. The system's reliability is demonstrated by quantifying reference materials and evaluating HER2 copy number variation in breast cancer. Its multiplexing capability is showcased with a quadruplex dPCR assay that detects key EGFR mutations, including 19Del, L858R, and T790M in lung cancer. Moreover, the digital stepwise melting analysis (dSMA) technique is introduced, enabling high-multiplex profiling of seven major EGFR variants spanning 35 subtypes. This innovative dPCR system presents a cost-effective and versatile alternative, overcoming existing limitations and paving the way for transformative advances in precision diagnostics.
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Affiliation(s)
- Caiming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 101408, China
| | - Nan Kang
- Department of Pathology, Peking University People's Hospital, Beijing, 100044, China
| | - Shun Ye
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Weihang Huang
- Center for Corpus Research, Department of English Language and Linguistics, University of Birmingham, Edgbaston, Birmingham, B152TT, UK
| | - Xia Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Cheng Wang
- Department of Breast Surgery Huangpu Branch, Shanghai Ninth People's Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Yuchen Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Biomedical Sciences College & Shandong Medical Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Yan-Fei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- Research Center for Analytical Sciences, Northeastern University, Shenyang, 110819, China
| | - Ying Lan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liang Ma
- Maccura Biotechnology Co., Ltd, Chengdu, 611730, China
| | - Yuhang Zhao
- Maccura Biotechnology Co., Ltd, Chengdu, 611730, China
| | - Yong Han
- Maccura Biotechnology Co., Ltd, Chengdu, 611730, China
| | - Jun Fu
- Maccura Biotechnology Co., Ltd, Chengdu, 611730, China
| | - Danhua Shen
- Department of Pathology, Peking University People's Hospital, Beijing, 100044, China
| | - Lianhua Dong
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, 100013, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 101408, China
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, 101408, China
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12
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Ganguly R, Lee CS. A Poisson-Independent Approach to Precision Nucleic Acid Quantification in Microdroplets. ACS APPLIED BIO MATERIALS 2024; 7:3441-3451. [PMID: 38658190 DOI: 10.1021/acsabm.4c00350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Digital PCR (dPCR) has become indispensable in nucleic acid (NA) detection across various fields, including viral diagnostics and mutant detection. However, misclassification of partitions in dPCR can significantly impact accuracy. Despite existing methods to minimize misclassification bias, accurate classification remains elusive, especially for nonamplified target partitions. To address these challenges, this study introduces an innovative microdroplet-based competitive PCR platform for nucleic acid quantification in microfluidic devices independent of Poisson statistics. In this approach, the target concentration (T) is determined from the concentration of competitor DNA (C) at the equivalence point (E.P.), where C/T is 1. Competitive PCR ensures that the ratio of target to competitor DNA remains constant during amplification, reflected in the resultant fluorescence intensity, allowing the quantification of target DNA concentration at the equivalence point. The unique amplification technique eliminates Poisson distribution, addressing misclassification challenges. Additionally, our approach reduces the need for post-PCR procedures and shortens analytical time. We envision this platform as versatile, reproducible, and easily adaptable for driving significant progress in molecular biology and diagnostics.
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Affiliation(s)
- Reya Ganguly
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Chang-Soo Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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13
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Sivaganesan M, Willis JR, Diedrich A, Shanks OC. A fecal score approximation model for analysis of real-time quantitative PCR fecal source identification measurements. WATER RESEARCH 2024; 255:121482. [PMID: 38598887 DOI: 10.1016/j.watres.2024.121482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 04/12/2024]
Abstract
Numerous qPCR-based methods are available to estimate the concentration of fecal pollution sources in surface waters. However, qPCR fecal source identification data sets often include a high proportion of non-detections (reactions failing to attain a prespecified minimal signal intensity for detection) and measurements below the assay lower limit of quantification (minimal signal intensity required to estimate target concentration), making it challenging to interpret results in a quantitative manner while accounting for error. In response, a Bayesian statistic based Fecal Score (FS) approach was developed that estimates the weighted average concentration of a fecal source identification genetic marker across a defined group of samples, mathematically incorporating qPCR measurements from all samples. Yet, implementation is technically demanding and computationally intensive requiring specialized training, the use of expert software, and access to high performance computing. To address these limitations, this study reports a novel approximation model for FS determination based on a frequentist approach. The performance of the Bayesian and Frequentist models are compared using fecal source identification qPCR data representative of different 'censored' data scenarios from a recently published study focusing on the impact of stormwater discharge in urban streams. In addition, data set eligibility recommendations for the responsible use of these models are presented. Findings indicate that the Frequentist model can generate similar average concentrations and uncertainty estimates for FS, compared to the original Bayesian approach. The Frequentist model should make calculations less computationally and technically intensive, allowing for the development of easier to use data analysis tools for fecal source identification applications.
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Affiliation(s)
- Mano Sivaganesan
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Jessica R Willis
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Adam Diedrich
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA
| | - Orin C Shanks
- U.S. Environmental Protection Agency, Office of Research and Development, Cincinnati, OH 45268, USA.
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14
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Jiang M, Wang ALW, Be NA, Mulakken N, Nelson KL, Kantor RS. Evaluation of the Impact of Concentration and Extraction Methods on the Targeted Sequencing of Human Viruses from Wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:8239-8250. [PMID: 38690747 PMCID: PMC11097627 DOI: 10.1021/acs.est.4c00580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/03/2024]
Abstract
Sequencing human viruses in wastewater is challenging due to their low abundance compared to the total microbial background. This study compared the impact of four virus concentration/extraction methods (Innovaprep, Nanotrap, Promega, and Solids extraction) on probe-capture enrichment for human viruses followed by sequencing. Different concentration/extraction methods yielded distinct virus profiles. Innovaprep ultrafiltration (following solids removal) had the highest sequencing sensitivity and richness, resulting in the successful assembly of several near-complete human virus genomes. However, it was less sensitive in detecting SARS-CoV-2 by digital polymerase chain reaction (dPCR) compared to Promega and Nanotrap. Across all preparation methods, astroviruses and polyomaviruses were the most highly abundant human viruses, and SARS-CoV-2 was rare. These findings suggest that sequencing success can be increased using methods that reduce nontarget nucleic acids in the extract, though the absolute concentration of total extracted nucleic acid, as indicated by Qubit, and targeted viruses, as indicated by dPCR, may not be directly related to targeted sequencing performance. Further, using broadly targeted sequencing panels may capture viral diversity but risks losing signals for specific low-abundance viruses. Overall, this study highlights the importance of aligning wet lab and bioinformatic methods with specific goals when employing probe-capture enrichment for human virus sequencing from wastewater.
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Affiliation(s)
- Minxi Jiang
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Audrey L. W. Wang
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Nicholas A. Be
- Physical
and Life Sciences Directorate, Lawrence
Livermore National Laboratory, Livermore, California 94550, United States
| | - Nisha Mulakken
- Computing
and Global Security Directorates, Lawrence
Livermore National Laboratory, Livermore, California 94550, United States
| | - Kara L. Nelson
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
| | - Rose S. Kantor
- Department
of Civil and Environmental Engineering, University of California, Berkeley, California 94720, United States
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15
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Grünwald NJ, Bock CH, Chang JH, De Souza AA, Ponte EMD, du Toit LJ, Dorrance AE, Dung J, Gent D, Goss EM, Lowe-Power TM, Madden LV, Martin FN, McDowell J, Naegele RP, Potnis N, Quesada-Ocampo LM, Sundin GW, Thiessen L, Vinatzer BA, Zeng Q. Open Access and Reproducibility in Plant Pathology Research: Guidelines and Best Practices. PHYTOPATHOLOGY 2024; 114:910-916. [PMID: 38330057 DOI: 10.1094/phyto-12-23-0483-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
The landscape of scientific publishing is experiencing a transformative shift toward open access, a paradigm that mandates the availability of research outputs such as data, code, materials, and publications. Open access provides increased reproducibility and allows for reuse of these resources. This article provides guidance for best publishing practices of scientific research, data, and associated resources, including code, in The American Phytopathological Society journals. Key areas such as diagnostic assays, experimental design, data sharing, and code deposition are explored in detail. This guidance aligns with that observed by other leading journals. We hope the information assembled in this paper will raise awareness of best practices and enable greater appraisal of the true effects of biological phenomena in plant pathology.
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Affiliation(s)
- Niklaus J Grünwald
- U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR 97331, U.S.A
| | - Clive H Bock
- U.S. Department of Agriculture-Agricultural Research Service, Southeastern Fruit and Tree Nut Research Station, Byron, GA 31008, U.S.A
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, U.S.A
| | | | - Emerson M Del Ponte
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Lindsey J du Toit
- Department of Plant Pathology, Washington State University, Mount Vernon, WA 98273, U.S.A
| | - Anne E Dorrance
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, U.S.A
| | - Jeremiah Dung
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research and Extension Center, Oregon State University, Madras, OR 97741, U.S.A
| | - David Gent
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331, U.S.A
| | - Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, U.S.A
| | - Tiffany M Lowe-Power
- Department of Plant Pathology, University of California Davis, Davis, CA 95616, U.S.A
| | - Laurence V Madden
- Department of Plant Pathology, College of Food, Agricultural and Environmental Sciences, The Ohio State University, Wooster, OH 44691, U.S.A
| | - Frank N Martin
- U.S. Department of Agriculture-Agricultural Research Service, Crop Protection and Improvement Research Center, Salinas, CA 93905, U.S.A
| | - John McDowell
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Rachel P Naegele
- U.S. Department of Agriculture-Agricultural Research Service, Sugarbeet and Bean Research Unit, East Lansing, MI 48824, U.S.A
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, U.S.A
| | - Lina M Quesada-Ocampo
- Department of Entomology and Plant Pathology and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27606, U.S.A
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Lindsey Thiessen
- Domestic and Emergency Scientific Support, U.S. Department of Agriculture-Animal & Plant Health Inspection Service-Plant Protection and Quarantine, Raleigh, NC 27606, U.S.A
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, U.S.A
| | - Quan Zeng
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT 06511, U.S.A
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16
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Xi BX, Cui XN, Shang SQ, Li GW, Dewer Y, Li CN, Hu GX, Wang Y. Antennal Transcriptome Evaluation and Analysis for Odorant-Binding Proteins, Chemosensory Proteins, and Suitable Reference Genes in the Leaf Beetle Pest Diorhabda rybakowi Weise (Coleoptera: Chrysomelidae). INSECTS 2024; 15:251. [PMID: 38667381 PMCID: PMC11050234 DOI: 10.3390/insects15040251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/14/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024]
Abstract
Diorhabda rybakowi Weise is one of the dominant pests feeding on Nitraria spp., a pioneer plant used for windbreaking and sand fixation purposes, and poses a threat to local livestock and ecosystems. To clarify the key olfactory genes of D. rybakowi and provide a theoretical basis for attractant and repellent development, the optimal reference genes under two different conditions (tissue and sex) were identified, and the bioinformatics and characterization of the tissue expression profiles of two categories of soluble olfactory proteins (OBPs and CSPs) were investigated. The results showed that the best reference genes were RPL13a and RPS18 for comparison among tissues, and RPL19 and RPS18 for comparison between sexes. Strong expressions of DrybOBP3, DrybOBP6, DrybOBP7, DrybOBP10, DrybOBP11, DrybCSP2, and DrybCSP5 were found in antennae, the most important olfactory organ for D. rybakowi. These findings not only provide a basis for further in-depth research on the olfactory molecular mechanisms of host-specialized pests but also provide a theoretical basis for the future development of new chemical attractants or repellents using volatiles to control D. rybakowi.
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Affiliation(s)
- Bo-Xin Xi
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (B.-X.X.); (Y.W.)
| | - Xiao-Ning Cui
- Key Laboratory for Grassland Ecosystem of Education Ministry, College of Pratacultural, Gansu Agricultural University, Lanzhou 730070, China; (C.-N.L.); (G.-X.H.)
| | - Su-Qin Shang
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (B.-X.X.); (Y.W.)
| | - Guang-Wei Li
- College of Life Science, Yan’an University, Yan’an 716000, China;
| | - Youssef Dewer
- Phytotoxicity Research Department, Central Agricultural Pesticide Laboratory, Agricultural Research Center, 7 Nadi El-Seid Street, Giza 12618, Egypt;
| | - Chang-Ning Li
- Key Laboratory for Grassland Ecosystem of Education Ministry, College of Pratacultural, Gansu Agricultural University, Lanzhou 730070, China; (C.-N.L.); (G.-X.H.)
| | - Gui-Xin Hu
- Key Laboratory for Grassland Ecosystem of Education Ministry, College of Pratacultural, Gansu Agricultural University, Lanzhou 730070, China; (C.-N.L.); (G.-X.H.)
| | - Yan Wang
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou 730070, China; (B.-X.X.); (Y.W.)
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17
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Bustin SA. Improving the quality of quantitative polymerase chain reaction experiments: 15 years of MIQE. Mol Aspects Med 2024; 96:101249. [PMID: 38290180 DOI: 10.1016/j.mam.2024.101249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/02/2024] [Accepted: 01/15/2024] [Indexed: 02/01/2024]
Abstract
The quantitative polymerase chain reaction (qPCR) is fundamental to molecular biology. It is not just a laboratory technique, qPCR is a bridge between research and clinical practice. Its theoretical foundations guide the design of experiments, while its practical implications extend to diagnostics, treatment, and research advancements in the life sciences, human and veterinary medicine, agriculture, and forensics. However, the accuracy, reliability and reproducibility of qPCR data face challenges arising from various factors associated with experimental design, execution, data analysis and inadequate reporting details. Addressing these concerns, the Minimum Information for the Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines have emerged as a cohesive framework offering a standardised set of recommendations that describe the essential information required for assessing qPCR experiments. By emphasising the importance of methodological rigour, the MIQE guidelines have made a major contribution to improving the trustworthiness, consistency, and transparency of many published qPCR results. However, major challenges related to awareness, resources, and publication pressures continue to affect their consistent application.
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Affiliation(s)
- Stephen A Bustin
- Medical Technology Research Centre, Anglia Ruskin University, Chelmsford, Essex, CM1 1SQ, UK.
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18
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Espira LM, Contreras JD, Felix-Arellano EE, Siebe C, Mazari-Hiriart M, Riojas-Rodríguez H, Eisenberg JNS. A comparative analysis of regional infection risk due to wastewater recontamination in the Mezquital Valley, Mexico. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170615. [PMID: 38316303 DOI: 10.1016/j.scitotenv.2024.170615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/07/2024]
Abstract
Urban wastewater reuse for agriculture provides reliable nutrient-rich water, reduces water stress, and strengthens food systems. However, wastewater reuse also presents health risks and characterizing the spatial dynamics of wastewater can help optimize risk mitigation. We conducted comparative risk analysis of exposure to wastewater in irrigation canals, where we compared those exposed to a) treated vs. untreated wastewater, and b) wastewater upstream vs. downstream from communities in the Mezquital Valley. The canal system with treated wastewater was sampled prior to being treated, directly after treatment, as well as before and after it flowed through a community. Along the canal system that carried untreated wastewater, we sampled before and after a community. We quantified the concentrations of bacterial, protozoal, and viral pathogens in the wastewater. Pathogen concentration data were used to calculate measures of relative risk between sampling points. Wastewater treatment reduced predicted bacterial pathogen infection risk in post-treatment locations (RR = 0.73, 95 % CI 0.61, 0.87), with no evidence of similar reductions in Giardia or viral pathogens (RR = 1.02, 95 % CI 0.56, 1.86 and RR = 1.18, 95 % CI 0.70, 2.02 respectively). Although infection risk decreased further down the canals, infection risk increased for bacterial pathogens after our sentinel community (RR = 1.94, 95 % 1.34, 2.86). For Giardia and viral pathogens infection risk was elevated but not significantly. We found similar evidence for increases in risk when comparing the treated section of the canal system with a canal section whose wastewater was not treated, i.e., the risk benefits of wastewater treatment were lost after our sentinel community for bacteria (RR = 5.27 vs. 2.08 for sampling points before and after our sentinel community respectively) and for Giardia (RR = 6.98 vs. 3.35 respectively). The increase in risk after transit through communities could have resulted from local community recontamination of the treated wastewater stream.
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Affiliation(s)
- Leon M Espira
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Jesse D Contreras
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48109, United States of America
| | - Eunice E Felix-Arellano
- Dirección de Salud Ambiental, Instituto Nacional de Salud Pública, Universidad No. 655 Colonia Santa María Ahuacatitlán, Cerrada Los Pinos y Caminera, 62100 Cuernavaca, Morelos, Mexico
| | - Christina Siebe
- Instituto de Geología, Universidad Nacional Autonóma de México, Circuito de la Investigación Científica s/n, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Marisa Mazari-Hiriart
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Circuito Exterior s/n. Anexo Jardín Botanico Exterior, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Horacio Riojas-Rodríguez
- Dirección de Salud Ambiental, Instituto Nacional de Salud Pública, Universidad No. 655 Colonia Santa María Ahuacatitlán, Cerrada Los Pinos y Caminera, 62100 Cuernavaca, Morelos, Mexico
| | - Joseph N S Eisenberg
- Department of Epidemiology, University of Michigan, Ann Arbor, MI 48109, United States of America.
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19
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Gross M, Dunthorn M, Mauvisseau Q, Stoeck T. Using digital PCR to predict ciliate abundance from ribosomal RNA gene copy numbers. Environ Microbiol 2024; 26:e16619. [PMID: 38649189 DOI: 10.1111/1462-2920.16619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/16/2024] [Indexed: 04/25/2024]
Abstract
Ciliates play a key role in most ecosystems. Their abundance in natural samples is crucial for answering many ecological questions. Traditional methods of quantifying individual species, which rely on microscopy, are often labour-intensive, time-consuming and can be highly biassed. As a result, we investigated the potential of digital polymerase chain reaction (dPCR) for quantifying ciliates. A significant challenge in this process is the high variation in the copy number of the taxonomic marker gene (ribosomal RNA [rRNA]). We first quantified the rRNA gene copy numbers (GCN) of the model ciliate, Paramecium tetraurelia, during different stages of the cell cycle and growth phases. The per-cell rRNA GCN varied between approximately 11,000 and 130,000, averaging around 50,000 copies per cell. Despite these variations in per-cell rRNA GCN, we found a highly significant correlation between GCN and cell numbers. This is likely due to the coexistence of different cellular stages in an uncontrolled (environmental) ciliate population. Thanks to the high sensitivity of dPCR, we were able to detect the target gene in a sample that contained only a single cell. The dPCR approach presented here is a valuable addition to the molecular toolbox in protistan ecology. It may guide future studies in quantifying and monitoring the abundance of targeted (even rare) ciliates in natural samples.
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Affiliation(s)
- Megan Gross
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Micah Dunthorn
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Thorsten Stoeck
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
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20
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Hunter-Schlichting DN, Vogel RI, Geller MA, Nelson HH. Quantification of low-level human cytomegalovirus and Epstein-Barr virus DNAemia by digital PCR. J Virol Methods 2024; 325:114876. [PMID: 38184072 DOI: 10.1016/j.jviromet.2023.114876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/13/2023] [Accepted: 12/31/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND Digital PCR (dPCR) can quantify cell-free viral DNA (DNAemia), a biomarker of active viral infection. To accelerate epidemiologic investigation into low-level viral reactivation in chronic disease, we have evaluated the performance of dPCR to detect cytomegalovirus (CMV) and Epstein-Barr virus (EBV) DNAemia across platforms and blood matrices. METHODS The droplet-based (BioRad) dPCR platform performance was compared to chip-based (BioMark), and assay validation followed dMIQE guidelines. CMV and EBV DNA reference materials were spiked into known negative plasma and serum samples. In addition, two independent cohorts of ovarian cancer patients were evaluated for viral DNAemia (n = 65 serum and 79 plasma samples). RESULTS The limit of quantification (LOQ) was at or slightly above 100 copies/mL for both instruments: 105-135 copies/mL for droplet-based detection and 100 copies/mL for chip-based detection. DNAemia in serum had a slightly lower LOQ (105-110 copies/mL) compared to plasma (LOQ; 115-135 copies/mL). The variation (CV) coefficients for each assay and machine were less than 5 %. In patient samples, CVs ranged from 4.5 - 7.4 % and were similar for cell-free DNA derived from serum or plasma. There was good correlation between DNAemia measurements in patient samples across dPCR platforms (r > 0.90 for each assay and matrix). CONCLUSION dPCR can quantify low-level herpes virus DNAemia with CVs below 8 %. Our results indicate that using serum-derived cell-free DNA and droplet-based dPCR is optimal for quantitating low-level viral DNAemia; however, plasma and chip-based approaches are acceptable alternatives and suitable for epidemiologic investigation.
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Affiliation(s)
- DeVon N Hunter-Schlichting
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States; Division of Epidemiology and Clinical Research, University of Minnesota, Minneapolis, MN, United States
| | - Rachel I Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States; Department of Obstetrics, Gynecology and Women's Health, School of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Melissa A Geller
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States; Department of Obstetrics, Gynecology and Women's Health, School of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Heather H Nelson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States; Division of Epidemiology and Clinical Research, University of Minnesota, Minneapolis, MN, United States.
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21
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Cleveland MH, He HJ, Milavec M, Bae YK, Vallone PM, Huggett JF. Digital PCR for the characterization of reference materials. Mol Aspects Med 2024; 96:101256. [PMID: 38359699 DOI: 10.1016/j.mam.2024.101256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
Well-characterized reference materials support harmonization and accuracy when conducting nucleic acid-based tests (such as qPCR); digital PCR (dPCR) can measure the absolute concentration of a specific nucleic acid sequence in a background of non-target sequences, making it ideal for the characterization of nucleic acid-based reference materials. National Metrology Institutes are increasingly using dPCR to characterize and certify their reference materials, as it offers several advantages over indirect methods, such as UV-spectroscopy. While dPCR is gaining widespread adoption, it requires optimization and has certain limitations and considerations that users should be aware of when characterizing reference materials. This review highlights the technical considerations of dPCR, as well as its role when developing and characterizing nucleic acid-based reference materials.
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Affiliation(s)
- Megan H Cleveland
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA.
| | - Hua-Jun He
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Young-Kyung Bae
- Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
| | - Peter M Vallone
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Jim F Huggett
- National Measurement Laboratory (NML), LGC, Queens Road, Teddington, TW11 0LY, Middlesex, UK; School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK
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22
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Vasseur A, Cabel L, Hego C, Takka W, Trabelsi Grati O, Renouf B, Lerebours F, Loirat D, Brain E, Cottu P, Sablin MP, Pierga JY, Callens C, Renault S, Bidard FC. Fulvestrant and everolimus efficacy after CDK4/6 inhibitor: a prospective study with circulating tumor DNA analysis. Oncogene 2024; 43:1214-1222. [PMID: 38413796 PMCID: PMC11014798 DOI: 10.1038/s41388-024-02986-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/29/2024]
Abstract
In a prospective study (NCT02866149), we assessed the efficacy of fulvestrant and everolimus in CDK4/6i pre-treated mBC patients and circulating tumor DNA (ctDNA) changes throughout therapy. Patients treated with fulvestrant and everolimus had their ctDNA assessed at baseline, after 3-5 weeks and at disease progression. Somatic mutations were identified in archived tumor tissues by targeted NGS and tracked in cell-free DNA by droplet digital PCR. ctDNA detection was then associated with clinicopathological characteristics and patients' progression-free survival (PFS), overall survival (OS) and best overall response (BOR). In the 57 included patients, median PFS and OS were 6.8 (95%CI [5.03-11.5]) and 38.2 (95%CI [30.0-not reached]) months, respectively. In 47 response-evaluable patients, BOR was a partial response or stable disease in 15 (31.9%) and 11 (23.4%) patients, respectively. Among patients with trackable somatic mutation and available plasma sample, N = 33/47 (70.2%) and N = 19/36 (52.8%) had ctDNA detected at baseline and at 3 weeks, respectively. ctDNA detection at baseline and PIK3CA mutation had an adverse prognostic impact on PFS and OS in multivariate analysis. This prospective cohort study documents the efficacy of fulvestrant and everolimus in CDK4/6i-pretreated ER + /HER2- mBC and highlights the clinical validity of early ctDNA changes as pharmacodynamic biomarker.
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Affiliation(s)
- Antoine Vasseur
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Luc Cabel
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Caroline Hego
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Wissam Takka
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France
| | - Olfa Trabelsi Grati
- Department of Genetics, Institut Curie, Paris Sciences & Lettres University, Paris, France
| | | | - Florence Lerebours
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Delphine Loirat
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Etienne Brain
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Paul Cottu
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Marie-Paule Sablin
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Jean-Yves Pierga
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
- Université Paris Cité, Paris, France
| | - Céline Callens
- Department of Genetics, Institut Curie, Paris Sciences & Lettres University, Paris, France
| | - Shufang Renault
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France.
| | - François-Clément Bidard
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France.
- Circulating Tumor Biomarkers Laboratory, INSERM CIC BT-1428, Institut Curie, Paris, France.
- UVSQ, Paris-Saclay University, Saint Cloud, France.
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23
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Terp SK, Pedersen IS, Stoico MP. Extraction of Cell-Free DNA: Evaluation of Efficiency, Quantity, and Quality. J Mol Diagn 2024; 26:310-319. [PMID: 38336350 DOI: 10.1016/j.jmoldx.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 02/12/2024] Open
Abstract
Cell-free DNA (cfDNA) serves as a valuable biomarker for early disease detection and monitoring. However, the use of cfDNA for analysis faces challenges owing to general low but variable abundance and fragmentation. Preanalytical factors, including cfDNA extraction, impact cfDNA quality and quantity. Efficient and robust cfDNA extraction is essential for reliable results in downstream applications, and various commercial extraction methods exist, each with trade-offs. To aid researchers and clinicians in choosing the proper cfDNA extraction method, manual, semiautomated, and automated methods were evaluated, including the QIAamp Circulating Nucleic Acid Kit (manual and QIAcube), QIAamp MinElute ccfDNA Kit (QIAcube), and QIAsymphony DSP Circulating DNA Kit (QIAsymphony). For each extraction method, cfDNA was extracted on two separate days, using samples obtained from 18 healthy donors. This study assessed extraction efficiency, quantity, and quality using droplet digital PCR and TapeStation. The QIAamp Circulating Nucleic Acid Kit, both manual and semiautomated, outperformed the QIAamp MinElute ccfDNA Kit (QIAcube) and QIAsymphony DSP Circulating DNA Kit (QIAsymphony), showing higher recovery rates and cfDNA quantity. All methods were reproducible, with no day-to-day variability and no contamination by high-molecular-weight DNA. The QIAamp Circulating Nucleic Acid Kit offers high yield without compromising quality. Implementation of the method should consider specific study and clinical needs, taking into account each method's advantages and limitations for optimal outcomes.
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Affiliation(s)
- Simone K Terp
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
| | - Inge S Pedersen
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Malene P Stoico
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark; Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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24
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Zhang J, Zhong H, Xuan N, Mushtaq R, Shao Y, Cao X, Wang P, Chen G. The Na + /Ca 2+ antiporter slr0681 affects carotenoid production in Synechocystis sp. PCC 6803 under high-light stress. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:3147-3155. [PMID: 38072645 DOI: 10.1002/jsfa.13205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 12/22/2023]
Abstract
BACKGROUND Carotenoids play key roles in photosynthesis and are widely used in foods as natural pigments, antioxidants, and health-promoting compounds. Enhancing carotenoid production in microalgae via biotechnology has become an important area of research. RESULTS We knocked out the Na+ /Ca2+ antiporter gene slr0681 in Synechocystis sp. PCC 6803 via homologous recombination and evaluated the effects on carotenoid production under normal (NL) and high-light (HL) conditions. On day 7 of NL treatment in calcium ion (Ca2+ )-free medium, the cell density of Δslr0681 decreased by 29% compared to the wild type (WT). After 8 days of HL treatment, the total carotenoid contents decreased by 35% in Δslr0681, and the contents of individual carotenoids were altered: myxoxanthophyll, echinenone, and β-carotene contents increased by 10%, 50%, and 40%, respectively, while zeaxanthin contents decreased by ~40% in Δslr0681 versus the WT. The expression patterns of carotenoid metabolic pathway genes also differed: ipi expression increased by 1.2- to 8.5-fold, whereas crtO and crtR expression decreased by ~90% and 60%, respectively, in ∆slr0681 versus the WT. In addition, in ∆slr0681, the expression level of psaB (encoding a photosystem I structural protein) doubled, whereas the expression levels of the photosystem II genes psbA2 and psbD decreased by ~53% and 84%, respectively, compared to the WT. CONCLUSION These findings suggest that slr0681 plays important roles in regulating carotenoid biosynthesis and structuring of the photosystems in Synechocystis sp. This study provides a theoretical basis for the genetic engineering of microalgae photosystems to increase their economic benefits and lays the foundation for developing microalgae germplasm resources with high carotenoid contents. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Jiaye Zhang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- School of Life Sciences, Shandong Normal University, Jinan, China
| | - Huairong Zhong
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Ning Xuan
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Rubina Mushtaq
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Yahui Shao
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Xue Cao
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- School of Life Sciences, Shandong Normal University, Jinan, China
| | - Pengchong Wang
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Gao Chen
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
- Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
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25
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Tanvetthayanont P, Yata T, Boonnil J, Temisak S, Ponglowhapan S. Advancing canine mammary tumor diagnostics: Unraveling the diagnostic potential of Cytokeratin 19 through droplet digital PCR analysis. Theriogenology 2024; 217:127-135. [PMID: 38271766 DOI: 10.1016/j.theriogenology.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/13/2024] [Accepted: 01/14/2024] [Indexed: 01/27/2024]
Abstract
Cytokeratin 19 (CK19) is a complex intracytoplasmic cytoskeletal protein primarily localized in the ducts of the mammary gland and skin epithelial cells. In humans, the expression of CK19 gene within circulating tumor cells (CTCs) extracted from blood samples of breast cancer patients reflects tumor cell activity, offering valuable insights for predicting early metastatic relapse or monitoring treatment effectiveness. However, knowledge of serum tumor markers is limited in veterinary oncology. Recently, droplet digital PCR (ddPCR), has been employed to explore rare target genes due to its heightened sensitivity and accuracy as a novel molecular diagnostic tool. The objectives of this study were to investigate the expression of the CK19 mRNA in CTCs, non-neoplastic mammary tissues, and both benign and malignant canine mammary tumors (CMTs) through ddPCR analysis. In Study I, we optimized the discard volume for blood samples to reduce CK19 contamination from skin epithelial cells post-venipuncture. The results revealed that discarding the initial 3 mL of blood was adequate and effective in eliminating CK19 mRNA contamination. In Study II, after the removal of the initial 3 mL of blood, we investigated CK19 mRNA-positive CTCs in the peripheral blood of normal healthy dogs, including those with benign and malignant CMTs. Intriguingly, CK19 mRNA was undetectable in all blood samples. The expression of CK19 mRNA in mammary tissues was investigated in Study III. The copy number (CN) ratios of the CK19 gene in non-neoplastic mammary tissues (14.77 ± 14.65) were significantly higher (P < 0.05) than those in benign (4.23 ± 3.35) and malignant groups (6.56 ± 5.64). Notably, no difference was observed between the benign and malignant groups. In conclusion, CK19 mRNA appeared unlikely to be a suitable candidate as a biomarker in the peripheral blood of CMTs, while the CN ratio in mammary tissues could serve as a potential discriminator between non-neoplastic and CMT groups, complementing the gold standard of histopathological examination.
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Affiliation(s)
- Potsawat Tanvetthayanont
- Department of Obstetric Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Teerapong Yata
- Unit of Biochemistry, Department of Physiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jiranun Boonnil
- National Institute of Metrology (NIMT), Pathumthani, 12120, Thailand
| | - Sasithon Temisak
- National Institute of Metrology (NIMT), Pathumthani, 12120, Thailand.
| | - Suppawiwat Ponglowhapan
- Department of Obstetric Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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Zhou Y, Wang Y, Song M, Jiang L, Sun C, Wang S, Yao H, Wang Z, Wang X, Liu C, Luo H, Song F. A high-throughput droplet digital PCR system aiming eight DNA methylation targets for age prediction. J Pharm Biomed Anal 2024; 240:115943. [PMID: 38181558 DOI: 10.1016/j.jpba.2023.115943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/19/2023] [Accepted: 12/23/2023] [Indexed: 01/07/2024]
Abstract
The droplet digital Polymerase Chain Reaction (ddPCR) has garnered recognition for its distinctive attribute of absolute quantification. And it has found practical utility in age prediction through DNA methylation profiles. However, a prevalent limitation in current ddPCR methodologies is the restricted capacity to detect only two targets concurrently in most instruments, leading to high costs, sample wastage, and labor-intensive procedures. To address the limitations, a novel high-throughput ddPCR system allowing for the simultaneous detection of eight targets was developed. Through the implementation of a new 8-plex ddPCR assay, coupled with comprehensive linear regression analyses involving primers and probes ratios, diverse inputs of single CpG sites with distinct primers and probes, and varying plex assay configurations, stable DNA methylation values for four CpGs and stable measurement precisions for distinct multiplex systems were consistently observed. These findings pave the way for advancing the field of chemistry science by enabling more efficient and cost-effective methods. Furthermore, the comparative validation of ddPCR and SNaPshot demonstrated a remarkable concordance in results, and the system also displayed well in the field of various aspects, including species specificity, DNA input, and aged samples. In this study, the recommended input of bisulfite-converted DNA was determined to be 10-50 ng due to the double-positive droplets. Notably, the Pearson correlation coefficient squared values of four CpGs were 0.4878 (ASPA), 0.4832 (IGSF1), 0.6881 (COL1A1), and 0.6475 (MEIS1-AS3). And the testing set exhibited a mean absolute error of 4.5923 years, indicating the robustness and accuracy of the age-predictive model.
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Affiliation(s)
- Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yanyun Wang
- Laboratory of Molecular Translational Medicine, West China Second University Hospital, Sichuan University, China
| | - Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, China; Med+ Molecular Diagnostics Institute of West China Hospital/West China School of Medicine, China
| | - Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Chaoran Sun
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shuangshuang Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Hewen Yao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zefei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xindi Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Chunhui Liu
- Scientific Support Center, Sniper Medical Technologies Co., Ltd., Suzhou 215000, China
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Turski MK, Albertolle ME. Utilizing droplet digital polymerase chain reaction for siRNA quantitation in rodent plasma and tissue via stem-loop reverse transcription. Bioanalysis 2024; 16:375-388. [PMID: 38380639 DOI: 10.4155/bio-2023-0228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
Background: siRNA is a promising therapeutic modality highlighted by several US FDA approvals since 2018, with many more oligonucleotide assets in clinical development. To support siRNA discovery and development, robust and sensitive quantitative platforms for bioanalysis must be established to assess pharmacokinetic/pharmacodynamic relationships and toxicology. Droplet digital PCR offers improved sensitivity and throughput, as well as reduced susceptibility to matrix effects, compared with other analytical platforms. Methodology: The authors developed a stem-loop reverse transcription droplet digital PCR method to measure siRNA in mouse plasma and liver extract using bioanalytical method qualification guidelines. Conclusion: This newly developed assay has been demonstrated to be a superior alternative to other platforms, with the added benefit of greater sensitivity, with dynamic range from 390 to 400,000 copies/reaction and readiness for FDA investigational new drug-enabling applications.
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Affiliation(s)
- Megan K Turski
- Global Drug Metabolism. Pharmacokinetics & Modeling, Takeda Development Center Americas, San Diego, CA, USA
| | - Matthew E Albertolle
- Global Drug Metabolism. Pharmacokinetics & Modeling, Takeda Development Center Americas, San Diego, CA, USA
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28
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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] [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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29
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Malla B, Shrestha S, Haramoto E. Optimization of the 5-plex digital PCR workflow for simultaneous monitoring of SARS-CoV-2 and other pathogenic viruses in wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169746. [PMID: 38159741 DOI: 10.1016/j.scitotenv.2023.169746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Wastewater-based epidemiology is a valuable tool for monitoring pathogenic viruses in the environment, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). While quantitative polymerase chain reaction (qPCR) is widely used for pathogen surveillance in wastewater, it can be affected by inhibition and is limited to relative quantification. Digital PCR (dPCR) offers potential solutions to these limitations. In this study, a 5-plex dPCR workflow was optimized for the simultaneous detection of SARS-CoV-2, influenza A virus, enteroviruses (EnV), and noroviruses of genogroups I (NoV-GI) and GII (NoV-GII) in wastewater samples. Wastewater samples (n = 36) were collected from a wastewater treatment plant in Japan between August and October 2022. The optimization included the evaluation of singleplex and 5-plex dPCR assays, and two different concentration methods, extraction kits, and dPCR approaches. The performance of singleplex and 5-plex dPCR assays showed comparable linearity and reliability, with the 5-plex assays showing greater efficiency. The polyethylene glycol (PEG) precipitation method showed better performance over the centrifugation method, two-step reverse transcription (RT)-dPCR over the one-step RT-dPCR, and AllPrep PowerViral DNA/RNA Kit showed better performance than the QIAamp Viral RNA Mini Kit. The optimal workflow therefore included PEG precipitation, the AllPrep PowerViral DNA/RNA Kit, and two-step RT-dPCR. This workflow was selected to monitor the presence of SARS-CoV-2 and other pathogenic viruses in wastewater samples in a 5-plex dPCR approach, yielding promising results. SARS-CoV-2 RNA was detected in the majority of samples, with NoV-GI, NoV-GII, and EnV also being detected. The successful optimization and application of the 5-plex dPCR assay for pathogen surveillance in wastewater offers significant benefits, including enhanced community health assessment and more effective responses to public health threats.
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Affiliation(s)
- Bikash Malla
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Sadhana Shrestha
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Eiji Haramoto
- Interdisciplinary Center for River Basin Environment, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan.
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30
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Hays A, Wissel M, Colletti K, Soon R, Azadeh M, Smith J, Doddareddy R, Chalfant M, Adamowicz W, Ramaswamy SS, Dholakiya SL, Guelman S, Gullick B, Durham J, Rennier K, Nagilla P, Muruganandham A, Diaz M, Tierney C, John K, Valentine J, Lockman T, Liu HY, Moritz B, Ouedraogo JP, Piche MS, Smet M, Murphy J, Koenig K, Zybura A, Vyhlidal C, Mercier J, Jani N, Kubista M, Birch D, Morse K, Johansson O. Recommendations for Method Development and Validation of qPCR and dPCR Assays in Support of Cell and Gene Therapy Drug Development. AAPS J 2024; 26:24. [PMID: 38316745 DOI: 10.1208/s12248-023-00880-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/06/2023] [Indexed: 02/07/2024] Open
Abstract
The emerging use of qPCR and dPCR in regulated bioanalysis and absence of regulatory guidance on assay validations for these platforms has resulted in discussions on lack of harmonization on assay design and appropriate acceptance criteria for these assays. Both qPCR and dPCR are extensively used to answer bioanalytical questions for novel modalities such as cell and gene therapies. Following cross-industry conversations on the lack of information and guidelines for these assays, an American Association of Pharmaceutical Scientists working group was formed to address these gaps by bringing together 37 industry experts from 24 organizations to discuss best practices to gain a better understanding in the industry and facilitate filings to health authorities. Herein, this team provides considerations on assay design, development, and validation testing for PCR assays that are used in cell and gene therapies including (1) biodistribution; (2) transgene expression; (3) viral shedding; (4) and persistence or cellular kinetics of cell therapies.
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Affiliation(s)
- Amanda Hays
- BioAgilytix Laboratories, Durham, North Carolina, USA.
| | - Mark Wissel
- Eurofins Viracor BioPharma Services, Inc., Lenexa, Kansas, USA
| | | | - Russell Soon
- BioMarin Pharmaceutical Inc., Novato, California, USA
| | - Mitra Azadeh
- Ultragenyx Pharmaceutical Inc., Novato, Calfornia, USA
| | | | | | | | - Wendy Adamowicz
- PPD Clinical Research, Thermo Fisher Scientific, Richmond, Virginia, USA
| | | | | | | | - Bryan Gullick
- BioAgilytix Laboratories, Durham, North Carolina, USA
| | | | | | - Pruthvi Nagilla
- Asher Biotherapeutics, Inc., South San Francisco, California, USA
| | | | - Manisha Diaz
- Eurofins Viracor BioPharma Services, Inc., Lenexa, Kansas, USA
| | | | | | | | - Timothy Lockman
- PPD Clinical Research, Thermo Fisher Scientific, Richmond, Virginia, USA
| | - Hsing-Yin Liu
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | | | | | | | | | - Jacqueline Murphy
- Janssen Research & Development, LLC, Spring House, Pennsylvania, USA
| | - Kaylyn Koenig
- Altasciences Preclinical Seattle LLC, Everett, Washington, USA
| | - Agnes Zybura
- Labcorp Drug Development, Greenfield, Indiana, USA
| | - Carrie Vyhlidal
- KCAS Bioanalytical and Biomarker Services, Shawnee, Kansas, USA
| | | | - Niketa Jani
- BioAgilytix Laboratories, Boston, Massachusetts, USA
| | - Mikael Kubista
- Institute of Biotechnology Czech Academy of Sciences, Prague, Czech Republic
| | - Donald Birch
- Altasciences Preclinical Seattle LLC, Everett, Washington, USA
| | - Karlin Morse
- Altasciences Preclinical Seattle LLC, Everett, Washington, USA
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31
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Mokhtar NFK, Shun YQ, Raja Nhari RMH, Mohamad NA, Shahidan NM, Warsanah IH, Mohd Hashim A. Nanoplate-based digital PCR for highly sensitive pork DNA detection targeting multi-copy nuclear and mitochondrial genes. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2024; 41:120-133. [PMID: 38190283 DOI: 10.1080/19440049.2023.2298476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024]
Abstract
The inclusion of ingredients derived from pigs in highly processed consumer products poses a significant challenge for DNA-targeted analytical enforcement, which could be overcome by using digital PCR. However, most species detection methods use digital PCR to target single-copy nuclear genes, which limits their sensitivity. In this work, we examined the performance of a nanoplate-based digital PCR method that targets multi-copy nuclear (MPRE42) and mitochondrial (Cytb) genes. Poor separation of positive and negative partitions, as well as a 'rain effect' were obtained in the porcine-specific MPRE42 assay. Among the optimization strategies examined, the inclusion of restriction enzymes slightly improved the separation of positive and negative partitions, but a more extensive 'rain effect' was observed. The high copy number of the MPRE42 amplicon is hypothesized to contribute to the saturation of the positive signal. In contrast, the porcine-specific Cytb assay achieved perfect separation of positive and negative partitions with no 'rain effect'. This assay can detect as little as 0.4 pg of pork DNA, with a sensitivity of 0.05% (w/w) in a pork-chicken mixture, proving its applicability for detecting pork in meat and meat-based products. For the MPRE42 assay, potential applications in highly degraded products such as gelatin and lard are anticipated.
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Affiliation(s)
- Nur Fadhilah Khairil Mokhtar
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
| | | | - Raja Mohd Hafidz Raja Nhari
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nurhidayatul Asma Mohamad
- Laboratory of Halal Services, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
| | - Nur Maisarah Shahidan
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
| | - Irwan Hanish Warsanah
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Amalia Mohd Hashim
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, Serdang, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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32
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Chen X, Wang F, Fu Y, Huang L, Li F, Zhao H, Guan X, Li Q, Li Q, Wang Y, Guo Y, Xie Z. Development and evaluation of a multiplex digital PCR method for sensitive and accurate detection of respiratory pathogens in children. Virology 2024; 590:109948. [PMID: 38064870 DOI: 10.1016/j.virol.2023.109948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/09/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024]
Abstract
The emergence of multiplex digital polymerase chain reaction (dPCR) and other detection technologies for respiratory pathogens in recent years has facilitated greater understanding of respiratory virus epidemics. In this study, a multiplex dPCR method was developed and evaluated as a means of detecting five respiratory pathogens in children with acute lower respiratory tract infection (ALRTI). With 139 nasopharyngeal swabs collected from children with ALRTI, pathogens were detected using dPCR and quantitative real-time PCR (qPCR) methods. Of those specimens, dPCR detected 86 positive cases, while qPCR identified 84. Moreover, dPCR exhibited higher sensitivity than qPCR, and displayed no cross-reactivity with common respiratory pathogens. These findings suggest that dPCR-based method could become one of the most promising options for acute respiratory pathogen detection.
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Affiliation(s)
- Xiangpeng Chen
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Fang Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Yiliang Fu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Luci Huang
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Fei Li
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Hongwei Zhao
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Xiaolei Guan
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Qiuping Li
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Qi Li
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yilu Wang
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China.
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, Research Unit of Critical Infection in Children, Chinese Academy of Medical Sciences, 2019RU016, Laboratory of Infection and Virology, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.
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33
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Gokemeijer J, Balasubramanian N, Ogasawara K, Grudzinska-Goebel J, Upreti VV, Mody H, Kasar S, Vepachedu VR, Xu W, Gupta S, Tarcsa E, Dodge R, Herr K, Yang TY, Tourdot S, Jawa V. An IQ Consortium Perspective on Best Practices for Bioanalytical and Immunogenicity Assessment Aspects of CAR-T and TCR-T Cellular Therapies Development. Clin Pharmacol Ther 2024; 115:188-200. [PMID: 37983584 DOI: 10.1002/cpt.3111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/05/2023] [Indexed: 11/22/2023]
Abstract
CAR-T therapies have shown remarkable efficacy against hematological malignancies in the clinic over the last decade and new studies indicate that progress is being made to use these novel therapies to target solid tumors as well as treat autoimmune disease. Innovation in the field, including TCR-T, allogeneic or "off the shelf" CAR-T, and autoantigen/armored CAR-Ts are likely to increase the efficacy and applications of these therapies. The unique aspects of these cell-based therapeutics; patient-derived cells, intracellular expression, in vivo expansion, and phenotypic changes provide unique bioanalytical challenges to develop pharmacokinetic and immunogenicity assessments. The International Consortium for Innovation and Quality in Pharmaceutical Development (IQ) Translational and ADME Sciences Leadership Group (TALG) has brought together a group of industry experts to discuss and consider these challenges. In this white paper, we present the IQ consortium perspective on the best practices and considerations for bioanalytical and immunogenicity aspects toward the optimal development of CAR-T and TCR-T cell therapies.
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Affiliation(s)
- Jochem Gokemeijer
- Discovery Biotherapeutics, Bristol Myers Squibb, Cambridge, Massachusetts, USA
| | - Nanda Balasubramanian
- Clinical Pharmacology, Pharmacometrics & Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | - Ken Ogasawara
- Clinical Pharmacology, Pharmacometrics & Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
| | | | - Vijay V Upreti
- Clinical Pharmacology, Modeling & Simulation, Amgen, Inc., South San Francisco, California, USA
| | - Hardik Mody
- Clinical Pharmacology, Genentech Inc., South San Francisco, California, USA
| | - Siddha Kasar
- Oncology Precision & Translational Medicine, Takeda Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Venkata R Vepachedu
- Bioanalytical Discovery & Development Sciences, Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Weifeng Xu
- Preclinical Development, Bioanalytical, Merck & Co., Inc., Rahway, New Jersey, USA
| | - Swati Gupta
- Development Biological Sciences, Immunology, AbbVie, Irvine, California, USA
| | - Edit Tarcsa
- Abbvie Bioresearch Center, Worcester, Massachusetts, USA
| | - Robert Dodge
- Novartis Institutes for BioMedical Research, One Health Plaza, East Hanover, New Jersey, USA
| | - Kate Herr
- Bioanalytical Discovery & Development Sciences, Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Tong-Yuan Yang
- Bioanalytical Discovery & Development Sciences, Johnson & Johnson Innovative Medicine, Spring House, Pennsylvania, USA
| | - Sophie Tourdot
- BioMedicine Design, Pfizer Inc., Andover, Massachusetts, USA
| | - Vibha Jawa
- Clinical Pharmacology, Pharmacometrics & Bioanalysis, Bristol Myers Squibb, Lawrenceville, New Jersey, USA
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Xu Q, Li J, Zhang Z, Yang Q, Zhang W, Yao J, Zhang Y, Zhang Y, Guo Z, Li C, Li S, Zhang C, Wang C, Du L, Li C, Zhou L. Precise determination of reaction conditions for accurate quantification in digital PCR by real-time fluorescence monitoring within microwells. Biosens Bioelectron 2024; 244:115798. [PMID: 37924656 DOI: 10.1016/j.bios.2023.115798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/27/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023]
Abstract
Real-time digital polymerase chain reaction (qdPCR) provides enhanced precision in the field of molecular diagnostics by integrating absolute quantification with process information. However, the optimal reaction conditions are traditionally determined through multiple iterative of experiments. Therefore, we proposed a novel approach to precisely determine the optimal reaction conditions for qdPCR using a standard process, employing real-time fluorescence monitoring within microwells. The temperature-sensitive fluorophore intensity presented the real temperature of each microwell. This enabled us to determine the optimal denaturation and annealing time for qdPCR based on the corresponding critical temperatures derived from the melting curves and amplification efficiency, respectively. To confirm this method, we developed an ultrathin laminated chip (UTL chip) and chose a target that need to be absolutely quantitative. The UTL chip was designed using a fluid‒solid‒thermal coupling simulation model and exhibited a faster thermal response than a commercial dPCR chip. By leveraging our precise determination of reaction conditions and utilizing the UTL chip, 40 cycles of amplification were achieved within 18 min. This was accomplished by precisely controlling the denaturation temperature at 2 s and the annealing temperature at 10 s. Furthermore, the absolutely quantitative of DNA showed good correlation (R2 > 0.999) with the concentration gradient detection using the optimal reaction conditions with the UTL chip for qdPCR. Our proposed method can significantly improve the accuracy and efficiency of determining qdPCR conditions, which holds great promise for application in molecular diagnostics.
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Affiliation(s)
- Qi Xu
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Jinze Li
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Zhiqi Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Suzhou CASENS Co., Ltd, Suzhou, 215163, China
| | - Qi Yang
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Wei Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Suzhou CASENS Co., Ltd, Suzhou, 215163, China; Ji Hua Laboratory, Foshan, 528000, China
| | - Jia Yao
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Yaxin Zhang
- Department of Mechanical and Electric Engineering, Changchun University of Science and Technology, Changchun, 130022, China
| | - Yueye Zhang
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Zhen Guo
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Chao Li
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Shuli Li
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Changsong Zhang
- Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou, 215153, China
| | - Chuanxin Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250033, China
| | - Lutao Du
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Shandong Provincial Key Laboratory of Innovation Technology in Laboratory Medicine, Jinan, 250012, China.
| | - Chuanyu Li
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China.
| | - Lianqun Zhou
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Suzhou CASENS Co., Ltd, Suzhou, 215163, China.
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Regazzo D, Avallone S, MacSweeney CP, Sergeev E, Howe D, Godwood A, Bennett KA, Brown AJH, Barnes M, Occhi G, Barbot M, Faggian D, Tropeano MP, Losa M, Lasio G, Scaroni C, Pecori Giraldi F. A novel somatostatin receptor ligand for human ACTH - and GH -secreting pituitary adenomas. Eur J Endocrinol 2024; 190:K8-K16. [PMID: 38123488 DOI: 10.1093/ejendo/lvad171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/11/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
OBJECTIVE Somatostatin receptor ligands have come to play a pivotal role in the treatment of both ACTH- and GH-secreting pituitary adenomas. Clinical efficacy averages 30-50%, thus a considerable number of patients with Cushing's disease or acromegaly remain unresponsive to this therapeutic approach. HTL0030310 is a new somatostatin receptor ligand selective for subtype 5 over subtype 2, thus with a different receptor profile compared to clinical somatostatin receptor ligands. DESIGN Assessment of the effect of HTL0030310 on hormone secretion in human ACTH- and GH-secreting pituitary adenomas in vitro. METHODS Primary cultures from 3 ACTH-secreting and 5 GH-secreting pituitary adenomas were treated with 1, 10 and 100 nM HTL0030310 alone or with 10 nM CRH or GHRH, respectively. Parallel incubations with 10 nM pasireotide were also carried out. ACTH and GH secretion were assessed after 4 and 24 hour incubation; SSTR2, SSTR3, SSTR5, GH and POMC expression were evaluated after 24 hours. RESULTS HTL0030310 reduced unchallenged ACTH and POMC levels up to 50% in 2 ACTH-secreting adenomas and blunted CRH-stimulated ACTH/POMC by 20-70% in all 3 specimens. A reduction in spontaneous GH secretion was observed in 4 GH-secreting adenomas and in 2 specimens during GHRH co-incubation. SSTRs expression was detected in all specimens. CONCLUSIONS This first study on a novel somatostatin receptor 5-preferring ligand indicates that HTL0030310 can inhibit hormonal secretion in human ACTH- and GH-secreting pituitary adenomas. These findings suggest a potential new avenue for somatostatin ligands in the treatment of Cushing's disease and acromegaly.
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Affiliation(s)
- Daniela Regazzo
- Endocrinology Unit, University Hospital of Padova, Padua 35143
| | - Serena Avallone
- Endocrinology Unit, University Hospital of Padova, Padua 35143
- Department of Clinical and Molecular Science, Università Politecnica delle Marche, Ancona 60126
| | | | | | - David Howe
- Sosei Heptares, Cambridge, CB21 6DG, United Kingdom
| | - Alex Godwood
- Sosei Heptares, Cambridge, CB21 6DG, United Kingdom
| | | | | | - Matt Barnes
- Sosei Heptares, Cambridge, CB21 6DG, United Kingdom
| | - Gianluca Occhi
- Department of Biology, University of Padova, Padua 35143
| | - Mattia Barbot
- Endocrinology Unit, University Hospital of Padova, Padua 35143
| | - Diego Faggian
- Laboratory Medicine, Department of Medicine, University Hospital of Padova, Padua 35143
| | - Maria Pia Tropeano
- Department of Neurosurgery, Humanitas Clinical and Research Center IRCCS, Rozzano 20089
| | - Marco Losa
- Department of Neurosurgery, Ospedale San Raffaele, Milan 20132
| | - Giovanni Lasio
- Department of Neurosurgery, Humanitas Clinical and Research Center IRCCS, Rozzano 20089
| | - Carla Scaroni
- Endocrinology Unit, University Hospital of Padova, Padua 35143
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Masante L, Susin G, Baudet ML. Droplet Digital PCR for the Detection and Quantification of Bona Fide CircRNAs. Methods Mol Biol 2024; 2765:107-126. [PMID: 38381336 DOI: 10.1007/978-1-0716-3678-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
CircRNAs are covalently closed RNA molecules gaining increasing attention over the years. Initially considered mere splicing errors, circRNAs are now recognized as a novel class of endogenous, conserved RNAs, expressed in many different species. The unique structure, the low levels of expression, and the almost complete sequence overlap with the cognate linear RNA make their detection and quantification challenging. Moreover, it has become crucial to prove the circular nature of the targeted transcript and unequivocally distinguish the circRNA from its linear counterpart. Nowadays, the most widely used technique to quantify circRNA expression is real-time quantitative PCR (qPCR). However, in the particular case of quantification of circles, it shows several technical shortcomings which affect the accuracy of the quantification. To precisely assess circRNA expression level, droplet digital PCR (ddPCR) is rapidly taking over for the more popular qPCR. In this chapter, we describe the detailed procedure based on droplets partitioning to quantify both linear and circRNA abundancy and demonstrate the circularity of the transcript under study with high precision, in a single experiment.
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Affiliation(s)
- Linda Masante
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Giorgia Susin
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy
| | - Marie-Laure Baudet
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento, Italy.
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Lehtokari VL, Sagath L, Davis M, Ho D, Kiiski K, Kettunen K, Demczko M, Stein R, Vatta M, Winder TL, Shohet A, Orenstein N, Krcho P, Bohuš P, Huovinen S, Udd B, Pelin K, Laing NG, Wallgren-Pettersson C. A recurrent ACTA1 amino acid change in mosaic form causes milder asymmetric myopathy. Neuromuscul Disord 2024; 34:32-40. [PMID: 38142473 DOI: 10.1016/j.nmd.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/25/2023] [Accepted: 11/26/2023] [Indexed: 12/26/2023]
Abstract
We describe three patients with asymmetric congenital myopathy without definite nemaline bodies and one patient with severe nemaline myopathy. In all four patients, the phenotype had been caused by pathogenic missense variants in ACTA1 leading to the same amino acid change, p.(Gly247Arg). The three patients with milder myopathy were mosaic for their variants. In contrast, in the severely affected patient, the missense variant was present in a de novo, constitutional form. The grade of mosaicism in the three mosaic patients ranged between 20 % and 40 %. We speculate that the milder clinical and histological manifestations of the same ACTA1 variant in the patients with mosaicism reflect the lower abundance of mutant actin in their muscle tissue. Similarly, the asymmetry of body growth and muscle weakness may be a consequence of the affected cells being unevenly distributed. The partial improvement in muscle strength with age in patients with mosaicism might be due to an increased proportion over time of nuclei carrying and expressing two normal alleles.
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Affiliation(s)
- Vilma-Lotta Lehtokari
- Folkhälsan Research Center, 00290 Helsinki, Finland; Department of Medical and Clinical Genetics, Medicum, 00014 University of Helsinki, Finland.
| | - Lydia Sagath
- Folkhälsan Research Center, 00290 Helsinki, Finland; Department of Medical and Clinical Genetics, Medicum, 00014 University of Helsinki, Finland
| | - Mark Davis
- Department of Diagnostic Genomics, PathWest Laboratory Medicine WA, Nedlands WA 6009, SA
| | - Desiree Ho
- Department of Diagnostic Genomics, PathWest Laboratory Medicine WA, Nedlands WA 6009, SA
| | - Kirsi Kiiski
- Folkhälsan Research Center, 00290 Helsinki, Finland; Laboratory of Genetics, Division of Genetics and Clinical Pharmacology, HUS Diagnostic Center, 00029 Helsinki University Hospital and 00014 University of Helsinki, Helsinki, Finland
| | - Kaisa Kettunen
- Laboratory of Genetics, Division of Genetics and Clinical Pharmacology, HUS Diagnostic Center, 00029 Helsinki University Hospital and 00014 University of Helsinki, Helsinki, Finland
| | - Matthew Demczko
- Division of Diagnostic Referral Services, Nemours Children's Hospital, Wilmington, DE 19803, United States
| | - Riki Stein
- Genetics Unit, Schneider Children's Medical Center, Petach Tikva 4920235, Israel
| | - Matteo Vatta
- Invitae Corporation, San Francisco, CA 94103, United States
| | | | - Adi Shohet
- Genetics Unit, Schneider Children's Medical Center, Petach Tikva 4920235, Israel
| | - Naama Orenstein
- Genetics Unit, Schneider Children's Medical Center, Petach Tikva 4920235, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Peter Krcho
- Department of Neonatology, Pavol Jozef Safarik University, 041 80 Košice, Slovakia
| | - Peter Bohuš
- Department of Pathology, L. Pasteur University Hospital, 040 11 Košice, Slovakia
| | - Sanna Huovinen
- Department of Pathology, Fimlab Laboratories, Tampere University Hospital, 33101 Tampere, Finland
| | - Bjarne Udd
- Folkhälsan Research Center, 00290 Helsinki, Finland; Neuromuscular Research Center, Department of Neurology, Tampere University and University Hospital, 33520 Tampere, Finland; Department of Neurology, Vaasa Central Hospital, 65130 Vaasa, Finland
| | - Katarina Pelin
- Folkhälsan Research Center, 00290 Helsinki, Finland; Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, 00014 University of Helsinki, Finland
| | - Nigel G Laing
- Department of Diagnostic Genomics, PathWest Laboratory Medicine WA, Nedlands WA 6009, SA; Harry Perkins Institute of Medical Research, and University of Western Australia Centre for Medical Research, Nedlands Western Australia 6009, Australia
| | - Carina Wallgren-Pettersson
- Folkhälsan Research Center, 00290 Helsinki, Finland; Department of Medical and Clinical Genetics, Medicum, 00014 University of Helsinki, Finland
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Kahana-Edwin S, Torpy J, Cain LE, Mullins A, McCowage G, Woodfield SE, Vasudevan SA, Shea DPT, Minoche AE, Espinoza AF, Kummerfeld S, Goldstein LD, Karpelowsky J. Quantitative ctDNA Detection in Hepatoblastoma: Implications for Precision Medicine. Cancers (Basel) 2023; 16:12. [PMID: 38201440 PMCID: PMC10778269 DOI: 10.3390/cancers16010012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Hepatoblastoma is characterized by driver mutations in CTNNB1, making it an attractive biomarker for a liquid biopsy approach utilizing circulating tumor DNA (ctDNA). This prospective observational study sought to ascertain the feasibility of ctDNA detection in patients with hepatoblastoma and explore its associations with established clinical indicators and biomarkers, including serum Alpha-fetoprotein (AFP). We obtained 38 plasma samples and 17 tumor samples from 20 patients with hepatoblastoma. These samples were collected at various stages: 10 at initial diagnosis, 17 during neoadjuvant chemotherapy, 6 post-operatively, and 5 at disease recurrence. Utilizing a bespoke sequencing assay we developed called QUENCH, we identified single nucleotide variants and deletions in CTNNB1 ctDNA. Our study demonstrated the capability to quantitate ctDNA down to a variant allele frequency of 0.3%, achieving a sensitivity of 90% for patients at initial diagnosis, and a specificity of 100% at the patient level. Notably, ctDNA positivity correlated with tumor burden, and ctDNA levels exhibited associations with macroscopic residual disease and treatment response. Our findings provide evidence for the utility of quantitative ctDNA detection in hepatoblastoma management. Given the distinct detection targets, ctDNA and AFP-based stratification and monitoring approaches could synergize to enhance clinical decision-making. Further research is needed to elucidate the interplay between ctDNA and AFP and determine the optimal clinical applications for both methods in risk stratification and residual disease detection.
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Affiliation(s)
- Smadar Kahana-Edwin
- Children’s Cancer Research Unit, Kids Research, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - James Torpy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Lucy E. Cain
- Cancer Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Anna Mullins
- Cancer Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Geoffrey McCowage
- Cancer Centre for Children, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Sarah E. Woodfield
- Divisions of Pediatric Surgery and Surgical Research, Michael E. DeBakey Department of Surgery, Pediatric Surgical Oncology Laboratory, Texas Children’s Surgical Oncology Program, Texas Children’s Liver Tumor Program, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sanjeev A. Vasudevan
- Divisions of Pediatric Surgery and Surgical Research, Michael E. DeBakey Department of Surgery, Pediatric Surgical Oncology Laboratory, Texas Children’s Surgical Oncology Program, Texas Children’s Liver Tumor Program, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dan P. T. Shea
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Andre E. Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Andres F. Espinoza
- Divisions of Pediatric Surgery and Surgical Research, Michael E. DeBakey Department of Surgery, Pediatric Surgical Oncology Laboratory, Texas Children’s Surgical Oncology Program, Texas Children’s Liver Tumor Program, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Kummerfeld
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- St Vincent’s Clinical School, UNSW Sydney, Sydney, NSW 2217, Australia
| | - Leonard D. Goldstein
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- St Vincent’s Clinical School, UNSW Sydney, Sydney, NSW 2217, Australia
| | - Jonathan Karpelowsky
- Children’s Cancer Research Unit, Kids Research, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Paediatric Oncology and Thoracic Surgery, The Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Division of Child and Adolescent Health, The University of Sydney, Sydney, NSW 2050, Australia
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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] [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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Lorenzatti A, Piga EJ, Gismondi M, Binolfi A, Margarit E, Calcaterra N, Armas P. Genetic variations in G-quadruplex forming sequences affect the transcription of human disease-related genes. Nucleic Acids Res 2023; 51:12124-12139. [PMID: 37930868 PMCID: PMC10711447 DOI: 10.1093/nar/gkad948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/22/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023] Open
Abstract
Guanine-rich DNA strands can fold into non-canonical four-stranded secondary structures named G-quadruplexes (G4s). G4s folded in proximal promoter regions (PPR) are associated either with positive or negative transcriptional regulation. Given that single nucleotide variants (SNVs) affecting G4 folding (G4-Vars) may alter gene transcription, and that SNVs are associated with the human diseases' onset, we undertook a novel comprehensive study of the G4-Vars genome-wide (G4-variome) to find disease-associated G4-Vars located into PPRs. We developed a bioinformatics strategy to find disease-related SNVs located into PPRs simultaneously overlapping with putative G4-forming sequences (PQSs). We studied five G4-Vars disturbing in vitro the folding and stability of the G4s located into PPRs, which had been formerly associated with sporadic Alzheimer's disease (GRIN2B), a severe familiar coagulopathy (F7), atopic dermatitis (CSF2), myocardial infarction (SIRT1) and deafness (LHFPL5). Results obtained in cultured cells for these five G4-Vars suggest that the changes in the G4s affect the transcription, potentially contributing to the development of the mentioned diseases. Collectively, data reinforce the general idea that G4-Vars may impact on the different susceptibilities to human genetic diseases' onset, and could be novel targets for diagnosis and drug design in precision medicine.
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Affiliation(s)
- Agustín Lorenzatti
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
| | - Ernesto J Piga
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
| | - Mauro Gismondi
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, Rosario, Santa Fe, Argentina
| | - Andrés Binolfi
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica (PLABEM), Ocampo y Esmeralda, Rosario S200EZP, Santa Fe, Argentina
| | - Ezequiel Margarit
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, Rosario, Santa Fe, Argentina
| | - Nora B Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
| | - Pablo Armas
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Ocampo y Esmeralda, Rosario S2000EZP, Santa Fe, Argentina
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Wilhelm A, Schoth J, Meinert-Berning C, Bastian D, Blum H, Elsinga G, Graf A, Heijnen L, Ho J, Kluge M, Krebs S, Stange C, Uchaikina A, Dolny R, Wurzbacher C, Drewes JE, Medema G, Tiehm A, Ciesek S, Teichgräber B, Wintgens T, Weber FA, Widera M. Interlaboratory comparison using inactivated SARS-CoV-2 variants as a feasible tool for quality control in COVID-19 wastewater monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166540. [PMID: 37634730 DOI: 10.1016/j.scitotenv.2023.166540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/11/2023] [Accepted: 08/22/2023] [Indexed: 08/29/2023]
Abstract
Wastewater-based SARS-CoV-2 epidemiology (WBE) has proven as an excellent tool to monitor pandemic dynamics supporting individual testing strategies. WBE can also be used as an early warning system for monitoring the emergence of novel pathogens or viral variants. However, for a timely transmission of results, sophisticated sample logistics and analytics performed in decentralized laboratories close to the sampling sites are required. Since multiple decentralized laboratories commonly use custom in-house workflows for sample purification and PCR-analysis, comparative quality control of the analytical procedures is essential to report reliable and comparable results. In this study, we performed an interlaboratory comparison at laboratories specialized for PCR and high-throughput-sequencing (HTS)-based WBE analysis. Frozen reserve samples from low COVID-19 incidence periods were spiked with different inactivated authentic SARS-CoV-2 variants in graduated concentrations and ratios. Samples were sent to the participating laboratories for analysis using laboratory specific methods and the reported viral genome copy numbers and the detection of viral variants were compared with the expected values. All PCR-laboratories reported SARS-CoV-2 genome copy equivalents (GCE) for all spiked samples with a mean intra- and inter-laboratory variability of 19 % and 104 %, respectively, largely reproducing the spike-in scheme. PCR-based genotyping was, in dependence of the underlying PCR-assay performance, able to predict the relative amount of variant specific substitutions even in samples with low spike-in amount. The identification of variants by HTS, however, required >100 copies/ml wastewater and had limited predictive value when analyzing at a genome coverage below 60 %. This interlaboratory test demonstrates that despite highly heterogeneous isolation and analysis procedures, overall SARS-CoV-2 GCE and mutations were determined accurately. Hence, decentralized SARS-CoV-2 wastewater monitoring is feasible to generate comparable analysis results. However, since not all assays detected the correct variant, prior evaluation of PCR and sequencing workflows as well as sustained quality control such as interlaboratory comparisons are mandatory for correct variant detection.
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Affiliation(s)
- Alexander Wilhelm
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany
| | - Jens Schoth
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, D-45128 Essen, Germany
| | | | - Daniel Bastian
- FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15-17, D-52056 Aachen, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Feodor-Lynen-Straße 25, D-81377 Munich, Germany
| | - Goffe Elsinga
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Feodor-Lynen-Straße 25, D-81377 Munich, Germany
| | - Leo Heijnen
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Johannes Ho
- TZW: DVGW-Technologiezentrum Wasser, Karlsruher Str. 84, 76139 Karlsruhe, Germany
| | - Mariana Kluge
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU München, Feodor-Lynen-Straße 25, D-81377 Munich, Germany
| | - Claudia Stange
- TZW: DVGW-Technologiezentrum Wasser, Karlsruher Str. 84, 76139 Karlsruhe, Germany
| | - Anna Uchaikina
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Regina Dolny
- Institute of Environmental Engineering, RWTH Aachen University, Mies-van-der-Rohe-Strasse 1, D-52074 Aachen, Germany
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Jörg E Drewes
- Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, D-85748 Garching, Germany
| | - Gertjan Medema
- KWR Water Research Institute, Groningenhaven 7, 3433 PE Nieuwegein, the Netherlands
| | - Andreas Tiehm
- TZW: DVGW-Technologiezentrum Wasser, Karlsruher Str. 84, 76139 Karlsruhe, Germany
| | - Sandra Ciesek
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany; German Center for Infection Research (DZIF), 38124 Braunschweig, Germany; Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D 60595 Frankfurt am Main, Germany
| | - Burkhard Teichgräber
- Emschergenossenschaft/Lippeverband, Kronprinzenstraße 24, D-45128 Essen, Germany
| | - Thomas Wintgens
- Institute of Environmental Engineering, RWTH Aachen University, Mies-van-der-Rohe-Strasse 1, D-52074 Aachen, Germany
| | - Frank-Andreas Weber
- FiW e.V., Research Institute for Water Management and Climate Future at RWTH Aachen University, Kackertstraße 15-17, D-52056 Aachen, Germany
| | - Marek Widera
- Goethe University Frankfurt, University Hospital, Institute for Medical Virology, Paul-Ehrlich-Str. 40, D-60596 Frankfurt, Germany.
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Snyder ED, Tank JL, Brandão-Dias PFP, Bibby K, Shogren AJ, Bivins AW, Peters B, Curtis EM, Bolster D, Egan SP, Lamberti GA. Environmental DNA (eDNA) removal rates in streams differ by particle size under varying substrate and light conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 903:166469. [PMID: 37633388 DOI: 10.1016/j.scitotenv.2023.166469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 08/17/2023] [Accepted: 08/19/2023] [Indexed: 08/28/2023]
Abstract
The use of environmental DNA (eDNA) as a sampling tool offers insights into the detection of invasive and/or rare aquatic species and enables biodiversity assessment without traditional sampling approaches, which are often labor-intensive. However, our understanding of the environmental factors that impact eDNA removal (i.e., how rapidly eDNA is removed from the water column by the combination of decay and physical removal) in flowing waters is limited. This limitation constrains predictions about the location and density of target organisms after positive detection. To address this question, we spiked Common Carp (Cyprinus carpio) eDNA into recirculating mesocosms (n = 24) under varying light (shaded versus open) and benthic substrate conditions (no substrate, bare substrate, and biofilm-colonized substrate). We then collected water samples from each mesocosm at four time points (40 min, 6 h, 18 h, and 48 h), and sequentially filtered the samples through 10, 1.0, and 0.2 μm filters to quantify removal rates for different eDNA particle sizes under varying light and substrate conditions. Combining all size classes, total eDNA removal rates were higher for mesocosms with biofilm-colonized substrate compared to those with no substrate or bare (i.e., no biofilm) substrate, which is consistent with previous findings linking biofilm colonization with increased eDNA removal and degradation. Additionally, when biofilm was present, light availability increased eDNA removal; eDNA levels fell below detection after 6-18 h for open mesocosms versus 18-48 h for shaded mesocosms. Among size classes, larger particles (>10 μm) were removed faster than small particles (1.0-0.2 μm). These results suggest that changes in the distribution of eDNA size classes over time (e.g., with downstream transport) and with differing environmental conditions could be used to predict the location of target organisms in flowing waters, which will advance the use of eDNA as a tool for species monitoring and management.
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Affiliation(s)
- Elise D Snyder
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA.
| | - Jennifer L Tank
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA.
| | | | - Kyle Bibby
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall of Engineering, Notre Dame, IN 46556, USA.
| | - Arial J Shogren
- Department of Biological Sciences, The University of Alabama, Science and Engineering Complex,1325 Hackberry Ln, Tuscaloosa, AL 35401, USA.
| | - Aaron W Bivins
- Department of Civil and Environmental Engineering, Louisiana State University, 3255 Patrick F. Taylor Hall, Baton Rouge, LA 70803, USA.
| | - Brett Peters
- Environmental Change Initiative, University of Notre Dame, 721 Flanner Hall, Notre Dame, IN 46556, USA.
| | - Erik M Curtis
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA.
| | - Diogo Bolster
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA; Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, 156 Fitzpatrick Hall of Engineering, Notre Dame, IN 46556, USA.
| | - Scott P Egan
- Department of BioSciences, Rice University, 6100 Main St, Houston, TX 77005-1827, USA.
| | - Gary A Lamberti
- Department of Biological Sciences, University of Notre Dame, 100 Galvin Life Sciences, Notre Dame, IN 46556, USA.
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43
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Kota PK, Vu HA, LeJeune D, Han M, Syed S, Baraniuk RG, Drezek RA. Expanded Multiplexing on Sensor-Constrained Microfluidic Partitioning Systems. Anal Chem 2023; 95:17458-17466. [PMID: 37971927 PMCID: PMC10759160 DOI: 10.1021/acs.analchem.3c01176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Microfluidics can split samples into thousands or millions of partitions, such as droplets or nanowells. Partitions capture analytes according to a Poisson distribution, and in diagnostics, the analyte concentration is commonly inferred with a closed-form solution via maximum likelihood estimation (MLE). Here, we present a new scalable approach to multiplexing analytes. We generalize MLE with microfluidic partitioning and extend our previously developed Sparse Poisson Recovery (SPoRe) inference algorithm. We also present the first in vitro demonstration of SPoRe with droplet digital PCR (ddPCR) toward infection diagnostics. Digital PCR is intrinsically highly sensitive, and SPoRe helps expand its multiplexing capacity by circumventing its channel limitations. We broadly amplify bacteria with 16S ddPCR and assign barcodes to nine pathogen genera by using five nonspecific probes. Given our two-channel ddPCR system, we measured two probes at a time in multiple groups of droplets. Although individual droplets are ambiguous in their bacterial contents, we recover the concentrations of bacteria in the sample from the pooled data. We achieve stable quantification down to approximately 200 total copies of the 16S gene per sample, enabling a suite of clinical applications given a robust upstream microbial DNA extraction procedure. We develop a new theory that generalizes the application of this framework to many realistic sensing modalities, and we prove scaling rules for system design to achieve further expanded multiplexing. The core principles demonstrated here could impact many biosensing applications with microfluidic partitioning.
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Affiliation(s)
- Pavan K. Kota
- Department of Bioengineering, Rice University, Houston, Texas 77005
| | - Hoang-Anh Vu
- Department of Bioengineering, Rice University, Houston, Texas 77005
| | - Daniel LeJeune
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005
| | - Margaret Han
- Department of Biosciences, Rice University, Houston, Texas 77005
| | - Saamiya Syed
- Department of Engineering Technology, University of Houston, Houston, Texas 77204
| | - Richard G. Baraniuk
- Department of Electrical and Computer Engineering, Rice University, Houston, Texas 77005
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Kongruang A, Limsuwanachot N, Magmuang S, Areesirisuk P, Niparuck P, Siriboonpiputtana T, Rerkamnuaychoke B. Committed change of real-time quantitative PCR to droplet digital PCR for monitoring BCR:: ABL1 transcripts in tyrosine kinase inhibitor treated CML. Hematology 2023; 28:2256199. [PMID: 37695125 DOI: 10.1080/16078454.2023.2256199] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 09/02/2023] [Indexed: 09/12/2023] Open
Abstract
OBJECTIVES We performed a feasibility study of an FDA-approved commercial ddPCR assay to measure BCR::ABL1 in CML patients treated using TKI therapy. METHODS Assay performance of standard RQ-PCR and commercially available FDA-approved ddPCR were compared to measure BCR::ABL1 p210 transcripts in RNA samples from 100 CML patients who received TKI therapy. RESULTS %BCR::ABL1/ABL1IS levels obtained from both methods were not statistically significant difference after normalization with batch-specific conversion factor (p = 0.0651). The correlation and agreement of %BCR::ABL1/ABL1IS between the two assays were high. Molecular response stratification data showed 56% concordance between RQ-PCR and ddPCR, and 37% higher residual disease detection using ddPCR. Furthermore, 21.21% (7/33) of RQ-PCR undetectable samples were detected by ddPCR, representing high sensitivity to quantify the low abundance of BCR::ABL1 transcripts. CONCLUSION ddPCR was proven to be a highly sensitive method with the potential to overcome some limitations of traditional RQ-PCR, and has the potential of being a valuable tool for monitoring BCR::ABL1 transcripts in CML during TKI therapy. (163 words).
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Affiliation(s)
- Adcharee Kongruang
- Human Genetic Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Nittaya Limsuwanachot
- Human Genetic Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sutada Magmuang
- Human Genetic Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Prapatsorn Areesirisuk
- Human Genetic Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pimjai Niparuck
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Teerapong Siriboonpiputtana
- Human Genetic Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Budsaba Rerkamnuaychoke
- Human Genetic Laboratory, Department of Pathology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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45
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Doğantürk YE, Dağ-Güzel A, Kuşkucu MA. Development of a Nanoplate-Based Digital PCR Test Method for Quantitative Detection of Human Adenovirus DNA. INFECTIOUS DISEASES & CLINICAL MICROBIOLOGY 2023; 5:353-366. [PMID: 38633848 PMCID: PMC10986707 DOI: 10.36519/idcm.2023.255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/04/2023] [Indexed: 04/19/2024]
Abstract
Objective Digital polymerase chain reaction (dPCR) assay is an advanced PCR technique that allows for the simultaneous detection and absolute quantification of diverse pathogens.Commercially validated kits available for detecting all subtypes of human adenovirus (HAdV) are limited. This study aimed to demonstrate the development of an in-house nanoplate-based dPCR assay with high sensitivity, even at low copy numbers. Materials and Methods In this methodological study, the standardized HAdV DNA was prepared by amplifying the specific hexon gene region with real-time PCR and purifying the HAdV DNA using magnetic beads from HAdV-positive extractions. Dilutions were tested in triplicate during three independent runs to determine the dynamic range, the limit of detection (LoD), the limit of quantification (LoQ), precision, and reproducibility. The primer and probe sequences used in the study were selected based on a literature review to ensure the detection of all HAdV serotypes in a single run. The selected primers were verified using the US National Center for Biotechnology Information (NBCI) nBLAST tools, and the target sequence was determined using the BioEdit software. The DNA concentration of the stock solution was measured using a Qubit fluorometer. The estimated copy number of the stock solution per milliliter was calculated based on the length of the amplified base sequence and fluorometer measurement. Results The dynamic range of the test was determined to be from 770.4 to 0.9476 cp/μl, with the LoD and LoQ values both being 0.9476 cp/μl. The coefficient of determination (r 2) value of the test was 0.9986. Conclusion The results demonstrated that the dPCR method could be an ideal tool for the diagnosis and absolute quantification of human adenoviruses, especially in low copy numbers. In order to determine the reproducibility of the test and validate the method for field use, it needs to be developed and adapted in various laboratories and supported by clinical studies.
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Affiliation(s)
- Yağmur Eylül Doğantürk
- Department of Medical Microbiology, İstanbul University-Cerrahpaşa School of Medicine, İstanbul, Türkiye
- Department of Medical Microbiology, İstanbul Aydın University School of Medicine, İstanbul, Türkiye
| | - Aylin Dağ-Güzel
- Department of Medical Microbiology, İstanbul University-Cerrahpaşa School of Medicine, İstanbul, Türkiye
- Medical Laboratory Techniques, Arel University Junior Technical Collage, İstanbul, Türkiye
| | - Mert Ahmet Kuşkucu
- Department of Medical Microbiology, İstanbul University-Cerrahpaşa School of Medicine, İstanbul, Türkiye
- Department of Medical Microbiology, Koç University School of Medicine, İstanbul, Türkiye
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46
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Bogožalec Košir A, Muller S, Žel J, Milavec M, Mallory AC, Dobnik D. Fast and Accurate Multiplex Identification and Quantification of Seven Genetically Modified Soybean Lines Using Six-Color Digital PCR. Foods 2023; 12:4156. [PMID: 38002213 PMCID: PMC10670894 DOI: 10.3390/foods12224156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
The proliferation of genetically modified organisms (GMOs) presents challenges to GMO testing laboratories and policymakers. Traditional methods, like quantitative real-time PCR (qPCR), face limitations in quantifying the increasing number of GMOs in a single sample. Digital PCR (dPCR), specifically multiplexing, offers a solution by enabling simultaneous quantification of multiple GMO targets. This study explores the use of the Naica six-color Crystal dPCR platform for quantifying five GM soybean lines within a single six-plex assay. Two four-color assays were also developed for added flexibility. These assays demonstrated high specificity, sensitivity (limit of detection or LOD < 25 copies per reaction) and precision (bias to an estimated copy number concentration <15%). Additionally, two approaches for the optimization of data analysis were implemented. By applying a limit-of-blank (LOB) correction, the limit of quantification (LOQ) and LOD could be more precisely determined. Pooling of reactions additionally lowered the LOD, with a two- to eight-fold increase in sensitivity. Real-life samples from routine testing were used to confirm the assays' applicability for quantifying GM soybean lines in complex samples. This study showcases the potential of the six-color Crystal dPCR platform to revolutionize GMO testing, facilitating comprehensive analysis of GMOs in complex samples.
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Affiliation(s)
- Alexandra Bogožalec Košir
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Sabine Muller
- Stilla Technologies, Biopark 1, Mail du Professeur Georges Mathé, 94800 Villejuif, France
| | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Allison C. Mallory
- Stilla Technologies, Biopark 1, Mail du Professeur Georges Mathé, 94800 Villejuif, France
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
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47
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Maiocchi S, Collins EN, Peterson AR, Alexander KC, McGlamery DJ, Cassidy NA, Ikonomidis JS, Akerman AW. Plasma microrna quantification protocol. VESSEL PLUS 2023; 7:27. [PMID: 38445249 PMCID: PMC10914336 DOI: 10.20517/2574-1209.2023.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate translation and are involved in many pathological processes. They have emerged as promising biomarkers for diagnosis of conditions such as aortic aneurysm disease. Quantifying miRNAs in plasma is uniquely challenging because of the lack of standardized reproducible protocols. To facilitate the independent verification of conclusions, it is necessary to provide a thorough disclosure of all pertinent experimental details. In this technical note, we present a comprehensive protocol for quantifying plasma miRNAs using droplet digital PCR. We detail the entire workflow, including blood collection, plasma processing, cryo-storage, miRNA isolation, reverse transcription, droplet generation, PCR amplification, fluorescence reading, and data analysis. We offer comprehensive guidance regarding optimization, assay conditions, expected results, and insight into the troubleshooting of common issues. The stepwise normalization and detailed methodological guide enhance reproducibility. Moreover, multiple portions of this protocol may be automated. The data provided in this technical note is demonstrative of the values typically obtained when following its steps. To facilitate standardization in data reporting, we include a table of expected aortic aneurysm-related miRNA levels in healthy human plasma. This versatile protocol can be easily adapted to quantify most circulating miRNAs in plasma, making it a valuable resource for diagnostic development.
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Affiliation(s)
- Sophie Maiocchi
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7545, USA
| | - Elizabeth N. Collins
- Department of Surgery, Division of Cardiothoracic Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7065, USA
| | - Andrew R. Peterson
- Department of Surgery, Division of Cardiothoracic Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7065, USA
| | - Kyle C. Alexander
- Department of Surgery, Division of Cardiothoracic Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7065, USA
| | - Dalton J. McGlamery
- Department of Surgery, Division of Cardiothoracic Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7065, USA
| | - Noah A. Cassidy
- University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - John S. Ikonomidis
- Department of Surgery, Division of Cardiothoracic Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7065, USA
| | - Adam W. Akerman
- Department of Surgery, Division of Cardiothoracic Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7065, USA
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Baril X, Constant P. Carbon amendments in soil microcosms induce uneven response on H2 oxidation activity and microbial community composition. FEMS Microbiol Ecol 2023; 99:fiad159. [PMID: 38040657 PMCID: PMC10716739 DOI: 10.1093/femsec/fiad159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 12/03/2023] Open
Abstract
High-affinity H2-oxidizing bacteria (HA-HOB) thriving in soil are responsible for the most important sink of atmospheric H2. Their activity increases with soil organic carbon content, but the incidence of different carbohydrate fractions on the process has received little attention. Here we tested the hypothesis that carbon amendments impact HA-HOB activity and diversity differentially depending on their recalcitrance and their concentration. Carbon sources (sucrose, starch, cellulose) and application doses (0, 0.1, 1, 3, 5% Ceq soildw-1) were manipulated in soil microcosms. Only 0.1% Ceq soildw-1 cellulose treatment stimulated the HA-HOB activity. Sucrose amendments induced the most significant changes, with an abatement of 50% activity at 1% Ceq soildw-1. This was accompanied with a loss of bacterial and fungal alpha diversity and a reduction of high-affinity group 1 h/5 [NiFe]-hydrogenase gene (hhyL) abundance. A quantitative classification framework was elaborated to assign carbon preference traits to 16S rRNA gene, ITS and hhyL genotypes. The response was uneven at the taxonomic level, making carbon preference a difficult trait to predict. Overall, the results suggest that HA-HOB activity is more susceptible to be stimulated by low doses of recalcitrant carbon, while labile carbon-rich environment is an unfavorable niche for HA-HOB, inducing catabolic repression of hydrogenase.
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Affiliation(s)
- Xavier Baril
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
| | - Philippe Constant
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, Laval, Québec H7V 1B7, Canada
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49
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Edwards RL, Takach JE, McAndrew MJ, Menteer J, Lestz RM, Whitman D, Baxter-Lowe LA. Next generation multiplexing for digital PCR using a novel melt-based hairpin probe design. Front Genet 2023; 14:1272964. [PMID: 38028620 PMCID: PMC10667681 DOI: 10.3389/fgene.2023.1272964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Digital PCR (dPCR) is a powerful tool for research and diagnostic applications that require absolute quantification of target molecules or detection of rare events, but the number of nucleic acid targets that can be distinguished within an assay has limited its usefulness. For most dPCR systems, one target is detected per optical channel and the total number of targets is limited by the number of optical channels on the platform. Higher-order multiplexing has the potential to dramatically increase the usefulness of dPCR, especially in scenarios with limited sample. Other potential benefits of multiplexing include lower cost, additional information generated by more probes, and higher throughput. To address this unmet need, we developed a novel melt-based hairpin probe design to provide a robust option for multiplexing digital PCR. A prototype multiplex digital PCR (mdPCR) assay using three melt-based hairpin probes per optical channel in a 16-well microfluidic digital PCR platform accurately distinguished and quantified 12 nucleic acid targets per well. For samples with 10,000 human genome equivalents, the probe-specific ranges for limit of blank were 0.00%-0.13%, and those for analytical limit of detection were 0.00%-0.20%. Inter-laboratory reproducibility was excellent (r 2 = 0.997). Importantly, this novel melt-based hairpin probe design has potential to achieve multiplexing beyond the 12 targets/well of this prototype assay. This easy-to-use mdPCR technology with excellent performance characteristics has the potential to revolutionize the use of digital PCR in research and diagnostic settings.
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Affiliation(s)
- Rebecca L. Edwards
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | | | | | - Jondavid Menteer
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Division of Cardiology, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Rachel M. Lestz
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Division of Nephrology, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Douglas Whitman
- Luminex Corporation, A Diasorin Company, Austin, TX, United States
| | - Lee Ann Baxter-Lowe
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, United States
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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Liu Z, Lin Y, Ge Y, Zhu Z, Yuan J, Yin Q, Liu B, He K, Hu M. Meta-analysis of microbial source tracking for the identification of fecal contamination in aquatic environments based on data-mining. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118800. [PMID: 37591102 DOI: 10.1016/j.jenvman.2023.118800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/29/2023] [Accepted: 08/10/2023] [Indexed: 08/19/2023]
Abstract
Microbial source tracking (MST) technology represents an innovative approach employed to trace fecal contamination in environmental water systems. The performance of primers may be affected by amplification techniques, target primer categories, and regional differences. To investigate the influence of these factors on primer recognition performance, a meta-analysis was conducted on the application of MST in water environments using three databases: Web of Science, Scopus, and PubMed (n = 2291). After data screening, 46 studies were included in the final analysis. The investigation encompassed Polymerase Chain Reaction (PCR)/quantitative PCR (qPCR) methodologies, dye-based (SYBR)/probe-based (TaqMan) techniques, and geographical differences of a human host-specific (HF183) primer and other 21 additional primers. The results indicated that the primers analyzed were capable of differentiating host specificity to a certain degree. Nonetheless, by comparing sensitivity and specificity outcomes, it was observed that virus-based primers exhibited superior specificity and recognition capacity, as well as a stronger correlation with human pathogenicity in water environments compared to bacteria-based primers. This finding highlights an important direction for future advancements. Moreover, within the same category, qPCR did not demonstrate significant benefits over conventional PCR amplification methods. In comparing dye-based and probe-based techniques, it was revealed that the probe-based method's advantage lay primarily in specificity, which may be associated with the increased propensity of dye-based methods to produce false positives. Furthermore, the heterogeneity of the HF183 primer was not detected in China, Canada, and Singapore respectively, indicating a low likelihood of regional differences. The variation among the 21 other primers may be attributable to regional differences, sample sources, detection techniques, or alternative factors. Finally, we identified that economic factors, climatic conditions, and geographical distribution significantly influence primer performance.
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Affiliation(s)
- Zejun Liu
- School of Civil Engineering, Sun Yat-Sen University, Zhuhai, 519082, China; Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Yingying Lin
- School of Civil Engineering, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Yanhong Ge
- Guangdong Infore Technology Co., Ltd, Foshan, 528322, China
| | - Ziyue Zhu
- School of Civil Engineering, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Jinlong Yuan
- School of Civil Engineering, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Qidong Yin
- School of Civil Engineering, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Bingjun Liu
- School of Civil Engineering, Sun Yat-Sen University, Zhuhai, 519082, China
| | - Kai He
- School of Civil Engineering, Sun Yat-Sen University, Zhuhai, 519082, China.
| | - Maochuan Hu
- School of Civil Engineering, Sun Yat-Sen University, Zhuhai, 519082, China; Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, 510070, China.
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